DataSheet1_Genomic Analyses for Selective Signatures and Genes Involved in Hot Adaptation Among Indigenous Chickens From Different Tropical Climate Regions.docx

Climate change, especially weather extremes like extreme cold or extreme hot, is a major challenge for global livestock. One of the animal breeding goals for sustainable livestock production should be to breed animals with excellent climate adaptability. Indigenous livestock and poultry are well adapted to the local climate, and they are good resources to study the genetic footprints and mechanism of the resilience to weather extremes. In order to identify selection signatures and genes that might be involved in hot adaptation in indigenous chickens from different tropical climates, we conducted a genomic analysis of 65 indigenous chickens that inhabit different climates. Several important unique positively selected genes (PSGs) were identified for each local chicken group by the cross-population extended haplotype homozygosity (XP-EHH). These PSGs, verified by composite likelihood ratio, genetic differentiation index, nucleotide diversity, Tajima’s D, and decorrelated composite of multiple signals, are related to nerve regulation, vascular function, immune function, lipid metabolism, kidney development, and function, which are involved in thermoregulation and hot adaptation. However, one common PSG was detected for all three tropical groups of chickens via XP-EHH but was not confirmed by other five types of selective sweep analyses. These results suggest that the hot adaptability of indigenous chickens from different tropical climate regions has evolved in parallel by taking different pathways with different sets of genes. The results from our study have provided reasonable explanations and insights for the rapid adaptation of chickens to diverse tropical climates and provide practical values for poultry breeding.

气候变化，尤其是极寒、极热等极端天气，是全球畜禽养殖业面临的重大挑战。实现可持续畜禽生产的核心育种目标之一，应当是培育气候适应性优异的畜禽品种。本土畜禽对当地气候具有良好的适应能力，是研究极端天气耐受能力的遗传足迹与分子机制的优质研究资源。为筛选不同热带气候区本土鸡的热适应相关选择信号与功能基因，本研究对65只栖息于不同气候区域的本土鸡开展了基因组分析。通过跨群体扩展单倍型纯合性（cross-population extended haplotype homozygosity, XP-EHH）分析，各地方鸡类群均被鉴定出若干关键特异性正选择基因（positively selected genes, PSGs）。这些正选择基因经复合似然比、遗传分化指数、核苷酸多样性、塔伊马D值（Tajima’s D）及去多重信号复合关联分析验证，与神经调节、血管功能、免疫功能、脂质代谢、肾脏发育及功能密切相关，上述通路均参与体温调节与热适应过程。不过，通过XP-EHH分析在全部3个热带鸡群中检测到的1个共通正选择基因，未通过其余5种选择性清除分析的验证。本研究结果表明，不同热带气候区本土鸡的热适应能力通过不同基因集参与的不同通路实现了平行演化。本研究结果为鸡类快速适应多样热带气候的机制提供了合理解释与研究视角，同时为畜禽育种实践提供了实用参考价值。