Comparative metabolomic and physiological analysis uncovers distinct drought tolerance mechanisms in four rice cultivars

Drought stress is a major abiotic challenge threatening global food security by negatively affecting rice morphology, physiology, and biochemistry. This study explored the morpho-physiological and metabolomic responses of four rice cultivars (Giza 179, Hassawi, Super 300, and Y EGY) to drought stress induced by 15% PEG for 14 days. Measurements included fresh weight, relative water content (RWC), proline content, and plant height, while leaf and root tissues underwent detailed GC-MS metabolomic profiling followed by multivariate analyses such as PCA, VIP scoring, volcano plots, and pathway enrichment. Results showed Y EGY experienced the greatest decline in fresh weight, whereas Giza 179 maintained higher biomass. Stress tolerance indices ranked the cultivars as Giza 179 (85.2%), Super 300 (65.5%), Hassawi (61.7%), and Y EGY (52.2%). Metabolomic analysis identified 114 leaf and 97 root metabolites, with 40 showing VIP > 1.0. Volcano plot analysis revealed distinct variety-specific responses: Giza 179 demonstrated broad metabolic activation with upregulation of methylgalactoside, glycerol-3-phosphate, and citric acid in leaves; Hassawi showed effective targeted responses with strategic trehalose upregulation, while Y EGY exhibited extensive root metabolic disruption. Pathway enrichment identified alanine, aspartate, and glutamate metabolism, arginine and proline metabolism, and the TCA cycle as most significantly affected in leaves, while the TCA cycle was the main response pathway in roots. Post-hoc analysis confirmed that drought-tolerant cultivars exhibited more balanced metabolic regulation. These findings suggest that superior drought tolerance is associated with either efficient targeted metabolic responses that conserve resources (Hassawi, Super 300) or robust integrated mechanisms that coordinate osmoregulation and metabolic reprogramming (Giza 179), providing valuable insights for breeding drought-tolerant rice varieties.