J Integr Plant Biol. ›› 2020, Vol. 62 ›› Issue (3): 314-329.DOI: 10.1111/jipb.12794

Special Issue: Nutrition and stress

• Plant-abiotic Interactions • Previous Articles     Next Articles

Natural variation in the promoter of OsHMA3 contributes to differential grain cadmium accumulation between Indica and Japonica rice

Chao-Lei Liu1,2†, Zhen-Yu Gao1†, Lian-Guang Shang3†, Chang-Hong Yang2,4, Ban-Pu Ruan1, Da-Li Zeng1, Long-Biao Guo1, Fang-Jie Zhao4, Chao-Feng Huang2,4* and Qian Qian1,3*   

  1. 1State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
    2Shanghai Center for Plant Stress Biology and National Key Laboratory of Plant Molecular Genetics, CAS Center of Excellence in Molecular Plant Sciences, the Chinese Academy of Sciences, Shanghai 200032, China
    3Agricultural Genomics Institute, the Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
    4State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China

    These authors contributed equally to this work.
    Email: Chao-Feng Huang (cfhuang@sibs.ac.cn); Qian Qian (qianqian188@hotmail.com, Dr. Qian is fully responsible for the distribution of all materials associated with this article)
  • Received:2019-01-14 Accepted:2019-02-18 Online:2019-02-21 Published:2020-03-01


Rice is a major source of cadmium (Cd) intake for Asian people. Indica rice usually accumulates more Cd in shoots and grains than Japonica rice. However, underlying genetic bases for differential Cd accumulation between Indica and Japonica rice are still unknown. In this study, we cloned a quantitative trait locus (QTL) grain Cd concentration on chromosome 7 (GCC7) responsible for differential grain Cd accumulation between two rice varieties by performing QTL analysis and map‐based cloning. We found that the two GCC7 alleles, GCC7PA64s and GCC793‐11, had different promoter activity of OsHMA3, leading to different OsHMA3 expression and different shoot and grain Cd concentrations. By analyzing the distribution of different haplotypes of GCC7 among diverse rice accessions, we discovered that the high and low Cd accumulation alleles, namely GCC793‐11 and GCC7PA64s, were preferentially distributed in Indica and Japonica rice, respectively. We further showed that the GCC7PA64s allele can be used to replace the GCC793‐11 allele in the super cultivar 93‐11 to reduce grain Cd concentration without adverse effect on agronomic traits. Our results thus reveal that the QTL GCC7 with sequence variation in the OsHMA3 promoter is an important determinant controlling differential grain Cd accumulation between Indica and Japonica rice.

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