An indication of major genes affecting hip and elbow dysplasia in four Finnish dog populations

Across-breed genetic investigation of canine hip dysplasia, elbow dysplasia, and anterior cruciate ligament rupture using whole-genome sequencing

Here, we report the use of genome-wide association study (GWAS) for the analysis of canine whole-genome sequencing (WGS) repository data using breed phenotypes. Single-nucleotide polymorphisms (SNPs) were called from WGS data from 648 dogs that included 119 breeds from the Dog10K Genomes Project. Next, we assigned breed phenotypes for hip dysplasia (Orthopedic Foundation for Animals (OFA) HD, n = 230 dogs from 27 breeds; hospital HD, n = 279 dogs from 38 breeds), elbow dysplasia (ED, n = 230 dogs from 27 breeds), and anterior cruciate ligament rupture (ACL rupture, n = 279 dogs from 38 breeds), the three most important canine spontaneous complex orthopedic diseases. Substantial morbidity is common with these diseases. Previous within- and between-breed GWAS for HD, ED, and ACL rupture using array SNPs have identified disease-associated loci. Individual disease phenotypes are lacking in repository data. There is a critical knowledge gap regarding the optimal approach to undertake categorical GWAS without individual phenotypes. We considered four GWAS approaches: a classical linear mixed model, a haplotype-based model, a binary case-control model, and a weighted least squares model using SNP average allelic frequency. We found that categorical GWAS was able to validate HD candidate loci. Additionally, we discovered novel candidate loci and genes for all three diseases, including FBX025, IL1A, IL1B, COL27A1, SPRED2 (HD), UGDH, FAF1 (ED), TGIF2 (ED & ACL rupture), and IL22, IL26, CSMD1, LDHA, and TNS1 (ACL rupture). Therefore, categorical GWAS of ancestral dog populations may contribute to the understanding of any disease for which breed epidemiological risk data are available, including diseases for which GWAS has not been performed and candidate loci remain elusive.

Genome-wide association studies for canine hip dysplasia in single and multiple populations - implications and potential novel risk loci

BACKGROUND

Association mapping studies of quantitative trait loci (QTL) for canine hip dysplasia (CHD) can contribute to the understanding of the genetic background of this common and debilitating disease and might contribute to its genetic improvement. The power of association studies for CHD is limited by relatively small sample numbers for CHD records within countries, suggesting potential benefits of joining data across countries. However, this is complicated due to the use of different scoring systems across countries. In this study, we incorporated routinely assessed CHD records and genotype data of German Shepherd dogs from two countries (UK and Sweden) to perform genome-wide association studies (GWAS) within populations using different variations of CHD phenotypes. As phenotypes, dogs were either classified into cases and controls based on the Fédération Cynologique Internationale (FCI) five-level grading of the worst hip or the FCI grade was treated as an ordinal trait. In a subsequent meta-analysis, we added publicly available data from a Finnish population and performed the GWAS across all populations. Genetic associations for the CHD phenotypes were evaluated in a linear mixed model using 62,089 SNPs.

RESULTS

Multiple SNPs with genome-wide significant and suggestive associations were detected in single-population GWAS and the meta-analysis. Few of these SNPs overlapped between populations or between single-population GWAS and the meta-analysis, suggesting that many CHD-related QTL are population-specific. More significant or suggestive SNPs were identified when FCI grades were used as phenotypes in comparison to the case-control approach. MED13 (Chr 9) and PLEKHA7 (Chr 21) emerged as novel positional candidate genes associated with hip dysplasia.

CONCLUSIONS

Our findings confirm the complex genetic nature of hip dysplasia in dogs, with multiple loci associated with the trait, most of which are population-specific. Routinely assessed CHD information collected across countries provide an opportunity to increase sample sizes and statistical power for association studies. While the lack of standardisation of CHD assessment schemes across countries poses a challenge, we showed that conversion of traits can be utilised to overcome this obstacle.

Effectiveness of Canine Hip Dysplasia and Elbow Dysplasia Improvement Programs in Six UK Pedigree Breeds

Hip and elbow dysplasia are common disorders in larger dog breeds and crosses, and a known contributory factor to osteoarthritis, lameness and reduced mobility. Screening schemes evaluating the severity of hip and elbow dysplasia in the UK are administered by the British Veterinary Association (BVA) and the Kennel Club (KC). The BVA/KC Hip Dysplasia scoring scheme is over 50 years old, having originated in 1965, and has operated in its current form since 1983. The BVA/KC Elbow Dysplasia grading scheme commenced more recently in 1998 and is based on the International Elbow Working Group guidelines. Hip score and elbow grade data on a considerable number of dogs in the UK have been generated from these two screening schemes. This study analyses data from dogs of six breeds scored from 1990 to present, to establish any determinable trends in hip score and elbow grade parameters, and to examine whether the implementation of such schemes has had a positive influence on hip and elbow health. A range of criteria, including the rate of participation in the screening schemes, hip score and elbow grade parameters (e.g., median, mean, standard deviation), and estimated breeding values (EBVs) were analyzed, both in the overall population and also among breeding animals. The results show a general decline in hip score parameters (median, mean, standard deviation, and 75th percentile), revealing a reduction in the prevalence and severity of hip dysplasia. There was a more modest decline in mean elbow grade within breeds. The proportion of sires and dams (of dogs born per year) with no hip score or elbow grade fell substantially over time, demonstrating good participation in the screening schemes. In most breeds, the scores of sires and dams are demonstrably improving. There is a declining genetic trend as ascertained by EBVs for both hip scores and elbow grades in most breeds, implying that the improvement observed is due in part to selection for improvement in hip and elbow health as described by the respective screening schemes.

Genetic dissection of canine hip dysplasia phenotypes and osteoarthritis reveals three novel loci

Background

Hip dysplasia and osteoarthritis continue to be prevalent problems in veterinary and human medicine. Canine hip dysplasia is particularly problematic as it massively affects several large-sized breeds and can cause a severe impairment of the quality of life. In Finland, the complex condition is categorized to five classes from normal to severe dysplasia, but the categorization includes several sub-traits: congruity of the joint, Norberg angle, subluxation degree of the joint, shape and depth of the acetabulum, and osteoarthritis. Hip dysplasia and osteoarthritis have been proposed to have separate genetic etiologies.

