Integrated analysis of transcriptomic and proteomic profiles identifies divergent regulatory networks for intramuscular fat in Chinese versus Western Pigs

Intramuscular fat (IMF) content is a key determinant of pork quality. In this study, the Chinese indigenous Huai pig (a fat-type breed) and the Western Duroc pig (a lean-type breed) were selected to investigate the molecular mechanisms underlying IMF deposition. Proteomic analysis identified 91 differentially expressed proteins (DEPs) between the two breeds. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that several key lipid metabolism-related pathways were significantly enriched, including the Lipid metabolic process, AMPK signaling pathway, nicotinate and nicotinamide metabolism, and Fat digestion and absorption. Western blotting further confirmed the reliability of the proteomic results. Integrated transcriptomic and proteomic analyses highlighted significant enrichment of the PPAR signaling pathway, which plays a central role in lipid metabolism. These findings suggest that enhanced fatty-acid uptake contributes to increased lipid deposition in muscle tissue. Additionally, several potential candidate genes associated with IMF deposition were identified, including CD36, SCARB2, ACADVL, ACADSB, ACADM, UNC119B, PAS-4, and APOA1. Collectively, this study provides valuable insights into the molecular regulation of IMF deposition in pigs and offers a theoretical basis and genetic resources for improving pork quality and advancing molecular breeding.