Heterosis-Based Identification of Candidate Genes Associated with Lipid Metabolism and Meat Quality in Crossbred Pigs

Heterosis or hybrid vigor is a well-recognized biological phenomenon, where crossbred progeny exhibit superior growth performance, stress tolerance, and productivity compared to their purebred parents. However, the molecular mechanisms underlying heterosis for meat quality traits in pigs remain poorly understood. In this study, we compared the longissimus dorsi muscle transcriptomes of Songliao Black Pig (SBP), Large White × Landrace pig (LWLDP), and their crossbred progeny (BXW) to uncover genetic mechanisms contributing to hybrid vigor in meat quality. Results identified 4290 differentially expressed genes (DEGs) in SBP vs. BXW and 3820 in LWLDP vs. BXW. Among these, 1358 genes displayed overdominant expression in BXW, indicating potential heterotic activation. Functional enrichment analysis identified key pathways involved in lipid metabolism, energy homeostasis, and muscle growth, including mTOR, AMPK, insulin, PI3K-Akt, MAPK, and calcium signaling. Over dominantly expressed genes such as <i>FASN</i>, <i>CPT1A</i>, <i>PPARG</i>, <i>ACACA</i>, <i>PPARA</i>, <i>SREBF1</i>, <i>FABP4</i>, <i>DGAT1</i>, <i>PPARGC1A</i>, <i>LIPC</i>, <i>ACSL5</i>, <i>PLCG2</i>, and members of the <i>COX family</i> were closely associated with intramuscular fat deposition, oxidative metabolism, and tenderness. Phenotypically, BXW exhibited improved meat color, moderate fat deposition, and lower shear force compared with parental breeds, clearly aligning with transcriptomic findings. These transcriptomic findings offer valuable insights into precision breeding strategies targeting superior meat quality through genomic selection and crossbreeding programs.