Li Donghua, Sun Guirong, Zhang Meng, Cao Yanfang, Zhang Chenxi, Fu Yawei, Li Fang, Li Guoxi, Jiang Ruirui, Han Ruili, Li Zhuanjian, Wang Yanbin, Tian Yadong, Liu Xiaojun, Li Wenting, Kang Xiangtao
College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.
Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450046, China.
BMC Genomics. 2020 Jul 23;21(1):511. doi: 10.1186/s12864-020-06900-8.
Domesticated chickens have a wide variety of phenotypes, in contrast with their wild progenitors. Unlike other chicken breeds, Xichuan black-bone chickens have blue-shelled eggs, and black meat, beaks, skin, bones, and legs. The breeding history and the economically important traits of this breed have not yet been explored at the genomic level. We therefore used whole genome resequencing to analyze the breeding history of the Xichuan black-bone chickens and to identify genes responsible for its unique phenotype.
Principal component and population structure analysis showed that Xichuan black-bone chicken is in a distinct clade apart from eight other breeds. Linkage disequilibrium analysis showed that the selection intensity of Xichuan black-bone chickens is higher than for other chicken breeds. The estimated time of divergence between the Xichuan black-bone chickens and other breeds is 2.89 ka years ago. Fst analysis identified a selective sweep that contains genes related to melanogenesis. This region is probably associated with the black skin of the Xichuan black-bone chickens and may be the product of long-term artificial selection. A combined analysis of genomic and transcriptomic data suggests that the candidate gene related to the black-bone trait, EDN3, might interact with the upstream ncRNA LOC101747896 to generate black skin color during melanogenesis.
These findings help explain the unique genetic and phenotypic characteristics of Xichuan black-bone chickens, and provide basic research data for studying melanin deposition in animals.
与野生祖先相比，家养鸡具有各种各样的表型。与其他鸡品种不同，淅川黑鸡产蓝壳蛋，且肉、喙、皮肤、骨骼和腿部均为黑色。该品种的育种历史及其经济重要性状在基因组水平上尚未得到探索。因此，我们使用全基因组重测序来分析淅川黑鸡的育种历史，并鉴定导致其独特表型的基因。
主成分分析和群体结构分析表明，淅川黑鸡与其他八个品种处于不同的进化分支。连锁不平衡分析表明，淅川黑鸡的选择强度高于其他鸡品种。淅川黑鸡与其他品种之间的估计分化时间为2890年前。Fst分析确定了一个包含与黑色素生成相关基因的选择性清除区域。该区域可能与淅川黑鸡的黑皮肤有关，可能是长期人工选择的产物。基因组和转录组数据的联合分析表明，与黑骨性状相关的候选基因EDN3可能与上游非编码RNA LOC101747896相互作用，在黑色素生成过程中产生黑色皮肤颜色。
这些发现有助于解释淅川黑鸡独特的遗传和表型特征，并为研究动物黑色素沉积提供基础研究数据。
