Differential gene expression drives muscle metabolic and structural differences in Liang Guang small spotted vs. large white pigs

Abstract

The Liang Guang Small Spotted (LGSS) pigs, an indigenous Chinese breed, are reported to exhibit desirable muscle attributes such as high intramuscular fat deposition, smaller muscle fiber diameter, and superior water-holding capacity. However, despite these merits, its commercial utility is constrained by suboptimal growth rates and diminished carcass yield. To explore transcriptomic differences potentially associated with distinct muscle phenotypes and identify targets for productivity enhancement, we performed integrated transcriptomic analysis of longissimus dorsi muscles (LDMs) from LGSS and Large White (LW) pigs. We characterized differentially expressed (DE) mRNAs, long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs), which were primarily enriched in key biological processes including glycolysis and carbon metabolism, structural organization, as well as signaling cascades such as HIF-1, AMPK, and PI3K-Akt. This study uncovers significant transcriptomic distinctions and identifies candidate regulatory molecules in LGSS pigs, offering potential biomarkers and a framework for future functional studies aimed at genetic improvement.

Keywords: Liang Guang Small Spotted pigs; Longissimus dorsi muscle; Pig; RNA sequencing; Whole-transcriptome sequencing.

Fig. 1

Gene expression profiles for LGSS and LW pigs. (A) Pearson correlation coefficient between all samples. (B) Principal component analysis (PCA) of all samples. (C) Differentially expressed (DE) genes between LGSS and LW samples. Volcano plots displaying the DE mRNAs (D) and known lncRNAs (E) for LGSS and LW samples.

Fig. 2

GO and KEGG enrichment analyses of DE mRNA for LGSS and LW pigs. (A) Bar plot of GO terms enriched using DE mRNAs. Only the top 10 terms are displayed. MF: molecular functions. CC: cellular components. BP: biological processes. (B) Dot plot of the KEGG pathways enriched using DE mRNAs. DE mRNAs that participate multiple KEGG pathways are listed on the left.

Fig. 3

KEGG and GO enrichment analyses of target genes of DE lncRNA, miRNA, and circRNA for LGSS and LW pigs. (A) Bar plot of GO terms enriched using the target genes of DE lncRNAs. Only the top 10 terms are displayed. (B) Dot plot of the top 20 KEGG pathways enriched using the target genes of DE lncRNAs. (C) Bar plot of GO terms enriched using the target genes of DE miRNAs and circRNAs. Only the top 10 GO terms are displayed.