Multi‐stage transcriptome analysis reveals genetic orchestration of rat testis development

BACKGROUND: Testicular development is a highly orchestrated process essential for male fertility, but its temporal genetic regulation remains incompletely resolved in many mammalian models. This study re-analyses rat testis transcriptomes across 15 stages from embryonic day 12 to postnatal week 16 using bulk RNA-sequencing data from a multispecies organ development atlas, generating a continuous, testis-focused temporal framework, and pinpointing key developmental transition windows and regulatory modules. RESULTS: Of 23,748 annotated genes, 17,717 were differentially expressed (DEGs), and hierarchical plus co-expression analyses identified four principal expression modules and five clusters capturing spermatogenic, morphogenetic, immune, and neurone-like programs. Four major transcriptional transition windows, embryonic day 14, embryonic day 19, postnatal week 2, and postnatal week 6, were defined, with the largest remodeling between 2 and 6 weeks coinciding with the onset of robust spermatogenesis and marking a particularly vulnerable window for environmental or toxicant-induced perturbation. Stage-specific spermatogenesis-associated gene sets at embryonic day 19 (n = 28), postnatal week 2 (n = 61), and week 6 (n = 735) showed minimal overlap, supporting sequential regulatory waves driving germ cell commitment, early meiosis, and terminal differentiation. Target enrichment analyses highlighted five conserved microRNAs (rno-miR-151-5p, rno-miR-29b-3p, rno-miR-384-5p, rno-miR-500-5p, rno-miR-672-5p) whose predicted and validated targets form modules related to extracellular matrix remodeling, apoptosis and cell-cycle control, ion-channel signaling, and neuronal-like pathways, with high sequence conservation to human homologs. Immune-related genes and blood-testis barrier components displayed coordinated expression dynamics, and a conserved core of 487 spermatogenesis genes showed strong cross-mammalian orthology, indicating a deeply shared transcriptional backbone on which species-specific regulatory nuances are layered. CONCLUSIONS: This multistage transcriptomic analysis delineates major developmental transitions, co-expression modules, and regulatory miRNA-mRNA networks that orchestrate rat testis maturation and highlight a critical P2W-P6W transition window. The resource complements existing multiorgan and single-cell datasets by providing a testis-focused temporal framework and identifies conserved gene sets and regulatory candidates of direct relevance to male infertility, toxicology, and cross-species translational studies.