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...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Oxford University Press
2021-12-01
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| Series: | Evolution Letters |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/evl3.263 |
| _version_ | 1797719362545647616 |
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| 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 |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-12T09:03:46Z |
| format | Article |
| id | doaj.art-765cf9358dee4da697e1e19678bd2f74 |
| institution | Directory Open Access Journal |
| issn | 2056-3744 |
| language | English |
| last_indexed | 2024-03-12T09:03:46Z |
| publishDate | 2021-12-01 |
| publisher | Oxford University Press |
| record_format | Article |
| series | Evolution Letters |
| spelling | doaj.art-765cf9358dee4da697e1e19678bd2f742023-09-02T15:28:47ZengOxford University PressEvolution Letters2056-37442021-12-015659560610.1002/evl3.263Using singleton densities to detect recent selection in Bos taurusMatthew Hartfield0Nina Aagaard Poulsen1Bernt Guldbrandtsen2Thomas Bataillon3Bioinformatics Research Centre Aarhus University Aarhus DK‐8000 DenmarkDepartment of Food Science Aarhus University Aarhus N DK‐8200 DenmarkCenter for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics Aarhus University Tjele DK‐8830 DenmarkBioinformatics Research Centre Aarhus University Aarhus DK‐8000 DenmarkAbstract 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.https://doi.org/10.1002/evl3.263Bos taurusgenomicsmilk fatmilk proteinselectionstature |
| spellingShingle | Matthew Hartfield Nina Aagaard Poulsen Bernt Guldbrandtsen Thomas Bataillon Using singleton densities to detect recent selection in Bos taurus Evolution Letters Bos taurus genomics milk fat milk protein selection stature |
| title | 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_short | Using singleton densities to detect recent selection in Bos taurus |
| title_sort | using singleton densities to detect recent selection in bos taurus |
| topic | Bos taurus genomics milk fat milk protein selection stature |
| url | https://doi.org/10.1002/evl3.263 |
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