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.

The ethylene response factors SNORKEL1 and SNORKEL2 allow rice to adapt to deep water

Abstract

Living organisms must acquire new biological functions to adapt to changing and hostile environments. Deepwater rice has evolved and adapted to flooding by acquiring the ability to significantly elongate its internodes, which have hollow structures and function as snorkels to allow gas exchange with the atmosphere, and thus prevent drowning1,2,3. Many physiological studies have shown that the phytohormones ethylene, gibberellin and abscisic acid are involved in this response4,5,6,7,8, but the gene(s) responsible for this trait has not been identified. Here we show the molecular mechanism of deepwater response through the identification of the genes SNORKEL1 and SNORKEL2, which trigger deepwater response by encoding ethylene response factors involved in ethylene signalling. Under deepwater conditions, ethylene accumulates in the plant and induces expression of these two genes. The products of SNORKEL1 and SNORKEL2 then trigger remarkable internode elongation via gibberellin. We also demonstrate that the introduction of three quantitative trait loci from deepwater rice into non-deepwater rice enabled the latter to become deepwater rice. This discovery will contribute to rice breeding in lowland areas that are frequently flooded during the rainy season.

Your institute does not have access to this article

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Figure 1: Identification of genes responsible for deepwater response in rice.
Figure 2: Molecular characterization of SK1 and SK2.
Figure 3: GA response and molecular mechanism of deepwater response.
Figure 4: SK genes in wild rice species and QTL pyramiding.

Accession codes

Primary accessions

DDBJ/GenBank/EMBL

Data deposits

The DDBJ accession numbers for SNORKEL1 and SNORKEL2 are as follows (rice variety, accession numbers): C9285, AB510478 and AB510479; Bhadua, AB510480 and AB510481; O. rufipogon (W0120), AB510482 and AB510483; and in O. nivara (W0106), AB510484 and AB510485. SNORKEL2 and SNORKEL2-like genes in O. glumaepatula (IRGC105668) are AB510486 and AB510487.

References

  1. Vergara, B. S., Jackson, B. & De Datta, S. K. in Climate and Rice (eds IRRI) 301–319 (IRRI, Los Baños, 1976)

    Google Scholar 

  2. Catling, D. Rice in Deepwater (Macmillan, London, 1992)

    Google Scholar 

  3. Kende, H., Van der Knaap, E. & Cho, H.-T. Deepwater rice: a model plant to study stem elongation. Plant Physiol. 118, 1105–1110 (1998)

    CAS  Article  Google Scholar 

  4. Métraux, J.-P. & Kende, H. The role of ethylene in the growth response of submerged deep water rice. Plant Physiol. 72, 441–446 (1983)

    Article  Google Scholar 

  5. Raskin, I. & Kende, H. Role of gibberellin in the growth response of submerged deep water rice. Plant Physiol. 76, 947–950 (1984)

    CAS  Article  Google Scholar 

  6. Hoffmann-Benning, S. & Kende, H. On the role of abscisic acid and gibberellin in the regulation of growth in rice. Plant Physiol. 99, 1156–1161 (1992)

    CAS  Article  Google Scholar 

  7. Azuma, T. et al. Involvement of the decrease in levels of abscisic acid in the internodal elongation of submerged floating rice. J. Plant Physiol. 14, 323–328 (1995)

    Article  Google Scholar 

  8. Bailey-Serres, J. & Voesenek, L. A. C. J. Flooding stress: acclimations and genetic diversity. Annu. Rev. Plant Biol. 59, 313–339 (2008)

    CAS  Article  Google Scholar 

  9. Hattori, Y. et al. A major QTL confers rapid internode elongation in response to water rise in deepwater rice. Breed. Sci. 57, 305–314 (2007)

    Article  Google Scholar 

  10. Hattori, Y. et al. Mapping of three QTLs that regulate internode elongation in deepwater rice. Breed. Sci. 58, 39–46 (2008)

    CAS  Article  Google Scholar 

  11. Nemoto, K. et al. Inheritance of early elongation ability in floating rice revealed by diallel and QTL analyses. Theor. Appl. Genet. 109, 42–47 (2004)

    CAS  Article  Google Scholar 

  12. Kawano, R. et al. Mapping of QTLs for floating ability in rice. Breed. Sci. 58, 47–53 (2008)

    CAS  Article  Google Scholar 

  13. Nakano, T., Suzuki, K., Fujimura, T. & Shinshi, H. Genome-wide analysis of the ERF gene family in Arabidopsis and Rice. Plant Physiol. 140, 411–432 (2006)

    CAS  Article  Google Scholar 

  14. Xu, K. et al. Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature 442, 705–708 (2006)

    ADS  CAS  Article  Google Scholar 

  15. Fukao, T., Xu, K., Ronald, P. C. & Bailey-Serres, J. A variable cluster of ethylene response factor-like genes regulates metabolic and developmental acclimation responses to submergence in rice. Plant Cell 18, 2021–2034 (2006)

    CAS  Article  Google Scholar 

  16. Solano, R., Stepanova, A., Chao, Q. & Ecker, J. R. Nuclear events in ethylene signaling: a transcriptional cascade mediated by ETHYLENE-INSENSITIVE3 and ETHYLENE-RESPONSE-FACTOR1. Genes Dev. 12, 3703–3714 (1998)

    CAS  Article  Google Scholar 

  17. Jackson, M. B. Ethylene and responses of plants to soil waterlogging and submergence. Annu. Rev. Plant Physiol. 36, 145–174 (1985)

