Dynamic transcriptomic landscape of myogenesis in Muscovy ducks (Cairina moschata): integrative analysis of hub genes posthatching

Objective: Post-hatching myogenesis is a critical determinant of meat yield and quality, with potential regulatory roles of specific genes remaining underexplored in Muscovy ducks (Cairina moschata). This study aimed to identify hub genes governing post-hatching myogenesis through transcriptomic profiling. Methods: Three white-feathered male Muscovy ducks at 1-day-old (1D) and 80-day-old (80D) were selected, respectively. Following humane euthanasia, the left leg muscles were collected for subsequent RNA extraction, library construction, genome alignment, and transcriptome sequencing. Differential gene expression analysis was performed using DESeq2 (ver. 1.16.1), with significant differentially expressed genes (DEGs) selected under the thresholds of |log2FC|>1 and p-value<0.05. Subsequent functional characterization included enrichment analyses (Gene Ontology, KEGG, and PANTHER pathways) implemented through DAVID and KOBAS, followed by protein-protein interaction network modeling via STRING. Topological analysis with CytoHubba further pinpointed hub genes functionally linked to myogenesis. Results: Totally 1,683 DEGs were identified between 80D and 1D muscles, including 865 upregulated and 818 downregulated genes. Totally ten hub genes, such as CD3E, ITK, COL4A6, and IVD, were prioritized as key regulators of myogenesis. Functional analysis revealed their enrichment in L-leucine catabolic processes and fatty acid β-oxidation. Pathway mapping further associated these genes with glycine/serine/threonine metabolism, and branched-chain amino acid degradation. Conclusion: This study delineates a molecular framework for post-hatching myogenesis in Muscovy ducks, highlighting ten hub genes that orchestrate myogenesis through metabolic reprogramming. These findings advance genetic strategies for improving poultry meat production and quality.