Whole genome resequencing reveals genetic markers for plumage colour in Jingyuan Chicken.

In order to investigate the basic genetic structure of plumage colour in Jingyuan chicken and to explore the genetic markers for plumage colour development, the present study was carried out to investigate the candidate key SNPs and candidate genes regulating black, linen and white plumage and plumage traits of Jingyuan chicken by using selection signal analysis and genome-wide association analysis. Selection signal analyses showed that including 30, 40 and 18 overlapping genes were associated with black, linen and white plumage colours in Jingyuan chicken. Meanwhile, integrative genomic analyses identified BCAT1, LMO3, and PIK3C2G as primary candidates for black plumage, and IL1RAPL1 for white plumage, with all genes showing convergent support across multiple complementary approaches. Further screening through Fst and θπ values identified 10 key candidate genes significantly associated with plumage colour traits, including ARFGEF2, VPS37A, SNX12, KIT, MET, ROS1, CSF1R, NGF, CDC42, and TEK. These results provide a fundamental theoretical basis for the genetic structure and formation of Jingyuan chicken plumage.