    CAS  Article  Google Scholar 

  18. Hooley, R. Gibberellins: perception, transduction and responses. Plant Mol. Biol. 26, 1529–1555 (1994)

    CAS  Article  Google Scholar 

  19. Cheng, C., Tsuchimoto, S., Ohtsubo, H. & Ohtsubo, E. Evolutionary relationships among rice species with AA genome based on SINE insertion analysis. Genes Genet. Syst. 77, 323–334 (2002)

    CAS  Article  Google Scholar 

  20. Vaughan, D. A., Lu, B.-R. & Tomooka, N. The evolving story of rice evolution. Plant Sci. 174, 394–408 (2008)

    CAS  Article  Google Scholar 

  21. Ashikari, M. et al. Cytokinin oxidase regulates rice grain production. Science 309, 741–745 (2005)

    ADS  CAS  Article  Google Scholar 

  22. Ashikari, M. & Matsuoka, M. Identification, isolation and pyramiding of quantitative trait loci for rice breeding. Trends Plant Sci. 11, 344–350 (2006)

    CAS  Article  Google Scholar 

  23. Fan, C. et al. GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor. Appl. Genet. 112, 1164–1171 (2006)

    CAS  Article  Google Scholar 

  24. Song, X.-J. et al. A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nature Genet. 39, 623–630 (2007)

    CAS  Article  Google Scholar 

  25. Shomura, A. et al. Deletion in a gene associated with grain size increased yields during rice domestication. Nature Genet. 40, 1023–1028 (2008)

    CAS  Article  Google Scholar 

  26. Huang, X. et al. Natural variation at the DEP1 locus enhances grain yield in rice. Nature Genet. 41, 494–497 (2009)

    CAS  Article  Google Scholar 

  27. Fukao, T. & Bailey-Serres, J. Submergence tolerance conferred by Sub1A is mediated by SLR1 and SLRL1 restriction of gibberellin responses in rice. Proc. Natl Acad. Sci. USA 105, 16814–16819 (2008)

    ADS  CAS  Article  Google Scholar 

  28. Morishima, H., Hinata, K. & Oka, H. I. Floating ability and drought resistance in wild and cultivated species of rice. Ind. J. Genet. Plant Breed. 22, 1–11 (1962)

    Google Scholar 

  29. Hood, E. E., Helmer, G. L., Fraley, R. T. & Chilton, M.-D. The hypervirulence of Agrobacterium tumefaciens A281 is encoded in a region of pTiBo542 outside of T-DNA. J. Bacteriol. 168, 1291–1301 (1986)

    CAS  Article  Google Scholar 

  30. Sambrook, J., Fritsch, E. F. & Maniatis, T. Molecular Cloning: A Laboratory Manual (Cold Spring Harbor Laboratory Press, 1989)

    Google Scholar 

  31. Kaneko, M. et al. Where do gibberellin biosynthesis and gibberellin signaling occur in rice plants? Plant J. 35, 104–115 (2003)

    CAS  Article  Google Scholar 

  32. Hiei, Y., Ohta, S., Komari, T. & Kumashiro, T. Efficient transformation of rice (Oryza sativa L.) mediated by Agrobacterium and sequence analysis of the boundaries of the T-DNA. Plant J. 6, 271–282 (1994)

    CAS  Article  Google Scholar 

  33. Hirano, K. et al. Comprehensive transcriptome analysis of phytohormone biosynthesis and signaling genes in microspore/pollen and tapetum of rice. Plant Cell Physiol. 49, 1429–1450 (2008)

    CAS  Article  Google Scholar 

  34. Mao, C., Wang, S., Jia, Q. & Wu, P. OsEIL1, a rice homolog of the Arabidopsis EIN3 regulates the ethylene response as a positive component. Plant Mol. Biol. 61, 141–152 (2006)

    CAS  Article  Google Scholar 

Download references

Acknowledgements

We thank I. Aichi for helping to produce the transgenic lines and M. Ito for helping to map the genes. We also thank P. Chaiyawat for the opportunity to photograph the deepwater rice specimen and M. Kojima for technical assistance with the hormone analysis. This work was supported by a grant from the Ministry of Agriculture, Forestry, and Fisheries of Japan (Integrated Research Project for Plants, Insects, and Animals using Genome Technology, QT-2003 and QT-4002) and a research fellowship from the Japan Society for the Promotion of Science (Y.H.). The wild rice lines used in this study were obtained from the National Institute of Genetics supported by the National Bioresource Project, MEXT, Japan and the International Rice Research Institute, Philippines.

Author Contributions M.A. conceived the project and designed the experiments. Y.H. identified the genes and Y.H., K.N., S.F., X.-J.S. and R.K. performed molecular characterization of the genes. H.S. and H.M. surveyed the hormone contents. J.W. and T.M. performed BAC clone analysis. A.Y., H.K. and M.M. provided advice regarding the experiments. M.A. and Y.H. wrote the manuscript.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Motoyuki Ashikari.

Supplementary information

Supplementary Information

This file contains Supplementary Notes, Supplementary Figures 1-11 with Legends and Supplementary Tables 1-4. (PDF 2255 kb)

Supplementary Movie 1

This movie shows temporal elongation phenotype under deepwater conditions. Plants were submerged in water up to 70% of the plant height, and the water level was then increased by 10 cm every day until the tank was full. Control, T65; DWR, C9285. (MOV 5759 kb)

Supplementary Movie 2

This movie shows temporal elongation phenotype under complete submergence. The tank was filled with water on the first day of the deepwater treatment. Control, T65; DWR, C9285. (MOV 6225 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Hattori, Y., Nagai, K., Furukawa, S. et al. The ethylene response factors SNORKEL1 and SNORKEL2 allow rice to adapt to deep water. Nature 460, 1026–1030 (2009). https://doi.org/10.1038/nature08258

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature08258

Further reading

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

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