Results

Using Fédération Cynologique Internationale -standardized ventrodorsal radiographs, German shepherds were rigorously phenotyped for osteoarthritis, and for joint incongruity by Norberg angle and femoral head center position in relation to dorsal acetabular edge. The affected dogs were categorized into mild, moderate and severe dysplastic phenotypes using official hip scores. Three different genome-wide significant loci were uncovered. The strongest candidate genes for hip joint incongruity were noggin (NOG), a bone and joint developmental gene on chromosome 9, and nanos C2HC-type zinc finger 1 (NANOS1), a regulator of matrix metalloproteinase 14 (MMP14) on chromosome 28. Osteoarthritis mapped to a long intergenic region on chromosome 1, between genes encoding for NADPH oxidase 3 (NOX3), an intriguing candidate for articular cartilage degradation, and AT-rich interactive domain 1B (ARID1B) that has been previously linked to joint laxity.

Conclusions

Our findings highlight the complexity of canine hip dysplasia phenotypes. In particular, the results of this study point to the potential involvement of specific and partially distinct loci and genes or pathways in the development of incongruity, mild dysplasia, moderate-to-severe dysplasia and osteoarthritis of canine hip joints. Further studies should unravel the unique and common mechanisms for the various sub-traits.

Prevalence of Canine Hip Dysplasia in Switzerland Between 1995 and 2016-A Retrospective Study in 5 Common Large Breeds

Canine hip dysplasia (CHD) is a genetic disease, modulated by epigenetic and environmental factors. To decrease the prevalence of CHD, the hip joints of many pure breed dogs are radiographed to identify dysplastic dogs not qualified for breeding. It has been shown that both, prevalence and severity of CHD may be reduced on the basis of phenotypic i.e., radiographic selection of breeding animals. The method has been used in many countries for over 50 years. In the present study, severity and prevalence of CHD in five common large breeds in Switzerland were evaluated since 1995. Both, prevalence and severity of CHD dropped in each breed between the periods 1995-1999 and 2010-2016. The prevalence decreased in Golden Retrievers from 25 to 9% and in Labrador Retrievers from 16 to 3%, respectively. In the Flat-Coated Retriever, prevalence in general was low, decreasing from 6 to 3%. In the Bernese mountain dog and the German shepherd dog, a decrease from 21 to 12% and from 46 to 18%, respectively, was observed. However, the rather low overall rate of radiographed dogs (Retrievers: 11 to 18%, Bernese Mountain dogs: 23% and German Shepherd dogs: 31%) does not allow to draw reliable conclusions regarding the true prevalence of CHD for the entire population of these breeds in Switzerland.

Novel protective and risk loci in hip dysplasia in German Shepherds

Canine hip dysplasia is a common, non-congenital, complex and hereditary disorder. It can inflict severe pain via secondary osteoarthritis and lead to euthanasia. An analogous disorder exists in humans. The genetic background of hip dysplasia in both species has remained ambiguous despite rigorous studies. We aimed to investigate the genetic causes of this disorder in one of the high-risk breeds, the German Shepherd. We performed genetic analyses with carefully phenotyped case-control cohorts comprising 525 German Shepherds. In our genome-wide association studies we identified four suggestive loci on chromosomes 1 and 9. Targeted resequencing of the two loci on chromosome 9 from 24 affected and 24 control German Shepherds revealed deletions of variable sizes in a putative enhancer element of the NOG gene. NOG encodes for noggin, a well-described bone morphogenetic protein inhibitor affecting multiple developmental processes, including joint development. The deletion was associated with the healthy controls and mildly dysplastic dogs suggesting a protective role against canine hip dysplasia. Two enhancer variants displayed a decreased activity in a dual luciferase reporter assay. Our study identifies novel loci and candidate genes for canine hip dysplasia, with potential regulatory variants in the NOG gene. Further research is warranted to elucidate how the identified variants affect the expression of noggin in canine hips, and what the potential effects of the other identified loci are.

Canine hip dysplasia: A natural animal model for human developmental dysplasia of the hip

Developmental dysplasia of the hip (DDH) in humans is a common condition that is associated with hip pain, functional limitations, and secondary osteoarthritis (OA). Surgical treatment of DDH has improved in the last decade, allowing excellent outcomes at short- and mid-term follow-up. Still, the etiology, mechanobiology, and pathology underlying this disease are not well understood. A pre-clinical animal model of DDH could help advance the field with a deeper understanding of specific pathways that initiate hip joint degeneration secondary to abnormal biomechanics. An animal model would also facilitate different interventional treatments that could be tested in a rigorous and controlled environment. The dog model exhibits several important characteristics that make it valuable as a pre-clinical animal model for human DDH. Dogs are naturally prone to develop canine hip dysplasia (CHD), which is treated in a similar manner as in humans. Comparable to human DDH, CHD is considered a pre-OA disease; if left untreated it will progress to OA. However, progression to OA is significantly faster in dogs than humans, with progression to OA within 1-2 years of age, associated with their shorter life span compared to humans. Animal studies could potentially reveal the underlying biochemical pathway(s), which can inform refined treatment modalities and provide opportunities for new treatment and prevention targets. Herein, we review the similarities and differences between the two species and outline the argument supporting CHD as an appropriate pre-clinical model of human DDH. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:1807-1817, 2018.

Phenotypic hip and elbow dysplasia trends in Rottweilers and Labrador retrievers in South Africa (2007-2015): Are we making progress?

