Integrating Transcriptomics and Metabolomics to Elucidate the Molecular Mechanisms Underlying Beef Quality Variations

Elucidating the molecular mechanisms underlying beef quality differences is crucial for precision breeding of high-quality cattle. In this study, we first characterized the myofibrillar morphology of high-quality (H group) and low-quality (L group) beef samples using hematoxylin-eosin (HE) staining. Transcriptomic and metabolomic analyses were then conducted to reveal the molecular regulatory basis of quality variation. HE staining revealed highly significant differences in muscle fiber area and diameter between H and L groups (p < 0.01), along with significant differences in muscle fiber density (p < 0.05), but no significant differences in muscle fiber perimeter. Furthermore, by focusing on five core metabolic pathways shared across the transcriptome and metabolome datasets, 30 differentially expressed genes (DEGs) and 14 differentially accumulated metabolites (DAMs) were identified. Pearson correlation analysis revealed synergistic regulation between DEGs and DAMs: AMPD2 modulates umami flavor by regulating inosine accumulation via the purine metabolism pathway; ACOX3 promotes unsaturated fatty acid synthesis and intramuscular fat deposition through carbohydrate metabolism; genes in the glycolysis/gluconeogenesis pathway maintain post-slaughter muscle pH homeostasis, thereby influencing beef tenderness. Collectively, this study integrates morphological and molecular evidence to elucidate the multi-level basis of beef quality formation, providing key candidate genes, metabolites, and pathways for molecular breeding. These findings offer comprehensive theoretical and technical support for the sustainable development of the premium beef industry.