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Breeding for low cadmium barley by introgression of a Sukkula-like transposable element

Nature Food volume 1, pages 489–499 (2020)Cite this article

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Abstract

Barley is the fourth most produced cereal crop in the world and one of the major dietary sources of cadmium (Cd), which poses serious threats to human health. Here, we identify a gene that encodes a P-type heavy metal ATPase 3 (HvHMA3) responsible for grain Cd accumulation in barley. HvHMA3 from the high Cd barley variety Haruna Nijo in Japan and the low Cd variety BCS318 in Afghanistan shared 97% identity at the amino acid level. In addition, the HvHMA3 from both varieties showed similar transport activity for Cd and the same subcellular localization at the tonoplast. However, the expression of HvHMA3 was double in BCS318 than in Haruna Nijo. A 3.3-kilobase Sukkula-like transposable element was found to be inserted upstream of the gene in the low Cd variety, which functioned as a promoter and enhanced the expression of HvHMA3. Introgression of this insertion to an elite barley cultivar through backcrossing resulted in decreased Cd accumulation in the grain grown in Cd-contaminated soil without yield penalty. The decreased Cd accumulation resulting from the insertion was also found in some other barley landraces in the world. Our results indicate that insertion of the Sukkula-like transposable element plays an important role in upregulating HvHMA3 expression.

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Fig. 1: Fine-mapping of a gene responsible for Cd accumulation in barley grain.
Fig. 2: Functional characterization of two alleles of HvHMA3.
Fig. 3: Expression pattern and genomic copy number of HvHMA3 in two barley varieties.
Fig. 4: Effect of the Sukkula-like transposable element insertion on HvHMA3 expression.
Fig. 5: Characterization of HvHMA3 RNAi lines.
Fig. 6: Characterization of BC3F2 lines derived from a backcross between BCS318 and Haruna Nijo.

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Data availability

The data that support the findings of this study are available from the corresponding author upon request. Sequence data relating to this article have been registered in the DDBJ/GenBank/European Molecular Biology Laboratory databases (https://www.ddbj.nig.ac.jp) under the accession numbers LC523824 (HvHMA3-H), LC523825 (HvHMA3-B), LC523826 (HvHMA3-H_promoter) and LC523827 (HvHMA3-B_promoter).

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Acknowledgements

This work was supported by a Grant-in-Aid for Specially Promoted Research (JSPS KAKENHI grant number 16H06296 to J.F.M.) and a grant from the Ministry of Agriculture, Forestry and Fisheries of Japan (Genomics-based Technology for Agricultural Improvement, TRS-1006 and Brain 25013A to J.F.M.). Barley seed samples and DNA were provided through the National Bioresource Project of Barley (MEXT, Japan).

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Authors and Affiliations

  1. Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan

    Gui Jie Lei, Miho Fujii-Kashino, De Zhi Wu, Hiroshi Hisano, Daisuke Saisho, Fenglin Deng, Naoki Yamaji, Kazuhiro Sato & Jian Feng Ma

  2. Institute of Crop Science, Zhejiang University, Hangzhou, China

    De Zhi Wu

  3. Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China

    Fenglin Deng

  4. State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China

    Fang-Jie Zhao

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  1. Gui Jie Lei
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Contributions

J.F.M. designed the research. G.J.L., M.F.-K., D.Z.W., H.H., D.S., F.D., K.S. and J.F.M. performed the research. G.J.L., M.F.-K., D.Z.W., D.S., N.Y., K.S., F.-J.Z. and J.F.M. analysed the data. G.J.L. and J.F.M. wrote the paper.

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Correspondence to Jian Feng Ma.

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Lei, G.J., Fujii-Kashino, M., Wu, D.Z. et al. Breeding for low cadmium barley by introgression of a Sukkula-like transposable element. Nat Food 1, 489–499 (2020). https://doi.org/10.1038/s43016-020-0130-x

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