Dissection of the gene regulatory network underlying sexual maturity divergence in Jining Bairi chickens through integrated RNA-seq and WGCNA analysis.

Sexual maturity is a pivotal reproductive trait in laying hens because it is directly related to egg production. The age at first egg is a definitive indicator of sexual maturity attainment in laying hens. Most Chinese indigenous chicken breeds exhibit a late onset of lay, significantly affecting their egg-laying performance. The Jining Bairi chicken, with its unique precocious sexual maturity (approximately 100 days of age at first lay), is an ideal model for deciphering the molecular mechanisms of avian sexual precocity. In this study, hypothalamic and ovarian tissues were systematically collected from Jining Bairi chickens at three developmental stages: 60 days (60 d), 100 days (100 d), and 140 days (140 d) of age. The 140 d cohort consisted of three non-laying (designated 140a) and three laying hens (designated 140b) for RNA-seq-based transcriptomic profiling and cross-tissue regulatory network construction. Bioinformatics approaches, including temporal expression clustering, protein-protein interaction networks, Venn analysis, and weighted gene co-expression network analysis, were employed to identify key genes and elucidate potential molecular regulatory networks governing sexual maturity differences. Results revealed significant enrichment of core reproductive pathways, including progesterone-mediated oocyte maturation, oocyte meiosis, gonadotropin-releasing hormone signaling, TGF-β signaling, Wnt signaling, and MAPK signaling pathways. Furthermore, pathways potentially implicated in sexual maturation regulation included FoxO signaling pathway, Toll-like receptor signaling pathway, mTOR signaling pathway, neuroactive ligand-receptor interaction, apelin signaling pathway, and necroptosis. Notably, neuroactive ligand-receptor interaction, apelin signaling pathway, and necroptosis were involved in regulating sexual maturation in chickens. Integrative screening revealed NPY4R, GALR1L, GRIN2C, POLR1B, ITGB3, ALDH18A1, PPP1R26, HTR1B, GABRA6, TSHB, APLNR, APELA, and GSL as hub genes contributing to phenotypic divergence between pre- and post-sexual maturity stages in chickens. These findings systematically delineate the molecular network underpinning sexual maturation through coordinated actions of hub genes and their associated signaling cascades.