Malania oleifera, the sole species of its genus, is an endangered tree endemic to the karst regions of China and a valuable woody oil crop. However, deep seed dormancy and slow germination severely limit its propagation and utilization. In this study, freshly harvested mature seeds of M. oleifera were soaked in gibberellic acid (GA₃) solutions at different concentrations. Germination traits and physiological and biochemical parameters were assessed, and transcriptome sequencing was performed to investigate the mechanisms underlying GA₃-promoted seed germination. Soaking seeds in GA₃ for 24 h significantly promoted germination in a concentration-dependent manner. The strongest response occurred at 600 mg·L⁻¹ GA₃, with germination potential and germination percentage reaching 34.2% and 60.0%, respectively. The beneficial effect declined at 800 mg·L⁻¹. Treatment with 600 mg·L⁻¹ GA₃ significantly increased superoxide dismutase (SOD) and peroxidase (POD) activities and reduced malondialdehyde (MDA) content, indicating that an appropriate GA₃ concentration helped maintain redox balance during germination. Transcriptome analysis identified 7548 and 3571 differentially expressed genes in UT_vs_W24 and W24_vs_GA24, respectively. These results indicated that water soaking initiated germination-related transcriptional changes that were further modified by GA₃ treatment. Functional enrichment analysis showed that transcriptional changes induced by water soaking mainly involved carbohydrate and lipid metabolism, secondary metabolism, and responses to stimuli, whereas GA₃ treatment further modulated redox processes, defense responses, plant hormone signal transduction, and the mitogen-activated protein kinase (MAPK) signaling pathway. Reconstruction of the plant hormone and MAPK signaling pathways showed that GA₃ markedly affected the expression of genes involved in gibberellin, abscisic acid, auxin, and brassinosteroid signaling. GA₃ also regulated the MKK–MPK cascade and downstream transcription factors, including WRKYs. Together, these findings characterize the physiological responses of M. oleifera seeds to GA₃ and reveal the molecular mechanisms underlying GA₃-promoted germination, providing a basis for improving the propagation efficiency of this valuable species.

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