Validation of Bovine Selective Sweeps Using High Resolution SNP Data

Within the genomes of different cattle breeds there are regions of reduced heterozygosity that arise from selection for a beneficial mutation. These mutations pull neighboring alleles into a haplotype which moves to fixation creating a region harboring a loss of variability called a selective sweep. Recently, selective sweeps in the bovine genome were identified using Illumina BovineSNP50 single nucleotide polymorphism (SNP) data. Our objective was to validate genomic regions identified as harboring selective sweeps and discover new regions using higher resolution SNP data from the Affymetrix prescreening array used to design the Axiom Genome-Wide BOS 1 array. This assay contains 2,575,339 SNPs which were scored in 58 individuals representing five phylogenetically diverse taurine and indicine breeds. We attempted to validate regions previously found using BovineSNP50 data by independently identifying putative selective sweeps using Affymetrix prescreening data and comparing minor allele frequencies and haplotypes in coinciding regions. This analysis indicated some regions were not characterized by a complete loss of variability as suggested by BovineSNP50 data and these regions were assessed for the presence of newly accumulated mutations. Using the high-density data, we detected regions ranging in size from 200 kb to 1 Mb. The across breed analysis identified common selected haplotypes among taurine breeds; however, none appear to be common between taurine and indicine breeds. The genes contained within these regions were examined to identify the likely phenotype affected by the beneficial mutations. Overall, detected regions appear to be due to breed formation and selective breeding events, not domestication events.