September 27-September 29, 2013 Boston, MA Thank

Transcription

September 27-September 29, 2013
Boston, MA
Thank you to our generous sponsors
Perpetual public-accessible conference proceedings website:
www.vin.com/tufts/2013
2
6th Tufts’ Canine and Feline
Breeding and Genetics Conference
Scientific Program
Saturday, September 28
Lecture Time: Title of Lecture:
Speaker:
8:30-9:10
Unraveling the Sources of Genetic Structure Within Breeds
Dr. Pam Wiener
9:10-9:50
Taking Advantage of Dog Breed Structure to Understand
Health
Dr. Elaine Ostrander
10:10-10:30
Genetics of Cat Populations and Breeds: Implications for
Breed Management for Health!
Dr. Leslie Lyons
10:30-11:10
Breeding Practices According to Breeds; Time, Place, and
Consequences
Dr. Grégoire Leroy
11:10-11:30
Inbreeding, Outbreeding, and Breed Evolution
Dr. Jerold Bell
1:15-1:55
Unraveling the Phenotypic and Genetic Complexity of
Canine Cystinuria
Dr. Paula Henthorn
1:55-2:35
How to Use and Interpret Genetic Tests for Heart Disease
in Cats and Dogs
Dr. Kathryn Meurs
2:55-3:35
Update on Genetic Tests for Diseases and Traits in Cats:
Implications for Cat Health, Breed Management and Human
Health
Dr. Leslie Lyons
3:35-4:15
Hereditary Gastric Cancer in Dogs
Dr. Elizabeth McNiel
3
The sources of genetic structure within breeds and its implications
Pam Wiener, Ph.D. The Roslin Institute, R(D)SVS, University of Edinburgh, Division of
Genetics and Genomics pam.wiener@roslin.ed.ac.uk
Genetic analyses of domesticated animal species have proved very useful for determining
relationships between breeds (Wiener et al., 2004), for illuminating the processes underlying
the domestication process (Wiener & Wilkinson, 2011), and for identifying genes associated
with specific traits (Georges, 2007). An important tool is the use of clustering-based
population genetic methods, in which populations are determined based on the genetic makeup of individuals, without prior population labelling. These techniques have been applied to
domesticated animal species in a number of studies and in most cases, have demonstrated
good correspondence between breeds and genetically-defined populations. Use of this
approach has proven to be particularly useful for identifying animals that do not fit the
general genetic profile of a given breed, for example, cross-bred or mis-classified individuals.
Within-breed genetic differentiation
In some cases, however, clustering techniques have revealed population structure below the
breed level, such that separate groupings are identified within breeds. This was demonstrated
in an analysis of British pig breeds, in which the British Saddleback breed showed internal
genetic structure (Wilkinson et al., 2008). There appeared to be greater differentiation
between the two British Saddleback clusters than between some breed pairs (Figure 1). A
similar finding was found for several British chicken breeds (Wilkinson et al., 2011), in
which within-breed differentiation was associated with different morphological types for
some breeds and with different flocks in others (Figure 2). The latter pattern indicates
restricted gene flow between breeders, which can lead to high rates of inbreeding.
Figure 2. Individual assignment based on clustering
analysis at K=35. Histograms demonstrate the proportion of each individual’s genome that originated from each of 24 populations. Each individual is represented by a vertical line corresponding to its membership coefficient (q). Genetic structure is seen within breeds such as Araucana, Leghorn , Maran, Silkie and Sussex. Reproduced from Wilkinson et al. (2011). Figure 1. A neighbour‐joining tree of British pigs constructed from allele‐sharing distances among all individuals. Bootstrap values greater than 500 are shown (out of 1000). British Saddleback individuals are found in two separate clusters. Reproduced from Wilkinson et al. (2008). 4
Several recent studies in dogs have also identified within-breed differentiation, which derives
from several sources. Quignon et al. (2007) analysed American and European samples from
four breeds and demonstrated a clear genetic separation of US and EU Golden retrievers.
They also identified genetic differentiation within Bernese mountain dogs, but it was not
clearly associated with geographical origin. Two other breeds in that study (Flat coated
retrievers and Rottweilers) did not show evidence of genetic structure. In other cases, genetic
differentiation is associated with phenotypic traits. Bjornfeldt et al. (2008) identified strong
genetic differentiation in poodles due to size and coat colour. Standard poodles were clearly
genetically distinct from all other poodles, while the smaller poodles were differentiated from
each other based on a combination of size and coat colour. A study on Schnauzer breeds
revealed a similar pattern of differentiation (Streitberger et al. 2011); the authors found that
Giant Schnauzers were strongly differentiated from the other Schnauzer breeds, while the
smaller Schnauzers clustered based on both coat colour and size. Mellanby et al. (2013) also
demonstrated genetic structure within UK Cavalier King Charles spaniels, although the
source of the differentiation was not clear. Preliminary analysis of UK Labrador retrievers
indicates within-breed genetic differentiation related to the role of dogs (i.e. working gun
dogs versus pets) as well as phenotypic characteristics (unpublished results).
Implications for managing recessive diseases: Strong population structure may lead to high
levels of inbreeding by creating partially independent sub-populations with relatively small
effective population sizes, increasing the role of genetic drift. This can thereby increase the
overall levels of homozygosity and thus, may also increase the numbers of individuals
homozygous for recessive disease alleles. Management practices that increase mixing within
the breed will reduce overall levels of inbreeding and therefore, may help reduce the levels of
such diseases. Somewhat ironically, in rare breeds, management strategies that involve
reduced breeding from a segment of the breed that carries known disease-associated variants
may exacerbate the problem at other loci by reducing the effective population size (Collins et
al., 2011) and thus these strategies must be designed with care and forethought.
Implications for genetic association studies and genetic evaluation: It is well established that
the existence of genetic structure can lead to spurious associations in genome-wide
association studies if the trait of interest is not evenly distributed with respect to genetic subgroups (Lander & Schork, 1994; Price et al., 2006). Therefore, it is recommended that in
such cases, stratification should be accounted for (Price et al., 2010). Population structure
may also influence the implementation of genomic evaluation schemes, in which breeding
decisions are based on genomic marker information; however, the implications of such
structure are less clear in this case. For example, Daetwyler et al. (2012) conclude that the
accuracy of prediction may be reduced by accounting for population stratification in some
situations (e.g. low or medium density markers). Further study is required on this issue.
References
Björnfeldt, S., F. Hailer, M. Nord & C. Vilà. (2008). Assortative mating and fragmentation within dog
breeds. BMC Evolutionary Biology 8:28.
Collins, L.M., L. Asher, J. Summers & P. McGreevy. (20110). Getting priorities straight: Risk
assessment and decision-making in the improvement of inherited disorders in pedigree dogs. The
Veterinary Journal 189: 147–154.
Daetwyler, H.D., K.E. Kemper, J.J.J. van der Werf & B.J. Hayes. (2012). Components of the accuracy
of genomic prediction in a multi-breed sheep population. Journal of Animal Science 90: 33753384.
Georges, M. (2007). Mapping, fine mapping, and molecular dissection of quantitative trait loci in
domestic animals. Annual Review of Genomics and Human Genetics 8: 131-162.
5
Lander, E.S. & N.J. Schork. (1994). Genetic dissection of complex traits. Science 265: 2037-2048.
Mellanby, R.J., R. Ogden, D.N. Clements, A.T. French, A.G. Gow, et al. (2013). Population structure
and genetic heterogeneity in popular dog breeds in the UK. The Veterinary Journal 196: 92-97.
Quignon, P., L. Herbin, E. Cadieu, E.F. Kirkness, B. Hédan, et al. (2007). Canine population
structure: assessment and impact of intra-breed stratification on SNP-based association studies.
PLOS one 12: e1324.
Price, A.L., N.J. Patterson, R.M. Plenge, M.E. Weinblatt, N.A. Shadick, et al. (2006). Principal
components analysis corrects for stratification in genome-wide association studies. Nature
Genetics 38: 904-909.
Price, A.L., N.A. Zaitlen, D. Reich & N.J. Patterson. (2010). New approaches to population
stratification in genome-wide association studies. Nature Reviews Genetics 11: 459-463.
Streitberger, K., M. Schweizer, R. Kropatsch, G. Dekomien, O. Distl, et al. (2011). Rapic genetic
diversification within dog breeds as evidenced by a case study on Schnauzers. Animal Genetics
43: 577-586.
Wiener, P., D. Burton and J.L. Williams. (2004). Breed relationships and definition of British cattle: a
genetic analysis. Heredity 93: 597-602.
Wiener, P. & S. Wilkinson (2011). Deciphering the genetic basis of animal domestication.
Proceedings of the Royal Society B: 278: 3161-3170.
Wilkinson, S., C.S. Haley, L. Alderson & P. Wiener. (2008). An empirical assessment of individualbased population genetic statistical techniques: application to British pig breeds. Heredity 106:
261-269.
Wilkinson, S., P. Wiener, D. Teverson, C.S. Haley & P.M. Hocking. (2011). Characterization of the
genetic diversity, structure and admixture of British chicken breeds. Animal Genetics 43: 552563.
6
The
n e w e ng l a n d j o u r na l
of
m e dic i n e
review article
franklin h. epstein lecture
Franklin H. Epstein, M.D., served the New England Journal of Medicine for more than 20 years.
A keen clinician, accomplished researcher, and outstanding teacher, Dr. Epstein was Chair and Professor of
Medicine at Beth Israel Deaconess Medical Center, Boston, where the Franklin H. Epstein, M.D., Memorial
Lectureship in Mechanisms of Disease has been established in his memory.
Both Ends of the Leash — The Human
Links to Good Dogs with Bad Genes
Elaine A. Ostrander, Ph.D.
From the National Human Genome Research Institute, National Institutes of
Health, Bethesda, MD. Address reprint
requests to Dr. Ostrander at the National
Human Genome Research Institute, National Institutes of Health, 50 South Dr.,
Bldg. 50, Rm. 5351, Bethesda, MD 20892,
or at eostrand@mail.nih.gov.
N Engl J Med 2012;367:636-46.
DOI: 10.1056/NEJMra1204453
Copyright © 2012 Massachusetts Medical Society.
F
or nearly 350 years, veterinary medicine and human medicine
have been separate entities, with one geared toward the diagnosis and treatment in animals and the other toward parallel goals in the owners. However,
that model no longer fits, since research on diseases of humans and companion
animals has coalesced.1-4 The catalyst for this union has been the completion of the
human genome sequence, coupled with draft sequence assemblies of genomes for
companion animals.5,6 Here, we summarize the critical events in canine genetics and
genomics that have led to this development, review major applications in canine
health that will be of interest to human caregivers, and discuss expectations for the
future.
Hum a n a nd C a nine Genomic s
In 2001, two independent draft versions of the human genome sequence and the concomitant identification of approximately 30,000 genes were the seminal events that
defined completion of the Human Genome Project.7,8 The genome was officially declared to be finished in 2004, with sequencing reported to include 99% of transcribing
DNA.9 By comparison, the genome of the domestic dog, Canis lupus familiaris, was sequenced twice, once to 1.5× density (i.e., covering the genome, in theory, 1.5 times)
and once to 7.8× density (providing sequencing for more than 95% of base pairs) in the
standard poodle and boxer, respectively.5,10 Subsequent contributions to the canine
genome have focused on better annotation to locate missing genes,11 understanding
chromosome structure,12 studying linkage disequilibrium,5,13 identifying copy-number
variants,14-16 and mapping the transcriptome.17
The use of the canine genome to understand the genetic underpinning of disorders that are difficult to disentangle in humans has been on the rise for nearly two
decades.1,2,18 The reason relates back to the domestication of dogs from gray wolves
(C. lupus), an event that began at least 30,000 years ago.19-21 Since their domestication,
dogs have undergone continual artificial selection at varying levels of intensity,
leading to the development of isolated populations or breeds5,22,23 (Fig. 1). Many
breeds were developed during Victorian times24 and have been in existence for only a
few hundred years, a drop in the evolutionary bucket.25 Most breeds are descended
from small numbers of founders and feature so-called popular sires (dogs that have
performed well at dog shows and therefore sire a large number of litters). Thus, the
genetic character of such founders is overrepresented in the population.25,26 These
facts, coupled with breeding programs that exert strong selection for particular
636
n engl j med 367;7 nejm.org august 16, 2012
The New England Journal
of Medicine
7
Downloaded from nejm.org at NIH on August 22, 2012. For personal use only. No other uses without permission.
Copyright © 2012 Massachusetts Medical Society. All rights reserved.
fr anklin h. epstein lecture
A
B
C
E
F
G
H
D
I
J
K
Figure 1. The Diversity of Dog Breeds.
Breeds vary according to many traits, including size, leg length, pelage (coat), color, and skull shape. Shown are borzoi
(Panel A), basset hound (Panel B), Chihuahua (Panel C), giant schnauzer (Panel D), bichon frise (Panel E), collie
(Panel F), French bulldog (Panel G), dachshund (Panel H), German shorthaired pointer (Panel I), papillon (Panel J),
and Neapolitan mastiff (Panel K). (Images courtesy of Mary Bloom, American Kennel Club.)
physical traits, mean that recessive diseases are
The Gene t ic P ow er of C a nine
common in purebred dogs,22,27,28 and many breeds
Fa mil ie s
are at increased risk for specific disorders.2,29 We,
and others, have chosen to take advantage of this One of the most striking features of canine famfact in order to identify genes of interest for hu- ilies is their large size, which makes them ameman and canine health.
nable to conventional linkage mapping. This fact
n engl j med 367;7
nejm.org
august 16, 2012
of Medicine
8
637
The
was particularly well illustrated in the search for
the canine gene for hereditary multifocal renal
cystadenocarcinoma and nodular dermatofibrosis (RCND) in German shepherds.30 Although rare,
RCND is a naturally occurring inherited cancer
syndrome that includes bilateral, multifocal tumors in kidneys and numerous, dense collagenbased nodules in the skin,31 a disorder that is
similar to the Birt–Hogg–Dubé syndrome (BHD)
in humans.32 In dogs, the disease allele is highly
penetrant and transmitted in an autosomal dominant fashion. The dog pedigree that was used for
mapping the disease included one affected founder male who sired several litters (Fig. 2). With DNA
available from nearly all dogs, this single pedigree
had sufficient power to localize the disease gene
to canine chromosome 5q12 with a logarithm of
odds (LOD) score of 4.6, giving odds of more
than 10,000 to 1 that the mapping was correct.30
After the localization of RCND, the human
BHD locus was mapped to human chromosome
17p12q11,33 which corresponds to canine chromosome 5q12. Both affected dogs and humans
were found to carry mutations in the same gene
encoding tumor-suppressor protein folliculin,34,35
which is hypothesized to interact with the energy
and nutrient-sensing signaling pathway consisting of AMP-activated protein kinase (AMPK) and
mammalian target of rapamycin (mTOR).36
Three issues about this example are striking.
First, the single, large dog pedigree was collected
and genotyped in a fraction of the time it took to
collect and characterize the many necessary human pedigrees. Second, BHD is associated with
substantial variability in disease presentation in
humans and may be hard to distinguish from
similar disorders.37 In the case of the large extended dog family, phenotyping was easy, since
every dog had the same genetic background and
the disease presentation was highly uniform. Also,
the dog locus was found before the human locus.
Other disease genes that were first mapped in dogs
for which there is a close human proxy include
narcolepsy,38 copper toxicosis,39,40 neuronal ceroid
lipofuscinosis,41 and ichthyosis,42 to name a few.
Each of such stories is illuminating in its own
way. In the case of narcolepsy in the Doberman
pinscher, the identification of a mutation in the
gene encoding hypocretin receptor 2 suggested a
newly recognized pathway that is involved in the
molecular biology of sleep. Another example is
canine neuronal ceroid lipofuscinosis, a late-onset
638
of
m e dic i n e
disorder of American Staffordshire terriers with
symptoms that are similar to a human adultonset form of the disorder known as Kuf’s disease.
In American Staffordshire terriers, neuronal ceroid
lipofuscinosis is caused by an R99H mutation in
exon 2 of the gene encoding arylsulfatase G
(ARSG), leading to a 75% decrease in sulfatase
activity. This study, therefore, both identified a new
gene for consideration in human neuronal ceroid
lipofuscinosis and provided new information regarding sulfatase deficiency and pathogenesis of
the disease.
Br eed S t ruc t ur e a nd Gene t ic
C ompl e x i t y Simpl ified
A recurring theme in the gene mapping of canine
diseases is the power of the breed structure (Fig.
3). To be a registered member of a breed, the dog’s
ancestors must have been registered members as
well.26 In 2011, the American Kennel Club (www
.akc.org) recognized 173 distinct dog breeds, with
European clubs taking the number of established
breeds to more than 400.24,43
Dog breeds offer the same advantage of reducing locus heterogeneity that is gained by studying
humans from geographically isolated countries
such as Finland or Iceland.29 For any given complex disease, a small number of genes and deleterious alleles will dominate the breed,3 much as the
999del5 BRCA2 mutation does in Icelandic women
with hereditary breast cancer.44
Epilepsy is a good example, since this disease
has been difficult to disentangle genetically in
humans because of indistinct clinical phenotypes
and a high degree of locus heterogeneity. The
disease affects 5% of dogs and is reported in
dozens of breeds. Remitting focal epilepsy in the
Lagotto Romagnolo breed45 is caused by variants
in LGI2, a homologue of the human epilepsy LGI1
gene. In contrast, miniature wire-haired dachshunds have a form of epilepsy reminiscent of the
progressive myoclonic disease known as Lafora’s
disease, which in humans is the most severe form
of teenage-onset epilepsy. The similar disease in
dachshunds is caused by an unusual expansion of
a dodecamer repeat46 within the gene encoding
malin (EPM2B) that modulates gene expression by
a factor of nearly 900. The presentation of epilepsy
is expectedly unique in other breeds.47 Thus, one
way to disentangle complex diseases like epilepsy
is to study the disorder in different dog breeds.
of Medicine
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august 16, 2012
The New England 10
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1
4
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+
4
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7
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+
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52
60
5
2
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NT
2
2
+
4
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3 NT
NT 2
1
3
4 NT
4
1
3
2
+
−
4
6
4
2
5
7
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2
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3
NT NT
2
4
2
4
+
+
4
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2 NT
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3
4
4
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4
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+
+
4
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3
59
51
5
3
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2
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NT NT
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4
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+
+
4
4
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50
58
3
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4
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+
4
3
5
3
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2
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NT NT
2
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+
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4
4
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2
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6
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3
+
1
4
7
1
1
2
1
2
−
8
2
57
30
1
7
2
1
2
1
NT NT
2
1
2
2
+
−
4
NT
4
3
3
2
3
4
4
4
+
6
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56
29
3
2
2
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4
5
+
4
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2
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2
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7
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4
6
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55
28
46
2
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2
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+
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1
1
7
2
1
2
3
4 NT
2
4
3
4
+
+
4
4
4
3
NT
3
2
2
2
3
NT NT
2
4
2
4
+
+
4
4
4
3
5
2
1
NT
3
3
+
4
4
54
27
45
3
2
3
4
4
4
+
4
3
3
2
3
4
4
4
+
6
2
FH2594 NT
FH2140 1
AHT141 1
ZuBeCa6 NT
GLUT4 4
C02608 4
RCND +
C05.771 4
FH2383 3
FH2594 NT
FH2140 1
AHT141 1
ZuBeCa6 2
GLUT4 4
C02608 4
RCND +
C05.771 4
FH2383 3
1
2
1
4
4
3
+
4
4
3
2
2
4
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3/5
+ +
4 4
4 4
1
2
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4
4
1
2
2
NT
2
2
−
4
4
53
NT
2
2
NT
2
3
+
4
4
Figure 2. Mapping Pedigree for Canine Renal Cystadenocarcinoma and Nodular Dermatofibrosis (RCND).
A single affected male dog carrying an autosomal dominant allele for RCND sired five litters of pups with five unique and unaffected females. Affected dogs are shown in black,
and unaffected dogs in white. Squares indicate males, circles females, and lines relationships. The portion of canine chromosome 5q14 showing linkage is indicated as a rectangle
below each square or circle. Black bars indicate the portion of the affected parental chromosome inherited by each offspring from the affected father, and white bars indicate the
portion inherited from the normal chromosome of the father. Alleles for each marker are indicated as numbers. Breakpoints allow the disease gene to be localized to a region
adjacent to marker ZuBeCa6. Reprinted from Jónasdóttir et al.,30 with the permission of the publisher.
?
12
FH2594
FH2140
AHT141
ZuBeCa6
GLUT4
C02608
RCND
C05.771
FH2383
?
NT
Unaffected
Affected
Diagnosis unknown
Not typed
Phase unknown
Mutant allele
Wild-type allele
FH2594
FH2140
AHT141
ZuBeCa6
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C02608
RCND
C05.771
FH2383
639
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The
m e dic i n e
The New England 11
Journal of Medicine
causative genes. Although progressive rod–cone
degeneration was initially mapped in miniature
and toy poodles, the disorder appears in more
than a dozen breeds and is phenotypically similar to one form of human adult-onset, autosomal
recessive retinitis pigmentosa. Analysis of additional SNPs allowed the investigators to reduce
the disease locus to a 106-kb haplotype that is
shared by affected dogs from 14 breeds. A mutation in a novel gene was ultimately determined to
cause the disease.50 Had there not been 14 affected breeds sharing the founder mutation, which
allowed the haplotype to be significantly reduced,
only next-generation sequencing could have ultimately localized the disease gene.
Although researchers could have correctly
guessed a subset of the breeds that shared the
same mutation at the causative locus for progressive rod–cone degeneration by knowing about
their shared heritage, common geographic origin,
or shared morphologic features, in many cases
the relationship among the breeds is too ancient
to be obvious. With the use of both cluster analysis51,52 and neighbor-joining trees,23 a clear picBr eed S t ruc t ur e a nd
ture is emerging regarding how breeds are reR educing R egions of L ink age
lated to one another genetically (Fig. 3). This
Disequil ibr ium
type of information highlights groups of breeds
The second way in which breed structure offers that probably share common founders (and hence
unique advantages to genetic mapping is that the same disease alleles) and facilitates experiwhen used judiciously, it allows researchers to mental design.
move quickly from linked or associated markers
to genes. In humans, linkage disequilibrium typMor phol o gic Fe at ur e s
ically extends on the order of kilobases, whereas
a nd Gene t ic Va r i at ion
within dog breeds it can extend for megabases.5,13
Long linkage disequilibrium means that although The examples discussed thus far have focused on
only a modest number of single-nucleotide poly- disease phenotypes. However, canine morphomorphisms (SNPs) are needed for an initial map- logic studies have been informative for both disping study, subsequent identification of the dis- covering new ways of perturbing the genome and
ease mutation can be difficult. This task is suggesting candidate genes for related diseases.
facilitated by leveraging interbreed relatedness. For instance, chondrodysplasia is a fixed trait for
Haplotypes in the region of interest can be com- more than 20 breeds with disproportionately
pared in related breeds with the same disorder, short legs recognized by the American Kennel
with the goal of identifying a segment that is Club, including the dachshund, corgi, and basset
shared by all affected dogs but absent in those hound (Fig. 5).53
lacking the trait (Fig. 4).
A genomewide association study comparing
Among the many investigators who have dem- 95 dogs from eight chondrodysplastic breeds with
onstrated this principle are Goldstein et al.,48,49 702 dogs from 64 breeds lacking the trait identiwho had previously mapped a form of canine fied a single strong association (P = 1.0×10–102)
progressive retinal atrophy called progressive rod– with canine chromosome 18. Although this very
cone degeneration to a 30-mb region. Progressive low P value is probably exaggerated because of
retinal atrophy is analogous to human retinitis the population structure, such a strong associapigmentosa, for which there are many forms and tion is not unusual when breeds sharing a trait
Figure 3 (facing page). Neighbor-Joining Tree
of Domestic Dogs.
On average, 10 to 12 dogs were genotyped for each of
approximately 80 breeds. Trees were constructed with
the use of data from each genotyped dog individually
or by grouping the data from each member of a breed
together, so each breed is represented as a single data
entry. Data were also analyzed in two ways: by considering adjacent 10 single-nucleotide-polymorphism
(SNP) windows or haplotypes or by considering each
SNP alone. The two analytic methods provided similar
results. Panel A shows the relationships among the
various dog breeds. The color groupings indicate
breeds that probably share common founders. Panel B
shows the historical relationship of the breeds with the
same color coding used in Panel A. In each case, breeds
that share either common behaviors or morphologic
traits are grouped together on the basis of DNA analysis,
indicating that they probably share common ancestors.
A black dot indicates at least 95% bootstrap support
(a measure of the likelihood that an evolutionary split
occurred in a given location in an evolutionary tree)
after the performance of 1000 replicates. Reprinted
from vonHoldt et al.23 with permission of the publisher.
The New England 12
Journal of Medicine
641
The
German Shepherd
*
Collie
*
Pembroke Welsh Corgi
*
Cardigan Welsh Corgi
*
of
m e dic i n e
lian genomes, turns out to be important in similar human diseases.
Other canine morphologic traits that include
such characteristics as body size, leg width, and
coat color have been mapped.22,28,54-58 Not surprisingly, loci that control both a morphologic
trait and a disease have been identified. This may
be a result of strong selection by breeders to
propagate dogs of a certain appearance, which
results in piggybacking of disease alleles, or in
some cases, diseases are associated with the same
genetic variants that create a morphologic effect.
This is best illustrated by dermoid sinus, a neuraltube defect in the ridgeback breed that is caused
by the same copy-number variant that produces
the hair ridge characteristic of the Rhodesian
ridgeback.59
M a pping Mult igenic T r a i t s
Giant Schnauzer
*
Figure 4. Comparing Haplotypes as a Method for Reducing a Region
of Association for a Given Mutation.
The mutation causing a hypothetical disease is indicated by a yellow star.
The various breeds with the disease are shown on the left; the chromosome
responsible for the disease is indicated by a horizontal bar. Within each
breed, meiotic breakpoints are indicated by the start and finish of the blue
bar for each breed. When all breeds are considered together, the minimal
associated region where the mutation must lie is between the red vertical
lines.
from a common founder are compared with a
large number of unrelated control breeds. In this
case, the trait is caused by expression of an fgf4
retrogene. This retrogene encodes fibroblast
growth factor 4 in which all fgf4 exons are present, but introns and regulatory signals are missing (Fig. 5). The spliced copy of the gene is located a large distance away from the source gene.
Although such an arrangement is common in
insects, this was the first report of an expressed
retrogene that alters a mammalian trait.53 Expression studies showed that the fgf4 retrogene
was expressed in the long bones of 4-week-old
puppies, suggesting that mistimed expression,
incorrect RNA levels, or mislocalization of the
retrogene product caused premature closure of
the growth plates in the long bones of the carrier breeds. It will be interesting to see whether
this gene, or this method of mutating mamma642
When the dog genome sequence was published
in 2005, Lindblad-Toh et al.5 hypothesized that
breed structure would enable mapping of simple
recessive traits in dogs with a genomewide association study of no more than 20 cases and controls each. They further reasoned that complex
traits that are controlled by, for instance, five
genes could be mapped with 97% certainty on
the basis of just 100 cases and 100 controls. This
was a bold prediction, since most genomewide
association studies of complex human disorders
require thousands of samples. But the investigators’ prediction proved to be correct, and many
genomewide association studies in dogs have successfully mapped complex traits on the basis of no
more than 50,000 SNPs and fewer than 200 dogs.
Recent work by Wilbe et al.60 that identifies
genes for systemic lupus erythematosus (SLE)–
related disease complex illustrates this point. Nova
Scotia duck-tolling retrievers have an abnormally
high rate of autoimmune diseases, including SLE.61
The breed is descended from a small number of
founders that survived two major outbreaks of
canine distemper virus in the early 1900s.62 It
has been hypothesized that autoimmune disorders develop in these dogs because they have a
particularly strong or reactive immune system,
which helped them to survive the distemper outbreaks. In an analysis of 81 cases and 57 controls in a genomewide association study of
22,000 SNPs, investigators found five associated
loci, three of which have already been validated.60 Candidate genes of particular interest in-
The New England 13
Journal of Medicine
A Breeds with Risk of Chondrodysplasia
B Observed Heterozygosity for Chondrodysplasia
0.4
Observed Heterozygosity
Figure 5. Mapping the Breed-Fixed Trait
of Chondrodysplasia.
Panel A shows examples of breeds that are associated
with chondrodysplasia, including the corgi, basset
hound, and wire-haired dachshund. Panel B shows observed heterozygosity for breeds that are at increased
risk for chondrodysplasia (red) and those that are not
at increased risk (black) within the associated 34-kb
region on canine chromosome 18. The x axis indicates
the chromosomal position of association, and the
y axis indicates observed heterozygosity. The red and
black lines indicate trends and highlight a 24-kb region
with low heterozygosity in the dogs at risk for chondrodysplasia that is absent in dogs that are not at increased
risk. Gene 1 is a pseudogene, a defective segment of
DNA that resembles a gene but cannot be transcribed,
called txndc1 (similar to the gene encoding thioredoxinrelated transmembrane protein 1), and gene 2 marks
the 3′ end of the gene encoding semaphorin 3C
(SEMA3C). The green boxes are conserved in both
sequence and context in all mammals for which data
are available. A 5-kb insertion (red rectangle), which
was observed only in dogs with an association with
chondrodysplasia and was found between the two putative regulatory elements, contains an fgf4 retrogene.
LINE denotes long interspersed nuclear element, and
SINE short interspersed nuclear element. Panel C shows
expression studies indicating that the fgf4 retrogene
is expressed in articular cartilage from the distal and
proximal humerus isolated from a 4-week-old dog with
chondrodysplasia. The retrogene and source gene are
distinguished by a single-nucleotide polymorphism,
which is cut by restriction enzyme BsrB1 in complementary DNA (cDNA) produced from the source gene,
resulting in two bands on a 2% agarose gel, but uncut
in the cDNA from the retrogene that is present in dogs
with chondrodysplasia, resulting in only one band. MW
denotes molecular weight marker. The source of control material is DNA isolated from the testes of a dog
with chondrodysplasia. Modified from Parker et al.,51
with the permission of the publisher.
0.3
0.2
0.1
0.0
23281978
23422559
23446056 23622780
Position on Chromosome 18
23425000
23430000
23435000
23440000
Gene 1
Insert
Putative regulatory region Putative regulatory region
Gene 2
SINEs
LINEs
C Expression of Retrogene
clude those associated with T-cell activation such
as PPP3CA, BANK1, and DAPPI.
700 —
600 —
500 —
400 —
300 —
Chondrodysplasia
cDNA
RetroFGF4 gene
1
2
3
4
MW +Control
—A
—G
—
200 —
100 —
No Chondrodysplasia
cDNA
cDNA
D o gs a nd C a ncer
700 —
600 —
500 —
400 —
300 —
MW FGF4
5
6
FGF4
7
8
MW +Control
Of all the disorders for which dogs are likely to
inform human health, canine cancer is likely to
have the greatest effect.63 Cancers are the most
200 —
frequent cause of disease-associated death in
dogs, and naturally occurring cancers are well
100 —
described in several breeds.3,64,65 Although considerable effort has gone into the study of common cancers, the dog has also served as a model
for studies of rare tumors, including histiocytic exist: a localized variant, in which skin and subsarcomas, which are highly aggressive, lethal, cutical tumors develop in a leg and metastasize
dendritic-cell neoplasms.66 In dogs, two forms to lymph nodes and blood vessels, and a dissemn engl j med 367;7
23445000
nejm.org
august 16, 2012
The New England 14
Journal of Medicine
—A
—G
—
643
The
inated multisystem form, in which tumors affect
the spleen, liver, and lungs.67 Histiocytic sarcomas
will develop in approximately 20% of Bernese
mountain dogs,68 and the condition is invariably
fatal.69 In humans, similar disorders such as
Langerhans’-cell histiocytosis have been well
characterized clinically, but the underlying cause
is unknown.70
Recently, a genomewide association study for
histiocytic sarcoma was undertaken in dogs.71
Because the disorder occurs in so few breeds,
Bernese mountain dogs from France, the United
States, and the Netherlands were included, with
the idea that these independently propagating
lines would offer the same advantages for reducing a region of association that distinct, but related, dog breeds provide.72 For this breed, this
assumption proved to be true, and two loci were
identified, one on chromosome 18. Fine mapping
and sequencing narrowed the locus to a single
risk-associated haplotype that spans the MTAP
gene and contains one or more variants that alter
the expression of the nearby INK4A–ARF–INK4B
locus but do not affect expression of MTAP itself.
Although 40% of a random sample of Bernese
mountain dogs in the United States are homozygous for the disease haplotype, histiocytic sarcoma develops in only about 20% of these dogs.
However, more than 60% of Bernese mountain
dogs eventually die of cancer. The disease-associated portion of chromosome 11 corresponds to
human chromosome 9p21, which has been associated with several types of cancer.73-75 We have
hypothesized that multiple distinct cancers in
Bernese mountain dogs may be related to variants within the MTAP–CDKN2A region and the
associated canine locus. Thus, studies of this
naturally occurring dog model not only illuminate a causative locus but also suggest a biologic
model for the study of germline variation in this
important cancer-susceptibility locus.
D o g Br eeds a nd Gene Ther a py
Although I have focused largely on the role of
dogs in the identification of genes that are associated with disease, dogs have also served an important role in the development of treatments.
One form of progressive retinal atrophy called
Leber’s congenital amaurosis type 2 is a disease
644
of
m e dic i n e
of dogs and humans that is caused by a loss of
the RPE65 protein owing to mutations in RPE65,
causing blindness shortly after birth. In a landmark study in 2001, Acland et al.76 used a recombinant adeno-associated virus carrying wild-type
RPE65 to restore vision in a dog that was homozygous for the RPE65 mutation. Replication was
successful,77 and treated dogs maintained stable
vision for at least 3 years.78 Humans with Leber’s
congenital amaurosis are now being successfully
treated for the disorder.79,80 Progressive retinal
atrophy occurs in more than 100 breeds of dogs,
suggesting dozens of naturally occurring models
for additional study. So far, 18 genes for canine
retinal diseases have been found.81
D o g Gene t ic s a nd Beh av ior
The canine system is valuable for mapping behaviors that are specific to both breed82 and species.23
Abnormal behaviors, including separation anxiety,
dominance aggression, and obsessive–compulsive
disorder, are most amenable to genetic studies.83
Partial success has been achieved with obsessive–
compulsive disorder in bull terriers and Doberman
pinschers.84,85 In Dobermans, the disease presents
as flank or blanket sucking and was recently
mapped to a 1.7-Mb region of chromosome 7 near
the CDH2 gene. CDH2 mediates synaptic activityregulated neuronal adhesion, but to date no functional studies have illuminated these findings and
no mutation has been reported.85
Sum m a r y
What we most wish to understand about dog
health is the very same thing we wish to know
about ourselves. When will we, or they, get sick?
How is the illness best treated? And what is the
likely outcome? Each half of a pet–human pair
wants to know what to expect from the other end
of the leash and how to prolong the relationship.
Finally, as the end of life approaches, we seek to
make both our canine companions and ourselves
comfortable, settled in the knowledge that a full
life has been achieved. When considered in that
frame, we are not so different from our canine
companions. As the scientific advances coalesce,
joining us ever closer to the one family member
we actually get to choose, it is worth bearing in
The New England 15
Journal of Medicine
mind that though our methods may be different,
our goals are the same: a healthy life well spent
in the best of company.
Disclosure forms provided by the author are available with the
full text of this article at NEJM.org.
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Copyright © 2012 Massachusetts Medical Society.
The New England 17
Journal of Medicine
Genetics of Cat Populations and Breeds: Implications for Breed Management
for Health!
Leslie A. Lyons, PhD, College of Veterinary Medicine, University of Missouri - Columbia
Lyonsla@missouri.edu
Introduction
Inclusive of feral domestic cats, the world-wide population of Felis silvestris catus is ~600
million, and represents on the order of 99% of all living individuals of the mammalian family
Felidae (Dauphiné, N. I. C. O., and ROBERT J. Cooper 2009). In the United States 38.4 million
households own cats, totaling 88 million individual animals, which incur $400 in expenditures
per year per household4. Cats incur veterinary health care costs in a direct fashion, but they may
be important vectors for pathogens which impact human behavior, such as Toxoplasma gondii.
Latent infection with Toxoplasma gondii has been implicated in cultural variation. Associations
with mental illness and infected status have also been reported. Thus the management of cat
populations is increasing in the public interest. Understanding the genetic relationships of help
to manage their health care and predict and prevent unwanted genetic diseases and traits.
Wildcat origins
The domestic cat, Felis catus,25,38 is one of 38 species in the cat family Felidae, being a member
of the Felis lineage.52 The Felis lineage is composed of three small African felids and four small
felids that may be the progenitors of the domestic cat, including Felis lybica (African wildcat),
Felis silvestris (European wildcat), Felis ornata (Asian wildcat), and Felis bieti (Chinese desert
cat).28,32 The domestic cat and the wildcat species can interbreed, producing fertile hybrids26;
thus their demarcation as subspecies and even distinct species can be disputed. Because the
common housecat is a domesticated derivative, the term Felis catus has been re-adopted and
does not clearly denote the genetic relationship to the progenitor wildcats or their subspecies.25
The relationship of the African, European, and two Asian wildcats is somewhat controversial;
currently, 21 subspecies are defined within these groupings.34 Other than the South African
subspecies of African wildcat, Felis lybica cafra, most species of wildcat and their associated
subspecies may be the progenitors of domestic cat populations,21,40 Felis lybica having the most
scientific support.
Domestic cats likely participated actively in their own domestication; both humans and felines
developed a symbiotic, commensal, mutual tolerance. Several independent sites of early
civilizations are known to have developed between 8000 and 3000 BCE, including the Huang He
River region of China; the Indus Valley in Pakistan; and the Fertile Crescent region, which
extends from Iraq, into Turkey, south along the Levant region of the Mediterranean coast, and,
arguably, into the Nile Valley of Egypt.8 As humans made the transition from hunter–gatherers
to the more sedentary lifestyle of the farmer and permanent settlements subsequently developed,
villages produced refuse piles and grain stores, attracting mice and rats,11 a primary prey species
for the small wildcat. To obtain these easy meals, bold wildcats perhaps began to tolerate
humans, and humans accepted the cat because of its utility in vermin control.
18
Domestic Populations
Random-bred and feral cats represent the overwhelming majority of cats throughout the world,
not fancy cat breed populations,3 although most genetic studies have focused on cat breeds to
date. Considering the worldwide distribution of cats, the United States likely has the highest
proportion of pedigreed cats. However, the proportion of pedigreed versus random-bred cats is
still fairly low; only 10% to 15% of feline patients at the University of California, Davis
Veterinary Medicine Teaching Hospital is represented by pedigreed cats.42 A general
understanding of cat breed development and a more in-depth understanding of a limited number
of foundation cat breeds will help predict health care problems on the basis of each cat’s genetic
background.
Genetic studies of over a thousand cats from worldwide populations have allowed the definition
of approximately ten genetically distinct cat populations from around the world. These
populations can be used as the foundation genetic pools for specific breeds. The first
documented cat show that judged cats on their aesthetic value occurred in London, England, at
the Crystal Palace in 1871.1 This competition presented only a handful of breeds, including the
British, Persian, Abyssinian, Angora, and Siamese. Thus, these early documented cat breeds
likely represented genetically distinct populations insofar as strict breeding programs were not
established at the time. However, now they are genetically distinct breeds, but their genetic
origins can be traced to their foundation populations.
Most worldwide cat fancy associations, such as the Cat Fanciers’ Association (CFA),16,17 The
International Cat Association (TICA),61 the Governing Council of the Cat Fancy (GCCF),2 and
the Fédération Internationale Féline (FIFe),22 recognize approximately 35 to 41 cat breeds,
although only a few breeds overwhelmingly dominate the census of the registries. Persian cats
and related breeds (e.g., Exotics, a shorthaired Persian variety) are among the most popular cat
breeds worldwide and represent an overwhelming majority of pedigreed cats. Although not all
cats produced by breeders are registered, perhaps only 20% to 30%, the CFA, one of the largest
cat registries worldwide, generally registers approximately 40,000 pedigreed cats annually.18
Approximately 16,000 to 20,000 are Persians, and approximately 3000 are Exotics; thus the
Persian group of cats represents more than 50% of the cat fancy population. Common breeds that
generally have at least 1000 annual registrants are Abyssinians, Maine Coons, and Siamese.
Other popular breeds include the Birman and Burmese, which are more prevalent in other areas,
such as the United Kingdom. Most of these popular breeds also represent the oldest and most
established cat breeds worldwide. However, because of different breeding standards in different
registries and population substructuring, not all cats identified as the same breed are genetically
alike. Disease frequencies may be different for breeds in different parts of the world. For
example, polycystic kidney disease has been shown to have about the same prevalence in Persian
cats around the world,5,6,10,15 but hypokalemia in the Burmese is more limited to cats in the
United Kingdom and Australia9,36 and not found in populations in the United States. Some lines
of Burmese in the United States segregate for a craniofacial defect, which is not commonly
found in Burmese cats outside the United States.50 The breed substructuring may be partially due
to rabies control measures that reduce migration of cats among countries, but it is also likely that
19
the known health concerns in the breeds have led to strong restrictions of imports and exports of
fancy-breed cats.
A more recently developed cat breed, the Bengal,31 which is a hybrid between the Asian Leopard
cat, Prionailurus bengalensis, and the domestic cat, has gained significant popularity throughout
the world, even though some registries currently do not recognize the breed. Because of limited
wildcat founders, the hybrid cats may have decreased genetic variation. These hybrid cats may
also have allelic incompatibilities for a given gene; the genes between the two species, leopard
cat and domestic cat, have millions of years of evolutionary divergence, which allows
differences at the DNA sequence level of a gene. Hence an accumulation of different genetic
variants that are functional within the species, but nonfunctional across the felid species, are
likely present in some Bengal cats. Thus hybrid cat breeds may have unexpected health problems
and infertility, creating a challenge for both genetic studies and primary health care.
Many modern cat breeds derived from an older “foundation” breed, thereby forming breed
families or groups. Approximately 22 breeds can be considered foundation or “natural” breeds.
Genetic studies have also shown that the foundation breeds have either significantly different
genetic pools or sufficient selection and inbreeding that created significant genetic distinction
(Figure 1). Cat breeds derived from the foundation breeds are often based on single gene
variants, such as longhaired and shorthaired varieties, or even a hairless variety, as found in the
Devon Rex and Sphynx grouping. Color variants also tend to demarcate breeds, such as the
“pointed” variety of the Persian, known as the Himalayan by many cat enthusiasts and as a
separate breed by some associations, such as TICA.61 These derived breeds are not genetically
significantly different and therefore share health concerns. Selkirk Rex, American Shorthair, and
British Shorthair all use Persians to help define their structure; thus these breeds also suffer from
polycystic kidney disease,43 and their genetic signatures are very similar to that of Persians,
nearly obscuring their original population foundations of U.S. and UK cats.
A population case study: Turkish Cats
The Lyons’ Feline Genetics laboratory has a standing interest in the dynamics of cat populations
and domestic cat breeds. Through interactions with cat breeders, both in the United States and
abroad, and also with collaborators from Turkish universities and animal shelters, the laboratory
performed three studies on the genetics of cats reportedly and documented to be from Turkey.
Round 1 - The first study was published in a scientific journal in 2007 and analyzed 14 Turkish
Angora and 21 Turkish Van. These cats were primarily from breeders within the United States
and cats were selected to have no grand-parents in common. Contributions from as many
different breeders was attempted to properly survey the gene pool and genetic structure of the
Turkish Angora and Turkish Van breeds in comparison to a variety of other breed cats from the
USA. Random bred cats from collaborators at Turkish universities were also analyzed. The
major outcomes of the first analyses of these breeds indicated:
20
1) Cats from the Mediterranean area, including Turkey, Israel, Cairo, Egypt and Italy are
genetically distinct from cats of Western Europe, Asia, and the Eastern coast of Kenya,
forming four major and distinct populations (races) of cats in the world.
2) Three cat breeds appear to have their ancient origins in the Mediterranean, including
Turkish Angora, Turkish Van and potentially the Egyptian Mau.
3) The Turkish Van and Turkish Angora are genetically distinct breeds.
4) The Turkish Angora had more genetic diversity and a lower inbreeding level in
comparison to Turkish Vans, suggesting they are slightly more genetically healthy.
5) Both Turkish Angora and Turkish Van were at the higher end of the spectrum of
inbreeding levels amongst the cats evaluated, suggesting minimal outcrossing may be
warranted.
6) The genetic variation of the random bred Turkish cats was amongst the highest of all cat
populations, suggesting the region was the origins of cat domestication.
Round 2 (Figure 2) – At the request of various Turkish Van breeders and because of the interest
to add genetic diversity to the Van breed by using cats from Turkey, the study was extended and
analyzed an additional 30 cats. These cats represented individuals supplied by several different
breeders from the USA, The Netherlands, Sweden, and Turkey. Four cats were included that
were listed as crosses with cats noted as Vankedisi. These cats were genetically compared to the
original 21 cats of the breed diversity study. The outcomes of this second study suggested:
1) Sixteen (16) of the 30 cats were highly significant similar genetically to the Turkish Vans
from the USA, suggesting these cats constitute the same breed. These cats were
designated Type A Turkish Vans (Fig. 2, red in Fig. 3).The three of four cats noted as
crosses with Vankedisi cats were in this grouping.
2) One cat was significantly similar to a Turkish Angora – (Type C in Fig. 2, blue in Fig. 3)
3) Thirteen (13) cats had genetics that were significantly different from Turkish Vans,
potentially from three different genetic sources designated at Type B, C and D.
Round 3 – After debate and complaints that breeders did not get to fairly contribute to the
second study, even though submissions were accepted for over a year, an additional 130 cats
were considered that were submitted by many different breeders. The breeders were asked to
prioritize cats as again. Ninety-three (93) had sufficient DNA for the analysis. In addition,
random bred cats from Cyprus, which were collected from the Malcolm Cat Sanctuary, as part of
a study with National Geographic, were available for comparison. A larger analysis was
performed that included Turkish Angoras, random bred cats from Turkey and Cyprus, all cats
submitted for the previous studies, and the new 93 cats, for a database of 248 cats. All cats were
considered in one large analysis. The analysis partitioned the cats based solely on genetic
variation, not by any other identification. Three major genetic groupings of cats were observed.
A cut-off value of 50% similarity was used to assign a cat to a group. The groupings were then
inspected to see what cats they contained. The overall summary of the Turkish cat study
suggested:
21
1) Results from the previous two studies are upheld and consistent.
2) Turkish Angora is a distinct breed and with significant contribution from Turkish random
bred cats. The Turkish Angora breed contains the most representative cats of Turkey.
3) Turkish Vans are a distinct breed and show significantly less influence from Turkish
random bred cats.
4) Cyprus cats are a distinct population within the Mediterranean.
5) Some limited migration of cats occurs between Cyprus and Turkey.
6) Type B, C and D cats from Round 2 were cats from Cyprus.
7) The Turkish Van is genetically similar to the four cats submitted as Vankedisi.
Conclusions
The analysis of cat populations supports several aspects of genetic research but importantly also
the management of cat breeds. Breeds that are genetically related all share the same health
concerns. These breed “families” would be starting candidates for discussions of outcrossing to
increase genetic diversity (Figure 4). In addition, by knowing the populations of origin, the
health concerns of the foundation populations could be at risk and need to be considered for
specific diseases and visa versa. Foundation, random bred cats could be used in outcorssing
programs to increase gene pools but likewise need to be monitored for unwanted genetic traits.
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Figure 1. Genetic distinction of domestic cat breeds.
Different colors represent genetically distinct groups of cats. Different breeds of the same color
imply they form a breed “family” in that these breeds are not genetically distinct from one
another.
23
Figure 2. Genetic analysis of Turkish Cats
Genetic profiles of Turkish Van cats analyzed in the Turkish cat study. Colors indicate
different genetic profiles. Each line is a different cat. Cats to the left are registered
Turkish Vans in the USA.
Figure 3. Genetic analysis of Turkish cats in comparison to street cats from
Cyprus and Turkey.
Genetic profiles of cats analyzed in the Turkish cat study. Colors indicate different genetic
profiles. Each line is a different cat. Blue = Turkish street cats and Turkish Angoras, Red =
Turkish Vans and Green = cats from Cyprus. Three genetic groupings were statistically
significant.
24
Figure 4. Estimating cat breed health with genetics
a. Genetic variation in cat breeds. Ho is average heterozygosity, F is the fixation index.
a. Genetic variation in random bred cats. Ho is average heterozygosity, F is the fixation
index.
25
Breeding practices according to breeds, time and place, and consequences
Leroy G., Rognon X., INRA, UMR1313 Génétique Animale et Biologie Intégrative, France
gregoire.leroy@agroparistech.fr
Abstract:
With companion animals, there is a large diversity in breeding practices, which may impact
genetic variability and health of selected breeds. Based on a survey, we illustrate the specificities
of scent hound dog breeders regarding either their breeding goals or their mating practices.
Mating between close relatives are also investigated in different cat breeds. Such mating are
more or less frequent according to breeds and countries, but seems to occur more rarely in the
last few years. Deleterious impact of inbreeding on fitness traits is also investigated for four dog
breeds. In most cases, litter size and longevity are found significantly reduced for individuals
with large inbreeding levels. These results illustrate how some breeding practices, such as mating
between close relatives, may have an impact on fitness and welfare in cat and dog breeds.
Introduction
Selection in companion animals such as dogs or cats differs from other domesticated species as
they are generally not raised by production or profits. A large majority of breeders are occasional
or hobby breeders and it seems to exist a large diversity of breeding practices according to those
breeders (Leroy et al. 2007). Recently, several reports have pointed out the potential deleterious
impact that may have some of those selection practices regarding the welfare of purebred dogs
(Nicholas 2011), in relation for instance to traits selection which, when taken to extremes, are
deleterious to health (Collins et al. 2011). Inbreeding has also been shown to have deleterious
impact on traits related to reproduction and occurrences of some diseases (Urfer 2009, Mäki et
al. 2001).
We propose here to show, on a few examples in dog and cat, the diversity of breeding practices,
between breeds, between countries, and over time. Impact of inbreeding depression on litter size
and longevity will also be illustrated based on some preliminary results on dog breeds.
Breeding practices according to breeds, results from a dog breeders survey
In dog species, where breeds shows a particularly large morphological diversity, in relation,
among others, to their different uses (pets, hunting, herding…), one may expect to find also a
large diversity of breeding goals according to breeds. To investigate if some differences could
also be found in relation to selection tools, management methods, and reproduction tools, a
survey composed of 55 questions was carried out in 2007 among 985 French dog breeders
(Leroy et al. 2007). Two main explanatory variables were used to analyses the results, namely
the number of litters produced, and the FCI group of the main breed raised.
26
Table 1: Average rank of breeding goals declared by dog breeders according to the
FCI breed group, the lower number being the best goal (there was no significant
effect of number of litters produced on the answers).
Whole
1
2
3
6
7
8
9
4-5-10
sample
Morphology***
2.4
2.1
1.8 1.7 2.1 2.5 2.6 1.7 1.9
Behaviour***
2.5 2.1 2.9 3.1 2.0 2.5 2.3
2.4
1.9
Health***
3.1
2.1 3.0 4.2 3.5 2.5 2.1 2.8
2.9
Work***
3.8
4.7 4.3 1.9 2.2 4.2 4.8 4.1
3.7
Others NS
4.9
4.9 4.8 4.9 4.8 4.8 4.9 4.9
4.9
NS non significant, *** P< 0.001 (From Leroy et al. 2007)
One of the main results of the study was related to the specificities of scent hound breeders,
considering either breeding objectives or mating practices. Indeed, if “morphology” was in
general considered as the first or the second breeding goal (see table 1), “working abilities” were
more important for scent hounds (FCI group 6) pointing dog groups (FCI group 7) breeders.
However, “health” as a selection goal appears completely secondary for scent hounds breeders,
and only 27% of them indicated it as a breeding objective versus 56% for pointing dog breeders
and 71% for overall breeders. It is difficult to interpret in what extent this result is related to a
low number of health problems in scent hounds, which infers that health does not appear as a
problem for breeders, or to the fact that scent hound breeders, who often raise their dogs in
packs, paying less attention to the health of their dogs, relative to breeders raising dogs more
“individually”. Scent hound breeders show other specificities in relation to mating practices.
When paying for a mating made by a sire which does not belong to them, the main modality used
is monetary payment, used by 85% of overall breeders, while in 6th group breeders, only 29% use
this modality. Indeed 85% Scent hound breeders prefer to give a puppy of the litter instead,
versus 28% on average. Scent hound breeders also indicate using less artificial insemination (AI)
than other breeders: 85% of those breeders indicate they never used AI, versus 58% on average.
Finally, according to the French Kennel Club, breeders of the 6th groups are also the only ones to
regularly register dogs with unknown origin, as in 2012, those registrations represented 5% of
the total registrations within the group, versus 0.1% for the other breeds. All those differences
show how some breeds may have their own specificities regarding breeding practices. Those
specificities may eventually be linked with specific patterns concerning within breed genetic
structure and variability, which can have consequences for health and welfare of those breeds.
Inbreeding practices according to breeds, countries and time: examples in cat breeds
Inbreeding practices correspond to intentional mating of related individuals, such as when
breeders attempt to fix or maintain specific traits from a common ancestor. This constitutes a
controversial practice, due to the eventual impact that inbreeding may have on the fitness of
litters produced (inbreeding depression). As a consequence, mating between close relatives (full
or half-sibs for instance) has been banned in several countries, such as the U.K. a few years ago.
It is therefore particularly interesting to investigate differences that may exist according to these
practices. In France, a recent study on 8 cat breeds and groups of breeds (Leroy et al. 2013a)
have shown for instance that the % of individuals inbred when considering 2 generations (i.e.
individuals which are the products of mating between sibs or direct parents), ranged from 2.7%
(Main Coon) to 8.4% (Persian/ Exotic Shorthair), illustrating the differences according to breeds.
27
Those differences may also exist within a given breed. As an illustration we analysed an
international pedigree database for Birman breed, provided by Jerold Bell. We computed the %
of individuals inbred when considering different generations.
Table 2: % of individuals inbred considering 2 or 3 generations during the 1991-2010
period according to four countries
Country
USA
UK
Sweden
Finland
Number of individuals
1185
1481
2820
1508
considered
% of individuals inbred
7%
4%
2%
0%
after 2 generations
% of individuals inbred
27%
26%
12%
7%
after 3 generations
As illustrated by table 2, when comparing different countries over the 1991-2000 period,
breeders from Nordic countries seem to make such mating rather rarely compared to the UK or
the USA. In these two countries 26% and 27% of kittens born over this period of time are inbred
when considering 3 generations, versus 7% and 12% in Finland and Sweden respectively.
% of individuals inbred considering
Figure 1: Evolution of % of Birman cats inbred according to different number of generations
considered, over the 1970-2010 period
It appears also that such mating practices are less and less frequents (see figure 1): from the 70s
to the 2000s, the percentage of individuals inbred considering 3 generations have decreased from
44% to less than 10%. These results are probably explained by the fact that welfare is a growing
concern, which is particularly taken into account in Nordic countries.
Inbreeding consequences on litter size and longevity: examples in dog
It is not easy to quantify the impact of inbreeding on breed health, since they depend on the
mating system, demographic history of the breed and the genetic mechanism involved (Ballou
1997). Here we propose to illustrate the consequences of inbreeding on prenatal and postnatal
survival of purebred dogs, considering litter size and longevity, based on births and deaths
declared for 4 breeds raised in France. Litters born over the 1990-2012 period as well as dogs
28
declared as dead over 2007-2012 were considered for this (see Leroy et al. 2013b). Here dogs
were divided into three inbreeding classes, considering either individuals with inbreeding
coefficient lower than 6.25% (corresponding to an inbreeding equivalent to a mating between
cousins), between 6.25 and 12.5% (mating between half-sibs), and 12.5% and larger.
Litter size
Longevity (in years)
Inbreeding
Figure 2: Evolution of litter size and longevity according to inbreeding coefficient for Bernese
Mountain Dog (BMD), German Shepherd Dog (GSD), Epagneul Breton (EPB) and West
Highland White Terrier (WHW) (95% standard error indicated)
Figure 2 shows the reduction in prolificacy and survival within dog breeds in relation to
inbreeding depression. In all case, except for longevity in West Highland White Terrier,
inbreeding classes were found to have a significant impact on the traits considered (P<0.001).
For instance, in the German Shepherd Dog breed, the average litter size decreased from 5.1 for
litters with low inbreeding coefficient, to 4.7 for litters with inbreeding coefficient larger than
12.5%. Similarly Epagneul Breton dogs with inbreeding coefficient lower than 6.25% showed an
average around 11.5 years, while this longevity was reduced to 10.4 years for dogs with
inbreeding larger than 12.5%. These results show that mating between close relatives clearly
impact the fitness of litters produced, even if there are other factors that affect more largely the
survival and the welfare of animals raised.
Discussion
As illustrated above, breeders of companion animals show a large diversity of breeding practices,
which may impact the genetic variability, as well as the health of populations and individuals
selected. Inbreeding practices may have, in theory, positive effects at the population level.
Indeed it is supposed to increase the exposure of recessive deleterious alleles to selection,
increasing inbreeding purge and reducing the risk of dissemination of a specific defect (Leroy
2011). Yet, given the deleterious consequences that high level of inbreeding may have on traits
related to fitness, namely the litter size and longevity, mating between close relatives should not
be recommended in any case. In practice, it is quite difficult to avoid any level of inbreeding in a
selection program, especially in breeds with small population size. However, one may be
recommend to limit rapid increase of inbreeding as, in theory, slow rates of inbreeding result in
more efficient selection against deleterious defects (Fu et al. 1998). At the population scale, the
over-use of some reproducers should also be avoided as it may increase the risk of dissemination
of genetic disorders (Leroy and Baumung 2011). Finally, choosing reproducers unrelated, or
eventually belonging to another breed, may constitute another option to introduce genetic
variability within a given kennel or breed. To conclude, it has to be emphasized that the
management of breed health have to be planned both at the breeder scale and at the breed club
29
scale. This is why to avoid health problem and get rid of inherited disease, the best chance for a
dog or cat breed is to have breeders and clubs fully cooperating in this common goal.
References
Collins LM, Asher L, Summers JF, McGreevy P (2011) Getting priorities straight: Risk assessment and
decision-making in the improvement of inherited disorders in pedigree dogs. Vet J 189(2): 147154.
Fu YB, Namkoong G, Carlson JE (1998) Comparison of breeding strategies for purging inbreeding
depression via simulation. Conserv Biol 12: 856-864.
Leroy G, Verrier E, Wisner-Bourgeois C, Rognon X (2007) Breeding goals and breeding practices of
French dog breeders: results from a large survey. Rev Med Vet 158: 496-503.
Leroy G (2011) Genetic diversity, inbreeding and breeding practices in dogs: Results from pedigree
analyses. Vet J 189: 177-182.
Leroy G, Baumung R (2011) Mating practices and the dissemination of genetic disorders in domestic
animals, based on the example of dog breeding. Anim Genet 42(1): 66-74.
Leroy G, Hedan B, Phocas F, Verrier E, Mary-Huard T (2013) Inbreeding impact on prolificacy and
longevity in dogs. 64th annual EAAP meeting. Nantes.
Leroy G, Vernet E, Pautet MB, Rognon X (2013a) An insight into population structure and gene flow
within purebred cats. J Anim Breed Genet.
Mäki K, Groen AF, Liinamo AE, Ojala M (2001) Population structure, inbreeding trend and their
association with hip and elbow dysplasia in dogs. Anim Sci 73: 217-228.
Nicholas FW (2011) Response to the documentary Pedigree Dogs Exposed: Three reports and their
recommendations. Vet J 189(2): 123-125.
Urfer SR (2009) Inbreeding and fertility in Irish Wolfhounds in Sweden: 1976 to 2007. Acta vet scand
51: 21.
30
Inbreeding, Outbreeding, and Breed Evolution
Jerold S Bell DVM, Tufts Cummings School of Veterinary Medicine, North Grafton. MA jerold.bell@tufts.edu
Pure-bred dog and pedigreed cat breeds evolved over time through selective breeding to standards.
These standards may have been conformational, behavioral, or working standards. The standards were
usually not organized and written at the inception of the breed, but instead written at a later date of breed
organization. Written standards are often updated over time – sometimes to clarify, and sometimes to
accommodate changes in the breed. Changes in breed standards may change the selective pressures on
what was bred for in the past, or what may be bred for in the future.
The pedigree record of a breed at its inception may be muddled with individuals of unknown ancestry,
or just individuals that fit the conformational or working standard of the breed. These are the breed’s
foundation stock. It is only at a time after an official “establishment” of a breed that a stud-book is
assembled, and soon closed to additional individuals of unknown ancestry. Some cat breeds maintained
open stud books for a period of time that allowed for the continued registration of cats adhering to a
conformational phenotype. This allowed added diversity to their gene pools.
Some breeds are formed through inbreeding on small kindreds of individuals who possess a particular
phenotypic trait. When original breed records are discovered, it is found that several familial lines of
ancestry during breed formation are often abandoned due to the expression of deleterious or undesirable
traits. It is only the lines that produce the desired characteristics and thrive through matings and
generations of breeding that become the mainstream ancestral “founders” of a breed.
Some breeds are formed through the cross-breeding of individuals from other established breeds. These
individuals would be members of established breeds that have already gone through the original
breeding and purging process. The new breed would still go through the typical expansion process.
The pedigree record of breeds shows that after formation, the breed will go through a significant
population expansion associated with increased average inbreeding coefficients. The Birman cat breed
and Cavalier King Charles Spaniel breeds are shown as examples.
Inbreeding coefficients show the genetic relatedness of the parents of individuals. Average inbreeding
coefficients of breed populations show trends in breed evolution. You can look at coefficients two
different ways – a total average inbreeding coefficient that accounts for all generations, and an average
inbreeding coefficient based on a set number of generations. The total generational average inbreeding
coefficient can only increase over time, unless importation from unrelated stock is added to the gene
pool. A 10 generation average inbreeding coefficient calculated from generation to generation (based on
decade of birth) will decrease in an expanding population where the average relatedness of breeding
pairs is less than the previous generation. The single most important factor increasing average 10
generation inbreeding coefficients is the popular sire syndrome. With this, the breed gene pool truncates
around a popular sire line, with the resultant loss of genetic influence of other quality male lines.
Molecular genetic studies of the chromosomal structure of dog breeds show large haplotype blocks
(identical sections of chromosomes) and linkage disequilibrium (LD) representing the results of
inbreeding and purging during breed development (vonHoldt BM et. al. Genome Res. 2011; 21:1294305). Studies of dog breeds estimate that they lose on average 35% of their genetic diversity through
breed formation (Gray MM et. al. Genetics 2009; 181:1493-505).
31
Molecular genetic studies of wolf populations over time mirror those of breed formation. A study of
Finnish Grey Wolves showed significant genetic diversity early on, due to migration from Russian
wolves. The population then went through a significant population expansion that coincided with
increased average inbreeding coefficients, decreased heterozygosity, and increases in the number of
family lines as well as effective breeding population size (Jansson E et. al. Mol Ecol. 2012; 21:5178-93).
Modern breeds of cats and dogs have gone through the above mentioned genetic selection, and are in
various stages of expanding their breeding population and gene pools. Some breeds may have small
effective population sizes and high homozygosity. However, if their offspring are generally healthy their
population can grow and expand. They are at stages of breed development where more populous breeds
were earlier in their development.
Population expansion is an important aspect of breed development and maintenance. It allows on
average the successive mating of individuals less related than the prior generation. It allows the creation
of new “family lines” and within-breed diversity. Population contraction is detrimental to breed
maintenance due to the loss of breeding lines and genetic diversity. Maintaining adequate numbers of
breeders and matings is important to breed vitality and survival.
As a consequence of breed formation dog and cat breeds have high homozygosity. This is the nature of
breed formation. Homozygosity by itself is not detrimental to breeds unless they carry a high genetic
load of deleterious receive genes. Some breeds may show decreased litter size, increased neonatal
mortality, or shorter average life spans with increases in inbreeding coefficients. These “inbreeding
depression” effects are due to the homozygous expression of specific deleterious genes that cause
specific disease. Direct selection against these genes and phenotypes is required to improve breed health.
If breed members are dying younger, what specific disease(s) is occurring in these individuals? If the
breed shows issues with fertility and fecundity, then breeders should specifically select for increased
fertility and fecundity.
Some advocates of dog and cat breeding call for organized outbreeding programs that mate the least
related individuals to each other. These mirror the Species Survival Plans (SSP) formulated for rare and
endangered species. The result of this effort will produce a randomized population and within-breed
increases in heterozygosity regarding gene distribution. However, this will have no effect on the
frequency of deleterious genes. Genes for breed-related genetic disorders that are already dispersed in
the gene pool will continue to produce affected individuals in a random fashion. This type of breeding
plan is also self-limiting, because as you remove the genetic differences between individuals it becomes
increasingly harder to outbreed (find mates that are genetically unlike each other). A healthy and diverse
breed gene pool should have many outbred clusters as well as different linebred families.
The genetic tools of linebreeding and outbreeding should be used for specific purposes. Breeders may
use different breeding tools with each mating that are either closer (linebreeding) or more distant
(outbreeding) than the average in the population based on their needs. Linebreeding concentrates the
genes of specific ancestors. Outbreeding brings in genes that are not present in the mate. When breeders
are each performing matings that are a little different from each other – some linebreeding in one line,
some outbreeding, some linebreeding in another line, etc., it maintains a diverse breed population.
The only way to decrease the frequency of deleterious genes in a population (and increase the frequency
of favorable genes) is through direct selection against (and for) those genes through genetic testing and
phenotypic evaluation. The rate and degree of genetic improvement through selection is directly
32
proportional to the amount of variation that exists between individuals within the breed. Randomizing a
population through outbreeding decreases the ability to apply selective pressure for genetic
improvement. Selective pressure requires lines of individuals who are unlike each other.
Some studies bemoan the homozygosity found in breeds, and call for selection to increase minor
frequency alleles and haplotypes. Molecular genetic tools can identify these, but in most cases the
phenotypic effects of increasing their frequency are unknown. It is possible that genetic selection for
quality and against undesirable traits reduced the frequency of these genes. Blindly selecting for them
without knowing their effect could significantly reverse selection-based breed improvement.
When breeds show high frequency of genetic disease, or significantly diminished fertility and fecundity,
they may have too high a genetic load of disease liability genes. In extreme instances they may require;
a SSP-type plan, opening the study book to importation, or cross-breeding to other related breeds.
However, most breeds do not find themselves in such dire situations, and only require proper selection
to improve their gene pools and genetic health.
The following conclusions can be made concerning breed evolution and health:
-The effects of inbreeding (homozygosity, large haplotype blocks and increased linkage disequilibrium)
are a natural consequence of breed formation.
-Healthy breed gene pools require expanding, or large stable populations.
-Breed health should be measured based on regular surveys of health and reproduction.
-Genetic selection for breed characteristics should avoid disease related phenotypes.
-Genetic selection for breed health should be directed against specific disease liability genes and
phenotypes.
-Breeders should avoid the overuse of popular sires – the most significant factor in limiting breed
genetic diversity.
33
Unraveling the Phenotypic and Genetic Complexity of Canine Cystinuria
Paula S. Henthorn and Urs Giger, Section of Medical Genetics (PennGen), University of
Pennsylvania, Philadelphia, PA henthorn@vet.upenn.edu
Cystinuria is a disease of disrupted amino acid transport in the collecting ducts of the kidney fail
to reclaim certain amino acids (cystine and the dibasic amino acids ornithine, lysine and arginine
referred to as COLA). The increased urinary COLA concentrations reach saturation levels for
cystine, which precipitates to form crystals and stones resulting in renal to urethral obstructions.
Mutations in the SLC3A1 and SLC7A9 genes give rise to cystinuria in the vast majority of
cystinuric humans, where the disease shows autosomal recessive or dominant inheritance
(reviewed in Palacin et al., 2001; Chillaron et al., 2010).
Cystine calculi have been reported from at least 70 dog breeds, with increased incidence in
several breeds (Ling et al., 1998; Osborne et al., 1999); in contrast cystinuria is rarely seen in
cats. We previously demonstrate autosomal recessively inherited cystinuria in Newfoundland
dogs (with less frequent urolithiasis in females due to anatomical urological differences) caused
by a mutation in the SLC3A1 gene that precludes the expression of a functional protein (Casal et
al. 1995; Henthorn et al. 2000). In addition we discovered a similar mutation in the SLC3A1
gene causing recessively inherited cystinuria, a dominantly inherited cystinuria due to a deletion
in SLC3A1, and a missense mutation in SLC7A9 gene associated with persistent cystinuria and
cystine stone formation in Labrador retriever, Australian cattle, and (European) miniature
pinscher dogs, respectively (Brons et al. 2013). These mutations and their consequences appear
to be consistent to those seen in human cystinuria.
However, for a number of other breeds examined for mutations in the SLC3A1 and SLC7A9 gene
protein-coding regions, no obvious mutations have been identified (Henthorn et al., 2000;
Harnevik et al. 2006; PH, UG unpublished data). In addition, it appears that in some breeds
(Mastiff and related breeds, Irish terriers), only adult, intact male dogs show elevated urine
COLA concentrations. In these breeds, the average age of stone formation is later than seen in
male Newfoundland dogs (Giger et al. 2011a,b; PH, UG unpublished data). Most importantly, in
these breeds, urinary aminoaciduria normalized after neutering, making neutering an effective
treatment for cystinuria in some, but not all breeds. Neuter status has no effect on cystinuria in
Newfoundlands, Labrador retrievers, Australian cattle dogs, and Miniature Pinschers (Brons et
al. 2013).
For Mastiffs and related breeds, we have determined that a non-conserved amino acid
substitution (Harnevik et al., 2006; PH unpublished data) as well as other DNA changes in the
SLC3A1 gene that may affect the expression levels of that gene are associated with stone
formation (PH, unpublished data). Intact male dogs that have two copies of this variant version
of the SLC3A1 gene appear to form stones between 1 and 4 years of age (older than
Newfoundlands, but younger than the average age of stone formation reported from the
Minnesota stone laboratory; Osborne et al., 1999). However, not all stone-forming Mastiffs are
homozygous (have two copies) of this variant allele. Additional genetic or environmental factors
may play a role for cystinuria in Mastiffs. This variant SLC3A1 allele is not found in androgendependent cystinuric dogs of other breeds, several in which cystinuria has a relatively high
incidence.
1
34
To simplify discussions of cystinuria, we have suggested a classification system for canine
cystinuria that encompasses both discriminating aspects of the phenotype (for example, gender
affected, androgen dependence, and mode of inheritance) and the gene associated with the
disease (Brons et al. 2013; see table below). We designate type I cystinuria when the disease
shows autosomal recessive inheritance, Type II when inheritance is autosomal dominant, and
Type III for sex-limited/androgen-dependent inheritance (PH, UG, unpublished data). Additional
types can be assigned if found. Specific mutations within each type should lead to phenotypes
that are sufficiently similar that the same medical management and breeding advice applies to all
cases within that type. Involvement of the SLC3A1 gene is indicated by adding –A, and similarly
addendum of –B indicated involvement of mutations in SLC7A9.
Phenotype
Type I - A
Type II - A
Type II - B
Type III -
Inheritance
Autosomal
recessive
Autosomal
dominant
Autosomal
dominant
Sex-limited
Gene
SLC3A1
SLC3A1
SLC7A9
Unknown
Gender
Males and
Females
Males and
Females
Males and
Females
Intact Adult
Males
Androgen dependent
No
No
No
Yes
≥ 8,000
≥ 8,000
nd
≤ 500
≥ 3,000
≥ 700
Newfoundland
Landseer
Labrador
Aust. cattle
dog
Min. Pinscher
Newfoundland
Landseer
Labrador
Aust. cattle
dog
Min. Pinscher
*COL
A
Homozygou
s
Heterozygou
s
Breeds affected
DNA-based genetic
test breeds
≤ 4,000
Mastiff &
related
Scot. Deerhound
Irish Terrier
†Mastiff &
related (risk for
earlier stone
formation)
* µmol/g creatinine, normal ≤ 500
† While we recommend DNA testing of Mastiffs and related breeds for cystinuria, be aware that
this DNA test alone does not completely predict the cystinuria status of every dog (particularly
for 1-2 dogs). Therefore, annual urinary nitroprusside testing is recommended for all adult
intact male dogs.
While there is still much left to discover, these findings advance our understanding of this
genetically complex disease. The characterization of the heterogeneity of cystinuria in different
canine breeds and our proposed new classification system have important ramifications for the
medical and genetic management of cystinuria in many dog breeds. Determining the molecular
mechanism of cystinuria in Mastiffs and other breeds will provide insight into the genetically
complex diseases. Most surprisingly, for cystinuria in some breeds, neutering can effectively
cure the disease, but we caution clinicians to contact us for cases where no studies of cystinuria
2
35
have yet been performed in the breed. And finally, these and future studies will have an impact
on the genetic control of cystinuria in future generations of dogs.
ACKNOWLEDGEMENTS
Dr. Henthorn's cystinuria research is performed in collaboration with Dr. Urs Giger (University
of Pennsylvania School of Veterinary Medicine) and Dr. Adrian Sewell (Department of
Pediatrics, University Children’s Hospital, Frankfurt am Main, Germany) Contributors at the
University of Pennsylvania include Dr. Ann-Kathrin Brons, Caitlin Fitzgerald, Michael Raducha,
JunLong Liu, and Karthik Raj. This work was supported by the University of Pennsylvania
School of Veterinary Medicine, the Canine Health Foundation, the National Institutes of Health
(OD 010939), the Mastiff and Scottish Deerhound national breed clubs, and by individual
breeders. We thank many veterinarians, dog owners and breeders for their participation in this
work.
