Abstract

BackgroundArtificial selection for economically important traits in cattle is expected to have left distinctive selection signatures on the genome. Access to high-density genotypes facilitates the accurate identification of genomic regions that have undergone positive selection. These findings help to better elucidate the mechanisms of selection and to identify candidate genes of interest to breeding programs.ResultsInformation on 705 243 autosomal single nucleotide polymorphisms (SNPs) in 3122 dairy and beef male animals from seven cattle breeds (Angus, Belgian Blue, Charolais, Hereford, Holstein-Friesian, Limousin and Simmental) were used to detect selection signatures by applying two complementary methods, integrated haplotype score (iHS) and global fixation index (FST). To control for false positive results, we used false discovery rate (FDR) adjustment to calculate adjusted iHS within each breed and the genome-wide significance level was about 0.003. Using the iHS method, 83, 92, 91, 101, 85, 101 and 86 significant genomic regions were detected for Angus, Belgian Blue, Charolais, Hereford, Holstein-Friesian, Limousin and Simmental cattle, respectively. None of these regions was common to all seven breeds. Using the FST approach, 704 individual SNPs were detected across breeds. Annotation of the regions of the genome that showed selection signatures revealed several interesting candidate genes i.e. DGAT1, ABCG2, MSTN, CAPN3, FABP3, CHCHD7, PLAG1, JAZF1, PRKG2, ACTC1, TBC1D1, GHR, BMP2, TSG1, LYN, KIT and MC1R that play a role in milk production, reproduction, body size, muscle formation or coat color. Fifty-seven common candidate genes were found by both the iHS and global FST methods across the seven breeds. Moreover, many novel genomic regions and genes were detected within the regions that showed selection signatures; for some candidate genes, signatures of positive selection exist in the human genome. Multilevel bioinformatic analyses of the detected candidate genes suggested that the PPAR pathway may have been subjected to positive selection.ConclusionsThis study provides a high-resolution bovine genomic map of positive selection signatures that are either specific to one breed or common to a subset of the seven breeds analyzed. Our results will contribute to the detection of functional candidate genes that have undergone positive selection in future studies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-015-0127-3) contains supplementary material, which is available to authorized users.

Highlights

  • Artificial selection in cattle has resulted in divergent breeds that are specialized for either milk or meat production or raised as dual-purpose breeds

  • IHS test The 705 243 single nucleotide polymorphism (SNP) used in our study covered 2512.08 Mbp of the bovine genome (UMD3.1), with a mean distance of 3.56 kb between adjacent SNPs

  • Vilas et al [36] recommended caution regarding the extent of false positive selection signatures which could be false positive results

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Summary

Introduction

Artificial selection in cattle has resulted in divergent breeds that are specialized for either milk or meat production or raised as dual-purpose breeds. The EHH test is useful to detect signatures of positive selection within a population using single nucleotide polymorphism (SNP) data [9,10,11]. This method that was first developed by Sabeti et al [1] exploits knowledge on the relationship between the frequency of an allele and the measures of LD with neighboring alleles. Access to high-density genotypes facilitates the accurate identification of genomic regions that have undergone positive selection. These findings help to better elucidate the mechanisms of selection and to identify candidate genes of interest to breeding programs

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