Unravelling mechanisms of drought tolerance in a soybean cultivar (Daewonkong roots): insights into integrative transcriptomic and metabolite analyses

Soybean (Glycine max L.), a major food crop in Korea, is highly vulnerable to drought, particularly under rain-fed cultivation. Although several transcriptomic studies have examined drought-responsive pathways in soybean leaves, research on root-specific responses and their association with isoflavone-mediated antioxidant defense remains limited. The Korean cultivar Daewonkong, which is widely cultivated but sensitive to drought, presents a useful candidate for investigating the molecular and metabolic mechanisms of stress susceptibility. RNA sequencing of Daewonkong roots under controlled and drought-stressed conditions identified 1,348 upregulated and 2,835 downregulated genes. Kyoto Encyclopedia of Genes and Genomes and MapMan analyses revealed enrichment of galactose, nitrogen, and glutathione metabolism among the upregulated genes, whereas cell wall, lipid, phenylpropanoid, and isoflavonoid biosynthesis were strongly repressed, suggesting a metabolic shift from growth-related processes to stress acclimation. When comparing the drought-sensitive Daewonkong cultivar with the drought-tolerant cultivar PI 471938, clear phenotypic and metabolic differences were observed. PI 471938 displayed a substantially higher survival rate after recovery from drought-induced stress and accumulated 2.5-fold greater levels of total isoflavones. Concurrently, this cultivar exhibited significantly enhanced antioxidant capacity, with higher polyphenol content and stronger radical scavenging activity [2,2′-Azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) and 2,2-Diphenyl-1-picrylhydrazyl (DPPH)] than Daewonkong. Furthermore, several drought-responsive genes, including GmMYB14, GmNFYA13, GmWRKY12, and GmFAD3A, were expressed at high levels in PI 471938, consistent with their roles in oxidative stress mitigation, membrane stability, and transcriptional regulation. Our findings demonstrate that drought tolerance in soybean is associated with enhanced antioxidant activity, increased isoflavone accumulation, and the coordinated induction of stress-responsive genes. These results provide molecular insights into soybean’s drought adaptation, establishing a foundation for breeding strategies to improve stress resilience.