Xu Nai-Yi, Liu Zhen-Yu, Yang Qi-Meng, Bian Pei-Pei, Li Ming, Zhao Xin
Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.
Department of Biology, University of Konstanz, Konstanz, Germany.
Front Genet. 2022 Jul 22;13:906447. doi: 10.3389/fgene.2022.906447. eCollection 2022.
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，尤其是极端寒冷或极端炎热等极端天气，是全球畜牧业面临的重大挑战。可持续畜牧业生产的动物育种目标之一应该是培育具有出色气候适应性的动物。本土畜禽对当地气候具有良好的适应性，是研究应对极端天气的遗传印记和机制的优质资源。为了识别可能参与不同热带气候地区本土鸡热适应的选择信号和基因，我们对栖息于不同气候环境的65只本土鸡进行了基因组分析。通过跨群体扩展单倍型纯合性（XP-EHH）为每个本地鸡群鉴定出了几个重要的独特正选择基因（PSG）。这些经复合似然比、遗传分化指数、核苷酸多样性、 Tajima's D以及多重信号去相关复合验证的PSG，与神经调节、血管功能、免疫功能、脂质代谢、肾脏发育和功能有关，这些都参与体温调节和热适应。然而，通过XP-EHH在所有三个热带鸡群中检测到了一个共同的PSG，但未得到其他五种选择扫描分析的证实。这些结果表明，来自不同热带气候区域的本土鸡的热适应性是通过不同的基因组合采取不同的途径平行进化的。我们的研究结果为鸡对不同热带气候的快速适应提供了合理的解释和见解，并为家禽育种提供了实用价值。
