Short‑chain fatty acid-related metabolism may be an important factor affecting intramuscular fat deposition in the longissimus dorsi muscle of Min pigs: evidence from integrated multi‑omics analysis

Objective: Intramuscular fat (IMF) deposition is an important determinant of pork quality. Although Northeast Min (Min) pigs are characterized by high IMF content, its molecular basis remains unclear. This study investigated the molecular basis of differential IMF deposition between Min and Duroc × Landrace × Yorkshire (DLY) pigs through integrated multi-omics analysis of longissimus dorsi muscle. Methods: Six Min and six DLY pigs raised under identical conditions were compared at a similar body weight (~100 kg). Longissimus dorsi samples were used for IMF determination and untargeted metabolomics, and four pigs per group were randomly selected for matched transcriptomic and proteomic analyses. Results: Min pigs had significantly higher IMF content than DLY pigs (p < 0.0001), and C16:0 and C16:1 were also significantly higher (p < 0.05). Proteomic analysis identified 672 differentially abundant proteins (341 upregulated, 331 downregulated), mainly enriched in energy metabolism, fatty acid metabolism, and short-chain fatty acid (SCFA)-related metabolic processes. Seven candidate proteins were significantly upregulated in Min pigs (raw p ≤ 0.05 and |log2FC| ≥ log2(1.5)). Metabolomic analysis identified 509 differential accumulated metabolites (166 upregulated, 343 downregulated), lysophosphatidylcholines, lysophosphatidylethanolamines, and several short-chain acylcarnitines were significantly increased in Min pigs(p < 0.05). Integrated analysis identified the TCA cycle and pyruvate metabolism as key shared pathways, suggesting enhanced mitochondrial oxidative metabolism. The seven candidate proteins also showed concordant upregulation at transcript and protein levels. Conclusion: Efficient IMF deposition in Min pigs may be associated with altered SCFA-related metabolic processes, providing insights into pork fat trait improvement and differential fat deposition.