Canine hip and elbow dysplasia are major orthopaedic problems prevalent the world over, and South Africa is no exception. Hip and elbow dysplasia phenotypic status is certified by a number of different radiographic schemes in the world. South Africa uses the Fédération Cynologique Internationale system to certify hips, and the International Elbow Working Group scheme to certify elbows. One way of reducing these often crippling conditions is by selective breeding using only dogs with no or marginal dysplastic joints. In South Africa, only seven breeds, including the Rottweiler, have breeding restrictions for hip dysplasia. There are no such restrictions for elbow dysplasia. This study assessed the prevalence of hip and elbow dysplasia over a 9-year-period in the Rottweiler and the Labrador retriever in South Africa as evaluated by official national scrutineers. Records from 1148 Rottweilers and 909 Labrador retrievers were obtained and were graded as normal or dysplastic, and numerical values were also evaluated. Data were compared between the two breeds, males and females as well as over time and were compared with similar data of the Orthopaedic Foundation for Animals in the United States. The prevalence values for hip dysplasia in Rottweilers and Labrador retrievers were 22% and 31%, respectively, whereas for elbow dysplasia the values were 39% and 19%, respectively. In Labrador retrievers, this incidence was much higher than in the American population. Rottweiler hip and elbow dysplasia numerical scores significantly improved over time, whereas in Labrador retrievers, only hip dysplasia showed a minor but significant improvement. This study proved that prescribing minimum breeding requirements, as in the Rottweiler in this study, significantly improved the breeding stock, suggesting that minimum hip and elbow breeding requirements should be initiated for all breeds at risk of these often crippling conditions.

Long-term genetic selection reduced prevalence of hip and elbow dysplasia in 60 dog breeds

Canine hip dysplasia (CHD) and elbow dysplasia (ED) impact the health and welfare of all dogs. The first formally organized assessment scheme to improve canine health centered on reducing the prevalence of these orthopedic disorders. Phenotypic screening of joint conformation remains the currently available strategy for breeders to make selection decisions. The present study evaluated the efficacy of employing phenotypic selection on breed improvement of hips and elbows using the Orthopedic Foundation for Animals complete database spanning the 1970–2015 time period. Sixty breeds having more than 1000 unique hip evaluations and 500 elbow evaluations (1,056,852 and 275,129 hip and elbow records, respectively) were interrogated to derive phenotypic improvement, sex and age at time of assessment effects, correlation between the two joints, heritability estimates, estimated breeding values (EBV), and effectiveness of maternal/paternal selection. The data demonstrated that there has been overall improvement in hip and elbow conformation with a reduction in EBV for disease liability, although the breeds differed in the magnitude of the response to selection. Heritabilities also differed substantially across the breeds as did the correlation of the joints; in the absence of a universal association of these differences with breed size, popularity, or participation in screening, it appears that the breeds themselves vary in genetic control. There was subtle, though again breed specific, impact of sex and older ages on CHD and ED. There was greater paternal impact on a reduction of CHD. In the absence of direct genetic tests for either of these two diseases, phenotypic selection has proven to be effective. Furthermore, the data underscore that selection schemes must be breed specific and that it is likely the genetic profiles will be unique across the breeds for these two conditions. Despite the advances achieved with phenotypic selection, incorporation of EBVs into selection schemes should accelerate advances in hip and elbow improvement.

Emerging insights into the genetic basis of canine hip dysplasia

Canine hip dysplasia (CHD) is the most common inherited polygenic orthopedic trait in dogs with the phenotype influenced also by environmental factors. This trait was described in the dog in 1935 and leads to a debilitating secondary hip osteoarthritis. The diagnosis is confirmed radiographically by evaluating signs of degenerative joint disease, incongruence, and/or passive hip joint laxity. There is no ideal medical or surgical treatment so prevention based on controlled breeding is the optimal approach. The definitive CHD diagnosis based on radiographic examination involves the exposure to ionizing radiation under general anesthesia or heavy sedation but the image does not reveal the underlying genetic quality of the dog. Phenotypic expression of CHD is modified by environmental factors and dogs with a normal phenotype can be carriers of some mutations and transmit these genes to their offspring. Programs based on selection of dogs with better individual phenotypes for breeding are effective when strictly applied but remain inferior to the selection of dogs based on estimation of breeding values. Molecular studies for dissecting the genetic basis of CHD are ongoing, but progress has been slow. In the future, the recommended method to improve hip quality in controlled breeding schemes, which will allow higher selection pressure, would be based on the estimation of the genomic breeding value. Since 2012, a commercial DNA test has been available for Labrador Retrievers using a blood sample and provides a probability for development of CHD but we await evidence that this test reduces the incidence or severity of CHD.

A genetic predictive model for canine hip dysplasia: integration of Genome Wide Association Study (GWAS) and candidate gene approaches

Canine hip dysplasia is one of the most prevalent developmental orthopedic diseases in dogs worldwide. Unfortunately, the success of eradication programs against this disease based on radiographic diagnosis is low. Adding the use of diagnostic genetic tools to the current phenotype-based approach might be beneficial. The aim of this study was to develop a genetic prognostic test for early diagnosis of hip dysplasia in Labrador Retrievers. To develop our DNA test, 775 Labrador Retrievers were recruited. For each dog, a blood sample and a ventrodorsal hip radiograph were taken. Dogs were divided into two groups according to their FCI hip score: control (A/B) and case (D/E). C dogs were not included in the sample. Genetic characterization combining a GWAS and a candidate gene strategy using SNPs allowed a case-control population association study. A mathematical model which included 7 SNPs was developed using logistic regression. The model showed a good accuracy (Area under the ROC curve = 0.85) and was validated in an independent population of 114 dogs. This prognostic genetic test represents a useful tool for choosing the most appropriate therapeutic approach once genetic predisposition to hip dysplasia is known. Therefore, it allows a more individualized management of the disease. It is also applicable during genetic selection processes, since breeders can benefit from the information given by this test as soon as a blood sample can be collected, and act accordingly. In the authors' opinion, a shift towards genomic screening might importantly contribute to reducing canine hip dysplasia in the future. In conclusion, based on genetic and radiographic information from Labrador Retrievers with hip dysplasia, we developed an accurate predictive genetic test for early diagnosis of hip dysplasia in Labrador Retrievers. However, further research is warranted in order to evaluate the validity of this genetic test in other dog breeds.

