A spatiotemporal atlas of gene expression in ovine fetal muscle reveals critical transitions and modular networks driving myogenesis

Skeletal muscle development is a complex biological process orchestrated by precisely regulated gene expression networks. Understanding the molecular mechanisms during fetal myogenesis is crucial for improving meat yield and quality in livestock. In this study, we performed RNA-seq analysis on skeletal muscle tissues from Chinese Merino sheep across 11 key developmental time points, from embryonic day 26 (D26) to near birth (D135). Using weighted gene co-expression network analysis (WGCNA), we identified nine distinct gene modules significantly associated with specific developmental stages. These modules revealed stage-specific biological processes, including myogenic progenitor cell (MPC) proliferation and differentiation, primary (PM) and secondary myofiber (SM) formation, energy metabolism, and muscle maturation. Key hub genes and signaling pathways-such as Wnt, TGF-β, MAPK, and PI3K-AKT-were further validated through functional enrichment and protein-protein interaction (PPI) networks. Notably, we identified critical developmental transition points at D29 (MPC differentiation initiation), D45 (embryonic-to-fetal transition), and D85 (myofiber maturation shift). Moreover, several novel hub genes, including CORIN, SMOC1/2, and ADAMTS family members, were identified. In summary, by identifying nine stage-specific co-expression modules, pinpointing three pivotal developmental transitions (D29, D45, D85), and uncovering novel hub genes of potential regulatory importance, this study provides a systems-level framework for understanding ovine fetal myogenesis and offers candidate targets for livestock genetic improvement. • A high-resolution spatiotemporal transcriptomic atlas of ovine fetal skeletal muscle across 11 developmental stages is constructed. • Nine stage-specific gene modules delineate three critical transitions at D29, D45, and D85 during myogenesis. • Novel hub genes, including CORIN, SMOC1/2, and ADAMTS family members, are identified as potential key regulators.