Integrated physiological and transcriptomic analysis revealed key genes and pathways related to continuous drought and salinity stress in Populus.

key messageIntegrated physiological and time-series transcriptomic analyses in poplar demonstrate drought prioritizes cell wall remodeling, while salt stress immediately activates ion transporters and JA signaling, defining distinct molecular adaptation mechanisms. Drought and salt stress were major abiotic factors that severely inhibited plant growth and productivity. Although frequently studied independently, the mechanisms by which plants differentially coordinated responses to these related stresses remained poorly understood. To elucidate the divergent adaptation strategies in Populus, we integrated physiological and time-series transcriptomic analyses in a hybrid poplar ((Populus simonii × P. nigra) × P. ussuriensis) under long-term drought and salt stress, followed by a recovery phase. Physiologically, drought stress induced delayed photosynthetic inhibition primarily via non-stomatal limitations, accompanied by sustained accumulation of proline and malondialdehyde (MDA), and high peroxidase (POD) activity even after rewatering. In contrast, salt stress caused rapid stomatal closure, leading to immediate photosynthetic decline. Notably, physiological recovery from salt stress was faster than from drought. Transcriptome sequencing identified 18,860 differentially expressed genes (DEGs). Time-course analyses revealed that drought stress prioritized activation of cell wall biogenesis (e.g., cutin, suberin, and lignin biosynthesis) and UDP-glucosyltransferase activity. Salt stress, however, immediately activated genes for ion transporters and jasmonic acid signaling. In addition, weighted gene co-expression network analysis (WGCNA) identified stress-specific modules and hub genes. In summary, this study could provide valuable insight for clarifying the physiological responses and molecular mechanisms of poplar in response to drought and salt stress.