Efficacy of an oral hyaluronate and collagen supplement as a preventive treatment of elbow dysplasia

One hundred and five Labrador dogs were randomly divided into two groups to determine the number of animals that develop elbow dysplasia when treated with an oral supplement compared to untreated ones. Efficacy of the oral treatment was also evaluated once illness was diagnosed. The supplement (Hyaloral) contained hyaluronic acid, hydrolysed collagen, glucosamine, chondroitin sulphate, and gamma oryzanol. Clinical evaluation of the elbow joints was completed at months 3, 6, 12, and 20 by orthopaedic evaluations, radiography, serologic and blood analysis, and veterinarian evaluation of dysplasia symptoms. All side effects were recorded. In the control group, 33.3% of the dogs developed radiographic evidence of elbow dysplasia compared to 18.5% in the treated group. Symptoms of dysplasia at 12 months differed between the treated (12.5%) and control (61.5%) animals, and were significantly different at 20 months (p < 0.05). Differences in lameness along with movement and swelling of the elbows between groups were observed after 12 months. The treated group had improved significantly by the last visit (p < 0.05). No adverse side effects were reported. In conclusion, oral treatment with Hyaloral may have a potential cumulative action that provides protection against dysplasia and significantly improves symptoms of elbow dysplasia.

Identification and validation of quantitative trait loci (QTL) for canine hip dysplasia (CHD) in German Shepherd Dogs

Canine hip dysplasia (CHD) is the most common hereditary skeletal disorder in dogs. To identify common alleles associated with CHD, we genotyped 96 German Shepherd Dogs affected by mild, moderate and severe CHD and 96 breed, sex, age and birth year matched controls using the Affymetrix canine high density SNP chip. A mixed linear model analysis identified five SNPs associated with CHD scores on dog chromosomes (CFA) 19, 24, 26 and 34. These five SNPs were validated in a by sex, age, birth year and coancestry stratified sample of 843 German Shepherd Dogs including 277 unaffected dogs and 566 CHD-affected dogs. Mean coancestry coefficients among and within cases and controls were <0.1%. Genotype effects of these SNPs explained 20–32% of the phenotypic variance of CHD in German Shepherd Dogs employed for validation. Genome-wide significance in the validation data set could be shown for each one CHD-associated SNP on CFA24, 26 and 34. These SNPs are located within or in close proximity of genes involved in bone formation and related through a joint network. The present study validated positional candidate genes within two previously known quantitative trait loci (QTL) and a novel QTL for CHD in German Shepherd Dogs.

Multiple loci associated with canine hip dysplasia (CHD) in German shepherd dogs

Canine hip dysplasia (CHD) is the most common hereditary skeletal disorder in dogs. To identify common alleles associated with CHD, we developed 37 informative single nucleotide polymorphisms (SNPs) within 13 quantitative trait loci (QTL) previously identified for German shepherd dogs. These SNPs were genotyped in 95 German shepherd dogs affected by CHD and 95 breed, sex, and birth year-matched controls. A total of ten SNPs significant at a nominal P value of 0.05 were validated in 843 German shepherd dogs including 277 unaffected dogs and 566 CHD-affected dogs. Cases and controls were sampled from the whole German shepherd dog population in Germany in such a way that mean coancestry coefficients were below 0.1 % within cases and controls as well as among cases and controls. We identified nine SNPs significantly associated with CHD within five QTL on dog chromosomes (CFA) 3, 9, 26, 33, and 34. Genotype effects of these nine SNPs explained between 22 and 34 % of the phenotypic variance of hip dysplasia in German shepherd dogs. The strongest associated SNPs were located on CFA33 and 34 within the candidate genes PNCP, TRIO, and SLC6A3. Thus, the present study validated positional candidate genes within five QTL for CHD.

Genome wide analysis indicates genes for basement membrane and cartilage matrix proteins as candidates for hip dysplasia in Labrador Retrievers

Hip dysplasia, an abnormal laxity of the hip joint, is seen in humans as well as dogs and is one of the most common skeletal disorders in dogs. Canine hip dysplasia is considered multifactorial and polygenic, and a variety of chromosomal regions have been associated with the disorder. We performed a genome-wide association study in Dutch Labrador Retrievers, comparing data of nearly 18,000 single nucleotide polymorphisms (SNPs) in 48 cases and 30 controls using two different statistical methods. An individual SNP analysis based on comparison of allele frequencies with a χ(2) statistic was used, as well as a simultaneous SNP analysis based on Bayesian variable selection. Significant association with canine hip dysplasia was observed on chromosome 8, as well as suggestive association on chromosomes 1, 5, 15, 20, 25 and 32. Next-generation DNA sequencing of the exons of genes of seven regions identified multiple associated alleles on chromosome 1, 5, 8, 20, 25 and 32 (p<0.001). Candidate genes located in the associated regions on chromosomes 1, 8 and 25 included LAMA2, LRR1 and COL6A3, respectively. The associated region on CFA20 contained candidate genes GDF15, COMP and CILP2. In conclusion, our study identified candidate genes that might affect susceptibility to canine hip dysplasia. These genes are involved in hypertrophic differentiation of chondrocytes and extracellular matrix integrity of basement membrane and cartilage. The functions of the genes are in agreement with the notion that disruptions in endochondral bone formation in combination with soft tissue defects are involved in the etiology of hip dysplasia.

Genetic correlations among canine hip dysplasia radiographic traits in a cohort of Australian German Shepherd Dogs, and implications for the design of a more effective genetic control program

Canine hip dysplasia (CHD) is a common musculoskeletal disease in pedigree dog populations. It can cause severe pain and dysfunction which may require extensive medication and/or surgical treatment and often ultimately requires humane euthanasia. CHD has been found to be moderately heritable and, given its impact on welfare, should be considered an imperative breeding priority. The British Veterinary Association/Kennel Club scoring method is one of several measures used to assess the genetic propensity of potential breeding stock for dysplastic changes to the hips based on radiographic examination. It is a complex measure composed of nine ordinal traits, intended to evaluate both early and late dysplastic changes. It would be highly desirable if estimated breeding values (EBVs) for these nine traits were consolidated into a simpler, EBV-based, selection index more easily usable by breeders. A multivariate analysis on the phenotype scores from an Australian cohort of 13,124 German Shepherd Dogs (GSDs) returned genetic correlations between 0.48–0.97 for the nine traits which fell into two trait groups, Group 1 reflecting early changes (“laxity”) and Group 2 reflecting late changes (“osteoarthritis”). Principal components analysis of the ordinal EBVs suggested the same pattern, with strong differentiation between “laxity” and “osteoarthritis” traits in the second component. Taking account of all results, we recommend interim use of two selection indexes: the first being the average of ordinal EBVs for “laxity” traits and the second being the average of ordinal EBVs for “osteoarthritis” traits. The correlation between these two selection indexes (0.771–0.774) is sufficiently less than unity enabling the selection of dogs with different genetic propensity for laxity and for osteoarthritic CHD changes in GSDs; this may also be applicable in other breeds. Dogs with low propensity for severe osteoarthritic change in the presence of laxity may be of interest both in molecular research and breeding programs.

