Genome-wide scan and analysis of positive selective signatures in Dwarf Brown-egg Layers and Silky Fowl chickens

Abstract

Chinese domestic chickens have been routinely subjected to artificial selection for the production of meats and eggs. Selection results in distinctive signatures in the genome that can reveal the genes underlying phenotypes of interest to breeders. In this study, we used the Chicken60K SNP chip to analyze DNA from Dwarf Brown-egg Layers (DB, n = 203) and Silky Fowls (SF, n = 181) and then examined the relative extended haplotype homozygosity (REHH) and fixation index (FST) to detect selection signatures. Since population structure analysis showed that SF was stratified into 2 subpopulations (SF1 and SF2), we removed the 20 SF1 chickens, and the remaining individuals (DB and SF2) were scanned for genome-wide selection signatures. A total of 939 selection signatures, including 446 candidate genes, were found to be potential selection targets using the FST test. REHH analysis identified 93 and 128 core regions, including 112 and 181 genes, in DB and SF2, respectively. Among the candidate genes, domestication-related genes such as NELL1 were found. After comparing the candidate genes with the Animal QTL database, we identified additional genes possibly associated with growth, reproduction, egg laying, and immune response, including GRHL3, CDK1, AKT1, and KMD3A. Functional enrichment analysis suggests that genes associated with muscle development have undergone positive selection. Our findings provide a genome-wide selection signature draft for DB and SF, and establish a resource that can be exploited in chicken breeding programs to manipulate the genes that underlie desired phenotypes.