Legume Genomics and Genetics 2026, Vol.17, No.1, 32-48 http://cropscipublisher.com/index.php/lgg 40 In an integrative analysis of multiple drought transcriptome datasets, 2168 robust DEGs were grouped into eight core modules, several of which were positively correlated with water-deficit stress and enriched for photosynthesis, cytokinin dehydrogenase activity, and systemic acquired resistance. Promoter motif mining across these DEGs uncovered over-represented cis-acting regulatory elements, including ABRE, DRE, W-box, and MYB-binding sites, implicating bZIP, AP2/ERF, NAC, WRKY, and MYB TF families as key upstream regulators . Protein-protein interaction (PPI) networks further refined these modules by highlighting central nodes such as GLYMA_04G209700 and GLYMA_06G030500 with high connectivity, which may integrate signals from multiple pathways and represent promising breeding targets. At the single-gene level, regulatory networks are being constructed around specific TFs and structural genes through a combination of transcriptomics, in silico network prediction, and targeted validation. For example, genome-wide analysis of the AP2/ERF family identified GmAP2/ERF144 as strongly induced by drought and salt stress; co-expression-based network prediction followed by RT-qPCR showed that several interacting genes were upregulated 3-30-fold in GmAP2/ERF144-overexpressing lines, suggesting that this TF acts as an upstream node activating a suite of stress-responsive genes (Wang et al., 2022). Similar strategies have mapped downstream targets of NAC TFs such as GmNAC3 and GmNAC19, which modulate genes involved in osmolyte metabolism, antioxidant defenses, and root development (Cui et al., 2024). More recently, data-driven feature-engineering pipelines have integrated multi-omics and non-omics datasets to prioritize candidate drought-tolerance genes and regulatory hubs with greater robustness than traditional WGCNA, providing a scalable framework for refining soybean drought regulatory networks. Together, these approaches are transforming lists of DEGs into structured gene regulatory networks that clarify how diverse signals converge on a relatively small number of master regulators. 5.2 The role of non-coding rnas in drought resistance regulation Non-coding RNAs (ncRNAs) add an additional, transcriptome-wide layer of control to soybean drought responses, complementing transcriptional regulation by TFs. In soybean, integrated small RNA, degradome, and mRNA sequencing under drought identified hundreds of miRNA-mRNA pairs with inverse expression, indicating widespread post-transcriptional repression in stress signaling networks. A notable example is gma-miR398c, which is strongly induced by drought and targets multiple peroxisome-related copper/zinc superoxide dismutase and copper chaperone genes (GmCSD1a/b, GmCSD2a/b/c, GmCCS) (Zhou et al., 2019). Overexpression of gma-miR398c in Arabidopsis and soybean reduced expression of these targets, impaired ROS scavenging capacity, increased electrolyte leakage, and promoted stomatal opening, leading to higher drought sensitivity (Zhou et al., 2019). Conversely, knockout of miR398c enhanced tolerance, demonstrating that this miRNA acts as a negative regulator of drought resistance by constraining antioxidant defenses. Alternative splicing of GmCSD1a/b was also observed, suggesting that isoform switching can partially bypass miRNA regulation and fine-tune stress responses. Beyond miR398, broader plant studies show that drought-responsive miRNAs commonly target TFs and hormone signaling components, embedding ncRNAs within both ABA-dependent and ABA-independent pathways (Singroha et al., 2021). For instance, conserved modules such as miR159-MYB and miR169-NF-YA modulate ABA signaling, while miR156-SPL and miR393-TIR1 regulate development and auxin responses, balancing growth and survival under water limitation (Singroha et al., 2021). Long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) further diversify regulatory possibilities by acting as scaffolds, decoys, or precursors in small RNA pathways, and by interfacing with chromatin states (Bolc et al., 2025). Although lncRNA and circRNA research in soybean drought responses is still in its infancy, evidence from other crops indicates that ncRNAs orchestrate hormone crosstalk, oxidative stress defenses, and root architecture, positioning them as tractable entry points for engineering drought resilience while managing yield trade-offs (Gelaw and Sanan-Mishra, 2021). Future integration of ncRNA catalogs with soybean TF-target networks and epigenomic maps will be essential to capture the full regulatory landscape of drought adaptation.
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