Abstract
Maintaining genetic diversity in dog breeds is an important consideration for the management of inherited diseases. We evaluated genetic diversity in Border Collies using molecular and genealogical methods, and examined changes to genetic diversity when carriers for Trapped Neutrophil Syndrome (TNS) and Neuronal Ceroid Lipofuscinosis (NCL) are removed from the genotyped population. Genotype data for 255 Border Collies and a pedigree database of 83,996 Border Collies were used for analysis. Molecular estimates revealed a mean multi-locus heterozygosity (MLH) of 0.311 (SD 0.027), 20.79% of the genome consisted of runs of homozygosity (ROH ) > 1 Mb, effective population size (Ne) was 84.7, and mean inbreeding (F) was 0.052 (SD 0.083). For 227 genotyped Border Collies that had available pedigree information (GenoPed), molecular and pedigree estimates of diversity were compared. A reference population (dogs born between 2005 and 2015, inclusive; N = 13,523; RefPop) and their ancestors (N = 12,478) were used to evaluate the diversity of the population that are contributing to the current generation. The reference population had a Ne of 123.5, a mean F of 0.095 (SD 0.082), 2276 founders (f), 205.5 effective founders (fe), 28 effective ancestors (fa) and 10.65 (SD 2.82) founder genomes (Ng). Removing TNS and NCL carriers from the genotyped population had a small impact on diversity measures (ROH > 1 Mb, MLH, heterozygosity), however, there was a loss of > 10% minor allele frequency for 89 SNPs around the TNS mutation (maximum loss of 12.7%), and a loss of > 5% for 5 SNPs around the NCL mutation (maximum 5.18%). A common ancestor was identified for 38 TNS-affected dogs and 64 TNS carriers, and a different common ancestor was identified for 33 NCL-affected dogs and 28 carriers, with some overlap of prominent individuals between both pedigrees. Overall, Border Collies have a high level of genetic diversity compared to other breeds.
Highlights
Study Location Number of Border Collies in pedigree Reference Population Ref. period Equivalent generations (EqG) Mean inbreeding coefficient (F) Rate of inbreeding (ΔF) Mean kinship coefficient (Φ) Generation Interval (I) Effective population size (Ne) Observed founders (f) Effective founders Effective ancestors Effective founder genomes (Ng) fe/f fa/fe number of founder genomes (Ng)/fe
Of the Genotyped dogs with pedigrees (GenoPed) population (227 dogs remaining that passed genotyped quality control and had pedigree information), 79.7% were from Australia, 10.6% were of unknown origin, 2.6% were from UK, 2.2% were from Japan, 1.8% were from USA, while the remaining 3.1% were from Belgium, Romania, New Zealand, Italy, Germany, and Finland
Maintaining diversity is conducive to health and well-being in populations of purebred dog breeds derived from a limited gene pool
Summary
Study Location Number of Border Collies in pedigree Reference Population Ref. period Equivalent generations (EqG) Mean inbreeding coefficient (F) Rate of inbreeding (ΔF) Mean kinship coefficient (Φ) Generation Interval (I) Effective population size (Ne) Observed founders (f) Effective founders (fe) Effective ancestors (fa) Effective founder genomes (Ng) fe/f fa/fe Ng/fe. All published molecular estimates of genetic diversity in Border Collies have been based on small panels of microsatellite m arkers[15,18,23,26]. The aims of this study were to assess genetic diversity in the Border Collie breed using SNP markers and compare these values to genealogical estimates of diversity, and to examine the impact of removing TNS- and NCL-affected and carriers dogs on genetic diversity
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