Whole-genome analysis reveals distinct adaptation signatures to diverse environments in Chinese domestic pigs  

作　　者：Zhen Wang Bangmin Song Jianyu Yao Xingzheng Li Yan Zhang Zhonglin Tang Guoqiang Yi 

机构地区：[1]Shenzhen Branch,Guangdong Laboratory of Lingnan Modern Agriculture,Key Laboratory of Livestock and Poultry Multi‑Omics of MARA,Agricultural Genomics Institute at Shenzhen,Chinese Academy of Agricultural Sciences,Shenzhen 518124,China [2]Kunpeng Institute of Modern Agriculture at Foshan,Agricultural Genomics Institute at Shenzhen,Chinese Academy of Agricultural Sciences,Foshan 528226,China [3]School of Life Sciences,Henan University,Kaifeng 475004,China [4]Shenzhen Research Institute of Henan University,Shenzhen 518000,China [5]State Key Laboratory of Pharmaceutical Biotechnology,The University of Hong Kong,Hong Kong SAR,China [6]Key Laboratory of Tropical Animal Breeding and Disease Research,Institute of Animal Science and Veterinary Medicine,Hainan Academy of Agricultural Sciences,Haikou 571100,China [7]Bama Yao Autonomous County Rural Revitalization Research Institute,Bama 547500,China

出　　处：《Journal of Animal Science and Biotechnology》2024年第5期1866-1880,共15页畜牧与生物技术杂志（英文版）

基　　金：supported by the National Key Research and Development Program of China(2021YFF1000600);the National Natural Science Foundation of China(32002150 and U23A20229);the Basic and Applied Basic Research Foundation of Guangdong Province(2020B1515120053);the Shenzhen Science and Technology Innovation Commission(JCYJ20190813114401691);the Central Government Guiding Funds for Local Science and Technology Development of China(He-Ke ZY220603);the Open Project of Hainan Provincial Key Laboratory of Tropical Animal Reproduction&Breeding and Epidemic Disease Research(HKL2020101)。

摘　　要：Background Long-term natural and artificial selection has resulted in many genetic footprints within the genomes of pig breeds across distinct agroecological zones.Nevertheless,the mechanisms by which these signatures contribute to phenotypic diversity and facilitate environmental adaptation remain unclear.Results Here,we leveraged whole-genome sequencing data from 82 individuals from 6 domestic pig breeds originating in tropical,high-altitude,and frigid regions.Population genetic analysis suggested that habitat isolation significantly shaped the genetic diversity and contributed to population stratification in local Chinese pig breeds.Analysis of selection signals revealed regions under selection for adaptation in tropical(55.5 Mb),high-altitude(43.6 Mb),and frigid(17.72 Mb)regions.The potential functions of the selective sweep regions were linked to certain complex traits that might play critical roles in different geographic environments,including fat coverage in frigid environments and blood indicators in tropical and high-altitude environments.Candidate genes under selection were significantly enriched in biological pathways involved in environmental adaptation.These pathways included blood circulation,protein degradation,and inflammation for adaptation to tropical environments;heart and lung development,hypoxia response,and DNA damage repair for high-altitude adaptation;and thermogenesis,cold-induced vasodilation(CIVD),and the cell cycle for adaptation to frigid environments.By examining the chromatin state of the selection signatures,we identified the lung and ileum as two candidate functional tissues for environmental adaptation.Finally,we identified a mutation(chr1:G246,175,129A)in the cis-regulatory region of ABCA1 as a plausible promising variant for adaptation to tropical environments.Conclusions In this study,we conducted a genome-wide exploration of the genetic mechanisms underlying the adaptability of local Chinese pig breeds to tropical,high-altitude,and frigid environments.Our findings shed light

关 键 词：Environmental adaptation Local Chinese breeds PIG Population genetics Selection signals Whole-genome resequencing 

分 类 号：S828.2[农业科学—畜牧学]