Integrative Multi-Omics Analysis Reveals Germplasm Advantages and Candidate Mechanisms Underlying High Intramuscular...

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.