Integrated ATAC-Seq and RNA-Seq Reveal Candidate Regulatory Genes and Chromatin Accessibility Associated with Intramuscular Fat Deposition: An Animal Trial in Hezuo Pigs.

Intramuscular fat content is a key determinant of pork quality, influencing traits such as tenderness, juiciness, and flavor. However, the molecular mechanisms regulating intramuscular fat deposition in indigenous pig breeds remain incompletely understood. This study aimed to identify genes and regulatory mechanisms associated with intramuscular fat accumulation in Hezuo pigs. Longissimus dorsi muscle samples from Hezuo pigs with extreme high and low intramuscular fat contents were subjected to chromatin accessibility profiling and transcriptome sequencing. Comparative analyses identified 2201 differentially accessible chromatin regions and 588 differentially expressed genes between the two groups. Functional enrichment analyses indicated that these genes were mainly involved in lipid metabolism, focal adhesion, extracellular matrix-receptor interaction, fatty acid metabolism, and adenosine monophosphate-activated protein kinase signaling. Integration of chromatin accessibility and gene expression datasets identified 92 co-regulated genes associated with intramuscular fat deposition, including MYLK3, PDGFC, PAK1, IGF1R, LAMA4, DIAPH1, SDC4, GADD45G, and RXRG. These findings reveal regulatory networks underlying intramuscular fat accumulation in Hezuo pigs and provide candidate genes and molecular resources for improving meat quality through genetic selection and breeding programs.