Letter

Expression of barley SUSIBA2 transcription factor yields high-starch low-methane rice

  • Nature volume 523, pages 602606 (30 July 2015)
  • doi:10.1038/nature14673
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Abstract

Atmospheric methane is the second most important greenhouse gas after carbon dioxide, and is responsible for about 20% of the global warming effect since pre-industrial times1,2. Rice paddies are the largest anthropogenic methane source and produce 7–17% of atmospheric methane2,3. Warm waterlogged soil and exuded nutrients from rice roots provide ideal conditions for methanogenesis in paddies with annual methane emissions of 25–100-million tonnes3,4. This scenario will be exacerbated by an expansion in rice cultivation needed to meet the escalating demand for food in the coming decades4. There is an urgent need to establish sustainable technologies for increasing rice production while reducing methane fluxes from rice paddies. However, ongoing efforts for methane mitigation in rice paddies are mainly based on farming practices and measures that are difficult to implement5. Despite proposed strategies to increase rice productivity and reduce methane emissions4,6, no high-starch low-methane-emission rice has been developed. Here we show that the addition of a single transcription factor gene, barley SUSIBA2 (refs 7, 8), conferred a shift of carbon flux to SUSIBA2 rice, favouring the allocation of photosynthates to aboveground biomass over allocation to roots. The altered allocation resulted in an increased biomass and starch content in the seeds and stems, and suppressed methanogenesis, possibly through a reduction in root exudates. Three-year field trials in China demonstrated that the cultivation of SUSIBA2 rice was associated with a significant reduction in methane emissions and a decrease in rhizospheric methanogen levels. SUSIBA2 rice offers a sustainable means of providing increased starch content for food production while reducing greenhouse gas emissions from rice cultivation. Approaches to increase rice productivity and reduce methane emissions as seen in SUSIBA2 rice may be particularly beneficial in a future climate with rising temperatures resulting in increased methane emissions from paddies9,10.

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Accessions

Primary accessions

GenBank/EMBL/DDBJ

Data deposits

The sequence of construct containing HvSBEIIb p:HvSUSIBA2 has been deposited in GenBank under accession number KR935231.

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Acknowledgements

Special thanks to S. Stymne. We would also like to thank B. Müller, X. Feng, M. Erikson, L. Sun, S. Isaksson, J. Ascue and S. Mayer for their help in determining concentrations of methane and methanogens, and B. Ingemarsson for discussions concerning the work layout. This work was funded by the following organisations and foundations: The Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning (Formas) for Project No 219-2014-1172; the joint Formas/Sida-funded programme (Project No 220-2009-2069) on sustainable development in developing countries; the SLU Lärosätesansökan Programme (TC4F) for Team 4 supported by Vinnova; the Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning (Formas) under the Strategic Research Area for the TCBB Programme; National Natural Science Foundation of China (projects no 30771298 and no 31370389); the SLU programme BarleyFunFood; the Carl Trygger Foundation for Project No CTS 11: 450; funding in part by the US Department of Energy Contract DE-AC05-76RL01830 with the Pacific Northwest National Laboratory.

Author information

Author notes

    • J. Su
    • , C. Hu
    •  & X. Yan

    These authors contributed equally to this work.

Affiliations

  1. Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China

    • J. Su
    • , C. Hu
    • , Z. Chen
    • , Q. Guan
    • , Y. Wang
    • , D. Zhong
    •  & F. Wang
  2. Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO Box 7080, SE-75007 Uppsala, Sweden

    • J. Su
    • , C. Hu
    • , X. Yan
    • , Y. Jin
    •  & C. Sun
  3. Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha 410128, China

    • Y. Jin
  4. The Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory, PO Box 999, K8-93 Richland, Washington 99352, USA

    • C. Jansson
  5. Department of Microbiology, Uppsala BioCenter, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden

    • A. Schnürer

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Contributions

J.S., Z.C., Q.G., Y.W. and D.Z. performed measurements of methane emissions from paddies; J.S. also performed western blot and zymogram analyses, methanogen quantification and starch determination. C.H. was responsible for plasmid constructions, rice transformation, Southern blot analysis and phenotypic trait characterization. X.Y. carried out gene expression analysis, starch determination, sugar induction experiments and phenotypic trait characterization. Y.J. performed plasmid validation, insertion site identification, methanogen quantification, measurements of methane emissions in phytotrons and sugar induction experiments, electrophoretic mobility shift assay (EMSA), qPCR and light microscopy. C.J. was involved in the initiation, layout and discussions concerning the work and manuscript revision. F.W. was involved in the planning of rice transformation and field trial settings. A.S. revised the manuscript and helped with methane and methanogen determinations. C.S. initiated and coordinated the work, designed the experiments, performed some experiments, and drafted and revised the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to F. Wang or C. Sun.

Extended data

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    This file contains Supplementary Table 1.

  2. 2.

    Supplementary Data

    This file contains the sequences of the construct and insertion sites in Extended Data Fig. 1.

Excel files

  1. 1.

    Supplementary Information

    This file contains Supplementary Table 2.

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