Integrated metabolomic and physiological profiling reveals mechanisms of drought tolerance in soybean.

BACKGROUND: Drought is a major constraint to soybean productivity, yet the metabolic mechanisms underlying genotypic variation in drought tolerance remain incompletely understood. This study investigated metabolic and physiological responses to water deficit in three Egyptian soybean breeding lines (L07, L34, and L74). RESULTS: Gas chromatography-mass spectrometry profiling identified 132 metabolites in leaves and 86 in roots, including amino acids, organic acids, carbohydrates, polyphenols, and lipids. Principal component analysis clearly separated control and drought-stressed plants, with the first two components explaining 55.7% and 54.4% of the variance in leaves and roots, respectively. L74 exhibited greater metabolic stability and accumulated higher levels of protective polyphenols (vanillic and benzoic acids), compatible solutes (trehalose and mannitol), and stress-related amino acids (γ-aminobutyric acid and proline) than L07 and L34. Partial least squares discriminant analysis identified trehalose, quercetin, chlorogenic acid, and phosphorylated sugars as major drought-responsive metabolites (variable importance in projection = 2.65-3.14). Pathway analysis revealed coordinated changes in carbohydrate metabolism, tricarboxylic acid cycle intermediates, and antioxidant metabolism. Physiologically, L74 maintained higher relative water content (81%) than L07 (71%) and L34 (69%), together with greater shoot biomass and antioxidant enzyme activities. CONCLUSION: Integrated metabolic and physiological analyses indicate that L74 achieves superior drought tolerance through coordinated metabolic homeostasis involving osmotic adjustment, antioxidant protection, and maintenance of primary metabolism. The identified metabolic signatures provide potential biomarkers for screening and breeding drought-tolerant soybean germplasm. © 2026 Society of Chemical Industry.