Sybeans have been grown by plant breeding for decades. As soybeans have very limited genetic variation, it is difficult for soybean breeders to find new genetic resources for abiotic stressors. Recently, soybeans have been exposed to flooding stress from intensive summer rainfall owing to climate change. Glycine soja, a wild soybean, is known to have greater genetic variation and greater resistance to a variety of biotic and abiotic stresses than ordinary soybeans. In this study, high-throughput transcriptome analysis was performed using flood-treated Glycine soja. Differentially expressed genes (DEGs) were analyzed using reads mapped to reference sequences, and gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed using selected DEGs. In addition, RT-qPCR analysis was performed to further analyze the expression of specific candidate genes. Several novel genes that could explain various mechanisms related to water stress were identified as related transcripts and adaptation mechanisms through cell wall expansion, alcoholic fermentation under anaerobic conditions, and structural changes. In addition, most of the isoflavonoid daidzein pathway genes exhibited upregulated expression under flooding stress. Interestingly, expression of the DIR (dirigent protein 1-like) gene, which is known to decrease in response to flooding stress in soybeans (Glycine max), was upregulated in Glycine soja. The expression of DIR revealed that DIR may play a key role in conferring flooding stress resistance in Glycine soja. This study provides useful information regarding the genes and comprehensive adaptation mechanisms related to flooding stress tolerance that can be utilized for cultivated soybeans through the Korean wild soybean.

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