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