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Mutations in Autosomal Recessive or Dominant Canine Cystinuria: A New Classification System. J
Vet Internal Medicine, accepted for publication.
Casal ML, Giger U, Bovee KC, Patterson DF. Inheritance of cystinuria and renal defect in
Newfoundlands. J Am Vet Med Assoc 1995;207:1585-1589.
Chillaron J, Font-Llitjos M, Fort J, Zorzano A, Goldfarb DS, Nunes V, Palacín M. Pathophysiology and
treatment of cystinuria. Nat Rev Nephrol 2010;6:424-434.
Giger U, Sewell AC, Lui J, Erat A, Sewell AC, Henthorn PS. Update on Fanconi Syndrome and
Cystinuria in Dogs: Amino Acidurias. In: ACVIM Forum, Denver, CO 2011a
Giger U, Lee JW, Cait Fitzgerald et al, Characterization Of Non-Type I Cystinuria In Irish Terriers, J Vet
Int Med, 2011b ACVIM Forum Abstracts, 2011b:25:718
Harnevik L, Hoppe A, Soderkvist P. SLC7A9 cDNA cloning and mutational analysis of SLC3A1 and
SLC7A9 in canine cystinuria. Mamm Genome 2006;17:769-776.
Henthorn PS, Liu J, Gidalevich T, Fang J, Casal ML, and Patterson DF. Canine cystinuria: polymorphism
in the canine SLC3A1 gene and identification of a nonsense mutation in cystinuric Newfoundland
dogs. Hum Genet 2000;107:295-303.
Ling GV, Franti CE, Ruby AL, and Johnson DL. Urolithiasis in dogs. II: Breed prevalence, and
interrelations of breed, sex, age, and mineral composition. Am J Vet Res 1998;59:630-642.
Osborne CA, Sanderson SL, Lulich JP, Bartges JW, Ulrich LK, Koehler LA, Bird KA, Swanson LL.
Canine cystine urolithiasis. Cause, detection, treatment, and prevention. Vet Clin N Am:Sm An Pract
1999; Jan;29(1):193-211, xiii.
Palacin M, Goodyer P, Nunes V, et al. Cystinuria. In: Scriver CR, ed. The metabolic and molecular bases
of inherited disease, 8th ed. New York: McGraw-Hill; 2001:4909-4932.
3
36
How to Use and Interpret Genetic Tests for Heart Disease in Cats and Dogs
Kathryn M. Meurs, DVM, PhD, Diplomate ACVIM (Cardiology), North Carolina State
University College of Veterinary Medicine, Raleigh, NC kate_meurs@ncsu.edu
Important definitions:
Congenital heart disease- present since birth, may be inherited or may not be inherited
Acquired heart disease- develops after the animal reached maturity, may be inherited or may not
be inherited
Heterozygote: has 1 copy of the mutated gene and 1 copy of a normal gene
Homozygote: has 2 copies of the mutated gene
Penetrance: Percentage of population with a mutation that show the disease
Expression: Severity of disease
Utilization of molecular information for screening and therapeutic issues
Increasingly heart disease in dogs and cats is found to be of inherited origin. This seminar
will discuss common testing for known genetic mutations for cats and dogs. Genetic tests are
generally a PCR test that identifies either a marker for the disease or that identifies the actual
genetic mutation. PCR is a method that takes a small amount of DNA provided by the clinician
or owner and amplifies a region of interest so it can be carefully inspected. DNA can be usually
provided in a blood sample in an EDTA tube, a buccal swab or even a semen sample. The DNA
will be inspected for the abnormality by the lab and the presence or absence of the marker or
mutation identified. However, breeders and owners should be cautioned and advised how to best
use the information. The results should be carefully considered and should be weighed against
the severity of the trait, the size of the breed’s gene pool, the mode of inheritance of the trait and
the positive traits that this individual animal brings to a breed. In some cases, strict screening and
removal programs may be very detrimental to small gene pools in specific breeds; breeding
recommendations should be carefully designed.
We will use two examples for illustration – Feline Hypertrophic Cardiomyopathy and Boxer
Arrhythmogenic Right Ventricular Cardiomyopathy (ARVC)
Feline Hypertrophic Cardiomyopathy
Hypertrophic cardiomyopathy is the most common form of heart disease in the cat. It is
an adult onset and known to be inherited in the Maine Coon and Ragdoll breeds and thought to
be inherited in Norwegian Forest, Siberian, Sphynx and Bengal cats among others. Causative
genetic mutations have now been identified in the Maine Coon and Ragdoll.
In the Maine Coon, a genetic mutation has been identified in the myosin binding protein
C (MYBPC3) gene. The penetrance of the disease is fairly low for heterozygotes (about 30%
37
show disease) but high for homozygotes (about 80%). The Maine Coon mutation appears to be
quite breed specific. It is unlikely to be associated with hypertrophic cardiomyopathy in other
breeds of cats unless they are closely related to the Maine Coon breed. Additionally, although
this mutation has been shown to lead to the development of this disease in this breed, not all cats
with the disease have this mutation so it is clear that there is more than 1 mutation in the maine
coon cat.
A substitution mutation has also been identified in the myosin binding protein C gene in
the Ragdoll cat. However, the Ragdoll mutation is different from the Maine Coon mutation and
is at a different location.
It is extremely unlikely that the Maine Coon and Ragdoll mutations were inherited from a
common ancestor since the mutations are different and are located in such different regions of
the gene. Additionally, it is very unlikely that other breeds of cats have the identical mutation.
Genetic testing is now available to test a cat for either mutation by submitting a DNA
sample to a reputable screening laboratory (http://www.ncstatevets.org/genetics/) . Good quality
DNA samples can be obtained either from a blood sample in an EDTA tube or by brushing the
oral gums of the cat with a special buccal swab, although many labs will even accept samples
submitted on a cotton swab.
The test results should verify that the cat is negative, heterozygous or homozygous for the
mutation. Cats that test negative do not have the mutation. This does not mean that they cannot
ever develop hypertrophic cardiomyopathy, it simply means that they will not develop the form
of the disease caused by the specific genetic mutation.
Due to an apparently fairly high prevalence of the mutation in both breeds, it would seem
to be unwise to recommend that all cats with the mutation be removed from the breeding
programs since this could result in dramatically altering the genetic makeup of these breeds.
Additionally, it should be emphasized that not all cats that have the mutation, particularly if they
are heterozygous, will develop a clinical form of the disease. Our current recommendations for
both breeds are to not use cats that are homozygous for the mutation for breeding purposes since
they will certainly pass on the mutation and they have the highest risk of developing the disease.
Heterozygous cats should be carefully evaluated. Cats that have many strong positive breed
attributes and are disease negative at time of breeding could be bred to a mutation negative cat.
Their lack of clinical disease may suggest that they have a less penetrant form of the disease or
that they just do not show evidence of this adult onset clinical disease yet. Therefore these cats
should only be used if they are exceptional for the breed and they should be clinically evaluated
for the disease every year. If they develop the clinical disease, they should no longer be kept in
the breeding program. The offspring of the mating of a positive heterozygous and a negative
should be screened for the mutation, and if possible, a mutation negative kitten with desirable
traits should be selected to replace the mutation positive parent in the breeding colony. Over a
few generations this will decrease the prevalence of the disease mutation in the population,
hopefully without greatly altering the genetic makeup of the breed too significantly. Finally,
disease negative but mutation positive cats should be evaluated annually for presence of disease.
38
Arrhythmogenic right ventricular cardiomyopathy in the boxer
Since the early 1980’s, the term boxer cardiomyopathy has been used to describe adult
boxer dogs that present with ventricular arrhythmias, and sometimes, syncope. Recent studies
have demonstrated that the disease has many similarities to a human disease called
Arrhythmogenic Right Ventricular Cardiomyopathy (ARVC). The similarities between the
diseases include clinical presentation, etiology and a fairly unique histopathology that includes a
fibrous fatty infiltrate of the right ventricular free wall. The disease is most commonly
characterized by ventricular arrhythmias, syncope and sudden death. However, systolic
dysfunction and ventricular dilation are seen in a small percentage of cases.
Arrhythmogenic right ventricular cardiomyopathy is a familial disease in the boxer and
appears to be inherited as an autosomal dominant trait. Unfortunately, the disease also appears to
be a disease of variable genetic penetrance and affected dogs can have many different
presentations including asymptomatic, syncope, sudden death and systolic dysfunction with
CHF. A genetic mutation has now been identified for boxer arrhythmogenic right ventricular
cardiomyopathy although it is not yet known if this will be responsible for all cases of the
disease since in human beings there are several known mutations. Individuals interested in
screening for the disease in breeding animals may do so with either a buccal swab or blood
sample. (http://www.ncstatevets.org/genetics/)
In human beings with ARVC, there are multiple genetic mutations that can lead to the
development of the disease. At this time we do not know if this mutation is the only cause in the
Boxer, therefore, clinical screening is still recommended. Since ARVC presents as an electrical
abnormality more often than one of myocardial dysfunction, screening efforts should be based on
annual Holter monitoring as well as annual echocardiography. Until a greater understanding of
disease inheritance and disease progression exists, caution should be used when advising
breeders to remove dogs from breeding programs. Overzealous removal of animals based on the
results of a single Holter monitor may have a significant negative impact on the breed.
Conclusions
Genetic testing is becoming increasingly available for the pet population. It should be
remembered that inherited disease is complex and that there is no perfect test. Results of the
genetic test should be carefully considered and should be weighed against the severity of the
trait, the size of the breed’s gene pool, the mode of inheritance of the trait and the positive traits
that this individual animal brings to a breed. In some cases, strict screening and removal
programs may be very detrimental to small gene pools in specific breeds; breeding
recommendations should be carefully designed.
39
Update on Genetic Tests for Diseases & Traits in Cats: Implications for Cat Health, Breed
Management & Human Health
Leslie A. Lyons, PhD, College of Veterinary Medicine, University of Missouri - Columbia
Lyonsla@missouri.edu
Below is an update of genetic tests for the domestic cat (30 July 2013). Text is modified from:
Genetic testing in domestic cats. Lyons LA. Mol Cell Probes. 2012 Dec;26(6):224-30. doi:
10.1016/j.mcp.2012.04.004. Epub 2012 Apr 21.
Introduction
Genetic testing has been available in the domestic cat since the 1960’s, but as like other species,
over the past 50 years, the level of resolution has improved from the chromosome level to the
sequence level. Knowing the direct causative mutation for a trait or disease assist cat breeders
with the breeding programs and can help clinicians determine heritable presentations versus
idiopathic versions of a health concern. Genetic tests cover all the various forms of DNA
variants, including chromosomal abnormalities, mtDNA variation, gene loss, translocations,
large inversions, small insertions and deletions and the simple nucleotide substitutions. Higher
throughput technologies have made genetic testing cheaper, simpler and faster, thereby making
cat genetic testing affordable to the lay public and small animal practice clinicians. The genetic
resources for cats and other animal species have also opened the doors for animal evidence to be
supportive in criminal investigations. This presentation will highlight the various tests available
for the domestic cat and their specific capabilities and role’s in cat health and management.
Cat Chromosomes
Some of the earliest genetic testing for any species was the examination of the chromosomes to
determine the presence of the normal and complete genomic complement. Early studies of
mitotic chromosomes of the domestic cat revealed an easily distinguishable karyotype consisting
of 18 autosomal chromosomes and the XY sex chromosome pair, resulting in a 2N complement
of 38 chromosomes for the cat genome [1]. Sex chromosome aneuploidies and trisomies of
small acrocentric chromosomes were typically associated with cases of decreased fertility and
syndromes that displayed distinct morphological presentations. Turner’s Syndrome (XO),
Klinefelter’s Syndrome (XXY) and chimerism has been documented in the domestic cat.
Because cat has a highly recognizable X-linked trait [2-5], Orange, and the X-inactivation
process was recognized [6], tortoiseshell and calico male cats were the first feline suspects of
chromosomal abnormalities. Karyotypic and now gene-based assays are common methods to
determine if a cat with ambiguous genitalia [7] or a poor reproductive history has a chromosomal
abnormality. Karyotypic studies of male tortoiseshell cats have shown that they are often
mosaics, or chimeras, being XX/XY in all or some tissues [5, 8-15]. The minor chromosomal
differences that are cytogenetically detectable between a domestic cat and an Asian leopard cat
are likely the cause of fertility problems in the Bengal cat breed, which is a hybrid between these
two species [16]. Other significant chromosomal abnormalities causing common “syndromes”
are not well documented in the cat. Several research and commercial laboratories can perform
cat chromosomal analyses when provided a living tissue, such as a fibroblast biopsy or whole
blood for the analysis of white blood cells.
40
Inherited Disease Tests
The candidate gene approach has been fruitful in domestic cat investigations for the
identification of many diseases and trait mutations. The first mutations identified were for a
gangliosidosis and muscular dystrophy, discovered in the early and mid-1990’s [17, 18], as these
diseases have well defined phenotypes and known genes with mutations that were as found in
humans. Most of the common diseases, coat colors, and coat types were deciphered in the cat
following the same candidate gene approach.
Most of the identified disease tests in cats that are very specific to breeds and populations are
available as commercial genetic tests (Table 1). Typically, diseases are identified in cat breeds,
which are a small percentage of the cat population of the world, perhaps at most 10 – 15% in the
USA [19]. However, some mutations that were found in a specific breed, such as
mucopolysaccharidosis in the Siamese [20, 21], were found in a specific individual and the
mutation is not of significant prevalence in the breed (Table 2). These genetic mutations should
not be part of routine screening by cat breeders and registries, but clinicians should know that
genetic tests are available for diagnostic purposes, especially from research groups with
specialized
expertise,
such
as
at
the
University
of
Pennsylvania
(http://research.vet.upenn.edu/penngen). Other diseases, such as polycystic kidney disease
(PKD), are prevalent, PKD in Persians is estimated at 30 – 38% worldwide [22-24]. Because of
cross breeding with Persians, many other breeds, such as British Shorthairs, American
Shorthairs, Selkirk Rex, and Scottish Folds, also need to be screened for PKD [25-27]. As PKD
testing begins to become less common, as breeders remove positive cats, other genetic tests are
becoming more popular, such as coat color and other disease traits (Figure 1).
Genetic Testing Concerns in Hybrid Cat Breeds
Several cat breeds were formed by crossing with different species of cats. The Bengal breed is
acknowledged worldwide and has become a highly popular breed. To create Bengals, Asian
leopard cats (Felis bengalensis) were and are bred with domestic cat breds like Egyptian Mau,
Abyssinian and other cats to form a very unique breed in both color and temperament [28]. An
Asian leopard cat had a common ancestor with the domestic cat about 6 million years ago, the
bobcat about 8 million years ago, the Serval about 9.5 million years ago [29]. The Jungle cat is
more closely related to a domestic cat than the leopard cat to the domestic cat. In addition, for
some of these wild felid species, different subspecies were incorporated into the breed. The
DNA sequence between a domestic cat and one of these wild felid species will have many
genetic differences, less for the Jungle cat, more for Serval as compared to a domestic cat. The
genetic differences are most likely silent mutations, but, the variation will interplay with genetic
assays and may cause more allelic drop-out than what would be normally anticipated. No
genetic tests are validated in the hybrid cats breeds, although the tests are typically used very
frequently in Bengal cats. Thus, the accuracy for any genetic test is not known for hybrid cat
breeds. A genetic test for the Charcoal coloration in Bengals will likely soon be available and is
unique due to the hybridization with leopard cats.
Race and Breed Identification
A newly developing test for the domestic cat is a race and breed identification panel. Based on
the studies by Lipinski et al. (2008) [30], and Kurushima et al. (2012, submitted), STRs have
been tested in a variety of random bred cats from around the world and a majority of the major
41
cat breeds of the USA and other regions. The genetic studies have been able to differentiate
eight worldwide populations of cats – races – and can distinguish the major breeds. Analyses of
the present day random bred cat populations suggest that the regional populations are highly
genetically distinct, hence analogous to humans, different races of cats. The regional genetic
differentiation is capture and displayed within the breeds that developed later from those
populations. The foundation population (race) of the Asian breeds, such as Burmese and
Siamese, are the street cats of Southeast Asia, whereas the foundation population (race) of the
Maine Coon and Norwegian Forest cat are Western European cats. Phenotypic markers help to
delineate breeds within specific breed families, such as the Persian, Burmese, and Siamese
families. The cat race and breed identification tests are similar to tests that have been developed
for the dog, such as the Mars, Inc. Wisdom Panel (http://www.wisdompanel.com/). Although
similar, domestic cats are random bred cats and not a concoction of pedigreed breed cats. Cat
breeds developed from the random bred populations that have existed in different regions of the
world for thousands of years. Therefore, the claims of the cat race and breed identification tests
are different than the dog tests, not claiming that most household cats are recent offspring of
pedigreed cats.
Implications for Cat Health & Breeding
To date, most cat genetic tests have been for traits that have nearly complete penetrance, having
little variability in expression, and early onset. These aspects are important when considering
management in the breed. If your cat has the PKD mutation – it will get kidney cysts – but the
development of renal failure is variable (variable expression). Therefore, some recognized
mutations in cats might be considered risk factors, predisposing an individual to health problem.
Excellent examples of mutations that confer a risk in cats are the DNA variants associated with
cardiac disease in cats. Hypertrophic cardiomyopathy (HCM) is a recognized genetic condition
[31]. In 2005, Drs. Meurs, Kittleson and colleagues published that a DNA alteration, A31P, in
the gene cardiac myosin-binding protein C 3 (MYBPC3) was strongly associated with HCM in a
long-term research colony of Maine Coon cats at UC Davis [32]. Recent studies have shown
that not all Maine Coon cats with the A31P mutation get HCM [33, 34] and one of those papers
has mistakenly interpreted this lack of penetrance as being evidence that the A31P mutation is
not causal [34]. This interpretation is misleading, causing debate as to the validity of the Maine
Coon HCM test. As true in humans with cardiac disease, the finding that not all cats with the
A31P mutation in MYBPC3 get HCM is actually usual in the field of HCM genetic testing.
Like cat HCM mutations, other disease mutations have shown variation in penetrance and
expression, such as the CEP290 PRA mutation in Abyssinians and some cats with the pyruvate
kinase deficiency can have very mild and subclinical presentations [35]. Thus, disease or trait
causing mutations may not be 100% penetrant, thus, they do not always cause clinically
detectable disease.
Conclusion
Many aspects of the population and the specific mutation must be considered during
management of a disease. Diseases with a low frequency in a large population could likely be
eliminated. Diseases in a very high frequency or present in a very small population need to be
slowly removed from the population with great care. Genetic testing is an important diagnostic
tool for the veterinarian, breeder, and owner. Genetic tests are not 100% foolproof and the
42
accuracy of the test procedure and the reputation and customer service of the genetic testing
laboratory needs to be considered. Some traits are highly desired and genetic testing can help
breeders to more accurately determine appropriate breedings, potentially becoming more
efficient breeders, thus lowering costs and excess cat production. Other traits or diseases are
undesired, thus genetic testing can be used to prevent disease and potentially eradicating the
concern from the population. Genetic tests for simple genetic traits are more consistent with
predicting the trait or disease presentation, but, as genomics progress for the cat, more tests that
confer risk will become more common.
43
Table 1. Common commercialized DNA tests for domestic cats.
MOI‡
Phenotype
Breeds
Gene
Mutation
Agouti (A+, a)[36]
AR
Banded fur to solid
All cats
ASIP
c.122_123delCA
Amber (E+, e)[37]
AR
Brown color variant
Norwegian
Forest
MC1R
c.250G>A
Brown (B+, b, bl)[38, 39]
AR
Brown, light brown color variants
All cats
TYRP1
b = c.8C>G, bl = c.298C>T
Color (C+, Cb, Cs, c)[39-41]
AR
Burmese, Siamese color pattern,
full albino
All breeds
TYR
cb = c.715G>T, cs = c.940G>A,
c = c.975delC
Dilution (D+, d)[42]
AR
Black to grey / blue,
All cats
MLPH
c.83delT
MC1R
c.250G>A
Disease / Trait (alleles)
Orange to cream
Extension (E+, e) – Amber
[37]
AR
Brown/red color variant
Norwegian
Forest
Fold (Fd, fd+)
AD
Ventral ear fold
Scottish Fold
Gloves (G+, g)[43]
AR
White feet
Birman
KIT
In Press
Hairless (Hr+, hr))[44]
AR
Atrichia
Sphynx
KRT71
c.816+1G>A
Inhibitor
AD
Absence of phaeomelanin
All cats
Long fur (L+, l)[45, 46]
AR
Long fur
All cats§
FGF5
c.356_367insT, c.406C>T,
c.474delT, c.475A>C
Manx (M, m+)
AD
Absence/short tail
Manx, American
Bobtail,
PixieBob
Rexing (R+, r)[47]
AR
Curly hair coat
Cornish Rex
44
In Press
c.998delT, c.1169delC, and
c.1199delC,
c.998_1014dup17delGCC
PYP2R5
c.250_253delTTTG
Rexing (Re+, re)[44]
AR
Curly hair coat
Devon Rex
KRT71
c.1108-4_1184del,
c.1184_1185insAGTTGGAG,
c.1196insT
Rexing[48]
AD
Curly hair coat
Selkirk Rex
KRT71
c.445-1G>C
Tabby[49]
AR
Blotched/classic pattern
All cats
AB Blood Type (A+, b)[50]
AR
Determines Type B
All cats
Craniofacial Defect
AR
Craniofacial Defect
Burmese
Gangliosidosis 1[51]
AR
Lipid storage disorder
Korat, Siamese
GBL1
c.1457G>C
AR
Burmese
HEXB
c.1356del-1_8,
c.1356_1362delGTTCTCA
AR
Korat
HEXB
c.39delC
Glycogen Storage Dis. IV[53]
AR
Glycogen storage disorder
Norwegian
Forest
GBE1
IVS11+1552_IVS12-1339
del6.2kb ins334 bp
Hypertrophic
Cardiomyopathy[32]
AD
Cardiac disease
Maine Coon
MYBPC
c.93G>C
Hypertrophic
Cardiomyopathy[54]
AD
Cardiac Disease
Ragdoll
MYBPC
c.2460C>T
Hypokalemia[55]
AR
Potassium deficiency
Burmese
WNK4
c.2899C>T
Progressive Retinal
Atropy[56]
AR
Late onset blindness
Abyssinian
CEP290
IVS50 + 9T>G
Progressive Retinal
Atropy[57]
AD
Early onset blindness
Abyssinian
CRX
c.546delC
Polycystic Kidney
Disease[27]
AD
Kidney cysts
Persian
PKD1
c.10063C>A
45
TAQPEP S59X, T139N, D228N, W841X
CMAH
c.1del-53_70, c.139G>A
In Press
Pyruvate Kinase Def.[58]
AR
Hemopathy
Abyssinian
PKLR
c.693+304G>A
Spinal Muscular Atrophy[59]
AR
Muscular atrophy
Maine Coon
LIX1-LNPEP
Partial gene deletions
‡ Mode of inheritance of the non-wildtype variant, § Long fur variants are more or less common depending on the breed. Not all
transcripts for a given gene may have been discovered or well documented in the cat, mutations presented as interpreted from
original publication.
46
Table 2. Other Mutations for Inherited Domestic Cat Diseases†.
Gene
Mutation‡
Disease
Gene
Mutation‡
CYP11B1
Exon 7 G>A
Mucopolysaccharidosis I[61]
IDUA
c.
1107_1109delCGA
or c. 1108_1110
GAC
Dihydropyrimidinase Def.
DPY8
c.1303G>A
Mucopolysaccharidosis VI[21]
ARSB
c.1427T>C
Fibrodysplasia Ossificans
Progressiva
ACVR1
G617A (R206H)
Mucopolysaccharidosis VI[20, 62]
ARSB
c.1558G>A
GLB1
c.1448G>C
HEXB
c.1467_1491inv
Mucopolysaccharidosis VII[65]
GUSB
c.1052A>G
HEXB
c.667C>T
Niemann-Pick C[67]
NPC
c.2864G>C
GM2A
c.390_393GGTC
Polydactyla[68]
SHH
c.479A>G
Hemophilia B[69]
F9
c.247G>A
Polydactyla[68]
SHH
c.257G>C,
c.481A>T
Hemophilia B[69]
F9
c.1014C>T
Porphyria (congenital
erythropoietic)[70]
UROS
c.140C>T,
c.331G>A
Hyperoxaluria[71]
GRHPR
G>A I4 acceptor site
Porphyria (acute intermittent)[72]
HMBS
c.842_844delGAG,
c.189dupT,
c.250G>A,
c.445C>T
LPL
c.1234G>A
Vitamin D Resistant Rickets[74]
CYP27B1
c.223G>A,
c.731delG
c.1748_1751delCCAG Vitamin D Resistant Rickets[76]
CYP27B1
c.637G>T
Disease
11b-hydroxylase
Def. (Congenital Adrenal
Hypoplasia) [60]
Lipoprotein Lipase Def.[73]
Mannosidosis, alpha[75]
LAMAN
47
Mucolipidosis II[77]
GNPTA
c.2655C>T
† The presented conditions are not prevalent in breeds or populations but may have been established into research colonies. ‡ Not
all transcripts for a given gene may have been discovered or well documented in the cat, mutations presented as interpreted from
original publication.
48
Figure 1. Trends of genetic testing in the domestic cat. DNA-based genetic tests are presented for the cat. Parentage
and individual identification (DNA) has not increased as cats do not require testing for registration. One of the most
popular tests, PKD, is presented separately to show that the testing requests are decreasing as breeders are eliminating
positive cats from breeding programs. Other disease tests and color tests are becoming more popular tests in the cat
market.
49
Figure 2. The slippery slope of mutation lethality. Some mutations are so severe, they cause death in utero, such as PKD
and taillessness. Some have high and severe penetrance while others have low and mild penetrance. All these factors
and others should be considered when managing a cat population.
50
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2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
12.
13.
14.
15.
16.
17.
18.
19.
20.
21.
22.
23.
24.
25.
26.
27.
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Peterschmitt, M., et al., Mutation in the melanocortin 1 receptor is associated with amber colour in the
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That Defines the Cornish Rex Cat Breed. PLoS One, 2013. 8(6): p. e67105.
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De Maria, R., et al., Beta-galactosidase deficiency in a Korat cat: a new form of feline GM1gangliosidosis. . Acta Neuropathol (Berl), 1998. 96: p. 307-14.
Bradbury, A.M., et al., Neurodegenerative lysosomal storage disease in European Burmese cats with
hexosaminidase beta-subunit deficiency. Mol Genet Metab, 2009. 97(1): p. 53-9.
Muldoon, L.L., et al., Characterization of the molecular defect in a feline model for type II GM2gangliosidosis (Sandhoff disease). Am J Pathol, 1994. 144(5): p. 1109-18.
Martin, D.R., et al., Mutation of the GM2 activator protein in a feline model of GM2 gangliosidosis. Acta
Neuropathol, 2005. 110(5): p. 443-50.
Meurs, K.M., et al., A cardiac myosin binding protein C mutation in the Maine Coon cat with familial
hypertrophic cardiomyopathy. Hum Mol Genet, 2005. 14(23): p. 3587-93.
Meurs, K.M., et al., A substitution mutation in the myosin binding protein C gene in ragdoll hypertrophic
cardiomyopathy. Genomics, 2007. 90(2): p. 261-4.
Gandolfi, B., et al., First WNK4-hypokalemia animal model identified by genome-wide association in
Burmese cats. PLoS One, 2012. 7(12): p. e53173.
Menotti-Raymond, M., et al., Mutation in CEP290 discovered for cat model of human retinal degeneration.
J Hered, 2007. 98(3): p. 211-20.
Menotti-Raymond, M., et al., Mutation discovered in a feline model of human congenital retinal blinding
disease. Invest Ophthalmol Vis Sci. , 2010. 51(6): p. 2852-9.
Lyons, L.A., et al., Feline polycystic kidney disease mutation identified in PKD1. J Am Soc Nephrol, 2004.
15(10): p. 2548-55.
Grahn, R.A., et al., Erythrocyte Pyruvate Kinase Deficiency mutation identified in multiple breeds of
domestic cats. BMC Vet Res, 2012. 8(1): p. 207.
Fyfe, J.C., et al., An approximately 140-kb deletion associated with feline spinal muscular atrophy implies
an essential LIX1 function for motor neuron survival. Genome Res, 2006. 16(9): p. 1084-90.
51
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29.
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31.
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gene in a cat. J Vet Intern Med, 2012. 26(5): p. 1221-6.
He, X., et al., Identification and characterization of the molecular lesion causing mucopolysaccharidosis
type I in cats. Mol Genet Metab, 1999. 67(2): p. 106-12.
Yogalingam, G., et al., Feline mucopolysaccharidosis type VI. Characterization of recombinant Nacetylgalactosamine 4-sulfatase and identification of a mutation causing the disease. J Biol Chem, 1996.
271(44): p. 27259-65.
Yogalingam, G., et al., Mild feline mucopolysaccharidosis type VI. Identification of an Nacetylgalactosamine-4-sulfatase mutation causing instability and increased specific activity. J Biol Chem,
1998. 273(22): p. 13421-9.
Crawley, A.C., et al., Two mutations within a feline mucopolysaccharidosis type VI colony cause three
different clinical phenotypes. J Clin Invest, 1998. 101(1): p. 109-19.
Uddin, M.M., et al., Identification of Bangladeshi domestic cats with GM1 gangliosidosis caused by the
c.1448G>C mutation of the feline GLB1 gene: case study. J Vet Med Sci, 2013. 75(3): p. 395-7.
Martin, D.R., et al., An inversion of 25 base pairs causes feline GM2 gangliosidosis variant. Exp Neurol,
2004. 187(1): p. 30-7.
Fyfe, J.C., et al., Molecular basis of feline beta-glucuronidase deficiency: an animal model of
mucopolysaccharidosis VII. Genomics, 1999. 58(2): p. 121-8.
Kanae, Y., et al., Nonsense mutation of feline beta-hexosaminidase beta-subunit (HEXB) gene causing
Sandhoff disease in a family of Japanese domestic cats. Res Vet Sci, 2007. 82(1): p. 54-60.
Somers, K., et al., Mutation analysis of feline Niemann-Pick C1 disease. Mol Genet Metab. , 2003. 79: p.
99-103.
Lettice, L.A., et al., Point mutations in a distant sonic hedgehog cis-regulator generate a variable
regulatory output responsible for preaxial polydactyly. Hum Mol Genet, 2008. 17(7): p. 978-85.
Goree, M., et al., Characterization of the mutations causing hemophilia B in 2 domestic cats. J Vet Intern
Med, 2005. 19(2): p. 200-4.
Clavero, S., et al., Feline congenital erythropoietic porphyria: two homozygous UROS missense mutations
cause the enzyme deficiency and porphyrin accumulation. Mol Med, 2010. 16(9-10): p. 381-8.
Goldstein, R., et al., Primary Hyperoxaluria in cats caused by a mutation in the feline GRHPR gene. J
Hered, 2009. 100(Supplement 1): p. S2-S7.
Clavero, S., et al., Feline acute intermittent porphyria: a phenocopy masquerading as an erythropoietic
porphyria due to dominant and recessive hydroxymethylbilane synthase mutations. Hum Mol Genet, 2010.
19(4): p. 584-96.
Ginzinger, D.G., et al., A mutation in the lipoprotein lipase gene is the molecular basis of chylomicronemia
in a colony of domestic cats. J Clin Invest, 1996. 97(5): p. 1257-66.
Geisen, V., K. Weber, and K. Hartmann, Vitamin D-dependent hereditary rickets type I in a cat. J Vet
Intern Med, 2009. 23(1): p. 196-9.
Berg, T., et al., Purification of feline lysosomal alpha-mannosidase, determination of its cDNA sequence
and identification of a mutation causing alpha-mannosidosis in Persian cats. Biochem J, 1997. 328 ( Pt 3):
p. 863-70.
Grahn, R., et al., No bones about it! A novel CYP27B1 mutation results in feline vitamin D-dependent
Rickets Type I (VDDR-1). in preparation, 2011.
Mazrier, H., et al., Inheritance, biochemical abnormalities, and clinical features of feline mucolipidosis II:
the first animal model of human I-cell disease. J Hered, 2003. 94(5): p. 363-73.
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domestic cat. Genomics, 2006.
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of Birman cats. . submitted, 2010.
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associated with the domestic cat AB blood group. BMC Genet, 2007. 8: p. 27.
De Maria, R., et al., Beta-galactosidase deficiency in a Korat cat: a new form of feline GM1gangliosidosis. . Acta Neuropathol (Berl), 1998. 96: p. 307-14.
Bradbury, A.M., et al., Neurodegenerative lysosomal storage disease in European Burmese cats with
hexosaminidase beta-subunit deficiency. Mol Genet Metab, 2009. 97(1): p. 53-9.
Martin, D.R., et al., Mutation of the GM2 activator protein in a feline model of GM2 gangliosidosis. Acta
Neuropathol, 2005. 110(5): p. 443-50.
Meurs, K.M., et al., A substitution mutation in the myosin binding protein C gene in ragdoll hypertrophic
cardiomyopathy. Genomics, 2007. 90(2): p. 261-4.
Gandolfi, B., et al., First WNK4-hypokalemia animal model identified by genome-wide association in
Burmese cats. PLoS One, 2012. 7(12): p. e53173.
Menotti-Raymond, M., et al., Mutation in CEP290 discovered for cat model of human retinal degeneration.
J Hered, 2007. 98(3): p. 211-20.
Menotti-Raymond, M., et al., Mutation discovered in a feline model of human congenital retinal blinding
disease. Invest Ophthalmol Vis Sci., 2010. 51(6): p. 2852-9.
Grahn, R.A., et al., Erythrocyte Pyruvate Kinase Deficiency mutation identified in multiple breeds of
domestic cats. BMC Vet Res, 2012. 8(1): p. 207.
Fyfe, J.C., et al., An approximately 140-kb deletion associated with feline spinal muscular atrophy implies
an essential LIX1 function for motor neuron survival. Genome Res, 2006. 16(9): p. 1084-90.
54
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gene in a cat. J Vet Intern Med, 2012. 26(5): p. 1221-6.
He, X., et al., Identification and characterization of the molecular lesion causing mucopolysaccharidosis
type I in cats. Mol Genet Metab, 1999. 67(2): p. 106-12.
Crawley, A.C., et al., Two mutations within a feline mucopolysaccharidosis type VI colony cause three
different clinical phenotypes. J Clin Invest, 1998. 101(1): p. 109-19.
Uddin, M.M., et al., Identification of Bangladeshi domestic cats with GM1 gangliosidosis caused by the
c.1448G>C mutation of the feline GLB1 gene: case study. J Vet Med Sci, 2013. 75(3): p. 395-7.
Martin, D.R., et al., An inversion of 25 base pairs causes feline GM2 gangliosidosis variant. Exp Neurol,
2004. 187(1): p. 30-7.
Fyfe, J.C., et al., Molecular basis of feline beta-glucuronidase deficiency: an animal model of
mucopolysaccharidosis VII. Genomics, 1999. 58(2): p. 121-8.
Kanae, Y., et al., Nonsense mutation of feline beta-hexosaminidase beta-subunit (HEXB) gene causing
Sandhoff disease in a family of Japanese domestic cats. Res Vet Sci, 2007. 82(1): p. 54-60.
Somers, K., et al., Mutation analysis of feline Niemann-Pick C1 disease. Mol Genet Metab. , 2003. 79: p.
99-103.
Lettice, L.A., et al., Point mutations in a distant sonic hedgehog cis-regulator generate a variable
regulatory output responsible for preaxial polydactyly. Hum Mol Genet, 2008. 17(7): p. 978-85.
Goree, M., et al., Characterization of the mutations causing hemophilia B in 2 domestic cats. J Vet Intern
Med, 2005. 19(2): p. 200-4.
Clavero, S., et al., Feline congenital erythropoietic porphyria: two homozygous UROS missense mutations
cause the enzyme deficiency and porphyrin accumulation. Mol Med, 2010. 16(9-10): p. 381-8.
Goldstein, R., et al., Primary Hyperoxaluria in cats caused by a mutation in the feline GRHPR gene. J
Hered, 2009. 100(Supplement 1): p. S2-S7.
Clavero, S., et al., Feline acute intermittent porphyria: a phenocopy masquerading as an erythropoietic
porphyria due to dominant and recessive hydroxymethylbilane synthase mutations. Hum Mol Genet, 2010.
19(4): p. 584-96.
Ginzinger, D.G., et al., A mutation in the lipoprotein lipase gene is the molecular basis of chylomicronemia
in a colony of domestic cats. J Clin Invest, 1996. 97(5): p. 1257-66.
Geisen, V., K. Weber, and K. Hartmann, Vitamin D-dependent hereditary rickets type I in a cat. J Vet
Intern Med, 2009. 23(1): p. 196-9.
Berg, T., et al., Purification of feline lysosomal alpha-mannosidase, determination of its cDNA sequence
and identification of a mutation causing alpha-mannosidosis in Persian cats. Biochem J, 1997. 328 ( Pt 3):
p. 863-70.
Grahn, R., et al., No bones about it! A novel CYP27B1 mutation results in feline vitamin D-dependent
Rickets Type I (VDDR-1). in preparation, 2011.
Mazrier, H., et al., Inheritance, biochemical abnormalities, and clinical features of feline mucolipidosis II:
the first animal model of human I-cell disease. J Hered, 2003. 94(5): p. 363-73.
55
Hereditary Gastric Cancer in Dogs
Elizabeth McNiel, DVM, PhD, Tufts Cummings School of Veterinary Medicine, Tufts Medical
Center Molecular Oncology Research Institute Elizabeth.McNiel@tufts.edu
Stomach cancer (gastric carcinoma) is considered a rare cancer in dogs, an impression that is
reinforced by published literature on this disease. Most papers feature fewer than 20 cases, thus
providing a very limited sketch of this disease. Several years ago, we reported that Chow Chows
have a significantly increased risk for gastric cancer and began to study the disease in this breed.
Subsequently, we have expanded our research to include other breeds at high risk including the
Belgian Tervuren, Belgian Sheepdog, Keeshond, Irish Setter, Bouvier, Norwegian Elkhound,
Akita, and Scottish Terrier. Other breeds may also be at risk. We suspect that difficulty in
accurately diagnosing dogs with this cancer may result in underreporting of its prevalence in dogs
of all breeds, although in certain breeds the disease is quite common.
Several years ago we established the Canine Gastric Cancer Repository and Database to provide a
tool to learn about canine gastric cancer and to develop strategies to prevent, diagnose and treat
this aggressive and nearly uniformly fatal disease.
What is gastric cancer?
Cancer develops from cells that grow uncontrollably and invade normal tissues. Cancer in the
stomach can derive from a number of different cell types, therefore many types of cancer can
occur in the stomach. However, most cancers in the stomach derive from the epithelium or lining
cells and are called gastric carcinoma (or adenocarcinoma).Therefore, most of the time, gastric
cancer is considered synonymous with gastric carcinoma.
A variety of classification systems that are based on microscopic appearance and position of the
cancer in the stomach have been used to classify stomach cancer in people. One of the traditional
systems (the Lauren System) consists of two groups: Intestinal Type and Diffuse Type. Intestinal
type forms lumps or masses on the surface while diffuse type invades directly into the wall of the
stomach causing thickness without the development of a surface mass. While dogs appear to be
capable of developing both types of gastric carcinoma, it appears that diffuse type is most
common. A systematic review of the histology from more than 100 canine gastric cancer cases is
currently underway.
What causes gastric cancer in dogs?
The short answer to this question is that we don’t know. However, in humans both environmental
causes and genetics play a role. Environmental contributors including diet (salt and nitrites) and a
bacterial organism called Helicobacter pylori. H. Pylori does not appear to naturally infect dogs.
The occurrence of gastric cancer in particular breeds, strongly suggests that genetics are important
in the canine disease. We have found families with multiple individuals affected over multiple
generations which also support this notion. Other evidence for this includes the high prevalence of
diffuse carcinoma in dogs which is associated with familial gastric cancer in people. The mode of
inheritance is not clear. We are collaborating with Elaine Ostrander’s lab at the NHGRI to
identify gene(s) that cause canine gastric carcinoma.
56
What are the signs of gastric cancer in dogs?
The signs of gastric cancer are usually insidious, particularly in the early stages. Consistently, we
see loss of appetite and weight loss. In many cases, we also see vomiting, although it may be very
intermittent and easy to ignore because all else seems normal. Occasionally there is diarrhea or
dark tarry stool which indicates intestinal bleeding. Because the signs of stomach cancer are very
vague and nonspecific, it is unusual for veterinarians to see a dog until the disease is quite
advanced.
How is a diagnosis of gastric cancer made?
A presumptive diagnosis of gastric cancer can often be made based on abdominal
ultrasonography. The difficulty is that gas in the stomach interferes with this imaging.
Furthermore, a distinct mass is often lacking in these cases. Thickness of the gastric wall may be
the best indication of cancer. This underscores the importance of routinely evaluating wall
thickness, particularly in dogs of high risk breeds with gastro-intestinal signs.
Definitive diagnosis of gastric cancer is based on biopsy. The least invasive way to obtain a
biopsy is with endoscopic biopsy. However, in many cases the diagnosis is missed on endoscopy.
The inaccuracies in endoscopic biopsy stem from the nature of most stomach cancers in dogs in
which the surface lining may look relatively normal even though there is substantial infiltration of
the stomach wall by cancer cells. Therefore many times veterinarians cannot determine where
biopsies should be collecting. Furthermore, endoscopic biopsies are may miss the cancer cells that
are more deeply embedded. Finally, the areas of affected stomach often become very firm and
almost rubbery in consistency and biopsying these areas may yield inadequate tissue.
Surgical biopsy has the best chance of providing an accurate diagnosis, but this is, of course, more
invasive. However, in addition to biopsy, there may also be the opportunity to surgically remove
the cancer.
How is gastric cancer treated?
Surgery is the treatment of choice for gastric carcinoma. However, the removal a cancer from the
stomach is challenging. When the cancer is very advanced involving a large proportion of the
stomach removal is not usually feasible. The location of the cancer is also a deciding factor. In
our experience, removal of the cancer is not always possible and it is uncommon for the surgeon
to be able to remove it completely. Even partial removal can provide some relief to the dog,
though this is not always true. We are aware of a single dog that lived for an additional 5 years
following removal of a gastric tumor and several others that survived for a year or more.
However, the vast majority of dogs will die of stomach cancer in time.
Several chemotherapy drugs have been used in dogs with stomach cancer although the
effectiveness of these is questionable.
The future of the management of stomach cancer will rely on development of genetic tests to
identify at risk individuals, selective breeding in some cases, development of screening tests, and
the development of new agents that target the molecular constitution of stomach cancer. These
types of advances are only possible with better understanding of the genetics and molecular
biology of canine stomach cancer.
57
Scientific Program
Sunday, September 29
Lecture Time: Title of Lecture:
Speaker:
8:10-8:50
Dr. Åke Hedhammar
Half A Century with Canine Hip Dysplasia
8:50-9:30
The Othopedic Foundation for Animals Hip Displasia Database: Dr. G. Greg Keller
A Review
9:50-10:30
The genetics of hip dysplasia and implications for selection
Dr. Tom Lewis
10:30-11:10
Genetic and Genomic Tools for Breeding Dogs With Healthy
Hips
Dr. Rory Todhunter
12:55-1:35
Holistic Management of Genetic Traits
Dr. Anita Oberbauer
1:35-2:15
From FUS to Pandora Syndrome - The Role of Epigenetics
and Environment in Pathophysiology, Treatment, and
Prevention
Dr. Tony Buffington
2:35-2:55
Breed Specific Breeding Strategies
Dr. Åke Hedhammar
2:55-3:15
UK initiatives for breeding healthier pedigree dogs
Dr. Tom Lewis
3:15-3:55
Genetic Tests: Understanding Their Power, and Using Their
Force for Good
Dr. Jerold Bell
58
Half a Century with Canine Hip Dysplasia
Åke A Hedhammar, DVM, M Sc, Ph D, Dipl. Internal Medicine -Companion Animals
Dept. of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
Malformations of the hips in dogs was described by Dr Schnelle already in 1937, but it was
not until about a century ago that it was made evident that it was a widely spread entity
affecting not only German shepherds.
Since then great attention and efforts have been paid worldwide by researchers as well as
breeders to reveal the mechanisms behind it and to decrease its prevalence.
The following is an attempt to briefly review knowledge attained and achievements
made over these years.
The perspective is from a veterinarian, neither a surgeon or radiologist nor a geneticist. It’s
the perspective of someone involved in some research on the effect of genes and environment
and as consultant to the Swedish kennel club in the institution of screening and breeding
programs to assist in the selection of suitable breeding stock.. Neither surgical nor medical
treatment will be covered. With reference to lectures to follow by Drs Keller, Lewis and
Todhunter on the OFA database, genetics and genomic tools respectively those aspects will
not be covered very extensively.
ETIOLOGY AND RISK FACORS
Definition of CHD “varying degree of laxity of the hip joint permitting subluxation during
early life, giving rise to varying degrees of shallow acetabulum and flattening of the femoral
head, finally inevitably leading to osteoarthritis."
Contrary to human hip dysplasia it soon became evident that Canine Hip Dysplasia (CHD) is
a developmental and degenerative disease rather than congenital /present already at birth.
Knowledge
We have learned that its structural and functional properties during its development and its
clinical course by degenerative processes are affected by genes as well as environmental
factors.
Achievements
Based on that knowledge we have got various tools to handle genetic as well environmental
factors in individuals and breed populations.
To be further known and achieved
The true etiology bye genes involved and their expression is still to be revealed as well as the
interaction between genes and environmental factors.
SCREENING PROCEDURES AND REGISTRIES
Screening for early signs of CHD have been proven to predict clinical outcome as well as
genetic transmission (disposition for early signs as well clinically manifest CHD).
59
Knowledge
Various screening methods have been investigated and validated for its purpose.
Radiographic methods in standardized stressed or non stressed positioning have proven to be
more useful than palpation as practiced in human HD. The outcome of any radiological
screening is strongly affected by age at screening, positioning and level of sedation calling
for standardizations of this parameters.
Achievements
Based on that knowledge screening programs have been extensively established by various
bodies worldwide.
Registries on results from these programs nowadays most commonly contain positive as well
as negative results on permanently identified individuals, open to the public and accessible on
line and supporting computerized information on national breed populations.
Earlier and more simple and inexpensive screening methods would enhance a more extensive
usage.. An ongoing dispute regarding the value of different screening methods hampers the
inclination to screen by any method. By computerization of results from many individuals the
prediction of the genotype is much more accurate than any screening of an individual dog.
Exchange of results from national registries is hampered by differences in procedure and
recordings and calls for an international harmonization.
EPIDEMIOLOGY AND PREVALENCE
CHD do affect almost all large sized breeds to variable extent and not just purebred/pedigree
dogs. The prevalence is affected by type of dogs, mollosoid dogs to high extent and scent
hounds to less than other.
Knowledge
The prevalence is known and documented in populations with extensive screening but most
commonly restricted to clinically unaffected animals at age of screening.
Achievements
A decreased prevalence is proven to be achieved in populations in which breeding stock i
routinely have been selected for hip status by standardized measures.
The prevalence in most populations - pedigree and non pedigree - is still unknown and scarce
regarding clinically affected individuals.
GENETICS AND BREEDING PROGRAMS
Based on known genetics and established screening programs structured breeding programs
have been instituted in a couple of countries on national breed populations.
Knowledge
The advancement of tools in both population genetics and molecular genetics have enhanced
our knowledge on how to handle the selection of breeding stock with reference to CHD.
60
Achievements
Structured breeding programs have proven to be very effective in purpose bred populations of
dogs for police, armed forces and as guide dogs as well as in national populations on
condition that a significant fraction of the population is screened and that the result is taken
into account.
Breed specific breeding programs would beneficially account for breed variations in
prevalence, population structure and other traits to take into account.
The extent of breeding programs - not just screening is needed to significantly affect the true
prevalence in most national breed populations. International breeding programs would
enhance the effect by exchange of results from different screening programs.
NUTRITIONAL IMPACT
The detrimental effect of over nutrition, i.e. excessive amounts of food (overfeeding) and
excessive amounts of specific nutrients (over supplementation) have been proven for many
orthopedics conditions in large sized breeds including CHD.
Knowledge
Already at an early stage it was proven how ad lib feeding increase prevalence and severity of
skeletal disorders including CHD. Contrary to earlier believe no specific nutrient can prevent
from CHD by given in excessive amounts.
Achievements
Feeding practices of large sized dogs have to some extent changed from “the more-the better”
to feeding moderate amount of complete and balanced diet resulting in optimal skeletal
conformation rather than maximal rate of growth.
Despite extensive promotion of chondro-protective products very little is still known on how
to prevent from arthritis in developmental disorders as CHD.
SUMMING UP
By attention and efforts by researchers as well as cynological organizations and breeders
worldwide extensive knowledge have been accumulated and effective tools have been
developed to control for CHD. The full effect of this is however hampered by lack of a wider
implementation.
A wider implementation of current screening methods and thereon based breeding programs
is much more important than any refinement to reveal more of the phenotypic expression of
CHD.
References and further readings
Schnelle GB.
135(4):234-5
Congenital dysplasia of the hip in dogs. As referred in J Am Vet Med Assoc. 1959;
61
Henricson B, Olson SE. Hereditary acetabular dysplasia in German shepherd dogs. J Am Vet Med
Assoc. 1959; 135(4):207-10.
Hedhammar Å, Wu Fu-ming, Krook L, Schryver HF, Lahunta A, Whalen JP et al. Overnutrition and
skeletal disease. An experimental study in growing Great Dane Dogs. Cornell Vet 1974; 64 Suppl 5.
Kasström H. Nutrition, weight gain and the development of hip dysplasia. Acta Radiol 1975; 344
Suppl: 135- 79.
Hedhammar A, Olsson SE, Andersson SA, Persson L, Pettersson L, Olausson A, Sundgren PE.
Canine hip dysplasia: study of heritability in 401 litters of German Shepherd dogs. J Am Vet Med
Assoc. 1979 May 1; 174(9):1012-6. http://www.ncbi.nlm.nih.gov/pubmed/570968
Swenson L, Audell L, Hedhammar A. 1997 Prevalence and inheritance of and selection for hip
dysplasia in seven breeds of dogs in Sweden and benefit: cost analysis of a screening and control
program. J Am Vet Med Assoc. 1997; Jan 15; 210(2):207-14.
http://www.ncbi.nlm.nih.gov/pubmed?cmd=Retrieve&db=PubMed&list_uids=9018354&dopt=Abstra
ct
Hedhammar 1998 ACTIVITIES BY FEDERATION CYNOLOGIC INTERNATIONAL (FCI) TO
COMBAT ELBOW AND HIP DYSPLASIA at the Website of the International Elbow Working
Group. http://www.vet-iewg.org/joomla/index.php/archive/13-1998-bologna/20-hedhammar-1998
Hedhammar A; Swensson L; Egenwall A 1999 Elbow arthrosis and hip dysplasia in Swedish dogs as
reflected by screening programmes and insurance data. The European journal of companion animal
practice 1999; 9:2.
Hedhammar A. Nutrition and selection of breeding stock with reference to skeletal health in large
growing Dogs - Swedish experiences over 25 years. Presented at IAMS Large Breed Health Care
Symposium, Venice, Italy November 17th, 2001.
Sallander M, Hedhammar Å, Trogen M. Diet, excercise and weight as risk factors in Hip Dysplasia
and Elbow Arthrosis in Labrador Retrievers. Journal of Nutrition 2006; 136:2050S-2052S.
http://jn.nutrition.org/content/136/7/2050S.full
Malm S, Strandberg E, Danell B, Audell L, Swenson L, Hedhammar A. Impact of sedation method on
the diagnosis of hip and elbow dysplasia in Swedish dogs. Prev Vet Med. 2007 Mar 17;78(3-4):196209.
Hedhammar A. Canine hip dysplasia as influenced by genetic and environmental factors The
European journal of companion animal practice 2007; 17(2):141-143.
http://www.docstoc.com/docs/80460727/Canine-Hip-Dysplasia-as-influenced-by-genetic-andenvironmental
Comhaire FH, Snaps F.Comparison of two canine registry databases on the prevalence
of hip dysplasia by breed and the relationship of dysplasia with body weight and height. Am J Vet
Res. 2008 Mar; 69(3):330-3.
Malm S, Fikse F, Egenvall A, Bonnett BN, Gunnarsson L, Hedhammar A, Strandberg E. Association
between radiographic assessment of hip status and subsequent incidence of veterinary care and
mortality related to hip dysplasia in insured Swedish dogs. Prev Vet Med. 2010 Feb 1;93(2-3):222-32.
62
Wilson B, Nicholas F, Thomson P. Selection against canine hip dysplasia: Success or failure? The
Veterinary Journal 2011; 189 (2011) 160–168.
http://actualidadveterinaria.files.wordpress.com/2011/08/selection-against-canine-hip-dysplasiasuccess-or-failure.pdf
Dennis R. 2012 Interpretation and use of BVA/KC hip scores in dogs. In Practice 2012; April
Volume 34: 178–194. Down loaded from inpractice.bmj.com on May 2, 2012.
http://actualidadveterinaria.files.wordpress.com/2011/08/selection-against-canine-hip-dysplasiasuccess-or-failure.pdf
Fikse WF, Malm S, Lewis TW. Opportunities for international collaboration in dog breeding from the
sharing of pedigree and health data. Vet J. 2013 Aug 8. pii: S1090-0233(13)00197-4. doi:
10.1016/j.tvjl.2013.04.025. [Epub ahead of print]
Hazewinkel HAW, Goedegebuure SA, Poulos PW, Wolvekamp WThC. Influences of chronic
calcium excess on the skeletal development of growing Great Danes. J Am Anim Hosp Assoc 1985;
21: 377- 91.
Lavelle RB. The effects of overfeeding of a balanced complete commercial diet to a group of growing
Great Danes I: Burger IH, RiversJPS, red. Nutrition of the dog and cat. Cambridge: Cambridge
University Press 1989:303- 14.
Comhaire FH, Snaps F 2008 Comparison of two canine registry databases on the prevalence
of hip dysplasia by breed and the relationship of dysplasia with body weight and height. Am J Vet
Res. 2008 Mar;69(3):330-3.
63
The Orthopedic Foundation for Animals Hip Dysplasia Database: A Review
Greg Keller, D.V.M, DACVR, Orthopedic Foundation for Animals, Inc., Columbia, MO
ofa@offa.org
The Orthopedic Foundation for Animals, Inc. (OFA) is a private not-for-profit foundation which
formed a voluntary hip dysplasia control database in 1966 with the following objectives:
1.) To collate and disseminate information concerning orthopedic and genetic disease of
animals.
2.) To advise, encourage and establish control programs to lower the incidence of
orthopedic and genetic diseases.
3.) To encourage and finance research in orthopedic and genetic disease in animals.
4.) To receive funds and make grants to carry out these objectives.
The OFA’s voluntary database serves all breeds of dogs and has the world’s largest all breed hip
databank on radiographic evaluations of the hip.
Due to breed variation by size, shape and pelvic conformation the OFA hip evaluation is based
on comparison among individuals of the same breed and approximate age. Like most hip
schemes the OFA employs the hip extended ventrodorsal view of the pelvis. Hip phenotypes are
categorized as normal (excellent-1, good-2 and fair-3), borderline-4 and dysplastic (mild-5,
moderate-6 and severe-7). Unlike most hip schemes the dog must be at least 24 months of age
and the consensus evaluation is derived from three independent evaluations by board certified
radiologists (1). Breed improvement, the reduction in hip dysplasia, is dependent on the degree
of genetic variation within the breed, the accuracy of identifying a superior phenotype and the
selection of pressure exerted upon the trait by individual and/or the breed club. There are
numerous reports of dramatic reduction in hip dysplasia in closed populations (2, 3 & 4). The
OFA database, even though the submissions are voluntary, has seen a similar improvement in
most breeds (5). There is a strong correlation between the hip phenotype of the sire, dam and
grandparents with a reduction in the prevalence for hip dysplasia in the progeny (6). Figure one
64
represents hip phenotype data on 490,966 progeny where the hip phenotype is also known on
sire and dam.
It is assumed that radiographs submitted to OFA are generally prescreened by the veterinarian
and the more obvious cases of hip dysplasia are probably not submitted. Therefore the actual
frequency of hip dysplasia in the general population is unknown, but has been approximated by
Corley and Rettenmaier to be higher than reported by OFA (7 & 8). However, the main
objective of the OFA is to identify phenotypically normal animals as potential breeding
candidates in order to reduce the frequency of hip dysplasia. A review of the OFA hip database
using a minimum of 5,000 evaluations yielded 44 breeds (Table 1). Regardless of the breed the
general trend is for an increase in the percent excellent phenotype and a reduction in the percent
dysplastic. Breed differences in the trend rate could be due to initial breed variations in hip
dysplasia, the size of the gene pool and the selection pressure exerted by individuals and/or breed
clubs.
OFA is approaching 1.6 million individual hip records and the real power in this data is the
ability for the public to access data through the Canine Health Information Center (CHIC)
www.caninehealthinfo.org and primarily from the OFA website (www.offa.org).
To 1980
AFGHAN HOUND
AIREDALE TERRIER
AKITA
ALASKAN MALAMUTE
AUSTRALIAN SHEPHERD
BELGIAN TERVUREN
BERNESE MOUNTAIN DOG
BORDER COLLIE
BOUVIER DES FLANDRES
BOXER
BRITTANY
BULLMASTIFF
1986 to
1990
1991 to 1995
1996 to 2000
2001 to 2005
2006 to 2010
Total
Ex %
Dys % Total
dogs
24.4
5.4
2703
27.6
5.6
695
31.9
6.4
787
37.0
4.6
736
34.5
6.6
714
35.5
5.2
620
38.1
3.8
452
30.0
5.4
6720
Ex %
Dys % Total
dogs
4.6
13.8
484
5.8
17.4
604
7.3
15.0
923
8.7
10.5
1056
8.6
6.8
1115
6.2
8.4
1057
8.8
8.5
624
7.4
10.9
5886
Ex %
Dys %
Total dogs
7.5
17.2
2047
11.3
17.2
2529
15.5
14.4
3366
20.7
9.8
3464
29.3
8.9
2219
31.8
5.6
1412
33.2
6.1
964
19.3
12.2
16047
Ex %
Dys %
Total dogs
10.7
13.7
3547
15.2
12.3
2012
17.9
11.4
2263
17.9
9.9
2068
24.1
7.4
1686
21.3
8.8
1292
23.9
8.1
869
17.1
10.9
13777
Ex %
Dys % Total
dogs
10.6
7.8
2028
10.6
7.3
1992
13.1
5.9
3523
14.7
5.2
5573
19.3
4.6
6711
17.8
5.0
6552
21.4
4.6
5311
16.8
5.3
31885
Ex %
Dys % Total
dogs
14.3
5.1
610
16.5
4.8
559
21.7
3.5
807
26.2
3.0
981
32.6
2.3
1040
31.6
2.3
1069
32.9
2.9
763
26.5
3.2
5859
Ex %
Dys % Total
dogs
2.9
31.2
554
4.1
25.0
929
7.1
19.7
1708
10.5
14.4
2557
15.2
12.5
2918
15.8
13.7
4519
20.3
12.5
4092
Ex %
Dys % Total
dogs
21.2
99
8.0
14.3
426
9.5
13.1
957
10.7
11.4
1750
14.1
9.7
2420
13.7
9.7
2843
16.9
8.2
2499
13.4
10.2
11137
Ex %
Dys % Total
dogs
3.1
19.1
768
3.8
19.0
1119
5.3
17.0
1428
6.7
11.4
1648
7.3
10.9
1312
6.7
12.0
976
12.4
10.1
742
6.4
14.1
8033
Ex %
Dys % Total
dogs
1.2
16.9
242
.9
16.1
217
3.7
13.4
536
3.3
8.2
1075
4.4
8.6
1292
2.7
10.6
1241
5.5
10.0
789
3.6
10.4
5411
Ex %
Dys % Total
dogs
5.9
19.9
2632
5.7
18.6
1916
6.4
16.7
2667
8.2
11.7
3048
12.1
11.6
2916
11.0
10.9
2896
13.7
8.3
1950
9.0
13.8
18109
Ex %
Dys % Total
dogs
1.6
30.5
367
.7
32.4
299
3.0
29.3
543
3.6
21.4
1276
6.1
22.3
1204
3.3
22.7
1043
5.7
20.1
716
4.0
23.6
5470
1981 to 1985
65
14.1
15.0
17525
To 1980
CAVALIER KING CHARLES
SPANIEL
CHESAPEAKE
BAY RETRIEVER
CHINESE SHAR-PEI
CHOW CHOW
COCKER SPANIEL
DOBERMAN PINSCHER
ENGLISH COCKER SPANIEL
ENGLISH SETTER
ENGLISH
SPRINGER
SPANIEL
FLAT-COATED RETRIEVER
GERMAN SHEPHERD DOG
GERMAN
SHORTHAIRED
POINTER
GOLDEN RETRIEVER
GORDON SETTER
GREAT DANE
GREAT PYRENEES
IRISH SETTER
LABRADOR RETRIEVER
MASTIFF
NEWFOUNDLAND
OLD ENGLISH SHEEPDOG
1981 to 1985
1986 to 1990
1991 to
1995
2001 to 2005
2006 to 2010
Total
3.1
10.8
732
4.7
9.9
1277
4.1
11.7
1967
4.2
11.8
1639
4.2
11.2
6275
11.0
20.6
2196
16.6
17.9
2182
18.3
13.9
1895
19.9
13.1
1268
12.7
19.5
12622
33.3
15
7.4
12.4
162
Ex %
Dys % Total
dogs
6.1
24.9
1633
7.0
22.8
1629
Ex %
Dys % Total
dogs
5.2
21.5
135
6.5
19.6
1660
8.8
14.2
3588
8.6
9.3
1885
13.3
8.9
1040
12.3
9.4
756
13.1
7.6
487
9.3
13.0
9563
Ex %
Dys %
Total dogs
4.5
22.0
673
4.3
23.7
1042
6.3
21.7
1236
9.0
14.4
812
10.6
13.7
584
8.7
13.5
541
14.2
15.9
366
7.4
18.9
5266
Ex %
Dys %
Total dogs
12.8
8.1
531
9.2
8.9
1164
9.5
7.0
1967
8.5
5.4
2328
12.8
4.4
2636
11.2
5.4
2689
13.4
5.4
1608
10.9
5.9
12991
Ex %
Dys % Total
dogs
13.1
7.7
2251
13.7
7.6
1541
17.9
5.6
2263
19.6
4.4
2787
22.8
5.0
2475
19.0
5.0
2182
19.1
5.0
1856
18.2
5.6
15406
Ex %
Dys % Total
dogs
12.1
7.3
713
10.7
6.7
805
16.5
5.3
1124
17.5
4.0
1207
21.7
5.2
1057
24.4
5.0
1143
28.4
4.9
843
19.1
5.3
6916
Ex %
Dys % Total
dogs
3.3
28.0
1423
3.5
17.6
1214
7.9
15.7
1405
10.5
12.7
1668
14.1
12.2
1690
15.4
11.1
1616
20.1
9.7
1212
10.8
15.1
10272
Ex %
Dys % Total
dogs
7.2
19.7
1791
5.2
18.0
1352
7.3
15.7
2029
9.0
10.8
2433
10.0
9.5
2443
9.9
9.1
2678
13.1
8.0
2007
9.1
12.3
14792
Ex %
Dys % Total
dogs
9.0
3.6
333
8.7
3.5
540
19.0
7.0
675
18.4
4.2
933
21.7
3.4
1029
24.8
3.0
1051
26.8
3.0
866
20.1
3.8
5464
Ex %
Dys % Total
dogs
2.6
20.3
11723
1.9
22.1
11679
3.1
20.5
17243
3.7
17.2
22022
4.8
16.5
16766
5.3
17.8
14525
7.2
17.9
10968
4.1
18.7
105443
Ex %
Dys % Total
dogs
19.8
6.9
1371
18.4
7.6
1196
22.2
5.6
2059
24.2
3.7
2866
29.9
3.0
2916
28.3
2.8
3096
33.4
1.7
2126
26.3
3.9
15711
Ex %
Dys % Total
dogs
1.9
23.1
16621
2.1
23.2
16290
2.8
22.5
19966
4.1
17.8
23139
5.4
16.1
22386
5.8
16.1
19099
8.9
13.2
13839
4.4
18.8
132110
Ex %
Dys % Total
dogs
4.1
25.9
1051
4.4
20.8
923
8.2
20.4
1128
9.4
17.0
959
13.1
12.0
786
12.0
15.7
669
19.1
9.7
476
9.1
18.4
6025
Ex %
Dys % Total
dogs
6.5
13.0
2050
8.7
15.1
981
12.3
11.4
1396
13.5
9.7
1750
15.0
10.0
2108
11.9
11.8
2426
13.6
10.5
1844
Ex %
Dys % Total
dogs
9.2
9.3
774
11.7
10.5
759
12.9
9.9
1031
16.2
8.3
1134
16.5
8.3
920
16.0
6.9
756
18.0
7.9
494
14.3
8.7
5890
Ex %
Dys % Total
dogs
5.1
14.8
3740
6.5
11.3
1257
8.6
12.2
1413
10.3
9.9
1463
13.8
8.8
1295
14.1
7.2
1200
17.9
6.4
825
9.3
11.3
11226
Ex %
Dys % Total
dogs
10.8
14.2
14088
11.5
14.7
16564
17.4
11.9
43244
20.3
11.0
51208
20.3
9.8
45458
25.3
8.0
27973
18.5
11.3
228094
Ex %
Dys % Total
dogs
2.5
19.9
322
5.4
22.7
503
5.1
23.2
986
6.3
17.2
2249
9.7
16.5
2778
9.2
18.1
2350
10.2
18.0
1398
8.1
18.2
10626
Ex %
Dys % Total
dogs
3.5
31.6
1696
2.9
31.4
1709
6.7
25.8
2338
8.4
21.4
2514
10.6
23.1
2420
11.8
21.3
2561
15.1
20.3
1780
8.7
24.4
15094
Ex %
Dys % Total
dogs
7.8
22.9
4434
9.4
18.8
1438
15.5
12.9
1091
17.7
11.3
947
17.2
10.3
816
21.8
10.0
578
11.9
18.0
10637
Ex %
Dys % Total
dogs
3.8
8.9
425
1996 to 2000
10.3
23.0
1769
15.2
13.3
28242
13.8
18.0
1299
66
11.8
114
12625
To 1980
PEMBROKE WELSH CORGI
POODLE
PORTUGUESE WATER DOG
RHODESIAN RIDGEBACK
ROTTWEILER
SAMOYED
SHETLAND SHEEPDOG
SIBERIAN HUSKY
SOFT COATED WHEATEN
TERRIER
WEIMARANER
1986 to 1990
1991 to 1995
1996 to 2000
2001 to 2005
2006 to
2010
Total
Ex %
Dys %
Total dogs
19.2
99
1.1
20.7
787
1.9
18.1
1583
2.4
14.3
2056
5.5
13.7
2257
3.7
17.3
2275
3.1
18.1
1598
3.3
16.5
10733
Ex %
Dys %
Total dogs
8.0
17.4
2273
7.2
14.1
1821
9.1
14.2
2442
11.0
9.9
3401
14.1
9.9
4058
13.1
9.6
4945
16.6
8.7
3799
12.1
11.2
22908
Ex %
Dys %
Total dogs
1.0
26.2
103
5.0
22.8
303
9.6
16.1
795
11.7
11.3
1271
16.2
10.1
1539
14.6
9.5
1955
20.6
8.7
1739
14.8
11.1
7790
Ex %
Dys %
Total dogs
13.9
11.8
1123
19.1
8.5
993
19.2
5.9
1450
23.4
2.9
1879
24.7
2.9
1968
23.3
2.9
2064
27.2
2.5
1575
22.3
4.6
11130
Ex %
Dys %
Total dogs
4.3
23.4
5901
5.2
22.8
16624
7.4
22.0
27339
9.2
17.6
22597
13.0
15.8
8973
11.9
15.8
6123
14.2
15.1
4921
8.4
19.8
92692
Ex %
Dys %
Total dogs
8.3
13.4
3767
7.4
12.2
2460
9.1
10.8
2593
10.9
8.8
2090
13.1
7.1
1787
14.4
8.7
1671
19.1
6.9
1416
10.8
10.4
15862
Ex %
Dys %
Total dogs
26.0
5.6
515
29.7
9.8
549
25.8
6.2
2676
27.6
3.8
4254
28.7
4.0
4640
25.3
3.5
4225
32.5
2.9
2876
27.9
4.2
19842
Ex %
Dys %
Total dogs
24.6
2.7
4453
28.7
2.2
2495
37.6
1.9
2588
38.0
1.2
2616
41.6
1.2
2102
39.1
1.5
1759
41.4
1.2
1396
34.0
1.8
17470
Ex %
Dys %
Total dogs
12.1
6.9
504
12.1
4.5
877
16.1
4.5
964
16.6
2.5
1030
22.2
4.0
1072
16.9
4.9
892
23.1
5.0
624
17.3
4.4
5992
Ex %
Dys %
Total dogs
12.7
10.4
1527
12.2
8.0
1068
14.0
7.4
1407
16.5
4.7
2004
19.6
6.0
2468
17.9
5.9
2865
21.0
4.4
2098
17.1
6.3
13547
Ex %
Dys %
Total dogs
13.1
11.8
1586
12.6
11.1
1040
19.8
8.5
1514
22.4
7.2
2252
25.8
5.9
2410
24.7
7.7
1959
28.1
5.5
1138
21.6
7.9
11946
VIZSLA
1981 to 1985
1.) Keller, GG et al: The Use of Health Databases and Selective Breeding
2.) Hedhammer A, Olsson SE, et al: Study of Heritability in 401 Litters of German Shepherd Dogs.
JAVMA, Vol. 1974; 1012-1016, 1979.
3.) Swensen L et al: Prevalence and inheritance of and Selection for Hip Dysplasia in Seven Breeds
of Dogs in Sweden and Benefit: Cost Analysis of a Screening and Control Program. JAVMA,
210:2, 1997, pp 207-214.
4.) Leighton EA: Genetics of Canine Hip Dysplasia. JAVMA, Vol. 210, No. 10, 1997, pp. 1474-1479.
5.) Kaneene JB et al: Update of a Retrospective Cohort Study of Changes in Hip Joint Phenotype of
Dogs Evaluated by the OFA in the United States, 1989 – 2003. Veterinary Surgery, 38: 398-405,
2009.
6.) Keller GG, et al: How the Orthopedic Foundation for Animals (OFA) is tackling inherited
disorders in the USA: Using hip and elbow dysplasia as examples. The Veterinary Journal (2011),
doi: 10.1016/j. tvjl.2011.06.19
7.) Corley EA, et al: Reliability of Early Radiographic Evaluation for Canine Hip Dysplasia Obtained
from the Standard Ventrodorsal Radiographic Projection. JAVMA, 211:9, 1997, pp. 1142-1146.
8.) Rettenmaier JL, Keller GG, et al: Prevalence of Canine Hip Dysplasia in a Veterinary Teaching
Hospital Population. Vet. Rad. & Ultrasound, Vol. 43, No. 4, 2002, p. 313-318. 67
The Genetics of Hip Dysplasia and Implications for Selection
Tom Lewis PhD, Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk, UK
tom.lewis@aht.org.uk
Hip dysplasia is a complex disease. When a trait or disease is described as ‘complex’ it is
usually meant that the trait is influenced by both genetic and non-genetic, or environmental,
effects. This makes it very difficult to determine the mode of inheritance, since the phenotype
(the observable manifestation of the trait) is not necessarily an accurate indicator of the
genetics; the genetics is only a part of the picture and is ‘overlaid’ by environmental
influences (‘good’ genetics may be masked by detrimental environment and vice versa).
Furthermore, the trait is often under the control of more than one (and usually many) genes
meaning that we can no longer categorise individuals as clear, carriers or affected. In this
lecture I will attempt to demonstrate the presumed genetic architecture of complex traits and
show how we can achieve more effective selection in spite of the problems bequeathed by
this complexity.
You are probably all familiar with Mendelian inheritance which Gregor Mendel
demonstrated with a 3:1 ratio of yellow to green peas. This ratio allowed him to infer that the
trait of pea colour was determined by 2 variants (alleles) at a single gene; the yellow allele
(A) being ‘dominant’ and the green allele (a) being ‘recessive’. This meant that the two
possible phenotypes of pea colour (yellow and green) were in fact produced by three possible
genotypes. Homozygotes (so called as both alleles are the same variety) with two yellow
alleles (AA) produced yellow peas and those with two green alleles (aa) produced green peas.
Heterozygotes having one green and one yellow allele (Aa) were yellow in appearance
(phenotype), the dominant yellow allele masking the recessive green. This is important since
it allows phenotypic variations, in this example the green pea colour, to apparently disappear
for a number of generations before suddenly reappearing.
Heterozygotes produce half their gametes (sex cells) with the A allele and half with the a
allele. Therefore progeny of two heterozygotes will have the genotypes AA : Aa : aa in the
ratio 1 : 2 : 1, but because the yellow allele A is dominant the phenotypic ratio is 3:1 (see
figure 1). However, this 1 : 2 : 1 ratio is very important – because the ‘dominance’ we have
encountered up to this point is not universal or complete across all traits or diseases.
