Integrative analysis of genome and transcriptome reveals a novel regulator for pork intramuscular fat content

Pork is a primary source of animal protein worldwide, and intramuscular fat (IMF) content is a key determinant of meat quality and consumer preference. To identify genetic regulators of IMF content, we leveraged RNA sequencing and whole-genome resequencing data from 79 Laiwu pigs renowned for high IMF content to conduct expression quantitative trait locus (eQTL) mapping. We integrated eQTL results with genome-wide association study (GWAS) data from 453 Chinese Lulai Black pigs (a crossbreed of Laiwu and Yorkshire pigs), and systematically identified candidate regulatory genes for IMF content by incorporating weighted gene co-expression network analysis (WGCNA) and correlation analysis in this population.

We identified 9,763 cis-eQTLs at the genome-wide level (p < 5E-08) and 1,337 cis-eQTLs at the suggestive level (p < 5E-06). A 2.02 Mb cis-QTL region on Sus scrofa chromosome 9, containing 587 cis-eQTLs regulating MED17 expression, overlapped with an IMF-associated QTL detected by GWAS in Lulai Black pigs, a Laiwu-Yorkshire crossbreed. WGCNA identified three critical co-expression modules related to IMF content, with MED17 acting as a critical gene in a module linked to adipogenesis and lipid metabolism. Correlation analysis showed MED17 expression was negatively correlated with IMF content (FDR = 1.58E-02). In 3T3-L1 preadipocytes, adenovirus-mediated Med17 overexpression significantly reduced adipogenic differentiation and altered expression of adipogenesis-related genes (Pparg, Adipoq, Srebf1, Cpt1a, and Atgl), indicating that Med17 modulates adipocyte differentiation and lipid metabolism.

This study identifies MED17 as a novel regulator of IMF content in pigs, bridging genomic variation, gene expression networks, and phenotypic traits. These findings provide mechanistic insights into IMF deposition and highlight the potential of integrative multi-omics approaches for genetic improvement of pork quality traits in breeding programs.