College of Animal Science and Technology, Hunan Agricultural University, Changsha, China.
Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Meizhou, China.
PLoS One. 2020 Oct 23;15(10):e0241137. doi: 10.1371/journal.pone.0241137. eCollection 2020.
Wuhua yellow chicken (WHYC) is an important traditional yellow-feathered chicken from China, which is characterized by its white tail feathers, white flight feathers, and strong disease resistance. However, the genomic basis of these unique traits associated with WHYC is poorly understood. In this study, whole-genome resequencing was performed with an average coverage of 20.77-fold to investigate heritable variation and identify selection signals in WHYC. Reads were mapped onto the chicken reference genome (Galgal5) with a coverage of 85.95%. After quality control, 11,953,471 single nucleotide polymorphisms and 1,069,574 insertion/deletions were obtained. In addition, 41,408 structural variants and 33,278 copy number variants were found. Comparative genomic analysis of WHYC and other yellow-feathered chicken breeds showed that selected regions were enriched in genes involved in transport and catabolism, immune system, infectious diseases, signal transduction, and signaling molecules and interactions. Several genes associated with disease resistance were also identified, including IFNA, IFNB, CD86, IL18, IL11RA, VEGFC, and ATG10. Furthermore, our results suggest that PMEL and TYRP1 may contribute to the white feather coloring in WHYC. These findings can improve our understanding of the genetic characteristics of WHYC and may contribute to future breed improvement.
五华黄鸡（WHYC）是中国重要的传统黄色羽肉鸡，其特征是白色尾羽、白色飞羽和较强的抗病能力。然而，与 WHYC 相关的这些独特特征的基因组基础知之甚少。在这项研究中，进行了全基因组重测序，平均覆盖度为 20.77 倍，以研究 WHYC 的可遗传变异和鉴定选择信号。读取序列与鸡参考基因组（Galgal5）的覆盖度为 85.95%。经过质量控制，获得了 11,953,471 个单核苷酸多态性和 1,069,574 个插入/缺失。此外，还发现了 41,408 个结构变异和 33,278 个拷贝数变异。WHYC 与其他黄色羽肉鸡品种的比较基因组分析表明，选择区域富集了参与运输和分解代谢、免疫系统、传染病、信号转导以及信号分子和相互作用的基因。还鉴定出了几个与抗病性相关的基因，包括 IFNA、IFNB、CD86、IL18、IL11RA、VEGFC 和 ATG10。此外，我们的结果表明 PMEL 和 TYRP1 可能有助于 WHYC 的白色羽毛着色。这些发现可以提高我们对 WHYC 遗传特征的理解，并可能有助于未来的品种改良。
