The integration of WGCNA and ceRNA analysis provides insights into bovine intramuscular fat deposition.

Abstract

Background: Intramuscular fat (IMF) content is a crucial determinant of beef quality and a key indicator in cattle breeding and production. However, the molecular regulatory mechanisms governing IMF deposition remain poorly understood.

Results: This study preliminarily explored the molecular mechanisms underlying IMF deposition by integrating weighted gene co-expression network analysis (WGCNA) and competitive endogenous RNA (ceRNA) network analysis. Sequencing of longissimus dorsi muscle samples from crossbred Wagyu cattle with varying IMF deposition levels revealed 172 differentially expressed circular RNAs (circRNAs), which were subsequently annotated and used to construct regulatory networks. Protein-protein interaction (PPI) network analysis predicted possible several lipid metabolism-related genes, including EZH2, AKT3, APP and SMARCA5. By combining the miRNA and mRNA data from our previous studies, we constructed circRNA-mRNA coexpression networks and circRNA-miRNA-mRNA regulatory networks. Functional enrichment analysis revealed that the identified circRNAs are involved primarily in lipid metabolism-related pathways, including phosphatidylinositol metabolism and the cGMP-PKG signaling pathway. Additionally, several circRNAs were predicted to function as molecular sponges based on coexpression patterns.

Conclusion: This study provides novel insights into the molecular mechanisms underlying IMF deposition in hybrid cattle and provides candidate regulatory mechanisms for further validation in selective breeding.