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Genomic inbreeding trends, influential sire lines and selection in the global Thoroughbred horse population
The Thoroughbred horse is a highly valued domestic animal population under strong selection for athletic phenotypes. Here we present a high resolution genomics-based analysis of inbreeding in the population that may form the basis for evidence-based discussion amid concerns in the breeding industry...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Nature Publishing Group UK
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6965197/ https://www.ncbi.nlm.nih.gov/pubmed/31949252 http://dx.doi.org/10.1038/s41598-019-57389-5 |
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author | McGivney, Beatrice A. Han, Haige Corduff, Leanne R. Katz, Lisa M. Tozaki, Teruaki MacHugh, David E. Hill, Emmeline W. |
author_facet | McGivney, Beatrice A. Han, Haige Corduff, Leanne R. Katz, Lisa M. Tozaki, Teruaki MacHugh, David E. Hill, Emmeline W. |
author_sort | McGivney, Beatrice A. |
collection | PubMed |
description | The Thoroughbred horse is a highly valued domestic animal population under strong selection for athletic phenotypes. Here we present a high resolution genomics-based analysis of inbreeding in the population that may form the basis for evidence-based discussion amid concerns in the breeding industry over the increasing use of small numbers of popular sire lines, which may accelerate a loss of genetic diversity. In the most comprehensive globally representative sample of Thoroughbreds to-date (n = 10,118), including prominent stallions (n = 305) from the major bloodstock regions of the world, we show using pan-genomic SNP genotypes that there has been a highly significant decline in global genetic diversity during the last five decades (F(IS) R(2) = 0.942, P = 2.19 × 10(−13); F(ROH) R(2) = 0.88, P = 1.81 × 10(−10)) that has likely been influenced by the use of popular sire lines. Estimates of effective population size in the global and regional populations indicate that there is some level of regional variation that may be exploited to improve global genetic diversity. Inbreeding is often a consequence of selection, which in managed animal populations tends to be driven by preferences for cultural, aesthetic or economically advantageous phenotypes. Using a composite selection signals approach, we show that centuries of selection for favourable athletic traits among Thoroughbreds acts on genes with functions in behaviour, musculoskeletal conformation and metabolism. As well as classical selective sweeps at core loci, polygenic adaptation for functional modalities in cardiovascular signalling, organismal growth and development, cellular stress and injury, metabolic pathways and neurotransmitters and other nervous system signalling has shaped the Thoroughbred athletic phenotype. Our results demonstrate that genomics-based approaches to identify genetic outcrosses will add valuable objectivity to augment traditional methods of stallion selection and that genomics-based methods will be beneficial to actively monitor the population to address the marked inbreeding trend. |
format | Online Article Text |
id | pubmed-6965197 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-69651972020-01-23 Genomic inbreeding trends, influential sire lines and selection in the global Thoroughbred horse population McGivney, Beatrice A. Han, Haige Corduff, Leanne R. Katz, Lisa M. Tozaki, Teruaki MacHugh, David E. Hill, Emmeline W. Sci Rep Article The Thoroughbred horse is a highly valued domestic animal population under strong selection for athletic phenotypes. Here we present a high resolution genomics-based analysis of inbreeding in the population that may form the basis for evidence-based discussion amid concerns in the breeding industry over the increasing use of small numbers of popular sire lines, which may accelerate a loss of genetic diversity. In the most comprehensive globally representative sample of Thoroughbreds to-date (n = 10,118), including prominent stallions (n = 305) from the major bloodstock regions of the world, we show using pan-genomic SNP genotypes that there has been a highly significant decline in global genetic diversity during the last five decades (F(IS) R(2) = 0.942, P = 2.19 × 10(−13); F(ROH) R(2) = 0.88, P = 1.81 × 10(−10)) that has likely been influenced by the use of popular sire lines. Estimates of effective population size in the global and regional populations indicate that there is some level of regional variation that may be exploited to improve global genetic diversity. Inbreeding is often a consequence of selection, which in managed animal populations tends to be driven by preferences for cultural, aesthetic or economically advantageous phenotypes. Using a composite selection signals approach, we show that centuries of selection for favourable athletic traits among Thoroughbreds acts on genes with functions in behaviour, musculoskeletal conformation and metabolism. As well as classical selective sweeps at core loci, polygenic adaptation for functional modalities in cardiovascular signalling, organismal growth and development, cellular stress and injury, metabolic pathways and neurotransmitters and other nervous system signalling has shaped the Thoroughbred athletic phenotype. Our results demonstrate that genomics-based approaches to identify genetic outcrosses will add valuable objectivity to augment traditional methods of stallion selection and that genomics-based methods will be beneficial to actively monitor the population to address the marked inbreeding trend. Nature Publishing Group UK 2020-01-16 /pmc/articles/PMC6965197/ /pubmed/31949252 http://dx.doi.org/10.1038/s41598-019-57389-5 Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article McGivney, Beatrice A. Han, Haige Corduff, Leanne R. Katz, Lisa M. Tozaki, Teruaki MacHugh, David E. Hill, Emmeline W. Genomic inbreeding trends, influential sire lines and selection in the global Thoroughbred horse population |
title | Genomic inbreeding trends, influential sire lines and selection in the global Thoroughbred horse population |
title_full | Genomic inbreeding trends, influential sire lines and selection in the global Thoroughbred horse population |
title_fullStr | Genomic inbreeding trends, influential sire lines and selection in the global Thoroughbred horse population |
title_full_unstemmed | Genomic inbreeding trends, influential sire lines and selection in the global Thoroughbred horse population |
title_short | Genomic inbreeding trends, influential sire lines and selection in the global Thoroughbred horse population |
title_sort | genomic inbreeding trends, influential sire lines and selection in the global thoroughbred horse population |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6965197/ https://www.ncbi.nlm.nih.gov/pubmed/31949252 http://dx.doi.org/10.1038/s41598-019-57389-5 |
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