Gametes from parent 2
(A )
Gametes from parent 1 (Aa)
A
a
A
AA
Aa
a
Aa
aa
Figure 1: Punnett square showing the genotypes and phenotypes from crossing two heterozygote
parents.
68
Consider for a moment (hypothetically) that gene A (with 2 alleles A and a) determines the
quantity of peas rather than their colour. So AA might yield 9 peas in each pod, while aa
yields only 3. If the A allele is completely dominant, then we expect the heterozygote to show
the same phenotype as the dominant homozygote; so in this hypothetical example Aa yields 9
peas per pod. However, as mentioned above, dominance is not universal or always complete.
For example, imagine that instead the heterozygote yielded 6 peas per pod – half way
between the two homozygotes. We can begin to look at things more quantitatively, plotting
the number of peas per pod against the number of A alleles:
Figure 2: hypothetical examples of complete dominance (L) and completely additive (R) A allele.
These are two important examples; the chart on the left in figure 2 shows complete
dominance, i.e. the heterozygote (Aa) is the same phenotypically as the AA homozygote. The
chart on the right shows no dominance, or complete additivity (i.e. the heterozygote is the
intermediate of the two homozygotes, and each A allele adds 3 peas per pod). Additivity is an
important concept as we move on to consider ‘genetic variation’.
Complete additivity at a single gene will give us a 1 : 2 : 1 ratio of phenotypes (reflecting the
genotype ratio). However, as stated earlier, many quantitative or complex traits are
influenced by multiple genes. As we consider perfect additivity over an increasing number of
genes (figure 3) we can see the phenotypic distribution (discounting non-genetic effects for a
moment) approaching a ‘normal distribution’ (also known as the ‘bell curve’, and very
important in statistics). Figure 3 shows (from left to right) the genetic distributions of traits
controlled by 1, 3 and 6 genes respectively, followed by a normal distribution on the far right.
Hopefully you can see that increasing the number of genes increases the number of
phenotypic categories and begins to produce continuous genetic variation for the trait or
disease in question. Thus, we have moved from thinking in terms of ‘clear’, ‘carrier’ and
‘affected’, to thinking in terms of a continuous scale of liability or risk.
69
Figure 3: (L to R) genotype frequency distributions for 1, 3 and 6 completely additive genes, and a
normal distribution (far right).
This is probably not as novel a concept as it may appear; think about when you hear news
reports about scientists having found a gene for cancer, heart disease, diabetes, Alzheimer’s
etc. – it’s always a gene, not the gene. There isn’t a single gene for any of these diseases just
as there isn’t a single gene for height or weight. So, for complex diseases like hip dysplasia
we will have to deal with the concept of genetic variation and risk.
But the complexity doesn’t end here. As mentioned at the outset complex traits are influenced
by both genetic and environmental factors. While the genes (and so the genetic risk) are
determined at conception, this risk is subsequently modified by the effects of numerous
known and unknown non-genetic or environmental influences. Think of heart disease; I may
have a moderate genetic risk, but if I smoke, eat a poor diet, eat too much, take no exercise
and have a stressful lifestyle my actual risk creeps up. My actual risk when I’m 50 may be
higher than a 50 year old with a higher genetic risk, but who watches their weight, eats
healthily, has never smoked and has a low stress lifestyle. The same is true for hip dysplasia,
where known environmental effects include diet and early-life exercise regime.
Nevertheless, genetics makes an important contribution to the overall risk. The heritability of
a trait tells us how important genetics is relative to non-genetic effects – strictly it is the
proportion of phenotypic variation that is due to genetic variation. For hip dysplasia about
40% of the overall observable variation is due to genetic variation. This may not seem much it is less than half after all - but it is by far the biggest single component.
However, when it comes to breeding, it is only the genetic risk we are concerned with, as it is
only genetics that is passed across generations. This presents us with a problem – we are
using phenotypes (hip scores) to guide our selections, but we know that they are not
necessarily the best guide to genetics. We may unwittingly choose a dog with a good hip
score, not knowing that this is actually more to do with a beneficial environment and that the
genetic risk, which is passed to the progeny, is actually fairly high. But to date, hip scores are
all that breeders have had to guide them.
This is where estimated breeding values, or EBVs, come in. EBVs are a quantitative estimate
of the true genetic risk, or breeding value. We make the estimate using trait information, in
the case of hip dysplasia using the hip score, on an individual and all its relatives. We are
able to do this thanks to the availability of pedigree information, which allows us to quantify
the relationship between all the dogs therein. Information on relatives, who share genes to a
quantifiable degree, will allow us to make a better judgement on an individual’s genetics. For
example, we may feel very differently about using a stud dog with a poor hip score if we
knew that he had over 50 progeny scored with a very good average hip score. The
performance of the progeny tells us about the genetics of the parent. In fact, this aspect has
been key to the success of EBVs, which have been extensively used in the dairy industry for
over 20 years. Here we are concerned with milk production traits – traits that are only
70
expressed in females. Yet we have very accurate EBVs for dairy bulls based on the milking
performance of thousands of their daughters. Somewhat paradoxically, we know more about
a bull’s genetics with respect to milking traits than we do for any cow!
As with all estimates, it is useful to know how good an estimate the EBV really is. It is
intuitive that we will have more confidence in the genetics of the stud dog mentioned above,
with his own hip score and scores of 50 progeny known, than a stud dog with no information
on itself or its progeny. Just as EBVs are a quantitatively formal way of taking account of
relatives’ information in the assessment of an individual’s genetic liability, so we can
formally calculate the accuracy of our estimate of true genetic liability (the EBV).
So, EBVs are a more accurate indicator of genetics than an individual phenotype – and are
more abundant. Because we calculate the accuracy of each EBV we are able to quantify how
much more accurate selection using EBVs will be than selection using phenotype; with more
accurate selection delivering greater genetic progress. Results from research show that
selection using EBVs is an average of 1.16 times more accurate than using hip scores, across
16 breeds (Lewis et al, 2013). Furthermore, EBVs are available for all animals in the
pedigree. Selection using EBVs of dogs too young to have their own hip score is on average
1.30 times more accurate than selection using the parental phenotypes (Lewis et al, 2013).
We also showed that a far greater proportion of animals had an EBV more accurate than
knowing both parental hip scores, than actually had both parental hip scores known,
demonstrating that EBVs are an effective way of providing more reliable information on a far
greater proportion of the breed or population.
Further improvements in the accuracy of selection have been shown to be available from the
way we use the phenotypes. For example, we have shown with selection index methodology
that for Labradors EBVs for elbow dysplasia score are up to 10% more accurate when
computed from a bivariate analysis of elbow and hip scores than from a univariate analysis of
elbow scores alone. A positive genetic correlation between hip and elbow score means that
hip score acts as a much more abundant, if slightly less accurate, indicator of elbow dysplasia
(Lewis et al, 2011). This method was also used to determine a more effective combination of
the nine component traits of the UK hip score than a simple aggregate total (Lewis et al,
2010b), again delivering more accurate selection.
Finally, it is important to remember that EBVs are simply a more effective way of using the
hip score data in selection – they are NOT a direct replacement! Quality data is critical for the
calculation of accurate EBVs. Furthermore, hip scores themselves have significant prognostic
value for individual dogs.
References:
Lewis, T.W., Blott, S.C., Woolliams, J.A.W. (2010a) Genetic evaluation of hip score in UK Labrador
Retrievers. PLoS ONE, 5(10): e12797
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0012797
Lewis, T. W., Woolliams, J.A.W, Blott, S.C. (2010b) Genetic evaluation of the nine component
features of hip score in UK Labrador Retrievers. PLoS ONE, 5(10): e13610
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0013610
Lewis, T.W., Ilska, J.J., Blott, S.C., Woolliams, J.A.W. (2011) Genetic evaluation of elbow scores
and the relationship with hip scores in UK Labrador Retrivers. The Veterinary Journal 189: 227-233.
http://www.sciencedirect.com/science/article/pii/S1090023311002383
71
Lewis, T.W., Blott, S.C., Woolliams, J.A.W. (2013) Comparative analysis of genetic trends and
prospect of selection against hip and elbow dysplasia in 15 UK dog breeds. BMC Genetics 14:16
http://www.biomedcentral.com/1471-2156/14/16
72
Genetic and Genomic Tools for Breeding Dogs with Better Hips
Rory J. Todhunter, BVSc, MS, PhD, DACVS, Department of Clinical Sciences, College of
Veterinary Medicine, Cornell University, Ithaca NY rjt2@cornell.edu
Canine hip dysplasia (CHD) is a developmental trait primarily affecting medium and
large breed dogs. CHD is characterized by faulty conformation and laxity of the hip joint that
usually affects both hips. Clinically, the osteoarthritis that results from hip dysplasia is
characterized by hind limb lameness, reduced exercise tolerance, reluctance to jump, poor hind
limb muscle mass, and laxity or pain in the hip joint. CHD can be detected radiographically as
subluxation of the affected hip. CHD results in synovitis accompanied by effusion and
osteoarthritis of the affected joint. Osteoarthritis is detected on a radiograph as osteophytes
around the femoral neck (so-called Morgan’s line), femoral head and acetabulum and a flattening
of the femoral head with a shallow, open acetabulum. Radiographs are insensitive to the presence
of incipient osteoarthritis of upper limb joints like the hip. In addition, the radiographic
alterations associated with hip dysplasia can be subtle and even an “unaffected” dog, as assessed
by a radiograph, can still carry some of the mutations that contribute to the disorder.
Genetics
CHD in dogs is an inherited, polygenic trait in which mutations in several genes [the
regions where these genes reside in the genome are called quantitative trait loci (QTLs)] are
involved in its clinical expression. The molecular genetic basis of CHD is currently unknown.
Many dogs with normal hips on radiographs carry at least a modicum of the trait-causing
mutations but not all that are necessary to cause physical expression of the trait. CHD is a
quantitative or complex trait that is expressed as a continuum from imperceptible to severe
forms. This continuum in trait expression observed as the hip phenotype represented in the
radiographic image is due to the additive nature of the genes and their alleles that underlie the
trait. Some alleles increase trait expression and some contribute resistance to the trait. This
continuum of trait expression is affected by environmental influences (such as plane of nutrition
and exercise, and many unknown epigenetic factors) which interact with the genetic constitution
to affect the degree to which the trait is manifested. CHD has a heritability between 0.25-0.7
depending on the pedigree in which it is estimated and the method used to measure the trait. We
have found one gene, fibrillin 2, which has a deletion that segregates with CHD across several
breeds represented in our genetic banking archive. Other candidate genes are under investigation.
We recently genotyped about 1,000 dogs on the High Density Illumina canine mapping array in
order to find markers and genes associated with CHD. Eventually, these genetic mapping
experiments will lead to discovery of the mutations that contribute to CHD.
It will take a concerted effort to rid breeds of the genetic mutations that contribute to
CHD expression or conversely, to introduce protective alleles at the loci that cause good hips.
Breeding two dysplastic dogs can yield a 75% incidence of CHD in offspring, while mating two
unaffected dogs can yield a 25% incidence. Selective breeding using normal dogs from normal
parents and grandparents, as well as progeny testing, should decrease the incidence of CHD. The
message here is that until we have a genetic test for CHD so we can detect genetically
susceptible dogs, the best indication of a dog's genetic makeup is where it came from (its' parents
and grandparents), what it produces (its' offspring), and the phenotype of its' siblings or half sibs.
73
To test whether a sire or dam carries mutations for CHD (even if the dog has OFA-good hips), it
should be bred to sires or dams with good hips and the proportion of affected offspring recorded
(progeny testing). As many as 20 offspring would be needed to be reasonably estimate a dog’s
genetic value for CHD.
Hip Conformation Screening
Because it is an inherited trait, the traditional strategy to control CHD has been through
establishment of registries. Registries can be voluntary or involuntary and each has its detractors.
In the USA, the Orthopedic Foundation for Animals (OFA) has provided a standard for
radiographic evaluation of hips based on breed, age, and conformation. Radiographs from dogs
under 2 years of age are given a provisional assessment of hip status and a definitive hip
certification is given to dogs 2 years or older. The OFA has far surpassed their one millionth
radiographic submission. Radiographic changes related to the osteoarthritis associated with CHD
may not be detected until two years of age or older. The sensitivity of the OFA radiograph at 12
months of age for detecting later development of osteoarthritis in affected hips ranges from 7799% depending on the severity of the CHD at the earlier age. Ninety to 95% of dysplastic dogs
have changes associated with CHD at 12 months of age. However, another study showed that of
all dogs developing hip osteoarthritis over their life span, only 53% had radiographic evidence of
a CHD at 2 years of age. Radiographs are insensitive to the presence of incipient osteoarthritis in
the hip. The joint is considered dysplastic when the femoral head conforms poorly to the
acetabulum or there are remodeling boney changes at the capsular attachment to the acetabulum
or femoral neck. Hip status is graded on a scale from excellent conformation to severe hip
dysplasia; there are 7 grades in all.
The PennHIP™ radiographic method measures the maximum amount of lateral
(distraction) hip joint laxity (distraction index). There is a positive relationship between the
distraction index and subsequent development of osteoarthritis. PennHIP radiographs include an
OFA style ventrodorsal projection, a compression and a distraction projection. The OFA style
film is evaluated for hip congruity and osteoarthritis. Labrador Retrievers with a low distraction
index (less than 0.3) at 8 months of age have about a 90% chance of being normal while those
with distraction indices greater than 0.8 have about a 90% chance of being dysplastic and
succumbing to secondary hip osteoarthritis. Most breeds have similar ranges and relationships
between the distraction index and the development of hip osteoarthritis. When choosing between
dogs for breeding, preferentially breed dogs with the lowest distraction indices of the available
pool. The optimum age for PennHIP™ screening is at early maturity (8-12 months of age for
medium to large breed dogs).
A radiographic imaging position called the dorsolateral subluxation (DLS) test was
developed at Cornell with an eye to improving the accuracy of hip evaluation. The PennHIP™
method finds dogs with laxity (a risk factor for CHD) but not all dogs with hip laxity develop
secondary hip osteoarthritis. Their hips presumably function normally when they ambulate. We
developed a method in which the hips are imaged in their normal functional position. The dogs
are imaged in ventral recumbency under heavy sedation (or general anesthesia). The stifles are
flexed and positioned under the hips so that the ischiatic table is superimposed over the stifles.
The DLS score equates with the proportion of the femoral head covered by the dorsal acetabular
74
rim. We compared the sensitivity (the percentage of dogs with osteoarthritis that were correctly
identified) and specificity (percentage of dogs without osteoarthritis that were correctly
identified) between the OFA-like extended-hip radiograph, the distraction index, and the
dorsolateral subluxation score (DLS) score. For a single test, the DLS score is the most accurate
in detection of both affected and unaffected dogs. A combination of the DLS score and Norberg
angle gave the best estimate of a dog’s likelihood of developing subsequent osteoarthritis than
any single test, including the DLS test. The Norberg angle is a measure of femoral head coverage
on the OFA style extended hip radiograph. The Norberg angle ranges from near zero for severely
subluxated hips to about 120º in the “best” hipped dogs. An angle over 105º seems to be
preferable. So we are back to needing two methods to adequately describe hip conformation.
This conclusion is supported by principal component analysis of the OFA score, the Norberg
angle, the DI, and the DLS score to measure hip conformation.
My recommendation for selection of a young to early mature pet dog (not for breeding)
with optimal hip quality is to examine the dog, palpate the hips for pain and Ortolani sign (under
sedation), and to confirm physical findings with at least one radiograph – either a DLS or an
extended hip radiograph. If the extended-hip (OFA style) image demonstrates subluxation
(dysplasia) then no need to go further. If the dog has a “normal” extended hip projection but a
positive Ortolani test, then that dog is at least susceptible to secondary osteoarthritis, if not
dysplastic, and to document the laxity, should have a laxity imaging projection like the DLS
method. A dog with optimal hip conformation should have palpated normally and have a DLS
score over 55% or a DI below 0.4.
The dilemma is how to select puppies with optimum hip conformation. For those breeds
with moderate to high risk for hip dysplasia, select pups from breeders where rigorous selection
practices are employed (phenotypes recorded on both the sire and dam lines) so the buyer can
review the breeding history. Both sides of the pedigree should be available. Information about
results of previous breedings is very helpful (roughly 15-20 offspring of the same parents must
be evaluated before one can have reasonable knowledge of the genetic quality of the same
parents). Application of estimated breeding values (EBVs) for CHD will result in faster gain than
basing breeding decisions on phenotype alone. Finally, marker-assisted selection will improve
genetic quality for complex or polygenetic traits like hip dysplasia far faster them breeding
“better than the average” and can replace the use of EBVs for those who can’t access them or
estimate them with much accuracy (which is the case for most breeders not aligned with Service
Organization like the Seeing Eye or Guiding Eyes for the Blind or military establishments).
Breeding Values for US Pure Breed Dogs Derived from the OFA Public Data Base
The breeding value in its earliest use was also called the selection index. The selection
index was based on integration of genetic (pedigree relationships) and phenotypic information
(OFA hip scores in our case) from each animal and its relatives and yields better results than
phenotypic selection alone for desirable traits. The accuracy of the selection index of a subject
increases when the OFA scores from its close relatives (e.g. progeny and ancestors) are included
in the estimation. The selection index was developed into the Best Linear Unbiased Prediction
(BLUP). The BLUP breeding strategy has been used successfully for genetic improvement,
particularly in livestock, and has also been applied in closed colonies of dogs with substantial
75
success. Variance components attributable to additive genetic and residual effects were estimated
for the OFA hip and elbow scores and pedigrees. Genetic parameters, including the additive
genetic variance and the residual variance were estimated using the REML procedure.
Heritability (h2) is the proportion of additive variance over the total variance which is the sum of
additive variance and residual variance. The general concept is to select dogs with the lower
EBVs as these are the individuals with the lowest or best hip and elbow conformation.
We derived EBVs (a measure of a dog’s genetic potential to produce offspring with
optimal characteristics for an inherited trait) and inbreeding coefficients for CHD in Labrador
retrievers based on OFA hip scores in the OFA database and provided them to the public in 2010
(http://www.vet.cornell.edu/research/bvhip/). The OFA hip scores and pedigrees of the Labrador
retrievers in the public data base were used for the genetic evaluation. Dogs were scored by the
OFA radiologists into seven categories: excellent, good, fair, borderline, mild, moderate and
severe hip dysplasia. The first three categories (excellent, good and fair) are generally considered
“normal” dogs although they will carry some of the mutations that contribute to hip dysplasia.
The last three categories (mild, moderate and severe) are considered “dysplastic” dogs. This
analysis was undertaken independently of the OFA. The seven hip score categories were
replaced with 7 numerical scores, starting with excellent as 1 and ending with severe as 7. A
numerical value of 2 was assigned to the combined category of “normal”. Our analysis of the
Labrador Retriever OFA hip breeding values over that period showed that there has been slow
but consistent genetic improvement (Hou et al., PLoS One 2010). The explanation and methods
that form the basis of the breeding values available in the search page of this web site were
published in the American Journal of Veterinary Research in 2008 by Zhang et al. and a PDF of
that paper is available in the publication section of my research home page in Clinical Sciences
at Cornell University.
Since 1974, the Orthopedic Foundation for Animals (OFA) has provided a voluntary
registry where the scores of hip and elbow radiographs of individual dogs and their pedigrees
have been deposited. Following on from the research we reported on Labrador Retriever hip
EBVs, we calculated estimated breeding values (EBVs) and inbreeding coefficients for a total of
1,264,422 dogs from 74 breeds which included at least 1,000 individuals. The analysis was
performed with a bi-variate (used both hip and elbow scores) mixed model across these 74
breeds to improve the accuracy of the EBVs, to compensate for the deficiency in voluntarily
reporting bias in the OFA public registry, and to provide an estimate of genetic correlation
between the hip and elbow scores. There were 760,455 and 135,409 dogs with their own hip and
elbow scores, respectively. The incidences of CHD and elbow dysplasia were 0.83% and 2.08%
across the 74 breeds (21 breeds for elbow dysplasia) and ranged from 0.07% to 6%, and 0.5% to
8% within breeds, respectively. These incidences were far lower than the incidence reported in
the hip and elbow dysplasia summary statistics by breed in the OFA web page
(http://www.offa.org/stats_hip.html). The heritability of hip and elbow scores was estimated at
0.23 and 0.16, respectively. Over the 40 years since 1974, the genetic improvement for hip
scores was 0.1 hip units or 16.4% of the average phenotypic standard deviation across the 74
breeds, which corresponded to a drop in the overall incidence of CHD of 3.37% clinically. For
elbow scores, the genetic improvement was 0.0021 elbow units or 1.1% of the phenotypic
standard deviation across the 21 breeds. Both genetic improvements were likely underestimated
due to the inevitable bias against reporting osteoarthritic records. Genetic change in EBVs for
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hip and elbow scores was breed specific; some breeds improved their genetic quality, some
demonstrated little improvement, while in a few breeds, genetic quality deteriorated. We
concluded that distinct breeding selection goals should be directed at improving the genetic
quality based on each breeds’ genetic characteristics and breed requirements and we provide the
first national hip and elbow EBVs by which to do so. The genetic and residual correlations
between hip and elbow scores were 0.12 and 0.08, respectively. The weak positive genetic
correlation suggested that selection based on hip scores would also slightly improve elbow
scores but it is necessary to allocate effort toward improvement of elbow scores alone (Hou et
al., 2013 PLoS One in press).
These estimated hip and elbow breeding values and inbreeding coefficients will be
accessible in this Cornell hip dysplasia web site. The dogs with low breeding value (low OFA
score means a better hip) and with higher accuracy (more related dogs measured, the higher the
accuracy) are the most desirable for breeding purposes. Low accuracy means that not many dogs
were available to estimate the breeding value.
Inbreeding
Inbreeding occurs when a mating is made with a relative or the parents shared common
ancestors. The closer an individual dog is to its ancestors with other dogs and the more common
ancestors, the stronger the inbreeding. The most severe inbreeding occurs in a sibling to sibling
mating or offspring to their parents. These matings commonly occur in an effort to preserve
features of a breed or line within a breed and is referred to as “line breeding”. The degree of
inbreeding can be mathematically expressed as an inbreeding coefficient. The inbreeding
coefficient of an individual is defined as the probability that any two homologous alleles (same
forms of the genetic locus) are identical by descent. That is, they were transferred from an
ancestor to the current generation. Inbreeding often occurs the deeper you trace a pedigree. It is
almost impossible to avoid inbreeding in a limited population, especially when the population
has experienced a bottle neck. Severe inbreeding could result in shorter lives and problems of
fitness including hip dysplasia. The level of inbreeding has continuously accumulated in US pure
breed dogs over the past 40 years with higher inbreeding occurring generally in the breeds with
total populations and therefore smaller breeding populations.
Questions & Answers about the Application of Hip and Elbow Estimated Breeding Values and
Inbreeding Coefficients to the Breeding and Selection of a Pup (taken from the Cornell Hip EBV
web site for the Labrador Retriever)
Once the new EBVs for other breeds are uploaded, then similar strategies for purchase
and breeding decisions will apply to other breeds.
Why is this search function to find Labrador Retrievers with better hip breeding values
useful? The breeding values and inbreeding coefficients recorded in this web site enable me to
find dogs with low hip score breeding values that belong to the current and recent generations.
The use of the dogs in the lower part of the breeding value range for breeding will likely improve
the hip quality of my breeding stock and puppies they produce. Purchase of puppies produced by
the sires and dams with the lower breeding values will likely produce puppies with better hips
77
than if I based breeding decisions on hip radiographs alone. The reason is that the selection of
dogs based on breeding values means that consideration has been given to both the dog's genetic
(pedigree) information and hip radiographic information combined. Selection of dogs based on
radiographs alone is very useful but faster genetic gain toward better hip conformation accrues
when breeding decisions are made based on genetic information as well.
Why does negative breeding values means a better hip? The question arises due to the
ambiguity of word “value”, which usually suggests the higher value the better. The breeding
value is an indicator for the genetic basis of the hip score variation. Consequently, breeding
values take the same unit and direction as the original phenotype – the OFA score. An OFA
score of 1 is for an excellent hip and an OFA score of 7 is for the most severe hip dysplasia.
What is the difference between expected progeny difference (EPD) and breeding value?
The breeding value is the prediction of the genetic basis of an individual OFA score. Half of the
genetic basis is contributed from one parent and half from the other. If an individual is mated
randomly, the expected difference of the progeny from the average (base) will be half of the
breeding value. Therefore, half of the breeding value is called the EPD. For example, sire A and
B have breeding values of -0.1 and 0.20, their EPDs will be -0.05 and 0.1. The progeny of sire A
is expected to be 0.15 lower than the progeny of sire B.
Will an inbred dog definitely have progeny with high inbreeding? Not really. The
progeny may not be inbred if the mate you select is not its relative. The inbreeding of an
individual depends if the parents are relatives or not.
Why can a breeding value be negative? The current reported breeding values were the
direct output of the solutions for each dog in the mixed linear model. The base of the breeding
value is the average breeding value among all the dogs evaluated. The base is a “floating” base
which can vary by adding new dogs which have better hips.
I wish to choose a pup from a litter and I know the parents who produced this litter? How
should I use the information in the hip EBV data base? Once you decide the qualities of the
parents you prefer, then gather the information about any inherited traits and diseases segregating
in the pedigree that you can. For a pup’s genetic potential to grow up with good hip quality, go
into the data base and look at the hip breeding values for the dogs you like. Then you can rank
those dogs based on their potential to produce pups with good hip conformation (the lowest hip
breeding value indicates the dog with the genetic potential to produce the best hip conformation
based on the OFA score). If only one parent is found in the data base, then that’s the best you can
do. Secondly, you can rank the parents according to their inbreeding coefficients. You should try
to choose pups produced from litters whose parents have the lowest inbreeding coefficients.
I wish to choose a pup from a litter but I don’t have information about the hip scores of
either parent? You can ask the breeder for any pertinent radiographic information they have
about their dog. They may have PennHIP information. They may not use the OFA method. They
may do no orthopedic screening at all. We also know that elbow dysplasia is a problem in the
Labrador Retriever breed. If you can obtain no information about orthopedic disease in a dog’s
pedigree, then I suggest you try another breeder.
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I wish to choose or buy a male dog as a potential breeder? How should I use the
information in the data base? Once you have selected the potential male dogs based on all the
breed qualities you prefer, then rank the dogs based on their genetic potential to produce
offspring with good hip conformation and on their inbreeding coefficients. Always breed to a
female dog with the best hip conformation and lowest inbreeding coefficient you can find along
with all the best qualities you can ascertain, orthopedic or otherwise.
I wish to choose or buy a female dog as a potential breeder? How should I use the
information in the data base? Once you have selected the potential female dogs based on all the
breed qualities you prefer, then rank them based on their genetic potential to produce offspring
with good hip conformation and on their inbreeding coefficients. Always breed to a male dog
with the best hip conformation and lowest inbreeding coefficient you can find along with all the
best qualities you can ascertain, orthopedic or otherwise.
I bought a pup already but just found this web site. How should I use the information in
the data base to decide if this puppy is at risk of hip dysplasia? If you can identify the parents in
the data base, look at the OFA breeding values of the parents. If they are above 0, then the pup
has a higher chance of developing hip dysplasia than if the breeding values are below 0. The
closer the breeding value is to 1, the greater the susceptibility to develop hip dysplasia. If you
decide the pup is susceptible, it should be examined regularly for hip instability by your
veterinarian. Depending on the dog’s age, medical or surgical intervention may be an option.
This is especially important if your dogs has clinical signs of hip dysplasia like reluctance to
jump, bunny hopping gait behind at speed (both hind legs moving forward together), soreness or
stiffness after exercise, a “wobbly” hind limb gait, poor muscle mass development behind
compared to its forequarter, difficulty getting up, placing extra body weight on its fore limbs
with a hunched back, a clicking sound when it walks, or reluctance to allow you to pet near its
hips. Any pup susceptible to hip dysplasia or any developmental orthopedic disease should be
watched for rapid body weight gain and if it is too fat, its food intake should be restricted under
advice of your veterinarian.
If a puppy is at risk for hip dysplasia based on the breeding value of its parents, what
should I do about it? Ask your veterinarian to examine your puppy’s hips regularly. This is
especially important if your dog has clinical signs of hip dysplasia like reluctance to jump, bunny
hopping gait behind at speed (both hind legs moving forward together), soreness or stiffness after
exercise, a “wobbly” hind limb gait, poor muscle mass development behind compared to its
forequarter, difficulty getting up, placing extra body weight on its fore limbs with a hunched
back, a clicking sound when it walks, or reluctance to allow you to pet near its hips. Any pup
susceptible to hip dysplasia or any developmental orthopedic disease should be watched for rapid
body weight gain and if it is too fat, its food intake should be restricted under advice of your
veterinarian.
I wish to choose a male dog for my female dog to produce a litter of pups with the best
hips I can. How do I select a dog from this data base? Rank the male dogs based on their OFA
hip breeding values scores and their inbreeding coefficients. Choose the dog with the qualities
you like as well as the best genetic potential to produce offspring with good hip conformation
and lower inbreeding co-efficient.
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Once I have identified a litter for puppy selection or a dog to which I'd like to breed, how
do I locate the owner or breeder? We can suggest trying Google, other Labrador Retriever
owners, breed/trade magazines like "Just Labs", contacting the Labrador Retriever breed clubs,
or the AKC, etc. You can also purchase a pedigree from the AKC and this will have an owner's
name on it. Eventually estimated breeding values and inbreeding coefficients for OFA hip scores
will be available for many breeds.
Genomic Reference Panel and Genomic Prediction
State-of-the-art for predicting the dogs that carry the best combination of alleles at the
genes that contribute to hip dysplasia is called genomic prediction. By genomic, I mean a method
that interrogates the whole genome of the individual dog. No gene has yet been identified that
contributes substantially, say 20%, to the overall genetic variation of the full range of hip
dysplasia. However, if the density of genetic markers or variants for which a dog is genotyped, is
sufficient to capture every gene that “lives” near a marker, then we can use the marker genotypes
as a surrogate for the genes. The marker(s) is so close to the gene that the form of its alleles is
always inherited with the gene i.e. recombination does not interfere with this relationship. There
are a couple of strategies that can be used to undertake the genomic prediction. A subset of
genetic markers called single nucleotide polymorphisms (SNPs) that span the genome are jointly
selected for their contribution to CHD (or any other complex trait). Or a set of SNPs that are
each significantly associated with the trait are used to build a multivariate linear model in a
forward or backward method keeping the markers in the model that accounts for the most
variation but eliminating redundant markers.
We employed the joint marker or Bayesian approach for our first effort. We used the
Norberg angle which is highly phenotypically and genetically correlated with the OFA hip score.
A reference population was established of dogs belonging to breeds susceptible or resistant to hip
dysplasia that have undergone genome wide SNP genotyping and that have accompanying
estimated hip breeding values calculated. A new dog of a breed that is in the reference
population is genotyped either across the genome or at the best subset of SNPs and its estimated
breeding value for optimal hip quality is estimated from the dogs in the reference panel based on
its own SNP genotypes. Modest correlations can also be made with the raw Norberg angle. The
best estimates of the genetic potential of two dogs to produce offspring with optimal hip quality
will be based on gene mutation tests but it will take resources and time to discover the genes that
contribute to CHD. In the mean time, SNP based selection will have to suffice to which we will
later add the mutations to improve the prediction model.
Currently, the largest reference population for genomic prediction we have available is
for the Labrador Retriever (Guo et al., 2011). For 180 Labrador Retrievers genotyped on the
Illumina version 1, 22K mapping array, genomic hip breeding values for the Norberg angle were
calculated in a Bayesian framework (Guo et al., 2011). This statistical method uses all the
available genotypes to explain the variability in the Norberg angle. The estimated hip breeding
values of these Labrador Retrievers were correlated with their genomic breeding values using the
most predictive (effective) 280 SNPs of the 22,000 markers in the version 1 array. 30% of the
variation in the Norberg angle of 108 Labrador Retrievers not used to develop the reference
genomic panel was explained by the genomic prediction. The accuracy for a true phenotype is
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about as expected because the heritability of HD as measured by the Norberg angle is only about
0.2-0.3. The accuracy of the genomic prediction for estimated hip breeding values on a subset of
the 108 naïve dogs was moderate at 57% of the variation. Ongoing research would combine
genomic prediction with the true hip radiographs of a genotyped dog to improve the accuracy of
the prediction by including newly genotyped and phenotyped dogs into the reference panel.
Other breeds might be added on which to predict genetic quality of hips. Recalculation of the
genomic prediction algorithm based on more individuals and denser genotyping using the
Illumina HD array should improve accuracy of the prediction. This iteration would be repeated
over and over.
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Holistic Management of Genetic Traits
Anita Oberbauer, Ph.D., Department of Animal Science, University of California, Davis, CA
AMOberbauer@UCDavis.Edu
In breeding any species, first and foremost there should be goals and objectives. Breeders have
different goals (improve the breed, optimize performance characteristics, win, financial
remuneration) and some may view their goals as being more noble than the goals of others.
Regardless, in any breeding endeavor one must strive for that specific goal(s) and in doing so
make concessions. The hallmarks of a successful breeder include making progress toward the
overall objective while minimizing the negative impact of tradeoffs.
Above, several possible breeding objectives were listed. An animal in a breeding pool is a
composite of numerous elements that include desired type, health, performance, reproductive
efficiency, structure, and temperament. When selecting breeding animals, these elements must be
prioritized and their relative importance to one another weighed. For example, a dog or cat that
is ideal in every category but lacks fertility fails to reach a breeding objective. A highly fertile
dog or cat that lacks desired type likewise fails to meet a breeding goal. Thus, in any breeding
program, one must achieve a balance blending often conflicting aspects.
Unfortunately, rather than looking at the long view and complexities of achieving breeding
goals, the majority of claims against concerted breeding programs (purebred dog or cat for
example) center on a perceived lack of concern by breeders to reduce harmful genetic conditions
in order to win, make money, satisfy ego, or (fill in the blank). Yet when breeders and owners
are asked to define “health” in relationship to dogs (or cats), definitions are many and varied.
Definitions can be pragmatic (not needing visits to the veterinarian), focused solely on physical
health, or focused solely on mental health; most commonly cited attributes of “health” are
absence of disease or injury concomitant with the ability to perform normal/expected body
functions and abilities. Most breeders or owners focus on the individual when considering
health. In contrast, livestock producers also include population health (so called “herd health”)
as a significant component of their concept of “health”. Herd health is especially critical for
large numbers of animals and/or densely populated animal groupings. Stepping back and
considering health in a broader perspective, herd health is definitely applicable to the dog
population as a whole or to a particular breed. One can consider genetic health of the population
as underpinning all the elements a breeder needs to attain a breeding goal.
An individual’s qualities (health, temperament, type, etc.) are a reflection of the population’s
genetic potential. When selecting an individual for breeding, the breeder should balance the
individual’s needs (a certain dog may need a mate who has a better shoulder assembly) with that
of the population as a whole (excessive use of a popular sire can reduce the genetic diversity for
future generations). Further, the breeder must make compromises. Even if the absolute perfect
breed specimen is produced, to perpetuate that individual one must breed to a mate that has
faults. What qualities should be emphasized in the less than perfect mate? One breeder will say
type (and that includes every attribute ranging from eye color, muzzle shape, ear placement,
length of back, to bend of stifle and beyond!) whereas a second breeder will insist that
temperament is most critical (and temperament also has a spectrum of qualifiers). Yet a third
breeder will insist upon health (as discussed above, health means different things to different
82
people). Despite the varied opinions each breeder should have a prioritized and weighted view
to a breeding program. Even then, the suite of traits that comprises the general element (type,
performance, etc.) each needs to be prioritized and weighted. While no breeder would knowingly
breed genetic defects, should one trade less than ideal eye color for better eye shape?
The domestication of the dog and cat reflected selection on traits that favored successful cohabitation with the human population. The inherent genetic diversity of the ancestral wolf
permitted the expression of many traits that favored domestication. Yet the domestication
process reduced some genetic diversity that was present in its ancestor; that is, bottlenecks in
which limited numbers of individuals established a relationship with humans created
subpopulations. Genetic diversity is critical to compensate for current and future challenges. For
example, the restricted genetic diversity in the endangered black-tailed prairie dog has resulted in
their susceptibility to an exotic, introduced pathogen that causes plague. Maintaining genetic
diversity maintains the health of the population. Thus, the founding dog population represented
a subset of the ancestral wolf and therefore dogs began with a smaller gene pool. The
establishment of breeds within the dog population as a whole further reduced the gene pools for
each breed.
The challenge in breeding is to fix the desirable traits while maintaining genetic diversity. Loss
of genetic variety within a unique population (read “breed”) is considered highly detrimental to
the overall genetic health of a breed. A population may begin with a limited gene pool.
Developing a new breed and then closing the registry for that breed equates to a small gene pool.
Using inbreeding schemes to fix desirable traits reduces genetic diversity by increasing the
genetic homozygosity, that is making both copies of a gene identical. Increased homozygosity
ensures that a particular desirable trait will be expressed it also potentiates the expression of
genetic disorders that are recessively inherited. Furthermore, loss of heterozygosity is
statistically correlated with greater autoimmune concerns. Taken together, although inbreeding,
enhances uniformity within litters and fixes characteristic, breed-defining traits, it also has
unintended consequences such as loss of rare alleles, increased homozygosity enabling
expression of recessive disorders, and reducing effective population size. Thus, inbreeding has
been the subject of much debate concerning the welfare and health of purebred dogs.
Similarly, extensive use of a popular sire also reduces heterozygosity effectively reducing the
population size. The use of a popular sire also proves to be more effective at dispersing
deleterious alleles within a breed than inbreeding (Leroy & Baumung, 2010) making disorders
that occur in a popular sire (or one for which he carries the mutant alleles) more difficult to
manage in the future. In humans the mutation rate resulting in random errors in DNA is one
mutation in every 100 million base pairs equaling ~ 60 new mutations per generation and more
mutations arise from the male (Conrad et al., 2011). Each human is estimated to carry
approximately 1,000 deleterious mutations (Sunyaev et al., 2001). Also in humans, it has been
demonstrated (Chun & Fay, 2011) that natural selection to eliminate some deleterious alleles
may increase the frequency of others; a deleterious allele may hitchhike along with a desirable
allele due to genetic linkage. In one review, all top 50 breeds the study evaluated had at least one
genetic disorder associated with the conformation demanded by the standard (Asher et al., 2009).
Deleterious mutations are difficult to eliminate from small populations and are likely to
accumulate.
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The association of deleterious with desirable traits has implications for proponents mandating
only individuals clear of deleterious alleles are permitted to breed. When considering genetic
health of an individual in relation to the population health, no single individual is free from all
genetic mutation. A dog, any dog, when all genetic diseases have been characterized will fail at
least one genetic test. Limiting breeding to those clear will further restrict the gene pool and
introduce unintended health consequences. That does not mean that genetic testing is
unwarranted. As Dr. Jerry Bell states, “breeding without genetic testing is irresponsible, and
unethical.” Using available test results in a holistic approach is key to maintaining the overall
genetic health of a breed.
In some cases the genetic test may indicate a risk, but not guarantee, of expression of a disease
(for example, degenerative myelopathy, Chang et al., 2013). Utilizing that information to inform
breeding decisions is critical but eliminating all dogs having a risk from the breeding population
is unwise. In other cases, the presence of an allele may be viewed as deleterious or an asset. A
particular allele for a behavioral trait is associated with highly productive working dogs although
owners should emphasize non-confrontational training methods to achieve optimal performance;
yet there is significant association between spontaneous episodic aggressive behaviors in dogs
with that allele (Lit et al., 2013). Maintaining that diversity within the gene pool permits
breeders to attain their individual goals.
A comment on crowd sourcing of health information: popular beliefs can be very wrong even if
commonly held. An example from history, it was universally believed that the world was flat—
even though there was consensus did not make that view factual. Just because “everyone” says
it’s true does not make it so and sensible caution should be applied to health statements. Much is
made of “healthy” mixed breeds; domesticated dogs carry deleterious mutations dating back to
the original domestication step. Thus, there are health conditions that will be present in a dog,
any dog, be it a purebred or mixed breed dog.
Concerted breeding to reduce unwanted traits is the only means to eliminate particular
conditions. Wisdom and stewardship of a breed is essential. The genetic health of a breed
depends upon wise sire and dam selection.
References
Asher, L. Diesel, G., Summers, J.F., McGreevy, P.D., and Collins, L.M. (2009) Inherited defects in
pedigree dogs. Part 1: Disorders related to breed standards. Veterinary Journal 182, 402-411.
Calboli, F.C.F., Sampson, J., Fretwell, N., and Balding D.J. (2008) Population structure and inbreeding
from pedigree analysis of purebred dogs. Genetics 179, 593-601.
Chang HS, Kamishina H, Mizukami K, Momoi Y, Katayama M, Rahman MM, Uddin MM, Yabuki A,
Kohyama M, Yamato O. (2013) Genotyping Assays for the Canine Degenerative Myelopathy-Associated
c.118G>A (p.E40K) Mutation of the SOD1 Gene Using Conventional and Real-Time PCR Methods: A
High Prevalence in the Pembroke Welsh Corgi Breed in Japan. Journal of Veterinary Medical Science.
75, 795-798
Chun S, Fay JC (2011) Evidence for Hitchhiking of Deleterious Mutations within the Human Genome.
PLoS Genet 7(8): e1002240.
http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002240
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Conrad et al. For the 1000 Genomes Project. (2011) Variation in genome-wide mutation rates within and
between human families. Nature Genetics 43, 712-714.
Leroy, G. and Baumung, R. (2010) Mating practices and the dissemination of genetic disorders in
domestic animals, based on the example of dog breeding. Animal Genetics doi 10.1111/j.13652052.2010.02079.x.
Lit L, Belanger JM, Boehm D, Lybarger N, Haverbeke A, Diederich C, Oberbauer AM. (2013)
Characterization of a dopamine transporter polymorphism and behavior in Belgian Malinois. BMC Genet.
2013 May 30;14:45. http://www.biomedcentral.com/1471-2156/14/45.
Sunyaev S, Ramensky V, Koch I, Lathe W, Kondrashov A, et al. (2001) Prediction of deleterious human
alleles. Hum Mol Genet 10: 591–597.
OMIA. Online Medelian Inheritance in Animals. Reprogen, Faculty of Veterinary Science, University of
Sydney, {December 2010}. World Wide Web URL: http://omia.angis.org.au/
85
From FUS to Pandora Syndrome - The Role of Epigenetics and Environment
in Pathophysiology, Treatment, and Prevention
C. A. Tony Buffington, DVM, PhD, DACVN, The Ohio State University Veterinary Hospital,
Columbus, OH buffington.1@osu.edu
INTRODUCTION
In an accurate clinical description of cats with lower urinary tract (LUT) disease
published in 1925,1 the disorder was reported to be very common, the roles of confinement and
highly nutritious food were discussed, and the common occurrence of the problem in Persian cats
was identified. In 1970, the term feline urologic syndrome (FUS) was coined by Osbaldiston
and Taussig to describe a problem, “characterized by dysuria, urethral obstruction, urolithiasis
(although no stones were reported) and hematuria”.2 They concluded from a review of 46 cases,
“the condition may not be a single disease entity, but rather a group of separate urologic
problems.”
During the 1980s, Osborne, et al., suggested that FUS should be considered synonymous
with feline lower urinary tract disease (FLUTD).3 Then, in 1995, the group4 suggested that the
acronym FUS be redefined as feline urologic signs to emphasize that FUS is not an etiologic
diagnosis of any particular LUT disease. They proposed that “when possible, refined diagnoses
of lower urinary tract disease should encompass descriptive terms pertaining to the site (e.g.,
urethra, bladder), pathophysiologic mechanisms (e.g., obstructive uropathy, reflex dyssynergia),
morphologic features (e.g., inflammation, neoplasia), and causes (e.g., anomalies, urolithiasis,
bacteria, fungi),” and suggested that confirmed and suspected causes of LUT diseases in
domestic cats be categorized as anatomic, iatrogenic, idiopathic, inflammatory (infectious and
noninfectious), metabolic, neoplastic, neurogenic, or traumatic. The terms FUS and FLUTD
have since been superseded by the ability of veterinarians to diagnose many distinct causes of the
well-known clinical signs of dysuria, stranguria, pollakiuria, hematuria, and inappropriate
urination (periuria) that, either individually or in some combination, cause clients to seek further
evaluation of their cats.5
Retrospective studies suggest that the majority of non-obstructed cats with LUT signs
have an idiopathic disorder, and that this percentage has not changed appreciably during the past
4 decades.2,6-9 The importance of LUT disorders to feline health is emphasized by the finding
that elimination disorders (the vast majority of which are urinary) result in destruction of
millions of cats in animal shelters in the United States every year.10 We defined idiopathic
cystitis as an acute or chronic disease of waxing and waning signs of irritative voiding (dysuria,
pollakiuria, hematuria, periuria), sterile urine, absence of cellular abnormalities suggesting
neoplasia, and failure to identify an alternative cause for these signs after appropriate lower
urinary tract (LUT) imaging procedures (combination of plain radiography, contrast radiography,
contrast urethrography, ultrasonography) in the absence of cystoscopic evaluation.8 Feline
interstitial cystitis (FIC), a subcategory of idiopathic cystitis, was defined as a chronic condition
describing cats that have frequent recurrences or persistence of clinical signs and cystoscopic
documentation of submucosal petechial hemorrhages (glomerulations) after bladder distension to
80 cm water pressure in the absence of an alternative explanation for these findings.9
1
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Based on a series of studies conducted during the past two decades, a variety of problems
beyond the urinary tract have been identified in cats with chronic, severe, recurrent LUT signs.11
These include epithelial, neurological, endocrine, immune and behavior abnormalities, as well as
a variety of comorbid disorders (which often precede development of LUT signs) affecting many
body systems. Enhanced central sympathetic drive in the face of inadequate adrenocortical
restraint, which seems to be related to maintaining the chronic disease process, also has been
identified. These systems appear to be driven by tonically increased activity of the central stress
response system, which may represent the outcome of a developmental accident that durably
sensitizes this system to the environment, possibly through epigenetic modulation of gene
expression.12 The repeated observation that most of these problems resolve after exposure to an
enriched environment provided additional evidence for a disorder of the central nervous system
resulting in a chronic multi-system illness variably affecting the bladder and other organs, as
opposed to a peripheral, organ-based problem.13-15
Diagnosis
Based on the evidence outlined above, I believe that some cats with chronic LUT signs
may have a “Pandora syndrome” (named for the Pandora myth, which reflects my experience in
studying this problem, and my optimism that hope for effective treatment remains).16 Based on
the currently available evidence, provisional criteria for diagnosis of a “Pandora syndrome”
might include:
1. Chronicity – persistence or recurrence of the condition(s) over months to years.
2. Comorbidity - evidence of problems in other body systems (particularly preceding the
presenting LUTS in the case of idiopathic cystitis. These may include behavioral,
endocrine gastrointestinal, respiratory, dermatological, etc.
3. A history of early adverse experience (orphaned, bottle fed, rescued).
4. Evidence of familial involvement. That is, parents and or littermates have a similar illness
profile.
Information about early experience and family members often cannot be obtained from
owners, and none of these criteria can be considered pathognomonic for anything. They may
serve only to raise one’s “index of suspicion” that a more systemic problem may be present. By
taking the time to obtain a comprehensive review of the cat’s history and conduct a thorough
physical examination before assuming that the cat has an isolated bladder (or other) disease, one
may find that some cats appear to have a disease affecting more than the organ attributed to the
presenting signs, which can helpfully inform one’s therapeutic recommendations. I urge others
to test this hypothesis for themselves.
Treatment
Based on current understanding of the role of the environment in chronic illness in cats,
environmental enrichment is the first line of therapy to reduce the risk of recurrence of whatever
clinical signs are present.13-15 Environmental enrichment for indoor-housed cats means provision
of all “necessary” resources listed below, refinement of interactions with owners, a tolerable
intensity of conflict, and thoughtful institution of change(s).5,17,18 The following areas all are
considered based on their influence on the health and welfare of indoor-housed cats.
2
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1. Food - Cats prefer to eat individually in quiet locations where they will not be startled by
other animals, sudden movement, or activity of an air duct or appliance that may begin
operation unexpectedly. Although canned food may be preferable for some cats due to the
increased water content or a more natural “mouth feel”, some cats may prefer dry foods. If a
diet change is appropriate, offering the new diet in a separate, adjacent container rather than
removing the usual food and replacing it with the new food permits the cat to express its
preferences. Natural cat feeding behavior also includes predatory activities such as stalking
and pouncing. These may be simulated by hiding small amounts of food around the house,
or by putting dry food in a container from which the cat has to extract individual pieces or
move to release the food pieces, if such interventions appeal to the cat. Also, some cats seem
to have specific prey preferences. For example, some cats prefer to catch birds, while others
may prefer to chase mice or bugs. Identifying a cat’s “prey preference” allows one to buy or
make toys that the cat will be more likely to play with. Specific ingredients or nutrients has
been found to be of minor significance to patient outcome when an enriched environment is
provided.13-15
2. Water - Cats also seem to have preferences for water that can be investigated. Water-related
factors to consider include freshness, taste, movement (water fountains, dripping faucets or
aquarium pump-bubbled air into a bowl), and shape of container (some cats seem to resent
having their vibrissae touch the sides of the container when drinking). As with foods,
changes in water-related factors should be offered in such a way that permits the cat to
express its preferences. Additionally, food and water bowls should be cleaned regularly
unless individual preference suggests otherwise.
3. Litter boxes - Litter boxes should be provided in different locations throughout the house to
the extent possible, particularly in multiple cat households. Placing litter boxes in quiet,
convenient locations that provide an escape route if necessary for the cat could help improve
conditions for normal elimination behaviors. If different litters are offered, it may be
preferable to test the cat’s preferences by providing them in separate boxes, since individual
preferences for litter type have been documented. For cats with a history of urinary
problems, unscented clumping litter should be considered. Litter boxes should be cleaned
regularly and replaced; some cats seem quite sensitive to dirty litter boxes. Litter box size
and whether or not it is open or covered also may be important to some cats.19
4. Space - Cats interact with both the physical structures and other animals, including humans,
in their environment. The physical environment should include opportunities for scratching
(both horizontal and vertical may be necessary), climbing, hiding and resting. Cats seem to
prefer to monitor their surroundings from elevated vantage points, so climbing frames,
hammocks, platforms, raised walkways, shelves or window seats may appeal to them.
Playing a radio to habituate cats to sudden changes in sound and human voices also may be
useful, and videotapes to provide visual stimulation are available.
5. Play - Some cats seem to prefer to be petted and groomed, whereas others may prefer play
interactions with owners. Cats also can be easily trained to perform behaviors (“tricks”);
owners just need to understand that cats respond much better to praise than to force, and
seem to be more amenable to learning when the behavior is shaped before feeding. Cats also
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may enjoy playing with toys, particularly those that are small, move, and that mimic prey
characteristics. Many cats also prefer novelty, so a variety of toys should be provided, and
rotated or replaced regularly to sustain their interest.
6. Conflict management - When cats’ perception of safety becomes threatened, they appear to
respond by attempting to restore their “perception of control”.20 During such responses,
some cats become aggressive, some become withdrawn, and some become ill.13 In our
experience, intercat conflict commonly is present when multiple cats are housed indoors
together and sickness behaviors are present in some of them.13 Signs of conflict between cats
can be open or silent. Cats in open conflict may stalk each other, hiss, and turn sideways
with legs straight and hair standing on end up to make themselves look larger. In contrast,
signs of silent conflict can be easily missed; threatened cats may avoid other cats, decrease
their activity, or both. They often spend increasingly large amounts of time away from the
family, stay in areas other cats do not use, or attempt to interact with family members only
when the assertive cat is elsewhere. Signs can result from two types of conflict; offensive
and defensive. In offensive conflict, the assertive cat moves closer to the other cats to control
the interaction. In defensive conflict situations, the threatened cat attempts to increase the
distance between itself and the perceived threat. Although cats engaged in either type of
conflict may spray or eliminate outside the litter box, we find that threatened cats are more
likely to develop elimination problems.
A common cause of conflict between indoor-housed cats is competition for resources;
space, food, water, litter boxes, perches, sunny areas, safe places where the cat can watch its
environment, or attention from people. There may be no limitation to access to these
resources apparent to the owner for conflict to develop; the cat's perceptions of how much
control it wants over the environment or its housemates' behaviors determines the outcome of
the situation.
Open conflict is most likely to occur when a new cat is introduced into the house, and
when cats that have known each other since kittenhood reach social maturity. Conflict
occurring when a new cat is introduced is easy to understand, and good directions are
available from many sources for introducing the new cat to the current residents.21 Clients
may be puzzled by conflict that starts when one of their cats becomes socially mature, or
when a socially mature cat perceives that one of its housemates is becoming socially mature.
When cats become socially mature, they may start to exert some control of the social groups
and their activities. This may lead to open conflict between males, between females, or
between males and females. And although the cats involved in the conflict may never be
“best friends”, they usually can live together without showing signs of conflict or conflictrelated illness. In severe cases, a behaviorist can be consulted for assistance in desensitizing
and counter conditioning of cats in conflict so they can share the same spaces more
comfortably if this is desired.
Treatment for conflict between cats involves providing a separate set of the listed
resources for each cat; in locations where cats can use them without being seen by other cats
if possible. This lets the cats avoid each other if they choose to without being deprived of
any essential resource. Cats may require and use more space than the average house or
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89
apartment affords them. The addition of elevated spaces such as shelves, “kitty condos”,
cardboard boxes, beds, or crates may provide enough three-dimensional space to reduce
conflict to a tolerable level. In severe situations, some cats may benefit from behaviormodifying medications. In our experience, however, medication can help when combined
with environmental enrichment has occurred, but cannot replace it. Conflict also can be
reduced by neutering all of the cats, and by keeping all nails trimmed as short as practicable.
Whenever the cats involved in the conflict can not be directly supervised, they may need to
be separated. This may mean that some of the cats in the household can stay together, but
that the threatened cat is provided a refuge from the other cats. This space should contain all
necessary resources for the cat staying in it.
Conflict with other animals, dogs, children, or adults is relatively straightforward. In
addition to being solitary hunters of small prey, cats are small prey themselves for other
carnivores, including dogs. Regardless of how sure the client is that their dog will not hurt
the cat, to the cat the dog may represent a predator. To ensure the cat’s safety, it must be
provided avenues of escape that can be used use at any time. For humans, it usually suffices
to explain that cats may not understand rough treatment as play, but as a predatory threat.
Most cats in urban areas in the United States are housed indoors and neutered, so conflict
with outside cats can occur when a new cat enters the area around the house the affected cat
lives in. To cats, windows offer no protection from a threatening cat outside. If outside cats
are the source of the problem, a variety of strategies to make ones garden less desirable to
them are available.
7. Pheromones - Pheromones are chemical substances that seem to transmit highly specific
information between animals of the same species. Although the exact mechanism of action
is unknown at this time and their effectiveness is not universally demonstrated,22 pheromones
appear to effect changes in the function of both the limbic system and the hypothalamus to
alter the animal’s emotional state. Feliway®, which contains a synthetic analogue of
naturally occurring feline facial pheromone and valerian, was developed to decrease anxietyrelated behaviors of cats. Use of this product has been reported to reduce the amount of
anxiety experienced by cats in unfamiliar circumstances, a response that may be helpful to
these patients and their owners. Decreased spraying in multi-cat households, decreased
marking, and a significant decrease in scratching behavior also has been reported subsequent
to its use. Feliway is not a panacea for unwanted cat behaviors, its effectiveness may be
improved by using it in combination with environmental enrichment, and/or drug therapies.
Because of the dearth of controlled trials, it currently is not possible to prioritize the
importance of any of these suggestions, or to predict which would be most appropriate in any
particular situation. Appropriately designed epidemiological studies might be able to identify
particularly important factors, after which intervention trials could be conducted to determine
their efficacy in circumstances where owners successfully implemented the suggested changes.
Follow-Up
One of the critical keys to any successful therapy program is to follow the progress of the
patient, which we generally delegate to a trained technician introduced to the client during the
clinic appointment. We tell clients what our follow-up schedule is, and ask them to agree to a
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preferred method and time to be contacted. Our first contact with the client occurs within a week
after initial recommendations are made usually over the telephone, followed by repeat in-house
“check-ins” at 3-6 weeks, 3 months, 6 months, and 1 year in uncomplicated cases (which need
less follow-up). This allows one to monitor the patient’s progress, to make adjustments as
needed, and to continue to coach the client. It also helps to determine when the owner is
becoming frustrated or is having problems with the plan so that encouragement or suggestions to
help them can be offered.
Conclusions
Many indoor housed cats appear to survive perfectly well by accommodating to less than
perfect surroundings. The neuro-endocrine-immune systems of some cats, however, do not seem
to permit the adaptive capacity that healthy cats enjoy, so these cats may be considered a
separate population with greater needs. Moreover, veterinarians are concerned more with
optimizing the environments of indoor cats than with identifying minimum requirements for
indoor survival. My current approach is to let the client choose the most appropriate intervention
for their particular situation, and to let trained technicians do the enrichment implementation
and follow-up (under veterinary supervision as appropriate).
Finally, the question of the relative merits of indoor housing to promote the welfare of
cats (and the different opinions on what constitutes animal welfare in general) is beyond the
present scope, and is a subject of controversy among experts. I hope to encourage extension of
the welfare efforts of individuals working in zoos, who have recognized the effects of the quality
of housing on the health on animals in their care and worked to enrich the environments of these
animals, to all “captive” animals in our care. I believe that chronic idiopathic cystitis and a
variety of related chronic health problems in cats may be better prevented than treated, and that
we have a great opportunity to encourage this husbandry approach in veterinary clinical practice.
Further information about environmental enrichment for indoor housed cats is available at:
http://indoorpet.osu.edu/
References
1.
Kirk H. Retention of urine and urine deposits In: Kirk H, ed. The Diseases of the Cat and
its General Management. London: Bailliere, Tindall and Cox, 1925;261-267.
2.
Osbaldiston GW, Taussig RA. Clinical report on 46 cases of feline urological syndrome.
Vet Med/Small Anim Clin 1970;65:461-468.
3.
Osborne CA, Johnston GR, Polzin DJ, et al. Redefinition of the feline urologic syndrome:
feline lower urinary tract disease with heterogeneous causes. Vet Clin North Am Small Anim Pract
1984;14:409-438.
4.
Osborne CA, Kruger JM, Lulich JP, et al. Feline Lower Urinary Tract Diseases In:
Ettinger SJ,Feldman EC, eds. Textbook of Veterinary Internal Medicine. 4 ed. Philadelphia: W.B.
Saunders, 1995;1805-1832.
5.
Westropp J, Buffington CAT. Lower Urinary Tract Disorders in Cats In: Ettinger
SJ,Feldman EC, eds. Textbook of Veterinary Internal Medicine. 7 ed. St. Louis: Elsevier-Saunders,
2010;2069-2086.
6.
Kruger JM, Osborne CA, Goyal SM, et al. Clinical evaluation of Cats with lower urinary
tract disease. Journal of the American Veterinary Medical Association 1991;199:211-216.
7.
Barsanti JA, Brown J, Marks A, et al. Relationship of lower urinary tract signs to
seropositivity for feline immunodeficiency virus in cats. Journal of Veterinary Internal Medicine
1996;10:34-38.
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8.
Buffington CA, Chew DJ, Kendall MS, et al. Clinical evaluation of cats with
nonobstructive urinary tract diseases. Journal of the American Veterinary Medical Association
1997;210:46-50.
9.
Buffington CAT, Chew DJ, Woodworth BE. Feline Interstitial Cystitis. Journal of the
American Veterinary Medical Association 1999;215:682-687.
10.
Patronek GJ, Glickman LT, Beck AM, et al. Risk factors for relinquishment of cats to an
animal shelter. Journal of the American Veterinary Medical Association 1996;209:582-588.
11.
Buffington CA. Idiopathic cystitis in domestic cats-beyond the lower urinary tract. J Vet
Intern Med 2011;25:784-796.
12.
Buffington CAT. Developmental Influences on Medically Unexplained Symptoms.
Psychotherapy and Psychosomatics 2009;78:139-144.
13.
Stella JL, Lord LK, Buffington CAT. Sickness behaviors in response to unusual external
events in healthy cats and cats with feline interstitial cystitis. Journal of the American Veterinary Medical
Association 2011;238:67-73.
14.
Westropp JL, Kass PH, Buffington CA. Evaluation of the effects of stress in cats with
idiopathic cystitis. Am J Vet Res 2006;67:731-736.
15.
Buffington CAT, Westropp JL, Chew DJ, et al. Clinical evaluation of multimodal
environmental modification (MEMO) in the management of cats with idiopathic cystitis. Journal of
Feline Medicine and Surgery 2006;8:261-268.
16.
Buffington CAT. Idiopathic Cystitis in Domestic Cats – Beyond the Lower Urinary
Tract. JVIM 2011;doi: 10.1111/j.1939-1676.2011.0732.x. [Epub ahead of print].
17.
Herron ME, Buffington CAT. Environmental enrichment for indoor cats. Compend
Contin Educ Pract Vet 2010;32:E1-E5.
18.
Herron ME, Buffington CA. Environmental enrichment for indoor cats: implementing
enrichment. Compend Contin Educ Vet 2012;34:E1-5.
19.
Herron ME. Advances in understanding and treatment of feline inappropriate elimination.
Top Companion Anim Med 2010;25:195-202.
20.
Moesta A, Crowell-Davis S. Intercat aggression - general considerations, prevention and
treatment. Tierarztliche Praxis Kleintiere 2011;39:97-104.
21.
Overall KL, Rodan I, Beaver BV, et al. Feline behavior guidelines from the American
Association of Feline Practitioners. Journal of the American Veterinary Medical Association
2005;227:70-84.
22.
Gunn-Moore DA, Cameron ME. A pilot study using synthetic feline facial pheromone for
the management of feline idiopathic cystitis. Journal of Feline Medicine and Surgery 2004;6:133-138.
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Breed Specific Breeding Straegies
Åke A Hedhammar, DVM, M Sc, Ph D, Dipl. Internal Medicine -Companion Animals
Dept. of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
Definition of a breeding program
•
•
•
planned breeding of a group of animals ( or plants ) , usually involving at least several
individuals and extending over several generations .
organized structure that is set up in order to realize the desired genetic improvement
of the population
agreed strategy to influence prevalence of a defined phenotype in a defined population
Breeding programs for specific traits have been established in many countries. They are most
commonly restricted to inherited disorders. Disease specific breeding programs have been
instituted for disorders as hip dysplasia, hereditary eye defects and a number of other
conditions possible to reveal by phenotypic or genotypic screening methods. Their values are
indisputable but do not very well account for breed variations in prevalence, population
structure and other traits to take into account. The goal for planned, organized and agreed
breeding plans is broader than just a few specified genetic disorders
This presentation will review Swedish experiences to establish breed specific breeding
programs taking into account not only disease specific breeding programs but also how
to handle other undesired as well as desired traits and to adapt them to population
structure and other differences between various breed populations.
Since 2004 the Swedish Kennel Club (SKC) have demanded every breed club to prepare a
breed specific breeding program for their strategy to handle future development regarding
desired as well as non-desired traits. It calls for a thorough description of current situation
and to prioritize actions that should be taken to reach common agreeable goals for their
national breed population.
Sources of information
To describe the breed population and the results from applicable screening programs for
inherited disorders as well as behavior test data SKC have extensive material available on the
web. Like in many other countries including US several breed clubs also have performed
breed surveys on various health issues that form a good basis for the situation regarding many
health issues.
In Sweden, more than 75 % of all Dogs are of known ancestral background and registered by
SKC. Moreover over 50 % have insurance for life and veterinary care and the majority in one
company- Agria Insurance.
Their database has been made available for population based epidemiological studies of a
number of diseases.
The breed specific disease pattern in German Shepherds has recently been published and the
breed specific disease patterns of more than 100 breeds are available as Agria Breed profiles.
93
Future perspective
As dog breeding is truly international breed specific breeding programs ideally should not
only be prepared for national breed population. International breed specific programs would
enhance exchange of breeding stock and vital breed populations. Country of origin would be
the nucleus in such efforts and the International Breeding societies should take the lead in
their preparation.
At The 1st International Workshop on Enhancement of Genetic Health in Purebred Dogs that
was arranged by the Swedish Kennel Club in Stockholm on June 2-3, 2012.one of the key
issues dealt with was Development of breed-specific breeding programs on national and
international levels.
References and suggested further readings
Agria Dog Breed Profiles (ADBP) (2011) http://www.agria.se/agria/artikel/agria-dog-breedprofiles-1
Special Breed Specific Instructions (BSI) regarding exaggerations in pedigree dogs (2011)
http://www.skk.se/Global/Dokument/Utstallning/special-breed-specific-instructions-A8.pdf
SKC (Swedish Kennel Club) (2011) Dog Health Workshop
http://www.skk.se/in-english/dog-health-workshop-2012/
Hedhammar ÅA, Malm S, Bonnett B (2011) International and collaborative strategies to
enhance genetic health in purebred dogs. Vet J. 189(2):189-96
BREEDING dogs in Sweden (2012)
SKK/Breeding-dogs-in-Sweden-2012_webb.pdf
http://www.skk.se/Global/Dokument/Om-
Code of Ethics for the Swedish Kennel Club (2013)
http://www.skk.se/Global/Dokument/Om-SKK/Code-of-ethics_breeding-policy_ethicalguidelines_webb.pdf
Vilson A., Bonnett B., Hamlin H., Hedhammar A. (2013) Disease patterns in 32,486 insured
German Shepherd Dogs in Sweden: 1995-2006, Vet. Record 2013 Aug 3;173(5):116
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UK Initiatives for breeding healthier pedigree dogs
Tom Lewis PhD, Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk, UK
tom.lewis@aht.org.uk
Selection against inherited disease is necessary for lasting and widespread improvement in
many aspects of canine welfare. Successful genetic selection requires 1) the motivation to
change a trait in the population; 2) data or information to differentiate between animals with
respect to that trait; and 3) sufficient control of breeding animals to direct specific matings.
These factors are demonstrated clearly in livestock, where the traits in question are associated
with food production (e.g. milk yield). For farmers the motivation in changing (increasing)
the milk yield in their herd is profit, since higher yields generate higher returns. They are
easily able to differentiate animal performance through assiduous recording of yields (which
are pretty much universal since payment is linked to quantity). Finally they have control over
the breeding of the entire herd (often hundreds of animals). These three factors have resulted
in the widespread genetic improvement in the performance of livestock and contributed to
dramatic improvements in yields over the last 60 years. Furthermore, as a result of the
overarching financial motivation, the abundance of data and complete control of breeding, it
has been possible to identify strategies that maximize genetic gain while minimizing the risk
of future problems due to inbreeding.
When it comes to breeding pedigree dogs the situation is less favourable to elicit widespread
genetic change. First, consider the motivation – what are most breeders’ principle objectives?
They are manifold; some breed primarily for success in the show ring or at field trials, some
for working ability (working gun dogs, herding dogs, guide dogs, sniffer dogs), but I suspect
most are hobby breeders and intend the puppies to go to pet homes. Thus, although health is
likely a universal consideration among dog breeders it is only one of a multitude of selection
objectives. Differentiation between breeding animals on ‘merit’ by dog breeders is highly
subjective and has often been achieved by eye, experience or anecdote (reflecting the
principle motivations). Finally, individual dog breeders have only very limited control over
the breeding population, usually one or very few animals. Given that dog breeders are quite
individualistic or self-reliant in terms of judgment of merit and scale of operation, the use of
health information to elicit widespread improvement in health is often sub-optimal. DNA
tests are an example of information that has been enthusiastically employed by dog breeders,
possibly because they offer a simple and definitive result (and one impossible to evaluate
visually), and they are consistent with individualistic operation.
The landscape of dog breeding means that some of the more sophisticated tools available to
livestock breeders to maximise genetic gain will not be directly transferable to dogs.
Nevertheless, there are measures that can be taken in several areas that will assist in
improving the efficacy of selection for health, by focusing on the motivation, the information
and the control. In this short talk I will highlight a few being undertaken in the UK.
Motivation
It is important to stress that in the majority of cases, health already is one of the primary
objectives of breeders. No one I’ve met explicitly intends to breed a dog with disease.
However, in some cases primary motivations may supersede the motivation to breed for
health; for example the trend for greater exaggeration of breed defining characteristics may
have [inadvertently] led to compromising the health of some breeds (e.g. Brachycephalic
airway disease in Bulldogs or Pugs, and skin conditions in Bassett Hounds).
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If health can be linked to the primary motivations of breeders, then it will become a de facto
selection objective. The introduction of vet checks at Crufts, barring progression of ‘Best of
Breed’ winners failing the checks to group finals, is a way of linking health to success in the
show ring. Health does appear to be a concern of puppy buyers. Raising awareness of and
providing information on health to the general public could help to elicit changes in demand.
Information
I covered a bit about the more effective use of health information in my earlier lecture (using
EBVs for hip score to elicit more accurate selection). We have also heard about the
importance of monitoring inbreeding in populations, and must consider appropriate breeding
strategies when there are DNA tests for simple Mendelian recessive diseases, i.e. multiobjective selection often within limited genepools. Mate Select currently provides
information on inbreeding coefficients of litters from potential matings, and shortly will
include EBVs for hip and elbow score, and a simple population analysis for most of the
breeds registered by the Kennel Club. The Kennel Club has a role to play, as the repository of
health data and pedigree in the UK, in providing more accurate information regarding health
and risks for both individual dogs and entire breeds.
Control
Compared to livestock breeders, dog breeders have control over the breeding of far fewer
animals. Coupled with a more individualistic or self-reliant ethos to dog breeding, possibly
due to differing objectives and maybe even competition, the sharing and use of data to direct
matings to meet common objectives is less widespread than in livestock sectors. However,
health is a common objective (or should be, and is a universal if not the principle objective),
and health information is increasingly available allowing breeders to be more discriminating
in mate selection. Therefore, breeders will continue to benefit from a range of tools designed
to allow them access to the most accurate information relating to health, and that will allow
them to use it in their own way since ‘herd-wise’ solution are not realistic. The Kennel Club’s
role in collating and presenting as much health information as possible is critical in
coordinating the efforts of a multitude of breeders to meet a universal selection objective.
96
Genetic Tests: Understanding Their Power, and Using Their Force for Good
Jerold S Bell DVM, Tufts Cummings School of Veterinary Medicine, North Grafton. MA jerold.bell@tufts.edu
Genetic tests are power tools, whose use can have a significant positive or negative impact on a breed’s
gene pool. As with all power tools, they should come with an instruction manual on safety and their
proper use.
The quantity and commercial availability of genetic tests offered for making breeding decisions are
rapidly increasing. Breeders must understand the types of genetic tests that are available (phenotypic
diagnostic tests, direct mutation DNA tests, linked marker-based DNA tests, susceptibility allele tests for
complexly inherited disorders, pedigree and molecular genetic coefficients, EBVs and GBVs, etc.), and
specifically what these tests tell them about the cats and dogs being tested. Along with the types of tests
available, breeders must understand their proper use. Many of these issues are discussed in the article
“Maneuvering
the
Maze
of
Genetic
Tests:
Interpretation
and
Utilization”
(http://www.vin.com/proceedings/Proceedings.plx?CID=TUFTSBG2011&Category=10236&PID=6825
6&O=Generic)
The fact that a genetic test exists does not automatically qualify it for global utilization. With the
plethora of genetic tests and their commercialization comes a realization that breeds can be tested into
oblivion with selection that often has no bearing on health or quality. There are historical records of how
improper use of genetic tests have reduced breed genetic diversity, as well as increased the frequency of
other deleterious genes.
Selection is what created breeds, and selection is what will maintain breeds and improve their genetic
health. Selection should be directed toward specific goals that directly improve the breed. Positive
selection towards breed standards should ensure that they are not linked to disease liability. These may
be conformational, behavioral, and/or working standards. Selection against disease liability should have
a goal of preventing genetic disease without significantly eliminating breeding lines or restricting breed
genetic diversity.
Genetic tests, pedigree and molecular genetic coefficients, and mating practices are tools that can allow
the breeder to achieve defined breeding goals. When breeders begin to use these tools as the goals
themselves, positive selective pressure is reduced, and breed gene pools will drift. Breeders must not
lose sight of the fact that they are breeding entire individuals, and not a heart, an eye, a hip, or a
coefficient number.
When evaluating an individual for breeding, the breeder must objectively assess the positive and
negative traits and disorders displayed. Knowledge of the common hereditary disorders in the breed is
important, as is their available genetic screening tests. For most dog breeds, these are listed in their
breed page on the Canine Health Information Center website (www.caninehealthinfo.org/breeds). A
similar website for cat breeds does not exist, however the Feline Advisory Bureau has a website
detailing genetic disorders of cat breeds (www.fabcats.org/breeders/inherited_disorders).
Traits requiring selection in a mating should be listed and prioritized. Disorders that cause morbidity or
mortality should have a high priority in selection. Traits and disorders caused by simple Mendelian
genes can be changed and eliminated in a single generation. However, breeders should recognize that
undesirable genes can be eliminated without eliminating breeding lines and affecting breed genetic
diversity.
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With testable simple Mendelian recessive genes causing genetic disorders, quality carriers can be breed
to normal-testing mates and never produce the disorder. Quality normal-testing offspring should replace
the carrier parent for breeding in the next generation to continue the breeding line. In this way, you lose
the single testable gene, but continue the breeding line. Genetic tests should increase the options for
breeding, and not limit them.
The typical response of a breeder on being informed of a carrier genetic test result is to remove the
prospective breeding individual from a breeding program. If a majority of breeders do this, it can
significantly limit the gene pool diversity of the breed. If an owner would breed an individual if it tested
normal for a genetic disease, then a carrier result should not change that decision. A direct genetic test
for a simple recessive trait does not alter WHO gets bred, only WHO THEY GET BRED TO (Henthorn
P, personal communication).
