Detection of genomic signatures of recent selection in commercial broiler chickens.

Weixuan Fu,Behnam Abasht,William R Lee

doi:10.1186/s12863-016-0430-1

Abstract

BackgroundIdentification of the genomic signatures of recent selection may help uncover causal polymorphisms controlling traits relevant to recent decades of selective breeding in livestock. In this study, we aimed at detecting signatures of recent selection in commercial broiler chickens using genotype information from single nucleotide polymorphisms (SNPs). A total of 565 chickens from five commercial purebred lines, including three broiler sire (male) lines and two broiler dam (female) lines, were genotyped using the 60K SNP Illumina iSelect chicken array. To detect genomic signatures of recent selection, we applied two methods based on population comparison, cross-population extended haplotype homozygosity (XP-EHH) and cross-population composite likelihood ratio (XP-CLR), and further analyzed the results to find genomic regions under recent selection in multiple purebred lines.ResultsA total of 321 candidate selection regions spanning approximately 1.45 % of the chicken genome in each line were detected by consensus of results of both XP-EHH and XP-CLR methods. To minimize false discovery due to genetic drift, only 42 of the candidate selection regions that were shared by 2 or more purebred lines were considered as high-confidence selection regions in the study. Of these 42 regions, 20 were 50 kb or less while 4 regions were larger than 0.5 Mb. In total, 91 genes could be found in the 42 regions, among which 19 regions contained only 1 or 2 genes, and 9 regions were located at gene deserts.ConclusionsOur results provide a genome-wide scan of recent selection signatures in five purebred lines of commercial broiler chickens. We found several candidate genes for recent selection in multiple lines, such as SOX6 (Sex Determining Region Y-Box 6) and cTR (Thyroid hormone receptor beta). These genes may have been under recent selection due to their essential roles in growth, development and reproduction in chickens. Furthermore, our results suggest that in some candidate regions, the same or opposite alleles have been under recent selection in multiple lines. Most of the candidate genes in the selection regions are novel, and as such they should be of great interest for future research into the genetic architecture of traits relevant to modern broiler breeding.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-016-0430-1) contains supplementary material, which is available to authorized users.

Highlights

Identification of the genomic signatures of recent selection may help uncover causal polymorphisms controlling traits relevant to recent decades of selective breeding in livestock
Approximately 11.09 % of the chicken genome was covered by regions detected by XP-extended haplotype homozygosity (EHH) methods, while approximately 2.58 % of the chicken genome was covered by regions detected by XP-composite likelihood ratio (CLR) methods
Selection regions detected by Cross-population extended haplotype homozygosity (XP-EHH) were much wider, mainly because the EHH test is an linkage disequilibrium (LD)-based method, and LD is expected to extend over longer distances in regions under recent selection [17]

Summary

Introduction

Identification of the genomic signatures of recent selection may help uncover causal polymorphisms controlling traits relevant to recent decades of selective breeding in livestock. The authors indicated that genetic selection contributed 85–90 % of the improvement in growth rate over the past 45 years. These dramatic phenotypic changes imply that the frequencies of the underlying causal polymorphisms themselves have been altered by selection for performance in these traits during the intervening time period. Detecting the genomic footprints of artificial selection should help researchers to identify the causal polymorphisms underlying phenotypic changes and to better understand the biological and genetic mechanism controlling these traits

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Discussion

Conclusion