Integrated analysis of transcriptome, metabolome, and lipidome revealed key genes associated with meat quality traits in pigs

With the improvement of people's living standards, public attention to pork quality has grown increasingly. This study aimed to identify the key genes affecting meat quality in pigs. Castrated Mashen (MS) pigs (n = 6) with an average body weight of 112.5 kg (300 days of age) and Duroc × (Landrace × Yorkshire) (DLY) pigs (n = 6) with an average body weight of 114.5 kg (165 days of age) were selected for slaughter. The longissimus dorsi muscle (LDM) was collected for meat quality traits determination and omics analyses. The results showed that MS pigs exhibited significantly superior meat color, intramuscular fat (IMF) content, marbling, shear force, and pH compared with DLY pigs (p < 0.05). A total of 1330 differentially expressed genes (DEGs), 94 differentially expressed lipids (DELs), and 185 differentially accumulated metabolites (DAMs) were screened between MS and DLY pigs (p < 0.05). Further weighted gene co-expression network analysis (WGCNA) revealed that glycerophospholipids (GP) and glycerolipids (GL) were key lipids affecting pork quality. Additionally, integration of lipidomic and metabolomic data identified "lipids-metabolites strong correlation pairs" influencing meat quality, such as the significant positive correlation between carnitine derivatives and various triglycerides (TG) (|r|> 0.8, p < 0.05). Furthermore, we conducted transcriptome-metabolome and transcriptome-lipidome correlation analyses based on expression abundance and functional annotations, and screened four key gene sets. Finally, after the intersection of these key genes, 19 core genes such as ALDOB, ASS1, CYP2A13, CYP2E1, DMGDH, PLCB1, and MAT1A may be related to pork quality. This study provides potential targets for further exploring the molecular mechanisms underlying pork quality by identifying several key genes linked to pork quality traits.