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Isolation and characterization of a rice line with high Cd accumulation for potential use in phytoremediation



To reduce cadmium (Cd) intake, remediation of Cd-contaminated soil and breeding crops with low Cd accumulation are important. This study aims to isolate rice mutants with altered accumulation of Cd.


We used rice seeds mutated by N-methyl-N-nitrosourea for screening. The mutant was physiologically, genetically, and molecularly characterized. Cd accumulation was compared among five rice varieties cultivated in a Cd-contaminated soil.


From 1000 lines screened, we isolated a line (TCM213) with high Cd accumulation. There was no difference in the root Cd uptake, but a higher root-to-shoot translocation of Cd was found in TCM213 compared with a common rice cultivar, T-65. The expression and sequence of OsNramp5 and OsHMA2 did not differ between TCM213 and T-65. However, several SNPs and deletion were found in the sequence of OsHMA3, although its expression and tissue localization were similar to those of T-65. Genetic analysis of an F2 population derived from T-65 and TCM213 showed that the variation of OsHMA3 explained 72 % of variation in total Cd accumulation. TCM213 accumulated the largest Cd amount in the shoots among five Cd-accumulating varieties.


High Cd accumulation in TCM213 results from loss of function of OsHMA3, and its high Cd accumulation has potential for efficient phytoremediation of Cd-contaminated soil.

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We thank Dr. Kumamaru for providing MNU-mutated seeds. This work was supported by Grant-in-Aid for Specially Promoted Research (JSPS KAKENHI grant no. 16H06296 to JFM), the National Key Basic Research Program of China (no. 2014CB441000 to RFS), the Natural Science Foundation of China (no. 41025005 to RFS), and the Ohara Foundation for Agriculture Research and Joint Research Program implemented at the Institute of Plant Science and Resources, Okayama University.

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Corresponding author

Correspondence to Jian Feng Ma.

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The authors declare that they have no conflict of interest.

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Responsible Editor: Fangjie Zhao .

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Fig. S1

CAPS marker fragment patterns. A CAPS marker was developed for genotyping OsHMA3 in F2 population divided from a cross between TCM213 and T-65. For details, refer to the text (PDF 126 kb)

Fig. S2

Phenotype of TCM213. Seedlings (34-day-old) of TCM213 and T-65 were exposed to 0.5 μM Cd in nutrient solution for 14 days. Picture was taken at harvest. Scale bar is 10 cm (PDF 159 kb)

Fig. S3

Alignment of OsHMA2 sequence in TCM213 and T-65 (PDF 135 kb)

Fig. S4

Alignment of OsNramp5 in TCM213 and T-65 (PDF 136 kb)

Fig. S5

Alignment of OsHMA3 sequence in TCM213, T-65, Anjana Dhan, and Choukokoku (PDF 155 kb)

Fig. S6

Phenotype of Cd-accumulating rice varieties. Seedlings (14-day-old) of TCM213, T-65, Anjana Dhan, Jarjan, and Choukokoku were transplanted to a Cd-contaminated soil. Picture was taken after 2-month growth. Scale bar is 20 cm (XLSX 38 kb) (PDF 175 kb)

Supplementary Table 1

Genotyping of TCM213, T-65, and other rice cultivars (XLSX 38 kb)

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Shao, J.F., Fujii-Kashino, M., Yamaji, N. et al. Isolation and characterization of a rice line with high Cd accumulation for potential use in phytoremediation. Plant Soil 410, 357–368 (2017).

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  • Biomass
  • Cadmium accumulation
  • OsHMA3
  • Phytoremediation
  • Rice