Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

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

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.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Purchase on Springer Link

Instant access to full article PDF

Prices may be subject to local taxes which are calculated during checkout

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.

Similar content being viewed by others

Data availability

Source data are available for Figs. 17 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.

References

  1. Flowers, T. J. Improving crop salt tolerance. J. Exp. Bot. 55, 307–319 (2004).

    CAS  PubMed  Google Scholar 

  2. Munns, R. & Tester, M. Mechanisms of salinity tolerance. Annu. Rev. Plant Biol. 59, 651–681 (2008).

    CAS  PubMed  Google Scholar 

  3. Zhu, J. K. Abiotic stress signaling and responses in plants. Cell 167, 313–324 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  4. Ismail, A. M. & Horie, T. Genomics, physiology, and molecular breeding approaches for improving salt tolerance. Annu. Rev. Plant Biol. 68, 405–434 (2017).

    CAS  PubMed  Google Scholar 

  5. Tester, M. & Davenport, R. Na+ tolerance and Na+ transport in higher plants. Ann. Bot. 5, 503–527 (2003).

    Google Scholar 

  6. Munns, R.et al. Energy costs of salt tolerance in crop plants. New Phytol. https://doi.org/10.1111/nph.15864 (2019).

  7. Greenway, H. & Munns, R. A. Mechanisms of salt tolerance in non-halophytes. Annu. Rev. Plant Physiol. 31, 149–190 (1980).

    CAS  Google Scholar 

  8. Rubio, F., Nieves-Cordones, M., Horie, T. & Shabala, S. Doing ‘business as usual’ comes with a cost: evaluating energy cost of maintaining plant intracellular K+ homeostasis under saline conditions. New Phytol. https://doi.org/10.1111/nph.15852 (2019).

  9. James, R. A. et al. Photosynthetic capacity is related to the cellular and subcellular partitioning of Na+, K+ and Cl in salt-affected barley and durum wheat. Plant Cell Environ. 29, 2185–2197 (2006).

    CAS  PubMed  Google Scholar 

  10. Horie, T., Hauser, F. & Schroeder, J. I. HKT transporter-mediated salinity resistance mechanisms in Arabidopsis and monocot crop plants. Trends Plant Sci. 14, 660–668 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Yang, Y. & Guo, Y. Elucidating the molecular mechanisms mediating plant salt-stress responses. New Phytol. 217, 523–539 (2018).

    CAS  PubMed  Google Scholar 

  12. Yang, Y. & Guo, Y. Unraveling salt stress signaling in plants. J. Integr. Plant Biol. 60, 796–804 (2018).

    CAS  PubMed  Google Scholar 

  13. Ren, Z. H. et al. A rice quantitative trait locus for salt tolerance encodes a sodium transporter. Nat. Genet. 37, 1141–1146 (2005).

    CAS  PubMed  Google Scholar 

  14. Munns, R. et al. Wheat grain yield on saline soils is improved by an ancestral Na+ transporter gene. Nat. Biotechnol. 30, 360–364 (2012).

    CAS  PubMed  Google Scholar 

  15. An, D. et al. AtHKT1 drives adaptation of Arabidopsis thaliana to salinity by reducing floral sodium content. PLoS Genet. 13, e1007086 (2017).

    PubMed  PubMed Central  Google Scholar 

  16. Campbell, M. T. et al. Allelic variants of OsHKT1;1 underlie the divergence between indica and japonica subspecies of rice (Oryza sativa) for root sodium content. PLoS Genet. 13, e1006823 (2017).

    PubMed  PubMed Central  Google Scholar 

  17. Busoms, S. et al. Fluctuating selection on migrant adaptive sodium transporter alleles in coastal Arabidopsis thaliana. Proc. Natl Acad. Sci. USA 115, 12443–12452 (2018).

    Google Scholar 

  18. Møller, I. S. et al. Shoot Na+ exclusion and increased salinity tolerance engineered by cell type-specific alteration of Na+ transport in Arabidopsis. Plant Cell 21, 2163–2178 (2009).

    PubMed  PubMed Central  Google Scholar 

  19. Byrt, C. S. et al. HKT1;5-like cation transporters linked to Na+ exclusion loci in wheat, Nax2 and Kna1. Plant Physiol. 143, 1918–1928 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Zhang, M. et al. A retrotransposon in an HKT1 family sodium transporter causes variation of leaf Na+ exclusion and salt tolerance in maize. New Phytol. 217, 1161–1176 (2018).