Estimated breeding values for canine hip dysplasia radiographic traits in a cohort of Australian German Shepherd dogs

Canine hip dysplasia (CHD) is a serious and common musculoskeletal disease of pedigree dogs and therefore represents both an important welfare concern and an imperative breeding priority. The typical heritability estimates for radiographic CHD traits suggest that the accuracy of breeding dog selection could be substantially improved by the use of estimated breeding values (EBVs) in place of selection based on phenotypes of individuals. The British Veterinary Association/Kennel Club scoring method is a complex measure composed of nine bilateral ordinal traits, intended to evaluate both early and late dysplastic changes. However, the ordinal nature of the traits may represent a technical challenge for calculation of EBVs using linear methods. The purpose of the current study was to calculate EBVs of British Veterinary Association/Kennel Club traits in the Australian population of German Shepherd Dogs, using linear (both as individual traits and a summed phenotype), binary and ordinal methods to determine the optimal method for EBV calculation. Ordinal EBVs correlated well with linear EBVs (r = 0.90–0.99) and somewhat well with EBVs for the sum of the individual traits (r = 0.58–0.92). Correlation of ordinal and binary EBVs varied widely (r = 0.24–0.99) depending on the trait and cut-point considered. The ordinal EBVs have increased accuracy (0.48–0.69) of selection compared with accuracies from individual phenotype-based selection (0.40–0.52). Despite the high correlations between linear and ordinal EBVs, the underlying relationship between EBVs calculated by the two methods was not always linear, leading us to suggest that ordinal models should be used wherever possible. As the population of German Shepherd Dogs which was studied was purportedly under selection for the traits studied, we examined the EBVs for evidence of a genetic trend in these traits and found substantial genetic improvement over time. This study suggests the use of ordinal EBVs could increase the rate of genetic improvement in this population.

Housing- and exercise-related risk factors associated with the development of hip dysplasia as determined by radiographic evaluation in a prospective cohort of Newfoundlands, Labrador Retrievers, Leonbergers, and Irish Wolfhounds in Norway

OBJECTIVE

To identify housing- and exercise-related risk factors associated with the development of hip dysplasia (HD) as determined by radiographic evaluation in Newfoundlands, Labrador Retrievers, Leonbergers, and Irish Wolfhounds in Norway.

ANIMALS

501 client-owned dogs from 103 litters.

PROCEDURES

Dogs were assessed from birth until official radiographic screening for HD at 12 (Labrador Retriever [n = 133] and Irish Wolfhound [63]) or 18 (Newfoundland [125] and Leonberger [180]) months of age. Information regarding housing and exercise conditions during the preweaning and postweaning periods was obtained with questionnaires. Multivariable random effects logistic regression models were used to identify housing- and exercise-related risk factors associated with the development of radiographically detectable HD.

RESULTS

Puppies walking on stairs from birth to 3 months of age had an increased risk of developing HD. Factors associated with a decreased risk of developing HD included off-leash exercise from birth to 3 months of age, birth during the spring and summer, and birth on a farm. Significant clustering of dogs with HD was detected within litters.

CONCLUSIONS AND CLINICAL RELEVANCE

Results indicated that puppies ≤ 3 months old should not be allowed access to stairs, but should be allowed outdoor exercise on soft ground in moderately rough terrain to decrease the risk for developing radiographically detectable HD. These findings could be used as practical recommendations for the prevention of HD in Newfoundlands, Labrador Retrievers, Leonbergers, and Irish Wolfhounds.

Heritability and phenotypic variation of canine hip dysplasia radiographic traits in a cohort of Australian German shepherd dogs

Canine Hip Dysplasia (CHD) is a common, painful and debilitating orthopaedic disorder of dogs with a partly genetic, multifactorial aetiology. Worldwide, potential breeding dogs are evaluated for CHD using radiographically based screening schemes such as the nine ordinally-scored British Veterinary Association Hip Traits (BVAHTs). The effectiveness of selective breeding based on screening results requires that a significant proportion of the phenotypic variation is caused by the presence of favourable alleles segregating in the population. This proportion, heritability, was measured in a cohort of 13,124 Australian German Shepherd Dogs born between 1976 and 2005, displaying phenotypic variation for BVAHTs, using ordinal, linear and binary mixed models fitted by a Restricted Maximum Likelihood method. Heritability estimates for the nine BVAHTs ranged from 0.14-0.24 (ordinal models), 0.14-0.25 (linear models) and 0.12-0.40 (binary models). Heritability for the summed BVAHT phenotype was 0.30 ± 0.02. The presence of heritable variation demonstrates that selection based on BVAHTs has the potential to improve BVAHT scores in the population. Assuming a genetic correlation between BVAHT scores and CHD-related pain and dysfunction, the welfare of Australian German Shepherds can be improved by continuing to consider BVAHT scores in the selection of breeding dogs, but that as heritability values are only moderate in magnitude the accuracy, and effectiveness, of selection could be improved by the use of Estimated Breeding Values in preference to solely phenotype based selection of breeding animals.

The S-measurement in the diagnosis of canine hip dysplasia

OBJECTIVE

To propose a direct measure of subluxation of the femoral head (S) in the assessment of hip joint laxity and evaluate it for clinical use.

STUDY DESIGN

Method comparison study.

ANIMALS

Dogs (n = 51).

