Pangenome Reveals Gene Content Variations and Structural Variants Contributing to Pig Characteristics

Pigs are one of the most essential sources of high-quality proteins in human diets. Structural variants (SVs) are a major source of genetic variants associated with diverse traits and evolutionary events. However, the current linear reference genome of pigs restricts the accurate presentation of position information for SVs. In this study, we generated a pangenome of pigs and a genome variation map of 599 deeply sequenced genomes across Eurasia. Additionally, we established a section-wide gene repertoire, revealing that core genes are more evolutionarily conserved than variable genes. Furthermore, we identified 546,137 SVs, their enrichment regions, and relationships with genomic features and found significant divergence across Eurasian pigs. More importantly, the pangenome-detected SVs could complement heritability estimates and genome-wide association studies based only on single nucleotide polymorphisms. Among the SVs shaped by selection, we identified an insertion in the promoter region of the TBX19 gene, which may be related to the development, growth, and timidity traits of Asian pigs and may affect the gene expression. The constructed pig pangenome and the identified SVs in this study provide rich resources for future functional genomic research on pigs.