    CAS  PubMed  Google Scholar 

  21. Rus, A. et al. Natural variants of AtHKT1 enhance Na+ accumulation in two wild populations of Arabidopsis. PLoS Genet. 2, 1964–1973 (2006).

    CAS  Google Scholar 

  22. Huang, S. et al. A sodium transporter (HKT7) is a candidate for Nax1, a gene for salt tolerance in durum wheat. Plant Physiol. 142, 1718–1727 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Hanks, R. J., Ashcroft, G. L., Rasmussen, V. P. & Wilson, G. D. Corn production as influenced by irrigation and salinity–Utah studies. Irrigation Sci. 1, 47–59 (1978).

    Google Scholar 

  24. Zhao, K. F., Song, J., Fan, H., Zhou, S. & Zhao, M. Growth response to ionic and osmotic stress of NaCl in salt-tolerant and salt-sensitive maize. J. Integr. Plant Biol. 52, 468–475 (2010).

    CAS  PubMed  Google Scholar 

  25. Luo, X. et al. Genome-wide association study dissects the genetic bases of salt tolerance in maize seedlings. J. Integr. Plant Biol. 61, 658–674 (2019).

    CAS  PubMed  Google Scholar 

  26. Jiao, Y. et al. Genome-wide genetic changes during modern breeding of maize. Nat. Genet. 44, 812–815 (2012).

    CAS  PubMed  Google Scholar 

  27. Wang, B. et al. Identification and fine-mapping of a major maize leaf width QTL in a re-sequenced large recombinant inbred lines population. Front. Plant Sci. 9, 101 (2018).

    PubMed  PubMed Central  Google Scholar 

  28. Zhang, Z. et al. Genome-wide analysis and identification of HAK potassium transporter gene family in maize (Zea mays L.). Mol. Biol. Rep. 39, 8465–8473 (2012).

    CAS  PubMed  Google Scholar 

  29. Tamura, K., Stecher, G., Peterson, D., Filipski, A. & Kumar, S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol. 30, 2725–2729 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Benito, B., Garciadeblas, B. & Rodriguez-Navarro, A. HAK transporters from Physcomitrella patens and Yarrowia lipolytica mediate sodium uptake. Plant Cell Physiol. 53, 1117–1123 (2012).

    CAS  PubMed  Google Scholar 

  31. Epstein, W. & Kim, B. S. Potassium transport loci in Escherichia coli K-12. J. Bacteriol. 108, 639–644 (1971).

    CAS  PubMed  PubMed Central  Google Scholar 

  32. Mäser, P. et al. Phylogenetic relationships within cation transporter families of Arabidopsis. Plant Physiol. 126, 1646–1667 (2001).

    PubMed  PubMed Central  Google Scholar 

  33. Fu, H. H. & Luan, S. AtKUP1: a dual-affinity K+ transporter from Arabidopsis. Plant Cell 10, 63–73 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  34. Santa María, G. E., Oliferuk, S. & Moriconi, J. I. A survey of sequences of KT-HAK-KUP transporters in green algae and basal land plants. Data Brief. 19, 2356–2363 (2018).

    PubMed  PubMed Central  Google Scholar 

  35. Batistic, O., Sorek, N., Schultke, S., Yalovsky, S. & Kudla, J. Dual fatty acyl modification determines the localization and plasma membrane targeting of CBL/CIPK Ca2+ signaling complexes in Arabidopsis. Plant Cell 20, 1346–1362 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  36. Calero, F., Gomez, N., Arino, J. & Ramos, J. Trk1 and Trk2 define the major K+ transport system in fission yeast. J. Bacteriol. 182, 394–399 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  37. Li, H. et al. NRT1.5/NPF7.3 functions as a proton-coupled H+/K+ antiporter for K+ loading into the xylem in Arabidopsis. Plant Cell 29, 2016–2026 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  38. Cao, Y., Liang, X., Yin, P., Zhang, M. & Jiang, C. A domestication-associated reduction in K+-preferring HKT transporter activity underlies maize shoot K+ accumulation and salt tolerance. New Phytol. 222, 301–317 (2018).

    PubMed  Google Scholar 

  39. Qin, Y. J., Wu, W. H. & Wang, Y. ZmHAK5 and ZmHAK1 function in K+ uptake and distribution in maize under low K+ conditions. J. Integr. Plant Biol. 61, 691–705 (2018).

