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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\u2009) &gt;\u20091\u00a0Mb, effective population size (<jats:italic>N<\/jats:italic><jats:sub>e<\/jats:sub>) 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\u2009=\u200913,523; RefPop) and their ancestors (N\u2009=\u200912,478) were used to evaluate the diversity of the population that are contributing to the current generation. The reference population had a<jats:italic>N<\/jats:italic><jats:sub>e<\/jats:sub>of 123.5, a mean F of 0.095 (SD 0.082), 2276 founders (<jats:italic>f<\/jats:italic>), 205.5 effective founders (<jats:italic>f<\/jats:italic><jats:sub>e<\/jats:sub>), 28 effective ancestors (<jats:italic>f<\/jats:italic><jats:sub>a<\/jats:sub>) and 10.65 (SD 2.82) founder genomes (<jats:italic>N<\/jats:italic><jats:sub>g<\/jats:sub>). Removing TNS and NCL carriers from the genotyped population had a small impact on diversity measures (ROH\u2009&gt;\u20091\u00a0Mb, MLH, heterozygosity), however, there was a loss of\u2009&gt;\u200910% minor allele frequency for 89 SNPs around the TNS mutation (maximum loss of 12.7%), and a loss of\u2009&gt;\u20095% 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.<\/jats:p>","DOI":"10.1038\/s41598-021-85262-x","type":"journal-article","created":{"date-parts":[[2021,3,18]],"date-time":"2021-03-18T16:47:41Z","timestamp":1616086061000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["Evaluation of genetic diversity and management of disease in Border Collie dogs"],"prefix":"10.1038","volume":"11","author":[{"given":"Pamela Xing Yi","family":"Soh","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wei Tse","family":"Hsu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mehar Singh","family":"Khatkar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter","family":"Williamson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2021,3,18]]},"reference":[{"key":"85262_CR1","doi-asserted-by":"publisher","first-page":"402","DOI":"10.1016\/j.tvjl.2009.08.033","volume":"182","author":"L Asher","year":"2009","unstructured":"Asher, L., Diesel, G., Summers, J. 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