Abstract
Simple SummaryWhole-genome re-sequencing data from 10 geographically isolated Tibetan pig populations were collected and analyzed in this study. Population genetic analyses, including Principal Component Analysis (PCA), phylogenic tree, genetic differentiation, deleterious variant, contribution to meta-population genetic diversity and selective sweep were performed. Limited genetic differentiation was identified among these Tibetan pig populations. Most deleterious variants were low-frequency mutations and population specific. Contribution to the meta-population was largest in the TT population, based on gene and allelic diversity. Genes under selection were involved in hypoxia adaptation, hard palate development, facial appearance, and perception of smell. Several geographically isolated populations of Tibetan pigs inhabit the high-altitude environment of the Tibetan Plateau. Their genetic relationships, contribution to the pool of genetic diversity, and their origin of domestication are unclear. In this study, whole-genome re-sequencing data from 10 geographically isolated Tibetan pig populations were collected and analyzed. Population genetic analyses revealed limited genetic differentiation among the Tibetan pig populations. Evidence from deleterious variant analysis indicated that population-specific deleterious variants were the major component of all mutational loci. Contribution to the meta-population was largest in the TT (Qinghai-Tibet Plateau) population, based on gene diversity or allelic diversity. Selective sweep analysis revealed numerous genes, including RXFP1, FZD1, OR1F1, TBX19, MSTN, ESR1, MC1R, HIF3A, and EGLN2 which are involved in lung development, hard palate development, coat color, hormone metabolism, facial appearance, and perception of smell. These findings increase our understanding of the origins and domestication of the Tibetan pig, and help optimize the strategy for their conservation.
Highlights
Tibetan pigs originated on the Tibetan Plateau, and the record of their breeding by humans can be traced back to the 7th century [1]
Results from SNP-chip data showed that the Tibetan pig was a domestic indigenous pig living on the Tibetan plateau and underwent genetic differentiation among three populations [4]
Gene and allelic diversity of each Tibetan pig population was calculated to identify their contributions to the population pool
Summary
Tibetan pigs originated on the Tibetan Plateau, and the record of their breeding by humans can be traced back to the 7th century [1]. Tibetan pigs are adapted to hypoxia, and a low temperature, low-pressure environment due to long-term natural selection [2,3,4,5]. Considerable research has focused on their origins, physiological features, and adaptation to their high-altitude environment. MtDNA evidence has revealed the origin centers of the Tibetan pig [6], and nuclear genome analysis has shown that the Tibetan pigs originated exclusively on the Tibetan plateau and survived in a wild state [7]. Considerable research has focused on their origins, physiological features, and adaptation to their high-altitude environment. mtDNA evidence has revealed the origin centers of the Tibetan pig [6], and nuclear genome analysis has shown that the Tibetan pigs originated exclusively on the Tibetan plateau and survived in a wild state [7].
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