Aside from preventing the production of affected individuals, breeders should select against placing new
carrier-testing offspring into breeding homes. Carrier to normal matings produce on average, 50%
carriers and 50% normal-testing offspring; a much higher carrier frequency than most breed-related
disease liability genes. It is important to progressively decrease the frequency of deleterious genes in a
breed, to increase breeding choices. This becomes especially important when there are several testable
genes in a breed. With high carrier frequencies, selection can become more of an effort to prevent
disease than to create the most desirable breed representative.
Complexly inherited traits will usually require more than one generation of selection to alter the genetic
load of liability genes. Genetic selection should rely on genetic tests or phenotypic evaluations that are
reflective and associated with causative genes. With complexly inherited traits (and with simple
recessive traits that have no test for carriers), the phenotype of first-degree relatives (siblings, parents,
and siblings of parents) best represent the range of liability genes that may be carried by the prospective
breeding individual. This “breadth of pedigree” analysis can be evaluated through estimated breeding
values (EBVs), or vertical pedigrees on the OFA website (www.offa.org).
Prospective mates should be listed and rated for the traits and disorders, in order to see which
individuals might provide the greatest selective pressure for the most important traits. If an individual is
highly desirable due to its traits and ability to pass them on, but also has several deleterious genes
identified through genetic testing; then a parent, sibling, or prior-born offspring may provide the desired
combination of traits and genetic test results.
Once a breeder has prioritized the traits and disorders that could undergo selection, (s)he must decide
which will undergo selection in the next mating. The more traits that are undergoing selection; there will
be less selective pressure that can be applied to any single trait.
As selection pressure is diminished by selection for test results that do not affect individual health and
fitness, these should be avoided. Some commercial companies counsel to use genetic tests or
coefficients as breeding goals. These include manipulation of MHC (major histocompatibility complex)
haplotypes, or whole-breed outbreeding recommendations.
Certain specific MHC haplotypes are found to be linked to susceptibility for specific genetic disorders.
However, general individual homozygosity or breed haplotype frequencies of the MHC loci by
themselves have not been linked to disease or impaired health. In a study of semi-feral village dogs from
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around the world, it was found that; 1) they share many of the same MHC haplotypes with pure-bred
dogs, 2) they have many unique haplotypes that are not found in pure-bred dogs, and 3) pure-bred dogs
also have many unique haplotypes that are not shared with village dogs. Pure-bred dogs do show
increased homozygosity of MHC loci consistent with their large haplotype blocks and long linkage
disequilibrium, however their predicted genetic depletion versus village dogs was not found (Kennedy
LJ, et. al.: Do village dogs retain more major histocompatibility complex diversity compared to pedigree
breed dogs? Poster presentation at the 7th International Conference on Advances in Canine and Feline
Genomics and Inherited Disease, Cambridge, MA).
There is a movement to recommend generalized outbreeding programs for breeds to ostensibly retain
genetic diversity. However, the types of matings used (linebreeding versus outbreeding) do not change
gene frequencies. It is the selection of breeding animals that alters gene frequencies. The lecture notes
“Inbreeding, Outbreeding and Breed Evolution” in the 6th Tufts Canine & Feline Breeding and
Genetics Conference proceedings provide further depth to this issue.
Breeders must be wary of commercial offerings of genetic tests for genes that have not been proven to
cause disease in their breed. This includes testing panels of collections of identified disease liability
genes. Just because a gene is linked to disease in one breed does not automatically mean that it is linked
to disease in all breeds. Causality or liability must be validated in each breed. If causality cannot be
documented, then unwarranted selection just puts unnecessary pressure on the breed gene pool, and
reduces the selective pressure on traits that are actually important to the breed.
Selection should be directed for specific desirable traits, and against disease liability genes. Efforts
should be made to avoid the loss of quality breeding lines and genetic diversity in mating decisions. The
most important aspect of maintaining breed genetic diversity is avoidance of the popular sire syndrome.
Expanding or large, stable breeding populations are the best buffer against gene loss. Genetic tests
provide excellent tools for breed improvement, and their proper utilization will allow breeders to see
continued improvement in health and quality.
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Poster Abstracts
Title:
Name:
A Web Resource on DNA Tests for Canine and Feline
Hereditary Diseases
Jeffrey Slutsky, Karthik Raj, Scott T Yuhnke,
and Urs Giger
Prevalence of Variant Alleles Associated with
Protein-losing Nephropathy in Soft Coated Wheaten
Terriers
Meryl P. Littman, Michael G. Raducha, and
Paula S. Henthorn
You’re getting on my nerves! The feline orofacial pain Barbara Gandolfi, Claire Rusbridge, Richard
syndrome
Malik and Leslie A. Lyons
The geographic diversification of domestic cats
Razib Khan, Alejandro Cortes, Hasan Alhaddad,
and Leslie Lyons
Who’s behind the mask and the cape? Asian Leopard
Cat’s agouti allele affects coat colour phenotype in
Bengal cat breed
Gershony LC, Cortes A, Penedo MCT, Davis
BW, Murphy WJ and Lyons LA
Genetic and Phenotypic Heterogeneity in Canine
Progressive Retinal Atrophy
Aušra Milano, Gustavo D. Aguirre, Gregory M.
Acland, Orly Goldstein, Sue Pearce-Kelling
Publishing health data using open access,
customised online platforms, and the benefits to
researchers, breeders, and the public
Nick Sutton, Aimee Llewellyn
Constrictive Myelopathy: a cause of hind limb ataxia
unique to Pug dogs?
Kathleen L. Smiler, Jon S. Patterson
Genetics and canine kidney disease: A risk locus in
Andrew L. Lundquist, Noriko Tonomura, Ross
Boxers with renal dysplasia identified by genome-wide Swofford, Michele Perloski, Katarina Tengvall,
association
Ake Hedhammar, Kerstin Lindblad-Toh
PennGen: Characterization of Metabolic and Molecular Caitlin A. Fitzgerald, Patricia O’Donnell, Karthik
Genetic Defects in Dogs and Cats
Raj, Michael Raducha, Ping Wang, Kate Berger,
Margaret L. Casal, Peter J Felsburg, Paula S
Henthorn, Mark E. Haskins, and Urs Giger
Congenital Hypothyroidism with Goiter in Cats due to
a TPO Mutation
Karthik Raj, Catherine V. Morrow, Anne Traas,
Angela M. Erat, Marisa Van Hoeven, Hamutal
Mazrier, Mark E. Haskins, and Urs Giger
Selection and the Co-Evolution of Breeds and
Disease-Liability Genes
Jerold S Bell
Population Genetic Studies and Gene Dynamics of
Dog and Cat Breeds
Jerold S Bell
100
A Web Resource on DNA Tests for Canine and Feline Hereditary Diseases
Jeffrey Slutsky, Karthik Raj, Scott T Yuhnke, and Urs Giger
and the WSAVA Hereditary Disease Committee
Section of Medical Genetics (PennGen), School of Veterinary Medicine, University of
Pennsylvania, Philadelphia, PA.
Following the first identification of a disease-causing mutation in dogs in 1989, and the more
recent completion of the canine and feline genome sequences, much progress has been made in
the molecular characterization of hereditary diseases in dogs and cats.
To increase access to information on diagnosing hereditary diseases in dogs and cats, a web
application has been developed to collect, organize and display information on available DNA
tests and other supporting information, including gene and chromosomal locations, mutations,
primary research citations, and disease descriptions. The DNA testing information can be
accessed at PennGen under the tab ‘Tests Available at Labs Worldwide’ at the URL:
http://research.vet.upenn.edu/WSAVA-LabSearch. There are currently 170 molecular genetic
tests available for hereditary diseases in dogs and cats offered by 54 laboratories worldwide.
This tool should provide clinicians, researchers, breeders and companion animal owners with a
single comprehensive, up-to-date and readily searchable webpage for information regarding
hereditary disease testing.
Supported in part by the WSAVA Hereditary Disease Committee, Waltham and NIH OD
010939.
101
Prevalence of Variant Alleles Associated with Protein-losing Nephropathy in
Soft Coated Wheaten Terriers
Meryl P. Littman (merylitt@vet.upenn.edu), Michael G. Raducha, and Paula S. Henthorn
University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA.
Variant alleles in NPHS1 and KIRREL2, the genes which encode the slit diaphragm proteins
nephrin and filtrin/Neph3, respectively, were previously found associated with protein-losing
nephropathy (PLN) in Soft Coated Wheaten Terriers (SCWT) by a genome-wide association
study and subsequent gene sequencing of candidate genes in a statistically significant interval
that differed among dogs with PLN compared with geriatric (14-18 year old) SCWT. Genotyping
assays were developed for both of the single nucleotide polymorphisms (SNPs) in these genes
that are in linkage disequilibrium in the breed. Homozygous positive dogs were shown to be at
highest risk for the development of PLN, heterozygous dogs were at intermediate risk, and
homozygous negative dogs were at low risk for the development of PLN.1
A prevalence study was performed to ascertain if breeders could safely remove carrier dogs in
one generation. Cheek swab, blood, or semen samples were tested from 1549 SCWT dogs of all
ages (median 4 yrs). Haplotypes are described as 1-1 (homozygous negative), 1-2
(heterozygous), and 2-2 (homozygous positive) for the PLN-associated variant alleles. The
following table shows the frequencies found in various countries.
USA, n=1095**
(Hardy-Weinberg expected frequencies in the USA)
Canada, n=155
Total USA and Canada, n=1250**
Nordic Countries, n=125
UK/Ireland, n=119
Other (Australia, Poland, Argentina), n=55*
Total all countries, n=1549 (Unknown Sex, n=13)
Females, n=898**
Males, n=639
*Includes 1 Mi, undetermined NPHS1; 1-2 KIRREL2
**Includes 1 Fi, 1-2 NPHS1; 1-1 KIRREL2
1-1
%
34
(33)
42.5
35
42
66
55.5
39
39
39
1-2
%
47
(49)
44.5
47
44
24
42
44
44
44
2-2
%
19
(18)
13
18
14
10
3.5
17
17
17
Variant Allele
Frequency (%)
43
35
42
36
22
25
39
39
39
Without genetic counseling with the knowledge of these haplotypes and assuming random
breeding, the variant allele frequency would remain 43% in the USA. This high frequency
indicates that it would be unwise to cull all carriers (1-2 or 2-2 dogs) of the variant alleles in one
generation, thereby risking loss of genetic diversity, increased inbreeding, and the potential of
increasing the incidence of other deleterious genetic traits. An approach to avoid producing high
102
risk homozygous positive (2-2) dogs would be to preferably breed desirable heterozygous (1-2)
or homozygous positive (2-2) dogs to homozygous negative (1-1) dogs.
Instructions for DNA submissions are available at www.scwtca.org/health/dnatest.htm.
1. Littman MP, Wiley CA, Raducha MG, Henthorn PS. Glomerulopathy and mutations in
NPHS1 and KIRREL2 in soft-coated Wheaten Terrier dogs. Mamm Genome
2013;24:119-126.
103
You’re getting on my nerves! The feline orofacial pain syndrome.
Barbara Gandolfi, Claire Rusbridge, Richard Malik and Leslie A. Lyons
The health of the Burmese breed is endangered by several diseases, such as hypokalemia,
Burmese craniofacial defect, flat-chested kittens, an acute teething disorder, diabetes mellitus ,
and Feline Orofacial Pain Syndrome (FOPS). FOPS is characterized by an episodic, typically
unilateral, discomfort with variable pain-free intervals. In many patients discomfort is triggered
by movements of the mouth such as eating, drinking or grooming. Affected cats are most
commonly presented with exaggerated licking and chewing movements, and pawing at the
mouth. More severe cases develop self-mutilation of tongue, lips and buccal mucosa. Due to the
severity of the lesions, many patients display anorexia. The syndrome is often recurrent and with
time may become unremitting, with up to 10% of the cases being euthanized as a consequence of
the condition. This condition is seen in a variety of feline populations, although Burmese cats
make up the great majority of cases, suggesting a genetic basis for the syndrome. A genomewide case-control association study that aimed to localize a the orofacial pain syndrome (FOPS),
using the Illumina Infinium Feline 63K iSelect DNA array was performed on 24 cases and 50
healthy controls. The study resulted in the identification of a locus on cat chromosome C1
associated with FOPS. Preliminary data suggest an association on cat chromosome C1, within
the low density lipoprotein receptor-related protein 1 gene (LRP1). The protein expressed in the
central nervous system has been implicated in other pain syndromes and recent studies
demonstrate that the gene is involved in migraine without aura. The length of the human
transcript is 14,897 bp translated into 4544 amino acids, the gene contains 89 coding exons and
is one of the largest genes in the human genome. Sequencing of the feline gene revealed several
polymorphisms under consideration.
104
The geographic diversification of domestic cats
Razib Khan1, Alejandro Cortes1, Hasan Alhaddad1, and Leslie Lyons1
Department of Population Health and Reproduction1, University of California, Davis, CA 95616
Felis silvestris catus, the domestic cat, diverged ~10,000 years ago from populations of Felis
silvestris lybica, the African wildcat. This result is supported by remains of cats inhumed with
humans on the island of Cyprus and mtDNA phylogenies. More recently, within the last ~150
years there has been development of “fancy” breeds such as the Persian. But there are gaps in the
evolutionary history of the cat between the initial domestication events in the Middle East, and
the efforts of modern breed associations in developing specialized varieties.
To further explore variation in Felis silvestris with the aim of inferring historical dynamics,
phylogenetic analysis were performed on over 3,000 individuals from 30 breeds and 30 regional
populations using 38 autosomal microsatellites. These are inclusive of non-breed cats from six
continents, breeds, wildcats, and hybrids. Genetic diversity and distance estimates were
generated. Principle coordinate analysis was used to visualize distances. Analysis of population
clustering utilizing the STRUCTURE package was performed. Finally, the TREEMIX package
generated graphs of relationships across the populations, and migration events between lineages.
Over the data STRUCTURE analyses with >20 explicit clusters were less informative. The initial
bifurcation occurred between domestic lineages and wildcats. Subsequent splits occurred
between European, Middle Eastern, and Asian lineages. Known breeds’ attested histories were
confirmed in terms of derivation from specific regional populations. Breed specific admixture
events were identified. Geopolitical contours were recapitulated by genetic population structure.
The cats of Iran and Iraq formed a distinct cluster from those of the Levant, possibly reflecting
ancient divisions in the Middle East. Other genetic relationships are only comprehensible
through understanding of local histories of colonialism. The population structure of domestic
cats reflects local interactions with humans. Finally, preliminary replications of some of these
analyses using 150 and 63,000 SNP data sets were examined.
105
Who’s behind the mask and the cape? Asian Leopard Cat’s agouti allele
affects coat colour phenotype in Bengal cat breed
Gershony LC1, Cortes A1, Penedo MCT2, Davis BW3, Murphy WJ3 and Lyons LA1
1
Department of Population Health and Reproduction, School of Veterinary Medicine, University
of California - Davis, Davis, CA, USA
2
Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
3
Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and
Biomedical Sciences, Texas A&M University, College Station, TX, USA.
Coat colours and patterns are highly variable in cats and determined by several genes. The
charcoal coat pattern inheritance in Bengal cats appears as an incomplete melanism, thus the
agouti signalling protein gene (ASIP) was investigated as a candidate gene for this phenotype.
DNA was isolated from buccal swabs obtained from 72 Bengal cats, where 49 were presumed to
be charcoal. The coding region of ASIP was amplified by polymerase chain reaction and
subsequently directly sequenced. The resulting sequences were compared to that of ten Asian
leopard cats and three control domestic cats. Polymorphisms were investigated within the gene.
Two non-synonymous SNPs were observed in exon 2 (c.41G>C and c.142T>C) when comparing
the control domestic cat sequence with the leopard cat sequence, resulting in amino acid changes
in the leopard cat (Cys14Ser and Ser48Pro, respectively). One synonymous single-nucleotide
polymorphism (SNP) was found in exon 3, substituting a cytosine for adenine in the leopard cat
(c.162C>A). Forty-three charcoal cats presented as compound heterozygotes at ASIP, consisting
of an Asian leopard cat allele and a domestic cat non-agouti allele (a). The compound
heterozygote state suggests that the interaction between the Asian leopard cat allele and the
domestic cat allele allowed for the recessive non-agouti allele to influence the markings of the
hybrid Bengal cat producing a darker, yet not completely melanistic, coat pattern. This study
presents the first validation of a Leopard cat allele segregating in the Bengal breed affecting the
overall phenotype of the pelage.
1) Further investigation should be conducted to assess similar interactions in other genes, and
how they would affect the accuracy of genetic tests within this breed.
2) Further investigation should be performed to better illuminate the potential allelic interactions,
and consequential phenotypic expression, within this hybrid breed.
106
Genetic and Phenotypic Heterogeneity in Canine Progressive Retinal Atrophy
Aušra Milano1, Gustavo D. Aguirre2, Gregory M. Acland3, Orly Goldstein3, Sue Pearce-Kelling1
1
Optigen, LLC, Ithaca, NY; 2 School of Veterinary Medicine, University of Pennsylvania,
Philadelphia, PA 3 Baker Institute, Cornell School of Veterinary Medicine, Ithaca, NY
Mutations causing Progressive Retinal Atrophy (PRA) are the predominant cause of hereditary
blindness in the domestic dog. Although over a dozen PRA mutations have been identified,
including prcd-PRA which has been observed in over 25 breeds, many PRA mutations remain
uncharacterized. During its nearly 15 years of operation, OptiGen has collected DNA, pedigrees
and detailed phenotype descriptions from hundreds of dogs that have been diagnosed with PRA
by veterinary ophthalmologists. This PRA research sample set includes over 500 samples and
100 breeds. DNA testing of these samples has revealed that many breeds harbor multiple forms
of PRA, often with similar clinical symptoms. Here we present the distribution of prcd and other
PRA-causing mutations that have been assayed within OptiGen’s PRA research sample set.
Breeds in which multiple forms of PRA are known to segregate are presented as well as
phenotypic variations in the PRA cases. Collaborative research projects that can make use of
these samples are encouraged.
107
Publishing health data using open access, customised online platforms, and
the benefits to researchers, breeders, and the public
Nick Sutton, Aimee Llewellyn
The Kennel Club, 1-5 Clarges Street, Piccadilly, London W1J 8AB
aimee.llewellyn@thekennelclub.org.uk
The Kennel Club has been recording and publishing health test results for DNA tests and the
British Veterinary Association/Kennel Club Health Schemes (hip dysplasia, elbow dysplasia,
and eye schemes) since 1965 in firstly the Kennel Club Gazette, and latterly the Breed Record
Supplement. The Kennel Club initially launched Online Services to provide general health
information. Then in May 2011 the bespoke online interface, Mate Select, was established
specifically to publish and disseminate breed population and health data recorded on the
Kennel Club Breed Register. Now, 2 years on, Mate Select, as an online publication resource
is being reviewed with the objective to establish what, if any, impact this method of health
data reporting has had on the accessibility of canine health information.
Prior to the launch of Mate Select, it had been recognised that while publishing health
information was valuable to dog breeders, there were numerous practical limitations to doing
so in hard-copy publications, such as the Breed Record Supplement. A primary limitation
being that this form of publication is not open-access, or easily searchable - particularly over
time. Records were published in the quarterly Breed Record Supplement, at an average of
approximately 40,000 individuals each year. Conversely, Mate Select is a free unrestricted
online interactive tool which receives approximately 300,000 searches each month, designed
to provide breeders with free, accessible health information for individual dogs. This provides
access to any breeder, enabling them to make informed choices which can have a positive
impact on the health of any potential puppies produced, as well as the breed in general. The
system was produced with expansion in mind and is able to accommodate advances in
molecular and population genetics. All of the results published are linked to each individual
dog’s record within the Kennel Club database, allowing imputation using customisable,
defined criteria for on-going assessment and monitoring. This resource is particularly useful
as guidance when prioritising health conditions or, establishing breeding restrictions such as
Kennel Club DNA Control Schemes.
Mate Select in its current state, is divided into tools that reflect an individual dogs health
(such as gene test results), and resources for considering breed-wide implications of
individual mating selections, such as inbreeding. Together, this provides dog breeders with
efficient and practical resources for reducing the risks of specific heritable condition and
incorporating inbreeding and genetic bottle-neck mitigation strategies into their breeding
plans, particularly in the selection of breeding stock. The Health Test Results Finder, which
manages over 100,000 online searches each month, publishes all health results for
approximately 80 breed-specific, individual single-gene mutation DNA tests. BVA/KC
Health Schemes published records currently consist of over 260,000 hip scores, 21,000 elbow
scores, 116 Chiari malformation/Syringomyelia (CM/SM) scores (introduced in 2012), as
well as the results for over 134,000 clinical eye examinations. Recording of either DNA test
results, or clinical examination “schemes” is expandable under the system and allows for
improvements to the confirmation of data – such as parentage profiling (in the case of
assigning hereditarily clear status) and notations where examined dogs have been microchipconfirmed for DNA tests. In addition, the data yielded from dogs undergoing clinical
examination schemes allows for the development of tools for the future, such as Estimated
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Breeding Values (EBVs). Linking the data to a pedigree or dog registration record adds
confidence to the examination status recorded and allows population geneticist to review
scheme uptake and results to calculate a threshold at which EBVs for a population can be
developed with confidence. Publication of tools that require frequent updating and recalculation, such as EBVs would be impossible without an online interface.
By definition, the development of a breed creates a population that can be increasingly
limited without outcrossing or otherwise introducing new genes into the system. Therefore,
tools that can provide a means to slow the rate of inbreeding, and/or reduce individual litter
inbreeding coefficients are of value to dog breeders. Mate Select tools, developed in
conjunction with the Kennel Club Genetics Centre at the Animal Health Trust, provides three
coefficient of inbreeding (COI) “calculators”: Breed COI, Individual (dog) COI, and the
Mating COI. For the dog breeder, the tool most practical is the Mating COI calculator. This
allows dog breeders to perform hypothetical matings using a dam and sire they are
considering to estimate the inbreeding coefficient for the resulting puppies. This number can
then be compared to the breed average (which is provided for comparison after each search),
to encourage breeding below the breed average and thus a decrease in the overall degree of
inbreeding. This is, again, a resource that would be impossible without an interactive online
interface. In the long term, breed-wide COI data can be assessed to monitor change, and
encourage improvement.
In summary, by recording health test results against pedigree data Mate Select provides a
robust, diverse and unique data resource that enables the public to make informed decisions.
Using a freely accessible, searchable, and interactive interface has significant advantages
over hard-copy publication. There is every indication that publishing health test results allows
for the reduction or elimination of some heritable diseases, and therefore any robust method
that makes this information more efficient and available is to every dog’s benefit. Although
it is too early to determine the full impact that Mate Select has had on the health of the UK
canine population, it is hoped that through improved accessibility and transparency of
published test results, breeding trends towards the production of healthier dogs will occur
more rapidly.
109
Constrictive Myelopathy: a cause of hind limb ataxia unique to Pug dogs?
Kathleen L. Smiler, DVM, DACLAM, Consultant, PO Box 429, Lakeville, MI 48366, Email
smilerk@mindspring.com (248)-953-3182
Jon S. Patterson, DVM, PhD, DACVP, Michigan State University College of Veterinary
Medicine, 163 DCPAH Building, 4125 Beaumont Rd., Lansing, MI 48910-8104, Email
patter12@msu.edu (517) 353-9471
BACKGROUND
Recently, a previously unreported condition termed “constrictive
myelopathy” was described in 11 adult Pug dogs (J Am Vet Med Assoc 2013; 242:223-229). The
paper reported a progressive incoordination and weakness of the hind limbs resulting from a
constriction of the spinal cord at the thoracolumbar junction, and associated with malformations
of the articulations of vertebrae in this area. The degenerative condition often progressed to
paraplegia, with urinary and/or fecal incontinence. Despite surgical treatment, neurologic disease
persisted or progressed. This myelopathy is seemingly unique to and reportedly rare in purebred
Pug dogs, although anecdotal evidence suggests that the vertebral malformations (hypoplasia
and/or aplasia of caudal articular processes) are relatively common in the breed, as supported by
imaging studies. Authors of the published study hypothesize that the vertebral anomalies may
represent a heritable condition in Pugs, and that instability at the thoracolumbar junction
associated with the anomalies leads to the formation of a circumferential fibrous band which
constricts the spinal cord. A case study of one Pug diagnosed with constrictive myelopathy at age
6.5 years, and euthanized at age 14 years is presented.
CASE DESCRIPTION
A spayed female purebred Pug dog, was initially observed at age
6.5 years to have reluctance climbing stairs and urinary and fecal incontinence. Neurologic
examination revealed bilateral hind limb weakness and ataxia, with increased tone in the left
hind. Hind limb proprioceptive deficits were present bilaterally, and the cutaneous trunci
response was absent caudal to T13. Radiographs and computed tomography (CT) suggested
hypoplasia of caudal articular processes of T10-T12, and MRI suggested spinal cord
compression at T12-T13. A diagnosis of "pug myelopathy" was made, and a dorsal laminectomy
was performed in the area of compression. At surgery, a circumferential band of mature fibrous
tissue, seen to compress the spinal cord, was removed. After surgery, the dog had improved hind
limb function, and better control of urination and defecation. Approximately 6-7 months after
surgery, however, the hind limb ataxia worsened, and a CT/myelogram suggested a
demyelinating condition. The dog was treated with various doses of prednisone and underwent
acupuncture therapy for 3 months at age 7.5 years. By age 8, the dog had complete urinary
retention incontinence, and by age 9, would walk only if supported, and relied on front limbs to
pull herself along. At age 12, a DNA sample was tested at University of Missouri for the
degenerative myelopathy (DM) gene mutation, and results were negative. Approximately 1 week
prior to euthanasia, the dog began having difficulty using one front limb, and euthanasia was
elected.
Complete necropsy was done at the Michigan State University Diagnostic Center for Population
and Animal Health (DCPAH). There was marked bilateral atrophy of the caudal thigh muscles,
muscles over the pelvis, and epaxial muscles of the thoracic and lumbar spine. Slight scoliosis of
110
the vertebral column to the right was noted at the level of T6-T7, and there was mild bridging
spondylosis on the ventral aspect of the vertebral bodies at theT6-T7 intervertebral space.
The entire vertebral column, containing the spinal cord, was placed in 10% neutral buffered
formalin, and following fixation, the spinal cord was removed and vertebrae were disarticulated
and examined. It was difficult to draw conclusions regarding the caudal articular processes of the
T11, T12, and T13 vertebrae, at the site of surgery 8 years prior, but there appeared to be
asymmetry with respect to size for the paired articular processes (right vs. left) of T12 and T13.
Histologically, there was severe segmental chronic myelomalacia in the T12 and T13 spinal cord
segments, with Wallerian degeneration cranial and caudal to this area. The leptomeninges were
moderately to markedly thickened by dense fibrous tissue from T10-T13, with areas of arachnoid
hyperplasia and dural fibrosis. Focal poliomyelomalacia in the C6 spinal cord segment was
noted, and close inspection of the cervical vertebral column revealed dry, flaky intervertebral
disc material at C5-C6 and C6-C7, suggesting a disc degeneration.
The final diagnosis was severe segmental chronic degenerative myelopathy at T12-T13, with
meningeal fibrosis (T10-T13) and Wallerian degeneration. This appeared to be the major lesion,
consistent with the 7 to 8-year history of progressive hind limb weakness, ataxia, and paralysis,
and consistent with what was described by the surgeons who treated the dog. The more recent
spinal cord lesion in the C6 segment involved primarily the gray matter and was consistent with
an acute intervertebral disc extrusion that then became chronic.
CONCLUSIONS AND SIGNIFICANCE The Pug Dog Club of America (PDCA) has
recognized the widespread anecdotal reports of hind limb ataxia and paralysis in Pugs and is
committed to encouraging research to better understand spinal disease including “constrictive
myelopathy,” and to effective strategies to manage the condition and reduce its incidence. The
poster authors have initiated proposals to better characterize both the vertebral and neurological
lesions, and to identify unique features which might distinguish constrictive myelopathy from
other conditions with similar clinical presentations in Pugs. Blood and tissue samples will be
banked for eventual DNA analysis as genetic components of this disease are considered.
To enhance awareness and accumulate data, a public outreach for case histories of Pugs with
hind limb ataxia and weakness is ongoing, utilizing social media, announcements to Pug group
media, presence at a national breed club dog show, and specific contacts with Pug rescue
organizations. The Pug rescue organizations are increasingly burdened by the surrender of ataxic
and paralyzed dogs, and it is difficult to find foster or permanent homes that will provide the
skilled care required (especially those with urinary incontinence complications). The diagnostic
procedures and long-term care will incur substantial costs for veterinary and rehabilitation
palliative therapy. The complex of diseases causing hind limb ataxia and weakness in Pugs,
possibly complicated by inherent vertebral malformations, is a formidable problem in the breed.
Figures in the poster will include various imaging results obtained for this case. MRI, CT
myelogram, radiographs including post mortem; photographs of gross vertebrae after dissection,
and photomicrographs of histopath of cord, etc.
111
Genetics and canine kidney disease: A risk locus in Boxers with renal
dysplasia identified by genome-wide association
Andrew L. Lundquist1, Noriko Tonomura1,2, Ross Swofford1, Michele Perloski1, Katarina
Tengvall3, Ake Hedhammar4, Kerstin Lindblad-Toh1,3
1 Broad Institute of Harvard and MIT, Cambridge, MA, USA, 2 Cummings School of Veterinary
Medicine, Tufts University, North Gratton, MA, USA, 3 Science for Life Laboratory,
Department of Medical Biochemistry and Microbiology, Uppsala University, Sweden, 4
Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
Email: andrewl@broadinstitute.org
Kidney disease is common in dogs and many breeds are affected. Dogs can be affected early in
life by various forms of inherited kidney disease or chronic kidney disease can manifest later in
life from a variety of causes. Previous studies have shown that renal failure is among the top
five causes of death in dogs and up to 30% of geriatric dogs have chronic kidney disease.
Historically, certain breeds have been affected with a specific type of kidney disease, suggesting
a genetic cause. Current canine genetic tests available include testing for hereditary nephritis in
Samoyed and Cocker Spaniel (vetGen), cystinuria in Newfoundland (vetGen), and primary
hyperparathyroidism in Keeshonden (Cornell University). Our group is focused on identifying
the genetic cause of various forms of inherited canine nephropathy through genetic association
studies. We are looking for collaborations with owners, breed clubs, and veterinarians to identify
cases of canine kidney disease including: breed specific inherited nephropathies, isolated or litter
specific cases of spontaneous kidney disease, and cases of adult dogs with chronic kidney
disease. Previously, we helped identify the risk alleles for renal amyloidosis in Shar Peis and
primary hyperparathyroidism in Keeshonden. Here we will discuss our efforts to identify risk
alleles for renal dysplasia in Boxers.
Identification of genetic risk factors for renal dysplasia in dogs is essential as there is no
treatment and affected dogs progress to renal failure and death at a young age. A genetic test for
renal dysplasia is available, however its validity across species has come into question and the
scientific community has called for additional validation of the test. We previously conducted a
genome-wide association study using the Canine HD BeadChip comparing 17 US Boxers with
renal dysplasia (age < 5) to 40 older Boxers (age > 10) with no known kidney disease. No
association was detected at the locus defined by the currently available genetic test. Association
analyses suggest a risk allele adjacent to a gene previously implicated in human hypodysplasia, a
common cause of pediatric kidney disease. Sequencing the coding region of our candidate gene
did not reveal a causative mutation, though variants nearby suggest a haplotype associated with
disease. We are currently analyzing a 4 MB region surrounding the risk locus with targeted
sequence capture to identify the causative variant(s) and we are working to acquire additional
cases of renal dysplasia in Boxers and other breeds as these are essential to help validate our
findings. These studies will help us dissect the genetics of canine renal dysplasia, improve our
understanding of renal development in dogs and humans, and determine the appropriate genetic
testing strategies for prevention.
112
PennGen: Characterization of Metabolic and Molecular Genetic Defects in
Dogs and Cats
Caitlin A. Fitzgerald, Patricia O’Donnell, Karthik Raj, Michael Raducha, Ping Wang, Kate
Berger, Margaret L. Casal, Peter J Felsburg, Paula S Henthorn, Mark E. Haskins, and Urs Giger
Section of Medical Genetics, School of Veterinary Medicine, University of Pennsylvania,
Philadelphia, PA.
The Section of Medical Genetics at University of Pennsylvania School of Veterinary Medicine
has actively pursued the diagnosis and management of hereditary diseases and genetic
predispositions to disease in companion animals for the past 4 decades.
The specialty Pediatrics and Genetics Clinic and diagnostic and research laboratories have been
characterizing many inherited traits in dogs and cats from the clinical features to the metabolic
and molecular genetic defects.
The Metabolic Genetics Screening Laboratory supported by an NIH grant conducts routine
analyses of amino acids, organic acids, and carbohydrates in urine samples for various inborn
errors of metabolism such as many storage diseases, lactic and methylmalonic aciduria,
cystinuria, and Fanconi syndrome.
Particularly, the NIH grant also focuses on
mucopolysaccharidosis (MPS), mannosidosis, and gangliosidosis, which are diagnosed by
urinary spot tests and enzyme assays. Moreover, affected animals serve as excellent disease
models of human disease.
Another area are hereditary blood disorders such anemia due to red cell defects (PK, PFK,
osmotic fragility), bleeding disorders caused by coagulation factor (Factor VII and XI), and
platelet disorders along with predisposition to infection resulting from white blood cell problems
(X-SCID, LAD, avian tuberculosis). This laboratory also investigates canine and feline blood
types and is offering typing service in case of incompatibility issues.
PennGen and the Josephine Deubler Laboratory, named in honor of Dr. Deubler (veterinarian,
dog breeder, and dog show judge) were specifically established to provide genetic tests for
veterinarians, breeders, and pet owners to assist in their effort to provide precise diagnosis and
help with breeding of animals free of hereditary diseases known to particular breeds. The
Laboratory offers DNA tests for genetic diseases found in dogs and cats mostly based upon the
research performed by the investigators at Penn to identify affected, carrier (asymptomatic) or
normal (clear) genotypes in pets. Tests offered by PennGen as well as other DNA testing
laboratories worldwide can be found at http://research.vet.upenn.edu/WSAVALabSearch which
is a searchable database by disease, breed, and laboratory.
PennGen provides various diagnostic genetic services and consultations for primary care
veterinarians, veterinary specialists, breeders and pet owners in order to produce the healthiest
dogs in each breed and to gain new knowledge and insight to these genetic diseases.
Supported in part by the National Institutes of Health (OD 010939), Canine Health, Winn Feline,
and other foundations.
113
Congenital Hypothyroidism with Goiter in Cats due to a TPO Mutation
Karthik Raj, Catherine V. Morrow, Anne Traas, Angela M. Erat, Marisa Van Hoeven, Hamutal
Mazrier, Mark E. Haskins, and Urs Giger
Section of Medical Genetics, School of Veterinary Medicine, University of Pennsylvania,
Philadelphia, PA.
Congenital hypothyroidism (CH) has been reported in many species; the hereditary forms can be
divided into thyroid dysmorphogenesis and dyshormonogenesis. While thyroid hypoplasia has
been described in dogs and cats, the molecular basis remains unknown. In contrast several breeds
of dogs with goiterous CH, studied by Fyfe et al, were found to have deficient thyroid peroxidase
(TPO) activity and disease-causing TPO gene mutations. The purpose of our study was to
characterize a family of domestic shorthair cats with goiterous CH.
Clinical features included dwarfism and dullness, known as cretinism and seen with CH in all
species, but also constipation and megacolon which are unique to cats with CH. Pedigree
analysis documented an autosomal recessive mode of inheritance. Affected kittens developed a
goiter and had low serum thyroxine (T4) and triiodothyronine (T3) when compared to controls,
but high thyroid stimulating (TSH) hormone levels indicating thyroid dyshormonogenesis. Oral
thyroid supplementation corrected the progression of clinical signs and prevented further
constipation and reversed the megacolon.
The TPO enzyme activity was extremely low in hypothyroid cats when compared to that of
normal cats. Genomic DNA and cDNA from affected, carrier, and normal cats were extracted
and sequenced based upon primers developed from the feline genome database. A homozygous
missense point mutation (c.1333G>A) in TPO, which results in an amino acid change
(p.Ala445Thr), was discovered in affected cats and the mutant allele segregated within the
family with goiterous CH. This is the first report of a TPO deficiency in cats. Unrelated
domestic shorthair cats with goiterous CH did not have this same TPO mutation. The prevalence
of this TPO mutation in the domestic cat population seems low, but CH is likely underreported in
cats.
Supported in part by NIH OD 010939.
114
Selection and the Co-Evolution of Breeds and Disease-Liability Genes
Jerold S Bell, Tufts Cummings School of Veterinary Medicine, N. Grafton, MA USA
Jerold.bell@tufts.edu
Natural selection works against inherited traits and disorders that would reduce the ability to
survive, thrive, and reproduce. Artificial selection can; reduce the frequency of disease-liability
genes, be neutral to their propagation, or sometimes preferentially select for them. Selection must
be appropriately applied in order to improve breed health.
Pure-bred dog and pedigree cat breeds evolved through selection for conformational, behavioral,
and/or working standards. With extreme phenotypic selection, breeders have purposely selected
for disease-liability, such as; the brachycephalic syndrome, excessive amounts of skin or skin
folds, and overangulation.
Selection for traits has been linked to disease-liability, such as; hyperuricosuria (SLC2A9) in
Dalmatians, cranio-facial defect (unpublished, Lyons) in Burmese, dermoid sinus (FGF3, FGF4,
FGF19 and ORAOV1 duplication) in Ridgebacks, and osteochondrodysplasia (unidentified) in
Scottish Folds. In some cases, the preferred trait can be genetically separated from the disease
liability. In other cases, they are pleiotropic expressions of the same genotype.
Other disease liability genes are not linked to selection, but lay in the genetic background of
breeds. Many of these are ancient mutations that preceded the separation of, and are shared by
many breeds. These include complex disorders, such as; hip dysplasia, patella luxation, and
diabetes mellitus (Types 1 & 2). Several ancestrally ancient mutations cause simple Mendelian
disorders, such as; progressive rod-cone degeneration (prcd), multifocal retinopathy (cmr1), and
hyperuricosuria (SLC2A9). Without direct selection, these can increase in frequency through the
popular sire effect or genetic drift.
Some recommendations to improve the genetic health of breeds concentrate on selection to
increase heterozygosity or minor allele frequencies. These methods; 1) do not select against
disease-liability genes, 2) will not prevent the phenotypic expression of dispersed genes, and 3)
may reverse the effects of positive selection through blind manipulation of minor alleles. Healthbased selection should be specifically directed against deleterious traits and genes.
115
Population Genetic Studies and Gene Dynamics of Dog and Cat Breeds
Jerold S Bell DVM, Clinical Associate Professor, Dept. of Clinical Sciences, Tufts Cummings School of
Veterinary Medicine jerold.bell@tufts.edu
(This article is based on a poster presented at the 7th International Conference on Advances in Canine and Feline Genomics
and Inherited Diseases, Sweden 2012. It can be reproduced with the permission of the author.)
Breed Gene Dynamics
Each dog and cat breed has its own evolutionary history of founders, accumulated deleterious genes,
population bottlenecks, popular sires, and geographical fragmentation. Some studies of dog and cat
breeds focus on the inbreeding coefficients of individuals, and the effective population size of breeds as
a measurement of their genetic vitality and ability to maintain themselves as pure breeds (Calboli et al.
2008, Genetics 179:593-601).
Most breeds started from a limited number of founders. As the population expands within a closed gene
pool, it allows mating choices between individuals that are less closely related than the previous
generation. This is shown by evaluating average 10 generation inbreeding coefficients (Mean 10 Gen IC).
Early in breed development, inbreeding coefficients can be high due to inbreeding on a small founder
population (as seen in the Borzoi and Burmese breeds), or breeding with a more diverse founder
population (as seen in the Siberian Husky, Gordon Setter, and Cavalier King Charles Spaniel breeds).
116
As generational pedigrees extend beyond 10 generations, the IC Mean 10 Gen can decrease as
populations utilize the breadth of their gene pool and the number of unique ancestors increase. When
the Mean 10 Gen IC increases, it is usually because breeders are concentrating on popular sires. The
Mean All Gen IC (homozygosity) necessarily goes up over time as a function of breed evolution. (The
Mean All Gen IC of Burmese goes down in this example due to importation of Burmese with incomplete
pedigrees.) The genetic health of dog and cat breeds is not a direct function of homozygosity or
heterozygosity; but of the accumulation and propagation of disease liability genes.
Several researchers have found that dog breed genetic diversity is not a function of population size or
average inbreeding levels (James 2011: Vet Journal 189:211-213, Bjornerfeld et al. 2008, BMC Evol Biol
8:28). Shariflou et al. (2011, Vet Journal 189:203-210 ) found that genetic diversity is not related to the
117
size of the breed, but to breeding practices and the even contribution of founding lines. The popular sire
syndrome is the single most influential factor in restricting breed gene pool diversity.
Molecular genetic studies of cattle show limited genetic diversity in evolutionary founder populations
(Bollongino et al. 2012, Mol Biol Evol. 2012 Sep;29(9):2101-4., The Bovine HapMap Consortium 2009
Science 324(5926):528-532). In spite of this, cattle breeds have propagated and are second only to dogs
in mammalian genetic diversity.
Breed genetic health does not have to do with existing breed inbreeding coefficients, homozygosity,
estimated number of founders, or other statistics. It has to do with reproductive ability and
accumulated disease liability genes. Breed genetic health should be judged based on current breed
health surveys.
Breeding Strategies
Some organizations have embraced the belief that close breeding is the cause of impaired breed health.
They have adopted programs that restrict close breeding, and promote outbreeding to the least related
individuals. This involves lowering mean inbreeding coefficients and/or increasing heterozygosity of
SNPs or haplotypes.
Outbreeding programs are akin to a Species Survival Plan (SSP) that is utilized when attempting to
“rescue” an endangered species. The vast majority of dog and cat breeds do not show evidence of
genetic depletion such as; low reproductive success, and increased stillborn and neonatal mortality.
Recommendations to outbreed (only breed to those least related) homogenizes breeds and erases the
genetic difference between individuals. It is a self-limiting process that requires matings be done
between individuals who are genetically different from each other. Eventually there will be no more
“lines” with differences. Everyone will be in the center, and no one at the periphery.
118
By erasing the genetic difference between individuals, this averts selective pressure for improvement.
Breed gene pool diversity requires distinct lines in order to create selective pressure. A mix of breeding
individuals from different lines within the breed maintains allelic polymorphism.
Breeders strive to select for healthy conformational, behavioral, and working standards for their breeds.
Selection over time allows more individuals to conform to a standard.
Attempts to create heterozygosity for SNPs and haplotypes that have no defined positive or negative
gene effect have as much a chance of reversing selection-based improvements as they have for being
beneficial to a breed’s genetic health.
This has been shown in cattle breeds: Prioritization based on neutral genetic diversity may fail to
conserve important characteristics in cattle breeds (Hall et al. 2012 J Anim Breed Genet 129(3):218225).
Prudent breeding practices allow some linebreeding, some outbreeding, and even occasional
inbreeding; with different breeders maintaining breeding lines or crossing lines as they see fit. It is the
different opinion and breeding actions of breeders that maintain breed diversity.
Genetic Health
We see increased genetic disease in pure-bred and cross-bred animals due to a lack of genetic testing
and selection of breeding animals, and an associated increase in disease liability genes. Different mating
types (inbreeding, linebreeding, outbreeding) are responsible for the expression of alleles in gene pairs,
but not in allele propagation. Selection of breeding stock for the next generation, and their fecundity is
what alters allele frequencies.
Genetic homozygosity is a function of speciation and breed formation. It is only detrimental if related
to disease liability genes or impaired health. We must ensure that our selection recommendations
improve breeds, and do not impede breeder efforts for progress in breed health, conformation, and
function.
119
Articles
Title:
Name:
A web resource on DNA tests for canine and feline
hereditary diseases
Slutsky J, Raj K, Yuhnke S, Bell J, Fretwell N,
Hedhammar A, Wade C, Giger U.
Deciphering the genetic basis of animal domestication Wiener P & Wilkinson S
Both Ends of the Leash — The Human Links to Good
Dogs with Bad Genes
Elaine A Ostrander
Variation of cats under domestication: genetic
Kurushima JD, Lipinski MJ, Gandolfi
assignment of domestic cats to breeds and worldwide Froenicke L, Grahn JC, Grahn RA, Lyons LA
random-bred populations
An insight into population structure and gene flow
within purebred cats
Leroy G, Vernet E, Pautet MB, Rognon X
Assessing the impact of breeding strategies on
inherited disorders and genetic diversity in dogs
Leroy G & Rognon X
B,
How the Orthopedic Foundation for Animals (OFA) is
Keller GG, Dziuk E, Bell JS
tackling inherited disorders in the USA: Using hip and
elbow dysplasia as examples
Comparative analyses of genetic trends and prospects Lewis TW, Blott SC and Woolliams JA
for selection against hip and elbow dysplasia in 15 UK
dog breeds
Prevalence of inherited disorders among mixed-breed Bellumori TP, Famula TR,
and purebred dogs: 27,254 cases (1995-2010)
Belanger JM, Oberbauer AM
Idiopathic Cystitis in Domestic Cats—Beyond the
Lower Urinary Tract
C.A.T. Buffington
120
Bannasch
DL,
The Veterinary Journal 197 (2013) 182–187
Contents lists available at SciVerse ScienceDirect
The Veterinary Journal
journal homepage: www.elsevier.com/locate/tvjl
A web resource on DNA tests for canine and feline hereditary diseases
Jeffrey Slutsky a, Karthik Raj a, Scott Yuhnke a, Jerold Bell b, Neale Fretwell c, Ake Hedhammar d,
Claire Wade e, Urs Giger a,⇑
a
School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
Department of Clinical Sciences, Tufts Cummings School of Veterinary Medicine, North Grafton, MA, USA
c
UK Waltham Centre for Pet Nutrition, Freeby Lane, Fretwell, Leicestershire, UK
d
Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
e
Faculty of Veterinary Science, University of Sydney, New South Wales 2006, Australia
b
a r t i c l e
i n f o
Article history:
Accepted 24 February 2013
Keywords:
Canine
Feline
Genetics
Database
Mutations
a b s t r a c t
Following the first identification of a disease-causing mutation in dogs in 1989 and the more recent completion of canine and feline genome sequences, much progress has been made in the molecular characterization of hereditary diseases in dogs and cats. To increase access to information on diagnosing
hereditary diseases in dogs and cats, a web application has been developed to collect, organize and display information on available DNA tests and other supporting information, including gene and chromosomal locations, mutations, primary research citations and disease descriptions. The DNA testing
information can be accessed at the URL: http://research.vet.upenn.edu/WSAVA-LabSearch. There are currently 131 molecular genetic tests available for hereditary diseases in dogs and cats offered by 43 laboratories worldwide. This tool should provide clinicians, researchers, breeders and companion animal
owners with a single comprehensive, up-to-date and readily searchable webpage for information on
hereditary disease testing.
Ó 2013 Elsevier Ltd. All rights reserved.
Introduction
Next to humans, the largest number of naturally occurring
hereditary disorders and genetic predispositions to disease has
been reported in dogs (Sargan, 2003; Giger et al., 2006; Bell
et al., 2012), followed by cats (Giger and Haskins, 2006; Pontius
et al., 2007; Lyons, 2010, 2012). Notably, many hereditary disorders in dogs and cats represent true homologues of genetic diseases in humans and thus serve as valuable naturally occurring
disease models (Marschall and Distl, 2010; Mellersh, 2011). Since
many of these disorders are recessively inherited and occur with
high frequency in specific or related breeds due to common
inbreeding practices, they represent a serious health problem for
companion animals (Padgett, 1998; Vella et al., 1999; Giger et al.,
2006; Asher, 2009; Hedhammar and Indrebø, 2011; Bell et al.,
2012). To address this issue, a thorough investigation of hereditary
disorders, from clinicopathologic features to the molecular genetic
basis of disease, has become a high priority.
Much progress has been made in the molecular characterization
of hereditary diseases in dogs and cats since the initial identification of the genetic basis for canine hemophilia B in 1989 (Evans
et al., 1989), aided by the completion of the canine (Lindblah-Toh
et al., 2005) and feline (Pontius et al., 2007) genome sequences,
and their recent improved coverages and annotations (National
Center for Biotechnology Information, NCBI).1 Thus far, most of
the characterized hereditary disorders involve single gene defects
with simple Mendelian inheritance and are mostly breed specific
(Giger and Haskins, 2006; Giger et al., 2006).
Knowing the specific molecular defect for a hereditary disease is
valuable, since it offers the best opportunity to make a precise diagnosis for an animal with clinical signs, helps to screen animals at risk
of developing the disease, permits identification of carrier animals
(heterozygous for a mutant allele but clinically healthy) and can
be used to test animals prior to breeding to assure that affected animals are not produced in future generations (Giger et al., 2006;
Lyons, 2010; Mellersh, 2011). The original research laboratories
where a disease-specific mutation is first discovered in a particular
breed may or may not continue testing animals subsequent to the
completion of the relevant research. However, other university or
for-profit laboratories may offer these tests following the publication of the mutation, depending on patent and licensure restrictions.
The extent of information that is provided to the public varies from
one testing laboratory to another, but usually comprehensive information on either the disease or mutation is unavailable.
⇑ Corresponding author. Tel.: +1 215 8988830.
1
E-mail address: giger@vet.upenn.edu (U. Giger).
1090-0233/$ - see front matter Ó 2013 Elsevier Ltd. All rights reserved.
http://dx.doi.org/10.1016/j.tvjl.2013.02.021
121
See: http://www.ncbi.nlm.nih.gov/.
183
J. Slutsky et al. / The Veterinary Journal 197 (2013) 182–187
Table 1
Sources of genetic disease information.
OMIA
CIDD
LIDA
IDID
OFA
CHF
Fabcats
University of Sydney
University of Prince Edward Island
University of Sydney
Cambridge University
Orthopedic Foundation of America
Canine Health Foundation
Feline Advisory Bureau
http://omia.angis.org.au/home; http://www.ncbi.nlm.nih.gov/omia/?term=omia
www.upei.ca/cidd
www.sydney.edu.au/vetscience/lida
http://server.vet.cam.ac.uk
http://www.offa.org
http://www.akcchf.org
http://www.fabcats.org/breeders/inherited_disorders
It is often daunting for veterinary clinicians, breeders and
researchers to keep up with rapid advances in diagnostic opportunities. Despite a number of sources of genetic disease information currently available on-line (Table 1), a few books (Bell et al., 2012), book
chapters, review articles and websites that have attempted to
gather information on genetic disease testing laboratories, the
number of disease-associated mutations, tests offered and laboratories involved continue to grow and change, rapidly rendering many
of these sources obsolete (Nicholas et al., 2011; Mellersh, 2012).
To provide a comprehensive resource to find up-to-date, verified information on the currently available DNA tests for inherited
diseases in dogs and cats, the Hereditary Disease Committee of the
World Small Animal Veterinary Association (WSAVA) has developed a web application featuring an interface that allows users
to search the underlying database, which we describe below.
Materials and methods
The Canine and Feline Hereditary Disease (DNA) Testing Laboratories2 web
application was developed using Microsoft ASP.net and a Microsoft SQL server database. The pages and database for this application are hosted on servers at the School
of Veterinary Medicine of the University of Pennsylvania (PennGen).
We screened the scientific literature for the molecular characterization of
hereditary diseases and genetic predispositions to disease in dogs and cats using
PubMed3 and Commonwealth Agricultural Bureau (CAB) Abstracts.4 We also searched
the Internet for laboratories that offer DNA testing for genetic diseases in dogs and
cats. We further checked the availability of DNA tests with dog and cat fancier associations, e.g. American Kennel Club (AKC), The Kennel Club (KC) UK, Fédération Cynologique Internationale (FCI), Cat Fancier Association (CFA) and The International Cat
Association (TICA), and organizations involved with genetic health issues in dogs or
cats, e.g. Canine Health Foundation (CHF), Orthopedic Foundation of Animals (OFA)
and Winn Feline Foundation. Each laboratory was contacted directly and asked for
specific information on each test, including which mutation(s) the laboratory tests
for, which species and breeds are affected by each mutation tested for, if testing is still
available for each DNA test and if additional DNA tests are offered.
In addition to reviewing the published studies and research abstracts in which
mutations were first described, we also verified unpublished information with research laboratories to identify additional disease-causing mutations and/or breeds
affected by the same or different mutations in the same gene for which tests are
now offered. The veracity of all unpublished information has not been verified by
the authors, but generally the information is from established laboratories. Genetic
information regarding the diseases listed, including gene affected, chromosome and
mutation description, was obtained mainly through original research papers and
published research on NCBI and PubMed. Mutations were described using the standard nomenclature as described by the Human Genome Variation Society.5 In addition, genome and other databases in NCBI and the Genome Annotation Resource
Fields – Felis catus (GARField) in the National Cancer Institute’s Laboratory of Genomic
Diversity (Pontius and O’Brien, 2007)6 were used to describe the chromosomal loci of
the genes in dogs and cats, respectively.
In some cases, the mutation in the database may be listed slightly differently to
that in the published literature due to new information on gene structure, release of
updated genome assemblies, use of non-standard nomenclature and occasional errors in mutation descriptions. Online Mendelian Inheritance in Animals (OMIA) and
Online Mendelian Inheritance in Man (OMIM) numbers were collected from their
websites or based on information provided by laboratory responses. During the
analysis, it became evident that the NCBI used a different numbering system than
OMIA for trait IDs, which caused confusion; fortunately, this has been corrected
2
3
4
5
6
See:
See:
See:
See:
See:
http://research.vet.upenn.edu/WSAVA-LabSearch.
www.ncbi.nlm.nih.gov/pubmed.
www.cabi.org.
http://www.hgvs.org/mutnomen.
http://lgd.abcc.ncifcrf.gov.
Table 2
Information available in the Canine and Feline Hereditary Disease (DNA) Testing
Laboratories web application.
Disease information
Genetic information
Laboratory information
Disease name
Related terms/synonyms
Commonly used code
OMIA/OMIM number
Breeds affected
Clinical disease
description
Chromosome
Gene
Mutation description
Research citation
Research hyperlink
Laboratory name
Website URL (hyperlink)
E-mail contact
Mailing address
Country
by NCBI following consultation. Descriptions on each hereditary disease are continuously being collected from the Veterinary Information Network (VIN) Associate
ebook for Hereditary Diseases.7
For the purposes of the data contained in this application, we defined a single
heritable disease as an illness characterized by typical signs and routine laboratory
tests and/or imaging abnormalities that occur due to a mutation in a particular
gene. Therefore, if two breeds present with similar disease phenotypes, but differ
in the gene mutated, the resulting disorders would be classified as separate diseases. However, in the case where there are distinct mutations in the same gene
in different breeds, causing the same illness, all these mutations would be listed
as the same disease.
Only dog breeds recognized by the AKC, FCI and KC were included in the database and we have not included information on mixed breeds unless they uniquely
express a specific mutation not seen in any purebreds. Any disease seen in a purebred dog or cat can, of course, occur in a mixed breed animal. For cats, we have included domestic shorthair and domestic longhair cats as their own ‘breeds’, along
with the standard pure breeds, as stated by CFA and TICA. Since our data focuses
on disease-specific mutations, tests for parentage and coat color, length and texture
are excluded, unless directly associated with a disease. Finally, inclusion of affected
breeds was limited to those backed by specific research, although on certain occasions we have allowed a broader interpretation, where the mutation has been found
through testing, but not confirmed in a published original study. No DNA mutation
screen panels are included in the data.
Results
The verified information on available DNA tests for hereditary
diseases and genetic predispositions to diseases in dogs and cats
is displayed on a website.8 We summarize here the information
contained in the database to mid-2012 (Tables 2–6). It was discovered that four laboratories stopped offering DNA tests during the collection period and are therefore not included in the data. Forty-four
laboratories offered DNA tests for hereditary diseases in dogs and
cats, 43 of which were included in the database and whose data
we report on below; one corporate laboratory requested to be excluded from the database. The name, address and website for each
laboratory, as well as details of each DNA test are provided.
Twenty-two of the 43 testing sites are the laboratories and/or the
investigators that originally identified the mutation. These usually
only test for a single mutation or a small group of (related) genetic
diseases; 14 laboratories only test for a single disease and nine of
these only test samples from a single breed bearing the mutation.
7
See: http://www.vin.com/Members/Associate/Associate.plx?Book=1&Browse
Chapter=&SpeciesID=5#Jump.
8
See: http://research.vet.upenn.edu/WSAVA-LabSearch.
122
184
Table 3
Information available from ‘View Disease Details’ link.
Disease name/synonyms
General description
Description in species
Mode of inheritance
Etiology
Breed, sex and age predilection
Clinical findings and signs
Diagnostic procedures
Treatment and management
Prevention
Differential diagnosis
Human disease homologue
Available tests
Research references
Contributor’s name and date
Of 43 laboratories that offered DNA testing, 21 were commercial laboratories that specialize in genetic disease testing. Twenty-eight laboratories offered DNA tests for dogs only, five for cats only and 10 for
dogs and cats. No laboratory offers all available tests, due to
restrictions by patents, limited licensure, through a specific disease
Table 6
Inheritance patterns of diseases with known mutations.
Autosomal recessive
Autosomal dominant
X-linked recessive
X-linked dominant
Mitochondrial
Dogs
Cats
Total
107
13
1
8
1
19
4
2
0
0
126
17
3
8
1
focus of the laboratories and/or through a lack of demand to test
for mutations that occur very rarely in a particular breed population
(Table 5).
A total of 155 hereditary diseases (130 in dogs, 25 in cats) have
been characterized at the molecular level and 125 currently can be
assessed in laboratories (111 in dogs, 20 in cats). Although 94 disorders can be tested for by several laboratories (85 in dogs, 9 in
cats), the rest are offered only by a single laboratory (Table 4),
either due to patent and license restrictions, lack of published
information and/or because the mutation is believed to occur very
rarely in a particular breed population. More than one mutation
has been reported in the same gene for several disorders
Table 4
Summary of disease information in the database.
Number of disease tests
Diseases with a single mutation
Diseases with multiple mutations
Total mutations tested for
Single breed mutations
Mutations affecting multiple breeds
Total breed specific tests tested forb
Commercial breed specific tests
Non-profit breed specific test
Breed tests available at only one laboratory
Breed tests available at multiple laboratories
Maximum number of laboratories performing a test
Maximum number of mutations in a single disease
Maximum number of breeds tested for a single mutation
Average number of laboratories testing a single breed specific mutation
Median number of laboratories
Average number of mutations for a specific disease
Median number of mutations
Average number of breeds for a specific mutation
Median number of breeds
a
b
c
d
e
f
g
h
i
j
Dog
Cat
Total
111
87
24
143
100
43
361c
306
176
123
238
10e
6g
22i
3.6
3
1.3
1
2.3
1
20
15
5
24
15
9
56d
41
35
13
43
10f
2h
16j
3.0
1
1.4
1
2.9
1
125a
102
29
167
115
52
417
347
211
136
281
Includes six diseases where the mutation has been found in both species and a test is available in both species.
Total of the tests for each specific mutation available in a specific breed (i.e. a specific disease/mutation/breed combination).
There are 121 breed specific tests for dogs available at both commercial and non-profit laboratories.
There are 20 breed specific tests for cats available at both commercial and non-profit laboratories.
Multiple instances.
Blood type B mutation.
Factor IX deficiency (hemophilia B).
Multiple instances.
Primary lens luxation.
Progressive retinal atrophy (Rdac mutation), although Blood type B is offered for all breeds.
Table 5
Summary of laboratory information in the database.
Number of laboratories
Average number of diseases tested by one laboratory
Median number of diseases tested by one laboratory
Maximum number of diseases tested by one laboratory
Minimum number of diseases tested by one laboratory
Average number of breed mutation tests by one laboratory
Median number of breed mutation tests by one laboratory
Maximum number of breed mutation tests by one laboratory
Minimum number of breed mutation tests by one laboratory
123
Non-profit
Corporate
Total
22
5.0
2
27
1
13.5
4.5
60
1
21
20.0
15
67
1
57.2
47
195
1
43
12.4
4.0
34.8
(24 disorders in dogs, five in cats); frequently, individual mutations
are breed specific. The pattern of inheritance of the majority of
diseases in dogs and cats with known mutations is autosomal
recessive; mutations that are inherited as autosomal dominant,
X-linked recessive, X-linked dominant or mitochondrial traits have
also been identified (Table 6). Tests for several complex traits with
multiple gene defects need to be investigated further.
185
Many mutations were found only in a single breed (69% of the
mutations listed in the database), whereas some mutations have
been found in multiple breeds, up to 22 for primary lens luxation.
Some disorders have only been identified in a single animal or family and may not be present in the general breed population, e.g. Xlinked severe combined immunodeficiency in dogs maintained in a
research colony (Henthorn et al., 1994); routine testing for such
Fig. 1. A sample disease test search for a coagulopathy in Beagles. (A) Searches can be done by disease/test, breed or laboratory. (B) Information regarding the selection is
used to narrow down the results. (C) Information about the specific disease in this breed is displayed. (D) Information about the laboratories doing the specific test in this
breed is displayed.
124
186
specific mutations usually is not offered. There are also cases
where there are separate mutations affecting the same breed, causing different forms of the disease, e.g. porphyria in domestic shorthair cats (Clavero et al., 2010).
Discussion
In the past two decades, much progress has been made in the
characterization of disease-causing mutations in dogs and cats.
Through DNA testing, this new information permits specific diagnosis in an animal affected by a specific hereditary disease or
allows an animal at risk of becoming ill because of a particular disease-causing mutation to be identified. Most genetic diseases are
inherited recessively and may occur commonly in one or more
breeds due to particular breeding practices, such as deliberate
inbreeding or the extensive use of a popular sire (Wade, 2011).
Therefore, knowledge of the mutation allows screening of the
breeding stock and, by permitting selection of appropriate breeding animals, can eliminate the disease from future generations.
DNA tests are the most desirable tools for the detection of
mutations causing hereditary diseases; they allow determination
of homozygosity and heterozygosity for a certain mutant/disease
allele, only require small samples (such as blood or cheek swabs,
which can be shipped by regular mail), are relatively simple to perform in the laboratory, are standardized and are potentially less
expensive than most other tests. There are many different techniques, from manual to robotically automated, for identification
of the normal and mutant allele for a disease. This web application
does not provide information on these detailed laboratory techniques, which often change with new technologies. Moreover, currently there is no official quality control system for DNA testing in
veterinary medicine and the application presented here cannot assess the quality of testing of any laboratory listed.
Although biochemical laboratory tests and imaging studies are
used to diagnose some hereditary diseases in companion animals,
genomic DNA tests for single gene defects are considered to be the
most accurate in clinical medicine and thus only DNA tests are included here. Allowing for human errors from identifying animals,
labeling and mixing up samples, these DNA tests are considered
to be accurate, assuming that regular laboratory standards, with
appropriate positive and negative controls, are followed.
Current information on mutant allele frequency is limited, since
the data generally are based upon a few rather small and frequently biased, rather than randomized, surveys or open registries.
Also, common mutations may disappear from a population (breed)
due to the success of a DNA screening program.
Recently, one company involved in canine disease testing has
offered a multiple single nucleotide polymorphism (SNP) panel
analysis that screens for disease-causing mutations in mixed breed
dogs (Mars Veterinary). This company was not included on the
website, since panel analysis screens are not considered to be a
specific breed test. The results of the panel are not reported as a
definitive diagnosis in affected animals, but alert the submitter if
a mutation is found, so that further specific testing can be pursued
at a DNA genetic disease testing laboratory. Unless patents and
licensures restrict its future use, such panel analyses may be used
for all known DNA mutations in a species, making this method a
simple and cost effective tool to screen for hereditary diseases in
companion animals.
Our website is arranged by general categories: disease, breed,
and laboratory, each of which can be searched separately
(Fig. 1A). After selecting an initial category to search, the users
may select the specific disease, species (canine/feline) and breed
they are interested in. If there is more than one mutation known
to cause a disease, the specific mutation can be selected. As an
example, we have chosen to search for factor VII deficiency, a common coagulopathy (Callan et al., 2006) (Fig. 1B). The application
displays the pertinent genetic information regarding the hereditary disease (Fig. 1C), as well as the laboratories that offer the test
(Fig. 1D). If further clinical details on the disease are desired, they
may be accessed via the hyperlink through the ‘View Disease Details’ option to download a PDF file (Fig. 1C; Table 3).
In the example shown in Fig. 1, three testing laboratories are
identified. The first laboratory listed will be the laboratory that
originally identified the particular breed-specific disease mutation,
if they are still testing for the mutation, or a laboratory that is directly affiliated with the research group. The research article first
describing the mutation may be accessed (Fig. 1C) through the textual citation or through a hyperlink (in this case freely accessible
by the hyperlink to PubMed Central). This disease example also reveals that two other breeds have Factor VII deficiency caused by
the same mutation (Alaskan Klee Kai and Scottish deerhound).
While this coagulopathy has also been described in Great Pyrenees
and English springer spaniels, the disease-causing mutation(s) in
these breeds have not yet been identified. Since the DNA test
may not be helpful for these and other breeds, currently they are
not contained in the database under this mutation test.
Conclusions
This web-based application represents a source of up-to-date
information on hereditary diseases in companion animals for veterinary clinicians looking for a laboratory to perform a test,
researchers searching for information on hereditary diseases and
owners/breeders with affected animals or animals at risk of developing a particular disease or passing on the mutant allele (carriers).
We intend to keep this web application updated by regular review
of the pertinent literature, correspondence with testing laboratories and through feedback from those involved in research on comparative medical genetics. This service will be continued by the
WSAVA Hereditary Disease Committee.
Conflict of interest statement
The authors from the University of Pennsylvania are associated
with PennGen, one of the not-for-profit laboratories offering DNA
tests, and the work was funded by the WSAVA through contributions from Waltham.
Acknowledgements
This study was supported in part by the WSAVA, Waltham and
the USA National Institutes of Health grant NIH RR002152 and NIH
OD010939. The authors would like to acknowledge the assistance
of VIN and especially Dr Linda Shell in the development of the disease information files in the Associate program, as well as many
veterinary clinicians and scientists who provided valuable specific
disease information.
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doi:10.1098/rspb.2011.1376
Published online 1 September 2011
Review
Deciphering the genetic basis of animal
domestication
Pamela Wiener* and Samantha Wilkinson
The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush,
Midlothian EH25 9RG, UK
Genomic technologies for livestock and companion animal species have revolutionized the study of
animal domestication, allowing an increasingly detailed description of the genetic changes accompanying
domestication and breed development. This review describes important recent results derived from the
application of population and quantitative genetic approaches to the study of genetic changes in the
major domesticated species. These include findings of regions of the genome that show between-breed
differentiation, evidence of selective sweeps within individual genomes and signatures of demographic
events. Particular attention is focused on the study of the genetics of behavioural traits and the implications for domestication. Despite the operation of severe bottlenecks, high levels of inbreeding and
intensive selection during the history of domestication, most domestic animal species are genetically
diverse. Possible explanations for this phenomenon are discussed. The major insights from the surveyed
studies are highlighted and directions for future study are suggested.
Keywords: animal domestication; breed differentiation; selective sweep; population bottleneck
1. INTRODUCTION
Understanding the history of domestication has been of
interest to biologists at least since Darwin. He appreciated
the wide variation within domesticated species, and
throughout On the origin of species [1] (and later, in his two
volumes of Variation under domestication [2]) he used them
as examples of his theories. It is now well accepted that the
process of animal domestication has involved a combination
of human-imposed selection and non-selective forces, the
latter including various forms of interference with the
demography and mating programme of these species.
It is only recently, with advances in genetic and statistical
technologies, that the genetic changes that have accompanied
animal domestication and breed development can be characterized. A rapidly increasing number of species now have
full-genome sequences. High-density, genome-wide single
nucleotide polymorphism (SNP) panels have been produced
for humans, as well as many other plant and animal species.
A variety of statistical techniques have concurrently been
developed to analyse this data. One of the key aspects of
this analysis is to use genomic data in order to make inferences about the selective and demographic forces that have
operated on individual species.
This review discusses the contribution that genetic
data have made to our understanding of both selective
and non-selective processes of evolutionary change in
domesticated animal species, and the insights into the
domestication process that have been revealed by these
studies. Applications of various population geneticbased methods for the detection of genomic regions
* Author for correspondence (pam.wiener@roslin.ed.ac.uk).
Electronic supplementary material is available at http://dx.doi.org/
10.1098/rspb.2011.1376 or via http://rspb.royalsocietypublishing.org.
Received 5 July 2011
Accepted 12 August 2011
127
under selection are presented, as well as methods for elucidating non-selective processes; many of these, if not all,
were first developed for human genetic analysis. This
article does not attempt to review all the relevant literature, but rather to use specific examples to illustrate
common themes. The examples presented are primarily
taken from cattle, pigs, chickens and dogs, where the
most advanced genetic resources are available.
2. SELECTIVE FORCES
The assumption underlying the detection of signatures of
selection in the genome is that selection is locus-specific.
By comparison, the effects of other evolutionary forces
(random genetic drift, mutation and inbreeding) should
be expressed genome-wide. Under this premise, the
methods for detecting selected loci attempt to identify
those at which allele frequencies have changed in a pattern consistent with positive selection. The methods
differ in the information they use to find such loci (particularly as there are very few data on historical allele
frequencies), which will be outlined further.
(a) Candidate gene studies
One approach adopted in domestication genetics is to
examine patterns of diversity around candidate genes
that, based on their function, are likely to have been targets
of selection. Two such genes are growth differentiation
factor 8 (GDF-8), associated with muscle conformation,
and melanocortion 1 receptor (MC1R), associated with
coat colour.
GDF-8 (myostatin) is a negative regulator of skeletal
muscle growth, and naturally occurring mutations in this
gene have been associated with increased levels of muscle
conformation in cattle, dogs, sheep and humans. There is
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This journal is q 2011 The Royal Society
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P. Wiener & S. Wilkinson
Review. Genetics of animal domestication
(a)
(b)
1.0
heterozygosity
0.8
0.6
0.4
0.2
0
0
1
2
3
4
5
distance from GDF-8 (cM)
6
Figure 1. Selection for muscle conformation in cattle. (a). Belgian Blue cows from early (top) and late (bottom) in the 20th
century (photos reprinted from Compere et al. [5]; stitches in the more recent photo indicate that the calf was delivered by
caesarean section, which is common in Belgian Blue cattle and associated with the large size of double-muscled calves [5]).
(b). Relationship between heterozygosity and genomic distance from the GDF-8 (myostatin) gene for Belgian Blue and
South Devon cattle homozygous for the 11 bp deletion (MH/MH) associated with double muscling (data from Wiener
et al. [6] and Wiener & Gutierrez-Gil [7]). Blue circles, Belgian Blue; red circles, MH/MH South Devons.
substantial diversity in GDF-8 across cattle breeds [3,4],
including, at the extreme, two independent loss-offunction mutations that are associated with the ‘double
muscling’ phenotype, in which animals have highly exaggerated muscle conformation. At the beginning of the
twentieth century, the majority of Belgian Blue cattle had
conventional conformation, and were used for both milk
and beef production [5] (figure 1a). However, after less
than a century of animal breeding, the double muscling
phenotype is now nearly fixed in the breed, suggesting
that there has been strong selection in favour of this trait,
presumably owing to the increased amount of derived
meat [8,9]. Analysis of microsatellite diversity in the
region flanking the GDF-8 gene revealed a significant
decrease in heterozygosity with increasing proximity to
GDF-8 in three primarily double-muscled breeds, including the Belgian Blue, as well as in the sub-group of
double-muscled South Devon cattle [6,7] (figure 1b),
which was not seen in most non-double-muscled breeds.
The pattern of heterozygosity in both Belgian Blue and
South Devon cattle is consistent with strong selection on
this gene. While evidence of a signature of selection near
myostatin has not yet been published for other species, it
is likely to exist as variation in this gene has been shown
to influence traits of economic interest in breeds of dogs
[10] and sheep [11].
Coat colour and pattern are key traits in the development of livestock and companion animal breeds, as they
were under selection well before breed development [12].
A number of genes have been associated with coat colour
in mammals, including the MC1R gene. MC1R influences the relative levels of eumelanin (black/brown) and
Proc. R. Soc. B (2011)
phaeomelanin (yellow/red) pigments, and appears to have
been a target for selection in pigs and other domesticated
animal species. For example, there has been independent
evolution of black coat colour in Asian and European
pigs, and selection for this phenotype appears to have
been particularly strong in Chinese pigs, where animals
with the black coat were used preferentially in animal sacrifice rituals during the Neolithic period, because they were
considered sacred [13]. Asian wild boar (the closest relative
to the domestic pig) show extensive nucleotide variation at
MC1R; however, nearly all European and Asian wild boar
genotyped so far express the same MC1R protein, with
genotypes differing primarily by synonymous substitutions
[13,14]. This wild-type protein allows complete expression
of both eumelanin and phaeomelanin pigments, and produces a coat in variable shades of brown [15]. In contrast,
in domestic pigs, there is reduced synonymous variation
relative to wild boar but at least nine different MC1R
proteins in addition to the wild-type [14], which are associated with coat colour phenotypes ranging from red to black
and including a variety of spotting patterns (white coat
and spotting are determined by a different gene, KIT)
(figure 2). Therefore, it appears that wild boar have been
subject to purifying selection for a camouflaged coat,
whereas a relaxation of this form of natural selection in
combination with human-mediated selection for distinctive
coat patterns has occurred in domestic pigs [14].
