Molecular Mechanisms Underlying Divergent Biochemical Compositions in Longissimus Dorsi of Huainan and Yunan Black Pigs: Insights from Fatty Acids, Amino Acids, and Transcriptomic Profiling

This study investigated meat quality, nutritional characteristics, and transcriptomic regulation in Yunan (YN) black pigs and Huainan (HN) black pigs (n = 6 each). Analysis of fatty acid composition revealed that HN black pigs possessed significantly higher levels of most fatty acids compared to YN black pigs. Notably, the contents of monounsaturated fatty acid C18:1n9c and polyunsaturated fatty acid C18:2n6c in HN black pigs were 1.94-fold and 2.65-fold higher, respectively, than those in YN black pigs. The α-linolenic acid content was also significantly elevated in HN black pigs, indicating an overall higher fatty acid content. Regarding amino acid differences, HN black pigs exhibited significantly higher levels of aspartic acid, glutamic acid, histidine, as well as superior composition of total amino acids, total umami amino acids, and essential amino acids, which contribute to enhanced flavor characteristics and nutritional balance. Transcriptome analysis identified 526 differentially expressed genes in HN vs. YN. KEGG enrichment analysis showed that these genes were involved in many adipogenesis and lipid metabolism signaling pathways, such as biosynthesis of unsaturated fatty acids, fatty acid elongation, apelin signaling pathway and lysine degradation. By integrating transcriptome and protein–protein interaction (PPI) network analyses, we identified key meat quality-related genes: ELOVL6, PRKAG3, ROCK2, and MYH11. miRNA profiling identified ssc-miR-133b, ssc-miR-206, and miR-205 as key regulators of meat quality. This study provides a valuable theoretical foundation for understanding the molecular mechanisms underlying pork quality and offers insights for its future improvement.