miRNA-mRNA Co-regulatory Network Analysis of Longissimus Dorsi Muscle in Shaziling Pig and Yorkshire Pig

doi:10.3969/j.issn.1001-0769.2025.01.009

Abstract：MicroRNAs (miRNAs) are a class of small non-coding RNAs with approximately 22 nucleotides in length. This study analyzed the expression profile chip and transcriptome data of the longissimus dorsi muscle tissue of Shaziling pigs and Yorkshire pigs to reveal the differential expression characteristics of miRNAs and messenger RNAs (mRNAs) between these two pig breeds and their regulatory networks. Small RNA sequencing identified a total of 307 miRNAs, among which 9 were significantly differentially expressed (5 upregulated and 4 downregulated), and 4 and 5 specific miRNAs were identified in Shaziling pigs and Yorkshire pigs, respectively. Transcriptome analysis identified 553 differentially expressed genes (DEGs), including 341 upregulated and 212 downregulated. Integrated analysis revealed that 8 differentially expressed miRNAs (DEMs) formed 70 regulatory pairs with 59 DEGs, and a key co-regulatory network was constructed. Gene Ontology (GO) enrichment analysis showed that the target genes were significantly involved in biological processes such as muscle contraction regulation and fatty acid oxidation. KEGG pathway analysis revealed significant enrichment of metabolic regulatory pathways, including the mitogen-activated protein kinase (MAPK) signaling pathway, the FoxO (Forkhead box O) signaling pathway, and ferroptosis. Among them, the MAPK14 gene participated in both endocrine resistance and immune regulation, while the ACOX1 gene played a dual role in propionate and carbon metabolism. These findings systematically elucidated the key differences in electrophysiological properties, energy metabolism, and molecular regulation levels of muscle tissues between Shaziling pigs and Yorkshire pigs, providing new insights into the molecular mechanisms underlying the formation of pig germplasm traits.