Integrative Multi-Omics Analysis Reveals Germplasm Advantages and Candidate Mechanisms Underlying High Intramuscular Fat Deposition in Wuhuang Pigs

Intramuscular fat (IMF) content is a key indicator of pork eating quality. Wuhuang pigs, a fat-type local breed of Sichuan, exhibit high IMF, but the underlying mechanisms remain unclear. Here, Wuhuang and foreign-breed pigs were compared by integrated phenotypic, transcriptomic, metabolomic and 16S rRNA analyses. Crude fat reached 6.40%, 288% higher than in foreign breeds (p < 0.001), with lower dressing percentage, loin-eye area, lean percentage (p < 0.01) and smaller muscle fibers (p < 0.05). Transcriptomics identified 157 differentially expressed genes (DEGs), with core lipogenic genes (SCD, FASN, DGAT2, and SREBF1) upregulated; metabolomics identified 47 differential metabolites enriched in sphingolipids, fatty acids, acylcarnitines and bile acids. Integrated pathway analysis revealed co-directional gene–metabolite changes in common pathways and an SCD/FASN-centered association network. The gut Firmicutes/Bacteroidetes ratio was elevated (about 3.8 vs. 1.9), and 70 differential genera were enriched in short-chain-fatty-acid producers (e.g., Bifidobacterium, Streptococcus, and Lachnospiraceae) and bile-acid metabolizers (e.g., Parasutterella). High IMF may thus be associated with coordinated changes along the “gut microbiota–host metabolism–gene expression–fat deposition” axis, providing candidate genes, metabolites and microbial taxa that may help conserve this local breed and improve pork quality.