Comparative Analysis of the Transcriptome of the Chicken Breast Muscle at Different Developmental Stages

Chickens are a primary source of protein in the human diet, with demand increasing annually. However, research on genes that promote chicken meat development remains relatively limited. Therefore, in this study, breast muscle samples (pectoralis major, n = 10 per group) from chickens at five developmental stages (D1, D35, D70, D105, and D140) were selected to investigate genetic-level changes and identify additional genes influencing chicken meat development. Differential expression analysis between adjacent stages (|FC| > 1.5, p < 0.05) revealed 42 differentially expressed genes (DEGs) shared across four comparisons, primarily enriched in muscle development pathways such as focal adhesion, the regulation of the actin cytoskeleton, and Wnt signaling. Weighted gene coexpression network analysis (WGCNA) revealed that four modules were significantly correlated with body weight and breast muscle weight phenotypes. By integrating the hub genes of the four modules and the DEGs, we identified key genes, including MEGF10, MYOM2, TM4SF1, HNMT, NR4A3, and Wnt5a. Furthermore, we conducted a comparative analysis of key gene expression trends across commercial broilers (CBs) and Beijing You (BJY) chickens. MYOM2 and Wnt5a exhibited distinct expression patterns during the early developmental stage of Xianju (XJ) chickens, suggesting that these genes may be critical factors distinguishing XJ chicken breast muscle development from that of other breeds. In all three chicken breeds analyzed, the expression levels of HNMT and MEGF10 gradually decreased with increasing age, indicating that their functions are universal in poultry muscle development. In summary, our findings revealed key regulatory genes that influence breast muscle development, offering candidate targets for marker-assisted selection in poultry breeding programs.