Abstract
BackgroundMeishan is a pig breed indigenous to China and famous for its high fecundity. The traits of Meishan are strongly associated with its distinct evolutionary history and domestication. However, the genomic evidence linking the domestication of Meishan pigs with its unique features is still poorly understood. The goal of this study is to investigate the genomic signatures and evolutionary evidence related to the phenotypic traits of Meishan via large-scale sequencing.ResultsWe found that the unique domestication of Meishan pigs occurred in the Taihu Basin area between the Majiabang and Liangzhu Cultures, during which 300 protein-coding genes have underwent positive selection. Notably, enrichment of the FoxO signaling pathway with significant enrichment signal and the harbored gene IGF1R were likely associated with the high fertility of Meishan pigs. Moreover, NFKB1 exhibited strong selective sweep signals and positively participated in hyaluronan biosynthesis as the key gene of NF-kB signaling, which may have resulted in the wrinkled skin and face of Meishan pigs. Particularly, three population-specific synonymous single-nucleotide variants occurred in PYROXD1, MC1R, and FAM83G genes; the T305C substitution in the MCIR gene explained the black coat of the Meishan pigs well. In addition, the shared haplotypes between Meishan and Duroc breeds confirmed the previous Asian-derived introgression and demonstrated the specific contribution of Meishan pigs.ConclusionsThese findings will help us explain the unique genetic and phenotypic characteristics of Meishan pigs and offer a plausible method for their utilization of Meishan pigs as valuable genetic resources in pig breeding and as an animal model for human wrinkled skin disease research.
Highlights
Meishan is a pig breed indigenous to China and famous for its high fecundity
Three population-specific synonymous single-nucleotide variants occurred in PYROXD1, Melanocortin 1 receptor (MC1R), and FAM83G genes; the T305C substitution in the MCIR gene explained the black coat of the Meishan pigs well
To detect genome-wide variation in Meishan pig breeds, we performed whole-genome resequencing of 32 unrelated Meishan pigs aligned against the Sus scrofa 10.2 reference genome using the Burrows-Wheeler Alignment tool (BWA) [14]; this generated a total of 732.76 Gb of sequence data with > 8× mapped read depth on average (Table S1)
Summary
Meishan is a pig breed indigenous to China and famous for its high fecundity. The traits of Meishan are strongly associated with its distinct evolutionary history and domestication. The comparison of the Duroc pig (Sus scrofa) genome with wholegenome sequences from different pig populations provides a favorable opportunity to trace the history of pig domestication and to exploit evidence of long-term gene flow and artificial selection [1]. Previous studies demonstrated that the distinct phenotypic characteristics between European and Asian pig breeds were due to the independent domestication of local wild boar populations in Asia and Europe. After the split between European and Asian pigs, the gene flow between Eurasian wild and domestic pig genomes, and human-mediated introgression have affected breed haplotypes [6, 7]. Artificial selection affected behavior and morphology and led to different domestic traits in European and Asian pigs [6, 8, 9]
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