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Data from: Using singleton densities to detect recent selection in Bos taurus

Citation

Hartfield, Matthew; Poulsen, Nina Aagaard; Guldbrandtsen, Bernt; Bataillon, Thomas (2021), Data from: Using singleton densities to detect recent selection in Bos taurus, Dryad, Dataset, https://doi.org/10.5061/dryad.547d7wm8q

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’, 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 since B. taurus recently experienced a population bottleneck, singleton numbers are reduced limiting the power of SDS methods. 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.

Methods

This depository contains (i) SDS scores for Bos taurus, Holstein breed autosomes, excluding Chromosome 25; (ii) polarisation information for Bos taurus SNPs. Further details on the methods are available in the publication.

Usage Notes

This depository contains the raw data only. Scripts for analysing the data are available from https://github.com/MattHartfield/CattleSDS.