ArticleBMC genomics2009
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.
Article in BMC genomics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers, 1 of them a synthesis that pooled it.
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50 citing papers in PubMed, 1 synthesis or guideline pooled it, 113 citations in OpenAlex.
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- Detection of copy number variation and selection signatures on the X chromosome in Chinese indigenous sheep with different types of tail.Asian-Australasian journal of animal sciences · 2020Article
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- Genome changes due to artificial selection in U.S. Holstein cattle.BMC genomics · 2019Article
- Artificial selection increased body weight but induced increase of runs of homozygosity in Hanwoo cattle.PloS one · 2018Article
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- Identification of selective sweeps reveals divergent selection between Chinese Holstein and Simmental cattle populations.Genetics, selection, evolution : GSE · 2016Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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 (N(e)) 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 N(e) 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 N(e) 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.
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