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 higher than that in japonica. However, the mechanism underlying this discrepancy has not been elucidated. Thus, understanding the genetic and molecular basis of Cd stress between indica and japonica is highly 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 (the 3rd and 5th day) were selected for dynamic gene analysis by the transcriptome method. The results showed that CH891 was more sensitive to Cd than 02428, and a total of 7,204 and 6,670 differentially expressed genes (DEGs) associated with Cd stress were detected on the 3rd day and 5th day, respectively. 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 pathway analysis of DEGs preferentially expressed in a stage-specific and cultivar-specific manner showed that secondary metabolic processes were enriched in SCR, while protein metabolism and plant hormones were enriched in RCR. The diverted metabolic pathways might be the major reason for the different response mechanisms of Cd in indica and japonica rice.Conclusion: These results provide novel insights regarding 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 help to elucidate the mechanisms of the indica and japonica rice Cd response differences.