Joint analysis of transcriptome and metabolome revealed the difference in carbohydrate metabolism between super hybrid rice and conventional rice under salt stress

With the increasingly severe problem of soil salinization worldwide, the molecular mechanism of salt tolerance of super hybrid rice has become an important scientific issue. In this study, the super hybrid rice Chaoyou1000 was used as the research object, and the conventional rice Huanghuazhan was used as the control to explore the molecular mechanism of salt tolerance in super hybrid rice. The joint analysis of transcriptome and metabolome found 4661 DEGs, of which 2130 were up-regulated and 2531 were down-regulated; 70 and 32 named differential metabolites were found in positive and negative ion modes, respectively. KEGG enrichment analysis showed that the carbohydrate metabolism-related pathways enriched by DEGs and differential metabolites were "starch and sucrose metabolism", "galactose metabolism", "glyoxylate and dicarboxylate metabolism", and "citrate cycle (TCA cycle)". Specifically, we found that some critical genes involved in carbohydrate metabolism, such as LOC107281310, LOC4325448, and LOC4341069, were up-regulated; some key metabolites, such as cis-aconitate, sucrose, and raffinose, were up-regulated. The difference in the expressions of these critical genes and metabolites between the two varieties is one of the most important reasons for the high yield and high resistance of Chaoyou1000. In addition, this study found that a large number of DEGs had a strong correlation with D-pipecolic acid, niveusin C, Gly Val Ala Ile, 2-(3-hydroxyphenyl)ethanol 1′-glucoside, 2,6-dimethyl-7-octene-1,6-diol 8-O-glucoside, (+)-syringaresinol, 2-indanone, 2-keto-6-acetamidocaproate, 3-dehydroquinate, IRETOL, and estrone glucuronide, suggesting that these genes and corresponding metabolites may exist with functional associations and regulatory relationships. The results of this study will provide a reference for the breeding of salt-tolerant rice.