Multi-omics analysis reveals differences in altitude adaptation and meat quality across cattle, cattle-yak, and yak

1. The abundance of water-soluble small-molecule metabolites in YLT was the highest 2. YLT was enriched with inosine, while CLT contained a higher content of L -tyrosine 3. YLT showed strongest upregulation of AMPK/PPAR pathway genes (e.g., CPT1A ) 4. ECM-related genes were distinctly regulated, explaining the tenderness differences Cattle (distributed below 2000 meters), yaks (distributed above 3000 meters), and their hybrid offspring, cattle-yaks (distributed at 2500–3500 meters), inhabit distinct altitude gradients and exhibit unique environmental adaptations. This study compared the longissimus thoracis muscle of cattle (CLT), cattle-yak (CYLT), and yak (YLT) to evaluate meat quality differences and their molecular regulatory mechanisms under different altitude adaptation using transcriptomics and metabolomics. Results indicated that YLT had higher protein and mineral content, darker color, and lower tenderness than CLT, while CYLT exhibited intermediate traits. Metabolomics revealed that total metabolite abundance in YLT was 11.83% higher than in CLT and 4.98% higher than in CYLT. YLT exhibited higher abundances of umami amino acids and flavor nucleotides (e.g., alanine, inosine 5’-monophosphate), indicating a greater flavor potential. In contrast, CLT showed higher levels of functional amino acids, such as L -leucine. Transcriptomics suggested that yak and cattle-yak adapt to hypoxia by upregulating hypoxia-responsive genes (e.g., RYR2 ) and activating the AMPK/PPAR signaling pathway, enhancing muscle contractility, oxygen transport, and fatty acid oxidation. High expression of extracellular matrix-related genes was associated with the tougher texture of YLT. These findings provide a theoretical basis for meat quality differences in cattle at different altitudes.