Legume Genomics and Genetics 2026, Vol.17, No.1, 32-48 http://cropscipublisher.com/index.php/lgg 33 2022). Physiologically, drought reduces leaf water potential and stomatal conductance, impairs chlorophyll content and gas exchange, and induces oxidative damage, as evidenced by elevated malondialdehyde levels and enhanced activities of antioxidant enzymes such as superoxide dismutase and peroxidase (Sekhurwane et al., 2025; Wang et al., 2025). While agronomic and physiological studies have clarified how and when drought damages soybean, the underlying molecular programs that orchestrate these responses-and that distinguish tolerant from sensitive genotypes-are only partially understood. Over the past two decades, substantial progress has been made in elucidating the molecular mechanisms of plant drought stress responses in model and crop species. Drought is now recognized as a complex stimulus that triggers interconnected signaling networks involving Ca2+ fluxes, reactive oxygen species (ROS), and phytohormones, most prominently abscisic acid (ABA) (Razi and Muneer, 2021). ABA-dependent and ABA-independent pathways converge on a wide array of transcription factors (TFs), including members of the DREB/CBF, NAC, bZIP, MYB, and WRKY families, which regulate suites of stress-responsive genes involved in osmotic adjustment, cell protection, and growth modulation (Aslam et al., 2022; Geng et al., 2024; Yue et al., 2025). These downstream genes encode late embryogenesis abundant (LEA) proteins, dehydrins, heat shock proteins, antioxidant enzymes, and transporters that collectively mitigate dehydration, membrane damage, and metabolic perturbation (Haghpanah et al., 2024). Multi-level regulation further includes post-transcriptional and epigenetic controls, such as alternative splicing, microRNAs, and DNA or RNA methylation, which fine-tune transcript stability and translation under fluctuating stress conditions (Fan et al., 2025). Insights from rice, sorghum, tomato, and other crops highlight the conservation and diversification of drought regulatory networks. In rice and other cereals, key drought-responsive genes and pathways have been extensively catalogued, including ABA signaling modules, MAPK cascades, and transcriptional networks that modulate root architecture, stomatal behavior, and chloroplast function (Fan et al., 2025; Yue et al., 2025). Reviews integrating physiological and molecular perspectives emphasize that drought tolerance is a polygenic, systems-level trait, shaped by signaling crosstalk among hormones and by networked gene modules acting at signaling, transcriptional, and effector levels (Razi and Muneer, 2021; Haghpanah et al., 2024). In soybean, functional studies such as CRISPR/Cas9 editing of specific transcription factors (e.g., GmHdz4) have demonstrated that targeted manipulation of drought-related regulatory genes can significantly enhance tolerance, underlining the translational potential of molecular knowledge for breeding (Ali et al., 2025). Despite these advances, many components of soybean-specific drought regulatory circuits and their dynamic coordination across development remain to be defined. Transcriptomics has emerged as a central tool to dissect plant drought responses at genome-wide scale. RNA sequencing (RNA-seq) enables quantitative profiling of gene expression changes across tissues, developmental stages, and contrasting genotypes, allowing the identification of differentially expressed genes (DEGs), coexpression modules, and enriched pathways under water deficit (Fracasso et al., 2016; Privitera et al., 2024; Yue et al., 2025). Comparative transcriptome studies in sorghum, tomato, Brassica, and other species have revealed that drought induces large transcriptional reprogramming in pathways such as phenylpropanoid and flavonoid biosynthesis, starch and sucrose metabolism, amino acid metabolism, ROS detoxification, and hormone signaling (Privitera et al., 2024; Yue et al., 2025). In soybean, integrated transcriptomic and metabolomic analyses under PEG-simulated drought at the seedling stage have demonstrated that tolerance involves coordinated adjustments in TCA cycle activity, glycolysis, secondary metabolism (especially flavonoids and isoflavones), and multiple hormone pathways, including ABA, auxin, gibberellin, and brassinosteroids (Wang et al., 2022). These studies not only identify candidate genes and metabolites associated with drought resistance, but also highlight cultivar-specific strategies for maintaining growth under water deficit (Wang et al., 2022). As sequencing technologies advance and costs decline, transcriptomics is increasingly being combined with other omics layers-metabolomics, proteomics, and even chromatin accessibility assays such as ATAC-seq-to build systems-level models of drought adaptation (Privitera et al., 2024; Shen et al., 2025). Multi-omics integration has
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