Transcriptomic analysis identifies candidate genes associated with striated muscle contraction during breast muscle development in meat-type ducks

The development of the breast muscle is critical for meat yield and quality in meat-type ducks. However, the transcriptional changes underlying breast muscle development in meat-type ducks remain poorly understood. In this study, we integrated phenotypic, histological, and myogenic regulatory factor analyses to characterize the developmental trajectory of the breast muscle, identifying embryonic day 19 (E19) as a pivotal transition point marked by peak muscle growth rate and maximal expression of MYOD, MYOG, and MYF5. Consequently, transcriptomic profiling of the pectoralis major muscle was conducted at three representative developmental stages, embryonic day 11 (E11), E19, and day of hatching (D1) using 15 cDNA libraries for RNA sequencing (RNA-seq). Pairwise comparisons identified 5,300, 5,167, and 8,393 differentially expressed genes (DEGs) in the E11 vs. E19, E19 vs. D1, and E11 vs. D1 comparisons, respectively. These DEGs were subsequently subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Following the identification of common DEGs across the three developmental stages, protein-protein interaction (PPI) network analysis was integrated with gene set enrichment analysis (GSEA). This analysis revealed 24 common key genes involved in breast muscle development during meat-type duck growth, which converged our investigation specifically on the striated muscle contraction gene set. Furthermore, by integrating CytoHubba ranking and GSEA, we identified a core set of six candidate genes associated with striated muscle contraction during breast muscle development in ducks, namely ACTN2, MYH11, MYL1, TNNC1, TNNI1, and TNNI2. In conclusion, our findings delineate the dynamic transcriptomic landscape of duck breast muscle development and identify candidate genes associated with striated muscle contraction, which would be useful for future functional investigations of these genes and for developing molecular markers in ducks.