Plants coevolved with their antioxidant defense systems, which detoxify and adjust levels of reactive oxygen species (ROS) under multiple plant stresses. We performed whole-genome identification of ascorbate peroxidase (APX) and catalase (CAT) families in cultivated and wild soybeans. In cultivated and wild soybean genomes, we identified 11 and 10 APX genes, respectively, whereas the numbers of identified CAT genes were four in each species. Comparative phylogenetic analysis revealed more homology among cultivated and wild soybeans relative to other legumes. Exon/intron structure, motif and synteny blocks are conserved in cultivated and wild species. According to the Ka/Ks value, purifying selection is a major force for evolution of these gene families in wild soybean; however, the APX gene family was evolved by both positive and purifying selection in cultivated soybean. Segmental duplication was a major factor involved in the expansion of APX and CAT genes. Expression patterns revealed that APX and CAT genes are differentially expressed across fourteen different soybean tissues under water deficit (WD), heat stress (HS) and combined drought plus heat stress (WD + HS). Altogether, the current study provides broad insights into these gene families in soybeans. Our results indicate that APX and CAT gene families modulate multiple stress response in soybeans.

Magnesium (Mg) is essential for plant growth and development and plays critical roles in physiological and biochemical processes. Mg deficiency adversely affects growth of plants by limiting shoot and root development, disturbing the structure and membranes of the grana, reducing photosynthesis efficiency, and lowering net CO2 assimilation. The MGT (Magnesium transporter) family is responsible for the absorption and transportation of magnesium in plants. Although the MGT family has been identified in different plant species, research regarding the soybean MGT genes is limited. In the current study, a total of 39 MGT genes distributed on 17 different chromosomes were identified in soybean. Phylogenetic analysis classified GmMGTs into three subgroups, NIPA, MRS2/MGT, and CorA, which showed little homology with MGTs of Arabidopsis thaliana and Oryza sativa members and clustered tightly with GmMGTs. Gene structure and conserved motif analysis also confirmed similar grouping in GmMGTs. The expansion of the GmMGT members in NIPA and MRS2/MGT was predicted, while CorA was identified as the most conserved group in G. max. Segmental duplication under purifying selection pressure was identified as the major driving force in the expansion of MGTs in soybean. GmMGTs showed diverse tissue-specific and stress-response expression patterns due to the presence of stress-related cis-regulatory elements in their promoter regions. Under Mg-deficiency and surplus stress conditions, a decrease in root length, shoot length, and root and shoot fresh as well dry weight in susceptible genotypes showed the variegated expression of MGTs in soybean genotypes. Furthermore, the upregulation of GmMGT2 and GmMGT29 in tolerant genotypes in response to Mg-deficiency as well as surplus stress conditions in leaves suggested the essential role of GmMGT genes in the absorption and transportation of Mg in soybean leaves. This study presents a comprehensive analysis of the MGT gene family in soybean, providing insights into their evolutionary relationships, gene classification, protein structures, and expression patterns under both Mg deficiency and Mg surplus conditions.

Soybean (Glycine max L.) is grown worldwide to obtain edible oil, livestock feed, and biodiesel. However, drought and salt stress are becoming serious challenges to global soybean cultivation as they retard the growth of soybean plants and cause significant yield losses. Voltage-dependent anion-selective channel (VDAC) proteins are well-known for their role in drought and salt tolerance in crop plants. In this study, we identified 111 putative VDAC genes randomly distributed in genomes of 14 plant species, including cultivated soybean (Glycine max) and wild soybean (Glycine soja). The comparative phylogenetic studies classified these genes into six different clades and found the highest structural similarities among VDAC genes of G. max and G. soja. From the conserved domain database, porin-3 (PF01459) was found to be the conserved domain in all VDAC proteins. Furthermore, gene annotation studies revealed the role of GmaVDAC proteins in voltage-gated anion channel activity. These proteins were also found to interact with other proteins, especially mitochondrial receptors. A total of 103 miRNAs were predicted to target fifteen GmaVDAC genes. In G. max, these genes were found to be segmentally duplicated and randomly distributed on twelve chromosomes. Transcriptomic analysis revealed that the GmaVDAC18.2 gene showed overexpression in root nodules, whereas the GmaVDAC9.1, GmaVDAC18.1, and GmaVDAC18.2 genes showed overexpression under drought and salt stress conditions.

Drought and salinity are two major factors limiting soybean productivity worldwide, and both stresses can negatively affect plant growth in similar manners by disrupting cellular redox homeostasis and metabolism. However, the regulatory networks coordinating transcriptional control and metabolic adaptation under both types of stress remain poorly understood. Here, we demonstrate that the R2R3–MYB transcription factors GmMYB60a and GmMYB60b serve as core negative regulators of drought and salt tolerance in soybean. Loss‐of‐function mutations in GmMYB60a/b clearly increased stress tolerance, which was associated with reduced reactive oxygen species accumulation and increased antioxidant capacity. The GmMYB60 proteins directly bind to and transcriptionally repress GmCYS20 , a key gene involved in cysteine biosynthesis, thereby reducing cellular cysteine and glutathione pools. Notably, the GmCYS20 protein physically interacts with GmMYB60 in the nucleus and weakens its ability to bind DNA, resulting in the formation of a transcription–metabolic feedback loop that stabilizes redox homeostasis under stress. Furthermore, the stress‐responsive NAC transcription factor GmNAC3 directly suppresses GmMYB60 expression, thereby linking environmental signals to metabolic regulation. Together, these findings reveal a hierarchical GmNAC3–GmMYB60–GmCYS20 regulatory module that coordinates cysteine homeostasis and oxidative stress responses by integrating transcriptional repression with metabolic feedback. This work provides mechanistic insights into soybean stress adaptation and identifies promising genetic targets for improving soybean resistance to drought and salinity.