Evaluation of genetic diversity and management of disease in Border Collie dogs

Pamela Xing Yi Soh; Wei Tse Hsu; Mehar Singh Khatkar; Peter Williamson

doi:10.1038/s41598-021-85262-x

Evaluation of genetic diversity and management of disease in Border Collie dogs

Sci Rep. 2021 Mar 18;11(1):6243. doi: 10.1038/s41598-021-85262-x.

Authors

Pamela Xing Yi Soh¹, Wei Tse Hsu¹, Mehar Singh Khatkar², Peter Williamson³

Affiliations

¹ School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, 2006, Australia.
² Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW, 2006, Australia.
³ School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, 2006, Australia. p.williamson@sydney.edu.au.

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 (N_e) 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 N_e of 123.5, a mean F of 0.095 (SD 0.082), 2276 founders (f), 205.5 effective founders (f_e), 28 effective ancestors (f_a) and 10.65 (SD 2.82) founder genomes (N_g). 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.

MeSH terms

Alleles
Animals
Chromosome Mapping
Databases, Genetic
Disease Management
Dog Diseases / diagnosis
Dog Diseases / genetics*
Dog Diseases / pathology
Dogs
Female
Gene Frequency
Genetic Variation*
Genome*
Genotype
Heterozygote
Homozygote
Male
Neuronal Ceroid-Lipofuscinoses / diagnosis
Neuronal Ceroid-Lipofuscinoses / genetics*
Neuronal Ceroid-Lipofuscinoses / pathology
Pedigree
Polymorphism, Single Nucleotide*
Primary Immunodeficiency Diseases / diagnosis
Primary Immunodeficiency Diseases / genetics*
Primary Immunodeficiency Diseases / pathology

Supplementary concepts

Neutrophil Immunodeficiency Syndrome