Unique Transcriptome and Gene Expression Analysis of Rice Seedling Reveals Different Cadmium Response Regulatory Mechanisms Between Indica and Japonica Rice

Abstract Background: In general, the Cd content in indica rice is usually higher than that in japonica. However, the mechanism for this discrepancy is unclear. Thus, understanding the genetic and molecular basis of Cd stress between indica and japonica is extremely important for rice improvement programs.Results: In this study, two varieties of rice, japonica 02428 and indica CH891, were continuously exposed to Cd and seedlings of the two varieties at two critical stages (3rd and 5th day) were selected for the dynamic genes analysis by transcriptome method. The results showed that CH891 was more sensitive to Cd than 02428, and a total of 7,204 and 6,670 differently expressed genes (DEGs) associated with Cd stress were detected at 3rd day and 5th day. Furthermore, we divided these DEGs into three categories: SCR (sensitive variety with Cd-responsive), RCR (resistant variety with Cd-responsive) and CCR (common Cd-responsive). The enriched metabolic pathways analysis of DEGs preferentially expressed in a stage-specific and cultivars-specific manner, and secondary metabolic processes were enriched in SCR while protein metabolism and plant hormone were enriched in RCR. The diverted metabolic pathways might be the major cause for different response mechanism of Cd in indica and japonica rice. Conclusion: These results provide a novel insight into the Cd response mechanism in rice seedlings between different varieties, and these important Cd-responsive DEGs were frequently involved in specific biological processes and metabolic pathways that might provide a novel insight over indica and japonica rice Cd response mechanism difference.