Multi-omics analysis reveals signatures of selection and loci associated with complex traits in pigs

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 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.

show abstract

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

Wang,

Song,

Yao

et al. 2024

Preprint

Self Cite

View full text Add to dashboard Cite

Background:Long-term natural and artificial selection resulted in many genetic footprints within the genomes of pig breeds across distinct agroecological zones. Nevertheless, the mechanisms of how these signatures contribute to phenotypic diversity and facilitate environmental adaptation remain unclear. Results: Here, we leveraged whole-genome sequencing data of 82 individuals from six domestic pig breeds originating in tropical, frigid, and high-altitude regions. Population genetic analysis suggested that environmental adaptations significantly contributed to population stratification in Chinese local pig breeds. Analysis of selection signals identified regions under selection for tropical adaptation (55.5 Mb), high-altitude adaptation (43.6 Mb), and frigid adaptation (17.72 Mb). 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 the biological pathways involved in environmental adaptations. These pathways contained blood circulation, protein degradation, and inflammation for tropical adaptation; heart and lung development, hypoxia response, and DNA damage repair for high-altitude adaptation; andthermogenesis, cold-induced vasodilation (CIVD), and cell cycle for frigid adaptation. By examining the chromatin state of the selection signatures, we detected the lung and ileum as two critically functional tissues for environmental adaptations. Finally, we unveiled a mutation (chr1: G246,175,129A) in cis-regulatory regions of ABCA1 as a plausible promising variant for tropical adaptation. Conclusions: In this study, we conducted a genome-wide exploration of the genetic mechanisms underlying the tropical, frigid, and high-altitude adaptability of Chinese local pig breeds. Our findings shed light on the prominent role of cis-regulatory elements in impacting environmental adaptation in pigs and may serve as a vital biomodel on human plateau-related disorders and cardiovascular diseases.

show abstract

Multi-omics analysis reveals signatures of selection and loci associated with complex traits in pigs

Cited by 4 publications

References 101 publications

Dynamics of DNA methylation during osteogenic differentiation of porcine synovial membrane mesenchymal stem cells from two metabolically distinct breeds

Dynamics of DNA methylation during osteogenic differentiation of porcine synovial membrane mesenchymal stem cells from two metabolically distinct breeds

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

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

Contact Info

Product

Resources

About