Genome-wide characterization of soybean malate dehydrogenase genes reveals a positive role for GmMDH2 in the salt stress response

Malate dehydrogenase (MDH) is a widely expressed enzyme that plays a key role in plant growth, development, and stress responses. However, information on MDH genes in the soybean genome is limited. Seventeen members of the soybean MDH family were identified by genome-wide analysis, and the genes were analyzed for the presence of conserved protein motifs. The genes were divided into five clusters according to their phylogenetic relationships. The intracellular localizations of six GmMDHs were determined by confocal microscopy of Arabidopsis mesophyll protoplasts. Transcripts of GmMDHs were significantly increased by abiotic stress (drought, salt, and alkalinity) and hormone treatments, as shown by an analysis of cis-regulatory elements and quantitative real-time polymerase chain reaction (qRT-PCR). The GmMDHs displayed unique expression patterns in various soybean tissues. Notably, the expression levels of a chloroplast isoform (GmMDH2) were unusually high under salt stress, presumably indicating a critical role in soybean responses to salinity. Expression of GmMDH2 in Escherichia coli showed that the recombinant enzyme has nicotinamide adenine dinucleotide phosphate (NADP)-dependent MDH activity. The redox states of the NADP (reduced form) (NADPH) pool and antioxidant activities were shown to be modulated by GmMDH2 gene overexpression, which in turn reduced reactive oxygen species (ROS) formation in transgenic soybean, significantly enhancing the salt stress resistance. Gene-based association analysis showed that variations in GmMDH2 were strongly linked to seedling salt tolerance. A polymorphism potentially associated with salt tolerance was discovered in the promoter region of GmMDH2. These findings not only improve our understanding of the stress response mechanism by identifying and characterizing the MDH gene family throughout the soybean genome but they also identified a potential candidate gene for the future enhancement of salt tolerance in soybean.