RNA Sequencing and Metabolomic Analyses Reveal Differences in Muscle Characteristics and Metabolic Profiles Between Purebred and Crossbred Huainan 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 <i>SLIT2</i>, <i>CH25H</i>, <i>NR4A2</i>, <i>NR4A1</i>, <i>FOSB</i>, <i>CRABP2</i>, <i>GDF10</i>, and <i>MRAP2</i> 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.