Integrated transcriptomic and metabolomic analyses reveal regulatory networks governing hub metabolic pathways in <i>Fraxinus hupehensis</i> seeds during germination

Efforts to protect germplasm resources of Fraxinus hupehensis (Oleaceae)-an endangered species endemic to Dahong Mountain, Hubei Province, China-are facing difficulties due to the deep dormancy of its seeds. To elucidate the molecular regulatory networks underlying dormancy release, an integrated investigation combining physiological profiling with transcriptomic and metabolomic analyses was performed on seeds of F. hupehensis during six critical germination stages. A decrease was observed in the contents of soluble sugar, soluble starch and crude fat as the germination process progressed, with glycolysis, the tricarboxylic acid cycle and the pentose phosphate pathways providing energy. Plant hormones such as abscisic acid and gibberellin 4 exerted coordinated regulatory effects throughout this process. Differentially expressed genes and metabolites were detected in metabolic pathways including sugar metabolism, respiratory metabolism, protein synthesis and degradation, along with lipid metabolism. Notably, structural hub genes and metabolites in metabolic pathways of starch and sucrose, respiratory, phenylalanine and linoleic acid played crucial regulatory roles in seed germination. Furthermore, hub transcription factors within the APETALA2/ethylene-responsive factor, basic helix-loop-helix and MYB families were identified by weighted gene correlation network analysis. This study unveiled the regulatory mechanisms of primary metabolic hub pathways during seed germination, providing a theoretical foundation for the breeding and conserving F. hupehensis and other endangered plant species.