Detection of selective sweeps in cattle using genome-wide SNP data

Holly R Ramey,Stephanie D Mckay,Jared E Decker,Jeremy F Taylor,Robert D Schnabel,Megan M Rolf

doi:10.1186/1471-2164-14-382

Holly R Ramey, Stephanie D Mckay + Show 4 more

Open Access

https://doi.org/10.1186/1471-2164-14-382

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Abstract

BackgroundThe domestication and subsequent selection by humans to create breeds and biological types of cattle undoubtedly altered the patterning of variation within their genomes. Strong selection to fix advantageous large-effect mutations underlying domesticability, breed characteristics or productivity created selective sweeps in which variation was lost in the chromosomal region flanking the selected allele. Selective sweeps have now been identified in the genomes of many animal species including humans, dogs, horses, and chickens. Here, we attempt to identify and characterise regions of the bovine genome that have been subjected to selective sweeps.ResultsTwo datasets were used for the discovery and validation of selective sweeps via the fixation of alleles at a series of contiguous SNP loci. BovineSNP50 data were used to identify 28 putative sweep regions among 14 diverse cattle breeds. Affymetrix BOS 1 prescreening assay data for five breeds were used to identify 85 regions and validate 5 regions identified using the BovineSNP50 data. Many genes are located within these regions and the lack of sequence data for the analysed breeds precludes the nomination of selected genes or variants and limits the prediction of the selected phenotypes. However, phenotypes that we predict to have historically been under strong selection include horned-polled, coat colour, stature, ear morphology, and behaviour.ConclusionsThe bias towards common SNPs in the design of the BovineSNP50 assay led to the identification of recent selective sweeps associated with breed formation and common to only a small number of breeds rather than ancient events associated with domestication which could potentially be common to all European taurines. The limited SNP density, or marker resolution, of the BovineSNP50 assay significantly impacted the rate of false discovery of selective sweeps, however, we found sweeps in common between breeds which were confirmed using an ultra-high-density assay scored in a small number of animals from a subset of the breeds. No sweep regions were shared between indicine and taurine breeds reflecting their divergent selection histories and the very different environmental habitats to which these sub-species have adapted.

Highlights

The domestication and subsequent selection by humans to create breeds and biological types of cattle undoubtedly altered the patterning of variation within their genomes
The average number of selective sweeps found in Charolais, Hanwoo, Salers, Brown Swiss and Jersey was 3.8 while the average number detected in Hereford, Angus and Holstein was 4.0 (Table 2) suggesting that variation in sample size did not play a significant role in elevating the false positive rate in the breeds with small sample sizes
Rather than characterising sweeps that occurred during the domestication of cattle and that should be common, e.g., among European taurine breeds that descended from cattle that were domesticated in the Fertile Crescent, these sweeps are much more likely to have occurred during the formation of breeds and will reflect selection to fix phenotypes such as coat colour or the absence of horns within specific breeds

Summary

Introduction

The domestication and subsequent selection by humans to create breeds and biological types of cattle undoubtedly altered the patterning of variation within their genomes. Strong selection to fix advantageous large-effect mutations underlying domesticability, breed characteristics or productivity created selective sweeps in which variation was lost in the chromosomal region flanking the selected allele. Strong on-going selection for variants of large effect leads to a loss of variation within the chromosomal region flanking the selected variant and the complete fixation of the haplotype which harbours the variant. This phenomenon is known as the “hitch-hiking effect” [9] and a region of the genome in which artificial selection has driven a haplotype to complete fixation is defined as having been subjected to a “selective sweep”. An important reason for seeking selective sweeps is that these regions can elucidate the identities of genes and mutations with large phenotypic effect even if they are no longer segregating within any one population and cannot be detected by forward genetics without the formation of expensive crosses

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