Whole-genome resequencing analysis of Pengxian Yellow Chicken to identify genome-wide SNPs and signatures of selection

Chinese indigenous chickens have experienced strong selective pressure in genes or genomic regions controlling critical agricultural traits. To exploit the genetic features that may be useful in agriculture and are caused by artificial selection, we performed whole-genome sequencing of six Pengxian Yellow Chickens and downloaded the sequence data of five Red Jungle fowls from the NCBI. Through selective sweep analysis, we detected several regions with strong selection signals, containing 497 protein-coding genes. These genes were involved in developmental processes, metabolic processes, the response to external stimuli and other biological processes including digestion (ABCG5, ABCG8 and ADRB1), muscle development and growth (SMPD3, NELL1, and BICC1) and reduced immune function (CD86 and MTA3). Interestingly, we identified several genes with extremely strong selection signals associated with the loss of visual capability of domestic chickens relative to their wild ancestors. Amongst them, we propose that CTNND2 is involved in the evolutionary changes of domestic chickens toward reduced visual ability through the diopter system. VAT1 was also likely to contribute to these processes through its regulation of mitochondrial fusion. In summary, these data illustrate the patterns of genetic changes in Pengxian yellow chickens during domestication and provide valuable genetic resources that facilitate the utilization of chickens in agricultural production.