Short-term watering regimes efficiently induce functional compounds in the endangered medicinal plant Syringa pinnatifolia

The protracted formation time of bioactive metabolites in rare woody medicinal plants limits both wild resource conservation and near‑term economic returns from cultivation. Syringa pinnatifolia is an endangered medicinal shrub from cold and arid regions of Inner Mongolia, accumulating pharmacologically valuable lignans and the sesquiterpenoid zerumbone. Despite medicinal progress, neither large-scale artificial cultivation nor early quality induction has been established for this endangered species. We subjected two‑year‑old cultivated plantlets to four watering regimes, with metabolomic, transcriptomic and physiological profiling of peeled stems. Our results indicated that water‑deficit (Drought, DR) and alternating wet/dry (AW/D) redirected metabolism towards accumulation of lignans and zerumbone, whereas well‑watered conditions (MW and RW) favored phenolics, sesquiterpenoids and flavonols. Notably, AW/D induced the broadest lignan spectrum and elevated zerumbone to levels approaching those of 30-year-old wild stems, but also increased specific lignan glycosides beyond the wild benchmark, and exhibited a higher relative yield of functional compounds per unit area. Transcriptomic analysis indicated that these metabolic shifts were accompanied by transcriptional changes of phenylpropanoid and terpenoid pathways, with AW/D associated with higher expression of downstream lignan-assembly genes ( DIR ) and the zerumbone synthase TPS8–1 , while DR was associated with higher expression of T PS8–2 and CYP76S105–1 . Co-expression analysis suggested that WRKY and MYB transcription factors may participate in these responses. Our results demonstrate that an appropriate watering regime can efficiently induce target compound profiles in plantlets in common-garden experiment even far away from native habitat, offering a sustainable alternative to wild harvesting for this protected species, and providing a potential strategy to establish upstream production capacity and reduce the payback period in cultivation.