Peng Sucheng, Zhang Li, Ali Sadaqat, Lin Shudai, Liao Zengguang, Peng Qiaoqiao, Xie Panpan, Zhang Zihao
College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China.
College of Food Science and Engineering, Guangdong Ocean University, Zhanjiang 524088, China.
Poult Sci. 2025 Aug 13;104(11):105680. doi: 10.1016/j.psj.2025.105680.
Yuexi Frizzled Feather Chicken (YFC), an indigenous breed in China noted for its curly feathers, primarily comprises yellow, white, and black plumage color strains. However, the genetic mechanism underlying the regulation of plumage colors remains unknown. In this study, whole genome resequencing was employed to systematically analyze and evaluate the genetic diversity of these three distinctive plumage color strains, as well as to screen and identify crucial genes related to the plumage color. Population genetic structure analysis revealed that the YFC could be divided into 3 plumage color populations, with the yellow-feathered chickens showing the highest genetic diversity, whereas the black-feathered chickens exhibited the strongest signatures of artificial selection. Further, detection of selection signals through Fst, ROD, XPCLR indicated that 59 overlapping genes (including MC1R, CDH1, TCF25, and ZFHX3), 19 overlapping genes (including GRM5, TYR, CTSC, and RAB38), and 17 overlapping genes (including PTCH1, FBP1, and FBP2) were significantly associated with black, white, and yellow plumage color in YFC, respectively. GO annotation and KEGG pathway analysis indicated that the plumage color regulation primarily involved in cell adhesion and signal transduction, regulation and synthesis of melanin, and synthesis of biological molecules. Moreover, GWAS and Sanger sequencing revealed that the rs317806696 in the CDH1 gene was relevant to the black plumage color of YFC, while the rs317372610 and rs741501156 in the TYR gene was associated with the white plumage color. Hence, the objective of this study is to provide comprehensive genomic insights into the genetic diversity and plumage color regulation in YFC, which provide the foundation for protection of YFC genetic resources and selection of chicken breeding program for different plumage colors.
岳西卷羽鸡（YFC）是中国本土品种，以其卷曲的羽毛而闻名，主要包括黄色、白色和黑色羽色品系。然而，羽色调控的遗传机制尚不清楚。在本研究中，采用全基因组重测序系统分析和评估这三个独特羽色品系的遗传多样性，并筛选和鉴定与羽色相关的关键基因。群体遗传结构分析表明，YFC可分为3个羽色群体，黄羽鸡的遗传多样性最高，而黑羽鸡表现出最强的人工选择特征。此外，通过Fst、ROD、XPCLR检测选择信号表明，分别有59个重叠基因（包括MC1R、CDH1、TCF25和ZFHX3）、19个重叠基因（包括GRM5、TYR、CTSC和RAB38）和17个重叠基因（包括PTCH1、FBP1和FBP2）与YFC的黑、白、黄羽色显著相关。GO注释和KEGG通路分析表明，羽色调控主要涉及细胞黏附与信号转导、黑色素的调控与合成以及生物分子的合成。此外，GWAS和Sanger测序显示，CDH1基因中的rs317806696与YFC的黑羽色相关，而TYR基因中的rs317372610和rs741501156与白羽色相关。因此，本研究的目的是为YFC的遗传多样性和羽色调控提供全面的基因组见解，为YFC遗传资源的保护和不同羽色鸡育种计划的选择提供基础。
