Physiological Mechanisms of Flooding Tolerance in Rice: Transient Complete Submergence and Prolonged Standing Water

  • T. D. Colmer
  • W. Armstrong
  • H. GreenwayEmail author
  • A. M. Ismail
  • G. J. D. Kirk
  • B. J. Atwell
Part of the Progress in Botany book series (BOTANY, volume 75)


Partial or complete submergence of shoots of rice (Oryza sativa L.) poses a dual challenge: the roots have to function in anoxic soil and gas exchange between shoots and air becomes restricted to a small aerial portion or is abolished during complete submergence. Adaptation of roots to anoxic and chemically reduced waterlogged soils was reviewed by Kirk et al. (Prog Bot, 2014). With deeper floods the O2 provision to the roots may decline, because there is a high resistance for gas exchange between floodwater and the submerged part of the foliage. Floodwaters differ greatly in light levels and CO2 concentrations, thus restricting underwater photosynthesis by varying degrees. During the day, underwater photosynthesis largely determines the O2 concentrations within submerged rice, whereas, at night, tissue O2 declines, particularly so in roots. Deepwater rice establishes a ‘snorkel’ via elongation of aerenchymatous internodes and leaf sheaths; these responses are triggered by ethylene, which acts on two Snorkel genes encoding ethylene-responsive factor (ERF) transcriptional regulators to elicit the action of gibberellin. In addition, aquatic roots emerge from stem nodes. Perversely, pronounced shoot elongation can be catastrophic for lowland rice completely submerged during transient floods. In these circumstances tolerance is underpinned by suppression of elongation by SUB1A-1, an ERF transcriptional regulator that blocks ethylene responsiveness. However, many aspects of survival during transient complete submergence remain unclear, such as the role of carbohydrate depletion, photosynthesis under water, and anoxia tolerance in roots. After desubmergence, possible injury to shoots from water deficits and free radicals also requires further elucidation. This review is focused on the evaluation of the physiological mechanisms involved in the acclimation–adaptation of rice to these floods.


Gibberellic Acid Internode Elongation Leaf Elongation Submergence Tolerance Deepwater Rice 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

List of Abbreviations


Alcohol dehydrogenase


Pyruvate decarboxylase


Quantitative trait loci; regions of DNA containing or linked to the genes that underlie a quantitative trait (i.e. a phenotype, such as submergence tolerance)


Reactive oxygen species


A major QTL on chromosome 9 of rice conferring tolerance of transient complete submergence


The gene conferring submergence tolerance at the SUB1 QTL region. The allele of SUB1A that confers submergence tolerance is called SUB1A-1. SUB1A-1 contains a natural point mutation, as compared with the more common allele SUB1A-2. Most Indica genotypes have a SUB1A gene, whereas Japonica genotypes do not. SUB1A encodes an ethylene-responsive factor (ERF) transcriptional regulator. SUB1A-1 contains a point mutation resulting in leaf (mainly sheath) elongation being insensitive to ethylene and the lack of a significant underwater elongation response has been termed ‘quiescence’, which, together with other associated changes, endows submergence tolerance (described in text, with references)



We thank Tim Setter for incisive criticism of the review; Ole Pedersen, Mike Jackson and Rens Voesenek, for helpful comments on various sections of this review; and Anders Winkel for stimulating discussions on his recent field submergence experiments on rice. The following people are thanked for contributions to the figures: K.G. Srikanta Dani (re-drawing of Figs. 1 and 4a and formatting of Fig. 5), Ole Pedersen (photographs and graphs in Fig. 2); Udompan Promnart (photograph in Fig. 4b), and Jean Armstrong for the photograph in Fig. 3.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • T. D. Colmer
    • 1
  • W. Armstrong
    • 1
    • 2
  • H. Greenway
    • 1
    Email author
  • A. M. Ismail
    • 3
  • G. J. D. Kirk
    • 4
  • B. J. Atwell
    • 5
  1. 1.School of Plant Biology and the UWA Institute of AgricultureThe University of Western AustraliaCrawleyAustralia
  2. 2.Department of Biological SciencesUniversity of HullYorkshireUK
  3. 3.International Rice Research InstituteMetro ManilaPhilippines
  4. 4.Environmental Science and TechnologyCranfield UniversityBedfordshireEngland, UK
  5. 5.Department of Biological Sciences, Faculty of ScienceMacquarie UniversitySydneyAustralia

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