# RNA Sequencing and Metabolomic Analyses Reveal Differences in Muscle Characteristics and Metabolic Profiles Between Purebred and Crossbred Huainan Pigs

## TL;DR

Crossbreeding improved lean meat yield in Huainan pigs, with RNA and metabolomic analyses revealing genetic and metabolic differences between purebred and hybrid pigs.

## Contribution

First-time transcriptomic and metabolomic profiling of crossbred Huainan pigs to identify molecular mechanisms behind improved meat quality.

## Key findings

- Crossbreeding increased lean meat yield and altered muscle characteristics in Huainan pigs.
- Transcriptomic analysis identified key genes like SLIT2 and NR4A2 upregulated in hybrids.
- Metabolomic profiling revealed 31-36 differentially accumulated metabolites and linked pyruvate metabolism to all hybrid comparisons.

## Abstract

This study aimed to enhance the low lean meat yield and slow growth rate of Huainan (HN) pigs through crossbreeding, resulting in three hybrid combinations (BH, LH, and YH) by mating HN pigs with Berkshire, Landrace, and Yorkshire pigs, respectively. Offspring were assessed for muscle characteristics, and the longissimus dorsi (LD) muscle underwent extensive transcriptomic and metabolomic evaluations. Evaluation of meat quality assessment indicated that all three crossbreeding strategies increased the proportion of lean meat in HN pigs. Integrated transcriptomic and metabolomic profiling disclosed significant disparities among the genetic groups and identified crucial differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs). These findings offer valuable insights for improving the meat quality of Huainan pigs and elevating the standard of derived products.

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.