Using singleton densities to detect recent selection in Bos taurus

Abstract Many quantitative traits are subject to polygenic selection, where several genomic regions undergo small, simultaneous changes in allele frequency that collectively alter a phenotype. The widespread availability of genome data, along with novel statistical techniques, has made it easier to...

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Autores principales:	Matthew Hartfield, Nina Aagaard Poulsen, Bernt Guldbrandtsen, Thomas Bataillon
Formato:	article
Lenguaje:	EN
Publicado:	Wiley 2021
Materias:	Bos taurus genomics milk fat milk protein selection stature Evolution QH359-425
Acceso en línea:	https://doaj.org/article/765cf9358dee4da697e1e19678bd2f74
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id	oai:doaj.org-article:765cf9358dee4da697e1e19678bd2f74
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spelling	oai:doaj.org-article:765cf9358dee4da697e1e19678bd2f742021-12-05T14:03:53ZUsing singleton densities to detect recent selection in Bos taurus2056-374410.1002/evl3.263https://doaj.org/article/765cf9358dee4da697e1e19678bd2f742021-12-01T00:00:00Zhttps://doi.org/10.1002/evl3.263https://doaj.org/toc/2056-3744Abstract Many quantitative traits are subject to polygenic selection, where several genomic regions undergo small, simultaneous changes in allele frequency that collectively alter a phenotype. The widespread availability of genome data, along with novel statistical techniques, has made it easier to detect these changes. We apply one such method, the “Singleton Density Score” (SDS), to the Holstein breed of Bos taurus to detect recent selection (arising up to around 740 years ago). We identify several genes as candidates for targets of recent selection, including some relating to cell regulation, catabolic processes, neural‐cell adhesion and immunity. We do not find strong evidence that three traits that are important to humans—milk protein content, milk fat content, and stature—have been subject to directional selection. Simulations demonstrate that because B. taurus recently experienced a population bottleneck, singletons are depleted so the power of SDS methods is reduced. These results inform on which genes underlie recent genetic change in B. taurus, while providing information on how polygenic selection can be best investigated in future studies.Matthew HartfieldNina Aagaard PoulsenBernt GuldbrandtsenThomas BataillonWileyarticleBos taurusgenomicsmilk fatmilk proteinselectionstatureEvolutionQH359-425ENEvolution Letters, Vol 5, Iss 6, Pp 595-606 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Bos taurus genomics milk fat milk protein selection stature Evolution QH359-425
spellingShingle	Bos taurus genomics milk fat milk protein selection stature Evolution QH359-425 Matthew Hartfield Nina Aagaard Poulsen Bernt Guldbrandtsen Thomas Bataillon Using singleton densities to detect recent selection in Bos taurus
description	Abstract Many quantitative traits are subject to polygenic selection, where several genomic regions undergo small, simultaneous changes in allele frequency that collectively alter a phenotype. The widespread availability of genome data, along with novel statistical techniques, has made it easier to detect these changes. We apply one such method, the “Singleton Density Score” (SDS), to the Holstein breed of Bos taurus to detect recent selection (arising up to around 740 years ago). We identify several genes as candidates for targets of recent selection, including some relating to cell regulation, catabolic processes, neural‐cell adhesion and immunity. We do not find strong evidence that three traits that are important to humans—milk protein content, milk fat content, and stature—have been subject to directional selection. Simulations demonstrate that because B. taurus recently experienced a population bottleneck, singletons are depleted so the power of SDS methods is reduced. These results inform on which genes underlie recent genetic change in B. taurus, while providing information on how polygenic selection can be best investigated in future studies.
format	article
author	Matthew Hartfield Nina Aagaard Poulsen Bernt Guldbrandtsen Thomas Bataillon
author_facet	Matthew Hartfield Nina Aagaard Poulsen Bernt Guldbrandtsen Thomas Bataillon
author_sort	Matthew Hartfield
title	Using singleton densities to detect recent selection in Bos taurus
title_short	Using singleton densities to detect recent selection in Bos taurus
title_full	Using singleton densities to detect recent selection in Bos taurus
title_fullStr	Using singleton densities to detect recent selection in Bos taurus
title_full_unstemmed	Using singleton densities to detect recent selection in Bos taurus
title_sort	using singleton densities to detect recent selection in bos taurus
publisher	Wiley
publishDate	2021
url	https://doaj.org/article/765cf9358dee4da697e1e19678bd2f74
work_keys_str_mv	AT matthewhartfield usingsingletondensitiestodetectrecentselectioninbostaurus AT ninaaagaardpoulsen usingsingletondensitiestodetectrecentselectioninbostaurus AT berntguldbrandtsen usingsingletondensitiestodetectrecentselectioninbostaurus AT thomasbataillon usingsingletondensitiestodetectrecentselectioninbostaurus
_version_	1718371908739661824

Using singleton densities to detect recent selection in Bos taurus

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