Dataset Information

Genomic prediction of traits related to canine hip dysplasia.

ABSTRACT: Increased concern for the welfare of pedigree dogs has led to development of selection programs against inherited diseases. An example is canine hip dysplasia (CHD), which has a moderate heritability and a high prevalence in some large-sized breeds. To date, selection using phenotypes has led to only modest improvement, and alternative strategies such as genomic selection (GS) may prove more effective. The primary aims of this study were to compare the performance of pedigree- and genomic-based breeding against CHD in the UK Labrador retriever population and to evaluate the performance of different GS methods. A sample of 1179 Labrador Retrievers evaluated for CHD according to the UK scoring method (hip score, HS) was genotyped with the Illumina CanineHD BeadChip. Twelve functions of HS and its component traits were analyzed using different statistical methods (GBLUP, Bayes C and Single-Step methods), and results were compared with a pedigree-based approach (BLUP) using cross-validation. Genomic methods resulted in similar or higher accuracies than pedigree-based methods with training sets of 944 individuals for all but the untransformed HS, suggesting that GS is an effective strategy. GBLUP and Bayes C gave similar prediction accuracies for HS and related traits, indicating a polygenic architecture. This conclusion was also supported by the low accuracies obtained in additional GBLUP analyses performed using only the SNPs with highest test statistics, also indicating that marker-assisted selection (MAS) would not be as effective as GS. A Single-Step method that combines genomic and pedigree information also showed higher accuracy than GBLUP and Bayes C for the log-transformed HS, which is currently used for pedigree based evaluations in UK. In conclusion, GS is a promising alternative to pedigree-based selection against CHD, requiring more phenotypes with genomic data to improve further the accuracy of prediction.

SUBMITTER: Sanchez-Molano E

PROVIDER: S-EPMC4358223 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Genomic prediction of traits related to canine hip dysplasia.

Sánchez-Molano Enrique E Pong-Wong Ricardo R Clements Dylan N DN Blott Sarah C SC Wiener Pamela P Woolliams John A JA

Frontiers in genetics 20150313

Increased concern for the welfare of pedigree dogs has led to development of selection programs against inherited diseases. An example is canine hip dysplasia (CHD), which has a moderate heritability and a high prevalence in some large-sized breeds. To date, selection using phenotypes has led to only modest improvement, and alternative strategies such as genomic selection (GS) may prove more effective. The primary aims of this study were to compare the performance of pedigree- and genomic-based ...[more]

PMID: 25821457

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Project description: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.

Project description: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.

Dataset Information

Genomic prediction of traits related to canine hip dysplasia.

Publications

Genomic prediction of traits related to canine hip dysplasia.

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