Dynamic development of muscle during embryogenesis in Arbor Acres broilers and TaoYuan chickens revealed by RNA sequencing

Embryonic muscle development is a highly dynamic and complex process, coordinated by numerous genes and transcriptional regulators such as small RNAs. Here, we profiled transcriptomic dynamics in breast muscle from Arbor Acres (AA) broilers and TaoYuan (TY) chickens at three embryonic time points (E9, E13, and E18). While developmentally regulated genes enriched similar biological pathways in both breeds, the architecture of microRNA (miRNA)-mRNA interaction networks was distinct. Integrative analysis combining weighted gene co-expression network analysis, differential expression analysis, and time-series clustering identified 161 candidate genes, including a subset of 39 showing progressively decreasing expression. Differential expression analysis of miRNA revealed that gga-miR-1744-3p was uniquely up regulated at E13 and E18 in TY chickens. By integrating predictions from TargetScan and miRDB, we further identified two core genes (USP8 and ZBTB38) from the set of 39 candidate genes, which are predicted targets of gga-miR-1744-3p. This gene was differentially expressed in the heart, breast muscle, and adipose tissue, and exhibited significantly higher expression in TY chickens. Functional assays confirmed that gga-miR-1744-3p promotes proliferation of chicken primary myoblasts. This study provides a comprehensive understanding of the development patterns and molecular mechanisms of breast muscles in broilers during embryogenesis.