    Google Scholar 

  40. Bañuelos, M. A., Garciadeblas, B., Cubero, B. & Rodríguez-Navarro, A. Inventory and functional characterization of the HAK potassium transporters of rice. Plant Physiol. 130, 784–795 (2002).

    PubMed  PubMed Central  Google Scholar 

  41. Wu, H. J. et al. Insights into salt tolerance from the genome of Thellungiella salsuginea. Proc. Natl Acad. Sci. USA 109, 12219–12224 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  42. Zhang, H., Li, Y. & Zhu, J. K. Developing naturally stress-resistant crops for a sustainable agriculture. Nat. Plants 12, 989–996 (2018).

    Google Scholar 

  43. Baxter, I. et al. A coastal cline in sodium accumulation in Arabidopsis thaliana is driven by natural variation of the sodium transporter AtHKT1;1. PLoS Genet. 11, e1001193 (2010).

    Google Scholar 

  44. Yang, M. et al. Genome-wide association studies reveal the genetic basis of ionomic variation in rice. Plant Cell 30, 2720–2740 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  45. Qi, Z. et al. The high affinity K+ transporter AtHAK5 plays a physiological role in planta at very low K+ concentrations and provides a caesium uptake pathway in Arabidopsis. J. Exp. Bot. 59, 595–607 (2008).

    CAS  PubMed  Google Scholar 

  46. Chen, G. et al. Rice potassium transporter OsHAK1 is essential for maintaining potassium-mediated growth and functions in salt tolerance over low and high potassium concentration ranges. Plant Cell Environ. 38, 2747–2765 (2015).

    CAS  PubMed  Google Scholar 

  47. Yang, T. et al. The role of a potassium transporter OsHAK5 in potassium acquisition and transport from roots to shoots in rice at low potassium supply levels. Plant Physiol. 166, 945–959 (2014).

    PubMed  PubMed Central  Google Scholar 

  48. He, Y. et al. A quantitative trait locus, qSE3, promotes seed germination and seedling establishment under salinity stress in rice. Plant J. 97, 1089–1104 (2018).

    Google Scholar 

  49. Shen, Y. et al. The potassium transporter OsHAK21 functions in the maintenance of ion homeostasis and tolerance to salt stress in rice. Plant Cell Environ. 38, 2766–2779 (2015).

    CAS  PubMed  Google Scholar 

  50. Assaha, D. V. M., Ueda, A., Saneoka, H., Al-Yahyai, R. & Yaish, M. W. The role of Na+ and K+ transporters in salt stress adaptation in glycophytes. Front. Physiol. 8, 509 (2017).

    PubMed  PubMed Central  Google Scholar 

  51. Kang, H. M. et al. Variance component model to account for sample structure in genome-wide association studies. Nat. Genet. 42, 348–354 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  52. Li, H. et al. Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels. Nat. Genet. 45, 43–50 (2013).

    CAS  PubMed  Google Scholar 

  53. Li, J. et al. The Os-AKT1 channel is critical for K+ uptake in rice roots and is modulated by the rice CBL1–CIPK23 complex. Plant Cell 26, 3387–3402 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  54. Suzuki, K. et al. OsHKT1;4-mediated Na+ transport in stems contributes to Na+ exclusion from leaf blades of rice at the reproductive growth stage upon salt stress. BMC Plant Biol. 16, 22 (2016).

    PubMed  PubMed Central  Google Scholar 

Download references

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).

Author information

Authors and Affiliations

Authors

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).

Corresponding author

Correspondence to Caifu Jiang.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

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.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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

Supplementary information

Supplementary Information

Supplementary Figs. 1–6 and Supplementary Tables 1–8.

Reporting Summary

Source data

Source Data Fig. 1

Statistical Source Data.

Source Data Fig. 2

Statistical Source Data.

Source Data Fig. 3

Statistical Source Data.

Source Data Fig. 4

Statistical Source Data.

Source Data Fig. 5

Statistical Source Data.

Source Data Fig. 6

Statistical Source Data.

Source Data Fig. 7

Statistical Source Data.

Source Data Extended Data Fig. 3

Statistical Source Data.

Source Data Extended Data Fig. 4

Statistical Source Data.

Source Data Supplementary Fig. 1

Statistical Source Data.

Source Data Supplementary Fig. 3

Statistical Source Data.

Source Data Supplementary Fig. 6

Statistical Source Data.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

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

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41477-019-0565-y

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing