Combined transcriptomic and metabolomic profiling identifies candidate pathways associated with adventitious root inhibition by watermelon scions in pumpkin rootstocks

Background Adventitious root (AR) formation is essential for grafted seedling propagation, yet its suppression in specific scion-rootstock combinations remains a significant challenge. To investigate the molecular pathways associated with AR inhibition by watermelon scions in pumpkin rootstocks, this study utilized a double-root-cutting system across three comparative treatments: non-grafted pumpkin (P), self-grafted pumpkin (P/P), and watermelon-grafted pumpkin (W/P). Results Histological analysis revealed that the watermelon scion is associated with a severe inhibit in cellular dedifferentiation and primordium initiation in the rootstock. Hormonal profiling confirmed that W/P rootstocks contained significantly lower indole-3-acetic acid (IAA) and higher trans-zeatin riboside (tZR) levels than P and P/P treatments at 12 DAG, disrupting the requisite auxin-to-cytokinin ratio for AR induction. Exogenous IAA and lovastatin promoted AR formation in W/P, whereas 6-BA markedly suppressed AR formation in P/P. Metabolomic analysis revealed significant alterations in 32 key metabolites across the tryptophan, zeatin, and flavonoid/phenylpropanoid pathways, notably including indole-3-carboxylic acid, adenine, isopentenyladenosine, quercetin, and kaempferol. Transcriptomic profiling highlighted the profound enrichment of plant hormone signal transduction pathways, characterized by the systemic down-regulation of core auxin signaling components ( AUX1 , AUX , ARFs , SAUR ) and the simultaneous up-regulation of cytokinin signaling elements ( AHPs , ARRs ). Furthermore, WGCNA identified specific transcription factors ( CAMTA3 , ILR3 , AIL6 ) and functional hub genes ( GH3.6 , CYP735A , LOG , XTH , Pectinesterase ) highly correlated with the suppression of AR development. Conclusions Collectively, this study characterizes the scion-induced transcriptional and metabolic disruptions associated with impaired AR organogenesis. The identified hormonal imbalances and integrated transcriptomic and metabolomic alterations, along with the identified regulatory hub genes, provide crucial genetic targets for improving rooting efficiency in elite grafted cucurbits.