METHODS

Dogs were sedated or anesthetized for a dorsolateral subluxation (DLS) examination. Two sets of radiographs were acquired, 1 each by a different technologist. A calibrated measuring bar was included on the image at the height of the hip to assess magnification. The DLS was calculated for each hip and different persons unaware of these details measured the "S"-value. One person measured the S-value 3 times over 3 days. Box plots were used to determine a cut-off for the empiric (8 mm) and corrected (4 mm) S-value.

RESULTS

Of 51 dogs, 33 were dysplastic based on a DLS score <55%. Magnification and body weight were strongly correlated (r = 0.4922, P = .0006). Both empiric and corrected S measurements showed good agreement with the DLS score (κ = 0.688 and κ = 0.681, respectively). The corrected S measurement produced more false negatives. Bland-Altman analysis showed interobserver and technician variance acceptable for clinical use (limits of agreement < ±3 mm). Intraobserver repeatability was acceptable for the right hip (95% of differences were ≤1.3 mm and 100% ≤ 1.9) but not for the left hip.

CONCLUSION

Using a cut-off value of 5 mm, the empirical S measurement can be used to exclude hip dysplasia in young dogs of various body proportions.

Selection against canine hip dysplasia: success or failure?

Canine hip dysplasia (CHD) is a multifactorial skeletal disorder which is very common in pedigree dogs and represents a huge concern for canine welfare. Control schemes based on selective breeding have been in operation for decades. The aim of these schemes is to reduce the impact of CHD on canine welfare by selecting for reduced radiographic evidence of CHD pathology as assessed by a variety of phenotypes. There is less information regarding the genotypic correlation between these phenotypes and the impact of CHD on canine welfare. Although the phenotypes chosen as the basis for these control schemes have displayed heritable phenotypic variation in many studies, success in achieving improvement in the phenotypes has been mixed. There is significant room for improvement in the current schemes through the use of estimated breeding values (EBVs), which can combine a dog's CHD phenotype with CHD phenotypes of relatives, other phenotypes as they are proven to be genetically correlated with CHD (especially elbow dysplasia phenotypes), and information from genetic tests for population-relevant DNA markers, as such tests become available. Additionally, breed clubs should be encouraged and assisted to formulate rational, evidenced-based breeding recommendations for CHD which suit their individual circumstances and dynamically to adjust the breeding recommendations based on continuous tracking of CHD genetic trends. These improvements can assist in safely and effectively reducing the impact of CHD on pedigree dog welfare.

Symmetry of hip dysplasia traits in the German Shepherd Dog in Australia

Canine hip dysplasia (CHD) is a common and debilitating developmental condition of the canine coxofemoral (hip) joint, exhibiting a multifactorial pattern of inheritance. British Veterinary Association hip traits (BVAHTs) are nine radiographic features of hips used in several countries to ordinally score both the right and left hip of potential breeding candidates to assess their suitability for breeding. The objective of this study was to examine some aspects of the relationship between contralateral scores for each BVAHT in a cohort of 13 124 Australian-registered German Shepherd Dogs. Goodman and Kruskal gamma coefficients of 0.48-0.95 and correlation coefficients of 0.50-0.74 demonstrate that the association between right and left hip scores varies between moderate and strong for BVAHTs. Principal component analysis of scores detected a sizeable left-versus-right effect, a finding supported by symmetry and quasi-symmetry analyses which found that seven of the nine BVAHTs display significant marginal asymmetry. Dogs showing asymmetry for one BVAHT are significantly more likely to display asymmetry at other BVAHTs. When asymmetry is expressed as a binary trait (either symmetrical or asymmetrical), it displays low to moderate heritability. Estimates of genetic correlations between right and left scores are very high for all BVAHTs (>0.945), suggesting right and left scores for each BVAHT are largely determined by the same set of genes. The marginal asymmetries are therefore more likely to be of environmental and non-additive genetic origin. In breeding programmes for CHD, we recommend that scores from both hips be used to estimate breeding values, with a term for side-of-hip included in the model to account for score variation owing to asymmetry.

MQScore_SNP software for multipoint parametric linkage analysis of quantitative traits in large pedigrees

We describe software for multipoint parametric linkage analysis of quantitative traits using information about SNP genotypes. A mixed model of major gene and polygene inheritance is implemented in this software. Implementation of several algorithms to avoid computational underflow and decrease running time permits application of our software to the analysis of very large pedigrees collected in human genetically isolated populations. We tested our software by performing linkage analysis of adult height in a large pedigree from a Dutch isolated population. Three significant and four suggestive loci were identified with the help of our programs, whereas variance-component-based linkage analysis, which requires the pedigree fragmentation, demonstrated only three suggestive peaks. The software package MQScore_SNP is available at http://mga.bionet.nsc.ru/soft/index.html.

Simulation study on the effects of excluding offspring information for genetic evaluation versus using genomic markers for selection in dog breeding

Different modes of selection in dogs were studied with a special focus on the availability of disease information. Canine hip dysplasia (CHD) in the German shepherd dog was used as an example. The study was performed using a simulation model, comparing cases when selection was based on phenotype, true or predicted breeding value, or genomic breeding value. The parameters in the simulation model were drawn from the real population data. The data on all parents and 40% of their progeny were assumed to be available for the genetic evaluation carried out by Gibbs sampling. With respect to the use of disease records on progeny, three scenarios were considered: random exclusion of disease data (no restrictions, N), general exclusion of disease data (G) and exclusion of disease data for popular sires (P). One round of selection was considered, and the response was expressed as change of mean CHD score, proportion of dogs scored as normal, proportion of dogs scored as clearly affected and true mean breeding value in progeny of popular sires in comparison with all sires. When no restrictions on data were applied, selection on breeding value was three times more efficient than when some systematic exclusion was practised. Higher selection response than in the exclusion cases was achieved by selecting on the basis of genomic breeding value and CHD score. Genomic selection would therefore be the method of choice in the future.

Comparative rheumatology: what can be learnt from naturally occurring musculoskeletal disorders in domestic animals?

Examples of naturally occurring musculoskeletal disorders are extremely common in veterinary species and provide a valuable comparative research resource, which can provide compelling comparative data on the aetiopathogenesis and treatment of many common human musculoskeletal diseases. In particular, orthopaedic diseases are a common morbidity in both dogs and horses. In this review, we give an overview of the common musculoskeletal diseases encountered in these species: for instance, tendon and ligament injuries, arthropathies and stress fractures, as well as an insight into the basic biology of these conditions. In doing so, we aim to demonstrate the similarities and differences between these disorders and similar conditions in man.

