Abstract
BACKGROUND: Soybean (Glycine max (Linn.) Merr.) is one of the important grain crops in China and a significant oilseed and high-protein dual-purpose crop both in China and worldwide. During soybean cultivation, continuous cropping obstacles are often encountered, which impede the growth and development of the crop and significantly reduce its yield and quality. Enhancing soybean’s resistance to autotoxicity has become an important research direction. Exogenous silicon (Si) plays a crucial role in the stress resistance regulation of crops, but the mechanism by which it alleviates autotoxicity remains unclear. RESULTS: We used soybean seeds (“ Zhonghuang 13 “) to assess how exogenous silicon (20 mM) affected the growth, photosynthetic characteristics, and activities of antioxidant enzymes and flavonoid-related enzymes of soybean seedlings under 4 mM Cinnamic acid(CA)-induced autotoxicity. The results showed that 4 mM CA induced autotoxicity could significantly reduce stem weight, stem fresh weight, root dry weight, root fresh weight, plant height and nodule number of soybean seedlings. Exogenous silicon can significantly improve these indexes of soybean seedlings under CA stress, and can also improve the net photosynthetic rate, transpiration rate, stomatal conductance and intercellular CO(2) concentration of soybean seedlings under CA stress, and alleviate the inhibition of antioxidase activity induced by CA. In addition, exogenous silicon can reduce the flavonoid-related enzyme activity of soybean seedlings under CA stress, thus reducing the formation of lignin and alleviating the influence on root nodules. Through transcriptome analysis, it was found that under cinnamic acid stress, a total of 9235 differentially expressed genes (DEGs) were responsive to exogenous silicon and involved in a variety of metabolic pathways and biosynthesis, including phenylpropanoid metabolism, hydrogen peroxide metabolism, nitrogen metabolism, nodulation process, plant hormone signal transduction, isoflavone biosynthesis, etc. These major metabolic and biosynthetic pathways may be the potential mechanisms by which exogenous silicon alleviates cinnamic acid stress on soybean seedlings. In addition, some members of the transcription factor family, such as AP2/ERF, C2H2, MYB, NAC, bHLH, and WRKY, may also contribute to exogenous silicon reducing cinnamic acid stress tolerance in soybean plants. This study has far-reaching significance to overcome the obstacle. CONCLUSIONS: In conclusion, the phenotypic, physiological and transcriptomic results demonstrated that the autotoxic substance cinnamic acid significantly inhibited the growth of soybeans. Exogenous sodium silicate could enhance the plant’s resistance to cinnamic acid stress by regulating the activities of antioxidant enzymes and phenylpropanoid pathway-related enzymes, as well as the expression of genes related to auxin, plant hormone signal transduction and phenylpropanoid synthesis, thereby alleviating the damage. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-026-08425-w.