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A HAK family Na+ transporter confers natural variation of salt tolerance in maize

Nature Plants volume 5, pages 1297–1308 (2019)Cite this article

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Abstract

Excessive sodium ion (Na+) concentrations in cultivated land alter crop yield and quality worldwide. Previous studies have shown that shoot Na+ exclusion is essential in most crops for salt tolerance. Here, we show by a genome-wide association study that Zea may L. Na+ content 2 (ZmNC2), encoding the HAK family ion transporter ZmHAK4, confers the natural variation of shoot Na+ exclusion and salt tolerance in maize. The ZmHAK4 locus accounts for ~11% of the shoot Na+ variation, and a natural ZmHAK4-deficient allele displays a decreased ZmHAK4 expression level and an increased shoot Na+ content. ZmHAK4 is preferentially expressed in the root stele and encodes a novel membrane-localized Na+-selective transporter that mediates shoot Na+ exclusion, probably by retrieving Na+ from xylem sap. ZmHAK4 orthologues were identified in other plant species, and the orthologues of ZmHAK4 in rice and wheat show identical expression patterns and ion transport properties, suggesting that ZmHAK4 orthologues mediate an evolutionarily conserved salt-tolerance mechanism. Finally, we show that ZmHAK4 and ZmHKT1 (a HKT1 family Na+-selective transporter) confer distinct roles in promoting shoot Na+ exclusion and salt tolerance, indicating that the combination of the favourable alleles of ZmHKT1 and ZmHAK4 can facilitate the development of salt-tolerant maize varieties.

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Fig. 1: Identification and molecular characterization of ZmNC2.
Fig. 2: ZmNC2 encodes the HAK family ion transporter ZmHAK4.
Fig. 3: A 12,586-bp insertion (InDel8128) is significantly associated with the ZmHAK4 transcript level and shoot Na+ content.
Fig. 4: ZmNC2 encodes a high-affinity Na+-selective ion transporter.
Fig. 5: ZmHAK4 inhibits root-to-shoot Na+ translocation.
Fig. 6: The expression patterns and ion transport properties of ZmHAK4 orthologues in rice and wheat.
Fig. 7: ZmHAK4 and ZmHKT1 show distinct roles in regulating root-to-shoot Na+ translocation.

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Data availability

Source data are available for Figs. 1–7 and Extended Data Figs. 3 and 4. The genetic materials that support the findings of this study are available from the corresponding authors upon request.

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Acknowledgements

We thank Y. Wang, Y. He, R. Song and N. P. Harberd for stimulating discussions. We acknowledge financial support from the National Key R&D Program of China (2016YFD0100605 and 2016YFD0100404), the Ministry of Agriculture of China (2019ZX08010003-002-005) and the National Natural Science Foundation of China (grant 31470350).

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Authors and Affiliations

  1. State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China

    Ming Zhang, Xiaoyan Liang, Limin Wang, Yibo Cao & Caifu Jiang

  2. Laboratory of Agrobiotechnology and National Maize Improvement Center of China, Department of Agronomy and Biotechnology, China Agricultural University, Beijing, China

    Weibin Song, Junpeng Shi & Jinsheng Lai

  3. Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China

    Jinsheng Lai & Caifu Jiang

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Contributions

M.Z., X.L., L.W., Y.C., W.S., J.L. and C.J. planned and designed the research. M.Z. and Y.C. grew the GWAS and RIL populations and measured the ion contents. M.Z. generated the CRISPR–Cas9 knockout lines, and carried out the functional analysis. X.L. and J.S. carried out the bioinformatics analysis. M.Z. and C.J. wrote the manuscript (the other authors contributed).

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Correspondence to Caifu Jiang.

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Peer review information Nature Plants thanks Tomoaki Horie, Magdalena Julkowska, David Salt and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Extended data

Extended Data Fig. 1 Comparison of the full sequences of ZmHAK4 between HuangC and X178 by a combined application of Sanger sequencing and whole- genome resequencing.

a, The ZmHAK4 gene model and the locations of the primers used to amplify the full sequence of ZmHAK4. The blue boxes represent exons, yellow boxes represent introns and untranslated regions (UTRs), and the red box represents the 12,586-bp inserted sequence observed in X178. b-c, Integrated Genome Viewer visualization of the whole-genome sequencing data covering the ZmHAK4 region (b), the high resolution view of the insert site (c). d, Shown that the mismatched sequences flanking the insert site were mapped to the ends of a ~12.5-kb fragment on Chromosome1, suggesting that the ~12.5-kb DNA fragment from Chr.1 has been inserted into the 5F/5R region of X178 genome.

Extended Data Fig. 2 The pattern of the whole-genome sequencing data covering the donor site of the 12,586-bp insertion (the insert donor region).

a, Integrated Genome Viewer visualization of the whole-genome sequencing data covering the insert donor region. b, High resolution view of the left and right borders of the insert donor region. The dash line coupled the paired reads. We generated the resequencing library using uniform length DNA fragment of ~500 bp, therefore the average distance between two paired reads is ~500 bp. However, we found that the reads mapped to the left border of the insert donor region paired with the reads mapped to the right border of the insert donor (>12 kb away), indicating the sequence between the left and right border of the insert donor region has been deleted, thus indicating that the 12,586- bp insertion observed in ZmHAK4 of X178 is a translocation.

Extended Data Fig. 3 The transcript levels of ZmHKT1 in ZmHKT1crispr-1 and wild type plants.

Data were means ± s.d. of three independent experiments.

Source data

Extended Data Fig. 4 The transcript levels of ZmHAK4 and ZmHKT1 in the root tissue of maize inbred line 32990700.

Data were means ± s.d. of three independent experiments.

Source data

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Zhang, M., Liang, X., Wang, L. et al. A HAK family Na+ transporter confers natural variation of salt tolerance in maize. Nat. Plants 5, 1297–1308 (2019). https://doi.org/10.1038/s41477-019-0565-y

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