Mechanisms for coping with submergence and waterlogging in rice

1Plants require water for growth but excess water that occurs during submergence or waterlogging is harmful or even lethal. A submerged plant is defined as "a plant standing in water with at least part of the terminal above the water or completely covered with water" (Figure 1; ). Submergence subjects plants to the stresses of low light, limited gas diffusion, effusion of soil nutrients, mechanical damage, and increased susceptibility to pests and diseases. Basically, flooding (i.e., submergence) can be classified into "flash flooding" and "deepwater flooding" in accordance with the duration of flooding and the water depth. Flash flooding, which generally lasts less than a few weeks, is caused by heavy rain but the depth is not very deep. On the other hand, deepwater flooding, which lasts for several months, occurs during the rainy season, and the water depth reaches several meters.

2Waterlogging is defined as a condition of the soil in which excess water limits gas diffusion (Figure 1; ). Oxygen diffusivity in water is approximately 10,000 times slower than in air, and the flux of O2 into soils is approximately 320,000 times less when the soil pores are filled with water than when they are filled with gas. The principal cause of damage to plants grown in waterlogged soil is inadequate supply of oxygen to the submerged tissues as a result of slow diffusion of gases in water and rapid consumption of O2 by soil microorganisms. Oxygen deficiency in waterlogged soil occurs within a few hours under some conditions. In addition to the O2 deficiency, production of toxic substances such as Fe2+, Mn2+, and H2S by reduction of redox potential causes severe damage to plants under waterlogged conditions. Thus, growth and development of most plants, except for rice (Oryza sativa L.) and other wetland species, are impeded under waterlogged conditions.

3Unlike other crop plants, rice has some adaptive traits for tolerance of submergence. One of the traits is formation of the longitudinal interconnection of gas spaces, called aerenchyma, that enables internal aeration between shoot and roots Moreover, leaf gas films, which are a micro-layer of air trapped between submerged leaves and the surrounding water, contribute to the internal aeration during submergence, thereby increasing submergence tolerance in rice.

4Many lowland rice cultivars, despite having an ability of internal aeration, are still sensitive to complete submergence. Their leaves and stems moderately elongate under complete submergence to reach the air-water interface, but their elongation growth can exhaust energy reserves and cause death when the flooding depth is deep and the flooding period is long. However, some cultivars use two distinct strategies of growth controls to survive under submerged conditions. One of the strategies is a quiescence strategy [i.e., the low-oxygen quiescence syndrome] (Figure 1), in which shoot elongation is suppressed to preserve carbohydrates for a long period (10-14 days) under flash-flood conditions. Submergence-tolerant cultivars can restart their growth during desubmergence by using preserved carbohydrates. Another strategy is an escape strategy [i.e., the low-oxygen escape syndrome] (Figure 1), which involves fast elongation of internodes to rise above the water level and is used by deepwater rice cultivars. Both strategies depend on ethylene-responsive transcription factors.

5The main adaptation of lowland rice to soil waterlogging is the formation of aerenchyma, which permits relatively unhindered transport of O2 from well-aerated shoots to submerged roots (Figures 1, 2;; ). Longitudinal diffusion of O2 towards the root apex can be further enhanced by induction of a barrier to radial O2 loss (ROL) that minimizes loss of O2 to the surrounding environment (Figures 1, 2). Furthermore, this barrier may impede the movement of soil-derived toxins (i.e., reduced metal ions) and gases (e.g. methane, CO2, and ethylene) into the roots. Both upland and lowland rice species use these traits under waterlogged conditions.

6Some recent reviews summarized the mechanisms of flooding tolerance in plants. In this review, we include recent discoveries that were not covered in the previous reviews and summarize what is known about the physiological and molecular mechanisms that contribute to tolerance to, or avoidance of, submergence (i.e., internal aeration and growth controls) and also adaptation to waterlogging (i.e., formations of aerenchyma and a barrier to ROL) in rice and other gramineous plants.

7Effective internal aeration in plants is crucial to survive under submergence. In rice, aerenchyma is well developed in roots, internodes, sheaths, and the mid-rib of leaves and contributes to the effective internal aeration between shoots and roots. Submerged leaves have gas films that aid O2 and CO2 exchange between leaves and the surrounding water, and thus increase underwater net photosynthesis by supplying CO2 during the day (under light conditions) and promote O2 uptake for respiration at night. As a result, leaf gas films contribute to leaf sugar production by photosynthesis when under water, and in turn shoot and root dry mass. Removal of leaf gas films caused a decrease of O2 partial pressure (pO2) in roots when shoots were in darkness, suggesting that leaf gas films partially contribute to O2 transport from shoot to root. Taken together, these findings indicate that leaf gas films are important for submergence tolerance in rice.

