Identification of Key Genes Regulating Body Weight in Qingyuan Partridge Chickens During Development using RNA-Sequence Analysis

Background: The Qingyuan partridge chicken is a high-quality local chicken breed in China. Its weight gain directly affects breeding efficiency. This study used RNA sequencing to analyze gene expression dynamics in the breast muscle tissue of Qingyuan partridge chickens at 1, 35, 70, and 105 days of age. Methods: This study employed RNA-sequencing, integrated with differential expression analysis, weighted gene co-expression network analysis (WGCNA), and short time-series expression miner (STEM) analysis, to systematically investigate the transcriptomic dynamics in breast muscle tissue across four developmental stages. Results: Phenotypic analysis revealed a significant increase in both body weight (BW) and breast muscle weight with age (p < 0.05). Transcriptomic analysis identified 3521 genes specifically expressed at the age of one day compared with the other 3 ages. These were significantly enriched in pathways related to ribosomal biosynthesis, cytoskeletal regulation, and cell proliferation (p < 0.05). Turquoise and black modules were identified by WGCNA, containing 1563 hub genes, which significantly correlated with BW. Integration of differentially expressed genes and STEM analysis selected 26 BW-related key genes closely associated with muscle growth, including calmodulin 2 (CALM2), heat shock protein 90 alpha family class A member 1 (HSP90AA1), and cholinergic receptor nicotinic delta subunit (CHRND). Protein–protein interaction analysis revealed two functional networks centered around these genes. Enrichment analysis of the STEM profiles indicated that upregulated genes were significantly enriched in autophagy and the ErbB, FoxO, mTOR, and insulin signaling pathways, while genes related to the ribosome, cell cycle, and PPAR signaling pathways were downregulated. Conclusions: This study identified BW-related key genes and pathways, enriching our knowledge of the functional maintenance of chicken BW.