An examination of positive selection and changing effective population size in Angus and Holstein cattle populations (Bos taurus) using a high density SNP genotyping platform and the contribution of ancient polymorphism to genomic diversity in Domestic cattle

Sean Maceachern,Mike Goddard,Ben Hayes,John Mcewan

doi:10.1186/1471-2164-10-181

Abstract

BackgroundIdentifying recent positive selection signatures in domesticated animals could provide information on genome response to strong directional selection from domestication and artificial selection. With the completion of the cattle genome, private companies are now providing large numbers of polymorphic markers for probing variation in domestic cattle (Bos taurus). We analysed over 7,500 polymorphic single nucleotide polymorphisms (SNP) in beef (Angus) and dairy (Holstein) cattle and outgroup species Bison, Yak and Banteng in an indirect test of inbreeding and positive selection in Domestic cattle.ResultsOutgroup species: Bison, Yak and Banteng, were genotyped with high levels of success (90%) and used to determine ancestral and derived allele states in domestic cattle. Frequency spectrums of the derived alleles in Angus and Holstein were examined using Fay and Wu's H test. Significant divergences from the predicted frequency spectrums expected under neutrality were identified. This appeared to be the result of combined influences of positive selection, inbreeding and ascertainment bias for moderately frequent SNP. Approximately 10% of all polymorphisms identified as segregating in B. taurus were also segregating in Bison, Yak or Banteng; highlighting a large number of polymorphisms that are ancient in origin.ConclusionThese results suggest that a large effective population size (Ne) of approximately 90,000 or more existed in B. taurus since they shared a common ancestor with Bison, Yak and Banteng ~1–2 million years ago (MYA). More recently Ne decreased sharply probably associated with domestication. This may partially explain the paradox of high levels of polymorphism in Domestic cattle and the relatively small recent Ne in this species. The period of inbreeding caused Fay and Wu's H statistic to depart from its expectation under neutrality mimicking the effect of selection. However, there was also evidence for selection, because high frequency derived alleles tended to cluster near each other on the genome.

Highlights

Identifying recent positive selection signatures in domesticated animals could provide information on genome response to strong directional selection from domestication and artificial selection
Genotyping and wild specimens We have found that a high proportion (~0.9) of single nucleotide polymorphisms (SNP) markers, designed from the B. taurus genome, were successfully assayed in a number of wild relatives from the Bovina subtribe, which diverged from B. taurus between 1–2 million years ago (MYA), while no successful genotypes were recorded from the Bubalina subtribe, which diverged some < 9 MYA
We have examined the frequency distribution of polymorphisms in milking and beef breeds of B. taurus using Fay and Wu's H as a test to identify genomic positive selection

Summary

Introduction

Identifying recent positive selection signatures in domesticated animals could provide information on genome response to strong directional selection from domestication and artificial selection. With the completion of the cattle genome, private companies are providing large numbers of polymorphic markers for probing variation in domestic cattle (Bos taurus). Domestic animals provide a unique opportunity to detect positive selection due to their extensive diversity amongst breeds, increasing availability of sequence data and large databases of polymorphisms that are accruing in domestic species like Bos taurus. The neutral model with constant effective population size predicts that most polymorphisms will have one common allele and one rare allele. Tajima [13] suggests that changes in the frequency spectrum of neutral polymorphic alleles can be used to detect a hitchhiking effect due to the spread of linked advantageous mutations. Polymorphisms are discovered by methods that tend to find common variants and this ascertainment bias can generate an excess of polymorphisms with intermediate allele frequency

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