Genomic and Phenotypic Consequences of Bi-Directional Introgression Between Chinese and European Pig Breeds

Abstract

Historically, Chinese indigenous pigs were introduced to Europe centuries ago with the aim of enhancing economically important traits in European breeds. In recent decades, there has been a reciprocal introduction of European commercial breeds to China for indigenous pig breeding. Our study investigated the genomes of 418 pigs, revealing a genomics landscape of bi-directional introgression patterns between Chinese and European pig populations. We noted a common occurrence of incomplete linkage disequilibrium between structural variations (SVs) and adjacent single-nucleotide polymorphisms (SNPs) in our population, suggesting that conventional SNP-based analyses might not adequately capture the effect of SVs. Therefore, we examine both the roles of population-level SNPs and SVs in bi-directional introgression patterns, and highlight a show case centered around theBMP2gene. We identified introgressed haplotypes and SVs originating from Southern Chinese indigenous pigs, dispersing widely across various European pig breeds. Concurrently, we noted that the introgressed European haplotypes and SVs have attained high frequencies in Northern Chinese indigenous breeds, likely contributing to improvements in body size. In summary, these findings underscore the significant role of introgression in shaping the genetic composition and phenotypic traits in modern pig breeds.