Detection of Recent Selection Signatures in Commercial Broiler Chickens

Over the past 70 years, broiler chickens have been intensively selected for performance improvement. This strong human-driven selection has led to major changes in traits of economical importance, most likely through changes in the frequency of alleles conferring desired phenotypes. Therefore, identification of genomic regions of such alleles may help uncover genes responsible for economic traits. In our study, we applied two methods, cross-population extended haplotype homozygosity (XP-EHH) and cross-population composite likelihood ratio (XP-CLR), to preform a genome-wide scan of recent selection signatures in five commercial elite broiler chicken lines, including three broiler sire (male) lines and two broiler dam (female) lines. A total of 322 candidate selection regions were detected by both methods, representing approximately 1.5% of the genome in each line. Of all candidate selection regions, 42 regions were detected in multiple lines. Through analyzing haplotypes in candidate selection regions, we found evidence for selection acting on the same or opposite alleles in multiple lines. Two examples of genes in candidate regions detected in multiple lines are Sex determining region Y-box 6 (SOX6) and Thyroid hormone receptor beta (cTR). These genes may have been under recent selection because of their essential roles in chickens’ growth, development and reproduction. The candidate genes identified in the present study are of interests for future research into the genetic architecture of traits relevant to modern broiler breeding.