Exogenous gibberellic acid shortening after-ripening process and promoting seed germination in a medicinal plant Panax notoginseng

BACKGROUND: Panax notoginseng (Burk) F.H. Chen is an essential plant in the family of Araliaceae. Its seeds are classified as a type of morphophysiological dormancy (MPD), and are characterized by recalcitrance during the after-ripening process. However, it is not clear about the molecular mechanism on the after-ripening in recalcitrant seeds. RESULTS: In this study, exogenous supply of gibberellic acid (GA(3)) with different concentrations shortened after-ripening process and promoted the germination of P. notoginseng seeds. Among the identified plant hormone metabolites, exogenous GA(3) results in an increased level of endogenous hormone GA(3) through permeation. A total of 2971 and 9827 differentially expressed genes (DEGs) were identified in response to 50 mg L(−1) GA(3) (LG) and 500 mg L(−1) GA(3) (HG) treatment, respectively, and the plant hormone signal and related metabolic pathways regulated by GA(3) was significantly enriched. Weighted gene co-expression network analysis (WGCNA) revealed that GA(3) treatment enhances GA biosynthesis and accumulation, while inhibiting the gene expression related to ABA signal transduction. This effect was associated with higher expression of crucial seed embryo development and cell wall loosening genes, Leafy Contyledon1 (LEC1), Late Embryogenesis Abundant (LEA), expansins (EXP) and Pectinesterase (PME). CONCLUSIONS: Exogenous GA(3) application promotes germination and shorts the after-ripening process of P. notoginseng seeds by increasing GA(3) contents through permeation. Furthermore, the altered ratio of GA and ABA contributes to the development of the embryo, breaks the mechanical constraints of the seed coat and promotes the protrusion of the radicle in recalcitrant P. notoginseng seeds. These findings improve our knowledge of the contribution of GA to regulating the dormancy of MPD seeds during the after-ripening process, and provide new theoretical guidance for the application of recalcitrant seeds in agricultural production and storage. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-023-04084-3.