Genome and Transcriptome Identification of a Rice Germplasm with High Cadmium Uptake and Translocation

The safe production of food on Cd-polluted land is an urgent problem to be solved in South China. Phytoremediation or cultivation of rice varieties with low Cd are the main strategies to solve this problem. Therefore, it is very important to clarify the regulatory mechanism of Cd accumulation in rice. Here, we identified a rice variety with an unknown genetic background, YSD, with high Cd accumulation in its roots and shoots. The Cd content in the grains and stalks were 4.1 and 2.8 times that of a commonly used japonica rice variety, ZH11, respectively. The Cd accumulation in the shoots and roots of YSD at the seedling stage was higher than that of ZH11, depending on sampling time, and the long-distance transport of Cd in the xylem sap was high. Subcellular component analysis showed that the shoots, the cell wall, organelles, and soluble fractions of YSD, showed higher Cd accumulation than ZH11, while in the roots, only the cell wall pectin showed higher Cd accumulation. Genome-wide resequencing revealed mutations in 22 genes involved in cell wall modification, synthesis, and metabolic pathways. Transcriptome analysis in Cd-treated plants showed that the expression of pectin methylesterase genes was up-regulated and the expression of pectin methylesterase inhibitor genes was down-regulated in YSD roots, but there were no significant changes in the genes related to Cd uptake, translocation, or vacuole sequestration. The yield and tiller number per plant did not differ significantly between YSD and ZH11, but the dry weight and plant height of YSD were significantly higher than that of ZH11. YSD provides an excellent germplasm for the exploration of Cd accumulation genes, and the cell wall modification genes with sequence- and expression-level variations provide potential targets for phytoremediation.