Combined transcriptomic and metabolomic analysis of the molecular mechanism of seed dormancy release in Notopterygium incisum.

Background: Notopterygium incisum seeds have both morphological and physiological dormancy characteristics and require stratification to break seed dormancy, but the mechanism of seed dormancy release during stratification is still unclear. In this study, different stages of N. incisum seed stratification were employed as experimenta objects, and the dynamic changes during seed dormancy release were studied through embryo morphology, physiological index determination, transcriptome, and metabolome.

Results: (1) Stratification treatment reduced the content of stored nutrients in N. incisum seeds, significantly changed enzyme activity, reduced ABA content, and increased GA₃ and IAA contents. (2) A total of 110,539 differentially expressed genes (DEGs) and 1656 metabolites (DAMs) were identified during dormancy release. Transcriptome analysis showed that after the dormancy of N. incisum seeds was released, the expression of genes in the abscisic acid signaling pathway (ABI1, PP2CA, ABI5 and ABF4) and the gibberellin signaling pathway (GAI, GAI1 and RGL1) were significantly down-regulated, and there were significant changes in the differentially expressed genes in the auxin, cytokinin and ethylene signaling pathways. The genes related to starch and sucrose metabolism were up-regulated during dormancy release. The genes related to phenylpropanoid and flavonoid biosynthesis were significantly up-regulated after dormancy release. (3) Combined transcriptomics and metabolomics analysis showed that phenylpropanoid biosynthesis and flavonoid biosynthesis are the key pathways for the dormancy release of N. incisum seeds. (4) Metabolomics analysis showed that the accumulation of metabolites of the phenylpropanoid biosynthesis pathway (p-coumaric acid, coniferyl aldehyde, coniferyl glycoside, 5-caffeoylshikimic acid and sinapinic acid) decreased during and after the dormancy release of N. incisum seeds, while the accumulation of flavonoids such as quercetin, rutin, delphinidin and naringenin chalcone increased significantly after dormancy release.

Conclusion: Dormancy release in N. incisum seeds involves differential regulation of hormones, carbohydrates, phenylpropanoids, and flavonoid metabolites. Our results provide important insights into the molecular regulatory network of dormancy release in N. incisum seeds.