Multi-Omics Integration Reveals Molecular Signatures Associated with Pork Quality Differences Between Liaodan Black and Xinjin Pigs

This exploratory study investigated meat quality differences and associated molecular characteristics between Liaodan Black (LDM) and Xinjin (XJM) pigs, two local breeds from Northeast China, using meat quality, fatty acid, and total amino acid measurements together with transcriptomic, proteomic, and untargeted metabolomic analyses of the longissimus thoracis et lumborum muscle (n = 3 per breed for all analyses). XJM pigs had higher intramuscular fat content and lower shear force, whereas LDM pigs had higher cooking yield. After correction for multiple testing, XJM pigs had higher oleic acid content. Total amino acid analysis showed higher serine, arginine, proline, methionine, and phenylalanine contents in XJM pigs, whereas isoleucine and leucine contents were higher in LDM pigs. Transcriptomic and proteomic analyses identified 5678 differentially expressed genes and 533 differentially abundant proteins, respectively, while untargeted metabolomic analysis revealed 622 differential metabolites based on putative annotations. These molecular differences were mainly associated with cytoskeletal organization, oxidative phosphorylation, protein turnover, amino acid metabolism, and central carbon metabolism. Transcriptome–proteome integration identified 258 shared differential features, of which 139 showed concordant changes at the mRNA and protein levels. Integrated analysis identified nine candidate molecules. After Benjamini–Hochberg correction, exploratory correlation analysis showed that GOT1 and GLO1 protein abundances were negatively associated with shear force and cooking yield, whereas ESD protein abundance was positively associated with IMF content. qPCR analysis of selected DEGs showed good agreement with RNA-seq results (r = 0.883, p < 0.001). Overall, the differences observed between the sampled LDM and XJM groups were mainly associated with lipid deposition, muscle structure-related processes, and energy metabolism.