Integrated transcriptomic and metabolomic analysis of provenances and organ-specific responses to drought and rehydration in Pinus tabuliformis

Introduction Drought stress severely limits the survival and growth of Pinus tabuliformis seedlings during afforestation. However, the molecular mechanisms coordinating organ-specific responses across diverse geographical provenances remain inadequately characterized. Methods This study investigated the dynamic drought responses of two provenances of P. tabuliformis , originating from semi-arid (HLH) and semi-humid (SL) regions, through a time-course drought and rewatering experiment. Integrated transcriptomic and metabolomic analyses of roots and leaves revealed a clear functional specialization between these organs. Results Roots primarily initiated signal transduction and osmotic adjustment, whereas needles were predominantly engaged in minimizing water loss through transpiration. Notably, the HLH provenance demonstrated a rapid-response plasticity strategy, while the SL provenance exhibited a highly dynamic defensive strategy. Several key candidate genes, including Pt2G21940, Pt1G23820, and Pt5G10920, were identified. Furthermore, gene-metabolite correlation networks underpinning the dynamics of proline, jasmonic acid, and flavonoid metabolism were delineated. Discussion These findings provide a molecular foundation for deciphering the drought resistance mechanisms in P. tabuliformis and offer valuable genetic targets for breeding drought-tolerant conifers.