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.

Pig growth is an economically important trait regulated by multiple genes and signaling pathways. To explore the molecular mechanisms underlying muscle growth, RNA sequencing was conducted to compare the transcriptomic profiles of the longissimus dorsi muscle between indigenous Liaoning Black pigs (CH) and commercial Duroc pigs (HD). Muscle samples from six CH (three males and three females) and six HD (three males and three females) pigs were analyzed. Functional annotation, Gene Ontology (GO) and KEGG enrichment, and protein–protein interaction (PPI) analyses were performed. Sequencing yielded 12 high-quality datasets (Q20 > 97%, Q30 > 93%). Comparative analysis identified 5051 DEGs in females (CHF vs. HDF; 2310 upregulated and 2681 downregulated) and 9972 DEGs in males (CHM vs. HDM; 4984 upregulated and 4988 downregulated). GO terms were mainly enriched in organonitrogen compound and protein metabolic processes, while KEGG pathways were enriched in focal adhesion and insulin signaling. PPI analysis highlighted hub genes ITGB1, SRC, MYL2, PRKACA, and MAPK3. qPCR validation showed strong agreement with RNA-seq data. These findings provide valuable insights into the molecular basis of divergent muscle growth between pig breeds.