Drought stress is the main limiting factor of crop productivity. Wild soybean (Glycine soja) is a fine germplasm resource, which has a high tolerance to adverse environmental conditions. This study aimed to reveal the mechanism responsible for drought tolerance in drought-tolerant wild soybean. Here, the growth parameters and metabolomics of the two wild soybean varieties’ seedlings were analyzed under polyethylene glycol-simulated drought stress using gas chromatography–mass spectrometry. In total, 61 differentially accumulated metabolites were identified in leaves under polyethylene glycol-6000-simulated drought conditions. Compared with common wild soybean, the drought-tolerant wild soybean grew better. A metabolite profiling analysis suggested that the tricarboxylic acid cycle was enhanced in drought-tolerant wild soybean but inhibited in common wild soybean compared with the control group under simulated drought stress. Thus, the accumulation of osmotic compounds and the enhancement of energy and secondary antioxidant metabolism under drought-stress conditions are the mechanisms responsible for drought tolerance in drought-tolerant wild soybean. The results provide an important theoretical basis for utilizing wild soybean resources.
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