Integrated transcriptome analysis reveals ABA-dependent and ABA- independent regulatory networks underlying the early drought response in Poncirus trifoliata

Drought severely impacts plant growth and development. Plants have evolved multiple strategies to respond to drought stress, and ABA signaling plays a key role in this process; however, the precise mechanism by which ABA mediates the drought response in citrus plants requires further elucidation. In this study, we investigated the physiological characteristics and transcriptome landscape of leaves under dehydration treatment in trifoliate orange ( Poncirus trifoliata (L.)) plants. Transcriptome analysis revealed 667 and 1,932 differentially expressed genes (DEGs) at 3 h and 6 h postdehydration, respectively, compared with the control (0 h). KEGG and GO enrichment analyses revealed that DEGs whose expression started to be upregulated at 6 h (cluster 1) were significantly enriched in pathways related to plant hormone signal transduction, MAPK signaling, and galactose metabolism. In contrast, genes in cluster 3, which started being induced at 3 h, were enriched in secondary metabolite biosynthesis pathways, suggesting that early drought stress promoted the accumulation of metabolites and hormones, contributing to the establishment of drought tolerance. Among the 227 consistently upregulated hub genes during dehydration treatment, critical regulators, such as NCED3, RBOHD, ABI1 and WRKY40, which play central roles in the drought response, were identified. Transcriptome analysis of ABA-treated trifoliate orange plants at 3 h and 6 h revealed that clustering analysis distinguished DEGs regulated through ABA-dependent pathways from those regulated independently of ABA. Protein‒protein interaction (PPI) network analysis via STRING confirmed that genes such as CHS, OPR2, DUR3, and OMT were coinduced by both drought and ABA, whereas transcription factors such as WRKY50, WRKY53, and NAC029 were regulated independently of ABA. In summary, early drought stress in citrus plants triggers a coordinated response via both ABA-dependent and ABA-independent pathways, involving photosystem protection, membrane stability maintenance, ROS homeostasis, ABA signal regulation, and secondary metabolite accumulation. These findings provide novel insights into the molecular basis of the early drought response in citrus and identify promising genetic targets for improving drought tolerance.