Data_Sheet_1_Genomic Analyses Reveal Adaptation to Hot Arid and Harsh Environments in Native Chickens of China.PDF

The acute thermal response has been extensively studied in commercial chickens because of the adverse effects of heat stress on poultry production worldwide. Here, we performed whole-genome resequencing of autochthonous Niya chicken breed native to the Taklimakan Desert region as well as of 11 native chicken breeds that are widely distributed and reared under native humid and temperate areas. We used combined statistical analysis to search for putative genes that might be related to the adaptation of hot arid and harsh environment in Niya chickens. We obtained a list of intersected candidate genes with log2 θπ ratio, FST and XP-CLR (including 123 regions of 21 chromosomes with the average length of 54.4 kb) involved in different molecular processes and pathways implied complex genetic mechanisms of adaptation of native chickens to hot arid and harsh environments. We identified several selective regions containing genes that were associated with the circulatory system and blood vessel development (BVES, SMYD1, IL18, PDGFRA, NRP1, and CORIN), related to central nervous system development (SIM2 and NALCN), related to apoptosis (CLPTM1L, APP, CRADD, and PARK2) responded to stimuli (AHR, ESRRG FAS, and UBE4B) and involved in fatty acid metabolism (FABP1). Our findings provided the genomic evidence of the complex genetic mechanisms of adaptation to hot arid and harsh environments in chickens. These results may improve our understanding of thermal, drought, and harsh environment acclimation in chickens and may serve as a valuable resource for developing new biotechnological tools to breed stress-tolerant chicken lines and or breeds in the future.

鉴于热应激对全球家禽生产的不利影响，商品鸡的急性热响应已得到广泛研究。本研究对塔克拉玛干沙漠地区土生土长的尼雅鸡品种，以及11个广泛分布于原生湿润和温带地区、在当地饲养的本土鸡品种进行了全基因组重测序（whole-genome resequencing）。本研究采用联合统计分析策略，筛选与尼雅鸡适应高温干旱严酷环境相关的候选基因。基于log2 θπ比值、FST与XP-CLR分析，本研究筛选得到一组交集候选基因，覆盖21条染色体上的123个区域（平均长度54.4 kb），涉及多种分子过程与通路，揭示了本土鸡适应高温干旱严酷环境的复杂遗传机制。本研究鉴定出多个受选择区域，其中的基因分别与循环系统及血管发育相关（BVES、SMYD1、IL18、PDGFRA、NRP1与CORIN）、中枢神经系统发育相关（SIM2与NALCN）、细胞凋亡相关（CLPTM1L、APP、CRADD与PARK2）、应激响应相关（AHR、ESRRG、FAS与UBE4B）以及脂肪酸代谢相关（FABP1）。本研究结果为鸡适应高温干旱严酷环境的复杂遗传机制提供了基因组学证据。上述结果有助于加深我们对鸡的热适应、干旱耐受及严酷环境驯化机制的理解，并可为未来开发培育抗应激鸡品系或品种的新型生物技术工具提供宝贵的参考资源。