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

(1) Objectives: Understanding the genetic basis of muscle development and meat quality traits in divergent pig breeds is crucial for advancing precision breeding strategies. (2) Methods: This study investigated transcriptome differences in the <i>longissimus dorsi</i> muscle between Chinese Congjiang Xiang (CX) and Landrace (LAN) pigs. RNA sequencing was performed on muscle tissues from ten individuals of each breed, generating 874.5 million raw reads with an average mapping rate of 89.3% to the pig reference genome. (3) Results: Transcriptional profiling revealed distinct expression patterns with 785 genes exclusively expressed in CX pigs and 457 genes unique to LAN pigs, while 7099 co-expressed genes were shared by both breeds. Differential expression analysis identified 2459 significantly different genes (|log2FC| ≥ 1, adjusted <i>p</i>-value < 0.05), with 1745 up-regulated and 714 down-regulated in CX pigs. Among the most significantly up-regulated genes in CX pigs were flavor-associated genes (<i>ELOVL5/6</i>, <i>FASN</i>, <i>DGAT2</i>, <i>ALDH1A3</i>, <i>PPAR-γ</i>) with log2FC values ranging from 1.21 to 3.88. GO and KEGG pathway analyses revealed that up-regulated genes in CX pigs were significantly enriched in immune response pathways (adjusted <i>p</i>-value < 0.01), while down-regulated genes were primarily associated with myosin complex formation and <i>PPAR</i> signaling pathway. PPI network analysis identified <i>PPAR-γ</i> as a central hub gene with 16 direct interactions to other flavor-related genes. (4) Conclusions: These findings demonstrate that the superior meat flavor characteristics of indigenous Chinese pigs are driven by enhanced expression of lipid metabolism genes and distinctive immune-related pathways, providing specific molecular targets for breeding programs aimed at improving meat quality while maintaining production efficiency in commercial breeds.