High-Altitude Adaptation: Breed-Specific Variations in Meat Quality of Ruminants from Different Elevations

To compare the effects of altitude and breed on the meat quality of ruminants, this study selected high-altitude yaks (HNA) and low-altitude yellow cattle (MNA) as research subjects and conducted an analysis by combining 16S rRNA sequencing and muscle transcriptome. The results showed that a total of 2,524 differentially expressed genes (DEGs) were screened out, among which 1,220 were up-regulated and 1,304 were down-regulated. KEGG significantly enriched pathways indicated that ECM-receptor interaction, HIF-1 signaling pathway, PI3K-Akt signaling pathway, and Pentose phosphate pathway were significantly up-regulated (P < 0.05), while Adrenergic signaling in cardiomyocytes and Motor proteins were significantly down-regulated (P < 0.05), suggesting that these pathways affect meat color, tenderness, and flavor by regulating lipid deposition, muscle fiber transformation, or energy metabolism. Microbial community analysis showed that the two groups' main dominant phyla were Bacteroidota and Firmicutes, and the dominant genus was Prevotell. At the genus level, three significantly different species were identified (P < 0.05), with Acetitomaculum and Achromobacter up-regulated in the HNA group and Olsenella up-regulated in the MNA group. Correlation analysis showed that Acetitomaculum was extremely significantly negatively correlated with PLPP2 (P < 0.01) and significantly positively correlated with LPIN1 (P < 0.05); Olsenella was extremely significantly negatively correlated with VEGFA (P < 0.01) and extremely significantly positively correlated with SCD5 and FADS2 (P < 0.01). Among them, Acetitomaculum and Olsenella promoted intramuscular fat deposition, thereby suggesting that the meat quality could be affected by regulating intramuscular fat deposition-related genes. In conclusion, this study integrated the microbiome and muscle transcriptome to reveal the molecular basis of the interaction between altitude and breed in shaping meat quality, laying a theoretical foundation for related mechanism research.