Abstract
Tibetan pig is native to the Qinghai-Tibet Plateau and has adapted to the high-altitude environmental condition such as hypoxia. However, its origin and genetic mechanisms underlying high-altitude adaptation still remain controversial and enigmatic. Herein, we analyze 229 genomes of wild and domestic pigs from Eurasia, including 63 Tibetan pigs, and detect 49.6 million high-quality variants. Phylogenomic and structure analyses show that Tibetan pigs have a close relationship with low-land domestic pigs in China, implying a common domestication origin. Positively selected genes in Tibetan pigs involved in high-altitude physiology, such as hypoxia, cardiovascular systems, UV damage, DNA repair. Three of loci with strong signals of selection are associated with EPAS1, CYP4F2, and THSD7A genes, related to hypoxia and circulation. We validated four non-coding mutations nearby EPAS1 and CYP4F2 showing reduced transcriptional activity in Tibetan pigs. A high-frequency missense mutation is found in THSD7A (Lys561Arg) in Tibetan pigs. The selective sweeps in Tibetan pigs was found in association with selection against non-coding variants, indicating an important role of regulatory mutations in Tibetan pig evolution. This study is important in understanding the evolution of Tibetan pigs and advancing our knowledge on animal adaptation to high-altitude environments.
Highlights
The origin of Tibetan pigs is still under debate
We discovered that Tibetan pigs had a similar genetic structure with domestic pigs from northern group
Genome comparison between Tibetan pigs and low-land domestic pigs from northern group, unveiled signatures associated with high-altitude adaptation in Tibetan pig genomes
Summary
The origin of Tibetan pigs is still under debate. Earlier studies have proposed different origin models. The earliest study based on phylogenomic analysis of mitochondrial DNA (mtDNA) sequence variations in 567 domestic pigs (including 29 Tibetan pigs) and 155 wild boars across Asia conducted by Wu et al (2007) showed that majority of Tibetan pigs shared haplogroups with domestic pigs from Yangtze River and northern China[13]. Clarifying the relationship between Tibetan and other Chinese wild and domestic pigs will provide important information to guide the choice of research approach used to reveal genetic mechanism underlying high-altitude adaptation in Tibetan pigs. This study will provide useful information in resolving the origin and mechanism underlying high-altitude adaptation in Tibetan pigs and give signals on the importance of clear origin history before conducting evolutionary adaptation analysis of special population or species in the future study
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