Genes associated with translation and oxidative phosphorylation as components of the translational response in nodulated and water-restricted soybean

Abstract Background Soybean primarily acquires nitrogen through symbiosis with nitrogen-fixing bacteria. Water deficit (WD) is a major stress limiting crop yield. Nodulation may enhance drought tolerance in legumes by modulating nitrogen and hormone metabolism, osmotic adjustment, and antioxidant defenses. However, the molecular mechanisms underlying the differing WD responses in nodulated (N-fix) versus non-nodulated (N-fed) plants remain unclear. Translational control of gene expression is a key regulatory mechanism during stress. Results Here, we compared the transcriptome and translatome of soybean roots from N-fix and N-fed plants exposed to WD, analyzing four combined treatments. Our results showed that N-fix plants under WD exhibited more complex responses in terms of total differentially expressed genes (DEGs) compared to N-fed plants. This complexity was also evident in DEGs subject to translational regulation and in differentially expressed transcription factors. Co-expression analysis revealed modules associated with core biological processes, encompassing nodulation, water deficit, and most interestingly, their interplay. Conclusions Our research reveals that translational regulation of genes involved in oxidative phosphorylation and translation initiation emerged as a key response in N-fix plants under WD. These findings highlight distinct molecular adaptations in nodulated soybean roots under WD, with translational control playing a central role. We also identified promising transcription factor candidate genes under translational regulation in N-fix roots—for which no role in nodulation has been described—offering potential targets for improving drought tolerance in legumes once validated functionally.