New insights into the transcriptomic profile during the late stages of chicken embryonic development

While comprehensive transcriptomic characterization of muscle development during the hatching stage remains limited, we conducted an integrated analysis of coding and non-coding RNA profiles in the pectoral muscles of Arbor Acres (AA) broilers and TaoYuan (TY) chickens at embryonic days 17 (E17), 19 (E19), and 21 (E21). Our findings revealed notable phenotypic differences: AA broilers exhibited greater embryo weight and larger muscle fiber cross-sectional areas compared to TY chickens. Across three developmental stages, we identified 4,577 differentially expressed genes (DEGs), 143 differentially expressed microRNAs (DEMs), 90 differentially expressed circRNAs (DECs), and 3,159 differentially expressed lncRNAs (DELs). By integrating weighted gene co-expression network analysis (WGCNA) analysis with differential expression profiling, we prioritized five coding genes (FOSL2, PDE4B, TRIB1, THBS1, and FBXO32) as key regulators of muscle development. Pathway enrichment analysis further revealed significant activation of the glycolysis/gluconeogenesis pathway in TY chickens, likely supporting the energy demands of shell pipping. To elucidate transcriptional regulatory mechanisms, we constructed competing endogenous RNA (ceRNA) networks based on miRanda predictions. This analysis identified four microRNAs (gga-miR-206, gga-miR-383-3p, gga-miR-449a, and gga-miR-449c-5p) that may modulate developmental genes through lncRNA and circRNA mediated sponge interactions. These ceRNA networks provide novel insights and a valuable framework for investigating the molecular regulation of embryonic muscle development in AA broilers and TY chickens.