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

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 Syndr...

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Autores principales:	Pamela Xing Yi Soh, Wei Tse Hsu, Mehar Singh Khatkar, Peter Williamson
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/e9108f79cc1f45ce8aadf38183af446c
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spelling	oai:doaj.org-article:e9108f79cc1f45ce8aadf38183af446c2021-12-02T11:39:20ZEvaluation of genetic diversity and management of disease in Border Collie dogs10.1038/s41598-021-85262-x2045-2322https://doaj.org/article/e9108f79cc1f45ce8aadf38183af446c2021-03-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-85262-xhttps://doaj.org/toc/2045-2322Abstract 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.Pamela Xing Yi SohWei Tse HsuMehar Singh KhatkarPeter WilliamsonNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Pamela Xing Yi Soh Wei Tse Hsu Mehar Singh Khatkar Peter Williamson Evaluation of genetic diversity and management of disease in Border Collie dogs
description	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.
format	article
author	Pamela Xing Yi Soh Wei Tse Hsu Mehar Singh Khatkar Peter Williamson
author_facet	Pamela Xing Yi Soh Wei Tse Hsu Mehar Singh Khatkar Peter Williamson
author_sort	Pamela Xing Yi Soh
title	Evaluation of genetic diversity and management of disease in Border Collie dogs
title_short	Evaluation of genetic diversity and management of disease in Border Collie dogs
title_full	Evaluation of genetic diversity and management of disease in Border Collie dogs
title_fullStr	Evaluation of genetic diversity and management of disease in Border Collie dogs
title_full_unstemmed	Evaluation of genetic diversity and management of disease in Border Collie dogs
title_sort	evaluation of genetic diversity and management of disease in border collie dogs
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/e9108f79cc1f45ce8aadf38183af446c
work_keys_str_mv	AT pamelaxingyisoh evaluationofgeneticdiversityandmanagementofdiseaseinbordercolliedogs AT weitsehsu evaluationofgeneticdiversityandmanagementofdiseaseinbordercolliedogs AT meharsinghkhatkar evaluationofgeneticdiversityandmanagementofdiseaseinbordercolliedogs AT peterwilliamson evaluationofgeneticdiversityandmanagementofdiseaseinbordercolliedogs
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Evaluation of genetic diversity and management of disease in Border Collie dogs

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