(b) Differentiation-based approaches
Changes within breeds have occurred on an evolutionarily short timescale compared with natural animal
populations; however, there is considerable phenotypic
128
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Figure 2. Coat colour variation in pig breeds. Clockwise from top-left: Berkshire, British Saddleback, Gloucestershire Old
Spots, Large Black, Middle White and Tamworth (photos: S. Wilkinson).
variation between domesticated animal breeds, particularly in dogs. Recent studies in various species have
applied an approach where markers with strong evidence
of genetic differentiation (e.g. high levels of Wright’s FST,
a measure of genetic differentiation between populations,
or allele-frequency differences) are taken as signals of
differential selection across populations. This approach
originated in the days when genetic markers were limited
and sparse, and the focus was on specific markers [16,17],
but in the current environment of dense, genome-wide
markers for many species, genome scans of differentiation
have become a viable strategy to identify selected genes or
genomic regions using the tails of the genome-wide FST
distribution to define the significance threshold [18].
For this and other approaches, it has been recognized
that instead of using single-locus statistical values, a sliding window analysis removes the stochastic variation
between loci, and thus better highlights regions with
signals of selection [19,20]. Although the populationdifferentiation approach was developed originally for
analysis of human data (and is still used in this context
[18,21]), this technique is possibly even better suited to
studies of domesticated animals because breeds are in
general genetically similar entities and the differences
that do exist may reflect the relatively recent selection
for breed-specific characteristics.
Akey et al. [22] conducted an FST scan of the genome for
10 dog breeds and identified outliers, which they argued
were candidates for targets of selection. This interpretation
of the results was supported by the fact that five genes that
had previously been mapped through association with
‘hallmark’ breed traits were among the 155 outlier SNPs
(including the insulin-like growth factor 1 gene—IGF1,
associated with body size—and several coat colour
genes). Regarding the other outlier SNPs identified in
their study, one of the highest FST values was only found
in the Shar-Pei breed, which is characterized by its distinctive skin-folding phenotype. The region where the high FST
signal was found contains several genes, including HAS2,
the expression of which had previously been associated
with skin wrinkling in this breed [23]. A recently discovered
duplication upstream of this gene appears to be responsible
for the wrinkling phenotype [24]. A separate study looking
at genetic differentiation between 79 domestic dog breeds
found that the top 11 FST values measured across all
129
breeds were found in genomic regions associated with
morphological traits, including body size, skull and snout
shape, coat characteristics and ear type [25].
For cattle, the genetic-differentiation approach has highlighted genomic regions that include genes encoding coat
features or body size/conformation. Several studies have
identified high levels of between-breed genetic differentiation near coat colour loci, including MC1R (see §2a)
and the Charolais dilution factor (Dc locus), indicating
that these genes have been important in the establishment of cattle breeds [26,27]. Another gene that has
been implicated as a possible target of selection based on
allele-frequency differences between cattle breeds is the
growth hormone receptor (GHR) gene [26–28].
Although it is clear that large qualitative effects have
been detected using these methods, there are known to
be limitations to FST -based methods for detecting genes
with small or moderate effects. Wiener et al. [27] found
the overall correlation between FST and the statistical
signal from linkage mapping analysis (see §2e) to be low
in a study of two cattle breeds. While genes associated
with coat colour could be detected as regions of large
allele-frequency differences, the signals for loci associated
with quantitative traits were generally weaker.
(c) Frequency spectrum-based approaches
A common approach to test for selection in human and
wild plant and animal populations is to use ‘frequency spectrum’ tests in which empirical allele distributions are
compared with those predicted under a neutral model.
One set of methods involves searching the genome for
regions with allele-frequency patterns that differ either
from background (genome-wide) patterns or from those
predicted by a neutral model [29,30]. These methods
involve calculation of a composite log likelihood (CLL)
for sliding window sets of genotypic data and testing significance based on a likelihood ratio test [29,30] or by
permutation testing [31]. This approach has recently
been applied to genome-wide SNP data for the 19 cattle
breeds characterized by the Bovine HapMap Consortium
[32]. In a follow-up analysis of this dataset, Stella et al.
[31] calculated the difference for each SNP between the
major allele frequency for a group of breeds defined by phenotype and the overall frequency across all breeds. For
3164
black-coated breeds, there was a very strong signature of
selection on BTA18 for windows that include the MC1R
coat colour locus (see §2a). A signature of selection was
also observed for polled (hornless) breeds on BTA1
within a region previously associated with presence/absence
of horns. For dairy breeds, 699 putative signatures of selection were identified across the genome, with the highest
(negative) CLL value on BTA6 near the KIT gene, which
is associated with the level of white coat spotting in cattle.
To make sense of the large number of significant results,
the authors looked for cases where genes from the same
gene family were at the centre of the significant window
(e.g. potassium channel genes, integrins and arginine-/
serine-rich splicing factors), arguing that these gene families
may have been under selection during dairy cattle breeding.
Difficulties in applying frequency-spectrum-based tests
to SNP data have been raised because of the bias towards
high-frequency alleles inherent in SNP ascertainment,
and thus interpretation of results can be problematic.
While a number of solutions have been proposed to deal
with this issue [33], in the long term the best remedy will
involve use of full-genome sequence data in place of SNP
data. Developments in next-generation sequencing are
now making this a reality for many species (see §2d).
(d) Extended homozygosity approaches
Another population-genetic approach for the detection of
selective sweeps has been to look for extended homozygous
genomic regions. This approach is based on ‘hitchhiking’ theory [34], in which neutral variants increase in
frequency owing to linkage disequilibrium (LD, the statistical association between allele frequencies at different loci)
with alleles at a selected locus, resulting in reduced diversity
across the region.
One particularly convincing example of reduced diversity near a selected locus relates to chondrodysplasia
(shortened limbs) in dogs. A genome-wide SNP analysis
revealed a 24 kb region of reduced heterozygosity on
chromosome 18 in chondrodysplastic breeds (e.g. Dachshunds) relative to non-chondrodysplastic breeds [35].
This region includes an insertion of a retrogene encoding
fibroblast growth factor 4 (FGF4) in the chondrodysplastic dogs, the expression of which may result in altered
activation of one or more fibroblast growth factor receptors. A similar pattern of reduced heterozygosity near
the IGF1 gene was observed in small dogs [36].
A number of statistical methods aim to distinguish the
length of homozygous segments generated by selection
from those generated by neutral processes, which extends
the analysis beyond the heterozygosity of individual markers. One of the first methods introduced to exploit the
hitch-hiking phenomenon in the context of high-density
genotype data was the long-range haplotype (LRH) test
[37]. In this method, the age of each core haplotype in
a genomic region is assessed using the length of extended
haplotype homozygosity (EHH). Unusually, high EHH
values suggest a mutation that increased more quickly
than expected under a neutral model. In an alternative approach, the logarithm of the ratio of EHH for
an ancestral allele to that for a derived allele (iHS) is
used as the test statistic [38], such that large negative
(positive) values of iHS indicate selection for the derived
(ancestral) allele.
The extended haplotype-based methods have been
applied mainly to human genetic data, but they have also
been implemented for several cattle datasets. Studies by
Hayes et al. [28,39] found high values of iHS for SNPs in
several regions of bovine chromosome 6, including one
region with the ABCG2 gene, associated with several
dairy traits. The Bovine HapMap Consortium [32] also
applied the iHS test across the genomes of 19 breeds and
found high iHS values in one or more breeds on most
chromosomes; these included regions on BTA2 near
GDF-8, on BTA6 near ABCG2, and on BTA14 near a
region associated with intramuscular fat. There were
many other regions where a specific gene could not be
implicated as a selection target. More recently, Qanbari
et al. [40] applied the LRH test to denser (50 K SNP)
data from Holstein dairy cattle. Although there were significant or nearly significant signals of selection for SNPs
associated with some dairy-related candidate genes (e.g.
the casein gene cluster encoding milk proteins and the
DGAT1 gene associated with milk fat percentage), of the
SNPs with greatest significance levels, none were found
near these candidates.
The advent of whole-genome sequencing opens up new
possibilities for the detection of selection signatures. Rubin
et al. [41] sequenced whole genomes of eight pools of
chickens representing commercial lines, experimental
lines and breeds selected for specific traits. The genome
was searched for regions of low diversity by calculating a
normalized pooled heterozygosity measure in sliding windows. One of the lowest statistics (suggestive of positive
selection) was found in the region of the beta-carotene
dioxygenase 2 (BCDO2) gene, which is associated with
skin colour in chickens. One or more regulatory mutations
that inhibit expression of the BCDO2 gene appear to be
responsible for the yellow skin phenotype [42]. Most chickens used for commercial egg and meat production in
industrialized countries (as well as many local breeds
worldwide) have the yellow skin phenotype and are homozygous for the recessive yellow skin allele locus, whereas
other local chicken breeds have white skin and carry the
dominant wild-type allele. The yellow skin allele appears
to have been derived from a different ancestral species
(possibly the grey junglefowl) than most of the commercial
chicken genome (for which the red junglefowl is the
presumed wild ancestor), suggesting a hybrid origin of
commercial chickens (see §3b) [42].
The region with the lowest heterozygosity score across
all domestic lines included the locus-encoding thyroid
stimulating hormone receptor (TSHR) gene [41], which
is involved in metabolic regulation and reproduction.
This region was almost completely fixed over a 40 kb segment. Further analysis of this locus in domestic chickens
from a number of countries revealed that each animal carried at least one copy of the derived haplotype (264/271
were homozygous). The role of TSHR in the domestication
of chickens is still unknown; however, the authors suggest
that it may be involved in the loss of seasonal reproduction
present in non-domesticated relatives.
(e) Genotype – phenotype association analyses
A powerful approach for gene mapping in livestock species
is linkage mapping, in which regions of the genome associated with particular traits (quantitative trait loci, QTL) are
130
identified. Populations generated by breed or line crosses
have proved to be particularly useful for identifying the
regions of the genome that distinguish the population founders. Although this technique generally identifies fairly
wide intervals that include a large number of genes, in
some cases it has led to the identification of individual
genes that influence physical traits related to domestication,
breed development or breed improvement (e.g. IGF2 in
pigs [43], DGAT1 [44] and GHR [45] in cattle).
QTL-encoding physical traits may also be associated
with behavioural traits. One such instance is the PMEL17
gene encoding plumage colour in chickens, which was
identified from a cross between red junglefowl and the commercial White Leghorn. A 9 bp insertion in exon 10 acts in
a dominant fashion, such that birds homozygous for the
ancestral junglefowl allele (i) are black, whereas those carrying the White Leghorn allele (I) are white (heterozygotes
sometimes have minor pigmentation). It has been demonstrated that there are substantial behavioural differences
between birds carrying the junglefowl and White Leghorn
alleles, such that i/i individuals birds are more vocal, have
lower activity levels in a test measuring fear of humans,
and are more aggressive, social and explorative [46–48]
than I/I birds, suggesting either that PMEL17 has pleiotropic effects on behaviour or the existence of a closely
linked behavioural locus [48]. This locus may also be
associated with feather-pecking, a bullying behaviour that
can result in severe damage to the victim [49]. Darker
birds tend to suffer more from feather-pecking compared
with their white counterparts [46,50]. However, it remains
unresolved whether the effect on feather-pecking is due
solely to the plumage colour or whether the behaviour of
i/i birds makes them more likely to be targets of pecking.
The case of PMEL17 is particularly interesting in that it
demonstrates the possibility of selection for correlated traits
in domesticated animals. It is likely that the behavioural
traits associated with PMEL17 were not the target traits
in the development of the White Leghorn breed but may
have been co-selected owing to selection for white plumage.
Association between behavioural traits and coat colour
appears to be a common phenomenon. Genes in the melanocortin system (including MC1R and the agouti gene)
have been associated in mice and other vertebrate species
(e.g. lions, lizards and birds) with both coat colour and
various behavioural traits, including aggressiveness,
sexual behaviour and learning behaviour [51]. Eumelanin-based coloration is generally associated with more
aggressive behaviour. In her treatise on cattle breeds,
Felius [12] claims that the Romans and later Europeans
also associated coat colour with cattle performance traits:
a red coat (the most common phenotype) was associated
with a ‘fiery’ and hard-working character, whereas the
rare white coat was associated with a sluggish and lazy
disposition. However, the genetic association between
behavioural traits and coat colour is not universal, as
demonstrated by a study on rats in which ‘tameness’
QTL (see below) were on different chromosomes from a
QTL segregating for white coat spotting [52].
In some cases, correlated selection appears to go in the
other direction, such that selection for behavioural traits
may result in associated changes in more visible phenotypes, as has been seen in the well-described selection
experiment involving the silver fox (the ‘farm-fox experiment’) [53]. Initiated in 1959 in Novosibirsk, Siberia,
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the original fox population showed continuous variation
for tameness/aggressiveness. A breeding programme was
established with 100 females and 30 males, from which
foxes were selected for their tameness using severe selection criteria [54]. The resulting population of tame foxes
behaved much like domestic dogs. Behavioural traits
other than tameness also evolved (e.g. tail wagging, licking). Moreover, in addition to the changes in behaviour,
other morphological changes also occurred, some of
which are reminiscent of dog breeds. For example, traits
such as floppy ears, curly tails and shortened snouts
appeared in some foxes. Recent development of a linkage
map for the silver fox [55] has allowed QTL analysis of
backcross and intercross populations derived from the
tame population and an unselected (aggressive) population. QTL for several tameness-related behavioural
traits map to fox chromosome 12; however, it is still
unclear whether these are associated with a single locus
[56]. Furthermore, inconsistencies between results from
different crosses suggest a complex inheritance pattern
(e.g. strong epistatic interactions) for these traits.
The study of silver foxes suggests that laboratory selection for behavioural traits can emulate the process of
domestication. Other researchers from Novosibirsk conducted an experiment selecting for reduced or enhanced
aggression to humans in a population of wild-caught
rats [57]. Like the silver fox, this population has recently
been exploited using genetic techniques to map regions of
the genome associated with ‘tameness’ (as referred to
above), defined by a linear combination of a set of behavioural traits [52]. QTL analysis indicates that more than
one region is involved in the evolution of tameness in
these rats [52] and that individual QTL may comprise
multiple sites [58].
Modification of behaviour is believed to have been one
of the key aspects of animal domestication, including
selection for ‘reduced fear, increased sociability and
reduced anti-predator responses’ (p. 5 in [59]). As dog
breeders and owners know well, behaviour is also associated with breed differences. In an investigation of four
composite personality traits (playfulness, curiosity/fearlessness, sociability and aggressiveness) in 31 dog breeds,
Svartberg [60] found large differences between breeds for
all traits. For example, popular pet breeds tended to have
higher sociability and playfulness scores than less popular
breeds.
3. NON-SELECTIVE FORCES
While selection has clearly been an important force in the
history of animal domestication, as with wild species,
other non-selective mechanisms have strongly influenced
evolutionary change in these species. There are various
approaches that allow inferences about demographic
and mating processes using genetic data.
(a) Human-mediated modifications to
population size and structure
One important advance with the advent of dense markers is the ability to exploit the relationship between
LD and effective population size (Ne, the number of individuals in an idealized population that would have the
same rate of genetic drift as the actual population), such
that Ne and r 2 (the correlation between allele frequencies
3166
at two loci) are inversely related [61 – 63]. Hill [63] also
recognized that LD between tightly linked markers
reflects older Ne than the LD between loosely linked markers. Specifically, assuming linear population growth,
LD between loci with recombination rate c reflects
the Ne of 1/2c generations in the past [64]. With
dense genotype data, this relationship can now be exploited to make inferences about population demographic
history [64,65].
Using this approach, the Bovine HapMap Consortium
[32] found that LD declined rapidly with increasing physical distance between markers, but the rate of decline
varied between cattle breeds. Overall LD levels for cattle
were between those seen for humans (generally low) and
dogs. Ne appears to have declined recently for all breeds,
presumably owing to bottlenecks associated with domestication and breed formation. Comparing LD–distance
relationships across breeds can be used to understand the
different breed histories. Three Bos indicus (humped
cattle, originating in the Indian subcontinent) breeds examined had lower LD than the Bos taurus (humpless cattle,
originating in the Middle East) breeds at short distances
and intermediate values at long distances, indicating a relatively large ancestral population compared with the taurine
breeds [32]. This characterization of B. indicus breeds is
consistent with findings of higher nucleotide diversity in
B. indicus than in B. taurus breeds [32,66]. Estimates of
current Ne in several commercial taurine cattle breeds are
very low (150), and the pattern of LD suggests a severe
recent contraction consistent with breed formation and
modern breeding practices such as artificial insemination
[64,67,68].
Population contraction has also featured in the demographic history of dogs, as LD patterns suggest at least
two bottlenecks: one at the time of domestication and
another at the time of breed formation [69,70]. However,
there are known difficulties in getting precise Ne estimates
using LD patterns [71], and studies have therefore differed
in their estimates of the magnitude and timing of the domestication bottleneck. The study of Lindblad-Toh et al. [69]
suggests a substantial domestication-related bottleneck approximately 9000 generations ago, whereas that
of Gray et al. [70] supports a more modest contraction
approximately 5000 generations ago. In any case, the
high level of LD over extended regions within dog breeds
is consistent with a more severe contraction at the time
of breed-creation events [69,70]. Long runs of homozygosity (ROHs) are also common in most dog breeds,
indicating recent inbreeding [25]. There is variation in
levels of LD between breeds of dogs. For example,
Labrador retrievers have relatively low levels of LD (similar
to that of some wolf populations), presumably because of
high Ne [69,70].
A severe contraction in size will also lead to a reduction
in the level of genetic diversity within populations.
Muir et al. [72] used high-density SNP data in chickens
to estimate the proportion of ancestral alleles that are
absent from commercial chickens. In comparing the distribution of alleles from commercial lines with that of
various non-commercial and ancestral breeds, they estimated that at least 50 per cent of the diversity in
ancestral breeds is missing from commercial lines owing
to bottlenecks early in the commercialization process,
continued inbreeding and industry consolidation.
There is clear evidence of declining Ne in commercial
animal breeds, and in some cases this has resulted in extremely low variability. A feral British breed, Chillingham
cattle, was found to be homozygous at 24 out of 25 microsatellite loci [73], which is strikingly low when compared
with other British cattle breeds [74]. The high levels of
homozygosity in the Chillinghams presumably result
from a very severe bottleneck and absence of immigration.
Looking over a longer timescale, ancient B. taurus DNA
has revealed a reduction in diversity at several cattle
genes over the last 4000 years [75]. It is not yet clear
whether this is a genome-wide or loci-specific pattern.
(b) Introgression
Another human-related phenomenon that is manifested
in the architecture of genomes is that of introgression
between breeds. Animal breeders may practice crossbreeding to introduce certain desirable traits for breed
improvement. In the case of pig breeds, past human
activity has influenced the genetic composition of European breeds. In the 18th and 19th centuries, Asian
alleles were introduced into certain British pig breeds to
promote traits such as fattening and earlier maturation
[2]. Breeds that experienced genetic introgression
included Berkshire and Middle White, and Asian morphological characteristics such as the squashed face of
the Middle White are still evident (see figure 2). Molecular studies have since provided genetic evidence of the
introgression from Asia to Europe. A study examining
mitochondrial diversity in pigs revealed that a number
of European commercial pig breeds carry Asian-like
mtDNA haplotypes [76]. The levels of Asian genetic
introgression were highly variable, depending on the
breed and commercial line, with an average of 29 per
cent frequency of Asian mtDNA haplotypes across European breeds. Genetic introgression can also be nonhuman-mediated, such as gene flow from wild relatives
into the domestic pool and vice versa. For example, a
Chinese wild boar genotyped by Fang et al. [14] carried
an MC1R allele common in European domestic pigs,
which must have resulted from gene flow. It is not clear
whether the introgression of grey junglefowl into the
primarily red junglefowl background of commercial
chickens, suggested by the presence of the yellow skin
phenotype [42] (see §2d ), was a human-mediated event.
4. LEVELS OF GENETIC DIVERSITY
One of the most interesting and somewhat surprising findings arising from genetic studies of domesticated animals is
that despite the role of intensive selection, inbreeding and
population bottlenecks, many domesticated animal species
are characterized by a high degree of genetic diversity.
Cattle, particularly B. indicus breeds, have substantial
nucleotide diversity [32], indicating a large ancestral effective population size. There is also evidence from a number
of individual genes that nucleotide variation is relatively
high in domesticated pigs [77], where sustained gene flow
with their wild boar relatives (see §3b) appears to play an
important role [78]. Despite the extensive bottleneck and
associated loss of alleles that accompanied the commercialization of broiler and layer lines [72], domestic chickens
have extensive sequence diversity [79], again presumably
owing to a very large ancestral population which had even
132
greater levels of diversity (as also seen in present-day red
junglefowl [80]). These high levels of genetic diversity contribute to the continuing ability of breeders to select for
production traits. Despite the very low effective population
size of the Holstein, average milk yield has continued to
increase [81]. Similarly, heritability for growth in broiler
chickens has remained at a similar level despite intensive
selection over the last 50 years [82].
Certain livestock breeds with particularly low population size (such as Chillingham cattle, discussed in §3a)
and some purebred dogs appear to be exceptions to this
pattern. Many dog breeds were established with very low
initial sizes, resulting in highly inbred populations and a
high prevalence of inherited diseases (e.g. syringomyelia
in Cavalier King Charles Spaniels and atopic dermatitis
in various breeds [83]), presumably owing to the high frequency of individuals homozygous for recessive alleles.
This is reflected in the low level of nucleotide diversity
seen in the dog, when compared with chickens and cattle
(electronic supplementary material, table S1).
While there are many indicators to show that genetic
variation is being lost in domesticated animals, this
appears to be operating within an overall context of high
levels of diversity in most cases, and therefore can be
counteracted by informed breeding decisions. This is
not to suggest that conservation and breed management
is not required, but rather that animal breeding has not
yet reached a point of no return.
5. CONCLUSIONS
(a) Preliminary insights from genomic analyses
Although identification of the genes important in animal
domestication and breed development is still in its early
stages, some common themes have emerged. One is that
there are clearly strong signatures of selection near a
number of genes associated with coat colour and pattern
(e.g. MC1R, KIT). This should not be surprising in that
these visible phenotypes provide a clear-cut mechanism
for farmers and breeders to distinguish their animals
from others, and in some cases have served a cultural
role. Coat colour and pattern remain important features
of breeds and are still under selection. For example,
Red Angus cattle breeders have formed separate breed
societies from Black Angus in a number of countries in
part because the red coat (an MC1R variant) is thought
to be more heat- and sun-tolerant than black.
There are also genomic indicators that suggest selection
on genes related to growth and body composition. There is
clear evidence in several cattle breeds for selection on the
myostatin gene, associated with muscle composition, and
several studies also suggest that there may have been selection on the GHR gene, associated with growth rate and
various production traits. In dogs, there is also evidence of
strong selection on a number of genes associated with
growth (e.g. IGF1) and skeletal traits, many of which are
related to breed-specific characteristics. The genomic picture
of selection for dairy-related traits is somewhat cloudier than
that seen for other cattle production characteristics. There
is some indication of selection signals near the ABCG2
and DGAT1 genes, which have been associated with milkproduction traits, but this is not consistent across studies.
Although these studies have indicated several genes
that appear to have been under selection and have
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highlighted demographic events, they also suggest difficulties in fully characterizing the history of animal
domestication using genetic data because of the concurrent action of multiple factors. Both selective and
non-selective forces have clearly played key roles in the
history of most domesticated species, and it may be difficult to separate these factors. For example, extended
homozygosity and increased LD can derive from population contraction and/or inbreeding as well as strong
selection, leading to problems distinguishing between
these causes [84].
(b) Directions for further study
Improvement and further development of statistical
methods for identification of selection signals is an active
area of investigation. In addition to the need for better
ways of distinguishing between demographic and selection
processes, new approaches may be required to adequately
investigate the role of selection on quantitative traits such
as milk yield. Low power to detect selection on quantitative
traits [27] may help to explain the inconsistent picture of
selection signals seen in dairy cattle.
Another important area of further research is the identification of the genes that have been selected for their impact
on tameness and other domestication-related behavioural
traits. While progress is currently being made in this direction, the study of the genetic basis of these traits is still in its
infancy. Long-term experimental selection for tameness in
the silver fox has provided valuable insight into the domestication process and promises to provide even greater
understanding once genomic techniques are applied to
this population. The loci underlying the rat and the fox
tameness QTL do not map to orthologous regions [56],
and thus these studies have already demonstrated that
there are multiple genetic routes to evolving tameness.
As demonstrated by the silver fox and tame rat studies,
experimental populations may provide great insight into
the process of domestication. There have been several
recent studies examining genetic changes over the
course of experimental selection on Drosophila [85] and
chicken [86] lines. More extensive analysis of this type
of data, especially when genetic material is collected
from different stages of the experiment, may allow inference of the processes of domestication that cannot be
measured directly. A complementary and more direct
approach involves the analysis of ancient genetic material
from different historical periods. As techniques for working with these samples improve, they will increasingly
provide insights into the genetic changes that have
accompanied the domestication process [87].
The Roslin Institute is supported by a core strategic grant
from the UK Biotechnology and Biological Sciences
Research Council (BBSRC). S. Wilkinson is funded by a
CASE studentship from the BBSRC and Rare Breeds
Survival Trust.
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136
Both Ends of the Leash — The Human Links to Good Dogs with Bad Genes
Elaine A. Ostrander, Ph.D., National Human Genome Research Institute, National Institutes of
Health, Bethesda, MD
N Engl J Med. 2012 August 16; 367(7): 636–646. doi: 10.1056/NEJMra1204453
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3508784/pdf/nihms421280.pdf (See
Lecture notes for Dr. Ostrander’s lecture.)
also
in
Abstract.
For nearly 350 years, veterinary medicine and human medicine have been separate entities, with
one geared toward the diagnosis and treatment in animals and the other toward parallel goals in
the owners. However, that model no longer fits, since research on diseases of humans and
companion animals has coalesced.1–4 The catalyst for this union has been the completion of the
human genome sequence, coupled with draft sequence assemblies of genomes for companion
animals.5,6 Here, we summarize the critical events in canine genetics and genomics that have led
to this development, review major applications in canine health that will be of interest to human
caregivers, and discuss expectations for the future.
137
doi: 10.1111/age.12008
Variation of cats under domestication: genetic assignment of
domestic cats to breeds and worldwide random-bred populations
J. D. Kurushima, M. J. Lipinski, B. Gandolfi, L. Froenicke, J. C. Grahn, R. A. Grahn and L. A. Lyons
Department of Health & Reproduction, School of Veterinary Medicine, University of California – Davis, Davis, CA, 95616, USA.
Summary
Both cat breeders and the lay public have interests in the origins of their pets, not only in
the genetic identity of the purebred individuals, but also in the historical origins of common
household cats. The cat fancy is a relatively new institution with over 85% of its 40–50
breeds arising only in the past 75 years, primarily through selection on single-gene
aesthetic traits. The short, yet intense cat breed history poses a significant challenge to the
development of a genetic marker–based breed identification strategy. Using different breed
assignment strategies and methods, 477 cats representing 29 fancy breeds were analysed
with 38 short tandem repeats, 148 intergenic and five phenotypic single nucleotide
polymorphisms. Results suggest the frequentist method of Paetkau (single nucleotide
polymorphisms = 0.78, short tandem repeats = 0.88) surpasses the Bayesian method of
Rannala and Mountain (single nucleotide polymorphisms = 0.56, short tandem
repeats = 0.83) for accurate assignment of individuals to the correct breed. Additionally,
a post-assignment verification step with the five phenotypic single nucleotide polymorphisms accurately identified between 0.31 and 0.58 of the misassigned individuals raising
the sensitivity of assignment with the frequentist method to 0.89 and 0.92 for single
nucleotide polymorphisms and short tandem repeats respectively. This study provides a
novel multistep assignment strategy and suggests that, despite their short breed history and
breed family groupings, a majority of cats can be assigned to their proper breed or
population of origin, that is, race.
Keywords assignment testing, Felis catus, lineage, microsatellite, race, single nucleotide
polymorphisms, short tandem repeat
Introduction
Over the past 140 years, a plethora of pedigreed cat
varieties has developed due to mankind’s imposed artificial
selection on the process of cat domestication. Since the first
cat show in London in 1871, which showcased only five
breeds, the development of pedigreed cats has increased in
popularity (Penny Illustrated Paper 1871). In the USA, the
Cat Fanciers’ Association (CFA, http://www.cfa.org/) currently recognises 41 breeds for competition, and The
International Cat Association (TICA, http://www.tica.org/)
accepts 57 breeds. A majority of the breeds acknowledged
by these two large registries are also typical breeds around
the world; however, each breed registry has specific
Address for correspondence
L. A. Lyons, Department of Health & Reproduction, School of
Veterinary Medicine, 4206 VetMed 3A, University of California –
Davis, Davis, CA 95616, USA.
E-mail: lalyons@ucdavis.edu
Accepted for publication 23 August 2012
nuances for breed standards and breeding practices. Furthermore, cat breed standards are defined by phenotypic
characteristics. Many of these phenotypes, such as hair
length, coat patterning and colours, are single-gene traits
found at low to moderate levels in the general nonpedigreed cat population. Several commercial laboratories
are marketing genetic tests to elucidate the breed ancestry
of dogs, ‘your best friend’ (Wisdom Panel, http://www.
wisdompanel.com/; Canine Heritage Breed Test, http://
www.canineheritage.com/), prompting cat owners to
wonder about the ancestral origins of their own feline
companions.
Because random-bred house cats have a different history
compared to dogs, genetic testing for breed and population
assignments requires a slightly different approach. Whereas
the average canine found in the streets of most developed
countries is more likely a cross-bred individual from
multiple purebred lines, the average random-bred cat is
not a descendant of its pedigreed counterparts. For cats, the
opposite scenario is more likely – pedigreed feline stocks are
the descendants of common street cats from discrete parts of
© 2012 The Authors, Animal Genetics © 2012 Stichting International Foundation for Animal Genetics, 44, 311–324
138
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Kurushima et al.
the world that have been selected for one or more distinct
traits (Table 1). Random-bred cats are the original populations from which the breeds developed, not a population of
pedigreed cats gone feral. Also, converse to most dog
registries, to improve population health and reduce the
effects of inbreeding depression, cat breeding associations
often seek to diversify their breed populations with randombred cats from the breed’s presumed ancestral origin. For
this reason, most cat registries use the term ‘pedigreed’ and
not ‘purebred’.
Two studies have evaluated the genetic distinction of cat
breeds. Lipinski et al. (2008) defined the connections
between the random-bred cat populations and their
descendant pedigreed lines using a DNA marker panel
containing two tetranucleotide and 36 dinucleotide
microsatellites [a.k.a. short tandem repeat (STR)] markers.
Five hundred fifty-five individuals were demarcated into 20
breeds. Four breeds remained unresolved as the selected
markers lacked sufficient power for demarcation, suggesting the grouping of same cat breeds into breed families.
Table 1 Traditional cat breed origins.
Breed
Abyssinian
American Bobtail1
American Curl1
American Shorthair
American Wirehair
Australian Mist
Birman
British Shorthair
Burmese
Chartreux
Cornish Rex
Devon Rex1
Egyptian Mau
European Shorthair
Japanese Bobtail
Korat
LaPerm1
Maine Coon
Manx1
Munchkin1
Norwegian Forest
Ocicat
Ojos Azules
Persian
Ragdoll
Russian Blue
Scottish Fold1
Selkirk Rex1
Siamese
Siberian
Sokoke
Sphynx
Tonkinese1
Turkish Angora
Turkish Van
Fixed or hallmark1
phenotype2
Shorthair, ticked, agouti
Bobtail
Rostral curl to pinnea
Wired hair
Siamese points, gloves,
longhair
Non-agouti, Burmese
points
Dilute, non-agouti
Curly coat
Curly coat
Shorthair
Bobtail
Dilute, non-agouti
Curly coat
Longhair
No tail
Short legs
Longhair
Spots
Blue eyes
Longhair
Longhair
Dilute, non-agouti
Ventral fold to pinnea
Curly coat
Siamese Points, Shorthair,
Non-agouti
Longhair
Hairless
Shorthair, heterozygous Burmese
and Siamese points
Longhair
Longhair
Origin
Date of
establishment
India, Africa
Mutation-USA
Mutation-USA
USA
Mutation-USA
Mix-Australia
Burma
England
Burma
1868
1960
1981
1966
1966
1990s
<1868
1870s
1350–1767
France
Mutation-UK
Mutation-UK
Egypt
Europe
Japan
Thailand
Mutation-USA
USA
Isle of Man
USA
Norway
Crossbred
Mutation-USA
Persia
XIV century
1950
1960
1953
USA
Russia
Mutation
Mutation-USA
Thailand
1960s
<1868
1961
1980s
1350–1767
Russia
Africa
Canada
Crossbred
<1868
Ankara, Turkey
Van Lake, Turkey
XV century
<1868
VI–XII century
1350–1767
1986
1860s
<1868
1990s
<1868
1964
1980s
<1868
1960s
1950s
Derived breeds
Somali3
Several breeds
Snowshoe3
Asian, Bombay, Tiffanie3,
Malayan, Burmilla
Sphynx (1966)
Cymric3
Siamese 9 Abyssinian
Exotic3, Kashmir, Himalayan,
Peke-faced, Burmilla
Ragamuffin
Nebelung3
Highland Fold3 (Coupari)
Colorpoint3, Javanese3,
Balinese3, Oriental3
Havana Brown, Don
Sphynx, Peterbald
Devon Rex
Siamese 9 Burmese
Origins are according to: Gebhardt (1991), The Royal Canin Encyclopedia (2000), TICA (http://tica.org/) and Australian Mist Breed Council (http://
www.australianmist.info/Home.html).
1
Some breeds allow variants that do not have the hallmark trait, such as straight-eared American Curls or straight-coated Selkirk Rex. The Tonkinese
has colour variants that produce Siamese and Burmese colorations. These variants are available for breeding but not for competition.
2
Many breeds have limited colorations and patterns that vary between registries. Only the most definitive colourations and patterns across most
registries are presented.
3
Many derived breeds are long- or shorthaired varieties of the foundation breed but have different breed names; others are delineated by longhair or
shorthair in the breed name. Several additional rex-coated cat populations have not developed into viable populations or are extinct.
139
Variation of cats under domestication
Furthermore, the breeds sampled by Lipinski et al. were
shown to be similar to the populations of street cats found
in Europe, the Eastern Mediterranean and Southeast Asia.
Menotti-Raymond et al. (2008) used a panel of 11
tetranucleotide STR markers to characterise the delineation of cat breeds. Using only the STR markers, 1040
individuals were demarcated into eight individual breeds
and nine additional breed groups. Twenty breeds could not
be resolved at the breed level. These studies indicate that
distinct populations and breeds of cats can be defined
genetically, that breeds do have different worldwide
origins, tetranucleotide STRs do not perform as well as
dinucleotide markers defining cat breeds, and some breeds
are so closely related that they cannot be distinguished
with even the rapidly evolving dinucleotide STRs.
The 38 highly polymorphic markers of Lipinski et al.
(2008) and a recently developed panel of 148 intergenic
autosomal single nucleotide polymorphisms (SNPs) were
recently applied to an extensive sample of random-bred
street cats collected throughout the world (Kurushima
2011). Nine hundred forty-four samples were collected
from 37 locations spread throughout North and South
America, Europe, Africa and Asia. The study found both
marker sets to be efficient at distinguishing five longestablished races; however, a few geographically close
populations were better delineated with either SNPs or
STRs, most likely due to varying mutation rates between
the markers.
Many methods of assignment testing have been developed using a variety of both genetic markers and statistical
methods (Paetkau et al. 1995; Rannala & Mountain 1997;
Pritchard et al. 2000; Baudouin & Lebrun 2001). These
techniques have been applied to various breeding populations including pigs, cattle and dogs (Schelling et al. 2005;
Negrini et al. 2009; Boitard et al. 2010). In cattle, Negrini
et al. (2009) used 90 SNPs to both allocate and then
assign 24 breeds under both the Bayesian methods of
Pritchard et al. (2000), Rannala & Mountain (1997) and
Baudouin & Lebrun (2001), and the likelihood method of
Paetkau et al. (1995). Negrini et al. (2009) concluded that
the Bayesian and frequentist methods, implemented
respectively through Rannala & Mountain (1997; Bayesian) and Paetkau et al. (1995; frequentist), worked best
when attempting to assign unknown individuals to a
known database of representative samples from each
breed.
This article assesses the ability of a panel of 148 evenly
dispersed genome-wide SNPs for population assignment of
domestic cats. Different assignment techniques are examined in a species exhibiting many recent and extreme
population bottlenecks in addition to large numbers of
population migrants, also comparing the power and
efficiency of this 148 SNP panel to fourfold fewer STRs.
The strength of phenotypic DNA variants is tested for
sensitivity and specificity to support individual assignment,
in particular for closely related cat breeds that are demarcated by these single-gene traits.
Sample collection and genotyping
Twenty-nine breeds were represented by 477 cats. This
study included 354 cats from the work of Lipinski et al.
(2008) that analysed 22 breeds. The 123 newly collected
samples represented seven additional breeds, including
Scottish Fold, Cornish Rex, Ragdoll, Manx, Bengal, Ocicat
and Australian Mist. All cats were representatives of their
breed as found within the USA, except for the Australian
Mist Cats and a few Turkish Angora and Turkish Van
samples from international submissions. Additionally, all
cats were pedigreed and verified to be unrelated to the
grandparent level. Worldwide random-bred data (n = 944)
were included from the previous study of Kurushima (2011)
to assess the origins of each of the breed populations. New
samples were collected via a buccal (cheek) swab and
extracted using the Qiagen DNeasy Blood and Tissue kit
following the manufacturer’s protocol.
Thirty-eight STRs were genotyped in the 123 newly
acquired cats following the PCR and analysis procedures of
Lipinski et al. (2008). Unlinked non-coding autosomal SNPs
(n = 169) were selected to evenly represent all autosomes
from the 1.99 coverage cat genomic sequence, which was
defined by one Abyssinian cat as resequencing data were
not available at the time of selection (Pontius et al. 2007).
Primers were designed with the VeraCode Assay Designer
software (Illumina, Inc.). Only SNPs that received a design
score of 0.75 or higher (with a mean design score of 0.95)
(n = 162) were included in the analysis (Table S1). Five
additional phenotypic SNPs were also evaluated in all cats.
The phenotypic SNPs consisted of a causative mutation for
the most common form of longhair in cats [AANG0202725
0.1(FGF5):g.18442A>C] (Kehler et al. 2007), Burmese and
Siamese colour points [AANG02171092.1(TYR):g.11026G
>T and AANG02171093.1(TYR):g.1802G>A respectively]
(Lyons et al. 2005b) and the mutations for the colour
variants chocolate and cinnamon [AY804234S6(TYRP1):
g.593G>A and AANG02185848.1(TYRP1):g.10736C>T
respectively] (Lyons et al. 2005a).
Golden Gate Assay amplification and BeadXpress reads
were performed per the manufacturer’s protocol (Illumina,
Inc.) on 50–500 ng of DNA or whole-genome amplified
product. BEADSTUDIO software v. 3.1.3.0 with the Genotyping
module v. 3.2.23 (Illumina, Inc.) was used to analyse the
data. Samples with a call rate <0.80 (n = 21) were removed
from further clustering analysis. Additionally, only SNPs
with a GenTrain Score >0.55 (n = 148) were included in the
analysis (Table S1). Each run of the SNP assay contained
both an internal positive and negative control to validate
repeatability and detect contamination.
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Kurushima et al.
Population statistics
Hardy–Weinberg equilibrium (HWE) with associated chisquared tests, as well as observed and expected heterozygosity, was calculated by breed with GENALEX v.6.3 (Peakall &
Smouse 2006). Inbreeding coefficients (FIS) within each
breed and between-population variation values (FST) were
calculated with FSTAT v. 2.9.3.2 (Goudet 1995). Because of
the predicted recent separation (co-ancestry) and small
population sizes of the breeds under consideration, Reynold’s genetic distance was calculated between all pairs of
breeds with the SNP data set (Reynolds et al. 1983). Nei’s
genetic distance was used with the STR data set to
accommodate the rapid mutation rate characteristic of
STRs (Nei 1972). Both distances were implemented through
the software package PHYLIP v. 3.69 (Felsenstein 1989).
Population structuring
Bayesian clustering
Data sets were analysed with the Bayesian clustering
program STRUCTURE v.2.3.1 (Pritchard et al. 2000) under
the admixture model with correlated allele frequencies and
a burn in of 100 000 with 100 000 additional iterations.
Values of Q were calculated from K = 1 to K = 33; each run
was replicated 10 times. Posterior log-likelihoods were used
to calculate ΔK to best estimate the number of ancestral
populations through the program HARVESTER v.0.56.4
(Evanno et al. 2005). All 10 iterations were then combined
through the program CLUMPP v.1.1.2 (Jakobsson & Rosenberg 2007) to create a consensus clustering. To assess the
effects of varying marker types on the final results, analysis
using STRUCTURE was conducted with the two different data
sets, SNPs and STRs.
(Piry et al. 2004). Breeds were assigned to the race that
produced the highest log(likelihood) value.
Assignment testing
Ten sets of 50 individuals were selected randomly from the
sample set and assigned to a population of origin using the
remaining samples as the reference populations using
GENECLASS2 v.2.0.h (Piry et al. 2004). The Bayesian method
of Rannala & Mountain (1997) and the frequentist method
suggested by Paetkau et al. (1995) were compared, as these
methods performed best in the previous assignment study of
Negrini et al. (2009) when compared to the Pritchard et al.
(2000) and the Audoulin & Lebrun methods (2001).
Average probabilities were computed using the Paetkau
et al. (2004) Monte Carlo resampling method through a
simulation of 1000 individuals and a type I error rate (a) of
0.01. Additionally, the assignment tests were performed in
three iterations: intergenic SNPs, intergenic and phenotypic
SNPs combined and STRs. Tallies of type I error (an
individual not reassigned to its population of origin) and
type II error (an individual assigned to the wrong population) were used to calculate the sensitivity and specificity of
the assignment method (Negrini et al. 2009).
The differences of the STR and SNP assignments also
were compared, post-assignment, with and without the use
of phenotypic SNPs. Cats were considered misassigned if
they had genotypes exclusionary for the breed, for example,
an individual assigned to the Exotic Shorthair breed was
identified as misassigned if it was homozygous for longhair,
a recessive trait in cats not found in that breed (see Table 1
for phenotypic diagnostic to breeds).
Results
Principal coordinate analysis
Summary statistics
Principal coordinate analyses were conducted on the
Reynold’s (SNPs) and Nei’s (STRs) genetic distance matrices
using the software GENALEX v.6.3 (Peakall & Smouse 2006).
For the PCA plots, both the data in the present manuscript
and data from the worldwide random-bred populations
(Kurushima 2011) were considered to show the relationship of the cat breeds and their random-bred population
origins.
Pedigreed cats (n = 477), representing 29 recognised
breeds, were included in this study (Table 2). Analysis of
all cats from the previous Lipinski et al. (2007) study was
attempted; however, DNA quality and quantity caused
some sample loss, as did available SNP analysis resources.
The number of cats per breed ranged from 7 to 25 with an
average of 16.4 individuals per breed. STRs had an average
call rate of 88.2%, and SNPs had a 94.0% average call rate.
Although the chi-squared goodness-of-fit test indicated that
126 of the 148 SNPs and 36 of the 38 STRs were not in
HWE in at least one breed group, only one SNP marker
(AANG02147808.1:g.9376T>C) was not in HWE in more
than 50% of the breeds (Table S2). Twenty-seven breeds
have 10–25 loci not in HWE; however, the Russian Blue
and Turkish Van breeds have 31 and 33 of the 186 genetic
markers not in HWE respectively. The frequency of the
genotypes and alleles for the phenotypic SNPs are indicated
in Table 3. The FGF5 mutation AANG02027250.1:
Breed race assignment
Cat breed populations were assigned to the eight ancestral
races of random-bred worldwide populations of cats
(Europe, Mediterranean, Egypt, Iraq/Iran, Arabian Sea,
India, Southeast Asia and East Asia) identified in the
previous study by Kurushima (2011) by calculating log
(likelihood) values using the Bayesian population assignment methods available in the software GENECLASS2 v.2.0.h
141
Table 2 Population statistics of cat breeds.
Breed
n
Total
Alleles(SNP)
Total
Alleles(STR)
Abyssinian
American SH
Australian Mist
Bengal
Birman
British SH
Burmese
Chartreux
Cornish Rex
Egyptian Mau
Exotic SH
Havana Brown
Japanese Bobtail
Korat
Maine Coon
Manx
Norwegian Forest
Ocicat
Persian
Ragdoll
Russian Blue
Scottish Fold
Siamese
Siberian
Singapura
Sokoke
Sphynx
Turkish Angora
Turkish Van
Total
15
13
15
18
20
18
19
13
15
14
19
14
19
25
19
17
16
10
15
15
17
17
15
17
17
7
17
21
20
477
277
269
273
274
247
276
262
264
262
268
279
245
267
246
282
282
284
264
276
265
259
269
242
275
232
222
277
284
277
296
130
168
156
192
133
192
158
151
163
160
178
113
191
150
210
233
248
142
181
178
146
180
133
227
94
92
178
275
259
490
PAB(STR)
PAW(STR)
Na(SNP)
Na(STR)
Ho(SNP)
Ho(STR)
1
0
4
10
3
2
2
0
2
1
1
1
4
2
2
6
8
3
1
4
2
2
2
4
1
0
2
10
6
1
0
0
2
0
0
1
0
0
0
1
0
0
0
1
2
0
2
0
0
1
1
1
2
0
0
0
1
0
1.87
1.82
1.85
1.85
1.67
1.87
1.77
1.78
1.77
1.81
1.89
1.66
1.80
1.66
1.91
1.91
1.92
1.78
1.87
1.79
1.75
1.82
1.64
1.86
1.57
1.50
1.87
1.92
1.87
1.79
3.42
4.42
4.11
5.05
3.50
5.05
4.16
3.97
4.29
4.21
4.68
2.97
5.03
3.95
5.53
6.13
6.45
3.74
4.76
4.68
3.84
4.74
3.50
5.97
2.47
2.42
4.68
7.24
6.82
4.54
0.29
0.28
0.27
0.24
0.17
0.24
0.20
0.24
0.24
0.25
0.25
0.17
0.22
0.17
0.26
0.30
0.28
0.24
0.29
0.29
0.19
0.26
0.20
0.26
0.18
0.17
0.27
0.25
0.24
0.24
0.42
0.55
0.57
0.58
0.44
0.55
0.42
0.56
0.56
0.50
0.53
0.42
0.58
0.52
0.60
0.70
0.67
0.50
0.50
0.62
0.45
0.57
0.47
0.71
0.34
0.37
0.55
0.67
0.60
0.53
FIS
(SNP)
0.02
0.02
0.01
0.07
0.13
0.10
0.08
0.10
0.05
0.03
0.07
0.12
0.15
0.08
0.11
0.00
0.06
0.04
0.02
0.06
0.16
0.00
0.00
0.09
0.06
0.00
0.05
0.11
0.12
0.06
FIS
(STR)
0.11
0.04
0.05
0.03
0.03
0.06
0.16
0.04
0.03
0.11
0.07
0.02
0.08
0.03
0.04
0.02
0.02
0.05
0.15
0.00
0.06
0.05
0.02
0.06
0.02
0.00
0.05
0.06
0.12
0.04
n, number of samples; PAB, private alleles within breeds; PAW, private alleles within breeds and worldwide random-bred populations; Na, average
effective number of alleles; Ho, observed heterozygosity; SNPs, single nucleotide polymorphisms; STRs, short tandem repeats; FIS, inbreeding
coefficient. SNP statistics were calculated using intergenic SNPs only.
g.18442A>C causing longhaired cats in the homozygous
state was by far the most prevalent of the phenotypic SNPs,
which was found in all but eight of the breeds. In contrast,
coat colour cinnamon, caused by AANG02185848.1
(TYRP1):g.10736C>T, was observed in only five breeds,
two breeds having a frequency lower than 0.1.
Genetic diversity
The population’s genetic data are presented in Table 2.
Effective SNP alleles ranged from 1.50 to 1.92 with an across
breed average of 1.79. The average effective number of STR
alleles observed was 4.54 across breeds, ranging from 2.42 to
7.23. Private STR alleles within breeds ranged from 0 to 10.
However, when compared to worldwide random-bred populations, private alleles within breeds dropped to between 0
and 2 per breed (Table 2). No SNPs had private alleles in a
breed, although breeds had anywhere from 12 to 74 SNP
alleles fixed within their population (Turkish Angora and
Sokoke respectively), and the minor allele frequency averaged across all loci ranged from 0.22 in Bengal to 0.32 in
Abyssinian with a mean of 0.25 (data not shown).
The average SNP-based observed heterozygosity was
0.24, ranging from 0.17 to 0.30, whereas the average
STR-based observed heterozygosity was 0.53, ranging from
0.34 to 0.71 (Table 2, Fig. S1). FIS were lowest in the
Ragdoll ( 0.06) and Siberian ( 0.06) with SNPs and STRs
respectively and highest within the Australian Mist Cats
(0.16) and Burmese (0.16). Between-population variation
FST values were 0.24 ± 0.01 with SNPs and 0.27 ± 0.02
with STRs (data not shown).
Breed clustering
The most likely value of K, the number of structured
groupings, could not be decisively determined. A significant
difference between the log-likelihoods was not evident for
either marker type between K = 17–33 (Fig. S2); however, a
plateau was suggested near K = 21 for STRs and near
K = 17 for SNPs; the STRUCTURE plots are presented in Fig. 1.
As a result, a combination of the ΔK plots and common
sense directed selection of the most likely number of
populations. For STRs, at K > 24 (Fig. S3a), different
lineages (breed lines) within specific breeds, such as
142
315
143
15
13
13
16
19
18
19
10
15
12
17
11
14
23
14
15
13
8
15
15
15
16
15
14
16
6
16
20
18
Abyssinian
American SH
Australian Mist
Bengal
Birman
British SH
Burmese
Chartreux
Cornish Rex
Egyptian Mau
Exotic SH
Havana Brown
Japanese Bobtail
Korat
Maine Coon
Manx
Norwegian Forest
Ocicat
Persian
Ragdoll
Russian Blue
Scottish Fold
Siamese
Siberian
Singapura
Sokoke
Sphynx
Turkish Angora
Turkish Van
15
10
11
15
0
16
19
5
14
12
5
11
8
22
0
8
8
8
0
4
14
13
15
1
16
6
9
0
0
AA
0
2
2
1
0
2
0
5
1
0
10
0
2
1
0
6
3
0
1
3
0
3
0
3
0
0
1
0
0
AC
0
1
0
0
19
0
0
0
0
0
2
0
4
0
14
1
2
0
14
8
1
0
0
10
0
0
6
20
18
CC
0
0.15
0.08
0.03
1.00
0.06
0
0.25
0.03
0
0.41
0
0.36
0.02
1.00
0.27
0.27
0
0.97
0.63
0.07
0.09
0
0.82
0
0
0.41
1.00
1.00
Freq. C
15
13
15
18
20
18
19
13
15
14
19
14
18
25
18
17
16
10
15
15
17
17
15
16
15
7
16
21
19
n
1
15
11
2
16
20
18
0
13
15
14
19
14
18
25
18
17
16
10
15
15
16
17
15
16
0
7
6
21
19
GG
TYR 715G>T
0
2
0
2
0
0
1
0
0
0
0
0
0
0
0
0
0
0
0
0
1
0
0
0
0
0
6
0
0
GT
Burmese Points
0
0
13
0
0
0
18
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
15
0
4
0
0
TT
0
0.08
0.87
0.06
0
0
0.97
0
0
0
0
0
0
0
0
0
0
0
0
0
0.03
0
0
0
1.00
0
0.44
0
0
Freq. T
15
13
12
14
16
17
16
11
14
12
17
12
15
21
17
16
15
9
15
15
15
15
13
15
14
4
12
20
20
n
1
15
13
10
9
0
13
16
11
3
12
14
10
13
20
17
16
15
9
5
0
11
14
0
8
14
3
9
17
19
GG
0
0
1
4
0
0
0
0
4
0
2
1
2
1
0
0
0
0
4
0
3
1
0
6
0
0
1
1
1
GA
TYR 940G>A
Siamese Points
0
0
1
1
16
4
0
0
1
0
1
1
0
0
0
0
0
0
6
15
1
0
13
1
0
1
2
2
0
AA
0
0
0.13
0.21
1.00
0.24
0
0
0.21
0
0.12
0.13
0.07
0.02
0
0
0
0
0.53
1.00
0.17
0.03
1.00
0.27
0
0.25
0.21
0.13
0.03
Freq. A
15
13
15
18
20
18
19
13
14
14
19
14
19
25
19
17
16
10
15
15
17
17
15
17
17
6
17
20
19
N
1
12
12
6
16
12
11
9
13
13
14
15
0
19
1
16
16
15
4
12
13
17
13
2
16
17
5
8
15
14
GG
3
0
6
2
5
2
4
0
1
0
3
1
0
2
2
1
0
1
2
2
0
4
6
1
0
1
5
5
2
GA
0
1
3
0
3
5
6
0
0
0
1
13
0
22
1
0
1
5
1
0
0
0
7
0
0
0
4
0
3
AA
TYRP1 1373 + 5G>A
Chocolate
All individuals were attempted for all phenotypic single nucleotide polymorphisms (SNPs); differing sample sizes are due to assay dropout.
1
n*
Breed
FGF5 475A>C
Longhair
Table 3 Phenotypic SNP frequencies
0.10
0.08
0.40
0.06
0.28
0.33
0.42
0
0.04
0
0.13
0.96
0
0.92
0.11
0.03
0.06
0.55
0.13
0.07
0
0.12
0.67
0.03
0
0.08
0.38
0.13
0.21
Freq. A
15
13
15
17
20
18
19
13
15
14
19
14
19
25
19
17
16
10
15
15
17
17
15
17
17
7
17
21
20
n1
4
13
7
17
20
15
18
13
15
14
19
14
19
25
19
17
16
6
15
15
17
17
15
17
17
7
17
21
20
CC
6
0
7
0
0
3
0
0
0
0
0
0
0
0
0
0
0
3
0
0
0
0
0
0
0
0
0
0
0
CT
TYRP1 298C>T
Cinnamon
5
0
1
0
0
0
1
0
0
0
0
0
0
0
0
0
0
1
0
0
0
0
0
0
0
0
0
0
0
TT
0.53
0
0.30
0
0
0.08
0.05
0
0
0
0
0
0
0
0
0
0
0.25
0
0
0
0
0
0
0
0
0
0
0
Freq. T
316
Kurushima et al.
Figure 1 Bayesian clustering of cat breeds. Clustering of breeds at K = 17 and K = 21 as calculated with single nucleotide polymorphisms (SNPs)
and short tandem repeats (STRs) respectively. Each column represents an individual cat. The y-axis represents Q or the proportional estimate
of genetic membership to the given cluster (K). Each K cluster is indicated by a unique colour.
Norwegian Forest Cat and Turkish Angora, became apparent before five other breed groups would delineate: Persian/
Exotic SH, British SH/Scottish Fold, Australian Mist/Burmese, Birman/Korat and Siamese/Havana Brown. Similar
results were found for the SNP-based analyses; however, the
associations of the Asian-based breeds varied (Fig. S3b).
SNPs appear to resolve the Birman and Singapura breeds
from the other Asian breeds more readily. Considering both
SNPs and STRs, Persians appear to have influenced several
breeds: Exotic Shorthair, Scottish Fold, British Shorthair
and, to a lesser extent, Chartreux (Fig. 1). Within breeds of
Asian heritage, Siamese have a strong influence on the
Havana Brown, Korat and, to a lesser extent, Birman and
Singapura (Fig. 1).
The principal coordinate analyses indicated the relationship of the breeds and their likely closest random-bred
origins, that is, race (Fig. 2). The breeds that originated
solely from European and American random-bred cats
clustered with the random-bred populations of Europe and
America. Likewise, breeds with Asian descent grouped with
South Asian populations of random-bred cats. The breeds
that do not share similar coordinates with a random-bred
population, such as Russian Blue, Ocicat, Singapura,
Australian Mist and Birman, have a strong influence from
both Europe and Asia.
Using Bayesian clustering, the breeds were then assigned
back to the eight random-bred races of Kurushima (2011)
(Table S3a,b). Four regional areas seem to have contributed
to the development of the considered cat breeds. Asian
breeds, such as Birman, Burmese and Siamese, grouped
with Southern Asian cats; Western breeds, such as Persian,
Norwegian Forest Cat and Maine Coon, grouped with the
Western European random-bred cats; Turkish Angora and
Turkish Van assigned to the Eastern Mediterranean cats
and the Sokoke to the India/Arabian Sea region. Three
breeds showed regional variation depending on the marker
type used for assignment. When analysed with data from
SNPs and STRs, the Turkish Angora was assigned to Europe
or to the Eastern Mediterranean, Bengal was assigned to
Europe or to the Arabian Sea, and Ocicat was assigned to
South Asia or Europe.
Assignment testing
The accuracy of assignment testing varied depending upon
not only the assignment method but also the marker type
used to differentiate the cat breeds. For example, when
comparing the Bayesian method of Rannala & Mountain
(1997) versus the frequentist method of Paetkau et al.
(1995), the average sensitivity of assignment for the 148
non-phenotypic SNPs was 0.56 and 0.78 respectively
(Table 4a and b). When the five phenotypic SNPs were
included with the random SNPs, the average assignment
sensitivity was 0.54 ± 1.4 and 0.83 ± 0.09 respectively.
Overall, the STRs had higher average sensitivities of
0.83 ± 0.05 and 0.88 ± 0.04 respectively. In six breeds,
adding phenotypic SNPs into the frequentist assignment of
individuals reduced the sensitivity of the test, and in six
breeds, specificity was reduced.
The post-assignment allocation using the five phenotypic
SNPs was able to correctly classify 57.5% of the 221
animals originally misassigned by the Bayesian method
144
317
318
Kurushima et al.
(a)
(b)
Figure 2 Principal coordinate analysis of cat breeds and worldwide random-bred cat populations. Colour shades indicate the population membership
of the respective random-bred populations as determined by Kurushima (2011). Green, European or European-derived; light blue, Eastern
Mediterranean; dark blue, Egypt; purple, Iraq/Iran; light pink, Arabian Sea; dark pink, India; light orange, Southeast Asia; dark orange, East Asia;
white, pedigreed breed groups. (a) single nucleotide polymorphisms (SNPs) as calculated by Reynold’s genetic distance (Reynolds et al. 1983); (b)
short tandem repeats (STRs) as calculated by Nei’s genetic distance.
with the intergenic SNPs and 50% of the 110 individuals
originally misallocated by the frequentist method (Table 5).
The phenotypic-based corrections increased the sensitivity
and specificity of the Bayesian method to 0.75 and 0.77
respectively and the frequentist to 0.89 (both sensitivity
and specificity) and resulted in better resolution than did
the use of intergenic SNPs alone (data not shown). The
effect of using phenotypic SNPs post-assignment was less
effective in the STR assignments (identifying 27% and 32%
of the Bayesian and frequentist misassignments respectively). The influence of recent breed development on the
misassignment of individuals may be further visualised by
plotting the crossed assignment rate as a function of the
genetic distance between breeds (Fig. S4a,b). The crossed
assignment rate increased as the genetic distance between
breeds decreased.
145
Table 4 Assignment accuracy of cats to breeds using the (a) Bayesian method, (b) frequentist method.
Intergenic SNPs
Breed
(a) Bayesian method
Abyssinian
American SH
Australian Mist
Bengal
Birman
British SH
Burmese
Chartreux
Cornish Rex
Egyptian Mau
Exotic SH
Havana Brown
Japanese Bobtail
Korat
Maine Coon
Manx
Norwegian Forest
Ocicat
Persian
Ragdoll
Russian Blue
Scottish Fold
Siamese
Siberian
Singapura
Sokoke
Sphynx
Turkish Angora
Turkish Van
All Breeds
95% confidence
interval
(b) Frequentist method
Abyssinian
American SH
Australian Mist
Bengal
Birman
British SH
Burmese
Chartreux
Cornish Rex
Egyptian Mau
Exotic SH
Havana Brown
Japanese Bobtail
Korat
Maine Coon
Manx
Norwegian Forest
Ocicat
Persian
Ragdoll
Russian Blue
EI
n
Intergenic and phenotypic SNPs
EII
Sens.
Spec.
Ave.
Prob.
EI
Ave.
Prob.
STRs
EI
EII
Sens.
Spec.
Ave.
Prob.
1.00
1.00
1.00
0.99
1.00
0.99
2
4
2
0
1
7
4
1
5
1
6
0
1
2
6
4
2
1
2
5
3
6
1
1
2
0
3
11
3
0
0
15
0
0
1
1
1
0
0
1
0
0
0
1
16
25
0
13
0
0
0
0
9
0
0
0
2
3
0.82
0.76
0.90
1.00
0.95
0.59
0.75
0.91
0.78
0.93
0.73
1.00
0.94
0.92
0.78
0.82
0.88
0.86
0.83
0.69
0.84
0.68
0.95
0.89
0.89
1.00
0.88
0.39
0.79
1.00
1.00
0.55
1.00
1.00
0.91
0.92
0.91
1.00
1.00
0.94
1.00
1.00
1.00
0.95
0.53
0.36
1.00
0.43
1.00
1.00
1.00
1.00
0.47
1.00
1.00
1.00
0.78
0.79
0.54
0.54
0.92
0.79
0.72
0.24
0.86
0.61
0.58
0.59
0.69
0.93
0.55
0.55
0.61
0.48
0.41
0.63
0.57
0.6
0.93
0.67
0.63
0.27
0.86
0.81
0.34
0.46
0.69
EII
Sens.
Spec.
0
0
2
0
0
5
0
7
0
0
6
1
34
17
32
1
25
1
0
0
0
0
0
23
0
0
0
134
3
0.64
0.35
1.00
0.91
0.73
0.24
0.88
0.91
0.39
0.71
0.23
0.87
0.61
1.00
0.63
0.05
0.69
0.57
0.17
0
0.79
0.16
0
0.33
1.00
1.00
0.44
0.39
0.07
1.00
1.00
0.91
1.00
1.00
0.44
1.00
0.59
1.00
1.00
0.45
0.93
0.24
0.59
0.35
0.50
0.31
0.80
1.00
0.98
1.00
1.00
0.99
0.99
0.99
1.00
1.00
0.98
1.00
1.00
1.00
1.00
1.00
1.00
1.00
1.00
0.99
1
1
1.00
1.00
1.00
1.00
1
1
0.12
1.00
1.00
1.00
0.05
0.25
11
17
20
23
22
17
16
11
23
14
22
15
18
24
27
22
16
7
12
16
19
19
19
9
19
5
25
18
14
4
8
0
7
4
17
4
1
12
3
16
2
2
0
3
20
8
4
12
16
0
18
19
9
1
0
16
5
10
0
0
1
0
0
10
1
13
0
0
8
2
33
15
21
1
4
0
0
0
0
0
0
0
0
0
0
125
3
0.64
0.53
1.00
0.70
0.82
0
0.75
0.91
0.48
0.79
0.27
0.87
0.89
1.00
0.89
0.09
0.50
0.43
0
0
1
0.05
0
0
0.95
1.00
0.36
0.72
0.29
1.00
1.00
0.95
1.00
1.00
0
0.92
0.43
1.00
1.00
0.43
0.87
0.33
0.62
0.53
0.67
0.67
1.00
0.98
0.99
1.00
1.00
0.96
1.00
1.00
1.00
0.97
1.00
1.00
1.00
1.00
1.00
1.00
1.00
1.00
0.99
1
1
1
1
1.00
1.00
1.00
1.00
1
1
1
1
1.00
1.00
1.00
0.09
0.57
1.00
1.00
0.99
1.00
0.98
4
11
0
2
6
13
2
1
14
4
17
2
7
0
10
21
5
3
10
16
4
16
19
6
0
0
14
11
13
500
221
237
0.56
0.14
0.54
0.12
0.99
231
291
0.54
0.13
0.48
0.13
1.00
86
88
0.83
0.05
0.82
0.08
0.63
11
17
20
23
22
17
16
11
23
14
22
15
18
24
27
22
16
7
12
16
19
0
1
0
2
1
10
2
2
5
1
19
1
4
1
5
8
1
0
9
3
0
0
0
2
0
0
6
2
0
0
0
7
0
0
0
8
11
46
1
19
0
0
1.00
0.94
1.00
0.91
0.95
0.41
0.88
0.82
0.78
0.93
0.14
0.93
0.78
0.96
0.81
0.64
0.94
1.00
0.25
0.81
1.00
1.00
1.00
0.91
1.00
1.00
0.54
0.88
1.00
1.00
1.00
0.3
1.00
1.00
1.00
0.73
0.56
0.25
0.88
0.14
1.00
1.00
0.32
0.53
0.57
0.43
0.39
0.45
0.51
0.31
0.29
0.29
0.43
0.48
0.29
0.41
0.44
0.33
0.33
0.27
0.39
0.26
0.31
0
4
0
2
1
5
3
2
4
2
10
2
3
0
1
5
3
0
6
2
1
0
0
3
0
0
4
0
0
1
0
5
1
0
0
13
9
20
2
10
0
0
1.00
0.76
1.00
0.91
0.95
0.71
0.81
0.82
0.83
0.86
0.55
0.87
0.83
1.00
0.96
0.77
0.81
1.00
0.50
0.88
0.95
1.00
1.00
0.87
1.00
1.00
0.75
1.00
1.00
0.95
1.00
0.71
0.93
1.00
1.00
0.67
0.65
0.39
0.78
0.38
1.00
1.00
0.32
0.60
0.58
0.43
0.38
0.33
0.51
0.31
0.30
0.32
0.37
0.49
0.26
0.42
0.44
0.40
0.37
0.30
0.45
0.26
0.32
2
2
2
0
1
5
0
0
2
3
4
0
1
0
6
4
1
1
1
4
3
0
0
1
0
0
3
2
0
0
0
1
0
0
0
5
12
3
1
6
0
0
0.82
0.88
0.90
1.00
0.95
0.71
1.00
1.00
0.91
0.79
0.82
1.00
0.94
1.00
0.78
0.82
0.94
0.86
0.92
0.75
0.84
1.00
1.00
0.95
1.00
1.00
0.80
0.89
1.00
1.00
1.00
0.95
1.00
1.00
1.00
0.81
0.60
0.83
0.86
0.65
1.00
1.00
0.33
0.27
0.27
0.21
0.34
0.16
0.26
0.15
0.25
0.18
0.39
0.37
0.29
0.45
0.35
0.14
0.06
0.10
0.26
0.32
0.39
1
(continued)
146
319
320
Kurushima et al.
Table 4 (continued)
Intergenic SNPs
Breed
EI
n
EII
Intergenic and phenotypic SNPs
Sens.
Spec.
Ave.
Prob.
EI
EII
Sens.
Spec.
Ave.
Prob.
STRs
EI
EII
Sens.
Spec.
Ave.
Prob.
Scottish Fold
Siamese
Siberian
Singapura
Sokoke
Sphynx
Turkish Angora
Turkish Van
19
19
9
19
5
25
18
14
10
1
5
1
0
3
10
5
0
0
3
0
0
2
1
3
0.47
0.95
0.44
0.95
1.00
0.88
0.44
0.64
1.00
1.00
0.57
1.00
1.00
0.92
0.89
0.75
0.84
0.33
0.19
0.45
0.41
0.32
0.23
0.27
10
0
4
0
0
3
6
4
0
0
3
0
0
2
8
2
0.47
1.00
0.56
1.00
1.00
0.88
0.67
0.71
1.00
1.00
0.63
1.00
1.00
0.92
0.60
0.83
0.85
0.32
0.22
0.44
0.42
0.31
0.37
0.37
2
0
0
3
0
1
9
2
0
0
18
0
0
0
7
3
0.89
1.00
1.00
0.84
1.00
0.96
0.50
0.86
1.00
1.00
0.33
1.00
1.00
1.00
0.56
0.80
0.45
0.17
0.11
0.32
0.46
0.25
0.21
0.18
All Breeds
95% confidence
interval
500
110
111
0.78
0.09
0.78
0.10
0.39
83
83
0.83
0.06
0.83
0.07
0.39
59
62
0.88
0.04
0.88
0.06
0.27
Bayesian method of Rannala & Mountain (1997).
Frequentist method of Paetkau et al. (1995).
1
Essentially zero due to lack of sensitivity; n, number of samples from this breed tested over 10 iterations; EI, members of a breed that were incorrectly
assigned to another breed; EII, members of a different breed that were incorrectly assigned to the breed in question; Sens., sensitivity; SNPs, single
nucleotide polymorphisms; STRs, short tandem repeats; Spec., specificity; Ave. Prob., average probability of assignment as calculated by the Paetkau
et al. (2004) Monte Carlo resampling method.
Table 5 Total misassigned individuals identified post-assignment by phenotypic SNPs.
Assigned by SNPs
Bayesian
Longhair
Burmese Points
Siamese Points
Chocolate
Cinnamon
Total1
Assigned by STRs
Frequentist
Bayesian
Frequentist
Total
Freq.
Total
Freq.
Total
Freq.
Total
Freq.
105
15
15
8
14
127
0.49
0.07
0.07
0.04
0.07
0.58
37
3
16
0
5
55
0.34
0.03
0.15
0
0.05
0.50
11
1
6
2
4
22
0.13
0.02
0.07
0.02
0.05
0.26
11
2
3
0
4
19
0.18
0.03
0.05
0
0.07
0.32
Frequency (SNPs: Bayesian = 221, Frequentist = 110 STRs: Bayesian = 86, Frequentist = 59); SNPs, single nucleotide polymorphisms; STRs, short
tandem repeats.
1
A few individuals were identified as misassigned with multiple phenotypic SNPs.
Discussion
The artificial selection and population dynamics of domestic
cats and their associated fancy breeds are unique amongst
domesticated species. Cats are one of the more recent
mammalian domesticates, arguably existing in a unique
quasi-domesticated state. Although domestication is an
ongoing process, the earliest instance of cat taming is
credited to a Neolithic burial site on Cyprus dated to 9500–
9200 years ago (Vigne et al. 2004). Unlike other agricultural species and the domestic dog, until recently, cats have
had minimal artificial selection pressures on their form and
function as they have naturally performed their required
task of vermin control. Barriers to gene flow are mitigated
as cats are transported between countries via both purposeful and accidental human-mediated travel, although
recently rabies control legislation has reduced the migration
of cats between some countries. Overlapping niches
between the wildcat progenitors, random-bred feral cats,
random-bred house cats and fancy breeds likely produces
continual, however limited, horizontal gene flow throughout the domestic cat world.
The overall selection on the cat genome may be predicted
to be less intense than in other domesticated species. The cat
fancy is <150 years old, and a majority of cat breeds were
developed in the past 50–75 years. Human selection in cats
has focused on aesthetic qualities, such as coat colours and
fur types, as opposed to complex behaviours and qualities,
such as hunting skills and meat or milk production in dog
or in other livestock species. Many of the cat’s phenotypic
attributes, even those that affect body and appendage
morphologies, are traits with basic Mendelian inheritance
patterns. One simple genetic change, such as the longhair of
the Persian versus the shorthair of Exotic Shorthairs, is the
147
defining characteristic between these two breeds. Burmese
and Siamese points are found in a large metafamily of
breeds that includes Burmese, Siamese, Javanese, Tonkinese
and Birman, to name a few (Table 1). Brown colorations are
diagnostic in breeds such as the Havana Brown (chocolate)
and the Abyssinian (cinnamon). These selective pressures
are reflected in the causative SNP frequencies in Table 3.
Cat registries have recognised that some breeds are
‘natural’, such as the Korat and Turkish Van. These breeds
are specific population isolates, and random-bred cats of
similar origins can be used to augment their gene pools.
Other breeds are recognised as ‘hybrids’, developed from
purposeful cross-breeding of either different breeds or
species. One such example is the Ocicat, an intentional
Abyssinian and Siamese cross. The Bengal is a unique breed
that is an interspecies hybrid between an Asian leopard cat
and various domestic breeds (Johnson-Ory 1991). As a
result, some cat breeds may be a concoction of various
genetic backgrounds, including cats of different breeds but
having the same racial origins, cats of different breeds from
different racial origins and even different species.
The 29 breeds were selected to represent the major breeds
of the cat fancy. Some breeds may have developed from
natural populations, while most cat breeds developed in the
past 50 years. Several breeds that had clearly derived from
another breed, such as Persians and Exotic Shorthairs, were
purposely chosen, whereas others were selected because
they were recently developed hybrid breeds, such as the
Ocicat, Bengal and Australian Mist. Thus, STRs may be
better for breaking up breed families, whereas intergenic
SNPs may give us more insight into the natural populations. More slowly evolving SNPs and relatively quickly
evolving STRs were examined to assess their power to
resolve cat breeds that have different patterns, origins and
ages of ancestry.
Significant genetic variation is present in many cat breeds
and cannot be predicted entirely by effective population size
(popularity amongst cat breeders) or breeding practices
alone. The Turkish Angora, originating from Turkey, an
area near the seat of cat domestication (Driscoll et al. 2007;
Lipinski et al. 2008), had the highest effective number of
alleles for both SNPs and STRs. A wide distribution of
heterozygosity levels and inbreeding values was found
throughout the remainder of the cat breeds. However, the
SNPs and STRs were not always concordant (as can be seen
in Fig. S1). A previous study found STRs often underestimate FST compared to SNPs, most likely due to a rapid STR
mutation rate, often leading to convergence (Sacks & Louie
2008). An alternative hypothesis is that long isolated breeds
of a large population size have had sufficient time and
opportunity to increase STR heteorzygosity through mutation, but not so for SNPs. Regardless, SNPs and STRs have
differing relative observed heterozygosity values for some of
the breeds (namely Abyssinians, Persians and Japanese
Bobtails) and is reflected in their FIS values.
