Different Substrates Drive Differential Responses of Rice to Salt Stress

Abstract Studying the salt tolerance mechanisms of rice under a single substrate has certain limitations. The salt tolerance strategies of rice may differ under different substrate conditions. This study established three substrate types by adjusting the proportions of laterite, peat moss, and river sand: S1 (high sand; low nutrient), S2 (medium sand; medium nutrient), and S3 (low sand; high nutrient). Compared with the respective fresh water control, the magnitude of dry weight reduction in each substrate gradually decreased (S1–S3), indicating that the salt stress was effectively alleviated. KEGG enrichment analysis of differentially expressed genes (DEGs) showed that Xiangliangyou900 may be more dependent on the remodeling of carbon metabolism pathway (compared to nitrogen metabolism) in S1, but the nitrogen metabolism pathway were more significant in S3. In S3, differential metabolites were significantly enriched in carbon and nitrogen metabolism pathways, but no such enrichment was found in S1, indicating that the S3 substrate, with its high nutrient and low river sand content, is more likely to trigger carbon and nitrogen metabolism remodeling. Under salt stress, the methylation level of C bases in the CHH type increased in S1 and decreased in S3. The methylation level of CHH-type C bases in the whole genome was more strongly correlated with the physicochemical parameters of the substrate (compared to CG and CHG types). This study speculated that rice may optimize its ability to adapt to salt stress by specifically regulating the methylation of CHH-type C bases to mediate gene expression. The results of this study help enrich the theoretical system of the rice salt stress response mechanism.