Introduction: The Huainan pig (HN) is known for its impressive litter size and exquisite meat quality. However, it also exhibits certain drawbacks such as excessive fat deposition, a relatively low percentage of lean meat percentage, and a slower growth rate. Crossbreeding with lean-type breeds, such as Large White, Landrace, and Berkshire can enhance offspring traits, and increase genetic diversity.Methods: In this study we employed RNA-seq technology to identify differentially expressed genes (DEGs) in subcutaneous adipose tissue (SAT) samples from HN pigs and their crosses with multiple breeds (with three replicates per group).Results: In the SAT of Huainan × Berkshire pigs (BH), Huainan × Yorkshire pigs (YH), and Huainan × Landrace pigs (LH), numerous key functional genes were identified, including LIPG, PLIN2, CPT1A, KLF9, CCND1, LDLR, ACSL1, ACLY and ANGPTL4. Functional enrichment analysis revealed that DEGs were primarily involved in several key pathways in BH, including the peroxisome proliferator-activated receptor (PPAR) signaling, metabolic pathways, arachidonic acid metabolism, and arginine/proline metabolism. Similarly, in LH, DEGs were associated with PPAR, cyclic adenosine monophosphate (cAMP) signaling, mitogen-activated protein kinase (MAPK), and the arginine/proline pathway. In contrast, the main pathways in YH were slightly different, including MAPK, fatty acid elongation, arginine/proline metabolism, and glycine/serine/threonine metabolism. Compared to HN, the differential genes in BH, LH, and YH showed a reduced fat deposition. However, in comparison, LH has a stronger subcutaneous fat deposition ability. Notably, LH exhibited a stronger tendency for subcutaneous fat deposition than the other two groups, while YH had the lowest fat deposition capacity.Conclusion: In conclusion, these findings offer valuable insights and provide a foundation for future research on the molecular mechanisms underlying fat deposition in pigs.

The HN pig, indigenous to Henan Province, is distinguished by its reduced lean meat yield and slower growth rates relative to commercial foreign breeds. To address these limitations, three hybrid combinations were generated through the crossbreeding of Huainan sows with Yorkshire, Landrace, and Berkshire sires. In this study, extensive transcriptomic and metabolomic analyses of the LD muscle were carried out for the first time, and carcass and meat quality characteristics were compared between hybrid and HN pigs. Slaughter and muscle quality assessments revealed that the lean meat percentage of LH and YH was significantly lower than that of HN, with YH exhibiting the lowest intramuscular fat level, indicating that this breed possesses enhanced lean meat production efficiency. Transcriptomic profiling revealed markedly increased expression of SLIT2, CH25H, NR4A2, NR4A1, FOSB, CRABP2, GDF10, and MRAP2 in all three hybrid groups compared to HN. Gene Ontology enrichment analysis identified that the skeletal muscle cell differentiation (GO:0035914) and transforming growth factor beta receptor signaling pathway (GO:0007179) were exclusively enriched in the YH vs. HN comparison. Non-targeted metabolomic analysis identified 31, 36, and 12 DAMs in BH vs. HN, LH vs. HN, and YH vs. HN comparisons, with pyruvate metabolism being the sole pathway common to all groups. An integrated multi-omics analysis revealed significant correlations between phytosphingosine levels and DEGs across all three comparisons. In summary, these results indicate that crossbreeding substantially improves lean meat yield in HN pigs while providing novel molecular insights into the underlying genetic and metabolic mechanisms.

To investigate the molecular mechanisms underlying muscle fiber development in different pig breeds and their impact on meat quality, this study collected the longissimus dorsi muscle of the indigenous Huainan pig and the commercial Large White pig at four developmental stages (0, 7, 14, and 21 days postnatal). Muscle fiber types were identified using myosin ATPase staining, while transcriptomics and non-targeted metabolomics were employed to analyze differences in gene expression and metabolite composition. The results showed that the Huainan pig had a higher proportion of oxidative muscle fibers, indicating superior aerobic metabolic capacity and meat quality. Transcriptome data identified 18 differentially expressed genes common to both pig breeds, including KLF4, NOS1, SH3KBP1, and TRARG1, which were upregulated in Huainan pigs to regulate muscle fiber type composition and meat quality by influencing mitochondrial function, nitric oxide synthesis, and glucose/lipid metabolism. Metabolomics analysis revealed significantly elevated levels of carnosine, citrulline, serine, and glycerol-3-phosphate in Huainan pigs, which are associated with metabolic pathways promoting muscle fiber transformation via enhancing energy supply, antioxidant capacity, and fatty acid oxidation. Notably, integrated transcriptome–metabolome analysis showed that oxidative metabolism genes (e.g., KLF4) and metabolites (e.g., citrulline) formed an AMPK-mediated ‘gene–metabolite’ loop in Huainan pigs, which synergistically promotes mitochondrial function and fiber differentiation. In summary, this study provides new insights into the molecular mechanisms underlying meat quality differences between pig breeds and offers a theoretical basis for the breeding and development of high-quality pork.