Multi-omics integration elucidates molecular mechanisms underlying distinctive meat quality in Liping cattle versus Angus hybrid and Simmental breeds.

Liping cattle, an indigenous Chinese breed, may possess unique meat quality characteristics, yet systematic comparisons with commercial breeds remain limited. This study systematically compared nutritional composition, amino acids, fatty acids, volatile flavor-related substances of longissimus dorsi muscle among Liping cattle (LP), Angus hybrid cattle (AG) and Simmental cattle (XM), and further adopted untargeted metabolomics and transcriptome sequencing to reveal the molecular basis for excellent meat quality of LP cattle. Nutritional detection demonstrated LP beef possessed typical advantages of high crude protein, low crude fat and low cholesterol. LP cattle accumulated higher contents of most essential and non-essential amino acids, accompanied by elevated functional n-3 polyunsaturated fatty acids and lower harmful trans fatty acids, which endows LP beef superior nutritional value and healthy fatty acid profile. Untargeted metabolomics identified numerous differential metabolites between LP and the two control breeds. Shared differential metabolites in LP cattle were mainly enriched in fructose and mannose metabolism, ferroptosis and carbohydrate metabolism pathways; characteristic metabolites related to nutrition, flavor and antioxidant capacity were significantly accumulated in LP muscle. Transcriptome screening uncovered a series of core differentially expressed genes. Consistently upregulated genes including MYH3, MSTN and PAX3 participated in skeletal muscle development, myofibril construction and lipid metabolism, while downregulated genes were mainly involved in inflammation and cell adhesion processes. Transcriptome-metabolome integrated analysis confirmed strong coordinated positive regulation between differential genes and metabolites. Fructose and mannose metabolism was identified as the shared critical pathway participating in forming the unique flavor traits of LP beef. In conclusion, the distinctive nutrient profile, abundant flavor precursors and coordinated transcription-metabolite regulation jointly shape the superior meat quality of LP cattle.