Legume Genomics and Genetics 2026, Vol.17, No.1, 32-48 http://cropscipublisher.com/index.php/lgg 38 and photosynthesis in drought responses (Wang et al., 2022; Kong et al., 2025). KEGG pathway and MapMan analyses further reveal coordinated changes in primary and secondary metabolism, including the TCA cycle, glycolysis, flavonoid and isoflavone biosynthesis, and cell wall remodeling, which have been repeatedly implicated in soybean drought tolerance (Wang et al., 2022; Kong et al., 2025). Network-based approaches, such as weighted gene co-expression network analysis (WGCNA), can identify co-expressed modules and hub genes associated with drought-tolerance traits or time-dependent responses (Li et al., 2022). By combining DEG lists with functional enrichment and network analyses, soybean RNA-seq studies have pinpointed key transcription factors, signaling components, and metabolic enzymes as candidate regulators of drought resistance, providing targets for functional validation and molecular breeding. 4 Identification and Functional Analysis of Differentially Expressed Genes in Soybean Under Drought Stress 4.1 Key differentially expressed genes induced by drought stress Transcriptomic profiling under water deficit has revealed thousands of differentially expressed genes (DEGs) in soybean, with both drought intensity and genotype strongly shaping expression patterns. In the drought-sensitive cultivar Liaodou 15, 2214, 3684 and 2985 DEGs were identified at mild, moderate and severe drought at flowering, respectively, indicating progressive transcriptional reprogramming as stress intensifies. Many of these DEGs are involved in antioxidant defenses, secondary metabolism and hormone signaling, and their induction is associated with increased activities of superoxide dismutase (SOD) and catalase (CAT) and elevated malondialdehyde (MDA), reflecting active but only partially effective stress mitigation (Li et al., 2022). Comparative analyses between tolerant and sensitive genotypes generally show a larger number of DEGs and stronger fold-changes in tolerant lines, suggesting that robust and timely transcriptional activation is a hallmark of drought resilience (Xuan et al., 2022). Across cultivars and developmental stages, a subset of drought-responsive genes appears conserved. Meta-analysis and co-expression network studies integrating multiple datasets identified 2168 robust DEGs and hub genes associated with photosynthesis, cytokinin dehydrogenase activity, glyceraldehyde-3-phosphate dehydrogenase, and systemic acquired resistance, pointing to central roles for carbon metabolism and stress signaling in drought tolerance (Shahriari et al., 2022). Specific metabolic genes, such as NCED1 and an SDR enzyme in abscisic acid (ABA) biosynthesis, and CHS, C4H, CAD, F3H, VTC and GST in flavonoid and ascorbate-glutathione pathways, have been repeatedly highlighted as key nodes linking ROS detoxification, secondary metabolism and yield maintenance under drought (Li et al., 2022). Lipid metabolism genes, including ADH and GPAT3, show consistent differential expression across several tolerant and sensitive cultivars and are proposed as universal drought-responsive markers (Yang et al., 2023). Integrative transcriptome-metabolome work further implicates genes in the tricarboxylic acid (TCA) cycle, glycolysis, and isoflavone biosynthesis as central regulators of energy supply and protective metabolites during water deficit (Wang et al., 2022). 4.2 Analysis of drought resistance-related transcription factor families Transcription factors (TFs) represent a major fraction of drought-induced DEGs and act as key switches in stress-responsive networks. Comparative RNA-seq of tolerant SS2-2 and sensitive Taekwang revealed strong SS2-2-specific upregulation of TFs from multiple families, including bZIP (GmbZIP), DREB, ERF, HD-ZIP, MYB, NAC and WRKY; in particular, one GmbZIP, one GmDREB, one GmHDZIP, five GmMYBs, six GmNACs, and 26 GmWRKYs were markedly induced only in the tolerant cultivar under severe water deficit (Yang et al., 2023). Weighted gene co-expression network analysis (WGCNA) in Liaodou 15 highlighted WRKY (e.g., Glyma.15G021900, Glyma.15G006800), MYB (Glyma.15G190100, Glyma.15G237900), and bZIP (Glyma.15G114800) TFs as central drought-responsive regulators (Li et al., 2022). A meta-network analysis across datasets likewise identified TF-rich co-expression modules and linked specific cis-regulatory motifs in DEG promoters to TF families such as bZIP, AP2/ERF, NAC and MYB, underscoring their pervasive roles in coordinating drought responses (Shahriari et al., 2022).
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