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Natural variation in the promoter of OsHMA3 contributes to differential grain cadmium accumulation between Indica and Japonica rice.
J Integr Plant Biol. 2020 Mar; 62(3):314-329.JI

Abstract

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.

Authors+Show Affiliations

State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China. Shanghai 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.State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.Agricultural Genomics Institute, the Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.Shanghai 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. State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.Shanghai 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. State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China. Agricultural Genomics Institute, the Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

30791211

Citation

Liu, Chao-Lei, et al. "Natural Variation in the Promoter of OsHMA3 Contributes to Differential Grain Cadmium Accumulation Between Indica and Japonica Rice." Journal of Integrative Plant Biology, vol. 62, no. 3, 2020, pp. 314-329.
Liu CL, Gao ZY, Shang LG, et al. Natural variation in the promoter of OsHMA3 contributes to differential grain cadmium accumulation between Indica and Japonica rice. J Integr Plant Biol. 2020;62(3):314-329.
Liu, C. L., Gao, Z. Y., Shang, L. G., Yang, C. H., Ruan, B. P., Zeng, D. L., Guo, L. B., Zhao, F. J., Huang, C. F., & Qian, Q. (2020). Natural variation in the promoter of OsHMA3 contributes to differential grain cadmium accumulation between Indica and Japonica rice. Journal of Integrative Plant Biology, 62(3), 314-329. https://doi.org/10.1111/jipb.12794
Liu CL, et al. Natural Variation in the Promoter of OsHMA3 Contributes to Differential Grain Cadmium Accumulation Between Indica and Japonica Rice. J Integr Plant Biol. 2020;62(3):314-329. PubMed PMID: 30791211.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Natural variation in the promoter of OsHMA3 contributes to differential grain cadmium accumulation between Indica and Japonica rice. AU - Liu,Chao-Lei, AU - Gao,Zhen-Yu, AU - Shang,Lian-Guang, AU - Yang,Chang-Hong, AU - Ruan,Ban-Pu, AU - Zeng,Da-Li, AU - Guo,Long-Biao, AU - Zhao,Fang-Jie, AU - Huang,Chao-Feng, AU - Qian,Qian, Y1 - 2019/05/06/ PY - 2019/01/14/received PY - 2019/02/18/accepted PY - 2019/2/23/pubmed PY - 2020/11/11/medline PY - 2019/2/22/entrez SP - 314 EP - 329 JF - Journal of integrative plant biology JO - J Integr Plant Biol VL - 62 IS - 3 N2 - 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. SN - 1744-7909 UR - https://www.unboundmedicine.com/medline/citation/30791211/Natural_variation_in_the_promoter_of_OsHMA3_contributes_to_differential_grain_cadmium_accumulation_between_Indica_and_Japonica_rice_ L2 - https://doi.org/10.1111/jipb.12794 DB - PRIME DP - Unbound Medicine ER -