Two of the most prevalent breeds are Persians and Bengals
(http://www.tica.org/). Persians were one of the first breeds
to be recognised, and Bengals, although only introduced in
the past 40 years, have risen to worldwide fame. Both breeds
had moderate levels of heterozygosity and inbreeding.
Several less popular breeds, such as the Cornish Rex,
contained fairly high levels of variation and low inbreeding,
whereas two recently developed breeds, the Siberian and
Ragdoll, revealed high variation, perhaps a reflection of their
recent development from random-bred populations. Thus,
levels of variation and inbreeding cannot entirely be
predicted based on breed popularity and breed age, implying
management by the cat breeders may be the most significant
dynamic for breed genetic population health.
The Bayesian cluster analysis supported the breed
demarcations from previous studies, especially the STR
analyses of Lipinski et al. (2008). Previously, 22 breeds,
which included 15 of 16 ‘foundation’ cat breeds designated
by the Cat Fanciers’ Association, delineated as 17–18
separate populations. This study added seven additional
breeds, including the missing 16th ‘foundation’ breed, the
Manx. However, the most likely value of K (number of
structured groupings) could not be decisively determined by
methods developed for wild populations. As STRUCTURE
creates a probability distribution of the breed populations
by inferring the previous generation’s genotypic frequencies
through the principles of HWE, several practices in cat
breeding result in genetic populations that do not always
align with the inferences of STRUCTURE. Cat breeds have
variation in age of establishment and significantly different
genetic population origins, and the dissimilarity in breeding
practices can create distinct lines within a single breed that
may be as unique as one of the more recently established
breeds. Additionally, many breeds were created through the
crossing of two, often highly divergent, populations of
cats resulting in a hybrid of sorts, whereas other breeds
still allow the introduction of cats from random-bred
populations. These instances confounded the log-likelihood
calculations, making an empirical determination difficult.
As in previous studies, the breeds that were not deemed
genetically distinct can be explained by the breed history
(Lipinski et al. 2008; Menotti-Raymond et al. 2008). The two
large breed families of Siamese and Persian types were reidentified, and the Persian family expanded with Scottish
Folds. The Australian Mist was added to the previously
recognised grouping of the Siamese/Havana Brown/Burmese, as this breed was created by cross-breeding with
Burmese. More recent breeds, such as the Ragdoll and Bengal,
are resolved as separate breed populations, suggesting STRs
alone can differentiate about 24 of 29 breeds, in addition to
Turkish- versus USA-originating Turkish Angoras. At
K = 17, SNPs could separate Birman from other Asiatic
breeds but not the Singapura. Thus, both sets of markers
provide valuable insight into the relationship of the breeds.
Because the breeds within the larger family groups are
148
321
322
Kurushima et al.
generally different by only a single-gene trait, an actual breed
designation may not be appropriate and perhaps should be
consider varieties within a breed. The cat fancy has precedence for this concept, the pointed Persian, a Himalayan, is
considered a variety in the CFA but a breed by TICA.
Regardless of the marker assayed, the principal coordinate and Bayesian assignment analyses clustered the
majority of breeds with the random-bred population that
was most influential to its creation, as suggested by popular
breed histories. Sixteen breeds originated from European
populations, six breeds from South Asian populations, two
breeds from the Eastern Mediterranean and the Sokoke from
the India or Arabian Sea region. However, some markerspecific differences were noted. When SNP and STR results
were compared through Bayesian assignment, the Turkish
Angora was assigned to Europe or the Eastern Mediterranean respectively, Bengal was assigned to Europe or the
Arabian Sea respectively and the Ocicat was assigned to
South Asia or Europe respectively. These dissimilarities were
not reflected in the PCA results that were remarkably
similar in both SNPs and STRs. This was most likely due to
offsetting the mutation rate differences with distance
matrices that accommodate these attributes.
Nonetheless, the aforementioned breeds have unique
histories that may explain the marker discrepancies with
Bayesian assignment to random-bred populations. The
Turkish Angora breed was reconstituted from the Persian
(European) pedigree post-World Wars, and their genetic
diversity has recently been supplemented via outcrossing to
Turkish random-bred cats. The identified subpopulations
within the breed may reflect the latest influx of random-bred
cats. The Bengal and the Ocicat clustering could be a result
of the contribution of breeds from very different regional
origins such as Abyssinian, Egyptian Mau and the Siamese.
Overall, the frequentist method of Paetkau et al. (1995)
outperformed the Bayesian method of Rannala & Mountain
(1997) in assigning unknown individuals to their breed of
origin. Both methods rely on a frequency distribution to
estimate the probability that an unknown arose in a given
population. The differences lie in how that frequency
distribution is established. Paetkau’s frequentist method
generates the frequency distribution based on the observed
alleles in each population, whereas the Bayesian method
begins with an initial distribution in which every population
in the data set has an equal allele density and then
calculates a posterior probability distribution based on the
initial assumption given the observed data. Both methods
assume the populations are in HWE; however, the frequentist method is able to accommodate populations with
drastically different allele frequencies – populations such as
those seen as a result of the cat fancy. Directed breeding,
such as that used in the development of pedigreed cats,
inherently violates the assumptions of HWE. Therefore, a
frequentist method that identifies an individual’s origin
based on the frequency of the genotypes in each potential
population should excel in assignment accuracy for inbred
populations.
Many breeds are defined by one genetic trait in the cat
fancy. Although many breeds can share a trait, such as
longhair, this same trait can exclude a breed (Table 3). Thus,
phenotypic traits were tested post-assignment, as many are
not highly breed selective pre-assignment. Although the 38
highly polymorphic STRs consistently outperformed the
SNPs, the addition of phenotypic SNPs as post-assignment
verification significantly improved the assignment rates. The
reduction in sensitivity and specificity when combing the
phenotypic SNPs in the assignment may be due to the
strength of selection imposed on these markers. In general,
breeds that were more inbred, not open to outcrosses and not
developed through the crossing of pre-existing breeds, had a
higher accuracy in reassignment; the Russian Blue, Sokoke
and Abyssinian are examples. In contrast, breeds where
outcrossing is common, either with other breeds or randombred populations, tended to confuse the assignment algorithm and had a high probability of both type I and II error,
such as the Persians, Turkish Angoras and Ragdoll. The most
common error in assignment by far was cross-assignment
between Exotic Shorthairs and Persians within this breed
family, a problem easily remedied by exploiting the FGF5 SNP
causing longhair in Persians.
Initially, cats could be localised to a regional population
and breed family by STRs and/or SNPs. Secondary differentiation within the breed family could be determined by
genotyping mutations for phenotypic traits, especially
traits that are specific to or fixed within a breed. Some traits
are required for breed membership; a Birman or Siamese
must be pointed, implying homozygosity for the
AANG02171093.1(TYR):g.1802G>A variant. Some traits
are grounds for exclusion: all Korats are solid blue, and no
other colours or patterns are acceptable. Therefore, a
trait such as the longhair AANG02027250.1(FGF5):
g.18442A>C variant could be used as a means for identifying
members of the Persian, Maine Coon, Turkish Angora,
Turkish Van and Birman breeds and, likewise, a means for
discrimination as an exclusion marker for breeds such as the
Abyssinian, Egyptian Mau, Sokoke and Ocicat. Other singlegene traits may be used to identify members of a small family
of cat breeds as well, such as the Burmese points,
AANG02171092.1(TYR):g.11026G>T, which is a prerequisite for membership to the Burmese and Singapura breeds.
The cinnamon mutation, AANG02185848.1(TYRP1):
g.10736C> T, is very rare in the general cat population, yet
is a defining characteristic of the red Abyssinian.
Cat fancy registries may not agree with assignments due
to variations in breeding practices between the registries for
a given breed. The Tonkinese, which is genetically a
compound heterozygote for the AANG02171092.1(TYR):
g.11026G>T and the AANG02171093.1(TYR):g.1802G>A
variants, can produce both pointed and sepia cats; thus,
Tonkinese can genetically resemble a Siamese or Burmese
149
respectively at the TYR locus. However, in some cases,
registration restrictions do not allow these Tonkinese
variants to be registered as Siamese or Burmese. In addition,
some breed registries allow colour and hair variants that
may not be permitted in another, confusing possible breed
assignments. Thus, the cats assigned in this study are more
likely specific to the cat fancy of the United States, and tests
for other breed populations that are registry- or regionalspecific may need to be developed. Since the development of
this SNP panel, additional phenotypic SNPs have been
discovered in cats including the Norwegian Forest Cat
colour variant amber (Peterschmitt et al. 2009), three
additional longhaired mutations (Kehler et al. 2007) and
the mutations responsible for hairlessness in Sphynx and
rexing of the Devon Rex (Gandolfi et al. 2010). These
additional mutations, as well as disease mutations, could
further delineate cat breeds.
Aside from the public interest in knowing whether their
prized family pet is descended from a celebrated pedigree,
breed assignment is a vital tool in tracing the spread of
genetically inherited diseases throughout the cat world.
Much like humans and dogs, certain populations of cats are
known to be at higher risk for particular diseases, such as
heart disease in the Maine Coon and Ragdoll (Meurs et al.
2005, 2007), polycystic kidney disease in the Persian
(Lyons et al. 2004) and progressive retinal atrophy in the
Abyssinian (Menotti-Raymond et al. 2007). Knowing
whether a particular feline descended from one of these
at-risk populations may influence treatments in a clinical
setting and help to better care for our animal companions.
In addition, understanding the population structuring of the
cat breeds can be of assistance to case–control studies for
genome-wide association studies. The current study defined
24 of 29 cat breeds and an additional three breeds using
phenotypic SNPs. With additional phenotypic and perhaps
disease-causing SNPs, the power of this STR/SNP panel to
accurately assign individuals to specific cat breeds, in
particular those breeds that are defined expressively by
single-gene traits, would be greatly increased.
Acknowledgements
We would like to thank the technical assistance of the
Veterinary Genetics Laboratory of the University of California – Davis and the University of California – Davis Genome
Center and those who graciously supplied us with buccal
swabs from their pets. Funding for this study was supplied in
part by National Geographic Expedition Grant (EC0360-07),
National Institutes of Health – National Center for Research
Resources (NCRR) grant R24 RR016094R24, now the
Office of Research Infrastructure Programs (ORIP) grant
R24OD010928, the University of California – Davis, Center
for Companion Animal Health, the Winn Feline Foundation,
and a gift from Illumina, Inc. (LAL), and the University of
California – Davis Wildlife Health Fellowship (JDK).
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Supporting information
Additional supporting information may be found in the
online version of this article.
Figure S1 Observed heterozygosity by breed.
Figure S2 Log likelihood and ΔK plots from the Bayesian
clustering of cat breeds.
Figure S3 (a) Alternate plots of short tandem repeat (STR)
Bayesian clustering analysis of cat breeds; (b) Alternate
plots of single nucleotide polymorphisms (SNP) Bayesian
clustering analysis of cat breeds.
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function of the Reynold’s genetic distance between populations using single nucleotide polymorphisms (SNPs); (b)
Crossed assignment rate between breeds as a function of the
Reynold’s genetic distance between populations using short
tandem repeats (STRs).
Table S1 FST by locus for genetic markers and design and
GenTrain score for single nucleotide polymorphisms (SNPs).
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bred cat populations.
151
J. Anim. Breed. Genet. ISSN 0931-2668
ORIGINAL ARTICLE
An insight into population structure and gene flow within
pure-bred cats
G. Leroy1,2, E. Vernet3, M.B. Pautet3 & X. Rognon1,2
ne
tique Animale et Biologie Inte
grative, AgroParisTech, Paris, France
1 UMR1313 Ge
ne
tique Animale et Biologie Inte
grative, INRA, Jouy-en-Josas, France
2 UMR1313 Ge
3 LOOF, Pantin, France
Summary
Keywords
Cat; gene flow; genetic variability; inbreeding;
population structure.
Correspondence
ne
tique Animale et
G. Leroy, UMR1313 Ge
Biologie Int
egrative, AgroParisTech, 16 rue
Claude Bernard, F-75231 Paris 05, France.
Tel: +33 (0) 1 44 08 17 46; Fax: +33 (0) 1 44 08
86 22; E-mail: gregoire.leroy@agroparistech.fr
Received: 29 October 2012;
accepted: 27 April 2013
Investigation of genetic structure on the basis of pedigree information
requires indicators adapted to the specific context of the populations studied. On the basis of pedigree-based estimates of diversity, we analysed
genetic diversity, mating practices and gene flow among eight cat populations raised in France, five of them being single breeds and three consisting of breed groups with varieties that may interbreed. When computed
on the basis of coancestry rate, effective population sizes ranged from 127
to 1406, while the contribution of founders from other breeds ranged from
0.7 to 16.4%. In the five breeds, FIS ranged between 0.96 and 1.83%, with
this result being related to mating practices such as close inbreeding (on
average 5% of individuals being inbred within two generations). Within
the three groups of varieties studied, FIT ranged from 1.59 to 3%, while
FST values were estimated between 0.04 and 0.91%, which was linked to
various amounts of gene exchanges between subpopulations at the parental level. The results indicate that cat breeds constitute populations submitted to low selection intensity, contrasting with relatively high
individual inbreeding level caused by close inbreeding practices.
Background
Genealogies constitute a profitable source of information to investigate breeding practices, diversity or
genetic structure in livestock, and companion and
captive animal populations. Based on Mendelian segregation rules, pedigree analysis can be used to follow
gene transmission from generation to generation and
between subsamples of an entire population, which
may be particularly useful for recently created animal
breeds.
Cat breeds may constitute an interesting example of
recent populations submitted to various gene flow.
Indeed, a majority of modern cat breeds has been
developed over the past 50 years, on the basis of simple phenotypical variants, with one or several former
populations (Lipinski et al. 2008). In companion animals, it has been found that some breeding practices
© 2013 Blackwell Verlag GmbH
and a suboptimal management of genetic variability,
such as popular sire effect, may lead to a dissemination of inherited disorders and an erosion of genetic
diversity. A subsequent increase in inbreeding may
eventually lead to an increased incidence of some disorders (Leroy & Baumung 2011) and a negative
impact on fitness traits (Boakes et al. 2007). These
issues have been well studied in dogs using pedigree
files, with investigations into breeding practices
(Leroy & Baumung 2011), the characterization of
genetic diversity (Leroy et al. 2006; Calboli et al. 2008;
Shariflou et al. 2011) or inbreeding effects (M€
aki et al.
2001). Cat breeds are, as well as dog populations,
threatened by genetic disorders with more than 250
inherited disorders reported by [Online Mendelian
Inheritance in Animals (OMIA), omia.angis.org.au].
Yet, pedigree investigations have been less frequently
conducted within this species (Mucha et al. 2011).
• J. Anim. Breed. Genet. (2013) 1–8
doi:10.1111/jbg.12043
152
G. Leroy et al.
Population structure within purebred cats
The aim of this study was to analyse the genetic
diversity of eight cat pure-bred populations raised in
France on the basis of pedigree data. There are two
main purposes: (i) to assess the level of genetic variability within cat breeds in relation to inbreeding
evolution and specific breeding practices, and (ii) to
investigate the recent gene flow explaining current
constitution and structure of cat populations.
Material and methods
Populations studied
In France, breed genealogies are managed in a unified
genealogical database handled by the Livre Officiel
des Origines Francßaises (LOOF). Among the 66 breeds
and varieties registered in France, five breeds and
three groups of breeds/varieties were chosen, showing
both relatively good pedigree knowledge and a variation in population size or geographical origin. The five
breeds are Maine Coon, Bengal, Birman, Chartreux
and Devon Rex. Maine Coon and Bengal breeds have
experienced a large population increase over the last
8 years (Figure 1): births increasing from 1325 to
4470 and from 136 to 1148, respectively, between
2003 and 2010. Birman and Chartreux breeds, the
only two populations of French origin among those
studied, have a relatively large number of births
(4015 and 2085 registrations in 2010, respectively).
By contrast, the Devon Rex breed was considered
here as an example of a breed with a small population
size (only 191 births in 2010).
The three groups include nine populations, which
can be considered as either breeds or varieties depending on countries and the breeding rules of the associations. For more clarity, subpopulations among groups
will be considered here as varieties.
The first group (PES) involved two varieties: Persian
and Exotic Shorthair. The Persian is one of the most
common breeds in the world and until 2010 showed
the largest number of births among breeds raised in
France (among PES kitties born in 2010, 4934 were
registered including 4209 declared as Persian). Crossbreeding is allowed with its shorthaired variety, the
Exotic Shorthair breed (725 registrations for 2010).
PES is also the only population among those analysed
with a decrease in number of births (13%) between
2003 and 2010 (Figure 1, Table 1). The second group
(BSH) involved five varieties (outcrossing being
allowed between these populations in France): British
Shorthair (1492 births in 2010), its longhair phenotypical variant (295 births), the Scottish variety (504
births), the Highland variety (Scottish longhair variant, 133 births) and the Selkirk variety (140 births).
Finally, the Abyssinian population (288 births in
2010) and its long haired Somali variety (139 births in
2010) were also analysed together (ABS).
For each breed or group of varieties, current generation was defined based on individuals registered
between 2008 and 2010 with both parents known.
Methods
We computed the number of equivalent complete
generations traced (EqG) and generation intervals as
described in Leroy et al. (2006). Identity-by-descent
(IBD) estimators, that is, coefficients of inbreeding F
and coancestry C, were computed and averaged over
the current generations. To characterize genetic structure within breeds and varieties, we computed fixation index FIS using the following equation (Leroy &
Table 1 Demographic parameters of the breeds studied
Evolution
of births
(2003–
2010) %
Breed or
group of
varieties
Figure 1 Evolution of births according to breeds over the 2003–2008
period.
Abyssinian/
Somali (ABS)
Bengal
Birman
British Shorthair/
British Longhair/
Highland/Scottish/
Selkirk (BSH)
Chartreux
Devon Rex
Maine Coon
Persian/Exotic
Shorthair (PES)
Reference population (individuals
registered with both parents known
over 2008–2010)
Nb of
breeders
153
Nb of
sires
Nb of
dams
+61
115
1 307
163
297
+781
+86
+198
241
1076
452
2896
11 109
6758
367
1087
809
645
2352
1401
+6
+96
+225
13
514
42
690
1300
6494
469
11 642
14 921
477
82
1215
2201
1052
128
2178
3812
2
Nb of
individuals
G. Leroy et al.
Baumung 2011),
FIS ¼
FC
:
1C
For each group (AbS, BSH and PES), we differentiated F~ and C~ averaged within all varieties, and C as
coancestry averaged over the entire group (Caballero
& Toro 2002), in order to compute F-statistics, using
the following equations,
FIS ¼
F~ C~
F~ C
C~ C
; FIT ¼
;
; F ST ¼
1C
1C
1 C~
The effective population size was estimated on the
basis of individual rates of inbreeding ΔFi and coancestry ΔCij (Cervantes et al. 2011), considering Fi is the
inbreeding coefficient of individual i, Cij the coancestry coefficient between individuals i and j, and EqGi
and EqGj their respective equivalent complete traced
generations:
pffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffi
DFi ¼ 1 EqGi 1 ð1 Fi Þ and
qffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffi
DCij ¼ 1 ðEqGi þEqGj Þ=2 ð1 Cij Þ:
Effective population sizes were estimated by averaging ΔFi over the current generation and ΔCij over
100 000 pairs of individuals randomly sampled among
the current generation, using the following formulas:
N eFi ¼ 1=2DF and N eCi ¼ 1=2DC:
Percentages of inbred individuals were computed
using the Van Raden (1992) method taking into
account only two and three generations. The evolution of average inbreeding coefficient according to the
number of generations considered was also estimated
for the current population.
On the basis of the breed origin of each founder
(ancestors of the current generation without parents
known), contribution of different breeds to each gene
pool was computed for the different breeds and
groups of breeds, considering either founders or
parental origins, that is, origins of parents of individuals of the reference generations. The analyses
were performed using the PEDIG software (http://
dga.jouy.inra.fr/sgqa/article.php3?id_article=110, Boichard 2002).
Results
2003 and 2010, the number of breeders ranged
between 87 (Devon Rex) and 2,428 (PES). Between
2008 and 2010, current generation sizes ranged from
469 (Devon Rex) to 14,921 (PES). On average, sires
produced 8.8 kittens, ranging from 5.7 (Devon Rex)
to 13.6 (Chartreux), and dams produced 4.7 kittens,
ranging from 3.7 (Devon Rex) to 6.2 (Chartreux). We
found on average 1 sire for 1.8 dams. All the breeds
show good pedigree knowledge (EqG = 7.2 on average), the highest values being found for Birman (8.1)
and Chartreux (8.3), while generation intervals ranged from 2.2 (Bengal) to 3.3 years (PES). Between
2003 and 2010, the number of kittens born and used
as reproducers followed the same trend as the number
of births (Figure S1): on average overall breeds, 17%
of kitties (including 5% of male and 12% of female)
later became reproducers, the proportion ranging
from 11% (Chartreux) to 22% (Bengal).
Diversity indicators
Table 2 shows the IBD estimators for the eight breeds
and groups of breeds/varieties. According to the breed,
F ranged from 2% (Maine Coon) to 4.4% (Chartreux).
These inbreeding levels could be explained by pedigree
knowledge, population size and also by mating between
close relatives (close inbreeding): the proportion of
inbred individuals, based on two and three generations,
ranged from 2.7 (Maine Coon) to 8.4% (Devon Rex)
and from 7.7 (Maine Coon) to 22.5% (Devon Rex),
respectively. For each breed considered, there was a
large increase in inbreeding coefficients during the first
generations (Figure 2). Over the following generations,
inbreeding increase was smoother and more regular,
indicating no strong bottleneck event.
Average coancestry C was always lower than
inbreeding, which is illustrated by a positive FIS value
for all the breeds, ranging between 0.96% (Maine
Coon) and 1.83% (Birman). In BSH and PES groups,
average C were lower than 1%, while the maximum
value was for the Chartreux breed (approximately
2.8%). Therefore, when using C instead of F to compute Ne, effective population size increased largely,
with NeCi and NeFi ranging between 127 (Devon Rex)
and 1406 (PES) and between 64 (Devon Rex) and 161
(Maine Coon), respectively.
Demographic and genealogical parameters
Gene flow within and between breeds and groups of
varieties
The eight breeds and groups of breeds studied showed
a wide range of situations, regarding population size
or numbers of breeders (Figure 1, Table 1). Between
By breed, the proportion of founders originating from
outside the breed was variable: based on founder
approaches, the contribution of external origins ran-
3
154
G. Leroy et al.
Table 2 Genealogical parameters of the breeds considering current generation (2008–2010)
Inbreeding
Coancestry
% of individuals inbred after
Main founder
origins outside
the breed (%)
NeFi
2
generations
3
generations
Overall
generations
C (%)
NeCi
FIS
(%)
2.71
95
6
13.1
67.6
1.14
266
a
0.7
Unknown (0.5)
2.19
2.83
97
3.6
11
95.2
1.78
182
1.07
5.7
8.07
6.73
3.18
2.69
2.93
2.6
115
105
4
5.2
13.5
13.9
95.1
80.7
1.12
0.61
365
553
1.83
a
5.3
16
American
Shorthair (2.2)
Balinais (2.7)
Persian (10.5)
6494
8.29
2.9
4.41
78
4.5
13.5
98.5
2.78
146
1.68
11.5
469
11 642
14 921
6.47
7.27
7.39
2.44
2.41
3.28
4.29
1.98
3.25
64
161
91
5.1
2.7
8.4
22.5
7.7
18
65.1
91.3
88.7
2.54
1.03
0.26
127
363
1406
1.79
0.96
a
5.9
1.2
1.7
Breed or group
of varieties
Nb of
individuals
EqG
T
F (%)
Abyssinian/Somali
(ABS)
Bengal
1307
6.31
2.77
2896
6.68
Birman
British Shorthair/
British Longhair/
Highland/
Scottish/
Selkirk (BSH)
Chartreux
11 109
6758
Devon Rex
Maine Coon
Persian/Exotic
Shorthair (PES)
Out
(%)
British
Shorthair (6.1)
Burmese (2.6)
Persian (0.9)
British
Shorthair (1)
EqG, number of equivalent generations; T, generation intervals in years; F, average inbreeding coefficient; NeFi, inbreeding effective population sizes;
C, average coancestry coefficient; NeCi, coancestry effective population sizes; FIS, breed fixation index; Out, % of founder origins outside the breed.
aSee Table 3.
Figure 2 Evolution of average inbreeding coefficients for the current
population according to the number of generations considered. All: all
generations considered.
ged from 0.7 (ABS) to 16% (BSH) of the gene pool
(Table 2). Most of the time, those external origins
were mainly related to one breed: for instance, the
British Shorthair contributed up to 50% or more of
the external origins for two breeds (namely Chartreux
and PES). However, considering the parental origins
of the current generation, gene flow was much more
limited, and in each population, <1% of those origins
belonged to external breeds (Figure 3).
As illustrated by Figure 3, the three groups of
varieties show contrasting situations with regard to
gene flow among subpopulations. As aforementioned,
in BSH, external origins contributed largely to the
gene pool. Within this group, the British Shorthair
constituted the largest population (64% of the total
population group), and it was also the main origin for
the different varieties of the group. Thus, founder origins from the British Shorthair ranged from 59.6%
(Selkirk) to 83.1% (British Shorthair) (Table S1). The
contribution of the British Shorthair variety remained
relatively important even considering its parental origins, with its contribution ranging between 22.6%
(Highland) and 91% (British Shorthair) (Figure 3).
Within the group, all varieties but one (Selkirk) were
involved as contributors of other ones. In the PES
group, the Persian constituted by far the main origin,
contributing to 86.6% of founder origins of the Exotic
Shorthair variety. However, considering the last generation, 67.3% of parental origin in Exotic Shorthair
belonged to the Exotic Shorthair. The two varieties of
the ABS group constituted more independent subpopulations, with most of the founder and parental contributions in the Abyssinian and the Somali coming
from Abyssinians and Somalis, respectively.
According to Table 3, within each of the three
groups, the average coancestry was relatively low
between each variety, ranging from 0.19 (Abyssinian
and Somali) to 0.67% (Scottish and Highland). As
expected, the contrast between inbreeding and
coancestry was lower when considering each variety
4
155
G. Leroy et al.
British Shorthair
(4342)
91.0
5.9
54.3
44.7
2.5
41.1
British
Longhair
(768)
0.6
2.1
Scottish
(1008)
44.7
3.1
2.4
0.1
7.9
17.3
3.7
0.1
22.6
22.8
26.8
Selkirk
(383)
BSH group
73.4
Highland
(255)
33.3
British Longhair
94.8
67.3
Persian
(12898)
British Shorthair
Exotic
Shorthair
(2023)
32.5
5.2
PES group
0.1
0.3
Scottish
Highland
Selkirk
Persian
96.4
95.6
Exotic Shorthair
Abyssinian
Figure 3 Founder contributions and parental
origins for BSH, PES and ABS groups. Circles
indicate repartition of founder contribution
according to the probability of gene origins,
while arrows represent parental origins (values
in%). Sizes of arrows and circles are proportional to contributions and population size
(current generation size in parenthesis).
Abyssinian
(895)
4.4
3.6
Within breed/
variety contribution
Discussion
The aim of this study was to assess genetic diversity and
gene flow within and between cat breeds, using, among
Somali
Origins outside the
group
AbS group
independently than when considering groups of
breeds. Indeed FIS values (1.76, 2.96 and 0.69% for
BSH, PES, and ABS, respectively, Table S2) were
lower than FIT (2, 3 and 1.59%, respectively), FST values being contrasted according to groups (0.24, 0.04
and 0.91%, respectively). Yet we noticed that for British Shorthair and Exotic Shorthair varieties, FIS was
slightly higher (2.2 and 3.1%, respectively) than
when considering FIT for BSH and PES groups (2 and
3%, respectively), indicating the existence of a substructure remaining among those varieties.
Somali
(412)
Contribution from another
variety of the group
Origins outside
the group
others, F-statistics adapted to pedigree analysis. Cat
breeds have rarely been investigated in the past, and the
only study based on pedigree analysis (Mucha et al.
2011) showed average inbreeding around 3%, concluding that cat populations are not threatened by negative
effects of inbreeding. Considering coancestry as the
parameter to minimize for conservational purpose
(Baumung & S€
olkner 2003), the breeds studied here
also show remarkably high levels of diversity, effective
population sizes computed based on coancestry (NeCi)
ranging between 127 and 1406. The average coancestry
was indeed found to be quite low in comparison with
dog breeds. As an illustration, for the eight breeds or
groups of varieties, average coancestries ranged
between 0.3 and 2.8% (1.4% on average), with current
generation sizes ranging from 469 to 14 921 (6949 on
5
156
G. Leroy et al.
Group of varieties
F (%)
FIS (%)
BSH
British Longhair
British Shorthair
Scottish
Highland
Selkirk
2.08
2.9
2.12
2.18
1.74
1.24
2.18
1.30
0.82
0.20
PES
Persian
Exotic Shorthair
ABS
Abyssinian
Somali
3.23
3.4
2.44
3.3
C (%) within and between varieties
British
British
Longhair
Shorthair
Scottish
0.85
0.57
0.74
2.72
3.14
0.44
0.02
0.5
0.56
0.83
Highland
Selkirk
0.68
0.52
0.67
1.37
0.25
0.28
0.21
0.22
1.94
Persian
Exotic Shorthair
0.27
0.21
0.52
Abyssinian
Somali
1.65
0.19
2.88
Table 3 Average coefficients of inbreeding F
and coancestry C within and between varieties
of BSH, PES and ABS groups
FIS, within variety fixation index.
average), with the average EqG around 7.2. By comparison, in 24 dog breeds with an EqG larger than 6 (7.1 on
average), Leroy et al. (2009) found average coancestries
to be twice as high (2.8%, ranging between 0.6 and
8.8%), with average current generation sizes approximately 8 times larger (54 645, ranging from 2167 to
156 492). This difference is probably related to the low
number of offspring per reproducer in cat breeds. In this
study, during a generation interval (around 3 years),
sires and dams produced on average 8.8 and 4.7 kittens,
respectively. By comparison, in dog breeds (Leroy &
Baumung 2011), sires and dams produced 16.4 and 8.3
puppies, respectively, during a generation interval
(4 years). The average number of offspring produced
per breeder was also on average smaller in cats (12.6
estimated from Table 1) than in dogs (18, see Leroy
et al. 2009). Therefore, in comparison with dog breeders, a large majority of cat breeders are occasional ones.
These breeders used their reproducers with low intensity, the females producing on average one litter during
the 2008–2010 period (litter size being found on average around 3.4, data not shown). This has a clear positive impact on genetic diversity, but does not mean that
regular bottlenecks do not occur within breeds, which
may lead to the dissemination of inherited diseases
(Wellmann & Pfeiffer 2009).
In comparison with coancestries (1.4% on average),
average inbreeding values were high (3.1% on average), leading to an underestimation of effective population sizes when using inbreeding instead of
coancestry (Table 2). These differences, indicating
deviations from random-mating conditions and illus-
trated through F-statistics variations, can be explained
by three non-exclusive phenomena: intentional mating between close relatives (close and line breeding),
existence of subpopulations (Wahlund effect) and low
effective population size.
First, there is a tendency among breeders to plan mating between closely related cats. On average, approximately 5% of kittens were inbred after two generations,
meaning their parents were sharing at least one parent.
According to an analysis of dog breeds and simulated
populations, an increase of approximately 0.7–1% of FIS
could be expected for such a proportion of mating
between half- and full-sibs (Leroy & Baumung 2011).
This result was in agreement with the large inbreeding
increase observed considering the first generations, relative to the following ones (Figure 2).
Secondly, positive FIT values could also be explained
by the existence of more or less differentiated subpopulations within breeds or groups. Two of the three
groups of varieties (BSH, PES) show relatively high FIT
values, which could, at first sight, be explained through
preferential mating within varieties. As illustrated by
Table 3, between-subpopulation coancestry was
always lower than within-subpopulation coancestry.
However, Figure 3 shows that gene exchanges were
relatively frequent among varieties of BSH and PES
groups, while in the AbS, only a small proportion of
parents originated from the other variety. This was in
agreement with the very low FST values estimated for
the BSH and the PES (0.24 and 0.04%) in comparison
with the ABS (0.91%) where the level of genetic differentiation between Abyssinians and Somalis was larger.
6
157
G. Leroy et al.
Finally, FIT and FIS variations could also be explained
by the effective population size of breeds, a limited population size decreasing fixation index and eventually
leading to negative values. This phenomenon can be
interpreted considering the evolution of IBD estimators. Indeed, in panmixia, inbreeding and coancestry
are supposed to differ only by ΔIBD (i.e. 1/(2Ne)), the
average coancestry between reproducers corresponding
to the average inbreeding of the next generation. This
is why, for a given generation and in random-mating
conditions at least, we should expect C to be larger than
F. Therefore, FIT (FIS respectively) should tend to
decrease in breeds (varieties respectively) with a small
effective population size. It may explain the low average FIS (0.69%) in AbS (related to the small population
size of Abyssinian and Somali varieties) and therefore
the moderate FIT (1.59%) within the group, despite the
large subpopulation differentiation FST index (0.91%).
A small effective population size also explains why the
Devon Rex breed, despite the largest proportion of individuals inbred after three generations (22.5%), showed
only a moderate FIS value (1.79%).
In a large group like the PES (considering population size), the high FIT (3.0%) value estimated was
finally less due to the subpopulation differentiation
ðFST ¼ 0:04Þ than to close inbreeding practices.
Indeed, 8.4 and 18% of individuals were found inbred
after two and three generations, respectively, explaining the large FIS value (2.96%). By contrast, in the
Maine Coon breed, where the smallest proportion of
individuals inbred after two and three generations
was found (2.7 and 7.7%, respectively), one of the
lowest FIS was also computed (0.96%). These different
examples illustrate quite well how the fixation index
can be influenced by the breeding practice and the
demographic situation of domestic populations.
A comparison between founder and parental origins
illustrates the variation in gene flow over time. When
considering the parental origins, only a low amount of
outcrossing was detected within each breed (implying
<1% of parents). Based on these results, we can consider each of the eight populations studied as almost
closed, which justifies the grouping choices we made.
However, the founder approach results highlight that
crossbreeding events have occurred in the past, with
more or less important effect on genetic diversity,
depending on the breed studied.
The French unified genealogical database was set
up in 2000, with founder individuals born during the
1980–2000 period. At this time, each of the breeds
and varieties studied were already recognized, which
underlines the fact that external contributions are
mainly related to recurrent cross-breeding events after
the creation of the breeds. Several explanations can
be given for such gene flow. For instance, in the Chartreux breed, the large amount of British Shorthair
contribution (6.1%) is probably due to regular registrations of blue British Shorthair individuals within
the breed (breeders’ personal communication). In the
BSH group, breeders in the past have probably used
Persian reproducers to improve the quality of their
coat, explaining their large contribution (10.5%) as
founders. Today, on the basis of the pedigree file, such
cross-breeding events rarely occur in France, where
they are only exceptionally allowed by LOOF, but
may exist in other countries depending on different
breeding rules. Development of DNA identification
will help to monitor the occurrence of false parentage
among cat breeds, as well as the level of introgression
of unofficial outcrossings. Studies based on molecular
markers may also bring further information on breed
relationships. For instance, Lipinski et al. (2008) and
Kurushima et al. (2012) seem to confirm introgression
of Persian individuals into British Shorthair populations, as well as British Shorthair individuals into the
Chartreux breed. Using molecular markers, MenottiRaymond et al. (2008) were not able to differentiate
Exotic/Persian, Abyssinian/Somali and British Shorthair/Scottish varieties. According to the same study,
Selkirk was, however, found to be different from British Shorthair and Scottish varieties, in contradiction
with our results, given the amount of gene flow
observed from British Shorthair to Selkirk varieties.
Such discrepancies could eventually be explained by
the breeding rules existing in the USA, where only
Persian and Exotic Shorthairs are permitted for crossbreeding with Selkirk individuals.
From a practical point of view, the NeCi values, found
larger than 100 for each of the breeds studied, indicate
that those populations are probably submitted to a limited genetic drift. By contrast, the large inbreeding values, connected to lower NeFi, may increase the
proportion of individuals affected by monogenic recessive genetic disorders, in relation to their allele frequency (Leroy & Baumung 2011). Some measures
should therefore be recommended to limit close
inbreeding practices, at least for breeds with NeFi lower
than 100, and particularly for Devon Rex, where 22.5%
of individuals were inbred after three generations.
Conclusions
To conclude, we can state that cat breeds constitute
populations submitted to relatively low selection
intensity, with various levels of genetic structure,
according to breeding practices and/or the existence
7
158
G. Leroy et al.
of varieties, involving more or less important gene
flow within a given population. If at the population
level, genetic drift is expected to be limited, high individual inbreeding level found by contrast led us to
recommend that particular attention should be paid
to population structure and inbreeding practices.
Each of the breeds studied has been submitted to
cross-breeding events in the last 30 years, with different
impacts on breed genetic diversity. Yet, the eight populations studied are currently almost closed to foreign
influence, with, however, regular gene flow remaining
among varieties. Studies like this one may provide useful information to define current population subdivisions more clearly. They also give insight into former
gene flow, which could be useful for gene association
studies (Quignon et al. 2007) or when considering
authorization of new cross breed events. Cross-breeding
may constitute an interesting option for introducing
genetic diversity within a given breed and/or improving
it, especially in relation to its health status. Further studies could consider more widely the potential impacts of
those breeding practices (close breeding, line breeding
and outcrossing) on animal welfare and health.
Acknowledgements
The authors would like to thank Emily Heppner and
Wendy Brand Williams for linguistic revision.
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Supporting Information
Additional Supporting Information may be found in
the online version of this article:
Figure S1 Evolution of number of reproducers
born and used according to breeds over the 2003–
2008 period.
Table S1 Origins of founders among varieties of
BSH, PES and ABS groups.
Table S2 Fixation index for BSH, PES and AbS
groups.
8
159
Contents lists available at SciVerse ScienceDirect
Assessing the impact of breeding strategies on inherited disorders and genetic
diversity in dogs
Grégoire Leroy ⇑, Xavier Rognon
AgroParisTech, UMR 1313, Génétique Animale et Biologie Intégrative, F-75231 Paris, France
INRA, UMR 1313, Génétique Animale et Biologie Intégrative, F-78352 Jouy-en-Josas, France
a r t i c l e
i n f o
Article history:
Accepted 18 June 2012
Keywords:
Canine
Pedigree analysis
Genetic diversity
Popular sire effect
Inherited disorders
a b s t r a c t
In the context of management of genetic diversity and control of genetic disorders within dog breeds, a
method is proposed for assessing the impact of different breeding strategies that takes into account the
genealogical information specific to a given breed. Two types of strategies were investigated: (1) eradication of an identified monogenic recessive disorder, taking into account three different mating limitations and various initial allele frequencies; and (2) control of the population sire effect by limiting the
number of offspring per reproducer. The method was tested on four dog breeds: Braque Saint Germain,
Berger des Pyrénées, Coton de Tulear and Epagneul Breton. Breeding policies, such as the removal of all
carriers from the reproduction pool, may have a range of effects on genetic diversity, depending on the
breed and the frequency of deleterious alleles. Limiting the number of offspring per reproducer may also
have a positive impact on genetic diversity.
Introduction
Management of inherited diseases and genetic diversity in different breeds of dogs is a growing concern for breeders, owners
and the general public (Nicholas, 2011). According to Online Mendelian Inheritance in Animals (OMIA)1 more than 575 disorders/
traits have been reported in dogs and at least 200 have monogenic
determinism (Nicholas et al., 2011). The prevalence of a genetic disorder can be >50% within a given population (Collins et al., 2011) and
the consequences for canine health may vary substantially, depending on the severity of the disorder and its frequency.
Increases in inbreeding and widespread dissemination of genetic disorders may have a deleterious impact on welfare of purebred
dogs, as shown with hip dysplasia in German shepherd dogs and
Golden retrievers (Mäki et al., 2001) or fertility in Irish wolfhounds
(Urfer, 2009). Founder effects and extensive use of popular sires are
considered to be the main reasons for the dissemination of genetic
disorders and are linked to a reduction in genetic diversity within a
breed (Leroy and Baumung, 2011). It has been suggested that the
prevalence of genetic diseases could be reduced through careful
selection and better management of genetic drift and inbreeding
(Lewis et al., 2010).
The Federation Cynologique Internationale (FCI) recommends
that the number of offspring per dog should not be >5% of the number of puppies registered in the breed population during a 5 year
period.2 In parallel, about 20% of disorders/traits reported in OMIA
have been characterised at the molecular level (Nicholas et al.,
2011). However, even when a genetic test is available, members of
breed societies often do not know which is the best strategy to adopt
to reduce the prevalence of genetic disorders. This is especially
important when considering the use of valuable stud animals that
may be disease carriers. There is also a need for members of breed
societies to be aware of the impact of different policies on genetic
diversity. Windig et al. (2004) modelled the consequences of a policy
for eradication of genetic disorders in sheep using simulated populations. There is a need to extend such studies to take into account the
level of complexity existing in real breeds, including non-random
mating, importations and bottleneck events.
In this paper, we propose a method to assess the impact of
breeding strategies on the frequency of deleterious alleles and
genetic diversity, taking into consideration the genealogical information available for a given breed. Two strategies were investigated: (1) eradication of an identified monogenic recessive
disorder using three different mating limitations and various initial
allele frequencies; and (2) control of the popular sire effect through
limitation of the number of offspring per reproducer.
⇑ Corresponding author. Tel.: +33 144081746.
1
E-mail address: gregoire.leroy@agroparistech.fr (G. Leroy).
See: omia.angis.org.au/.
2
http://dx.doi.org/10.1016/j.tvjl.2012.06.025
160
See: http://www.fci.be/uploaded_files/29-2010-annex-en.pdf.
344
G. Leroy, X. Rognon / The Veterinary Journal 194 (2012) 343–348
mating restriction was applied from the first year of the programme. Three different
thresholds for the number of offspring were considered for all breeds: 50 (ps50),
100 (ps100) and 200 (ps200). A limitation of 25 offspring per reproducer (ps25)
was also considered for BSG and BRP, but could not be applied to COT or EPB, since
sires of these breeds produce, on average, a number of offspring close to or >25
(Table 1).
In the two scenarios, we supposed a random replacement of reproducers. To
test what would happen if new sires or dams were more or less related to those replaced, we studied the possibility that, among the simulations, 50% of the replacement sires (or dams) were sampled among the 10th percentile of the most (or least)
related sire (or dam) of individuals born in the same year. This procedure was tested
for one breed (COT) considering two of the sub-scenarios (ps50 and erC for an initial
frequency of 50%). Each scenario was programmed in Fortran 90, repeated and averaged over 100 iterations (see Appendix A: Supplementary file 1).
To investigate the evolution of the frequency of a deleterious allele, we considered a single gene with two alleles (A and a), homozygous individuals aa being regarded as affected by the genetic defect. The initial allele frequencies of a were set
at 20% and 50%, respectively. Carriers were randomly distributed among founders
(i.e. individuals without known parents) of a given pedigree, with alleles being
transmitted according to Mendelian segregation rules. It was assumed that there
was no selection of the allele before the beginning of the breeding strategy.
Breeds selected for analysis
Four French breeds of dogs with different population sizes were selected for
analysis: Braque Saint Germain (BSG), Berger des Pyrénées (BRP), Coton de Tulear
(COT) and Epagneul Breton (EPB) (Table 1). The numbers of dogs registered in
France for each breed from 2006 to 2010 ranged from 283 (BSG) to 27,326 (EPB).
Generation intervals (T) were computed for each breed for dogs born from 2001
to 2010.
The number of equivalent complete generations (EqG), inbreeding coefficient (F)
and kinship coefficient (U; also known as ‘co-ancestry’, which corresponds to the
degree of inbreeding of a potential offspring of a pair of individuals) were averaged
for the 2006–2010 period (Leroy et al., 2006). Kinship was averaged over 10,000
pairs of dogs born during a given period. When considering simulated sub-scenarios, kinship was averaged over 100 pairs sampled over 100 iterations. The evolution
of genetic diversity was assessed considering the evolution of yearly average U. For
each scenario, kinship rate was computed per generation DU using the formula
DUt = (Ut+1 Ut)/(1 Ut), considering Ut and Ut+1 as average kinship in 2000 (year
before implementation of the breeding strategy) and 2010 (end of the period investigated) and correcting it by period considered and generation intervals.
Results
The four breeds had a high level of pedigree completeness, EqG
values for the period 2006–2010 ranging from 6.98 (COT) to 9.33
(EPB) (Table 1). In the same period, F ranged from 0.056 (EPB) to
0.091 (BRP) and U ranged from 0.036 (EPB) to 0.103 (BSG). As illustrated in Fig. 1, there was a global increase in kinship for each
breed over the whole period.
Eradication of recessive disorder
As illustrated in Fig. 2, the three breeding strategies had different impacts on the frequency of the deleterious allele. Removing all
carriers from reproduction (sub-scenario erC) directly decreased
the frequency to a value close to 0, whatever the initial frequency.
Due to importations of some dogs (without known parents and
considered here as founders), allele frequency was not exactly
equal to 0 during the period. When heterozygotes were allowed
to reproduce (sub-scenario erA), the consequences were limited;
for COT, the allele frequency decreased over 10 years to 22% when
the initial frequency was 50% and to 13% when the initial frequency was 20%.
When heterozygote offspring of carriers were not allowed to
reproduce (sub-scenario erI), the decrease in allele frequency was
amplified and reached values close to 0 after 10 years. These results were similar for all four breeds (see Appendix A: Supplementary Fig. 1).
When considering the impact of the different strategies on genetic diversity, more reproducers were removed from the reproductive pool and the kinship increase was larger with increased
severity of selection against disorders and larger initial frequencies
of the deleterious allele (see Appendix A: Supplementary Table 1).
Breeds with small populations were affected more than breeds
with larger populations (Fig. 1). When the initial allele frequency
was set to 20%, kinship increase was, in general, limited. For example, when all carriers were removed from the reproductive pool
(sub-scenario erC) in 2010, U for BSG increased from 0.135 to
0.154 (+14%, P < 0.0001), while there was no change for EPB
(0.037 in each case, P > 0.05).
Simulation process: ‘what if’
Given the genealogical file of a breed, the ‘what if’ simulation process investigated ‘what’ would have happened ‘if’ a given breeding strategy had been applied
over a 10 year period (2001–2010). Evolution of genetic diversity and allele frequencies were compared between the original and the modified pedigree files. Pedigrees were modified using the rule that, for a litter born during the 2001–2010
period, if its sire (or dam) was affected by the mating restriction corresponding
to the breeding policy (see below), the parent was replaced by the sire (or dam)
of another dog randomly sampled from dogs born in the same year and not affected
by the mating restriction. If all potential parents were affected by the mating
restriction, then the sampling was made among dogs born in the preceding year.
Mating restrictions were modelled according to two different breeding scenarios:
Scenario ‘er’
In this scenario, we analysed strategies aiming to eradicate a monogenic recessive disorder, assuming that carriers may be identified early (e.g. through a genetic
test). We compared three sub-scenarios of breeding strategies with an increasing
severity of selection against the disorder. For each sub-scenario, the two initial allele frequencies were considered (20% and 50%): (1) sub-scenario erA, in which,
from the first year of the programme, dogs affected by the disease (i.e. homozygote
aa) were removed from the reproductive pool; (2) sub-scenario erI, an ‘intermediate’
policy in which, from the first year of the programme, dogs affected by the disease
(i.e. homozygote aa) were also removed from the reproductive pool; heterozygote
dogs (Aa) were allowed to reproduce, but their carrier offspring (i.e. heterozygote
Aa or homozygote aa) were removed from the reproductive pool; and (3) sub-scenario erC, in which, from the first year of the programme, carriers (i.e. heterozygote
Aa or homozygote aa) were removed from the reproductive pool.
Scenario ‘ps’
The aim of this scenario was to control the popular sire effect through a limitation on the number of offspring allowed per sire. When a reproducer had exceeded
the maximum number of offspring, it was not allowed to reproduce any more; this
Table 1
Demographic and genealogical characteristics of the four breeds studied.
Breed name
Number of dogs in pedigree file
T
2006–2010 period
Number of dogs
FCI threshold
283
3630
10,784
27,325
14
182
539
1366
Average number of offspring per
reproducer (maximal number observed)
Sires
Braque Saint Germain
Berger des Pyrénées
Coton de Tulear
Epagneul Breton
1999
28,834
40,563
183,181
4.69
4.77
4.37
4.88
14.8
13.2
27.4
18.6
EqG
F
U
7.73
7.22
6.98
9.33
0.073
0.091
0.061
0.056
0.103
0.054
0.039
0.036
Dams
(62)
(82)
(233)
(297)
7.6
7.4
9.8
9.6
(30)
(40)
(39)
(54)
T, generation interval; FCI threshold: 5% of the number of dogs produced during the 2006–2010 period; EqG, number of equivalent generations; F, mean inbreeding
coefficient; U, mean kinship coefficient.
161
345
BSG
0.25
0.25
0.20
0.2
0.15
0.15
0.10
0.1
BRP
0.05
1990
COT
2000
2005
2010
0.05
1990
0.08
0.08
0.07
0.07
0.06
0.06
0.05
0.05
0.04
0.04
0.03
1990
1995
2000
2005
2010
0.03
1990
0.06
0.06
0.05
0.05
0.04
0.04
0.03
0.03
0.02
1990
EPB
1995
1995
2000
2005
2010
0.02
1990
0.05
0.05
0.04
0.04
0.03
0.03
0.02
1990
1995
2000
2005
2010
0.02
1990
1995
2000
2005
2010
1995
2000
2005
2010
1995
2000
2005
2010
1995
2000
2005
2010
Year
Year
Initial frequency: 20%
Fig. 1. Evolution of average kinship (U) over 10 years according to scenarios related to the eradication of a monogenic recessive disorder. BSG, Braque Saint Germain; BRP,
Observed evolution;
scenario erA; scenario erI;
scenario erC.
Berger des Pyrénées; COT, Coton de Tulear; EPB, Epagneul Breton.
Allele frequency
0.25
0.60
0.2
0.40
0.15
0.1
0.20
0.05
0
1990
1995
2000
2005
2010
0.00
1990
1995
2000
2005
Year
Year
2010
Fig. 2. Evolution of the frequency of a deleterious allele over 10 years according to scenarios related to the eradication of a monogenic recessive disorder in the Coton de
Observed evolution;
scenario erA; scenario erI;
scenario erC.
Tulear.
When the initial allele frequency was set to 50%, kinship increase was much higher. In 2010 for BSG, U increased from
0.135 to 0.154 for erA (+14%, P < 0.0001), 0.19 for erI (+41%,
P < 0.0001) and 0.21 for erC (+56%, P < 0.0001). However, the impacts were limited for EPB when considering the last year of simulation. Proportionally to absolute kinship increase, DU
computed from 2000 to 2010 was also affected (see Appendix A:
Supplementary Table 2), e.g. for BSG, DU increased from 1.3% to
5.3% per generation when the erC scenario was applied with an initial allele frequency of 50%.
162
Limitation of popular sire effect
Application of sub-scenarios involving increasing constraints on
the number of offspring had an impact on the proportion of replaced
parents (Table 2), as well as the average kinship (Fig. 3). When
limiting the number of offspring to 200 per reproducer (ps200), only
a small proportion of matings were affected. There was no impact on
U for BSG and BRP, while there were small decreases in U
from 0.038 to 0.036 ( 6%, P < 0.0001) and from 0.038 to 0.037
( 4%, P < 0.0001) for COT and EPB, respectively, in 2010.
346
Table 2
Proportion of sires and dams changed over the 2001–2010 period depending on the maximum number of offspring allowed per reproducer (ps scenarios).
Breed name
Proportion of sires and dams changed (%)
Threshold: 25
Braque Saint Germain
Berger des Pyrénées
Coton de Tulear
Epagneul Breton
Threshold: 50
Threshold: 100
Threshold: 200
Sire
Dam
Sire
Dam
Sire
Dam
Sire
Dam
22.8
67.0
–
–
5.8
10.0
–
–
2.9
19.0
76.9
49.0
0
0.1
0.3
1.3
0
2.8
35.7
22.7
0
0
0
0
0
0.3
6.8
4.6
0
0
0
0
Non-random replacement of reproducers
0.15
BSG
0.13
0.11
0.09
0.07
0.05
1990
1995
2000
2005
2010
Fig. 4 illustrates the evolution of kinship in COT when breeders
tend to choose replacement sires and dams more related or less related to the replaced one under two scenarios (erC initial allele frequency = 50% and ps50). The replacement of reproducers by related
animals tended to increase average kinship, while choosing unrelated reproducers tended to decrease kinship.
0.07
Discussion
BRP
0.06
0.05
0.04
0.03
1990
1995
2000
2005
2010
1995
2000
2005
2010
1995
2000
2005
2010
COT
0.05
0.04
0.03
0.02
1990
EPB
0.05
0.04
0.03
0.02
1990
Year
Fig. 3. Evolution of average kinship (U) over 10 years according to scenarios related
to the limitation of the number of offspring allowed per reproducer. BSG, Braque
Saint Germain; BRP, Berger des Pyrénées; COT, Coton de Tulear; EPB, Epagneul
Observed evolution;
scenario ps200;
scenario ps100;
scenario
Breton.
scenario ps25 (only for BSG and BRP).
ps50;
When a smaller number of offspring was allowed, the proportion of affected matings increased dramatically, modifying kinship
evolution at the same time. When the number of permitted offspring was limited to 50, sires were replaced for 77% of COT individuals, leading to a decrease in U from 0.038 to 0.032 for this
breed in 2010 ( 15%, P < 0.0001), while sires were replaced for
19% of BRP individuals, resulting in a decrease in U from 0.061
to 0.055 ( 10%, P < 0.0001). In BSG, there was little change in evolution of diversity in consecutive ps sub-scenarios. When the number of offspring per reproducer was limited to 25, there was an
unexpected increase of U from 0.135 to 0.149 in 2010 (+10%,
P < 0.0001).
Management of genetic diversity constitutes an important issue
for controlling the dissemination of inherited diseases and hence
the welfare of dogs. In the present study, we used kinship to investigate the evolution of genetic diversity, since it is a key component
of breed conservation (Baumung and Sölkner, 2003) and is directly
related to the number of founder genome equivalents, i.e., theoretical remaining alleles inherited from founders (Caballero and Toro,
2000). Therefore, the risk of spreading new inherited disorders is
proportional to kinship increase. In an ideal closed population,
average kinship increases steadily over time. However, in practice,
fluctuations in its evolution may occur due to practices such as
importation of dogs without known pedigree.
The ‘what if’ procedure developed in this study was used to
investigate the consequences of breeding practices based on real
pedigree data. It takes into account parameters that are difficult
to include together in classical population simulations, such as
overlapping generations, non-random mating and bottleneck
events. Using sub-scenario erI, in which heterozygotes were allowed to reproduce, but their carrier offspring were removed from
reproduction, it was estimated that a deleterious allele could be
eliminated after 10 years of selection.
In practice, the FCI recommendations concerning the number of
offspring per reproducer are not applicable for the BRP, COT and
EPB (Table 1), since the maximum number of puppies produced
by all reproducers in the period from 2006 to 2010 was less than
the recommended threshold specific to each breed. Furthermore,
the FCI recommendation would be difficult to implement for the
BSG breed, since sires currently produce more offspring on average
than the recommended threshold. However, our simulation approach enables specific recommendations to be provided within
the context of a given breed.
The approach used in this study relies on several hypotheses
and simplifications. We assumed that the current genetic structure
would be similar to that of 10 years previously, but this may lead
to bias if the breed has undergone a large change in population
size. We also assumed that there was random replacement of
reproducers, which seldom happens in real populations. As illustrated in Fig. 4, a non-random choice of replacement sires or dams
may have an effect on the evolution of diversity. It is difficult to
estimate if, and at which level, breeders may choose reproducers
more related or less related to the replaced ones; however, future
163
347
Year
Year
Scenario erC (Initial allele frequency = 50%)
Scenario ps50
Fig. 4. Evolution of average kinship (U) over 10 years for scenarios erC (initial allele frequency = 50%) and ps50 in the Coton de Tulear, according to the level of relatedness
between replaced sires and dams and sires and dams chosen for replacement. U, Kinship;
observed evolution; scenario with random replacement;
scenario with
scenario with 50% of replacement sires (or dams) sampled
50% of replacement sires (or dams) sampled among the 10th percentile of the most related sire (or dam);
among the 10th percentile of the least related sire (or dam).
surveys could be implemented to give an indication about such
choices.
On the basis of these results, some recommendations can be
made for each of the four breeds included in this study, considering
either an absolute increase in kinship or evolution of DU over the
10 year period according to scenario. To limit the extent of
inbreeding depression, it is generally considered that acceptable
values of inbreeding (or kinship) rate per generation should not
be >0.5–1% (Bijma, 2000). This value could be somewhat larger
or smaller than the threshold for the BRP and COT, depending on
the various scenarios considered in this study. Note that in scenarios aiming to eradicate a monogenic recessive disorder, a brief increase of rate in kinship was followed by more stable kinship
evolution once the disease had been removed.
Given its small population size, the situation with the BSG
seems to be the most problematic. In order to remove a deleterious
allele with a large frequency (50%) from the breed, the most efficient eradication policies (erI and erC) should be excluded, given
their potential negative impact on genetic diversity. For a moderate frequency of the allele (20%), it is more conceivable to use such
policies, even if the predicted impact on genetic diversity (a relative increase in kinship level of 14% in 2010) is not negligible.
Otherwise, given the efforts already implemented for the management of genetic diversity within the breed, imposing a reasonable
threshold of number of offspring will not improve the situation
substantially. The two sires used the most in 2010 show a low level
of kinship with the current population, explaining why kinship was
increased when applying the ps25 scenario. The recommendation
could be made to increase the number of reproducers or to implement more binding breeding schemes, for example minimising
kinship (Fernandez et al., 2005). Outcrossing may be an interesting
option for the BSG and is periodically used by the breed society.
In the BRP and COT, the same recommendations could be given
regarding eradication of a specific disease. For a large allele frequency (50%), directly removing all carriers (erC) is not desirable,
since DU computed over the period would increase from 0.5% to
1.2% and from 0.1% to 0.8%, respectively (see Appendix A: Supplementary Table 2), exceeding recommended thresholds. An intermediate policy (erI) would have a moderate impact on genetic
diversity (a relative increase in kinship level of 11% and 18% for
BRP and COT in 2010, respectively). For an allele frequency close
to 20%, direct removal of carriers (erC) would have a limited effect
on kinship (a relative increase of 5% and 8% in 2010, respectively).
A greater contrast may be observed between the BRP and COT
when limits are imposed on popular sire effects given a more
‘intensive’ use of reproducers in the COT. In this breed, in order
to have a relative decrease of kinship level of 15%, no reproducer
should produce more than 50 offspring, which in turn would affect
164
77% of the matings with respect to sire replacement. It would be
more reasonable to recommend a threshold around 100 (36% of
mating affected regarding sire pathway), even if the impact on genetic diversity will be more limited (a relative decrease of U of
10%). In the BRP, a threshold of 50 would allow kinship rate to
decrease from 0.5% to 0.2%.
In the EPB, even with a high frequency of a deleterious allele, direct removal of carriers would not affect genetic diversity substantially and erC policy can be recommended in any case. Given the
large number of reproducers within the breed, even when a large
number of individuals are removed from reproduction, the probability of a complete loss of genetically original families is small.
Therefore, the risk of occurrence of a bottleneck in relation to
breeding strategies is more limited within the EPB breed. An offspring threshold of 100 should be adequate for the breed, since
changing only 23% of sires in 2010 would have led to a predicted
relative decrease of kinship of 12%.
Conclusions
The simulation method developed here sought to assess the impact of different breeding strategies on the frequency of a deleterious allele and on genetic diversity for four French dog breeds. By
simulating changes occurring within a pedigree file after implementation of a chosen breeding strategy, we have provided breed-specific recommendations relating to issues such as the removal of an
inherited disease or limitation of number of offspring per reproducer. The choice of a given strategy is also highly dependent on
the existence of other traits to be selected, such as those related to
behaviour and to severity of the disease. For a same frequency, a disease with a dramatic impact on viability will likely require a stricter
breeding policy than a mildly deleterious one. Adaptation of the
procedure to more complex situations (more complex inheritance,
segregation of several diseases) could be the subject of further
studies.
None of the authors of this paper has a financial or personal
relationship with other people or organisations that could inappropriately influence or bias the content of the paper.
Acknowledgements
The authors would like to thank the Société Centrale Canine for
the providing data, Michèle Tixier Boichard for useful discussions,
and Andrea Rau and Wendy Brand-Williams for linguistic revision.
348
Appendix A. Supplementary material
Supplementary data associated with this article can be found, in
the online version, at http://dx.doi.org/10.1016/j.tvjl.2012.06.025.
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165
Contents lists available at ScienceDirect
How the Orthopedic Foundation for Animals (OFA) is tackling inherited disorders
in the USA: Using hip and elbow dysplasia as examples
G. Gregory Keller a,⇑, Edmund Dziuk a, Jerold S. Bell a,b
a
b
Orthopedic Foundation for Animals, Columbia, MO 65201-3806, USA
Department of Clinical Sciences, Tufts Cummings School of Veterinary Medicine, North Grafton, MA 01536-1895, USA
a r t i c l e
i n f o
Keywords:
Canine
Inherited disorders
Hip dysplasia
Elbow dysplasia
Genetic registry
a b s t r a c t
The Orthopedic Foundation for Animals (OFA) maintains an on-line health pedigree database for inherited disorders of animals. With the American Kennel Club Canine Health Foundation, the OFA maintains
the Canine Health Information Center (CHIC) for parent breed clubs to identify breed-specific required
health tests. Analysis of the results of OFA evaluations in the hip and elbow registries show that selection
based on phenotype improves conformation. Disorders with complex inheritance respond best to selection based on depth (ancestors) and breadth (siblings) of pedigree health test results. This information
can be derived from vertical pedigrees generated on the OFA website.
Introduction
A prominent businessman in the United States, John M. Olin,
was also an avid sportsman and recognized the impact of canine
hip dysplasia on his Labrador retrievers. Along with the Golden Retriever Club of America, German Shepherd Club of America and the
veterinary community, he organized a meeting that eventually led
to the formation of the Orthopedic Foundation for Animals (OFA) in
1966. The OFA is guided by the following four specific objectives:
(1) To collate and disseminate information concerning orthopedic and genetic diseases of animals.
(2) To advise, encourage and establish control programs to
lower the incidence of orthopedic and genetic diseases.
(3) To encourage and finance research in orthopedic and genetic
disease in animals.
(4) To receive funds and make grants to carry out these
objectives.
The OFA is governed by a voluntary Board of Directors. As a notfor-profit organization, the revenue over expenses is either held in
the operating reserve or donated to support animal health-related
research. Most funding is channeled through the American Kennel
Club Canine Health Foundation (AKC-CHF)1 or Morris Animal Foundation, with occasional direct funding. OFA has supported research
⇑ Corresponding author. Tel.: +1 800 4420418x223.
1
E-mail address: ofa@offa.org (G.G. Keller).
See: www.akcchf.org.
doi:10.1016/j.tvjl.2011.06.019
166
not only in orthopedic diseases but also for cancer, cardiac, hepatic,
nephritic, neurologic, ocular and thyroid disease.
While the OFA’s initial focus was canine hip dysplasia, the
mission has broadened to include cats and other genetic
diseases, including elbow dysplasia, patella luxation, autoimmune thyroiditis, congenital heart disease, Legg–Calve–Perthes
disease, osteochondrosis dissecans (shoulder osteochondrosis),
sebaceous adenitis and congenital deafness. The methodology
and criteria for evaluating the test results for each disorder are
independently established by veterinary scientists from their
respective specialty areas and the standards used are generally
accepted throughout the world. Disorders present on the OFA
website include those that have a defined test for normalcy. Disorders such as epilepsy, gastric dilatation/volvulus and cancers
that do not have defined phenotypic or genotypic tests are not
included. If genetic markers for disease liability are identified
in the future, these can be added as tools for genetic disease
control.
The power of the OFA genetic database lies in the compilation
and integration of all health screening information in a single location. For dogs with an existing OFA record, examination results
from the Canine Eye Registry Foundation (CERF) are incorporated
in their OFA record. In addition, the results of genotypic tests that
are either submitted by the owner or through a cooperative agreement with the parent club are also included in the OFA genetic
database. Cutting-edge advancements in molecular genetics now
account for over 90 DNA tests involving over 145 breeds of dogs
and cats.
The collection of such data is meaningless unless the data can
be disseminated to parties of interest. The OFA maintains an
198
G.G. Keller et al. / The Veterinary Journal 189 (2011) 197–202
on-line database of >1 million phenotypic and genotypic test results.2 All normal or grades of normal results in the OFA database
are available on-line. Abnormal or grades of abnormal results are
available on-line if released by the owner, or if the results are part
of a breed club program where all (normal and abnormal) test results are published.
The Canine Health Information Center (CHIC)3 is a program that
is dually sponsored by the OFA and the AKC-CHF. The parent clubs
determine the breed-specific health issues for CHIC certification
and encourage breeder participation in the program. The CHIC program is not about normalcy; it is about health consciousness. Dogs
receive CHIC certification if they have completed the required
breed-specific health testing, regardless of the test results. Other
requirements include permanent identification (tattoo or microchip)
and release to the open database of abnormal results. CHIC encourages health screening to improve the overall health of breeds. There
are presently over 139 parent breed clubs participating, with over
64,500 dogs achieving CHIC certification.
The acceptance of the CHIC certification program by parent
breed clubs and breeders provides an avenue for the only proven
method of genetic disease control: breed-specific phenotypic and
genotypic screening of prospective breeding stock. The CHIC program provides a standard for breeders to practice health-conscious
breeding. It also allows pet owners to screen prospective purchases
for evidence of health-conscious breeding.
Another goal of the CHIC program is to collect and store canine
DNA samples, along with corresponding genealogic and phenotypic information, to facilitate future research and testing aimed
at reducing the incidence of inherited disease in dogs. Researchers
have been hampered by the lack of appropriate DNA samples and
the DNA repository addresses this need. To date, the CHIC DNA
Repository contains DNA from over 12,500 dogs and has received
17 requests from researchers, resulting in the distribution of over
2,200 DNA samples with their appropriate health and pedigree
information.
To evaluate hip dysplasia, the OFA employs the ventrodorsal
hip-extended positioning recommended by the American Veterinary Medical Association (AVMA Council on Veterinary Service,
1961). The in-house radiologist is the sole evaluator for preliminary evaluation of dogs <24 months of age. The reliability of preliminary hip evaluations for predicting of-age OFA ratings was
demonstrated by Corley et al. (1997). Dogs or cats must be
P24 months of age to receive OFA hip certification. Radiographs
are independently evaluated by three board-certified veterinary
radiologists out of a pool of consultants maintained by the OFA.
The consensus rating of these three radiologists becomes the hip
rating that is reported to the owner and referring veterinarian.
There is a high degree of inter- and intra-reader correlation for
conventional and digital images (Corley, 1992; Essman and Sherman, 2006).
Seven OFA hip ratings are reported: Excellent, Good, Fair, Borderline, Mild, Moderate or Severe. The first three ratings are considered to be normal, while the last three ratings are regarded as
dysplastic. A Borderline rating is given when there is no clear consensus between radiologists to place the hips in a category of normal or dysplastic. It is recommended that dogs with this rating
have a repeat radiograph submitted after a minimum of 6 months.
The OFA elbow dysplasia registry employs the protocol established by the International Elbow Working Group (IEWG),4 which
consists of Normal or Grades I, II or III Dysplastic based on the severity of secondary osteoarthritis/degenerative joint disease present on
an extreme flexed mediolateral view (International Elbow Working
Group, 2001). When a specific component of elbow dysplasia is observed, it is reported in addition to the Grade as ununited anconeal
process, osteochondrosis or fragmented medical coronoid process.
Elbow radiographs are subjected to the same of-age or preliminary
evaluation and certification process as hip radiographs.
Diseases with complex inheritance can respond to selective
pressure based on phenotype (Keller, 2006; Pirchner, 1983). In this
manuscript, the OFA hip and elbow registries are used to illustrate
this response.
The OFA hip registry of 1,187,831 evaluations was queried for hip ratings of
progeny where both parents also had known of-age hip ratings. Data were collected
on progeny with of-age or preliminary hip confirmation ratings of normal (Excellent, 1; Good, 2; Fair, 3) or dysplastic (Mild, 5; Moderate, 6; Severe, 7). Progeny with
Borderline (4) hip ratings were not included. The hip ratings of both parents were
recorded, including all seven grades. A hip Combined Parent Score (CPS) for each
mating was determined by adding together the numbers corresponding to the
hip rating for each parent; for two OFA Excellent parents the CPS was 2 and for
two OFA Severe parents the CPS was 14. Matings with the same CPS were combined
together for analysis; e.g. Good mated to Borderline, Fair mated to Fair and Excellent mated to Mild all have a CPS of 6.
The OFA elbow registry of 260,195 evaluations was queried for elbow ratings of
progeny where both parents had known of-age elbow ratings. Data were collected
on progeny with preliminary or of-age elbow confirmation ratings of Normal (1) or
dysplastic (Grade I, 2; Grade II, 3; Grade III, 4). An elbow CPS for each mating was
determined by adding together the numbers corresponding to the elbow rating for
each parent; for two OFA Normal parents the CPS was 2 and for two OFA Grade III
parents the CPS was 8. Matings with the same CPS were combined together for
analysis.
Pearson correlation analysis was performed to compare the CPS of matings to
the observed percentages of hip dysplasia or elbow dysplasia in the progeny.
Results
Table 1 shows the hip ratings for 490,966 progeny in the OFA
hip registry with known sire and dam hip ratings. The percentage
of dysplastic progeny increased as the parental hip scores increased. The total number of hip radiograph submissions from parents with normal hip ratings was significantly greater than those
from parents with dysplastic hip ratings (P > 0.05).
Fig. 1 shows the relationship between the CPS and the percentage of dysplastic progeny. Matings with the same CPS (on the diagonal of Table 1) were strongly correlated with increasing
percentages of dysplastic progeny (Pearson correlation coefficient
r = 0.96; P > 0.05). The single CPS that did not reflect this trend
was for matings between two severely dysplastic parents, where
only 18 progeny were submitted for evaluation.
Table 2 shows the elbow ratings for 67,599 progeny in the OFA
elbow registry with known sire and dam elbow ratings. Matings
including one normal parent had significantly lower percentages
of progeny with elbow dysplasia (12.4%) than those between two
parents with elbow dysplasia (45.4%) (P > 0.05). Matings involving
a parent with Grade I elbow dysplasia produced significantly more
elbow dysplasia (25.6%) than matings including a parent with normal elbows (v2 = 0.77, 6 df, P = 0.99).
Fig. 2 shows the relationship between the CPS and the percentage of progeny with elbow dysplasia. The Pearson correlation coefficient between the CPS and percentage of dysplastic progeny was
r = 0.06. The lack of correlation is due to the low percentage of dysplasia in progeny of Grade III sires bred to Grade II dams, and Grade
III parents bred to each other. The total number of progeny from
these matings numbered 14 and 3, respectively.
Discussion
2
3
4
See: www.offa.org.
See: www.caninehealthinfo.org.
See: www.iewg-vet.org/.
The OFA hip data and CPS demonstrate that hip dysplasia is
inherited in an additive and quantitative manner. This verifies
167
199
Table 1
Progeny results of matings between parents with known hip scores.
Sire rating
Excellent (1)
Dysplastic (%)
Total
Good (2)
Dysplastic (%)
Total
Fair (3)
Dysplastic (%)
Total
Borderline (4)
Dysplastic (%)
Total
Mild (5)
Dysplastic (%)
Total
Moderate (6)
Dysplastic (%)
Total
Severe (7)
Dysplastic (%)
Total
Total
Dam rating
Total
Excellent (1)
Good (2)
Fair (3)
Borderline (4)
Mild (5)
Moderate (6)
Severe (7)
3.6
17,972
6.1
52,784
9.6
9039
12.3
155
13.4
1271
18.7
729
18.5
65
82,015
5.8
50,485
9.6
217,938
14.6
49,212
17.5
811
18.9
6930
23.0
3973
31.5
461
329,810
9.4
6241
14.1
41,628
19.8
13,513
22.8
263
26.5
2301
32.2
1328
37.1
167
65,441
8.9
79
17.7
532
20.2
168
22.2
9
30.8
39
50.0
30
50.0
4
861
16.4
807
18.3
4531
27.2
1532
36.2
47
29.6
459
41.4
239
45.0
40
7655
18.9
428
22.8
2618
31.6
896
34.4
32
35.0
266
38.0
213
65.3
49
4502
22.0
59
24.2
360
36.0
136
44.4
9
39.6
48
55.8
52
44.4
18
682
76,071
320,391
74,496
1326
11,314
6564
804
490,966
Fig. 1. Relationship of Combined Parent Score to percentage of hip dysplastic progeny.
the conclusions of other researchers that canine hip dysplasia is
inherited as a quantitative trait (Leighton, 1997; Zhu et al., 2009;
Hou et al., 2010). Hou et al. (2010) analyzed all Labrador retrievers
in the open-access OFA hip database and calculated an heritability
of 0.21, which confirms hip dysplasia acting as a moderately heritable disease. They also confirmed a steady genetic improvement
168
of OFA hip ratings in the breed over a 40 year period. These results
validate the OFA recommendation that using parents with better
phenotypic hip conformation produces offspring with better hips.
