Transcriptomic and Metabolomic Integrated Analysis of the Effect of Exogenous Nano-silicon on Rice Salt Tolerance Under Salt Stress

Objective Exploring the potential physiological and molecular mechanisms of nano-silicon soaking on salt tolerance in rice, especially the synergistic transcriptional and metabolic responses, to provide theoretical basis and technical guidance for stress resistant cultivation of rice in saline soil.

Method Rice cultivar '9311' was used as the experimental material, with four treatments: Seed soaking with distilled water without NaCl treatment (control, CK), seed soaking with 2.00 mmol/L exogenous nano-silicon without NaCl treatment (exogenous nano-silicon, N), seed soaking with distilled water + 60 mmol/L NaCl treatment (salt stress, S), and seed soaking with 2.00 mmol/L exogenous nano-silicon + 60.00 mmol/L NaCl treatment (nano-silicon + salt stress, N+S). Samples were collected at three-leaf-one-heart stage to measure morphological indicaes, antioxidant enzyme activities, osmotic regulatory substances, and endogenous hormones in leaves and roots. Transcriptomic and metabolomic analyses were integrated to identify differentially expressed genes(DEGs) and differentially accumulated metabolites (DAMs).

Result Salt stress markedly inhibited the growth of rice seedlings. In comparison to the CK, the aboveground dry weight and root dry weight of seedlings subjected to S decreased significantly by 35.53% and 50.69%, respectively. Additionally, the activities of POD in leaves and roots increased significantly by 32.02% and 38.14%, respectively, while MDA content rose significantly by 55.57% in leaves and 18.23% in roots. The Na⁺ content increased significantly by 1 382.48% and 951.52%, respectively. Compared with the S treatment, the N+S treatment significantly increased the aboveground dry weight and root dry weight of seedlings by 26.28% and 49.53%, respectively. The activities of SOD, POD, and CAT in the root system increased significantly by 57.14%, 20.53%, and 80.59%, respectively. The contents of SP and Pro in the leaves increased by 14.37% and 21.86%, respectively. Furthermore, the MDA content in leaves and roots decreased by 26.37% and 10.20%, respectively, and the Na⁺ content decreased by 38.20% and 25.75%, respectively. Transcriptomic analysis indicated that, compared to S treatment, N+S treatment identified 61 and 276 DEGs in leaves and roots, respectively. The DEGs in leaves treated with N+S were significantly enriched in pathways such as lysine biosynthesis and ABC transporters. In contrast, the DEGs in roots were significantly enriched in pathways related to plant hormone signal transduction and linoleic acid metabolism. Metabolomics analysis identified 104 and 64 DAMs in leaves and roots treated with N+S, respectively, compared to S treatment. Further analysis revealed that the metabolism of nicotinate and nicotinamide was significantly enriched in leaves treated with N+S, while the metabolism of linoleic acid, cysteine, and methionine in roots was significantly enriched. Through the integrated analysis of transcriptomics and metabolomics, compared to S treatment, the DEGs and DAMs in the leaves treated with N+S were enriched in pyrimidine metabolism and pyruvate metabolism, whereas those in the root system were enriched in zeatin biosynthesis.

Conclusion Exogenous nano-silicon seed soaking treatment activates the antioxidant system, enhances osmotic regulation, and balances ion homeostasis and endogenous hormone levels by modulating the transcriptional and metabolic pathways involved in zeatin biosynthesis, thereby mitigating salt stress damage in rice seedlings..