Abstract

Simple SummaryTibetan sheep living on the Qinghai–Tibet Plateau have evolved strong adaptability to cold and low-oxygen environments, but the molecular mechanism by which their rumen epithelium copes with high-altitude stress remains unclear. This study aimed to reveal the adaptive regulatory mechanism using mRNA-miRNA transcriptome analysis. We identified many differentially expressed genes and microRNAs in the rumen epithelium of sheep at three altitudes. The results showed that with increasing altitude, Tibetan sheep enhance immune function and stress resistance by upregulating immune and heat shock genes, and maintain energy balance by adjusting metabolic pathways. Key miRNA-mRNA regulatory pairs were found to jointly control mitochondrial function and immune responses. These findings clarify the molecular mechanism of rumen epithelium adaptation to high altitude, providing a scientific basis for breeding livestock that can adapt well to plateau environments.The rumen epithelium of Tibetan sheep plays a critical role in energy metabolism and immune defense; however, its post-transcriptional regulatory mechanisms under high-altitude hypoxia stress remain unclear. In this study, we employed integrated mRNA and miRNA transcriptome sequencing to analyze the adaptive strategies of the rumen epithelium in Tibetan sheep at different altitudes. A total of 2183 differentially expressed genes (DEGs) and 135 differentially expressed miRNAs (DEmiRNAs) were identified. Functional enrichment analysis revealed that DEGs and their target genes were significantly enriched in immune-related pathways such as the NF-κB signaling pathway and cytokine–cytokine receptor interaction, as well as metabolic pathways including oxidative phosphorylation and branched-chain amino acid degradation. Integrated network analysis highlighted key regulatory pairs, includingoar-miR-370-3ptargetingPCK2andIL1R2, andnovel-miR-781regulatingPIK3R5, suggesting coordinated modulation between mitochondrial