Coordinated flavonoid pathway deficiency defines drought sensitivity in Casuarina equisetifolia roots: a multi-omics...

Drought stress impairs the ecological functioning of Casuarina equisetifolia in coastal ecosystems. Elucidating the molecular mechanisms underlying drought tolerance is essential for molecular breeding, yet systematic insights into genotype-specific root responses to dynamic drought and rehydration remain scarce. Here, we integrated root transcriptomic, metabolomic, and physiological analyses of drought-tolerant (DT) and drought-sensitive (DS) genotypes across a full drought-rehydration cycle to unravel root-based drought resistance mechanisms. Under non-stress conditions, DT roots exhibited a constitutive pre-adaptive state characterized by elevated basal phenylpropanoid and α-Linolenic acid pathway activities and low-cost antioxidant homeostasis. During drought, DT roots deployed temporally ordered transcriptional reprogramming to enable staged defense activation, metabolic optimization, and efficient post-rehydration recovery. In contrast, DS roots exhibited distinct expression patterns characterised by early and sustained suppression of the phenylpropanoid and flavonoid pathways. Multi-omics analysis revealed that DS roots displayed coordinated transcriptional and metabolic downregulation of flavonoid biosynthesis. This sustained molecular deficiency corresponded to reduced antioxidant capacity, severe oxidative damage, and poor recovery performance. Key transcription factors exhibited distinct genotypic regulatory patterns in roots. Our results demonstrate that the superior drought tolerance of DT roots relies on intrinsic pre-adaptation combined with dynamic, orderly multi-omics reprogramming, while drought susceptibility in DS roots is defined by irreversible flavonoid pathway dysfunction. This work provides precise molecular targets for breeding improved varieties.