It was expected that fewer radiographs would be submitted for
the progeny of two dysplastic parents, since fewer breeders perform such matings. The low numbers may also be due to pre-
200
Table 2
Progeny results of matings between parents with known elbow scores.
Sire rating
Normal (1)
Dysplastic
(%)
Total
Grade I (2)
Dysplastic
(%)
Total
Grade II (3)
Dysplastic
(%)
Total
Grade III (4)
Dysplastic
(%)
Total
Total
Dam rating
Total
Normal
(1)
Grade I
(2)
Grade II
(3)
Grade III
(4)
10.1
24.1
29.4
28.1
55,867
4309
875
167
22.0
41.0
46.9
52.2
3917
591
145
23
32.6
55.4
65.8
57.1
1121
222
38
14
23.9
38.1
14.3
0.0
251
42
14
3
61,156
5164
1072
207
61,218
4676
1395
310
67,599
screening of radiographs with obviously dysplastic hips by veterinarians; these radiographs may not be submitted to the OFA for
evaluation (Paster et al., 2005). This would reduce the resultant frequencies of dysplastic individuals. Prescreening of dysplastic
radiographs for OFA submission appears to be constant over time
(Reed et al., 2000).
Traits such as hip dysplasia and elbow dysplasia are complexly
(polygenically) inherited, with increasing incidence based on
increasing frequencies of susceptibility alleles at loci that contribute to variation in liability. Selection based on vertical or depth-ofpedigree hip ratings (parents and grandparents), when combined
with an individual’s own rating, increases the accuracy of selection
and hence response to selection. Similarly, selection based on horizontal or breadth-of-pedigree hip ratings (siblings), when combined with an individual’s own rating, increases accuracy of
selection and hence response to selection (Pirchner, 1983; Keller,
2006).
Breeding schemes that employ estimated breeding values
(EBVs) that combine phenotypic ratings from all known relatives
(weighted according to genetic relationship) provide the greatest
selective power, rather than single measurements on individual
dogs (Zhu et al., 2009; Hou et al., 2010). EBVs that utilize molecular
genetic markers for liability genes would be even more beneficial
(Stock and Distl, 2010; Zhou et al., 2010).
The open-access OFA health database website provides breeders with the information that helps them to make informed breeding decisions. When an individual dog’s record is accessed, detailed
information on all recorded health issues, including test results,
age at the time of testing and the resulting certification numbers,
are available. Sire and dam information are provided, as well as
information on full and half siblings and any offspring that may
be in the database. A vertical pedigree can be generated from a link
on the individual’s OFA page, providing traditional depth of pedigree and breadth of pedigree health information. This type of data
is extremely useful when trying to make selection decisions based
on phenotypic data.
The vertical hip pedigree of the Golden retriever Champion (Ch.)
Faera’s Starlight (Fig. 3) shows how parent, grandparent, offspring
and sibling information are combined in a single graphic format for
evaluation. Whilst this dog had hips with an Excellent rating, he
was bred from Fair- and Good-rated parents, with three Fair- and
one Good-rated grandparents. While he produced 92.4% normal
offspring with a preponderance of Good ratings, he produced more
Fair- than Excellent-rated offspring. The vertical pedigree provides
more information than the single individual rating. Vertical
Fig. 2. Relationship of Combined Parent Score to percentage of elbow dysplastic progeny.
169
201
Fig. 3. OFA vertical pedigree of Golden retriever Ch. Faera’s Starlight.
pedigrees of individual animals are available on the OFA website
for the hip, elbow, cardiac, thyroid, patella, CERF (eye) and degenerative myelopathy registries.
EBV technology would combine all of the phenotypic information in Fig. 3 into a single measurement that provides the most
accurate possible prediction of the average performance of the offspring of the dog in question (Faera’s Starlight). However, the individual’s OFA page and vertical pedigree allows the breeder to
determine where the liability comes from in the pedigree, the specific results from each mating and each dog’s strengths and weaknesses. These are useful tools for selection and genetic
improvement.
The distraction index (DI) measurement of the PennHIP method
for hip dysplasia control employs a mechanical distraction device
to measure maximal hip joint laxity as a predictor of future degenerative joint disease and osteoarthritis (Smith et al., 1990). PennHIP studies show that the OFA rating and DI measurement are
significantly associated (Powers et al., 2010) and DI measurements
submitted by their owners to the OFA are included in the hip dysplasia registry.
While the DI provides a measurement of laxity, it does not take
into account degenerative joint disease or osteoarthritic changes.
Studies have shown that liability for hip dysplasia and liability
for osteoarthritis are controlled by separate genes (Clements
et al., 2006; Zhou et al., 2010). The OFA hip rating incorporates
170
an evaluation of both subluxation on the ventrodorsal hip-extended view, as well as radiographic anatomy and secondary
boney changes.
The PennHIP method recommends selection based on the DI
measurement of individual dogs. Based on PennHIP data of dogs
presented to the University of Pennsylvania School of Veterinary
Medicine, 100% of Golden retrievers and 89% of Labrador retrievers
who received normal OFA ratings were deemed osteoarthritis-susceptible by their DI (Powers et al., 2010). Powers et al. (2010) also
raised the possibility that the Cardigan Welsh Corgi is genetically
fixed for hip dysplasia, based on DI measurements for the breed.
However, the clinical presentation of disease in these breeds does
not bear out these predictions, suggesting that there is a high falsepositive rate for DI prediction of clinical disease. A study correlating ventrodorsal hip-extended radiographic ratings to later insurance-related claims for hip dysplasia showed a strong association
(Malm et al., 2010). Data correlating DI measurements to morbidity from clinical disease have not been published.
Dog breeds have closed stud books and dog breeders have concerns about genetic diversity and the effects of artificial selection
on their gene pools (Calboli et al., 2008). The removal of 89% or
more of possible breeding stock for a single genetic disorder
(which would be required in order to breed only from those Labrador retrievers with acceptable DI) will doom any breed to extinction from genetic depletion. While breeding from only OFA
202
Excellent dogs will significantly improve hip ratings of progeny,
the elimination of the rest of the phenotypically normal dogs from
breeding (most of which produce predominantly normal dogs)
would also severely restrict the gene pools of breeds. Pragmatic
breeding recommendations include breeding from normal dogs
with increasing normalcy of parents, grandparents, siblings and
progeny, as shown on the OFA vertical pedigree, and through the
use of EBVs.
The significant difference between progeny from one parent
with normal elbows and progeny from two parents with dysplastic
elbows suggests a qualitative trait. However, it is established that
elbow dysplasia is a polygenic (multifactorial) trait (Engler et al.,
2009). Increasing CPS tended to increase the frequency of elbow
dysplasia in the progeny, but low numbers of submissions for some
mating types between dysplastic parents skewed the results, making the correlation inconclusive. Again, pre-screening and non-submission to OFA of obviously dysplastic radiographs may have
affected the data.
Grade I elbow dysplasia is a radiographic diagnosis that usually
does not produce clinical disease or morbidity in the dog. Some
breed groups counsel owners to ignore the diagnosis of Grade I elbow dysplasia and to treat these dogs as if they were normal. However, the data presented here demonstrates that progeny from a
parent with Grade I elbow dysplasia, when bred to mates from
all other rating classifications, have a significantly increased frequency of elbow dysplasia. These results are significantly different
from the results observed with progeny from one normal parent
bred to mates from all other rating classifications.
The data show that even two dogs with normal elbow radiographs may produce 10.1% progeny with elbow dysplasia. This is
where consideration of depth and breadth of pedigree information
becomes important. Any rating of elbow dysplasia in siblings of
dogs with a normal elbow rating provides evidence that the normal
dog may carry additional elbow dysplasia liability alleles.
Selection for increasing normalcy of depth and breadth of pedigree information provides a better selection tool for complexly
inherited disease. The use of the OFA vertical pedigree provides
the information necessary to make informed breeding decisions.
The addition of EBVs that combine all of this information (Engler
et al., 2009) and that also include genotypes of DNA markers for
liability genes (Stock and Distl, 2010; Zhou et al., 2010) would be
even more beneficial.
Conclusions
The OFA data show that hip and elbow conformation improve
with improving parental phenotypic ratings. The open access OFA
website provides health test results on individuals, as well as depth
and breadth of pedigree health information on closely related individuals. This information provides the best means for making
breeding decisions for both complexly inherited and Mendelian
disorders.
The authors are Chief of Veterinary Services (GGK), Chief Operating Officer (ED) and Director (JSB) of the not-for-profit Orthopedic Foundation for Animals.
Acknowledgement
The authors thank Ms. Rhonda Hovan for allowing use of the
pedigree of Ch. Faera’s Starlight.
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171
Comparative analyses of genetic trends and
prospects for selection against hip and elbow
dysplasia in 15 UK dog breeds
Lewis et al.
Lewis et al. BMC Genetics 2013, 14:16
172
RESEARCH ARTICLE
Open Access
Comparative analyses of genetic trends and
prospects for selection against hip and elbow
dysplasia in 15 UK dog breeds
Thomas W Lewis1*, Sarah C Blott1 and John A Woolliams2
Abstract
Background: Hip dysplasia remains one of the most serious hereditary diseases occurring in dogs despite
long-standing evaluation schemes designed to aid selection for healthy joints. Many researchers have
recommended the use of estimated breeding values (EBV) to improve the rate of genetic progress from selection
against hip and elbow dysplasia (another common developmental orthopaedic disorder), but few have empirically
quantified the benefits of their use. This study aimed to both determine recent genetic trends in hip and elbow
dysplasia, and evaluate the potential improvements in response to selection that publication of EBV for such
diseases would provide, across a wide range of pure-bred dog breeds.
Results: The genetic trend with respect to hip and elbow condition due to phenotypic selection had improved in
all breeds, except the Siberian Husky. However, derived selection intensities are extremely weak, equivalent to
excluding less than a maximum of 18% of the highest risk animals from breeding. EBV for hip and elbow score
were predicted to be on average between 1.16 and 1.34 times more accurate than selection on individual or both
parental phenotypes. Additionally, compared to the proportion of juvenile animals with both parental phenotypes,
the proportion with EBV of a greater accuracy than selection on such phenotypes increased by up to 3-fold for hip
score and up to 13-fold for elbow score.
Conclusions: EBV are shown to be both more accurate and abundant than phenotype, providing more reliable
information on the genetic risk of disease for a greater proportion of the population. Because the accuracy of
selection is directly related to genetic progress, use of EBV can be expected to benefit selection for the
improvement of canine health and welfare. Public availability of EBV for hip score for the fifteen breeds included in
this study will provide information on the genetic risk of disease in nearly a third of all dogs annually registered by
the UK Kennel Club, with in excess of a quarter having an EBV for elbow score as well.
Keywords: Canine, Hip dysplasia, Elbow dysplasia, Estimated breeding value, Selection, Accuracy, Genetic
correlation, Heritability, Welfare
Background
Hip dysplasia may be described as one of the most serious hereditary diseases occurring in pedigree dogs given
the popularity of susceptible breeds and the prevalence
therein [1,2]. It is also one of the most persistent, first
having been described over 50 years ago [3-5]. Hip dysplasia is a developmental orthopaedic disorder characterised
by the formation of a dysmorphic, lax (loose) coxo-
femoral (hip) joint [6]. Over time, particularly in larger
and giant breeds, the malformation and laxity lead to the
abnormal wearing of bone surfaces and the appearance of
the osteoarthritic signs of degenerative joint disease (DJD)
[7]. The resultant osteoarthritis (OA) is irreversible and so
the only way to effect a lasting and widespread improvement in the welfare of susceptible breeds is through genetic
selection. Hip dysplasia remains a significant problem,
despite the presence of several evaluation schemes across
the world designed to provide an empirical phenotype for
selection, partly due to its complexity; a polygenic background and multiple environmental influences ensure no
* Correspondence: tom.lewis@aht.org.uk
1
Kennel Club Genetics Centre at the Animal Health Trust, Lanwades Park,
Kentford, Newmarket, Suffolk CB8 7UU, UK
Full list of author information is available at the end of the article
© 2013 Lewis et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative
Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and
reproduction in any medium, provided the original work is properly cited.
173
Page 2 of 11
increased accuracy and abundance of reliable information that publication of EBV would provide.
clear pattern of inheritance. Furthermore, the breeding
guidelines accompanying evaluation schemes have often
elicited only very weak selection [8,9].
In contrast elbow dysplasia, despite also being a developmental orthopaedic abnormality long recognised as a
serious problem [10], has historically received less attention than hip dysplasia. As a result, schemes evaluating
elbow condition are younger than those examining hips,
and so data is less abundant. The term ‘elbow dysplasia’
commonly describes a number of abnormalities associated with developmental physiological incongruity of the
elbow joint that often result in OA [11].
This grouping of syndromes for both the pathology
and evaluation of elbow dysplasia may result in underestimates of heritability [12]; which range from 0.10 to
0.38 [13-17] among various breeds. Analyses of more
specific elbow abnormalities have estimated higher heritabilities; for example 0.57 for fragmented coronoid
process in German Shepherd Dogs [9]. Estimates of heritability of hip condition generally have a smaller range
but appear moderate in magnitude, from 0.20 to 0.43
across various breeds [8,14,16,18-20] despite using data
from different international scoring schemes and hips
being evaluated on both detectable laxity and OA. The
reported genetic correlation between hip and elbow condition varies even more, from −0.09 to 0.42 [9,14,16,17].
Many recent studies estimating the genetic parameters
of hip and elbow dysplasia score data have recommended selection using estimated breeding values (EBV;
[8,9,14,16,19-21]. EBV are the best linear unbiased predictor (BLUP) of every dog’s breeding value derived from
the pedigree information used in its calculation [1], and
are a more accurate estimate of the genetic liability of a
trait than the individual phenotype. However, attempts
to quantify the potential benefit to the response to selection against hip and elbow dysplasia that the increased
accuracy of selection using EBV would bring (compared
to phenotypic selection) are less common than parameter estimation, but have been made empirically by
Lewis et al. [8], and via simulation by Stock and Distl
[22] and Malm et al. [23]. Improvements in the rate of
genetic progress (which is directly related to the accuracy of selection, [24]) would be achieved not only
through EBV acting as a more accurate predicator of
genetic risk (i.e. the true breeding value) than phenotype,
but also through enhanced opportunities to increase selection intensity due to EBV being available for every
dog in the pedigree [25]. EBV would effectively provide
a greater quantity of more reliable information with respect to breeding. This study, therefore, aims to estimate
the genetic parameters of hip and elbow dysplasia in
the UK registered breeds for which score data is most
abundant, determine any genetic trends and evaluate
potential improvements in response to selection due to
Methods
Data
Phenotype data comprised results of the British Veterinary
Association (BVA)/UK Kennel Club (KC) hip and elbow
scoring schemes. Details of scoring protocols are given by
Gibbs [26] and Lewis et al. [17]. In brief, radiographs of
hips are scored bilaterally on 9 features according to the
degree of laxity and/or OA observed (8 features scored
0 to 6, one feature scored 0 to 5). The aggregate of the
18 scores reported ranges from 0 (indicating no malformation) to 106 (severe hip dysplasia). The BVA/KC elbow
scoring scheme was launched in 1998 based on guidelines
of the International Elbow Working Group (IEWG).
Elbow radiographs are scored according to the size of
detectable primary lesions and severity and extent of OA
observed, ranging from 0 (normal) to 3 (severe elbow dysplasia). The score of the worst elbow only is publically
reported. Pedigree data was provided by the KC and linked
to phenotype data via a unique registration number.
Fifteen breeds (Akita [AKT], Bearded Collie [BEARD],
Bernese Mountain Dog [BMD], Border Collie [BORD],
English Setter [ENG], Flat Coat Retriever [FCR], Gordon
Setter [GDN], Golden Retriever [GR], German Shepherd
Dog [GSD], Labrador Retriever [LAB], Newfoundland
[NEWF], Rottweiler [ROTT], Rhodesian Ridgeback [RR],
Siberian Husky [SHUSK] and Tibetan Terrier [TT])
were included in the study. For 5 breeds (BMD, GR,
GSD, LAB and ROTT) the genetic parameters of hip
and elbow score were estimated using bivariate analyses.
For the remaining 10 breeds, the genetic parameters of
hip score only were estimated using univariate analyses.
For the ten breeds with hip score only, genetic parameters and EBV were estimated simultaneously using data
from dogs evaluated at 365–1459 days old and between
1990 and 2011 inclusive, and the entire KC electronically
recorded pedigree extending back to the early 1980s;
hip score having undergone transformation to improve
normality (see below). For BMD and ROTT genetic parameters and EBV were computed simultaneously for
hip and elbow data via bivariate REML analyses using
evaluations from dogs of the same age and study period
and the entire KC electronic pedigree. The pedigrees of
LAB, GSD and GR were too large to include in their entirety in bivariate parameter estimation on a desktop PC,
and so for parameter estimation in these breeds data
and/or depth of pedigree was truncated. For GSD and
GR genetic parameters of hip and elbow score were estimated using data from all dogs of the same age and
study period with a further 5 generations of pedigree.
For LAB genetic parameters of hip and elbow scores
were estimated using data from all dogs evaluated at the
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Page 3 of 11
same age and between 2000–2011, and 2 further generations of pedigree. The genetic parameters for LAB, GSD
and GR were then used in the calculation of BLUP EBV
using hip and elbow data from 1990–2011 and the entire
KC pedigrees of each breed (GR pedigree = 386,580 animals; GSD pedigree = 572,552 animals; LAB data = 59,077
evaluations, pedigree = 977,083 animals), undertaken by
Edinburgh Genetic Evaluation Service (EGENES) using
MiX99. The numbers of records used in the REML analyses of hip score for each breed are shown in Additional
file 1: Table S1.
Thus, data for EBV computation included 142,287 hip
scores from all fifteen breeds, which have a total mean
of 82,118 registrations per year (2000 to 2010 data), and
13,908 elbow scores from BMD, GR, GSD, LAB and
ROTT; these breeds having a total mean of 70,363 registrations per year (2000–2010 data).
effects. To extend this univariate model to bivariate analyses the variance terms such as σ2 a were replaced by
the appropriate bivariate covariance matrices (Σ) for the
traits using the Kronecker product, such as A ⊗ ΣA. The
phenotypic variance is denoted as σ2P, and heritability
(h2) is calculated as the proportion of phenotypic variance explained by the additive genetic variance (σ2A/σ2P).
Phenotypic, additive genetic and residual correlations
(rP, rA , rE) were computed from the genetic (co)variances
obtained.
Fixed effects included in the model were: sex, inbreeding coefficient (as calculated using the entire KC electronic pedigree), age in days at evaluation, absolute day
of birth (measured as days since 1st January 1980) and
year of evaluation. Age in days and absolute day of birth
were fitted with random smoothing splines to model
temporal trends [8].
Analyses
Meta-analysis of parameter estimates across breeds
Mixed linear models were fitted using ASREML [27].
For univariate analysis of hip score the model used was
as per Lewis et al. (2010) [8]. For bivariate analysis of
hip and elbow score the model used was as per Lewis
et al. (2011) [17].
Total hip score was log transformed (after adding 1 to
avoid necessitating the logarithm of zero) to improve
normality. Where applicable the untransformed mean of
left and right elbow score was included as a y-variate.
The possible transformation of observed values to more
closely correspond to the underlying liability [17] was
not undertaken as the benefits were found to be small
and because, importantly, the transformation depends
on the prevalence which may change over time. Data
from 3 year old animals (1095–1459 days) were included
for consistency with hip data and after preliminary analysis using Labrador data showed the genetic correlation
of elbow score at 365–1094 days and 1095–1495 days (i.e.
1–2 and 3 year olds) was indistinguishable from 1.
The general form of the univariate linear model was as
follows:
The spread of parameter estimates will be due to two
components: (i) sampling errors within a breed, and (ii)
variation in the true parameter among breeds. A metaanalysis of the parameter estimates was undertaken to
obtain the best estimate of the mean parameter for the
population of breeds, together with a standard error to
account for both sampling and population variation.
This followed the procedures of Corbin et al. [28]. The
analysis provides an estimate of the variance of the true
parameter among breeds, and if this is 0 then the pooled
mean is identical to that obtained from using a weight
for each breed equal to the reciprocal of its sampling
variance.
Accuracy of estimated breeding values
The accuracy (r) of each animal’s EBV was calculated as:
sffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffi
PEV
r ¼ 1
ð1 þ F Þσ 2A
(see Additional file 2), where PEV is the prediction
error variance of each EBV, F is the inbreeding coefficient for each animal and σ2 A is the estimated additive
genetic variance obtained from the mixed model analysis. ASREML provides both the estimates of the EBV
and their associated PEVs.
Potential advantages of using EBV in future selection
for lower hip/elbow scores were evaluated by comparison of mean EBV accuracies with the predicted accuracy
of phenotypic selection in all breeds. Firstly, the mean
EBV accuracy of phenotyped animals born in 2010 (with
no progeny phenotypes) was compared to the accuracy
of phenotypic selection (h, [24]). Secondly, mean accuracy of EBV for animals born in 2011 (<365 days old and
therefore without a phenotype), but for which both
Y ¼ Xb þ Za þ Wc þ e
where Y is the vector of observations, W, X and Z are
known incidence matrices, b is the vector of fixed effects; a is the vector of random additive genetic effects
with the distribution assumed to be multivariate normal
(MVN), with parameters (0, σ2 aA); c is the vector of random litter effects with the distribution assumed to be
MVN, with parameters (0, σ2 cIlitter), and e is the vector
of residuals distributed MVN with parameters (0, σ2 eI).
I represents an identity matrix of an appropriate size,
A is the additive genetic relationship matrix and σ2 denotes the variance of each of the respective random
175
Page 4 of 11
Results
parental phenotypes were available, was compared to the
accuracy of selection using these phenotypes (√(½).h, see
Additional file 3) to determine any potential improvement in the response to selection of breeding animals
prior to obtaining their own scores. Finally, the proportion of animals born in 2011 (so without a phenotype)
with EBV accuracy exceeding √(½).h was calculated and
compared to the proportion where both parental phenotypes were available.
Hips
An average of between 6% (GSD) and 19% (GDN) of all
dogs registered annually since 1990 had been hip scored.
The rate of scoring is higher for breeding animals, with
the mean percentage of breeding animals born annually
since 1990 having undergone hip scoring ranging from
27% of sires and 28% of dams (AKT) to 80% of sires
(GDN) and 86% of dams (BMD), Figure 1. There was
considerable variation in the distribution of total untransformed hip scores (Figure 2 and Additional file 1:
Table S1), with mean hip score ranging from 7.89
(SHUSK) to 23.35 (NEWF), mode from 6 to 10, median
from 8 to 14, and standard deviation from 4.38 (SHUSK)
to 20.49 (NEWF). All distributions were highly skewed,
with coefficient of skewness ranging from 1.46 (NEWF)
to 4.59 (FCR), reflecting the cumulative nature of the
scoring system [29].
The results of the analyses determined that the BEARD
displayed the smallest phenotypic variation (0.219) in log
transformed total hip score and the NEWF the largest
(0.605, Table 1). The FCR exhibited the smallest degree of
additive genetic variation (0.073) of log transformed total
hip score and the NEWF the largest (0.279). Estimates of
heritability of log transformed total hip score ranged from
0.28 (FCR) to 0.48 (SHUSK). Estimates of litter variance
as a proportion of phenotypic variance (not shown)
Assessment of genetic gain to date
The genetic gain as a proportion of genetic standard
deviation was calculated as: (mean EBVmaxyr-mean
EBVminyr)/ σA. For hip score minyr = 1990, and for elbow
score minyr = 2000; maxyr = 2011 for both traits. The
trends in genetic disposition to hip/elbow score were
discerned for each breed via regression of EBVs on date
of birth, and intensity of selection (i) applied estimated
by rearrangement of the following equation:
ΔG ¼ ih2 σ P =L
where ΔG is the genetic trend determined by regression
of EBV on date of birth, h2 is the heritability, σP is the
phenotypic standard deviation, and L is the generation
interval.
Figure 1 Average proportion of breeding animals hip scored. Mean proportion of male and female breeding animals born annually from
1990–2010 that are hip scored for all 15 breeds.
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Page 5 of 11
Figure 2 Hip score distribution for Newfoundland and Siberian Husky. Distribution of total hip score for the Newfoundland (top) and
Siberian Husky (bottom) breeds, from dogs evaluated between 1990–2011 and 365–1459 days old.
ranged from 0.017 (AKT) to 0.141 (GDN), although litter
was not a significant effect in all models. Meta-analysis of
estimates of heritability of hip score across the 15 breeds
indicated only a small degree of heterogeneity among
breeds, with a mean estimate of heritability across breeds
of 0.38 (s. e. 0.014). The estimate of variance of between
breed heritability estimates was 1.8 x 10-3.
Regression of EBV on date of birth showed recent improving (negative) genetic trends significantly different to
zero (P < 0.01) in all cases except that of the SHUSK,
where the genetic disposition towards higher (unfavourable) hip score, while still determinable (P < 0.01), increased at a rate of 0.8% per year (Table 2). Those breeds
showing an improving genetic trend ranged from a decline
in genetic propensity toward hip score of −0.13% per year
(FCR) to −1.98% per year (NEWF) on the untransformed
scale. However, of those breeds showing an improving
genetic trend the derived selection intensities are weak;
equivalent to excluding between less than 2% (BEARD,
FCR and RR) and less than 18% (GDN) of the highest risk
animals from breeding. As a result the genetic progress
made has been slow, with the difference in mean EBV
from animals born in 1990 and 2011 equating to between
only 0.12 (BEARD) and 0.82 (NEWF and GDN) of respective genetic standard deviations.
The mean accuracies of EBV of phenotyped animals
born in 2010 were higher than the predicted accuracy of
Table 1 Parameter estimates of hip score
σ2P
σ2A
h2
s.e.
AKT
0.478
0.187
0.39
0.053
BEARD
0.219
0.100
0.46
0.048
BORD
0.223
0.098
0.44
0.033
ENG
0.295
0.104
0.35
0.049
FCR
0.257
0.073
0.28
0.032
GDN
0.450
0.194
0.43
0.062
NEWF
0.605
0.279
0.46
0.041
RR
0.445
0.146
0.33
0.048
SHUSK
0.349
0.167
0.48
0.038
TT
0.246
0.084
0.34
0.048
BMD
0.355
0.129
0.36
0.040
GR
0.313
0.126
0.40
0.017
GSD
0.390
0.138
0.35
0.015
LAB
0.381
0.126
0.33
0.012
ROTT
0.308
0.120
0.39
Breed
0.028
Estimates of phenotypic and additive genetic variance (σ Pand σ A respectively)
and heritability (h2, with standard error) of hip score for 15 breeds. The top panel
shows parameters for 10 breeds derived from univariate analyses, while the
bottom panel shows parameters for 5 breeds derived from bivariate analyses of
hip and elbow score. Breed abbreviations: Akita [AKT], Bearded Collie [BEARD],
Bernese Mountain Dog [BMD], Border Collie [BORD], English Setter [ENG], Flat
Coat Retriever [FCR], Gordon Setter [GDN], Golden Retriever [GR], German
Shepherd Dog [GSD], Labrador Retriever [LAB], Newfoundland [NEWF], Rottweiler
[ROTT], Rhodesian Ridgeback [RR], Siberian Husky [SHUSK] and Tibetan
Terrier [TT].
2
2
177
Page 6 of 11
animals for which such phenotypes were actually available. The increment ranged from 2% (from 92.8% with
both parental phenotypes to 94.8% with EBV accuracy
> √½.h; ENG), to an increase of over three-fold (from
19.5% with both parental phenotypes to 59.7% with EBV
accuracy > √½.h; AKT). In some cases this jump was not
particularly large, ENG and GDN for example have increments of just 2% and 6% respectively, but in these
cases the increment in actual (mean) EBV accuracy compared to √½.h is large (47% and 32% respectively).
Table 2 Estimates of genetic progress and selection
pressure for hip and elbow score
Hips
Progress / σA
b (x10-2)
i
AKT
−0.28
−0.66
−0.08
<0.04
BEARD
−0.12
−0.16
−0.04
<0.02
p excluded
BORD
−0.36
−0.63
−0.13
<0.07
ENG
−0.67
−1.07
−0.24
<0.13
FCR
−0.17
−0.13
−0.04
<0.02
GDN
−0.82
−1.95
−0.32
<0.18
NEWF
−0.82
−2.00
−0.22
<0.12
RR
−0.19
−0.32
−0.06
<0.02
SHUSK
0.25
0.81
0.12
N/A
TT
−0.36
−0.52
−0.13
<0.06
BMD
−0.30
−0.68
−0.12
<0.06
GR
−0.71
−1.20
−0.23
<0.13
GSD
−0.48
−0.89
−0.16
<0.08
LAB
−0.77
−1.28
−0.28
<0.16
ROTT
−0.59
−0.78
−0.14
<0.07
−0.20
−0.72
−0.11
<0.06
Elbows
Since 2000 between 1% (GR, GSD, LAB) and 15%
(BMD) of all registered dogs of the 5 relevant breeds
have been elbow scored. The rate of scoring is higher for
breeding animals, with the mean percentage of breeding
animals born annually since 2000 having undergone
elbow scoring ranging from 8% of sires and 7% of dams
(ROTT) to 66% of sires and 77% of dams (BMD). There
was variation in the distribution of untransformed elbow
scores with mean elbow score ranging from 0.15 (LAB)
to 0.61 (ROTT), standard deviation from 0.46 (LAB) to
0.87 (BMD) and coefficient of skewness from 0.92
(ROTT) to 3.59 (LAB) (Additional file 4: Table S2). The
LAB displayed the smallest phenotypic variation (0.196)
and additive genetic variation (0.037) in elbow score and
the BMD the largest (0.760 and 0.201 respectively). Estimates of heritability of untransformed mean elbow score
ranged from 0.14 (ROTT) to 0.30 (GR) (Table 4). Metaanalysis of estimates of heritability of elbow score across
the 5 breeds indicated only a small degree of heterogeneity, with an across-breed estimate of heritability of
0.218 (s.e. 0.026). The estimate of variance of between
breed heritability estimates was similar to but smaller
than that for hip score at 0.8 x 10-3. Estimates of litter
variance as a proportion of phenotypic variance (not
shown) ranged from 0.007 (BMD) to 0.146 (ROTT), although litter was not a significant effect in all models.
The genetic correlation between hip and elbow scores
ranged from 0.005 (BMD) to 0.550 (ROTT). However,
the genetic correlation between the two traits was only
determinable as significantly different from zero in LAB
(P < 0.001). The deviation of the correlation from zero in
ROTT approached significance (P = 0.055), suggesting
that more data may have increased the power to detect
significance. Meta-analysis of estimates of genetic correlation between hip and elbow score across the 5 breeds
indicated a greater degree of heterogeneity among
breeds than found with the heritabilities, with an acrossbreed estimate of genetic correlation of 0.216 (s.e.
0.076). The estimate of variance of between breed genetic correlation estimates was 13.1 x 10-3.
Regression of EBV on date of birth showed a recent
slow but significantly (P < 0.05) improving genetic trend
Elbows
BMD
GR
−0.13
−0.31
−0.09
<0.04
GSD
−0.14
−0.21
−0.14
<0.07
LAB
−0.13
−0.18
−0.12
<0.06
ROTT
−0.21
−0.39
−0.15
<0.08
Genetic progress was estimated in two ways: total change as mean EBV2011mean EBV1990 (for hips, EBV2011-mean EBV2000 for elbows) as proportion of
genetic standard deviation (σA) and annually by the regression coefficient
(b) of EBV on date of birth. Selection pressure was described in two ways:
standardised selection intensity (i) against hip/elbow score, and the equivalent
proportion of breeding individuals excluded required to achieve that intensity
by truncation of the distribution. The top panel shows parameters for
10 breeds derived from univariate analyses of hip score and the middle panel
shows hip parameters for 5 breeds derived from bivariate analyses of hip and
elbow score. The bottom panel shows elbow parameters for 5 breeds derived
from bivariate analyses of hip and elbow score. Breed abbreviations: Akita
[AKT], Bearded Collie [BEARD], Bernese Mountain Dog [BMD], Border Collie
[BORD], English Setter [ENG], Flat Coat Retriever [FCR], Gordon Setter [GDN],
Golden Retriever [GR], German Shepherd Dog [GSD], Labrador Retriever [LAB],
Newfoundland [NEWF], Rottweiler [ROTT], Rhodesian Ridgeback [RR], Siberian
Husky [SHUSK] and Tibetan Terrier [TT].
selection on phenotype (h) for all breeds, ranging from
an improvement of 8% (BEARD and SHUSK) to 24%
(FCR) (Table 3). The mean accuracies of un-phenotyped
animals born in 2011 but with phenotyped parents were
higher than the anticipated accuracy of selection on parental phenotypes for all breeds by between 18%
(SHUSK) and 47% (ENG). Importantly the anticipated
accuracy of selection on parental phenotypes (√(½).h) is
optimistic since it ignores all potential biases from fixed
effects and changes in the addititive genetic variance
over generations due to selection [30]. The proportion
of all animals registered in 2011 with EBV accuracies
greater than that anticipated from selection on parental
phenotypes was always greater than the proportion of
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Page 7 of 11
Table 3 Increment in accuracy of selection for low hip score using EBV versus phenotype
Animals with phenotype
Proportion with r > √½.h
Animals with parental phenotype
h
mean r
n
incr
√½.h
mean r
n
incr
EBV
pheno
incr
AKT
0.62
0.74
23
1.18
0.44
0.64
129
1.45
0.597
0.195
3.05
BEARD
0.68
0.73
26
1.08
0.48
0.61
324
1.29
0.923
0.806
1.15
BORD
0.66
0.74
98
1.11
0.47
0.58
910
1.23
0.745
0.583
1.28
ENG
0.59
0.72
18
1.21
0.42
0.62
180
1.47
0.948
0.928
1.02
FCR
0.53
0.66
54
1.24
0.38
0.53
1067
1.39
0.998
0.866
1.15
GDN
0.66
0.73
30
1.12
0.46
0.61
145
1.32
0.928
0.873
1.06
NEWF
0.68
0.75
37
1.11
0.48
0.58
441
1.21
0.829
0.697
1.19
RR
0.57
0.66
20
1.16
0.40
0.52
521
1.28
0.844
0.502
1.68
SHUSK
0.69
0.74
12
1.08
0.49
0.58
288
1.18
0.478
0.209
2.29
TT
0.58
0.70
45
1.19
0.41
0.55
712
1.34
0.928
0.736
1.26
BMD
0.60
0.71
48
1.19
0.43
0.56
402
1.31
0.893
0.754
1.18
GR
0.63
0.73
277
1.15
0.45
0.54
5097
1.21
0.860
0.791
1.09
GSD
0.59
0.69
337
1.15
0.42
0.51
3343
1.21
0.571
0.441
1.29
LAB
0.57
0.70
1004
1.21
0.41
0.52
16160
1.28
0.685
0.494
1.39
ROTT
0.63
0.73
51
1.17
0.44
0.59
565
1.34
0.568
0.361
1.57
Mean
1.16
1.30
1.44
(Left panel) The mean accuracy (r) of EBV of phenotyped animals born in 2010 compared to accuracy of phenotypic selection (h), with the sample size (n) and
increment in accuracy (incr). (Middle panel) The mean accuracy of EBV of unphenotyped animals born in 2011, but with parental phenotypes, compared to the
accuracy of selection on parental phenotypes (√(½).h). (Right panel) The proportion of unphenotyped animals born in 2011 with EBV accuracy exceeding √(½).h
(EBV) compared to the proportion of 2011 born animals with parental phenotypes available (pheno). The top panel utilised parameters for 10 breeds derived from
univariate analyses, while the bottom panel utilised parameters for 5 breeds derived from bivariate analyses of hip and elbow score. Increments calculated prior
to rounding. Breed abbreviations: Akita [AKT], Bearded Collie [BEARD], Bernese Mountain Dog [BMD], Border Collie [BORD], English Setter [ENG], Flat Coat Retriever
[FCR], Gordon Setter [GDN], Golden Retriever [GR], German Shepherd Dog [GSD], Labrador Retriever [LAB], Newfoundland [NEWF], Rottweiler [ROTT], Rhodesian
Ridgeback [RR], Siberian Husky [SHUSK] and Tibetan Terrier [TT].
The mean accuracies of EBV of phenotyped animals
born in 2010 were higher than the predicted accuracy of
selection on phenotype (h) for all breeds, ranging from
an improvement of 17% (GR) to 52% (ROTT) (Table 5).
The mean accuracies of un-phenotyped animals born in
2011 but with phenotyped parents were similarly greater
than the anticipated accuracy of selection on parental
phenotypes by between 23% (GR) and 71% (ROTT). The
proportion of all animals registered in 2011 with EBV
accuracies greater than that anticipated from selection
on parental phenotypes was greater than the proportion
of animals for which both parental phenotypes were actually available in all 5 breeds, the increment ranging
from 23% (from 72.2% with both parental phenotypes to
88.9% with EBV accuracy > √½.h; BMD) to a greater than
10-fold increase (from 6% with both parental phenotypes
to 79.5% with EBV accuracy > √½.h; ROTT).
(Table 2) in all 5 breeds, ranging from a decline in genetic propensity toward elbow score of between −0.18%
per year (LAB) to −0.72% per year (BMD). The derived
selection intensities were very weak; equivalent to excluding between only less than 4-8% of the highest risk
animals from breeding. As a result the genetic progress
made has been slow, with the difference in mean EBV
from animals born in 2000 and 2011 equating to between only 0.13 (LAB) and 0.21 (ROTT) of respective
genetic standard deviations.
Table 4 Parameter estimates of elbow score
σ2P
σ2A
h2
s.e.
rA
s.e.
rE
s.e.
BMD
0.760
0.201
0.26
0.054
0.005
0.134
0.122
0.051
GR
0.278
0.084
0.30
0.054
0.137
0.098
0.095
0.050
GSD
0.265
0.048
0.18
0.062
0.203
0.140
−0.054
0.055
LAB
0.196
0.037
0.19
0.028
0.344
0.064
−0.003
0.024
The effect of inbreeding
ROTT
0.533
0.073
0.14
0.106
0.550
0.299
−0.091
0.091
The effects of inbreeding coefficient were typically very
small and not significantly different to zero in all cases,
except on hip score in the RR (−0.69, s.e. = 0.350) and
on elbow score in the GR (0.83, s.e. = 0.316). In the RR
this corresponds to a decline of 0.75 points for the
Estimates of phenotypic and genetic variance (σ2 Pand σ2 A respectively) and
heritability (h2) of elbow score and genetic and residual correlations (rA and rE
respectively, with standard errors) with hip score for 5 breeds. Breed
abbreviations: Bernese Mountain Dog [BMD], Golden Retriever [GR], German
Shepherd Dog [GSD], Labrador Retriever [LAB], Rottweiler [ROTT].
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Table 5 Increment in accuracy of selection for low elbow score using EBV versus phenotype
Animals with phenotype
Proportion with r > √½ h
Animals with parental phenotype
h
mean r
n
incr
√½ h
mean r
n
incr
EBV
pheno
incr
BMD
0.51
0.66
46
1.28
0.36
0.52
385
1.43
0.889
0.722
1.23
GR
0.55
0.64
136
1.17
0.39
0.48
959
1.23
0.385
0.149
2.59
GSD
0.42
0.51
197
1.21
0.30
0.38
535
1.26
0.272
0.071
3.85
LAB
0.43
0.59
579
1.37
0.31
0.45
3411
1.45
0.600
0.104
5.76
ROTT
0.37
0.56
28
1.52
0.26
0.45
95
1.71
0.795
0.061
13.09
Mean
1.23
1.34
3.14
(Left panel) The mean accuracy (r) of EBV of phenotyped animals born in 2010 compared to accuracy of phenotypic selection (h), with the sample size (n) and
increment in accuracy (incr). (Middle panel) The mean accuracy of EBV of unphenotyped animals born in 2011, but with parental phenotypes, compared to the
accuracy of selection on parental phenotypes (√(½).h). (Right panel) The proportion of unphenotyped animals born in 2011 with EBV accuracy exceeding √(½).h
(EBV) compared to the proportion of 2011 born animals with parental phenotypes available (pheno). Increments calculated prior to rounding. Breed abbreviations:
Bernese Mountain Dog [BMD], Golden Retriever [GR], German Shepherd Dog [GSD], Labrador Retriever [LAB], Rottweiler [ROTT].
known). Using EBV owners of breeding bitches would
be able to more accurately assess the genetic merit of
potential sires resulting in an improved response to selection, whether phenotypes are available or not. In
addition, EBV will be available for all registered animals
of the breed, increasing selection intensity opportunities.
For example: the projected time to achieve an improvement of 5 points in the median hip score via phenotypic
selection, under the guidelines which were in place for
the majority of the period covered by the data, range
from 30 to over 300 years (NEWF and BEARD respectively) mainly due to weak selection intensity [8]. Although these guidelines have now been amended to
promote selection from below the median rather than
the mean phenotype, the opportunity to increase selection intensity is more readily presented by EBV (their
universality within a breed removing the random sampling of genetic risk from the use of un-scored animals).
Selecting breeding stock with EBV below the breed
mean is projected to achieve such an improvement in
between 9 years for NEWF and 18 years for BEARD.
The increases in the proportion of animals with breeding
value accuracies greater than that provided by parental
phenotypes illustrate that EBV provide, per phenotype,
more information on more animals, enabling wider comparison by breeders. An additional benefit from publishing EBV could be the indirect introduction of selection
pressure through potential pet owners more accurately
differentiating the genetic risk of hip (and elbow) dysplasia among available litters.
It is crucial however that participation in the BVA/KC
screening schemes continues – the availability of EBV
does not mean scoring is no longer necessary. Phenotypes are the basis of accurate breeding values, and accuracies will rapidly decline if phenotypic information
were to become sparse. Theory predicts that EBV accuracy would be expected to increase with participation,
and a plot and regression of mean EBV accuracy at birth
median hip score of 8 (or a 4.24 point decrease from a
hip score of 50) comparing coefficient of inbreeding of
0.125 to 0 (values obtained for offspring of a half-sib and
unrelated matings respectively). In the GR there is an increase of 0.1 points in elbow score comparing coefficient
of inbreeding of 0.125 to 0.
Discussion
The results from this study demonstrate the potential
power of EBV to improve the predicted accuracy of
selection against hip and elbow dysplasia in many dog
breeds in the UK, including 3 of the 10 most popular
breeds. The mean accuracies of EBV are always higher
than would be obtained via selection on available phenotypes (using either individual or both parental phenotypes). Furthermore, a far greater proportion of juvenile
animals have EBV with a higher accuracy than can at
present be obtained by selection using both parental
phenotypes. Thus, reliable information is available on
much more of the population than currently exists,
which will allow breeders to make more accurate selections earlier in the life of the dog. The accuracy of selection is directly linked to genetic progress, meaning more
accurate selection will lead to greater progress in breeding for health. We have demonstrated this to be the case
in a wide range of breeds. The broader impact can be
realised by noting that the average annual number of
registrations of the 15 breeds included in this study, and
so that will each have an EBV, is in excess of 80,000, approximately 1/3 of all annual registrations with the UK
Kennel Club.
Substantially faster genetic improvement is expected
to come via both increased accuracy and greater selection intensity, as the provision of EBV could have a
major impact on the ways in which dogs are selected by
breeders and pet owners (accompanied by appropriate
user information). Currently mate selection is based on
ancestral phenotypes and two dogs’ own phenotypes (if
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Page 9 of 11
parameter. The slightly higher estimate of between breed
variance of heritability for hip score compared to that for
elbow score may reflect the greater number of breeds included in the analysis for that trait, and inclusion of additional breeds not currently in the sample may prove an
outlier to this current collection. Nevertheless, results
from the meta-analysis suggest that the heritability of both
hip and elbow score are remarkably consistent across
breeds, and that most of the observable variation in estimates is due to sampling variation. The across breed estimate of the residual correlation between hip and elbow
score is small (with a small s.e., 0.024 ± 0.035), and the
meta-analysis revealed only small between breed variation
in such estimates (Additional file 6: Table S3). This implies
that across breeds there is a large degree of independence
in non-genetic environmental risk factors on dysplasia of
the hip and elbow joint. This finding across multiple
breeds supports an earlier observation on the small environmental correlation between hip and elbow score in
LAB [17] and is somewhat surprising given that both dysplasias are developmental orthopaedic diseases.
All breeds included in this study showed an improving
genetic trend with respect to hip and elbow score, except
the SHUSK, suggesting that phenotypic selection to date
has had a small but beneficial impact. The increasing
genetic propensity towards hip dysplasia in the SHUSK
was matched by the phenotypic trend (regression of total
hip score on date of birth showing a yearly rise of 0.075
score points), which has been observed previously [31].
However, the SHUSK had the best hip scores of all the
15 breeds analysed here. It may be that the historical
role of the SHUSK as a sled dog has entailed de facto
selection against lameness, but that increasing popularity
as pets or show dogs has weakened this tacit selection
pressure. The popularity of the breed in the UK has
risen quickly recently, from 829 registered in 2000 to
2,209 in 2010. While the general hip condition of the
SHUSK remains better than for many other breeds,
breeders should be aware of the detrimental trend. It
serves as an example that the transition to a popular pet
breed be accompanied by tools, such as EBV, that protect the qualities of the breed for which it is valued.
The results presented here indicate that the GDN has
been subject to the greatest selection intensity for reduction in hip score, equivalent to excluding the 18% of animals with the worst hip scores from breeding. This is in
line with former breeding guidelines based on the mean
hip score and has been accompanied by a phenotypic
decline in hip score of over 0.6 points per year (from
regression of total hip score on date of birth) and a fall
in the mean hip score from 24.35 in 1990 to 14.77 in
2010. The GDN is not a numerous breed, with a mean
of 324 dogs registered per year from 2000–2010, but appears to have a large proportion of breeders committed
on the mean annual proportion of sires with hip scores
provides empirical support (Additional file 5: Figure S1).
Experience in livestock sectors reinforces the theory,
where widespread and routine data collection and very
large family sizes (i.e. thousands of progeny) can yield
EBV accuracies of >0.9, although, it must be noted, accuracies are rarely so high at the time of selection. The
resulting message to breeders is simple: continued scoring will maintain and further enhance the accuracy of
selection of breeding stock for healthy joints, as well as
increasing the pool of animals with reliable information.
Moreover, the phenotypic score is of value to breeders
and pet owners alike in providing an indicator of not
only the genetics but the environmental influence on an
individual animal’s hip/elbow joints. While the EBV
should guide breeding decisions, the phenotype is useful
to inform the appropriate care of the dog that may
ameliorate the severity of hip and elbow dysplasia where
it occurs.
The accumulation of phenotypes will be particularly
critical for future analyses of elbow dysplasia, where the
extent of recording is much less than for hip dysplasia,
and since elbow score is less heritable than hip score
(possibly due in part to the collection of traits described
by the elbow score). This study only managed to detect
a genetic correlation between hip and elbow scores with
enough precision to be statistically significantly different
to zero in the LAB. Previously, we demonstrated that bivariate analysis of hip and elbow data can confer significant benefits to the accuracy of EBV for elbow scores,
where a favourable genetic correlation exists [17]. Additional elbow score data will be essential to determine
more precise genetic correlations between hip and elbow
score in BMD, GR, GSD and ROTT, although reported
estimates from other studies indicate there may be wide
variation across breeds [9,14,16].
While genetic parameters are often (correctly) viewed
as specific to each breed, questions can arise as to
whether the genetic parameters (h2 and rA) from one
breed may be useful in BLUP analyses (EBV calculation)
of another. This is particularly relevant where small
population size means that breed-by-breed parameter
calculation is not feasible. The analysis of 15 breeds in this
study using the same model provided a good opportunity
to explore this matter. Results from the meta-analysis
indicate that there is more between breed variation in estimates of genetic correlation between hip and elbow score
than for heritability of elbow score, across the five breeds
for which both traits were analysed. While additional
elbow scoring data will therefore be expected to result in
more consistent estimates of heritability across breeds as
sampling variance is reduced, the estimates of genetic
correlation between hip and elbow score are expected to
reflect the greater between breed variation in the true
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through deterministic use of empirical data can then be
used in induction. The reported superiority of mean
EBV accuracies over the accuracy of selection on individual hip score phenotype reported here were smaller
than reported by Malm et al. using simulation [23], however there tended to be fewer animals with phenotypes
in our data, implying less information. Comparison of
EBV accuracy with selection on parental phenotypes
shows the improvement was of similar magnitude.
EBV for hip and elbow dysplasia are routinely computed and published in Norway, Finland and Denmark
for up to 38 breeds and in Sweden for 5 breeds (K Maki,
personal communication), in Germany for GSD, and in
the USA for LAB. The public release of EBV described
in this study is anticipated in the UK in 2013. The abundance of EBV for hip and elbow dysplasia in so many
countries raises the prospect of the globalisation of scoring and evaluation schemes. Analyses determining the
genetic correlations between individual scoring protocols
would enable dogs to be evaluated under any (participating) scheme (UK registered dogs evaluated under the
FCI scheme and Scandinavian dogs participating in the
BVA/KC scheme for example) while still having an EBV
in the country of registration [25]. It should be noted,
however, that not all scoring protocols may be equal in
terms of predicting the lameness associated with hip and
elbow dysplasia and consequential OA [33]. To address
this further research focussing on identifying OA and
lameness later in the life of scored dogs would be welcome. Fortunately, the manner in which EBV for canine
health are presented offers an ‘outward continuity’, allowing
improvements to be made to the computational model or
to the evaluation protocol, as well as the utilisation of
international data, without noticeable disruption to the
end user [25].
to including health traits in selection objectives; for example over 80% of sires and dams undergo hip scoring.
While slightly greater genetic progress was observed in
the NEWF, a larger estimate of heritability and shorter
generation interval meant that the derived selection intensity was smaller than for the GDN. However across
all breeds and traits, regression of genetic gain on the
proportion of breeding animals scored did not show significant association (P > 0.05). This demonstrates that
quantity of data alone does not guarantee genetic improvement, but that it must be accompanied by the appropriate breeding advice and the motivation by breeders to
act upon it. Across comparable breeds, the rates of genetic
progress calculated in this study were broadly typical of
those that have been previously reported [16].
Substantial improvements in the predicted accuracy of
selection, and therefore genetic progress, based on estimating breeding values have been quantifiably demonstrated here for a wide range of breeds, including a
number of the more uncommon breeds. For the more
uncommon breeds, selection against diseases such as hip
dysplasia is more problematic when based on phenotypes alone as there may be only a small number of the
candidates with a record, and so making a small breed
smaller. Therefore an approach to increasing numbers of
candidates with usable information, as demonstrated
here, should be welcome. Rarer breeds are more likely to
suffer the effects of genetic over-contribution of some
animals to future generations, usually through the widespread use of popular sires. Where selection does take
place in small populations (which it must do to improve
welfare where hip dysplasia is prevalent, as argued in the
introduction) a balance must be struck between genetic
progress in reducing the burden of disease on the one
hand, and minimising the risk of the emergence of a
novel genetic disease on the other, which can be measured by the rate of inbreeding. The inbreeding coefficient per se was found to be largely unrelated to, and
have only a small effect on, hip and elbow score in this
study. However, one drawback with the use of EBV
based on pedigrees and phenotypes is that they too can
promote greater rates of inbreeding in the course of generating more progress [32]. This need not be inevitable,
but instead places an emphasis on increasing awareness
of inbreeding among breeders, and making more tools
available to help them manage rates of inbreeding as
EBV are introduced.
In this study we elected to conduct a deterministic
prediction of the superiority of EBV accuracy over that
of selection using phenotype. An alternative method
would be to use simulation. However, simulations are
stochastic and can be prone to error in some situations.
A further disadvantage of simulation is a lack of insight
into the underlying causes, which when encountered
Conclusion
The use of EBV by dog breeders is projected to facilitate
considerable improvements in the response to selection for
healthier hip and elbow joints in a wide range of breeds,
through both enhanced accuracy and greater abundance of
information. Across the 15 breeds analysed here estimates
of heritability of hip and elbow score were remarkably consistent, and phenotypic selection has been successful in
eliciting genetic progress, albeit very slowly, in all breeds
except the SHUSK. However, substantial improvement in
the accuracy of selection via use of EBV was demonstrated
across all breeds, for both dogs with and without a phenotype. The availability of EBV for hip score for 15 UK registered pedigree dog breeds will provide information on the
genetic risk of disease in nearly a third of all dogs annually
registered by the UK KC, with in excess of a quarter having
an EBV for elbow score as well.
182
Page 11 of 11
Additional files
12. Bishop SC, Woolliams JA: On the genetic interpretation of disease data.
PLoS One 2010, 5(1):e8940.
13. Beuing R, et al: Prevalence and inheritance of canine elbow dysplasia in
German Rottweiler. J Anim Breed Genet 2000, 117(6):375–383.
14. Maki K, Groen AF, Liinamo AE, Ojala M: Genetic variances, trends and
mode of inheritance for hip and elbow dysplasia in Finnish dog
populations. Anim Sci 2002, 75:197–207.
15. Janutta V, et al: Genetic analysis of three different classification protocols
for the evaluation of elbow dysplasia in German shepherd dogs. J Small
Anim Pract 2006, 47(2):75–82.
16. Malm S, et al: Genetic variation and genetic trends in hip and elbow
dysplasia in Swedish Rottweiler and Bernese Mountain Dog. J Anim Breed
Genet 2008, 125(6):403–12.
17. Lewis TW, et al: Genetic evaluation of elbow scores and relationship with
hip scores in UK Labrador retrievers. Vet J 2011, 189:227–233.
18. Silvestre AM, et al: Comparison of estimates of hip dysplasia genetic
parameters in Estrela Mountain Dog using linear and threshold models.
J Anim Sci 2007, 85(8):1880–4.
19. Hou Y, et al: Retrospective analysis for genetic improvement of hip joints
of cohort Labrador retrievers in the United States: 1970–2007. PLoS One
2010, 5(2):e9410.
20. Wilson BJ, et al: Heritability and phenotypic variation of canine hip
dysplasia radiographic traits in a cohort of Australian German Sheperd
dogs. PLoS One 2012, 7(6):e39620.
21. Ginja MM, et al: Diagnosis, genetic control and preventive management
of canine hip dysplasia: a review. Vet J 2010, 184(3):269–76.
22. Stock KF, Distl O: Simulation study on the effects of excluding offspring
information for genetic evaluation versus using genomic markers for
selection in dog breeding. J Anim Breed Genet 2010, 127:42–52.
23. Malm S, et al: Efficient selection against categorically scored hip dysplasia
in dogs is possible using best linear unbiased prediction and optimum
contribution selection: a simulation study. J Anim Breed Genet 2012. http://
onlinelibrary.wiley.com/doi/10.1111/j.1439-0388.2012.01013.x/abstract.
24. Falconer DS, Mackay TFC: Introduction to Quantitative Genetics. 4th edition.
Longman: Edinburgh Gate, Harlow, Essex CM20 2JE; 1996.
25. Woolliams JA, Lewis TW, Blott SC: Canine hip and elbow dysplasia in UK
Labrador retrievers. Vet J 2011, 189:169–176.
26. Gibbs C: The BVA/KC scoring scheme for control of hip dysplasia:
interpretation of criteria. Vet Rec 1997, 141(11):275–84.
27. Gilmour AR, et al (Eds): ASReml user guide release 3.0. UK: VSN International
Ltd, Hemel Hempstead, HP1 1ES; 2009.
28. Corbin LJ, et al: Linkage disequilibrium and historical effective population
size in the Thoroughbred horse. Anim Genet 2010, 41(Suppl 2):8–15.
29. Lewis TW, Woolliams JA, Blott SC: Genetic evaluation of the nine
component features of Hip score in UK Labrador retrievers. PLoS One
2010, 5(10):e13610.
30. Bulmer MG: The effect of selection on genetic variability. Am Nat 1971,
105(943):201–211.
31. Willis MB: A review of the progress in canine hip dysplasia control in
Britain. J Am Vet Med Assoc 1997, 210(10):1480–2.
32. Verrier E, Colleau JJ, Foulley JL: Long-term effects of selection based on
the animal model BLUP in a finite population. Theortetical and Applied
Genetics 1993, 87:446–454.
33. Wilson B, Nicholas FW, Thomson PC: Selection against canine hip
dysplasia: Success or failure? Vet J 2011, 189:169–176.
Additional file 1: Table S1. Summary statistics of hip scores of all 15
breeds.
Additional file 2: Appendix 1. Derivation of accuracy of breeding
values including F.
Additional file 3: Appendix 2. Derivation of accuracy of mass
(phenotypic) selection.
Additional file 4: Table S2. Summary statistics of elbow scores for 5
breeds.
Additional file 5: Figure S1. Plot of EBV accuracy on proportion of
sires with phenotypes.
Additional file 6: Table S3. Summary of meta-analysis.
Competing interests
TWL is fully funded and SCB partly funded by the UK Kennel Club Charitable
Trust. The funders had no role in study design, data analysis, decision to
publish, or preparation of the manuscript. Hip and elbow score data and
pedigree was collated and provided by the UK Kennel Club. JAW declares no
competing interests.
Author contributions
TWL, SCB & JAW conceived and designed the analyses; TWL performed the
analyses; TWL & JAW analysed the results; TWL, SCB & JAW wrote the paper;
all authors read and approved the final manuscript.
Acknowledgements
The authors are grateful to the BVA hip and elbow scoring panellists for data
provided by their ongoing work, and to Dr M. Coffey and Dr K. Moore of
EGENES at Scotland’s Rural University College for provision of BLUP EBV on
the 3 most populous breeds. SCB and TWL gratefully acknowledge funding
from the Kennel Club Charitable Trust. JAW gratefully acknowledges funding
from the BBSRC.
Author details
1
Kennel Club Genetics Centre at the Animal Health Trust, Lanwades Park,
Kentford, Newmarket, Suffolk CB8 7UU, UK. 2The Roslin Institute and Royal
(Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush
Research Centre, Midlothian EH25 9RG, UK.
Received: 2 August 2012 Accepted: 25 February 2013
Published: 2 March 2013
References
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region, Part 1. North Am Vet 1937, 18:53–56.
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1956, 38:476.
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6. Brass W: Hip dysplasia in dogs. J Small Anim Pract 1989, 30:166–170.
7. Maki K: Breeding against hip and elbow dysplasia in dogs. In PhD thesis.
University of Helsinki, Department of Animal Science; 2004.
8. Lewis TW, Blott SC, Woolliams JA: Genetic Evaluation of Hip Score in UK
Labrador Retrievers. PLoS One 2010, 5(10):e12797.
9. Stock KF, et al: Genetic analyses of elbow and hip dysplasia in the
German shepherd dog. J Anim Breed Genet 2011, 128:219–229.
10. Hodgman S: Abnormalities and defects in pedigree dogs 1.
An investigation into the existence of abnormalities in pedigree dogs in the
British Isles. Journal of small animal practice 1963, 4(6):447–456.
11. Hazewinkel HAW: Elbow Dysplasia, definition and known aetiologies.
In 22nd annual meeting of the International Elbow Working Group. Munich,
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proceedings2007iewg.pdf (accessed 2 February 2011).
doi:10.1186/1471-2156-14-16
Cite this article as: Lewis et al.: Comparative analyses of genetic trends
and prospects for selection against hip and elbow dysplasia in 15 UK
dog breeds. BMC Genetics 2013 14:16.
183
SMALL ANIMALS
Prevalence of inherited disorders
among mixed-breed and purebred dogs:
27,254 cases (1995–2010)
Thomas P. Bellumori, MS; Thomas R. Famula, PhD; Danika L. Bannasch, PhD, DVM;
Janelle M. Belanger, MS; Anita M. Oberbauer, PhD
Objective—To determine the proportion of mixed-breed and purebred dogs with common
genetic disorders.
Design—Case-control study.
Animals—27,254 dogs with an inherited disorder.
Procedures—Electronic medical records were reviewed for 24 genetic disorders: hemangiosarcoma, lymphoma, mast cell tumor, osteosarcoma, aortic stenosis, dilated cardiomyopathy, hypertrophic cardiomyopathy, mitral valve dysplasia, patent ductus arteriosus,
ventricular septal defect, hyperadrenocorticism, hypoadrenocorticism, hypothyroidism, elbow dysplasia, hip dysplasia, intervertebral disk disease, patellar luxation, ruptured cranial
cruciate ligament, atopy or allergic dermatitis, bloat, cataracts, epilepsy, lens luxation, and
portosystemic shunt. For each disorder, healthy controls matched for age, body weight, and
sex to each affected dog were identified.
Results—Genetic disorders differed in expression. No differences in expression of 13 genetic disorders were detected between purebred dogs and mixed-breed dogs (ie, hip dysplasia, hypo- and hyperadrenocorticism, cancers, lens luxation, and patellar luxation). Purebred dogs were more likely to have 10 genetic disorders, including dilated cardiomyopathy,
elbow dysplasia, cataracts, and hypothyroidism. Mixed-breed dogs had a greater probability
of ruptured cranial cruciate ligament.
Conclusions and Clinical Relevance—Prevalence of genetic disorders in both populations
was related to the specific disorder. Recently derived breeds or those from similar lineages
appeared to be more susceptible to certain disorders that affect all closely related purebred dogs, whereas disorders with equal prevalence in the 2 populations suggested that
those disorders represented more ancient mutations that are widely spread through the
dog population. Results provided insight on how breeding practices may reduce prevalence
of a disorder. (J Am Vet Med Assoc 2013;242:1549–1555)
D
ogs are second only to humans in the number of
hereditary diseases identified in the population.1
Information about the prevalence and etiology of disorders in dogs may provide insight into preventative
measures and possible treatments for dogs with diseases as well as for humans sharing common disorders.2 Although no single registry maintains a record
of genetic disease in dogs, it has been suggested that
purebred dogs are more prone to genetic disorders than
are mixed-breed dogs.3 Breeding practices and selection pressures used by breeders of purebred dogs have
been implicated in the perceived high frequency of genetic disorders, whereas the random mating practices
of mixed-breed dogs have been suggested to increase
hybrid vigor (heterosis), resulting in healthier dogs.4
The increased homozygosity expected in purebred
dogs offers the potential for these animals to have traits
ABBREVIATIONS
AKC
CI
IVDD
American Kennel Club
Confidence interval
Intervertebral disk disease
influenced by recessive alleles in greater frequency than
their crossbred counterparts. The common assumption that a mixed-breed dog is healthier would not be
true if both parents carried deleterious mutations for
the same disorder. Few data have been compiled to accurately assess the question of whether purebred dogs
are at greater risk for genetic disorders, compared with
mixed-breed dogs. In a study5 of dogs affected with hip
dysplasia, no significant difference in prevalence was
observed between purebred and mixed-breed dogs.
Domestic dogs are thought to be derived from 3 to
5 wolf lineages.6 Each lineage would be derived from a
few common ancestors; thus, one might expect some
disorders would be common to all dogs, regardless of
breed. Genetic mutations that accompanied the domestication process would be expected to be widely distributed throughout the dog population, affecting dogs of
any breed, including admixtures of breeds. In contrast
From the Department of Animal Science, College of Agricultural and
Environmental Sciences (Bellumori, Famula, Belanger, Oberbauer),
and the Department of Population, Health and Reproduction, School
of Veterinary Medicine (Bannasch), University of California-Davis,
Davis, CA 95616.
Address correspondence to Dr. Oberbauer (amoberbauer@ucdavis.
edu).
JAVMA, Vol 242, No. 11, June 1, 2013
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SMALL ANIMALS
to more distant mutations, more recent selection pressure (eg, in Europe during the Victorian era7) would
influence the distribution of newer mutations, restricting those to subsets of the overall dog population. It
is likely that with breed refinement for specific tasks
and morphology, some mutations accompanied selection for those traits. Rigorous selection pressures to refine the breeds by inbreeding and bottlenecks4,8 would
contribute to a loss of genetic diversity, thereby increasing the likelihood of recessive disorders within a breed
population.
The AKC registers purebred dogs and records
ancestors. Although, in 2004, there were > 140 AKCregistered breeds, 10 breeds represented more than half
of the reported AKC-registered dogs, whereas the 100
least popular breeds represented < 15% of all AKC registrations.9 The less popular breeds, with many fewer
dogs registered each year, would be expected to have
smaller effective gene pools. For example, the current
population of Portuguese Water Dogs, ranked 56th
in registrations as of 2011, has been traced back to a
small number of dogs, mostly from 2 kennels, with approximately 6 ancestors comprising 80% of the current
gene pool.9 Breeds with smaller gene pools and reduced
genetic variation are more likely to phenotypically express a recessive disorder.1
Many studies have sought to describe the prevalence of disorders among individual breeds. Often, the
focus is on a single disorder and its inheritance pattern
in a particular breed to define possible mutations. Yet,
more global studies designed to assess the proportion of
mixed-breed and purebred dogs affected with heritable
disorders can prove useful toward reducing the prevalence of those disorders in the dog population. Describing disorders equivalently expressed within purebred
and mixed-breed dogs may identify disorders common in the overall population and suggest approaches
to reduce the prevalence. In contrast, disorders more
prevalent to a particular breed may be reduced by use
of concerted breeding practices.
A recent study10 found a direct correlation between
disorders inherited in purebred dogs and the morphological characteristics specified in the breed standard.
Although that finding underscores the fact that purebred dogs are considered at risk for disorders, it is unknown whether mixed-breed dogs have the same risk
of genetic disorders that is suggested for purebred dogs.
The purpose of the study reported here was to describe
the prevalence of genetic disorders in the dog population as a whole.
lowing categories were assessed: cancers (hemangiosarcoma, lymphoma, mast cell tumor, and osteosarcoma),
cardiac disorder (aortic stenosis, dilated cardiomyopathy,
hypertrophic cardiomyopathy, mitral valve dysplasia,
patent ductus arteriosus, and ventricular septal defect),
endocrine disorders (hyperadrenocorticism, hypoadrenocorticism, and hypothyroidism), orthopedic disorders (elbow dysplasia, hip dysplasia, IVDD, patellar
luxation, and ruptured cranial cruciate ligament), and
other (atopy or allergic dermatitis, bloat, cataracts, epilepsy, lens luxation, and portosystemic shunt). Mode
of inheritance was not a factor in the selection of the
conditions under study.
Medical records review—Patient records contained fields that included pertinent history, clinical
signs, clinical diagnosis, and other comments. Searches
for keywords and any synonym or alternative representation for the genetic disorders were conducted in all
fields. As an example, “Cushings,” “Cushing’s,” “Cushing,” and “hyperadrenocorticism” were all keyword
searches to extract data related to hyperadrenocorticism. From each individual keyword search, a single
database of patients was created for each disorder. In
addition to disorder status, patient identification number, breed, sex, species, body weight, date of birth, admissions date, discharge date, search-term field (eg,
pertinent history and clinical diagnoses), and keyword
in context were captured. Each record was screened for
accuracy, and only records with definitive confirmed
diagnoses by the veterinary medical teaching hospital staff or the referring veterinarian were included for
analyses. Any record that referred to suspected diseases,
a presumptive diagnosis pending test results, rule-out
diagnosis, or differential diagnosis or that included a
diagnosis that was in any other way unconfirmed was
omitted from analyses. For example, diagnoses of myxomatous mitral valvular disease were excluded from the
mitral valve dysplasia category. The sole exception was
epilepsy, for which the disorder was classified into 1 of
3 categories (confirmed, probable, or suspect) on the
basis of the recorded information. Because of the nature
of the records explaining specific vertebral problems,
any dog with a laminectomy was considered to have
IVDD, although laminectomy for cervical spondylomyelopathy was excluded. For each disorder, records were
excluded such that only patients with a confirmed and
reliable diagnosis of a particular disorder were retained.
Regardless of the number of visits, a given dog was
counted only once for a given disorder. To yield a comparison of healthy or diseased dogs with dogs evaluated
at hospital for other reasons, a search for records of all
dogs admitted after being hit by a car was also done.
The veterinary medical teaching hospital veterinary medical and administrative computer system was
again searched to collect information on all of the dogs
evaluated at the hospital from January 1, 1995, through
January 1, 2010. This data file contained all dogs evaluated at the clinic, including those with and without the
disorders that were under study, yielding information
for each of the 268,399 visits. Data from the confirmed
disorder files were matched to the full data file. In this
way, individual patient records were matched so that all
visit records for a single patient had the same diagno-
Materials and Methods
Case selection criteria—The data used in these
analyses were obtained by searching through the University of California-Davis Veterinary Medical Teaching Hospital electronic records of all patients evaluated
from January 1, 1995, through January 1, 2010. The
genetic disorders selected for the study represented
those expected to be present in the dog population at a
measurable prevalence and to be debilitating, with confidence in the reliability of diagnosis. Additionally, disorders that affected a variety of anatomic locations and
physiologic systems were chosen. Disorders in the fol1550
Scientific Reports
JAVMA, Vol 242, No. 11, June 1, 2013
185
addition, by counting the number of data sets (of 50),
the difference in disease risk between purebred and
mixed-breed dogs could be determined.
All analyses were conducted via statistical softwarea
with a logit link function for analysis of the binomial
variable of disease status. The model included terms for
age class, weight class, and sex as well as a term for purebred versus mixed-breed dog. Because each of the 50
data sets was balanced for age, weight, and sex groups,
the OR for any of these variables should be 1.0, and this
was monitored in all analyses as a test of the sampling
process. The OR for purebred versus mixed-breed status
for each of the 50 data sets was saved, as were the lower
and upper limits of the 95% CI for this estimate and its
associated P value. Also counted were the number of
times (of 50 tests) the P value was less than or equal to
the commonly used type I error rate of 0.05.
The number of dogs from each breed evaluated
at the veterinary medical teaching hospital was determined as well as the number of dogs of each breed that
were defined as control (no disorder) or affected (having ≥ 1 disorder). The percentage of each breed that was
control or affected was then calculated.
Statistical analysis—For each disorder, appropriate population controls were identified from the complete data file containing all dogs evaluated at the veterinary medical teaching hospital in the 15-year time
frame. Because the number of dogs lacking a given condition far exceeded the number of dogs with the condition, to create the control population against which the
dogs with the condition were compared, it was necessary to randomly sample the dogs lacking the condition. Dogs were first stratified by body weight, sex, and
age, and then each dog with a condition was matched
to a randomly selected dog from the control group having the same weight, sex, and age classification. This
sampling created control sets that represented the same
characteristics as the affected dogs except for breed status. Control dogs were matched for age (0 to 2 years,
> 2 to 7 years, or > 7 years), weight (0 to 12 kg [0
to 26.4 lb], > 12 to 20 kg [26.4 to 44 lb], or > 20 kg
[44 lb]), and sex (male, castrated male, female, or
spayed female) to each affected dog for each condition. The control dogs matched by the age, weight, and
sex criteria were randomly selected from the complete
data file, creating the control group for each disorder
in accordance with clinical research designs.11 Thus,
the controls were from the same population base from
which the dogs with disorders were derived.
To enhance the reliability of the analyses, the sampling set of healthy control dogs was repeated 50 times
for each condition investigated. That is, for any given
condition, an equal number of healthy dogs, stratified
by the age, body weight, and sex of the affected dogs,
were randomly selected 50 times to create repeated
control data sets matched to the affected dogs. In this
manner, the sole variable between the 50 randomly created data sets representing the control population was
the number of mixed-breed or purebred dogs. In this
way, 50 estimates (1 from each randomly selected set
of controls) of the OR for the comparison of purebred
with mixed-breed dogs as well as the mean 95% CI of
this ratio and the mean P value used to test this ratio
against the null hypothesis of 1.0 were calculated. In
Results
Of the 90,004 dogs examined at the veterinary
medical teaching hospital small animal clinic that had
an identified breed status (purebred, mixed, or pit bull–
type), 27,254 had ≥ 1 of the conditions under study
and 62,750 were control dogs (Table 1). In terms of the
percentage of dogs of each breed with ≥ 1 disorder, 15
breeds had < 20% of dogs with ≥ 1 disorder, 63 breeds
had from 21% to 30%, 41 breeds had from 31% to 40%,
and 10 breeds had > 40%. The mean age at the first visit
(assessed as the first appointment at the hospital with
a disorder diagnosis) was calculated for each disorder
(Table 2). Patent ductus arteriosus and ventricular septal defect were both diagnosed at a mean age of 1.32
years. Hyperadrenocorticism was diagnosed at a mean
age of 10.54 years, the oldest age of diagnosis for any
disorder. By comparison, dogs hit by a car had a mean
age of 4.87 years.
Of the 24 disorders assessed, 13 had no significant difference in the mean proportion of purebred and
mixed-breed dogs with the disorder when matched for
age, sex, and body weight (Table 2). Disorders without
a significant predisposition included all the neoplasms
(hemangiosarcoma, lymphoma, mast cell tumor, and
osteosarcoma), hypertrophic cardiomyopathy, mitral
valve dysplasia, patent ductus arteriosus, and ventricular
septal defect in the cardiac category; hip dysplasia and
patellar luxation in the orthopedic category; hypoadreTable 1—Breed distribution of dogs with (Condition) and without (Control) inherited disorders evaluated at the Veterinary
Medical Teaching Hospital, University of California-Davis, in a
15-year period.