The long (and winding) road to gene discovery for canine hip dysplasia

Hip dysplasia is a common inherited trait of dogs that results in secondary osteoarthritis. In this article the methods used to uncover the mutations contributing to this condition are reviewed, beginning with hip phenotyping. Coarse, genome-wide, microsatellite-based screens of pedigrees of greyhounds and dysplastic Labrador retrievers were used to identify linked quantitative trait loci (QTL). Fine-mapping across two chromosomes (CFA11 and 29) was employed using single nucleotide polymorphism (SNP) genotyping. Power analyses and preferential selection of dogs for ongoing SNP-based genotyping is described with the aim of refining the QTL intervals to 1-2 megabases on these and several additional chromosomes prior to candidate gene screening. The review considers how a mutation or a genetic marker such as a SNP or haplotype of SNPs might be combined with pedigree and phenotype information to create a 'breeding value' that could improve the accuracy of predicting a dog's hip conformation.

Fragmented coronoid process in the dog: a heritable disease

Fragmented coronoid process (FCP) is one of the main diseases associated with elbow dysplasia. FCP is often diagnosed in medium-to-large breed dogs with front leg lameness, for instance in Rottweilers, Labrador Retrievers and Bernese Mountain dogs. Dogs with FCP develop osteoarthrosis of the elbow joint despite conservative or surgical treatment. Although FCP is considered a hereditary condition, the gene or genes causing FCP have yet to be identified. This article provides an overview of different aspects of FCP, including elbow joint development, hypotheses about disease pathogenesis, the genetic background of FCP, and genetic methodology to identify gene or genes responsible for FCP.

PedStr software for cutting large pedigrees for haplotyping, IBD computation and multipoint linkage analysis

We propose an automatic heuristic algorithm for splitting large pedigrees into fragments of no more than a user-specified bit size. The algorithm specifically aims to split large pedigrees where many close relatives are genotyped and to produce a set of sub-pedigrees for haplotype reconstruction, IBD computation or multipoint linkage analysis with the help of the Lander-Green-Kruglyak algorithm. We demonstrate that a set of overlapping pedigree fragments constructed with the help of our algorithm allows fast and effective haplotype reconstruction and detection of an allele's parental origin. Moreover, we compared pedigree fragments constructed with the help of our algorithm and existing programs PedCut and Jenti for multipoint linkage analysis. Our algorithm demonstrated significantly higher linkage power than the algorithm of Jenti and significantly shorter running time than the algorithm of PedCut. The software package PedStr implementing our algorithms is available at http://mga.bionet.nsc.ru/soft/index.html.

Diagnosis, genetic control and preventive management of canine hip dysplasia: a review

Despite expensive screening and breeding programmes, hip dysplasia (HD) continues to be one of the most common orthopaedic diseases in dogs. The vast majority of dogs afflicted with HD show minimal to no clinical signs, but it can also be a highly debilitating condition for both working and pet dogs. Hip joint laxity is considered a major risk factor for the development of degenerative joint disease and a definitive diagnosis is made if characteristic signs are evident on a ventrodorsal view of the pelvis. Early prediction of the condition can be made using stress radiographic techniques to evaluate the passive hip laxity. The diagnosis of HD may be used for the purpose of selecting breeding stock or to decide on the best treatment approach. Breeding programmes based on individual dog phenotypes have been ineffective and a selection procedure based on breeding value (BV) estimation is recommended. Traditional conservative and surgical treatment approaches are reserved for dogs with overt clinical signs of the disease but such treatments can be expensive and aggressive, and are often ineffective in eliminating clinical signs or subluxation and in preventing the development of degenerative joint disease. The implementation of breeding programmes based on BVs and further research into early prediction/diagnosis of HD and effective preventive treatment approaches are essential.

Hip dysplasia in Estrela mountain dogs: prevalence and genetic trends 1991-2005

Three hundred and thirteen Estrela mountain dogs were examined for hip dysplasia (HD) using the standard ventrodorsal hip extended view, and graded into five categories (A, B, C, D and E) using the Fédération Cynologique Internationale's (FCI) scoring system. The Ortolani method was performed to evaluate hip joint laxity. Pedigree information was obtained from the Portuguese Kennel Club and the genetic trend was evaluated by calculating the mean breeding values (BVs) for the last 15 years, using the threshold model. HD was found in 66% of the dogs. There was low-moderate correlation between the results of the Ortolani test and FCI hip scores (r(s)=0.386; P<0.001). Grades of hip dysplasia were equal in both males and females (P=0.14) and in the animals' right and left sides (P=0.51). The mean BVs for HD were stable in dogs born between 1991 and 2003, and showed an improvement in 2004 and 2005. The data confirm the high prevalence and severity of HD in predisposed breeds that do not have breeding programmes in place. It also confirms an initial favourable change in BVs that is a likely consequence of the voluntary radiographic hip-screening programme.

Single nucleotide polymorphisms refine QTL intervals for hip joint laxity in dogs

Hip laxity is one characteristic of canine hip dysplasia (CHD), an inheritable disease that leads to hip osteoarthritis. Using a genome-wide screen with 250 microsatellites in a crossbreed pedigree of 159 dysplastic Labrador retrievers and unaffected greyhounds, we previously identified putative (P < 0.01) QTL on canine chromosomes 11 and 29 (CFA11 and CFA29). To refine these QTL locations, we have genotyped 257 dogs including 105 Labrador retrievers, seven greyhounds, four generations of their crossbreed offspring and three German shepherds for 111 and 171 SNPs on CFA11 and CFA29 respectively. The distraction index (DI, a measure of maximum hip laxity) was used as an intermediate phenotype that predicts whether a hip joint will or will not develop osteoarthritis. Using a multipoint linkage analysis, significant evidence (95% posterior probability) was found for QTL contributing to hip laxity in the 16.2-21 cM region on CFA11 that explained 15-18% of the total variance in DI. Evidence for an independent QTL on CFA29 was weaker than that on CFA11. Identification of the causative mutation(s) will lead to better understanding of biochemical pathways in both dogs and humans with hip laxity and dysplasia.

