Yang Lijuan, Zhao Wei, Chen Siyu, Xue Lin, Tian Jinli, Xu Hairong, Zhang Haibo, Wang Hua, Gu Yaling, Zhang Juan
College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China.
Ningxia Ninety-Three-Zero Ecological Agriculture and Animal Husbandry Co., Yinchuan 750200, China.
Poult Sci. 2025 Aug 6;104(11):105666. doi: 10.1016/j.psj.2025.105666.
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.
为了探究静原鸡羽毛颜色的基本遗传结构，并探索羽毛颜色发育的遗传标记，本研究通过选择信号分析和全基因组关联分析，对调控静原鸡黑色、麻色和白色羽毛及羽毛性状的候选关键单核苷酸多态性（SNPs）和候选基因进行了研究。选择信号分析表明，静原鸡中分别有30、40和18个重叠基因与黑色、麻色和白色羽毛颜色相关。同时，综合基因组分析确定BCAT1、LMO3和PIK3C2G为黑色羽毛的主要候选基因，IL1RAPL1为白色羽毛的主要候选基因，所有基因在多种互补方法中均得到了一致支持。通过Fst和θπ值进一步筛选，确定了10个与羽毛颜色性状显著相关的关键候选基因，包括ARFGEF2、VPS37A、SNX12、KIT、MET、ROS1、CSF1R、NGF、CDC42和TEK。这些结果为静原鸡羽毛的遗传结构和形成提供了基础理论依据。