Breed
Purebred
Mixed
Pit bull–type
Total
JAVMA, Vol 242, No. 11, June 1, 2013
Control
Condition
Total
45,015
16,693
1,042
62,750
20,937
5,990
327
27,254
65,952 (73.3%)
22,683 (25.2%)
1,369 (1.5%)
90,004 (100%)
Scientific Reports
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SMALL ANIMALS
sis and any patient that may not have had the disorder
listed for a specific visit was still classified as having
the disorder. A given dog could have been classified as
having multiple disorders if > 1 disorder was confirmed
via diagnostic evaluation. From this file containing all
unique dogs, control dogs were identified for use as
hospital controls in accordance with clinical research
designs.11 Specifically, none of the conditions under
study were diagnosed in these dogs.
Each patient had a breed designation. Dogs of
AKC-recognized breeds, AKC miscellaneous breeds,
or Foundation Stock Service breeds were considered to
be purebred dogs. All nondomesticated canine patients
(dingo or wolf) were removed. Pit bull–type dogs were
evaluated independently because of the inability to
validate purebred status. Any dog labeled as a mix was
considered to be a mixed-breed dog. From the records
collected, age at each visit could be calculated. For each
dog, the age of first recorded diagnosis at the veterinary
medical teaching hospital for each disorder was calculated and a mean age of first diagnosis was determined
for each disorder.
SMALL ANIMALS
Table 2—Distribution and descriptive statistics of mixed-breed and purebred dogs with inherited conditions diagnosed over a 15-year
period.
Disorder or injury
Cardiac
Aortic stenosis*
Dilated cardiomyopathy*
Hypertrophic cardiomyopathy
Mitral valve dysplasia
Patent ductus arteriosus
Ventricular septal defect
Cancer
Hemangiosarcoma
Lymphoma
Mast cell tumor
Osteosarcoma
Orthopedic
Elbow dysplasia*
Hip dysplasia
IVDD*
Patellar luxation
Ruptured cranial cruciate ligament†
Endocrine
Hyperadrenocorticism
Hypoadrenocorticism
Hypothyroidism*
Other
Atopy or allergic dermatitis*
Bloat*
Cataracts*
Epilepsy total*
Epilepsy confirmed
Epilepsy probable
Epilepsy suspect
Lens luxation
Portosystemic shunt*
Hit by car†
Mixed
Purebred
(No. of dogs) (No. of dogs)
Mean age
Total
at first
(No. of dogs) diagnosis (y)
Mean OR (95% CI)
Mean
P value
No. of times
breed was
significant
33
32
3
40
81
16
357
329
33
180
329
117
390
361
36
220
410
133
3.0
7.23
6.51
4.09
1.32
1.32
3.03 (1.96–4.76)
3.45 (2.22–5.26)
2.04 (0.40–10.0)
1.85 (0.73–1.96)
0.85 (0.60–1.22)
1.72 (0.86–3.45)
0.000
0.000
0.336
0.446
0.480
0.168
50
50
9
5
3
15
135
392
342
187
427
1,182
1,105
522
562
1,574
1,447
709
9.19
8.0
8.0
8.23
1.25 (0.95–1.64)
1.11 (0.94–1.30)
1.20 (1.01–1.43)
1.09 (0.86–1.39)
0.186
0.271
0.068
0.449
17
8
32
3
191
500
833
466
400
1,034
1,431
3,658
1,710
828
1,225
1,931
4,491
2,176
1,228
3.54
3.89
7.35
5.16
5.95
2.00 (1.63–2.50)
1.05 (0.91–1.23)
1.41 (1.26–1.56)
1.04 (0.90–1.20)
0.79 (0.67–0.94)
0.000
0.473
0.000
0.490
0.031
50
4
50
0
41
281
67
326
808
228
1,369
1,089
295
1,695
10.54
8.72
6.86
1.02 (0.84–1.23)
1.23 (0.83–1.79)
1.56 (1.33–1.85)
0.593
0.354
0.000
0
5
50
237
35
734
188
146
24
18
64
74
569
1,094
187
2,822
749
565
120
64
251
608
1,069
1,331
222
3,556
937
711
144
82
315
682
1,638
5.95
6.92
9.21
6.24
6.57
5.26
5.32
9.07
2.39
4.87
1.56 (1.30–1.89)
1.79 (1.10–2.94)
1.27 (1.12–1.41)
1.37 (1.10–1.69)
1.33 (1.03–1.79)
1.61 (0.88–2.94)
1.03 (0.48–2.22)
1.14 (0.78–1.69)
2.04 (1.49–2.77)
0.59 (0.51–0.69)
0.003
0.054
0.000
0.016
0.062
0.158
0.536
0.478
0.000
0.000
50
36
50
47
28
13
1
2
50
50
Mean P value indicates comparison of purebred dogs with matched control sampling sets. Number of times breed was significant = Number
of times (of 50) that comparison of affected dogs with matched control sampling sets indicated a significant (P < 0.05) difference in probability that
mixed-breed and purebred categories differed in expression of the condition. Mean OR (95% CI) indicates comparison of purebred dogs relative
to mixed-breed dogs.
*Purebred dogs had a greater probability of expressing the condition. †Mixed breeds had a greater probability of expressing the condition.
Epilepsy total consists of the sum of all 3 categories of epilepsy.
nocorticism and hyperadrenocorticism in the endocrine
category; and lens luxation in the other category.
In contrast, 10 disorders were more prevalent in purebred dogs, compared with those found in mixed-breed
dogs. Aortic stenosis and dilated cardiomyopathy in the
cardiac category, hypothyroidism in the endocrine category, elbow dysplasia and IVDD in the orthopedic category, and atopy or allergic dermatitis, bloat, cataracts, total
epilepsy, and portosystemic shunt were all diagnosed in
a greater proportion of purebred dogs than mixed-breed
dogs (P < 0.05). The OR for these disorders ranged from
1.27 (cataracts) to 3.45 (dilated cardiomyopathy) for
purebred dogs, relative to mixed-breed dogs, indicating a
greater probability of the condition in purebred dogs.
Cranial cruciate ligament rupture and being hit by
a car were more likely to be observed in mixed-breed
dogs than purebred dogs, with a 1.3- and 1.7-fold probability of the condition, respectively. Whereas the percentage of purebred dogs evaluated at the veterinary
medical teaching hospital during this time frame was
73.3% and for mixed-breed dogs was 25.2%, the percentage of mixed-breed dogs evaluated after being hit
by a car was 35% and significantly (P < 0.05) greater
than expected (Table 2); a similar higher-than-expected
percentage was observed for pit bull–type dogs.
1552
Ten genetic disorders had a significantly greater
probability of being found in purebred dogs. For aortic stenosis, the top 5 breeds affected on the basis of
the percentage of dogs of that breed affected and mixed
breeds were Newfoundland (6.80%), Boxer (4.49%),
Bull Terrier (4.10%), Irish Terrier (3.13%), Bouvier des
Flandres (2.38%), and mixed breed (0.15%); for dilated cardiomyopathy, breeds included Doberman Pinscher (7.32%), Great Dane (7.30%), Neapolitan Mastiff
(6.52%), Irish Wolfhound (6.08%), Saluki (5.88%),
and mixed breed (0.16%). Breeds affected with elbow
dysplasia included Bernese Mountain Dog (13.91%),
Newfoundland (10.28%), Mastiff (6.55%), Rottweiler (6.31%), Anatolian Shepherd Dog (5.41%), and
mixed breed (0.90%); for IVDD, Dachshund (34.92%),
French Bulldog (27.06%), Pekingese (20.59%), Pembroke Welsh Corgi (15.11%), Doberman Pinscher
(12.70%), and mixed breed (4.43%); for hypothyroidism, Giant Schnauzer (11.45%), Irish Setter (7.69%),
Keeshond (6.63%), Bouvier des Flandres (6.55%), Doberman Pinscher (6.30%), and mixed breed (1.54%);
for atopy or allergic dermatitis, West Highland White
Terrier (8.58%), Coonhound (8.33%), Wirehaired
Fox Terrier (8.16%), Cairn Terrier (6.91%), Tibetan
Terrier (5.86%), and mixed breed (1.08%); for bloat,
Scientific Reports
JAVMA, Vol 242, No. 11, June 1, 2013
187
would cause an overrepresentation of some disorders
in purebred dogs. Additionally, clients are willing to
pursue more extensive treatment at a referral hospital.13
Owners of purebred dogs are more likely to spend more
on their dogs than are owners of mixed-breed dogs,14
which would result in a greater proportion of purebred
dogs, as seen in the present study. Some dogs in the
present study not classified as having a particular condition may simply not have had that condition confirmed
because of the age of onset or the expense of definitive
diagnostic procedures. For example, epilepsy, atopy
(allergic dermatitis), and hypothyroidism, all of which
have higher probability in purebred dogs, require more
intensive diagnosis, and there may be sociological aspects in which dog owners who own mixed-breed dogs
may have less incentive to confirm the diagnosis.
Data for an acute onset of a disorder may have
been underrepresented in our data set if clients preferentially took the dog to their own veterinarian and not
a teaching hospital. Furthermore, the Veterinary Medical Teaching Hospital of the University of CaliforniaDavis represents a dog population primarily from the
west coast and may not represent dog populations in
other geographic regions. However, for 1 condition in
the present study (portosystemic shunt), the data and
the breeds preferentially affected mirrored data for all of
North America.15
All of these biases would be expected equally
among mixed-breed and purebred dogs in the population under study, or a bias specifically against the purebred dog population may have occurred; neither would
affect the objective of the study. Although these are potential limitations to the data, overall, the data set that
was evaluated is, in the authors’ opinion, one of the best
representations to include consistent diagnoses in large
numbers of purebred and mixed-breed dogs.
A previous study5 found no difference between
purebred and mixed-breed dogs with hip dysplasia.
Our results, which corroborate the findings of the previous study,5 indicated that in addition to hip dysplasia, several other disorders did not predominate among
purebred dogs. For genetic disorders that are found in
multiple breeds or are equally present in mixed-breed
dogs, causal mutations may have arisen multiple times
or the progenitors of the affected dogs may have been
derived from a common distant ancestor carrying the
defect. Mutations introduced into the dog genome early, in an ancestor closely associated with the wolf progenitor, would be spread through the dog population
at large. Perhaps the same desired traits that made dogs
a favorable species for domestication16 were linked to
alleles for hyperadrenocorticism, hypoadrenocorticism,
cancers, hip dysplasia, lens luxation, and some cardiac
disorders that were not found to be different between
purebred and mixed-breed dogs.
Alternatively, the selection for desirable morphological traits may be linked to the presence of deleterious alleles. Patellar luxation and lens luxation are
clear examples of size-oriented predisposition. These
disorders did not differ in prevalence between purebred
and mixed-breed dogs, yet appear to be more common
among smaller dogs. Another potential explanation for
a disorder’s equal prevalence in purebred and mixed-
Discussion
This study characterized the prevalence of genetic
disorders among purebred and mixed-breed dogs evaluated at the veterinary medical teaching hospital. The
study was designed specifically to evaluate purebred
dogs, compared with mixed-breed dogs in total, without attempting to evaluate individual breed prevalence.
One concern with this approach is that a breed-specific
disorder found in a high-population breed may inflate
the prevalence among purebred dogs, unduly influencing interpretation of the results. This did not appear to
be the case because in those conditions with a difference in prevalence between purebred and mixed-breed
dogs, none of the top 5 breeds (as a percentage of dogs
evaluated at the hospital) were high-population breeds.
The results indicated that genetic disorders were
individual in their expression throughout the dog population. Some genetic disorders were present with equal
prevalence among all dogs in the study, regardless of
purebred or mixed-breed status. Other genetic disorders were found in greater prevalence among purebred
dogs. Every disorder was seen in the mixed-breed population. Thus, on the basis of the data and analyses, the
proportion of mixed-breed and purebred dogs affected
by genetic disorders may be equal or differ, depending
on the specific disorder.
Although this study evaluated > 90,000 purebred
and mixed-breed dogs, there were limitations to the
study. The study population represented dogs evaluated
at a teaching hospital, and the proportions of the disorders in the purebred and mixed-breed dogs may have
been different from that in the general canine population. However, the study population did reflect the proportions of purebred and mixed-breed dogs evaluated
at private veterinary hospitals in the United States.12
In a referral hospital, breeds that are considered predisposed to a certain condition may be evaluated with
greater frequency and the condition may be diagnosed
at a higher rate than in other breeds or mixed-breed
dogs that do not have a recognized predisposition. This
JAVMA, Vol 242, No. 11, June 1, 2013
Scientific Reports
188
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SMALL ANIMALS
Saint Bernard (3.76%), Irish Setter (3.42%), Bloodhound (3.39%), Great Dane (2.80%), Irish Wolfhound
(2.70%), and mixed breed (0.20%); for cataracts, Silky
Terrier (22.76%), Miniature Poodle (21.49%), Brussels
Griffon (20.51%), Boston Terrier (19.61%), Tibetan
Terrier (18.92%), and mixed breed (4.04%); for epilepsy (total), Catahoula Leopard Dog (3.90%), Beagle
(3.57%), Schipperke (3.42%), Papillon (3.40%), Standard Poodle (3.19%), and mixed breed (0.91%); and for
portosystemic shunt, Yorkshire Terrier (10.86%), Norwich Terrier (7.41%), Pug (5.88%), Maltese (5.87%),
Havanese (4.35%), and mixed breed (0.35%). No single
breed dominated the listings. Labrador Retrievers and
mixed-breed dogs were more frequently evaluated at the
veterinary medical teaching hospital; therefore, those
dogs typically had a greater prevalence of every disorder.
However, the most frequent breeds affected by each disorder changed when adjusted for absolute numbers of
dogs of that breed evaluated at the clinic. Although some
breeds appeared multiple times in different disorders, no
breed dominated by the percentage of breed affected.
SMALL ANIMALS
breed dogs is that some tissues or organs may be less
resistant to genetic aberration and a number of different
mutations may induce a similar phenotypic defect, even
though the precise mutations differ in the 2 dog populations. Additionally, developmental abnormalities influenced by the environment or stochastic developmental
perturbations (eg, certain cardiac conditions)17 would
result in the same disease diagnosis. No significant difference was found for cancers between purebred and
mixed-breed dogs. Genes for cancer expression may be
spread widely among the dog population as a whole,
respond to environmental factors that affect all dogs, or
a combination of both.
For disorders that affected purebred dogs in higher
proportions, the underlying causal mutations likely occurred more recently, such as after the gene pools for
particular purebred dogs were developed, or were characteristic of particular lineages. In this study, 4 of the
top 5 breeds (by percentage) affected with elbow dysplasia are characterized as being from the Mastiff-like
dog lineage9: Bernese Mountain Dog, Newfoundland,
Mastiff, and Rottweiler. One could speculate that these
breeds, having been derived from a common ancestor,18
share mutations. Transmission of genetic disorders may
not only occur within a single antiquity lineage, but also
may occasionally cross to another lineage as a result of
desire for particular functional traits.8 A 1998 study19
supports this idea by revealing that certain disorders,
such as elbow dysplasia and portosystemic shunt, occurred in clusters of highly related dogs, whereas clusters of unrelated dogs were unaffected. Additionally, the
purebred population was at greater risk for atopy than
was the mixed-breed dogs. The published literature indicates that certain breeds are more likely to have atopy
than other breeds,20,21 suggesting that the high prevalence within individual breeds may result in the overall
purebred population being at greater risk than the population of mixed-breed dogs. Reports of mixed-breed
dogs having equivalent atopy prevalence to subsets of
purebred dogs22 support the existence of such an effect
and underscore the concept of clustering of disorders
among highly related dogs.
Disorders may be associated with breed derivation or with breed bottlenecks. Such an example is the
Irish Wolfhound, a breed with relatively few dogs registered annually. In the mid-1800s, the Irish Wolfhound
underwent a population bottleneck so severe that the
breed was thought to be extinct.23 The reduced effective
population size suggests a relationship with the concomitant increased risk of dilated cardiomyopathy in
Irish Wolfhounds. Indeed, as many as 1 in 3 Irish Wolfhounds may be affected with this disorder.23 In the present study, Irish Wolfhounds were in the top 5 purebred
dog breeds with dilated cardiomyopathy, corroborating
the high prevalence, compared with other breeds.
Other disorders appear to be more generalized and
more frequently observed in mixed-breed dogs. For example, metabolic disturbances have been implicated in
the onset of canine diabetes mellitus, for which the risk
of development is higher in mixed-breed dogs.24 In the
present study, dogs with cranial cruciate ligament rupture included purebred dogs from at least 3 lineages (ie,
Mastiff, Akita, and German Wirehaired Pointer),9 with
1554
mixed-breed dogs having a 30% greater risk for this disorder than did purebred dogs. The increased risk may
be caused by multiple musculoskeletal alleles from different physical conformations that, when combined, reduce the resilience of the ligament in the context of the
joint, as has been suggested for humans.25
Purebred dog owners, often devoted to a breed
and seeking to track the health of that breed, may have
created the impression that purebred dogs are not as
healthy as mixed-breed dogs. Overall, the prevalence of
disorders among purebred and mixed-breed dogs in the
present study depended on the condition, with some
having a clear distinction between purebred and mixedbreed dogs and others having no difference. Our results
confirmed those of other studies focused on hip dysplasia5 and congenital portosystemic shunts15 and expanded the potential for future genetic studies to focus on
several breeds when considering at-risk breeds to characterize the underlying genetic change. These results
also gave insight on the potential effects of breeding
practices to reduce prevalence. Reliable genetic tests or
screening at a young age may reduce some disorders
in the dog population as a whole. Additionally, some
disorders may require breed registry intervention to reduce conformational selection pressures that contribute to predisposing a breed to a disorder.
a.
Generalized linear function, R, version 12, R Foundation for Statistical Computing, Vienna, Austria. Available at: www.r-project.
org/. Accessed Feb 21, 2012.
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Brooks M, Sargan DR. Genetic aspects of disease in dogs. In: The
genetics of the dogs. Wallingford, Oxfordshire, England: CABI
Publishing, 2001;191–266.
Tsai KL, Clark LA, Murphy KE. Understanding hereditary diseases using the dog and human as companion model systems.
Mamm Genome 2007;18:444–451.
Karlsson EK, Lindblad-Toh K. Leader of the pack: gene mapping in
dogs and other model organisms. Nat Rev Genet 2008;9:713–725.
Leroy G. Genetic diversity, inbreeding and breeding practices in
dogs: results from pedigree analyses. Vet J 2011;189:177–182.
Rettenmaier JL, Keller GG, Lattimer JC, et al. Prevalence of canine hip dysplasia in a veterinary teaching hospital population.
Vet Radiol Ultrasound 2002;43:313–318.
Wayne RK, Ostrander EA. Origin, genetic diversity, and genome
structure of the domestic dog. Bioessays 1999;21:247–257.
Hedhammar ÅA, Malm S, Bonnett B. International and collaborative strategies to enhance genetic health in purebred dogs.
Vet J 2011;189:189–196.
Lindblad-Toh K, Wade CM, Mikkelsen TS, et al. Genome sequence, comparative analysis and haplotype structure of the
domestic dog. Nature 2005;438:803–819.
Parker HG, Ostrander EA. Canine genomics and genetics: running with the pack. PLoS Genet 2005;1:e58.
Asher L, Diesel G, Summers JF, et al. Inherited defects in pedigree dogs. Part 1: disorders related to breed standards. Vet J
2009;182:402–411.
Hulley SB. Designing clinical research. Philadelphia: Lippincott
Williams & Wilkins, 2007.
Trevejo R, Yang M, Lund EM. Epidemiology of surgical castration of dogs and cats in the United States. J Am Vet Med Assoc
2011;238:898–904.
Brown CM. The future of the North American veterinary teaching hospital. J Vet Med Educ 2003;30:197–202.
Dotson MJ, Hyatt EM. Understanding dog-human companionship. J Bus Res 2008;61:457–466.
Tobias KM, Rohrbach BW. Association of breed with the diagJAVMA, Vol 242, No. 11, June 1, 2013
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factors for atopic dermatitis in a Swedish population of insured
dogs. Vet Rec 2006;159:241–246.
Lund E. Epidemiology of canine atopic dermatitis. Vet Focus
2001;21:32–33.
Schick RO, Fadok VA. Responses of atopic dogs to regional allergens: 268 cases (1981–1984). J Am Vet Med Assoc
1986;189:1493–1496.
Parker HG, Meurs KM, Ostrander EA. Finding cardiovascular
disease genes in the dog. J Vet Cardiol 2006;8:115–127.
Guptill L, Glickman L, Glickman N. Time trends and risk factors for diabetes mellitus in dogs: analysis of veterinary medical
data base records (1970–1999). Vet J 2003;165:240–247.
Wahl CJ, Westermann RW, Blaisdell GY, et al. An association
of lateral knee sagittal anatomic factors with non-contact ACL
injury: sex or geometry? J Bone Joint Surg Am 2012;94:217–226.
From this month’s AJVR
Efficacy of decontamination and sterilization
of single-use single-incision laparoscopic surgery ports
James G. Coisman et al
Objective—To determine the efficacy of decontamination and sterilization of a disposable port
intended for use during single-incision laparoscopy.
Sample—5 material samples obtained from each of 3 laparoscopic surgery ports.
Procedures—Ports were assigned to undergo decontamination and ethylene oxide sterilization
without bacterial inoculation (negative control port), with bacterial inoculation (Staphylococcus aureus, Escherichia coli, and Mycobacterium fortuitum) and without decontamination and sterilization
(positive control port), or with bacterial inoculation followed by decontamination and ethylene oxide
sterilization (treated port). Each port underwent testing 5 times; during each time, a sample of the
foam portion of each port was obtained and bacteriologic culture testing was performed. Bacteriologic culture scores were determined for each port sample.
Results—None of the treated port samples had positive bacteriologic culture results. All 5 positive
control port samples had positive bacteriologic culture results. One negative control port sample had
positive bacteriologic culture results; a spore-forming Bacillus sp organism was cultured from that
port sample, which was thought to be an environmental contaminant. Bacteriologic culture scores
for the treated port samples were significantly lower than those for the positive control port samples.
Bacteriologic culture scores for the treated port samples were not significantly different from those
for negative control port samples.
Conclusions and Clinical Relevance—Results of this study indicated standard procedures for
decontamination and sterilization of a single-use port intended for use during single-incision laparoscopic surgery were effective for elimination of inoculated bacteria. Reuse of this port may be safe
for laparoscopic surgery of animals. (Am J Vet Res 2013;74:934–938)
JAVMA, Vol 242, No. 11, June 1, 2013
June 2013
See the midmonth issues
of JAVMA
for the expanded
table of contents
for the AJVR
or log on to
avmajournals.avma.org
for access
to all the abstracts.
Scientific Reports
190
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SMALL ANIMALS
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nosis of congenital portosystemic shunts in dogs: 2,400 cases
(1980–2002). J Am Vet Med Assoc 2003;223:1636–1639.
Vaysse A, Ratnakumar A, Derrien T, et al. Identification of genomic regions associated with phenotypic variation between dog
breeds using selection mapping. PLoS Genet 2011;7:e1002316.
Taussig HB. World survey of the common cardiac malformations: developmental error or genetic variant? Am J Cardiol
1982;50:544–559.
Vonholdt BM, Pollinger JP, Lohmueller KE, et al. Genome-wide
SNP and haplotype analyses reveal a rich history underlying dog
domestication. Nature 2010;464:898–902.
Ubbink GJ, Van de Broek J, Hazewinkel HA, et al. Cluster analysis of the genetic heterogeneity and disease distributions in
purebred dog populations. Vet Rec 1998;142:209–213.
Nødtvedt A, Egenvall A, Bergval K, et al. Incidence of and risk
J Vet Intern Med 2011;25:784–796
I d i o p a t h i c C y s t i t i s i n D o m es t i c C a t s — B e y o n d t h e L o w e r
Ur i n a r y T r a c t
C.A.T. Buffington
Signs of lower urinary tract (LUT) disease in domestic cats can be acute or chronic, and can result from variable combinations
of abnormalities within the lumen of the LUT, the parenchyma of the LUT itself, or other organ system(s) that then lead to
LUT dysfunction. In the majority of cats with chronic signs of LUT dysfunction, no specific underlying cause can be confirmed
after standard clinical evaluation of the LUT, so these cats typically are classified as having idiopathic cystitis. A syndrome in
human beings commonly known as interstitial cystitis (IC) shares many features in common with these cats, permitting comparisons between the two species. A wide range of similarities in abnormalities has been identified between these syndromes
outside as well as inside the LUT. A variety of potential familial and developmental risk factors also have been identified. These
results have permitted generation of the hypothesis that some of these people have a disorder affecting the LUT rather than a
disorder of the LUT. This perspective has suggested alternative diagnostic strategies and novel approaches to treatment, at least
in cats. The purpose of this review is to summarize research investigations into the various abnormalities present in cats, to
compare some of these findings with those identified in human beings, and to discuss how they might modify perceptions about
the etiopathogenesis, diagnosis, and treatment of cats with this disease.
Dedication: I dedicate this contribution to Professor Dennis J. Chew, whose collaboration, patience, and support made it all possible.
Key words: Comorbidity; Developmental biology; Etiology; Phenotype; Syndrome.
igns of lower urinary tract (LUT) dysfunction in
domestic cats (Felis silvestris catus) include variable
combinations of dysuria, hematuria, periuria, pollakiuria, and stranguria.1 A review article published in
1996 listed some 36 confirmed causes of LUT signs.2
These signs can be acute or chronic, and can result from
variable combinations of abnormalities within the lumen
of the LUT (local external abnormalities), in the LUT
itself (intrinsic abnormalities), or other organ system(s)
that then lead to LUT dysfunction (internal abnormalities). In the majority of cats with chronic signs of LUT
dysfunction, however, no specific underlying cause can
be confirmed after standard clinical evaluation of the
LUT. These cats typically are classified as cases of idiopathic causation, hence the name idiopathic cystitis.1
Beginning in 1993, results of a series of studies using
cats with chronic idiopathic LUT signs donated by owners
for whom they no longer were acceptable pets have been
published. Initial studies of these cats focused on identification of abnormalities of the LUT because the affected
cats were proposed to represent a naturally occurring
model of a chronic LUT syndrome in human beings called
interstitial cystitis (IC).3,4 These studies led to the proposal
in 1996 that cats having chronic idiopathic LUT signs be
described as having ‘‘feline interstitial cystitis’’ (FIC).5
During the ensuing years, evidence also has accumulated that additional problems outside the LUT are
commonly present in these cats, as well as in most
patients with IC. This evidence has led to reconsideration of the cause(s) of the syndrome in these individuals,
S
Abbreviations:
ACTH
FIC
GAG
IC
KCl
LUT
SRS
UTI
adrenocorticotropic hormone
feline interstitial cystitis
glycosaminoglycan
interstitial cystitis
potassium chloride
lower urinary tract
stress response system
urinary tract infection
as well as to considerable debate about the most appropriate name, diagnostic approach, and treatment
recommendations. This reconsideration is ongoing, and
has resulted in the generation of new hypotheses related
to the etiopathogenesis of the signs and symptoms in
both cats and human beings with this problem, as well as
novel approaches to treatment, at least in cats.
The purposes of this review are to summarize some of
the many research investigations into the external, intrinsic, and internal abnormalities that are present in these cats
(this organization was chosen because it roughly parallels
the chronology of studies of the syndrome over the past 3
decades), to compare these findings with those identified in
human beings with IC during this time, and to consider
how these results might modify perceptions about the
diagnosis and treatment of cats with this problem.
Nosology
From the Department of Veterinary Clinical Sciences, College of
Veterinary Medicine, The Ohio State University, Columbus, OH.
Corresponding author: C.A. Tony Buffington, Department of Veterinary Clinical Sciences, College of Veterinary Medicine, The Ohio
State University, 601 Vernon L. Tharp Street, Columbus, OH 432101089; e-mail: buffington.1@osu.edu.
Nosology refers to the naming of diseases. Diseases
can be named according to etiology, pathogenesis, and
affected organ system(s), and by presenting signs and
symptoms. A significant challenge to accurate nosology
exists because diseases can be named based on prominent
signs and symptoms long before research identifies
the etiology and pathogenesis. Whereas presenting
signs sometimes result in naming a disease for the organ
associated with the signs, the disease might not originate
Submitted December 10, 2010; Revised January 26, 2011;
Accepted March 28, 2011.
Copyright r 2011 by the American College of Veterinary Internal
Medicine
10.1111/j.1939-1676.2011.0732.x
191
Idiopathic Cystitis in Cats
785
Regardless of the name eventually chosen to describe
cats with chronic idiopathic LUT and other clinical signs,
current evidence suggests that restriction of the description of these cats to their LUT signs does not capture all
currently recognized features of the syndrome.15,16,18
Regardless of agreement on an accurate descriptive term
for the syndrome, it seems appropriate for clinicians to
conduct a more comprehensive evaluation of cats presented with these and other chronic idiopathic signs to
determine whether only these signs occur, or whether
variable combinations of comorbid somatic and behavioral abnormalities also are present. Such an evaluation
could result in a more complete diagnosis and implementation of additional approaches to treatment for some
cats, which has been associated with better outcomes.15
For the purposes of this review, I will retain the terminology used to describe patients in the studies referenced,
since it was what was used at the time the results were
published. This is done with some trepidation because of
the risk of reinforcing the focus on the LUT rather than a
more comprehensive assessment of the problem list of the
patients, but such was, and to a greater or lesser extent
still is, how studies have been reported.
in the affected organ, and many diseases affect more than
one organ. Thus, the name could reflect a subset of the
problems associated with an underlying disease. This
could have affected the nosology describing cats with
chronic idiopathic LUT signs6 and human beings with
IC.7 Feinstein8 recently concluded that ‘‘an important
principle in naming apparently new ailments is to avoid
etiologic titles until the etiologic agent has been suitably
demonstrated. A premature causal name can impair a
patient’s recovery from the syndrome, and impede research that might find the true cause.’’
Although terms such as ‘‘feline urological syndrome,’’9
‘‘feline lower urinary tract disease,’’10 and ‘‘feline interstitial cystitis’’11 fairly accurately capture the currently
recognized diagnostic criteria for LUT disorders, they
no longer seem to capture the extent of the problems
occurring in many cats. These terms all focus on the
LUT, reflecting the prominent presenting signs and
LUT-focused diagnostic testing rather than a thorough
evaluation of the entire cat. In human beings, more
comprehensive investigations of patients with IC and
a variety of other chronic idiopathic disorders have
resulted in the suggestion of names such as ‘‘medically
unexplained syndrome,’’12 ‘‘functional somatic syndrome,’’13 or ‘‘central sensitivity syndrome’’14 to
describe the multiple abnormalities observed in these
patients by physicians. The list of chronic disorders proposed to be covered by these names is long, and includes
problems addressed by most of the medical subspecialties. These names also seem to violate Feinstein’s
admonition, however, and it seems that some generic
umbrella term comparable to ‘‘cancer’’ or ‘‘infection’’
might be more appropriate. One possibility, which I will
use in this review when it seems appropriate, is to adopt
an interim name such as ‘‘Pandora’’ syndrome until the
most biologically appropriate nosological term is identified. Tentative criteria for diagnosis of a ‘‘Pandora’’
syndrome include:
Abnormalities Identified in FIC and IC
Many features in common have been identified in cats
and human beings with the syndrome.19 Variable combinations of LUT abnormalities have been identified in
patients of both species, who also often suffer multiple
comorbid disorders.16,20 Moreover, the occurrence of comorbid disorders often precedes the occurrence of LUT
signs and symptoms (C.A.T. Buffington, unpublished
observation).21,22 These comorbid disorders also appear
to occur more commonly in close relatives of human
patients,23,24 and evidence of adverse early experiences
has been reported in patients with FIC25 and IC.26
Two LUT forms of the syndrome have been reported,
nonulcerative (Type I) and ulcerative (Type II); other
forms also could exist.20 Cats almost always present with
the Type I form, although the Type II form has been
described,27 and in human beings, approximately 90% of
patients have the Type I form.28 The etiopathogenesis of
these 2 forms differs. The Type II form appears to be an
inflammatory disease intrinsic to the bladder, whereas
the Type I form might be neuropathic in origin.
Owners commonly request evaluation of obvious LUT
signs they observe in their cats, so a large amount of
research has been directed toward the bladder, resulting
in identification of a variety of abnormalities. The bladder is a deceptively sophisticated organ.29,30 Its internal
covering consists of an epithelium with its underlying neurovascular supporting tissue, which is surrounded by
both smooth and striated muscle.31 These structures engage in complex neuroendocrine communication with
the rest of the body to determine the appropriate conditions and timing for voiding. Bladder neural connections
include sensory afferent, central, and somatic, sympathetic, and parasympathetic efferent neurons that
interact throughout the neuraxis between the urothelium
and the cerebral cortex.32 In addition to a variety of
1. Presence of clinical signs referable to other organ systems in addition to the chronic idiopathic signs
prominently referable to a particular organ for which
the patient is being evaluated. For example, variable
combinations of clinical signs referable to other organ
systems such as the gastrointestinal tract, skin, lung,
cardiovascular, central nervous, endocrine, and
immune systems have been identified in cats with
chronic idiopathic LUT signs.15,16
2. Waxing and waning of severity of clinical signs associated with events that (presumably) activate the
central stress response system (SRS).15,17,18
3. Resolution of signs associated with effective environmental enrichment.15,17,18
A name like ‘‘Pandora’’ syndrome seems appropriate
for at least 2 reasons. First, it does not identify any specific cause or organ, and second, it seems to capture the
dismay and dispute associated with the identification of
so many problems (evils) outside the organ of interest of
any particular subspecialty.
192
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Buffington
such as the number of previous treatments, including
catheterization of male cats, also might have influenced
their results. Other studies have reported prevalence rates
of UTI from 15 to 43% in cats with compromised urinary
tract defense mechanisms, and 1 study reported a prevalence of 22% in cats with no apparent predisposing
factors.50 Some evidence suggests that colonization may
result from an underlying vulnerability in affected cats.
Perineal urethrostomy did not lead to postoperative bacterial infection in healthy cats, whereas it occurred
postoperatively in 22% of cats with histories of recurrent
or persistent urethral obstruction.51
There also might be a relationship between IC and
UTI in human beings. One recent study found evidence
of UTI within the past 2 years in 38% of the IC/painful
bladder syndrome patients they studied,52 although, ‘‘ . . .
the infection domain was not associated with any
increased symptoms.’’ Additionally, retrospective data
suggest that a proportion, probably a minority, of
women had evidence of UTI or inflammation at the
onset of symptoms of IC/painful bladder syndrome.53 It
also has been speculated that intrinsic abnormalities
make the LUT more vulnerable to microbial colonization,38 which might be consistent with the observation of
increased risk for bacterial UTI in these patients.
neurotransmitters, bladder function also is influenced by
both adrenocortical and sex hormones.33
Local External Abnormalities
Toxic and Protective Factors. The presence of some
toxin,34 abnormality of some protective factor,35,36 or
presence of some microorganism37,38 in the urine has
been proposed to explain the LUT signs and symptoms
in patients with FIC and IC. An abnormality of TammHorsfall protein that results in loss of protection of the
urothelium,39 the appearance of an ‘‘anti-proliferative
factor’’ and local growth factor abnormalities that might
disrupt cell signaling,40 and other changes in the urine of
patients with IC have been identified and are being
investigated.41,42 Whether these play causative roles in
FIC or IC remains to be determined, although the relevance of the Tamm-Horsfall protein abnormality was
diminished by the report of absence of voiding dysfunction or compatible histological abnormalities in TammHorsfall protein knockout mice.43
Microbial Agents. Given the similarity in symptoms
between cystitis resulting from bacterial urinary tract
infection (UTI) and FIC and IC, researchers have considered infection to be a cause of the LUT signs and
symptoms for nearly 100 years. Guy Hunner, for whom
the ‘‘Hunner’s ulcer’’ of the Type II form of the syndrome was named, publically speculated that a bacterial
infection was the cause of ‘‘a rare type of bladder ulcer in
women’’ in 1915.44 If microbes are associated with FIC
or IC, they could either cause the disorder, or be associated with it in some noncausal way.
A role for infectious agents such as viruses in the LUT
signs observed in cats has been investigated,37,45
although what relationship viruses play in the etiopathogenesis of these signs in cats with naturally occurring FIC
remains unclear at this time.46 Moreover, investigations
of what role infectious agents might play in the systemic
manifestations of the syndrome are yet to be reported.
In human beings, 2 recent studies concluded that ‘‘IC
is not associated with persistence of viral and bacterial
DNA in the bladder. A chronic infective etiology for the
condition is excluded by these findings,’’47 and, ‘‘these
data suggest that the symptom flares of IC are not usually associated with recurrent UTI and, therefore, are
likely due to a triggering of the other painful mechanisms
involved in IC patients who are culture-negative.’’48
Thus, the probability that an infectious agent commonly
causes the symptoms present in these patients seems
quite small.
Although microorganisms in the LUT might not commonly cause FIC or IC, this does not mean that microbes
have no association with the syndromes. A recent report
of 134 cats in Norway evaluated for LUT signs found
bacteriuria exceeding 103 CFU/mL in 44 (33%) cats, and
exceeding 104 in 33 (25%), either alone or with variable
combinations of crystals and uroliths.49 These results
suggested a prevalence of bacteriuria higher than
reported previously, which the authors speculated might
have resulted from differences between cases diagnosed
at primary and tertiary care facilities. Other variables,
Intrinsic Abnormalities
The Glycosaminoglycan (GAG) Layer. The internal
surface of the LUT is coated by a GAG layer that might
be abnormal in patients with FIC or IC. A wide variety
of sometimes-conflicting changes in the quantity and
quality of the GAG layer in patients with IC is
reported.54–56 Decreased total GAG,35,57 and a specific
GAG known as GP-51,58 has been reported in cats with
FIC. One group of investigators also found chondroitin
sulfate in the plasma of cats with feline urologic syndrome, leading them to conclude that the decreased
chondroitin concentration they found in urine could have
resulted from reabsorption back across a more permeable
urothelium.57 Limitations of most studies of urine GAG
include the difficulty of the GAG assay and the variety of
methods used, so what role the GAG layer plays in these
disorders currently remains unresolved.59
Experimental attempts to replenish the GAG layer
also have been reported. In cats, 2 studies of the effects
of GAG replacement therapies have been investigated,
but no benefit beyond placebo was found in either
study.60,61 In human beings, the beneficial effects of
polysulfated62,63 and other GAGs64 on symptoms of IC
or painful bladder syndrome/IC also appear to be small.
As noted in a recent editorial commentary, the shift in
perspective toward a more systemic view of IC ‘‘calls local treatments into question.’’59
Urothelium. A specialized epithelium called the urothelium lines the distal portion of the urinary tract, including the renal pelvis, ureters, bladder, upper urethra,
and glandular ducts of the prostate.65 The urothelium is
composed of a basal cell layer attached to a basement
membrane, an intermediate layer, and a superficial apical
layer.66 Although healthy urothelium maintains a tight
193
barrier to ion and solute flux, factors such as altered pH or
electrolyte concentrations, mechanical, chemical, or neurally mediated stimulation, and infectious agents all can
impair the integrity of the barrier.67
Both functional and anatomical abnormalities of the
urothelium have been reported in FIC and IC, although
their cause and significance are unknown. In cats with
FIC, significantly higher bladder permeability to sodium
salicylate,68 as well as reduced transepithelial resistance
and increased water and urea permeability after
hydrodistention of the bladder, has been reported.69 A
denuded urothelium with appearance of underlying cells
also was found in these cats by scanning and transmission electron microscopy, leading the authors to
conclude that the urothelial damage and dysfunction
identified might ‘‘suggest novel approaches toward
examining the etiology and therapy of IC.’’69 Ironically,
a paper published the same month70 reported strikingly
similar electron microscopic findings—in healthy female
mice exposed to constant illumination for 96 hours, after
which they were returned to conventional day-night illumination for 7 days before being killed. This report
showed that comparable urothelial injury also could
occur in healthy animals exposed to stressful external
events. Neither of these studies examined any other
tissues to determine if the observed abnormalities were
restricted to the bladder or had a more widespread
distribution.
Recent studies have revealed that urothelial cells
express a number of molecular ‘‘sensors’’ that confer
properties similar to both nociceptive and mechanosensitive type neurons on these cells. Thus, like superficial
cells on other epithelial surfaces,71,72 urothelial cells possess specialized sensory and signaling properties that
allow them to respond to their environment and to
engage in reciprocal communication with neighboring
urothelial and nerve cells.73 Alterations in the expression
of various receptors, channels, and transmitters involved
in both the ‘‘sensor’’ as well as ‘‘transducer’’ properties of
the urothelium at both gene and protein levels have been
found in urothelial cells from both cats and human beings
with the syndrome.30 Alterations in stretch-mediated
release of transmitters from the urothelium, including
increased nitric oxide74 and adenosine triphosphate75
release also may influence urothelial integrity and cell-cell
signaling.
Submucosa. Abnormalities also are present below the
urothelium, although the histological features of Type I
FIC76 and IC77 are somewhat unusual. Vasodilatation
and vascular leakage in the general absence of any significant mononuclear or polymorphonuclear infiltrate is
the most common finding, suggesting the presence of
neurogenic inflammation.78,79 Increased numbers of
mast cells have been observed in biopsy specimens from
about 20% of patients with Type I FIC76 and IC,28 and
are thought by some to be involved in the pathophysiology of the syndrome.80 The finding of mast cells in
the bladder is by no means specific to these syndromes.81
The role of mast cells in IC and comorbid disorders,
especially those exacerbated by stress, was recently
reviewed.82 It was concluded that mast cell activation
787
could be a neurally mediated byproduct of the stress
response associated with the disorder. One beneficial
action of the tricyclic antidepressant amitriptyline (if
such exists83) could be through inhibition of mast cell activation.84 In one recent report, however, no difference in
the degree of lymphocyte and mast cell infiltration, or in
neovascularization or staining for uroplakins, was found
between bladders of cats with feline idiopathic cystitis
and those with urolithiasis, and in this study urothelial
GAG staining was highest in tissues from affected cats.85
Detrusor Muscle. In contrast to the many abnormalities found on the luminal side of the lamina propria,
there is a paucity of data of etiopathogenic importance
implicating the bladder muscle in the pathophysiology of
FIC or IC.86 In cats with FIC, nonspecific inflammatory
changes in the detrusor,87 as well as in vitro evidence to
suggest that the muscle functions relatively normally,79
have been reported.
Intrinsic Abnormalities—Summary. The etiopathogenic
significance of local bladder abnormalities occurring in patients with FIC and IC remains to be established.
Moreover, in chronic diseases, clinical signs often do not
appear to correlate well with pathology in the bladder,28 or
elsewhere.88 For example, bladder lesions characteristically
associated with irritative voiding symptoms and pelvic
pain in patients diagnosed with IC also have been observed
in asymptomatic women undergoing tubal ligation.89
Some patients treated with cyclophosphamide also develop
a hemorrhagic cystitis and voiding dysfunction without the
pain often associated with IC.90 A similar situation also
occurs in the bowel. In one study, rectal perception of distention was actually attenuated in patients with ulcerative
colitis, whereas it was enhanced in patients with irritable
bowel syndrome.91 To paraphrase the conclusion of the
authors of this study, low-grade mucosal inflammation
alone is unlikely to be responsible for symptoms of functional disorders.
Most studies of FIC and IC also have failed to examine
tissues from other organs for comparison, so one cannot
determine whether the identified changes are restricted to
the LUT, or whether they also occur elsewhere in the
body of patients with the syndrome. Moreover, no temporal relationship has been established between these
abnormalities and the onset of clinical signs. Finally,
improvement in clinical signs has been reported to occur
in the absence of cystoscopic or histological changes in
cats92 or human beings,93 and cystectomy does not
resolve symptoms in human beings with the Type-I form
of the syndrome.94 These findings suggest that important
parts of the problem lie elsewhere.
Internal Abnormalities
Afferent Input. Sensory information is transmitted
from the bladder to the spinal cord by afferent neurons.
Mechanosensitive bladder afferent neurons were found
to exhibit a small increase in sensitivity to distension with
154 mM saline in cats affected with FIC as compared
with normal cats, albeit at higher than normal spontaneous micturition pressures.95 The effect of increasing
concentrations (80–300 mM) of potassium chloride
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Buffington
(KCl) on afferent firing also was examined, both because
intravesical KCl has been used as a diagnostic probe for
IC in human beings,96 and because it has been speculated,97 but never demonstrated, that the urine potassium
concentration plays a role in the pathophysiology of IC.
Increased afferent firing similar to that seen with saline
was observed during filling with KCl at concentrations
o150 mM; however, concentrations of 150–300 mM produced almost complete inhibition of afferent firing at
pressures between 30 and 80 cm of water, suggesting that
increased bladder permeability permits entry of sufficiently high concentrations of KCl into the submucosa
to dampen neural activity. These data suggest that
afferent nerves become more sensitive to stimuli in cats
with FIC.
A modest increase in Substance P, an 11 amino acid
sensory neurotransmitter peptide, immunoreactivity in
unmyelinated neurons has been detected in bladder tissue
from cats with FIC,98 and in some,99 but not all,100 studies of bladder tissue from human beings with IC. Bladder
Substance P receptor expression is significantly
increased in cats with FIC,101 and both increased102 and
decreased103 in patients with IC. Clinical trials of
the therapeutic properties of Substance P antagonists in
human beings to date have been disappointing, however,104,105 and recent evidence suggests that Substance P
might limit the severity of inflammatory reactions,106,107
opening the possibility that the changes observed in
patients with these syndromes may reflect some protective response.
A variety of abnormalities have been identified in dorsal root ganglion cell bodies of bladder-identified
neurons from cats with FIC. Cells from affected cats
were 30% larger, expressed altered neuropeptide profiles, and exhibited slowly desensitizing, capsaicininduced currents related to increased protein kinase
C-mediated phosphorylation of the transient receptor
potential vanilloid 1 receptor.108 Moreover, these abnormalities were not restricted to cells from bladderidentified neurons; similar findings were observed in
dorsal root ganglion cells throughout the lumbosacral
(L4-S3) spinal cord.108
Treatments targeting bladder sensory neurons have
been tested, but without success to date.109 Resiniferatoxin, a potent naturally occurring analog of capsaicin
that activates transient receptor potential vanilloid 1
receptors on nociceptive sensory neurons, reduced bladder compliance and capacity in a pilot study of
anesthetized cats with FIC.110 Controlled trials of both
capsaicin and resiniferatoxin in human beings with IC
also have failed to find significant benefits over placebo.111 As one expert recently concluded, ‘‘Intravesical
instillation therapy has basically not changed during the
last few years, although some studies have disconfirmed
some regimens. Intensive research may hopefully result
in more effective treatments in the future.’’112
Brain. Exacerbations of LUT signs in response to
external environmental challenges have been reported
both in laboratory studies17 and in client-owned cats
with FIC,113–117 as well as in patients with IC.118,119 In
the brain, significant increases in tyrosine hydroxylase,
the rate-limiting enzyme of catecholamine synthesis,
immunoreactivity have been identified in the pontine
locus coeruleus120 and the paraventricular nucleus of the
hypothalamus of cats with FIC.121
The locus coeruleus contains the largest number of
noradrenergic neurons, and is the most important source
of norepinephrine in the central nervous system. Afferent
input, including bladder distention, stimulates neuronal
activity in the locus coeruleus, which is the origin of the
descending excitatory pathway to the bladder.29 The locus coeruleus also is involved in such global brain
functions as vigilance and arousal. Increased tyrosine
hydroxylase activity in the locus coeruleus also can occur
in response to chronic external stressors,122 with accompanying increases in autonomic outflow.123 Moreover,
the locus coeruleus appears to mediate visceral responses
to external as well as internal input.124 The increased
immunoreactivity found in these nuclei might thus provide clues to the observation that the signs in cats117,125
and symptoms in human beings126,127 follow a waxing
and waning course that can be influenced by external as
well as internal events.
External environmental events that activate the SRS are
termed stressors.128 Examples of these events include sudden movements, unknown or loud noises, novel and
unfamiliar places and objects, and the approach of strangers. Inadequate perception of control and predictability
also can activate the SRS in animals because of interference with attempts to cope with their environments.129
Depending on the frequency, intensity, and duration,
chronic activation of the SRS can overtax homeostatic
regulatory systems, resulting in diminished welfare,130 abnormal conduct, and sickness behaviors.131,132
The acoustic startle response has been used as a probe of
sensitivity to external events in patients with FIC and IC.
This response is a brainstem reflex that responds to unexpected, loud stimuli, which has been shown to be increased
by both fear and anxiety mediated by higher brain structures.133 The acoustic startle response in cats with FIC is
greatest and most different from that of healthy cats during
stressful situations, but is still greater in cats with FIC than
in healthy cats even when adapted to enriched housing conditions.134 Exaggerated acoustic startle responses also have
been reported in women with IC.135,136
Efferent Output
Neural. Activation of the SRS by either internal or
external stimuli can result in stimulation of peripheral
neural, hormonal, and immune responses. In addition to
increased activity in the locus coeruleus, plasma catecholamine concentrations are significantly (P o .05)
higher in cats with FIC compared with healthy cats both
at rest125 as well as during exposure to a moderate stress
protocol.17 Furthermore, plasma catecholamine concentrations decreased in the healthy cats as they acclimated
to the stress, whereas even higher concentrations of
plasma norepinephrine and epinephrine were found in
cats with idiopathic cystitis.17
A functional desensitization of a-2 adrenergic receptors in affected cats also has been identified by evaluating
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789
These results, when combined with observations of increased concentrations of corticotrophin-releasing
factor121,149 and ACTH146 in response to stress in the absence of a comparable increase in plasma adrenocortical
hormone concentrations, suggest the presence of mild
primary adrenocortical insufficiency or decreased adrenocortical reserve in cats with FIC. Inappropriately low
plasma adrenocortical hormone concentrations also
have been observed in human beings with IC and chronic
idiopathic prostatic pain syndrome.20,150 Potential mechanisms underlying the stress-related reductions in
circulating adrenocortical steroid concentrations include
endocrine,151 neural,152,153 and developmental influences
on the adrenal gland.20
Immune. Studies of laboratory-housed17,154 and zooconfined cats155 have found that activation of the SRS is
associated with a variety of sickness behaviors.18 Sickness behaviors refer to variable combinations of
vomiting, diarrhea, anorexia or decreased food and
water intake, fever, lethargy, somnolence, enhanced
pain-like behaviors, as well as decreased general activity,
body care activities (grooming), and social interactions.156 Sickness behaviors are thought to reflect a
change in motivation toward withdrawal to promote recovery by inhibiting metabolically expensive (eg, foraging)
or dangerous (eg, exposure to predators) activities when
the animal is in a relatively vulnerable state. Sickness behaviors are found across mammalian species, and their
occurrence157 has been linked to immune activation and
proinflammatory cytokine release,158 as well as to changes
in mood and pathologic pain.132,159 Sickness behaviors
can result both from peripheral (bottom-up) and central
(top-down) activation of immune responses. In a recent
study of healthy cats and cats with FIC,18 (infra vide)
unusual environmental events, but not disease status,
resulted in a significant increase in total sickness behaviors when the results were controlled for other factors.
Recent studies have begun to map the pathways that
transduce activation of the SRS into cellular dysfunction.
Induction of the transcription factor nuclear factor-kB in
peripheral blood mononuclear cells was observed after
environmental activation of the SRS.160 Only norepinephrine induced this response, which was reduced
by both a(1)- and b-adrenergic inhibitors. The authors
concluded that norepinephrine-mediated activation of
nuclear factor-kB represented a downstream effector of
the response to stressful psychosocial events, linking
changes in the activity of the SRS to a bewildering array
of cellular responses via cell surface receptors.161 Cytokines and a variety of other inflammatory and metabolic
signals also can activate nuclear factor-kB by binding
to different cell surface receptors, further complicating interpretation of the source(s) of generation of cellular responses. Adrenocortical steroids tend to inhibit
activation of nuclear factor-kB.162,163 This and other
adrenocortical steroid-related protective mechanisms164–166
might be less efficient in hypoadrenocortical states such as
FIC and IC.
Comorbid Disorders. The possibility of an internal
cause in some patients with FIC and IC also is suggested
by the presence of multiple comorbid disorders in many
their response to the selective a-2 adrenergic receptor
agonist medetomidine in both in vivo137 and in vitro
studies.79 In vivo, heart rate decreased and pupil diameter increased significantly in healthy cats compared with
cats with idiopathic cystitis, which also had significantly
lower respiratory rates than did healthy cats after intramuscular administration of 20 mg medetomidine/kg body
weight. No significant differences in blood pressure or
sedation level were observed. In vitro, electrical field
stimulation of bladder strips from cats with FIC revealed
that atipamezole, an a-2 adrenergic receptor antagonist,
did not alter the relaxing effect of norepinephrine, further suggesting downregulation of a-2 adrenergic
receptors.79
Abnormalities of efferent nerves also appear to be
present. Bladder tissue from patients with FIC (A.J.
Reche and C.A.T. Buffington, unpublished observations,
2001) and IC99,100 contains increased tyrosine hydroxylase-immunoreactive neurons in both muscle and
urothelium. There is increased nitric oxide74 and norepinephrine (but not acetylcholine) release from bladder
strips in cats with FIC.79 In addition, tyrosine hydroxylase-containing nerves occur in or near the bladder
mucosa, suggesting an interaction between noradrenergic
nerves and the urothelium. Urothelial cells can express
both a- and b-adrenergic receptors, and adrenergic agonist stimulation of these receptors leads to nitric oxide
release. These data support the view that the urothelium
can be influenced by both afferent and efferent nerves,
which in turn can influence the function of a variety of cell
types and ultimately bladder function.138 Significant increases in local nerve growth factor concentrations also
have been found in affected cats,139 and human beings,140,141 which too can affect bladder nerve function,30
although the finding in humans was not specific to IC.140
The specificity of the finding in cats is not known.
Activation of the SRS also can increase epithelial permeability by neural mechanisms, permitting environmental agents greater access to sensory neurons,142 which
could result both in increased afferent firing and local
inflammation. Thus, the effects of the emotional state of
the animal may modulate perceived sensations from
peripheral organs, completing a loop that may be modulated by both central and peripheral neural activity.143
Hormonal. In addition to the sensory, central, and
efferent neural abnormalities identified, an ‘‘uncoupling’’
of SRS output, with a relative predominance of sympathetic nervous system to hypothalamic-pituitary-adrenal
activity,144 appears to be present in patients with FIC
and IC. Sympathoneural outflow normally is restrained
by adrenocortical output.145 In patients with FIC20,146
and IC,147,148 however, it increases without coactivation
of the adrenal cortex. Additionally, the adrenocortical
response to adrenocorticotropic hormone (ACTH) stimulation during stressful circumstances is reduced, and
cats with FIC often have small adrenal glands.25,146
Histopathological examination of these glands excluded
the presence of hemorrhage, inflammation, infection,
fibrosis or necrosis, and morphometric evaluation identified reduced size of the fasciculata and reticularis zones
of the adrenal cortex.
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Buffington
abnormalities suggest a genetic or familial susceptibility,
a developmental accident, or some combination of
these.20,26 When a pregnant female is exposed to a sufficiently harsh stressor, or is unusually sensitive to
environmental stressors herself, the hormonal products
of the ensuing stress response may cross the placenta and
affect the course of fetal development.172 The biological
‘‘purpose’’ of transmitting this response to the fetus
might be to program the development of the fetal SRS
and associated behaviors toward enhanced vigilance to
increase the probability of survival.173
The effects of maternal hormones on the fetus seem to
depend on the timing and magnitude of exposure in relation to the developmental ‘‘programs’’ that determine the
maturation of the various body systems during gestation
and early postnatal development.172 For example, if the
fetus is exposed before initiation of a developmental
program, there might be no effect on adrenal development. Adrenal development might be reduced, however,
if exposure occurs during the critical period when the
adrenocortical maturation program is running,20 or
increased if exposure occurs after the period of adrenocortical development.173
Postnatal stressors also can result in persistently
increased central corticotrophin-releasing factor activity
in animals.174 Behavioral abnormalities in adult rats can
result from adverse events during the neonatal period.175
These effects were mediated by epigenetic modification of
glucocorticoid receptor gene expression in the hippocampus by DNA methylation and histone acetylation.176
Adult mice subjected to chronic social stress have stressinduced epigenetic modulation of hippocampal gene
expression that is not restricted to the neonatal period.177
In addition, other studies of early environmental effects on
rat pups have found alterations in autonomic emotional
motor circuits,178 as well as in monoamine, g-amino
butyric acid, and glutaminergic circuits in adulthood.179
Studies in rodents also have shown that neonatal
inflammation of the bladder can result in impaired bladder function in adults when the bladder is rechallenged.180
Similar results also have been reported in the colon after
neonatal manipulation181 or maternal deprivation.182
These results support the hypothesis that events experienced during development may permanently affect
visceral sensory systems, representing an additional potential cause of chronic idiopathic disorders. Unfortunately, other organs were not evaluated in these studies,
so the full extent of the changes resulting from early
adverse experiences remains to be determined.
Recent studies in human beings also have demonstrated that early adverse experience can result in
durable alterations in endocrine and autonomic
responses to stress similar to those identified in IC.147,183
Although the dramatic adverse effects of abuse on the
SRS of human beings are well known,184 less extreme
parenting behaviors such as neglect, rejection, and hostility185 as well as a host of environmental events186 also
might play important mediating roles in the neuroendocrine abnormalities observed.187,188
Early life events also can confer resilience to adverse
experience. Both genetic and environmental resilience
patients, the absence of this pattern of comorbidity in
patients with other LUT diseases, and the unpredictable
order of appearance of the comorbidities. Cats with FIC
can have variable combinations of comorbid disorders,
including behavioral, cardiovascular, endocrine, and
gastrointestinal problems in addition to their LUT
signs.15,16,20,115,167 Most human beings with IC also
suffer from variable combinations of comorbid disorders
that affect a variety of other body systems.20,168–170 That
patients with FIC and IC have variable combinations of
other comorbid disorders raises the question of the
extent to which a different etiology affects each organ
versus the extent to which some common disorder affects
all organs, which then respond in their own characteristic
ways.
External, intrinsic, or both, bladder abnormalities
could lead to development of these other disorders.
Patients with extrinsic (eg, chronic UTI) or intrinsic
(eg, bladder cancer or ‘‘overactive bladder’’) urological
disorders, however, have not been reported to be at
comparable increased risk for development of the
many comorbid disorders that afflict patients with IC.
Moreover, appearance of FIC (C.A.T. Buffington, unpublished observation) or IC21,22 does not predictably
precede development of other syndromes, further suggesting that they are not a consequence but rather
independent events or separate manifestations of a common underlying disorder.
Internal Abnormalities—Summary. In addition to the
variety of local bladder abnormalities identified in
patients with FIC and IC, examination of other tissues
for comparison has revealed that many of the identified
changes are not restricted to the bladder, but also occur
elsewhere in the body of patients with the syndrome.
Moreover, comorbid disorders apparently are as likely to
precede as to follow the onset of the syndrome. The number, order of onset, and extent of abnormalities identified
outside the LUT in cats with FIC were unexpected, and it
seems likely that more will be identified in the future.
Moreover, many of the changes seem to be ‘‘functional,’’
waxing and waning with disease activity, rather than
structural. Disease activity also was found to change with
environmental circumstances, worsening during exposure to challenging (stressful) circumstances.
Although a variety of internal abnormalities in tissues
or systems distant to the bladder occur in patients with
FIC and IC, their etiopathologic significance has not
been established. Evidence also supports the observation
that both external (environmental) as well as internal
(visceral) events can activate the SRS, leading to activation of variable combinations of neural, hormonal, and
immune responses. These responses might help explain
the number, location, and variability of subsequent
health problems.171
Early Life Events
The findings of increased corticotrophin-releasing factor, ACTH, and sympathoneural activity in the presence
of reduced adrenocortical response and small adrenal
fasciculata and reticularis zones without other apparent
197
factors have been identified,189–191 and the effect of
external events on these factors on the developing nervous system might depend on the timing of exposure to
them.192 Thus, research has demonstrated that early life
experience can have a multitude of effects on the exposed
individual, from conferring susceptibility to reinforcing
resilience. Moreover, these effects can confer a susceptibility that might or might not eventually be unmasked by
later events,193,194 further complicating the story.
791
distal penis to attempt to dislodge any obstructions,
decompressive cystocentesis, and a darkened, low stress
environment that did not house any dogs resulted in resolution of urethral obstruction, defined as spontaneous
urination within 72 hours and subsequent discharge
from the hospital, without the need for urethral catheterization in 11/15 (73%) of male cats with urethral
obstruction.195 And in a laboratory study, sickness
behaviors were observed both in healthy cats and in cats
with FIC in response to unusual external events for
77 weeks after environmental enrichment.18 Increasing
age and weeks when unusual external events occurred,
but not disease status, resulted in a significant increase in
total sickness behaviors when controlled for other factors. A protective effect of male sex on food intake in
healthy cats was observed, as well as a small increased
risk of age for upper gastrointestinal (1.2) and avoidance
behaviors (1.7). In contrast, unusual external events were
associated with significantly increased risks for decreases in
food intake (9.3) and elimination (6.4), and increases in
defecation (9.8) and urination (1.6) outside the litter box.
These results suggest that some of the most commonly
observed abnormalities in client-owned cats occurred after
unusual external events in both groups. Because all cats
were comparably affected by unusual external events, clinicians may need to consider the possibility of exposure to
unusual external events in the differential diagnosis of cats
presented for care for these signs.
Additional Findings
The idea that a ‘‘Pandora’’ syndrome might be present
in some cats with chronic idiopathic LUT signs developed from a number of clinical and laboratory studies. In
the late 1990s, a prospective, multicenter, doubleblinded, placebo-controlled, randomized clinical trial
designed to evaluate the efficacy of pentosan polysulfate
for improving LUT signs in cats with FIC was conducted.60 Cats with at least 2 episodes of LUT signs
within the past 6 months, cystoscopic findings of diffuse
glomerulations present in at least 2 quadrants of the
bladder, and the absence of an alternative diagnosis after
appropriate clinical investigations were randomly assigned to receive either 0.0 (vehicle placebo), 2.0, 8.0, or
16.0 mg/kg pentosan polysulfate twice daily for 26 weeks.
Owners evaluated the cats weekly by rating hematuria,
stranguria, pollakiuria, periuria, and vocalization during
voiding attempts on a scale of 0–3 (none, mild, moderate,
severe), and additional cystoscopic examination was performed at the end of the study. All treatments were well
tolerated by the cats; adverse events were rare and no
consistent treatment-related pattern was evident. Average owner-recorded scores of signs of LUT dysfunction
decreased by approximately 75% in all groups, although
recurrent episodes occurred on some 35% of cats. While
these results suggest that nonspecific therapeutic
responses might occur in cats with FIC, possibly by
altering their perception of their surroundings, lack of a
‘‘usual care’’ control group require that the study be
interpreted with caution.
The hypothesis that LUT signs might be responsive to
environmental influences, while not novel,113,114 led to
additional investigations. Laboratory studies revealed
that environmental enrichment was associated not only
with reduction in LUT signs, but also with normalization
of circulating catecholamine concentrations, bladder
permeability, and cardiac function,17,137 and reduced responses to acoustic startle.134 Based on these findings,
environmental enrichment was evaluated in a 10-month
prospective observational study of client-owned cats
with moderate to severe feline idiopathic cystitis.15 In
addition to their usual care, clients were offered individualized recommendations for multimodal environmental
modification based on a detailed environmental history.
In addition to significant reductions in LUT signs,
decreased fearfulness, nervousness, signs referable to the
respiratory tract, and a trend toward reduced aggressive
behaviors were identified.15
Most recently, a clinical study of pharmacologic therapy, extrusion, inspection, and gentle massage of the
Clinical Implications
Based on the evidence available to date, some cats
evaluated for chronic signs of LUT dysfunction might
instead have a ‘‘Pandora’’ syndrome. Given the comorbid disorders sometimes found in cats with some other
chronic disorders, other presentations of the syndrome
seem likely. Based on these observations, and on the current limited understanding of the many factors
potentially involved, a reasonable diagnostic strategy
for cats with chronic clinical signs referable to a particular organ system might be to conduct a comprehensive
investigation of the animal’s history, environment, and
other organ system function. Additional supportive data
might include evidence of early adverse experience (orphaned, abandoned, etc.), presence of related signs in
family members, waxing and waning of signs related to
environmental threat, and the absence of evidence for an
alternative cause. Evidence for the presence of these
additional factors would support diagnosis of ‘‘Pandora’’ syndrome, whereas evidence of absence of these
factors would argue for an organ-specific disorder.
With regard to treatment, significant recovery from
signs referable to the LUT and other systems has been
reported in cats with LUT-predominant ‘‘Pandora’’ syndrome using tailored multimodal environmental
modification.15 The effectiveness of environmental
enrichment also suggests that pharmacological or other
therapeutic interventions face an important barrier to
demonstrate efficacy in the presence of the large therapeutic response to this approach in cats with the
syndrome. Moreover, pharmacological approaches that
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require force, such as pilling, also might result in activation
of the SRS. Given the lack of evidence for effectiveness of
most currently available pharmaceutical treatments for
cats with chronic idiopathic LUT signs at least, these
approaches should be undertaken with caution.
The prognosis for recovery of cats with LUT-predominant ‘‘Pandora’’ syndrome appears to depend on the
commitment of the owner, the modifiability of the environment, and the severity of the disorder in the cat.
Additionally, cats seem to retain the underlying vulnerability, however, even after long periods of time without
expressing clinical signs, if exposed to sufficiently severe
stressors.
5. Buffington CA, Chew DJ, DiBartola SP. Interstitial cystitis
in cats. Vet Clin North Am Small Anim Pract 1996;26:317–326.
6. Osborne CA, Kruger JM, Lulich JP, et al. Feline urologic
syndrome, feline lower urinary tract disease, feline interstitial cystitis: What’s in a name? J Am Vet Med Assoc 1999;214:1470–1480.
7. Hanno PM. Re-imagining interstitial cystitis. Urol Clin
North Am 2008;35:91–99.
8. Feinstein AR. The Blame-X syndrome: Problems and
lessons in nosology, spectrum, and etiology. J Clin Epidemiol 2001;
54:433–439.
9. Osbaldiston GW, Taussig RA. Clinical report on 46 cases
of feline urological syndrome. Vet Med/Small Anim Clin 1970;65:
461–468.
10. Osborne CA, Johnston GR, Polzin DJ, et al. Redefinition
of the feline urologic syndrome: Feline lower urinary tract disease
with heterogeneous causes. Vet Clin North Am Small Anim Pract
1984;14:409–438.
11. Buffington CAT, Chew DJ, Woodworth BE. Feline interstitial cystitis. J Am Vet Med Assoc 1999;215:682–687.
12. Schur EA, Afari N, Furberg H, et al. Feeling bad in more
ways than one: Comorbidity patterns of medically unexplained and
psychiatric conditions. J Gen Intern Med 2007;22:818–821.
13. Ablin K, Clauw DJ. From fibrositis to functional somatic
syndromes to a bell-shaped curve of pain and sensory sensitivity:
Evolution of a clinical construct. Rheum Dis Clin North Am 2009;
35:233–251.
14. Yunus MB. Central sensitivity syndromes: A new paradigm
and group nosology for fibromyalgia and overlapping conditions,
and the related issue of disease versus illness. Semin Arthritis
Rheum 2008;37:339–352.
15. Buffington CAT, Westropp JL, Chew DJ, et al. Clinical
evaluation of multimodal environmental modification (MEMO) in
the management of cats with idiopathic cystitis. J Feline Med Surg
2006;8:261–268.
16. Buffington CAT, Westropp JL, Chew DJ, et al. A case-control study of indoor-housed cats with lower urinary tract signs.
J Am Vet Med Assoc 2006;228:722–725.
17. Westropp JL, Kass PH, Buffington CAT. Evaluation of the
effects of stress in cats with idiopathic cystitis. Am J Vet Res
2006;67:731–736.
18. Stella JL, Lord LK, Buffington CAT. Sickness behaviors in
response to unusual external events in healthy cats and cats with feline interstitial cystitis. J Am Vet Med Assoc 2011;238:67–73.
19. Buffington CAT. Bladder pain syndrome/interstitial cystitis. In: Baranowski AP, Abrams P, Fall M, eds. Urogenital Pain in
Clinical Practice. New York: Informa Healthcare, USA; 2008:
169–183.
20. Buffington CAT. Comorbidity of interstitial cystitis with
other unexplained clinical conditions. J Urol 2004;172:1242–1248.
21. Wu EQ, Birnbaum H, Kang YJ, et al. A retrospective
claims database analysis to assess patterns of interstitial cystitis diagnosis. Curr Med Res Opin 2006;22:495–500.
22. Warren JW, Howard FM, Cross RK, et al. Antecedent
nonbladder syndromes in case-control study of interstitial cystitis/
painful bladder syndrome. Urology 2009;73:52–57.
23. Weissman MM, Gross R, Fyer A, et al. Interstitial cystitis
and panic disorder: A potential genetic syndrome. Arch Gen
Psychiatry 2004;I61:273–279.
24. Dimitrakov JD. A case of familial clustering of interstitial
cystitis and chronic pelvic pain syndrome. Urology 2001;58:281vi–viii.
25. Westropp JL, Welk KA, Buffington CAT. Small adrenal
glands in cats with feline interstitial cystitis. J Urol 2003;170:
2494–2497.
26. Buffington CAT. Developmental influences on medically
unexplained symptoms. Psychother Psychosom 2009;78:139–144.
27. Clasper M. A case of interstitial cystitis and Hunner’s ulcer
in a domestic shorthaired cat. N Z Vet J 1990;38:158–160.
Summary and Perspective
Currently available evidence suggests that many cases of
chronic idiopathic LUT signs presently diagnosed as having FIC actually may have a ‘‘Pandora’’ syndrome. The
syndrome might result from early adverse experiences that
sensitize the neuraxis to sensory input, increasing the frequency and duration of activation of the SRS when
the individual is housed in a provocative environment.
The chronic ‘‘wear and tear’’ of persistent activation of
the SRS, when superimposed on the (possibly familial)
variability of organ involvement, possibly explains the inconsistency of comorbid disorder presentation.171
The available data only suggest this scenario, however,
and permit generation of the hypothesis. Many of the findings are based on data obtained from small numbers of
severely affected animals recruited because of the severity
of their disease, and have not been independently replicated. One might imagine a number of additional
complementary or alternative ‘‘systemic’’ hypotheses
related to variable combinations of genetic, epigenetic,
and environmental influences; these remain to be explored.
Acknowledgments
The author expresses his heartfelt thanks to the many
mentors, colleagues, and students with whom he has
worked on research into this syndrome for their advice,
collegiality, and effort.
Supported by the National Institutes of Health P50
DK64539 Women’s Health and Functional Visceral Disorders Center, and DK47538.
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203
6th Tufts' Canine & Feline Breeding and Genetics Conference
Friday
27-Sep
7:00-8:00
8:00-8:10
8:10-8:30
8:30-9:10
9:10-9:50
9:50-10:10
10:10-10:30
10:30-11:10
Saturday Lectures
28-Sep
Breakfast & Registration
Introductions and Announcements
Illumina Presentation
Sunday Lectures
29-Sep
7:00-8:00
Breakfast
8:00-8:10
Introductions and Announcements
Breeds As Populations
Unraveling the Sources of Genetic Structure Within
8:10-8:50
Breeds - Dr. Pam Wiener
Taking Advantage of Dog Breed Structure to
8:50-9:30
Understand Health - Dr. Elaine Ostrander
Break
9:30-9:50
Genetics of Cat Populations and Breeds: Implications
for Breed Management for Health! - Dr. Leslie Lyons 9:50-10:30
Breeding Practices According to Breeds; Time, Place,
and Consequences - Dr. Grégoire Leroy
Canine Hip Dysplasia
Half A Century with Canine Hip Dysplasia
- Dr. Åke Hedhammar
The Othopedic Foundation for Animals Hip Displasia
Database: A Review - Dr. Greg Keller
Break
The genetics of hip dysplasia and implications for
selection - Dr. Tom Lewis
11:10-11:30
Inbreeding, Outbreeding, and Breed Evolution Dr. Jerold Bell
10:30-11:10
Genetic and Genomic Tools for Breeding Dogs With
Healthy Hips - Dr. Rory Todhunter
11:30-12:30
Panel Discussion
11:10-12:10
Panel Discussion
12:30-1:15
Lunch
12:10-12:55
Genetic Disorders
Lunch
Management of Genetic Disease
1:15-1:55
Unraveling the Phenotypic and Genetic Complexity of
Canine Cystinuria - Dr. Paula Henthorn
12:55-1:35
1:55-2:35
How to Use and Interpret Genetic Tests for Heart
Disease in Cats and Dogs - Dr. Kate Meurs
1:35-2:15
2:35-2:55
Break
2:15-2:35
Update on Genetic Tests for Diseases and Traits in
Cats: Implications for Cat Health, Breed Management
and Human Health - Dr. Leslie Lyons
2:35-2:55
2:55-3:35
3:35-4:15
Hereditary Gastric Cancer in Dogs Dr. Elizabeth McNiel
3:15-3:55
4:15-5:15
Panel Discussion
3:55-4:55
2:55-3:15
Holistic Management of Genetic Traits Dr. Anita Oberbauer
From FUS to Pandora Syndrome - The Role of
Epigenetics and Environment in Pathophysiology,
Treatment, and Prevention - Dr. Tony Buffington
Break
Breed Specific Breeding Strategies Dr. Åke Hedhammar
UK initiatives for breeding healthier pedigree dogs Dr. Tom Lewis
Genetic Tests: Understanding Their Power, and Using
Their Force for Good - Dr. Jerold Bell
Panel Discussion
6:00-8:00 Registration

September 27-September 29, 2013 Boston, MA Thank

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