Multi-omics insights into the regulation of yak longissimus dorsi muscle by dietary energy levels

Adipose deposition is a key determinant of meat quality and energy storage in yaks, bearing significant implications for livestock productivity in high-altitude regions. The yak ( Bos grunniens ), a distinctive cattle breed indigenous to the Qinghai–Tibet Plateau, is widely recognized for its remarkable adaptability to energy fluctuations. However, the molecular mechanisms by which dietary energy levels regulate muscle physiology and metabolism remain poorly understood. In this study, yaks were assigned to low-energy, medium-energy, and high-energy groups according to dietary composition and nutritional levels. Transcriptomic and metabolomic analyses were conducted to identify differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs), followed by KEGG enrichment analysis to construct relevant network interaction diagrams. Integrated transcriptome–metabolome analysis revealed that the DEGs and DAMs were significantly enriched in the mTOR signaling pathway, ABC transporters, central carbon metabolism in cancer, aminoacyl-tRNA biosynthesis, mineral absorption, biosynthesis of amino acids, glutathione metabolism, and 2-oxoglutarate metabolism pathways. Six DAMs were identified: L-ornithine, L-methionine, L-histidine, 3-methyl-L-histidine, L-isoleucine, and L-leucine. In the low‑energy versus high‑energy comparison, L‑isoleucine and L‑leucine showed correlative patterns related to fat deposition, with WARS identified as a candidate gene from multi‑omics correlation analysis. In the low‑energy versus medium‑energy comparison, L‑ornithine exhibited correlative patterns related to fat deposition, with GPX1 as a candidate hub gene. In the medium‑energy versus high‑energy comparison, correlative patterns of L‑ornithine and glycine were observed, with *ODC1*, *DOT1L*, and *AGT* proposed as candidate hub genes. Weighted gene co-expression network analysis (WGCNA) of the transcriptomic data, using the six DAMs as phenotypic traits, identified gene modules highly correlated with these metabolites. Corresponding enrichment analysis indicated that genes related to the metabolism of L-ornithine, L-methionine, L-histidine, L-isoleucine, and L-leucine were predominantly enriched in Gene Ontology terms such as cellular process, single-organism process, cell, cell part, binding, and catalytic activity. Pathways significantly enriched in relation to fat deposition included the PPAR signaling pathway, PI3K-Akt signaling pathway, and glycerolipid metabolism. Functional annotation suggested that CEBPA, GSK3B, CDKN1B, LPL, GPAT1/2, and FOS represent candidate genes potentially linked to adipogenesis based on existing literature; their actual biological functions in yak muscle require experimental validation. In conclusion, the significantly differentially expressed genes and metabolites show correlative patterns within the aforementioned metabolic pathways and represent promising candidate molecules for further investigation of muscle fat deposition in yaks.