Transcriptome and metabolome analysis demonstrate critical contribution of flavonoid biosynthesis and galactose metabolism to salt resistance of rice roots

Rice roots serve as the first line of defense to perceive salt stress. Therefore, in-depth exploration of the physiological and molecular regulatory mechanisms by which rice roots adapt to saline stress environments is crucial for understanding salt tolerance in rice. The physiological indicators, transcriptome and metabolome were performed on the roots of salt-tolerant cultivar HD961 and salt-sensitive cultivar IR29 at 0 h, 12 h and 72 h after salt stress (SS) treatment with 150 mM in this study. The physiological results showed that HD961 had stronger antioxidant capacity relative to IR29. The down-regulated differentially expressed genes (DEGs) were more than up-regulated DEGs in both rice cultivars through transcriptome comparative analysis. However, the results of the metabolomics were opposite. Comprehensive analysis of transcriptome and metabolome showed that flavonoid biosynthesis in both cultivars significantly responded to SS, and galactose metabolism was an important pathway to regulate HD961 salt resistance. Most of DEGs and significantly regulated metabolites (SRMs) in the flavonoid biosynthesis pathway under SS were upregulated in both cultivars. The LOC_Os04g01354, LOC_Os11g32650 and LOC_Os12g02370 might be plausible candidate genes for salt tolerance regulation by the flavonoid biosynthesis pathway. For galactose metabolism in HD961, 28 DEGs and 9 SRMs were identified, with D-sucrose being the highest content SRM and LOC_Os07g48830 being the DEG with highest expression. These results can provide a framework for further exploration of the molecular regulatory network of salt-tolerance.