Integrated transcriptome-metabolome analysis reveals a GmMYB093-GmCYP90A1-BR module supporting soybean adaptation to iron deficiency.

Iron deficiency is a major abiotic constraint that limits soybean growth, nodulation, symbiotic nitrogen fixation, and yield, yet objective criteria for evaluating low-Fe tolerance and the regulatory mechanisms linking root-nodule responses with shoot adaptation remain insufficiently defined. Here, we established an entropy-weight-based evaluation system using 62 soybean accessions and identified Wanhuang506 (Wh506) as a highly tolerant cultivar and Flyer as a highly sensitive cultivar. Physiological validation showed that Wh506 maintained higher Fe accumulation, chlorophyll retention, antioxidant enzyme activities, and nodule development than Flyer under low-Fe stress. To explore the molecular basis of this contrast, integrated transcriptomic and metabolomic profiling was performed in leaves and root-nodule complexes (RNCs). Compared with Flyer, Wh506 exhibited stronger RNC-centered transcriptional and metabolic reprogramming involving Fe-related redox processes, secondary metabolism, and brassinosteroid (BR) biosynthesis. Multi-omics integration prioritized GmCYP90A1, a BR biosynthetic cytochrome P450 gene, as a candidate component associated with low-Fe tolerance, while the MYB transcription factor GmMYB093 was specifically induced in Wh506 RNCs. Yeast one-hybrid and dual-luciferase assays demonstrated that GmMYB093 directly binds to the GmCYP90A1 promoter and activates its transcription. Hairy-root overexpression of GmMYB093 or GmCYP90A1 increased endogenous BR levels, improved Fe accumulation, enhanced antioxidant capacity, reduced lipid peroxidation, and alleviated chlorosis and growth inhibition under low-Fe stress. Exogenous BR application further mitigated Fe-deficiency-induced chlorosis, particularly in sensitive accessions. These findings support a model in which the GmMYB093-GmCYP90A1-BR module contributes to soybean low-Fe adaptation by coordinating Fe homeostasis, redox protection, and root-nodule performance, providing candidate targets for breeding Fe-efficient soybean cultivars.