Analysis of the canine genome and canine health: a commentary

Genomic data illuminates demography, genetic structure and selection of a popular dog breed

BACKGROUND

Genomic methods have proved to be important tools in the analysis of genetic diversity across the range of species and can be used to reveal processes underlying both short- and long-term evolutionary change. This study applied genomic methods to investigate population structure and inbreeding in a common UK dog breed, the Labrador Retriever.

RESULTS

We found substantial within-breed genetic differentiation, which was associated with the role of the dog (i.e. working, pet, show) and also with coat colour (i.e. black, yellow, brown). There was little evidence of geographical differentiation. Highly differentiated genomic regions contained genes and markers associated with skull shape, suggesting that at least some of the differentiation is related to human-imposed selection on this trait. We also found that the total length of homozygous segments (runs of homozygosity, ROHs) was highly correlated with inbreeding coefficient.

CONCLUSIONS

This study demonstrates that high-density genomic data can be used to quantify genetic diversity and to decipher demographic and selection processes. Analysis of genetically differentiated regions in the UK Labrador Retriever population suggests the possibility of human-imposed selection on craniofacial characteristics. The high correlation between estimates of inbreeding from genomic and pedigree data for this breed demonstrates that genomic approaches can be used to quantify inbreeding levels in dogs, which will be particularly useful where pedigree information is missing.

Visualization of Genome Diversity in German Shepherd Dogs

A loss of genetic diversity may lead to increased disease risks in subpopulations of dogs. The canine breed structure has contributed to relatively small effective population size in many breeds and can limit the options for selective breeding strategies to maintain diversity. With the completion of the canine genome sequencing project, and the subsequent reduction in the cost of genotyping on a genomic scale, evaluating diversity in dogs has become much more accurate and accessible. This provides a potential tool for advising dog breeders and developing breeding programs within a breed. A challenge in doing this is to present complex relationship data in a form that can be readily utilized. Here, we demonstrate the use of a pipeline, known as NetView, to visualize the network of relationships in a subpopulation of German Shepherd Dogs.

Genetics and behavior: a guide for practitioners

Phenotyping behavior is difficult, partly because behavior is almost always influenced by environment. Using objective terms/criteria to evaluate behaviors is best; the more objective the assessment, the more likely underlying genetic patterns will be identified. Behavioral pathologies, and highly desirable behavioral characteristics/traits, are likely complex, meaning that multiple genes are probably involved, and therefore simple genetic tests are less possible. Breeds can be improved using traditional quantitative genetic methods; unfortunately, this also creates the possibility of inadvertently selecting for covarying undesirable behaviors. Patterns of behaviors within families and breed lines are still the best guidelines for genetic counseling in dogs.

Inbreeding impact on litter size and survival in selected canine breeds

Data obtained from the French Kennel Club and the Fichier National Canin were used to estimate the effect of inbreeding on average litter size and survival in seven French breeds of dog. Depending on the breed, litter sizes were 3.5-6.3 puppies and longevities were 7.7-12.2 years. Estimated heritabilities were 6.0-10.9% for litter size and 6.1-10.1% for survival at 2 years of age. Regression coefficients indicated a negative effect of inbreeding on both individual survival and litter size. Although the impact of baseline inbreeding within breeds appears to be limited, the improper mating of close relatives will reduce biological fitness through significant reduction of litter size and longevity.