Abstract
The genetic basis of complex traits and phenotypic differentiation remains unclear in pigs. Using nine genomes-seven of which were newly generated, high-quality de novo assembled genomes-and 1081 resequencing genomes, we built a pan-genome and identified 134.24 Mb nonredundant nonreference sequences, 1099 novel protein-coding genes, 187,927 structural variations (SVs) and 30,143,962 single-nucleotide polymorphisms (SNPs). Analysis of selective domestication revealed BRCA1 associated with enhanced adipocyte growth and fat deposition, and ABCA3 linked to an alleviated immune response and reduced lung injury. Integrating 162 transcriptomes and 162 methylomes of skeletal muscle across 27 developmental stages revealed the regulatory mechanism of phenotypic differentiation between Eastern and Western breeds. Artificial selection reshaped local DNA methylation status and imparted regulatory effects on the progression patterns of heterochronic genes such as GHSR and BDH1, particularly during embryonic development. Altogether, our work provides valuable resources for understanding molecular mechanisms behind phenotypic variations and enhancing the genetic improvement programs in pigs.