Comparative transcriptome analysis reveals the potential mechanism of GA-induced dormancy release in black seeds.

Bunge produces dimorphic seeds on the same plant, with brown seeds displaying non-dormant characteristics and black seeds exhibiting intermediate physiological dormancy traits. Previous studies have shown that black seeds have a very low germination rate under natural conditions, but exogenous GA effectively enhanced the germination rate of black seeds. However, the physiological and molecular mechanisms underlying the effects of GA on black seeds are still unclear. In this study, transcriptomic profiles of seeds at different germination stages with and without GA treatment were analyzed and compared, and the TTF, HO, O , starch, and soluble sugar contents of the corresponding seed samples were determined. The results indicated that exogenous GA treatment significantly increased seed vigor, HO, and O contents but decreased starch and soluble sugar contents of black seeds during seed dormancy release. RNA-seq results showed that a total of 1136 DEGs were identified in three comparison groups and were involved mainly in plant hormone signal transduction, diterpenoid biosynthesis, flavonoid biosynthesis, phenylpropanoid biosynthesis, and carbohydrate metabolism pathway. Among them, the DEGs related to diterpenoid biosynthesis (, and ) and ABA signal transduction () could play important roles during seed dormancy release. Most genes involved in phenylpropanoid biosynthesis were activated under GA treatment conditions, especially many genes encoding peroxidase. In addition, exogenous GA treatment also significantly enhanced the expression of genes involved in flavonoid synthesis, which might be beneficial to seed dormancy release. In accordance with the decline in starch and soluble sugar contents, 15 genes involved in carbohydrate metabolism were significantly up-regulated during GA-induced dormancy release, such as , , and , etc. In a word, exogenous GA effectively increased the germination rate and seed vigor of black seeds by mediating the metabolic process or signal transduction of plant hormones, phenylpropanoid and flavonoid biosynthesis, and carbohydrate metabolism processes. Our results provide novel insights into the transcriptional regulation mechanism of exogenous GA on the dormancy release of black seeds. The candidate genes identified in this study may be further studied and used to enrich our knowledge of seed dormancy and germination.