Integrative analysis of GWAS, epigenomic, and 3D genomic reveals the genetic architecture of body mass index in pigs

Body mass index (BMI) is an important composite trait reflecting fat and muscle deposition, which is closely related to feed efficiency, carcass composition, and overall production performance in pigs. Optimizing BMI is crucial for achieving balanced growth and desirable meat quality in modern pig breeding programs. While numerous genetic loci associated with BMI have been reported in humans, studies in livestock remain scarce, and the genetic and regulatory mechanisms driving BMI variation are still largely unknown. To address this, we conducted genome-wide association study on 4,519 pigs representing three commercial breeds (Yorkshire, Landrace, and Duroc), performing analyses both at the single-breed level and in the combined population. By integrating Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq), Chromatin Immunoprecipitation followed by Sequencing (ChIP-seq), and in situ Hi-C followed by chromatin immunoprecipitation (HiChIP) datasets for functional genomics analyses, we identified five quantitative trait loci with potential regulatory function, two of which are homologous to enhancer regions in the human genome. We further prioritized a set of high-confidence candidate genes, including OSBPL10, PCCA, MYPN, PAWR, and PCDH7, which are closely associated with lipid metabolism and muscle development. These findings reflect breed differences in body composition, provide targets for improving meat production efficiency through breeding, and offer insights into the genetic and regulatory mechanisms underlying human metabolic disorders.