TY - JOUR

T1 - Using singleton densities to detect recent selection in Bos taurus

AU - Hartfield, Matthew

AU - Poulsen, Nina Aagaard

AU - Guldbrandtsen, Bernt

AU - Bataillon, Thomas

N1 - Funding Information: We would like to thank S. Boitard for sharing his results on demographic inference and S. Boitard, J. Slate, and two anonymous reviewers for providing feedback on the manuscript. MH is supported by a NERC Independent Research Fellowship (NE/R015686/1). NAP, BG, and TB are funded by a synergistic research grant from the Faculty of Science and Technology, Aarhus University, Denmark. MH and TB also acknowledge financial support from the European Research Council under the European Union's Seventh Framework Program (FP7/20072013, ERC Grant 311341). B. taurus Publisher Copyright: © 2021 The Authors. Evolution Letters published by Wiley Periodicals LLC on behalf of Society for the Study of Evolution (SSE) and European Society for Evolutionary Biology (ESEB).

PY - 2021

Y1 - 2021

N2 - 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.

AB - 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.

KW - Bos taurus

KW - genomics

KW - milk fat

KW - milk protein

KW - selection

KW - stature

U2 - 10.1002/evl3.263

DO - 10.1002/evl3.263

M3 - Letter

C2 - 34917399

AN - SCOPUS:85119624681

VL - 5

SP - 595

EP - 606

JO - Evolution Letters

JF - Evolution Letters

SN - 2056-3744

IS - 6

ER -