Multi-Omics Analysis Reveals Differences in Pork Quality and Skeletal Muscle Characteristics Between Tianfu Black and DLY Pigs

This study compared pork quality and muscle molecular profiles between Tianfu Black (TFB) and Duroc × (Landrace × Yorkshire) (DLY) pigs under a common-age finishing design. Forty-eight barrows (24 per group) were studied from 153 to 195 days of age; eight pigs per group contributed terminal measurements and six contributed each omics dataset. TFB pigs had lower drip loss, cooking loss, and shear force and higher intramuscular fat content, alongside higher oxidative MyHC markers. TFB also had lower serum triglyceride and total cholesterol concentrations despite greater fat deposition. DLY muscle had higher p-mTOR/mTOR and p-4EBP1/4EBP1 ratios. Transcriptomic analysis identified 989 differentially expressed genes, with 673 higher in TFB and 316 higher in DLY. Pathway-level analysis showed TFB enrichment of oxidative phosphorylation and protein export, and DLY enrichment of carbohydrate- and cholesterol-related pathways, cytoskeletal organization, and motor proteins. Metabolomic analysis identified 16 features that differed after multiple-testing correction, including putatively annotated 1-methylhistidine and N-acetyl-1-methylhistidine, both higher in TFB. Histidine metabolism was enriched in TFB after multiple-testing correction. CARNMT1 expression was also higher in TFB, placing a transcriptomic difference within the carnosine–anserine branch of histidine-related metabolism. Together, the muscle fiber, mitochondrial, and histidine-related profiles provide a molecular context for the observed pork quality differences.