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

TL;DR

This study identifies recent selective sweeps in cattle genomes using SNP data, revealing breed-specific regions linked to traits like horn status and coat color, with findings influenced by assay resolution limitations.

Contribution

It demonstrates the detection of breed-specific selective sweeps in cattle genomes and highlights the impact of assay resolution on results accuracy.

Findings

Identified 28 sweep regions in 14 breeds using BovineSNP50 data.

Validated 5 regions with Affymetrix BOS 1 assay data.

Detected breed-specific sweeps linked to phenotypes like horn status and coat color.

Abstract

The domestication and subsequent selection by humans to create breeds 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 been identified in the genomes of many species including humans, dogs, horses, and chickens. We attempt to identify regions of the bovine genome that have been subjected to selective sweeps. Two 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 cattle breeds. Affymetrix BOS 1 prescreening assay data for five breeds were used to identify 114 regions and validate 5 regions identified using the BovineSNP50 data. Many genes are located within these regions; however, phenotypes that we predict to have historically been under strong selection include horned-polled, coat color, stature, ear morphology, and behavior. The identified selective sweeps represent recent events associated with breed formation rather than ancient events associated with domestication. No sweep regions were shared between indicine and taurine breeds reflecting their divergent selection histories. A primary finding of this study is the sensitivity of results to assay resolution. Despite the bias towards common SNPs in the BovineSNP50 design, false positive sweep regions appear to be common due to the limited resolution of the assay. This assay design bias leads to the detection of breed-specific sweep regions, or regions shared by a small number of breeds, restricting the suite of selected phenotypes detected to primarily those associated with breed characteristics.