Abstract
Intramuscular fat (IMF) is a critical indicator of meat quality. Jingyuan chicken, a local breed in China, is highly valued by consumers for its superior meat quality. However, the molecular mechanisms that govern IMF deposition in Jingyuan chickens remain inadequately understood. In this study, we conducted transcriptomic, non-targeted metabolomic, and lipidomic analyses of the breast muscles from 42- to 180-d-old Jingyuan chickens to investigate the molecular mechanisms involved in IMF deposition. To identify key genes, metabolites, and lipids associated with IMF, we performed weighted gene co-expression network analysis (WGCNA) and statistical analyses using linear models. The significance of the associations was assessed using a threshold of P < 0.001, which was determined through a multiple test correction method. From the transcriptomic data, we identified 13 co-expression modules, with the green and yellow modules demonstrating significant associations with IMF (P < 0.001). Further analysis revealed 67 hub genes that were notably linked to IMF. The metabolomic analysis identified 36 co-expression modules, among which the magenta and cyan modules were significantly associated with IMF (P < 0.001). The 8 key metabolites related to IMF deposition were identified within these modules. In the lipidomic analysis, co-expressed lipids were classified into 24 modules. The green and blue modules exhibited significant correlations with IMF, and 28 key lipids within these modules were enriched in pathways related to glycerolipid metabolism, thermogenesis, and arachidonic acid metabolism (P < 0.001). Correlation analysis indicated that TNS1, FKBP1B, and HACD1 are pivotal functional genes regulating IMF deposition. HACD1 is involved in the elongation of very long-chain fatty acids (VLCFA), which are involved in various biological processes as precursors. To validate the gene function of HACD1, we performed RNA interference to silence HACD1 expression. We found by two-tailed t-test analysis that silencing HACD1 expression led to a significant reduction in the expression of adipose synthesis marker genes, and cell proliferation of adipocyte precursors was inhibited, thereby suppressing the accumulation of lipid droplets (P < 0.05).