Abstract
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 contrib-ute 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 origi-nating in tropical,high-altitude,and frigid regions.Population genetic analysis suggested that habitat isolation signifi-cantly 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 identi-fied a mutation(chr1:G246,175,129A)in the cis-regulatory region of ABCA1 as a plausible promising variant for adap-tation 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 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.
基金项目
National Key Research and Development Program of China(2021YFF1000600)
National Natural Science Foundation of China(32002150)
National Natural Science Foundation of China(U23A20229)
Basic and Applied Basic Research Foundation of Guangdong Province(2020B1515120053)
Shenzhen science and Technology Innovation Commission(JCYJ20190813114401691)
Central Government Guiding Funds for Local Science and Technology Development of China(He-Ke ZY220603)
Open Project of Hainan Provincial Key Laboratory of Tropical Animal Reproduction & Breeding and Epidemic Disease Research(HKL2020101)
维普
万方数据