Time-course transcriptomic information unravels the adaptation strategies of Nicotiana tabacum to drought stress through altered root system architecture

Introduction Drought stress, exacerbated by global climate change, poses a significant threat to agricultural productivity and global food security. Plants have evolved intricate adaptive mechanisms, with the root system playing a crucial role in sensing soil water deficits and acquiring essential resources. Methods This study investigated the time-course adaptation strategies of two Nicotiana tabacum varieties, ZC208 (drought-tolerant) and ZY100 (drought-sensitive), to different levels of drought stress through altered root system architecture (RSA) and transcriptomic regulations. Results RSA parameters generally decreased, while specific root length, surface area, and volume increased. Antioxidant enzyme activities (SOD, POD, CAT) and proline content in roots significantly increased, contrasting with a reduction in soluble sugars. This research provides valuable insights into the dynamic molecular and physiological mechanisms underlying drought adaptation in tobacco roots, offering potential targets for breeding drought-tolerant cultivars to enhance agricultural resilience in a changing climate. Analysis of the root transcriptome identified a large cohort of differentially expressed genes (DEGs), with more downregulated than upregulated DEGs across all drought stages in both varieties. Time-course analysis using STEM identified distinct expression profiles for ZC208 (6 profiles) and ZY100 (8 profiles), highlighting dynamic gene regulation over time. WGCNA identified modules strongly correlated with RSA parameters, with key pathways including ‘MAPK signaling pathway, plant’, ‘plant-pathogen interaction’, and ‘sesquiterpenoid and triterpenoid biosynthesis’. Genes involved in plant hormone signaling (e.g., AUX/IAA, PYR/PYL) and starch/sucrose metabolism (e.g., endoglucanase, β-glucosidase) showed differential expression patterns, indicating their crucial roles in drought response. Discussion This research provides valuable insights into the dynamic molecular and physiological mechanisms underlying drought adaptation in tobacco roots, offering potential targets for breeding drought-tolerant cultivars to enhance agricultural resilience in a changing climate.