Multi-omics reveals molecular basis of beef quality differences between Qinchuan and Nanyang cattle

Beef quality traits, such as intramuscular fat deposition, water-holding capacity, and tenderness, vary among breeds, yet their molecular basis remains unclear. In this study, we hypothesized that the regulation of muscle energy metabolism and lipid deposition is associated with differences in beef quality between Qinchuan and Nanyang cattle. To this end, we measured meat quality traits in the longissimus dorsi muscle of females from the two breeds ( n = 5 per group) and conducted integrative analyses using transcriptomic, proteomic, and metabolomic data. The results showed that Qinchuan cattle exhibited higher intramuscular fat content, marbling scores, and better tenderness and water-holding capacity. Multi-omics analysis identified 1011 differentially expressed genes, 895 differentially expressed proteins, and 12 differential metabolites, with some molecules showing consistent changes at both the transcriptional and protein levels. Pathway analysis revealed that glycolysis and energy metabolism pathways were enhanced in Nanyang cattle, whereas the PPAR signaling pathway was activated in Qinchuan cattle. Correlation network analysis indicated that energy metabolism-related molecules were positively correlated with shear force and water loss, while PPAR signaling pathway-related molecules were positively correlated with intramuscular fat content and marbling scores. l -serine was associated with PPAR-related molecules and intramuscular fat content, and promoted adipogenic differentiation of intramuscular preadipocytes in vitro by upregulating PPAR-related genes. This study reveals that the regulation of energy metabolism and lipid deposition is associated with breed-specific differences in meat quality, providing candidate molecular targets and metabolic biomarkers for improving meat quality in local cattle breeds. • Qinchuan cattle showed higher marbling, IMF, and tenderness than Nanyang cattle. • Multi-omics revealed lower glycolysis and higher lipid metabolism in Qinchuan beef. • Integrated networks connected energy metabolism, fat deposition, and meat quality traits. • PPAR signaling genes and proteins were upregulated and linked to superior beef quality. • l -serine was identified as a candidate metabolite promoting intramuscular adipogenesis.