文献类型： 外文期刊

作者： Wang, Zhen ¹ ; Song, Bangmin ¹ ; Yao, Jianyu ⁵ ; Li, Xingzheng ¹ ; Zhang, Yan ⁶ ; Tang, Zhonglin ¹ ; Yi, Guoqiang ¹ ;

作者机构： 1.Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Key Lab Livestock & Poultry Multiom MARA, Shenzhen Branch,Guangdong Lab Lingnan Modern Agr, Shenzhen 518124, Peoples R China

2.Chinese Acad Agr Sci, Kunpeng Inst Modern Agr Foshan, Agr Genom Inst Shenzhen, Foshan 528226, Peoples R China

3.Henan Univ, Sch Life Sci, Kaifeng 475004, Peoples R China

4.Henan Univ, Shenzhen Res Inst, Shenzhen 518000, Peoples R China

5.Univ Hong Kong, State Key Lab Pharmaceut Biotechnol, Hong Kong, Peoples R China

6.Hainan Acad Agr Sci, Inst Anim Sci & Vet Med, Key Lab Trop Anim Breeding & Dis Res, Haikou 571100, Peoples R China

7.Bama Yao Autonomous Cty Rural Revitalizat Res Inst, Bama 547500, Peoples R China

关键词： Environmental adaptation; Local Chinese breeds; Pig; Population genetics; Selection signals; Whole-genome resequencing

期刊名称：JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY （ 影响因子：6.3； 五年影响因子：6.4 ）

ISSN： 1674-9782

年卷期： 2024 年 15 卷 1 期

页码：

收录情况： SCI

摘要： BackgroundLong-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.ResultsHere, 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.ConclusionsIn 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 on the prominent role of cis-regulatory elements in environmental adaptation in pigs and may serve as a valuable biological model of human plateau-related disorders and cardiovascular diseases.