Transcriptome Profiling Reveals Genetic Basis of Muscle Development and Meat Quality Traits in Chinese Congjiang Xiang and Landrace Pigs

Understanding the genetic basis of muscle development and meat quality traits in divergent pig breeds is crucial for advancing precision breeding strategies. This study aimed to investigate transcriptome differences in the longissimus dorsi muscle between Chinese Congjiang Xiang (CX) and Landrace (LAN) pigs. RNA sequencing was performed on muscle tissues from ten individuals of each breed, with an average mapping rate of 89.3% to the pig reference genome. Transcriptional profiling revealed 785 genes exclusively expressed in CX pigs and 457 genes unique to LAN pigs, with 7,099 co-expressed genes shared by both breeds. Principal component analysis demonstrated clear separation between the breeds. Differential expression analysis identified 2,459 differentially expressed genes, with 1,745 up-regulated and 714 down-regulated in CX pigs. Notably, genes associated with meat flavor formation (ELOVL5/6, FASN, DGAT2, ALDH1A3, PPAR-γ) were significantly up-regulated in CX pigs. Functional enrichment analysis showed that up-regulated genes in CX pigs were primarily enriched in immune responses, while down-regulated genes were associated with myosin complex and PPAR signaling pathway. These findings provide novel insights into the molecular mechanisms underlying the distinctive meat characteristics of indigenous Chinese and commercial European pig breeds, offering valuable genetic resources for future breeding programs aimed at enhancing pork quality.