Legume Genomics and Genetics 2026, Vol.17, No.1, 32-48 http://cropscipublisher.com/index.php/lgg 34 uncovered key regulatory hubs, such as TFs or signaling components whose expression patterns tightly correlate with protective metabolites or physiological traits, and has begun to link chromatin state to transcriptional activation of drought-responsive genes (Shen et al., 2025). For soybean, these approaches provide an unprecedented opportunity to connect field-relevant drought phenotypes with underlying gene networks, thereby accelerating the discovery of robust biomarkers and targets for breeding. The present study leverages transcriptomic analyses in soybean under drought stress to deepen understanding of its molecular response architecture, focusing on the identification of core regulatory pathways and genotype-specific expression signatures that can inform breeding strategies for enhanced drought resilience. 2 Physiological and Molecular Bases of Soybean Drought Stress Response 2.1 Physiological changes in soybean under drought stress Drought stress triggers a cascade of physiological perturbations in soybean, affecting water status, photosynthesis, and growth. Water deficit reduces leaf water potential and relative water content, leading to stomatal closure that initially limits transpirational water loss but also constrains CO2 uptake and photosynthetic carbon assimilation (Xu et al., 2023; Wang et al., 2025). Under progressive or prolonged drought, soybean exhibits marked declines in net photosynthetic rate, stomatal conductance, intercellular CO2 concentration, and chlorophyll content, together with reduced leaf area, plant height, and biomass accumulation (Li et al., 2022; Wang et al., 2022). Chlorophyll fluorescence and OJIP analyses indicate impaired photosystem II efficiency, decreased electron transport, and enhanced non-photochemical quenching, reflecting both damage and photoprotective adjustments in the photosynthetic apparatus under severe water deficit (Falcioni et al., 2025). These physiological constraints are more pronounced at sensitive developmental stages, particularly flowering and grain filling, where decreases in photosynthesis and assimilate supply translate into reduced pod set, seed number, and seed weight, ultimately causing substantial yield losses (Li et al., 2022). Oxidative stress is a central component of the drought response. Water deficit promotes overproduction of reactive oxygen species (ROS) such as superoxide and hydrogen peroxide, inducing lipid peroxidation, protein oxidation, and membrane damage, which can be monitored via increased malondialdehyde (MDA) content and electrolyte leakage (Xuan et al., 2022; Shahriari et al., 2022). To mitigate ROS toxicity, soybean activates an antioxidant defense system, including enhanced activities of superoxide dismutase, catalase, peroxidases, and ascorbate peroxidase, alongside accumulation of non-enzymatic antioxidants and phenolic compounds (Li et al., 2022; Shahriari et al., 2022). Osmotic adjustment represents another key adaptive strategy: tolerant genotypes tend to maintain higher levels of compatible solutes such as proline, soluble sugars, and soluble proteins, helping to preserve cell turgor, stabilize proteins and membranes, and buffer redox status under drought (Figure 1) (Shahriari et al., 2022; Wang et al., 2022). Figure 1 Physiological responses of soybean to drought stress
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