Integrated transcriptome and co-expression network analysis reveals specific modules and hub genes underlying...

Magnolia sieboldii K. Koch is prized for its ornamental, medicinal, and economic value, yet its seeds exhibit morphophysiological dormancy, leading to difficult and unpredictable germination. This study investigates the mechanism of dormancy release in M. sieboldii seeds by exogenous gibberellic acid (GA₃). Germination tests confirmed that GA₃ treatment effectively broke seed dormancy, achieving over 80% germination, whereas seeds imbibed in distilled water (DW) did not. Physiological analysis revealed that GA₃ imbibition maintained a low abscisic acid (ABA)/GA ratio and significantly altered carbohydrate metabolism, characterized by a sharp decrease in starch and an increase in sucrose at 24 h after imbibition (HAI). RNA-seq analysis identified numerous differentially expressed genes (DEGs) in response to GA₃ across different imbibition times. GO enrichment analysis indicated that GA₃ rapidly activated pathways related to signal transduction and amylase activity. Weighted gene co-expression network analysis (WGCNA) further identified key gene modules strongly correlated with hormonal (ABA, GA₃) and metabolic (starch, sucrose, glucose) traits. Hub genes within these modules, such as MsrB2, DOF5.4, and WAKs, were implicated in dormancy release. Functional characterization of a candidate gene, MsDOG1, demonstrated its role in repressing germination, as its overexpression in Arabidopsis enhanced dormancy, an effect that was alleviated by low-temperature imbibition. Our findings that exogenous GA₃ promotes dormancy release in M. sieboldii seeds by remodeling the hormonal and metabolic landscape and gene expression networks thus provide a valuable resource for understanding the molecular mechanisms of morphophysiological dormancy.