Whole genome analyses reveal novel genes associated with chicken adaptation to tropical and frigid environments

作者：Shourong Shi, Dan Shao, Lingyun Yang, Qiqi Liang, Wei Han, Qian Xue, Liang Qu, Li Leng, Yishu Li, Xiaogang Zhao, Ping Dong, Muhammed Walugembe, Boniface B. Kayang, Amandus P. Muhairwa, Huaijun Zhou, Haibing Tong · 发表于：Journal of Advanced Research · 年份：2022 · DOI：10.1016/j.jare.2022.07.005 · 被引用次数：74 · 研究领域：Livestock and Poultry Management、Genetic and phenotypic traits in livestock、Animal Nutrition and Physiology

INTRODUCTION: Investigating the genetic footprints of historical temperature selection can get insights to the local adaptation and feasible influences of climate change on long-term population dynamics. OBJECT: Chicken is a significative species to study genetic adaptation on account of its similar domestication track related to human activity with the most diversified varieties. Yet, few studies have demonstrated the genetic signatures of its adaptation to naturally tropical and frigid environments. METHOD: Here, we generated whole genome resequencing of 119 domesticated chickens in China including the following breeds which are in order of breeding environmental temperature from more tropical to more frigid: Wenchang chicken (WCC), green-shell chicken (GSC), Tibetan chicken (TBC), and Lindian chicken (LDC). RESULTS: Our results showed WCC branched off earlier than LDC with an evident genetic admixture between WCC and LDC, suggesting their closer genetic relationship. Further comparative genomic analyses solute carrier family 33 member 1 (SLC33A1) and thyroid stimulating hormone receptor (TSHR) genes exhibited stronger signatures for positive selection in the genome of the more tropical WCC. Furthermore, genotype data from about 3,000 African local ecotypes confirmed that allele frequencies of single nucleotide polymorphisms (SNPs) in these 2 genes appeared strongly associated with tropical environment adaptation. In addition, the NADH:ubiquinone oxidoreductase subunit S4 (...