Global analysis of differentially expressed genes between japonica and indica rice roots reveals the molecular basis for enhanced cold tolerance in japonic a rice

Plant roots provide important support for plant growth, acquiring water and nutrients, and anchoring the plants. Rice varieties have been cultivated and improved through crossbreeding of japonica rice and indica rice varieties, which have various contrasting characteristics in important traits including root development. In this study, we performed genome-wide transcriptome analysis between Dongjin (japonica) and IR64 (indica) rice varieties to identify genes associated with important agricultural traits in rice roots. Using Agilent 44K array analysis, we isolated 564 genes from Dongjin that were significantly upregulated relative to expression in IR64 and 251 genes upregulated in IR64 compared with Dongjin. Gene ontology (GO) enrichment analysis revealed that genes related to glycine, cellular amino acid, carbohydrate metabolism, hydrogen peroxide, chitin, cell wall macromolecule catabolism, and response to oxidative stress are over-represented in Dongjin compared with IR64. Conversely, in IR64, enterobactin biosynthesis, response to oxidative stress, oxidation reduction, and metabolic process genes were upregulated. Through MapMan analysis, we determined that four ascorbate peroxidase (APX) and glutathione peroxidase (GPX)-related genes closely associated with response to oxidative stress from GO enrichment analysis were more important in the roots of Dongjin than in IR64. We further confirmed that the APX and GPX enzyme activities under cold stress were higher in Dongjin than in IR64. These results explain why the japonica cultivar is more resistant to cold stress than the indica cultivar. Our results can be used as an important basis for future studies on useful traits related to root development and abiotic stress tolerance in rice.