BACKGROUND: Long non-coding RNAs (lncRNAs) play crucial roles in testicular development and spermatogenesis. The seminiferous tubule, the exclusive site of spermatogenesis, houses all types of male germ cells, regulated by both lncRNAs and mRNAs. However, the expression patterns and functions of these molecules across different developmental stages of dairy goat seminiferous tubules remain poorly understood. RESULTS: In this study, we sequenced and identified lncRNAs and mRNAs expressed in the seminiferous tubules of Guanzhong dairy goats at two developmental stages: 45-day-old premature (G45) and 240-day-old mature (G240). Significant differences in testis index and seminiferous tubules morphology were observed between G45 and G240 (P <
0.05). Transcriptome analyses revealed 11,612 lncRNAs and 18,217 mRNAs, with 7,554 lncRNAs and 11,986 mRNAs showing significant differential expression between the two stages. Among these, 229 differentially expressed mRNAs related to spermatogenesis were identified. Key genes, such as Kit, Dmrt1, and Sox9, were down-regulated, whereas Ddx4, Sycp1, and Sycp3 were up-regulated after sexual maturity. Notably, signalling pathways including PI3K/Akt, MAPK, and Rap1 were implicated in the regulation of spermatogenesis. We constructed lncRNA-mRNA interaction networks, identifying specific lncRNAs and their target genes potentially critical for spermatogenesis. Additionally, single-cell transcriptome data validated the expression of key genes, revealing that Piwil4 and Dnmt3l were specifically expressed in spermatogonial clusters, whereas Piwil1, Piwil2, and Gtsf1 were predominantly expressed in spermatocyte clusters. CONCLUSIONS: These findings highlight the essential roles of specific genes in the maturation of seminiferous tubules in dairy goats. This study provides comprehensive transcriptomic profiles and lncRNA-mRNA interaction networks between the G45 and G240 stages, offering valuable insights into spermatogenesis and seminiferous tubules development in Guanzhong dairy goats.