Integrated transcriptomics and metabolomics reveal the molecular mechanisms of intramuscular fat deposition in Yanbian yellow cattle

Intramuscular fat (IMF) is a key determinant of beef sensory quality. In this study, 60 24-month-old Yanbian yellow cattle (n = 30 per group), reared under standardized environmental and dietary conditions, were categorized into high-IMF (HM) and low-IMF (LM) groups. HM beef exhibited significantly higher IMF (P < 0.05), increased monounsaturated fatty acids, and reduced saturated fatty acids compared to LM. Integrated transcriptomics and non-targeted metabolomics (n = 8 per group) revealed that IMF deposition is associated with a dual-layered regulatory framework: an upstream signaling layer (comprising PPAR, PI3K-Akt, and mTOR pathways) and a downstream metabolic execution layer (lysine degradation and cholesterol metabolism). Weighted Gene Co-expression Network Analysis (WGCNA) identified Acadm and Elovl6 as candidate hub genes within these networks. Furthermore, 9-hydroxyoctadecanoic acid (9-HODE) was identified as a differentially abundant metabolite; 100-ns molecular dynamics simulations suggested its high-affinity binding to the Thyrotropin-releasing hormone receptor (TRHR) receptor as a potential mechanism for lipid accumulation. These findings provide important biological insights and a mechanistic basis for understanding the molecular regulation of marbling in Yanbian yellow cattle.