Transcriptome and Metabolome Analyses Reveal the Mechanism by Which Uniconazole Affects Waterlogging Stress in Soybean

Waterlogging stress typically causes submergence or partial submergence stress in plants, which negatively impacts agricultural production, from seed germination to vegetative and reproductive growth. Uniconazole (S3307) was recently used to minimize the damage caused by waterlogging. Here, we investigate the effects of S3307 on the growth, development, and yield of soybean under waterlogging stress. Morphological and physiological indexes, as well as the transcriptome and metabolome of soybean were analyzed in control condition and waterlogged condition with (WS) or without (W) spraying S3307. The results showed that waterlogging stress led to growth inhibition and reduced activity of antioxidant enzymes in soybean plants, resulting in a large accumulation of MDA content and ultimately causing yield reduction. Foliar spraying of S3307 increased stem diameter, reduced plant height, increased dry matter accumulation, increased antioxidant enzyme activities, inhibited MDA accumulation, and alleviated the yield reduction. The combined transcriptomics and metabolomics investigation demonstrated that, compared to Control, both W and WS treatments generated similar directional changes in triterpenoid metabolism and stress response pathways, suggesting that waterlogging stress activated these defense-related pathways. Notably, the strength of these reactions was considerably greater in the WS treatment than in the W treatment. Under waterlogging stress, foliar application of S3307 increased the expression of genes involved in flavonoid production and increased the accumulation of unsaturated fatty acids-substances known to help in cell membrane stability-when compared to the W treatment. In summary, our findings show that S3307 does not alter the direction of waterlogging-induced reactions but rather greatly increases their strength, thereby positively regulating soybean waterlogging tolerance. This establishes a biochemical mechanism and theoretical foundation for using plant growth regulators to reduce stress.