Breaking loops in large complex pedigrees

For pedigrees with multiple loops, exact likelihoods could not be computed in an acceptable time frame and thus, approximate methods are used. Some of these methods are based on breaking loops and approximations of complex pedigree likelihoods using the exact likelihood of the corresponding zero-loop pedigree. Due to ignoring loops, this method results in a loss of genetic information and a decrease in the power to detect linkage. To minimize this loss, an optimal set of loop breakers has to be selected. In this paper, we present a graph theory based algorithm for automatic selection of an optimal set of loop breakers. We propose using a total relationship between measured pedigree members as a proxy to power. To minimize the loss of genetic information, we suggest selection of such breakers whose duplication in a pedigree would be accompanied by a minimal loss of total relationship between measured pedigree members. We show that our algorithm compares favorably with other existing loop-breaker selection algorithms in terms of conservation of genetic information, statistical power and CPU time of subsequent linkage analysis. We implemented our method in a software package LOOP_EDGE, which is available at http://mga.bionet.nsc.ru/nlru/.

Assessment of collagen genes involved in fragmented medial coronoid process development in Labrador Retrievers as determined by affected sibling-pair analysis

OBJECTIVE

To evaluate the involvement of various collagen genes in the development of fragmented medial coronoid process (FCP) in Labrador Retrievers.

SAMPLE POPULATION

93 dogs originating from 13 litters were used in the study; FCP was diagnosed in 35 dogs, and each affected dog had at least 1 sibling that was also affected. Twelve dams and sires were included in the analysis. All dogs were purebred Labrador Retrievers except for 2 litters (offspring of a female Golden Retriever-Labrador Retriever mixed-breed dog).

PROCEDURES

For each dog, DNA was isolated from blood samples. Polymorphic microsatellite markers adjacent to 14 candidate genes (ie, COL1A1, COL1A2, COL2A1, COL3A1, COL5A1, COL5A2, COL6A3, COL9A1, COL9A2, COL9A3, COL10A1, COL11A1, COL11A2, and COL24A1) were analyzed by use of PCR assays; genotypes were determined via automated detection of DNA products. The level of allele sharing between pairs of affected siblings was assessed.

RESULTS

Among the 93 dogs, allele sharing of the 14 collagen genes was determined as follows: COL1A1, 45%; COL1A2, 47%; COL2A1, 37%; COL3A1, 32%; COL5A1, 43%; COL5A2, 32%; COL6A3, 36%; COL9A1, 45%; COL9A2, 49%; COL9A3, 38%; COL10A1, 46%; COL11A1, 52%; COL11A2, 47%; and COL24A1, 47%.

CONCLUSIONS AND CLINICAL RELEVANCE

Because siblings share 50% of their genome at random, the fact that the percentages of allele sharing among the analyzed collagen genes were not significantly > 50% indicates that these genes are not determinant candidates for FCP in Labrador Retrievers. The gene for the vitamin D receptor could also be excluded because of its proximity to COL2A1.

Inheritance of litter size at birth in farmed arctic foxes (Alopex lagopus, Canidae, Carnivora)

Natural populations of the arctic fox (Alopex lagopus, Canidae, Carnivora) differ drastically in their reproductive strategy. Coastal foxes, which depend on stable food resources, produce litters of moderate size. Inland foxes feed on small rodents, whose populations are characterized by cycling fluctuation. In the years with low food supply, inland fox populations have a very low rate of reproduction. In the years with high food supply, they undergo a population explosion. To gain insight into the genetic basis of the reproductive strategy of this species, we performed complex segregation analysis of the litter size in the extended pedigree of the farmed arctic foxes involving 20,665 interrelated animals. Complex segregation analysis was performed using a mixed model assuming that the trait was under control of a major gene and a large number of additive genetic and random factors. To check the significance of any major gene effect, we used Elston-Stewart transmission probability test. Our analysis demonstrated that the inheritance of this trait can be described within the frameworks of a major gene model with recessive control of low litter size. This model was also supported by the pattern of its familial segregation and by comparison of the distributions observed in the population and that expected under our model. We suggest that a system of balanced polymorphism for litter size in the farmed population might have been established in natural populations of arctic foxes as a result of adaptation to the drastic fluctuations in prey availability.

Canine genomics and genetics: running with the pack

The domestication of the dog from its wolf ancestors is perhaps the most complex genetic experiment in history, and certainly the most extensive. Beginning with the wolf, man has created dog breeds that are hunters or herders, big or small, lean or squat, and independent or loyal. Most breeds were established in the 1800s by dog fanciers, using a small number of founders that featured traits of particular interest. Popular sire effects, population bottlenecks, and strict breeding programs designed to expand populations with desirable traits led to the development of what are now closed breeding populations, with limited phenotypic and genetic heterogeneity, but which are ideal for genetic dissection of complex traits. In this review, we first discuss the advances in mapping and sequencing that accelerated the field in recent years. We then highlight findings of interest related to disease gene mapping and population structure. Finally, we summarize novel results on the genetics of morphologic variation.

Complex Segregation Analysis of Canine Hip Dysplasia in German Shepherd Dogs

Complex segregation analyses were carried out to clarify the mode of inheritance of canine hip dysplasia (CHD) in German shepherd dogs. Data were used from 8,567 animals examined for CHD from 20 families with three to four generations. The existence of a major gene in addition to polygenic gene effects was detected. In the present study, a mixed model with a dominant major gene effect seemed to be most probable for dichotomous encoding (0: dogs without signs of CHD; 1: dogs with borderline/slight to severe CHD). In addition, mixed major gene inheritance was shown for a binary trait where borderline was assigned to dogs scored free from CHD and for a trichotomously encoded trait (0: dogs without signs of CHD; 1: borderline CHD; 2: mild to severe CHD). Although only small frequencies were found for the unfavorable homozygotic genotype AA, the probability of the AB genotype was high in affected animals. Selection schemes to reduce the frequency of the allele A should therefore efficiently improve existing breeding programmes in German shepherd dogs.