8defined submergence tolerance as "the ability of a rice plant to survive 10-14 days of complete submergence and renew its growth when the water subsides; there is no stem elongation during submergence." Under this definition, submergence tolerance indicates flash-flood tolerance. Generally, the seedlings of many lowland rice cultivars elongate their leaves to get oxygen at the water's surface under submerged conditions. However, because this shoot elongation requires large amounts of energy, most rice cultivars (i.e., flash-flood-intolerant cultivars) have poor ability to recover fully after the water recedes and eventually sustain severe damage or die. By contrast, the flash-flood-tolerant East Indian rice cultivar FR13A shows restricted shoot elongation and reduced energy consumption under submergence. The energy in FR13A plants is preserved during submergence, and upon desubmergence their growth can be restarted by using this energy. There is therefore a negative correlation between shoot elongation and survival rate under complete submergence.

9FR13A has the Submergence-1 (SUB1) locus on chromosome 9. discovered that the SUB1 locus contains SUB1A, SUB1B, and SUB1C, all of which encode ethylene response factors and are upregulated under submergence, but only SUB1A is responsible for the flash-flood tolerance. The near-isogenic line M202(SUB1), which was generated by introgression of the SUB1 region from FR13A into the flash-flood-intolerant cultivar M202, shows restricted shoot elongation under submergence, as does FR13A. To preserve energy and carbohydrates, M202(SUB1) suppresses the expression of genes encoding α-amylase and sucrose synthase, which are involved in starch and sucrose metabolism. In addition, SUB1A positively regulates the genes involved in alcohol fermentation and thus promotes acclimation of plants to flash-flood conditions. reported that SUB1A also enhances the expression of genes encoding SLENDER RICE-1 (SLR1) and SLR1 like 1 (SLRL1), which are key repressors of gibberellin (GA) signaling in rice; it also negatively regulates the GA response in order to restrict shoot elongation under submergence. Recently, it was shown that SUB1A expression is also induced by drought and oxidative stress upon desubmergence. SUB1A positively regulates the expressions of genes involved in ABA-mediated acclimation to drought conditions. Moreover, under oxidative stress, SUB1A promotes the expression of genes related to the detoxification of reactive oxygen species (ROS) and reduces the accumulation of ROS. As a result, M202(SUB1) has a higher drought and oxidative tolerance than M202. In rain-fed rice fields, inadequate water management is prone to cause flooding and drought. Thus, as submergence and drought stresses can cause severe decreases in rice production in rain-fed rice fields, introgression of the SUB1A gene into rice cultivars intolerant of submergence and drought is a promising way of increasing rice productivity in these fields.

10Deepwater flooding lasts for several months, and O2 deficiency causes energy depletion in plants. To survive under deepwater-flood conditions, rice plants must escape from the flooding. A unique trait of deepwater rice is that its internodes rapidly and substantially elongate to avoid deepwater flooding. Remarkably, some deepwater rice cultivars can increase their height by 25 cm/day. This rapid elongation allows the leaf tips to extend above the water surface and enables the rice plants to efficiently photosynthesize and exchange gases for respiration. During internode elongation, ethylene biosynthesis is activated and the accumulated ethylene regulates the increases in GA content and decrease in ABA content. As internode elongation is promoted by GA or repressed by ABA, the increased GA/ABA ratio contributes to the elongation. Indeed, GA activates the expression of cell division-related genes, and thus active cell division is observed at the intercalary meristem in the internode under submergence. Moreover, high levels of expression of genes encoding expansin, which is involved in cell-wall loosening, and changes in the orientation of cellulose microfibrils are observed in the internode during internode elongation. Aerenchyma formation occurs in the internodes simultaneously with their elongation, and is enhanced by ethylene. Growth of adventitious roots, which is preceded by death of epidermal cells that cover the root primordia, is also promoted by ethylene.

11Recently, identified the SNORKEL1 (SK1) and SNORKEL2 (SK2) genes responsible for internode elongation in deepwater rice. Non-deepwater rice (i.e., lowland rice) into which SK1 or SK2 had been introduced showed internode elongation in the same way as deepwater rice, indicating that the SK genes are key factors for the escape strategy of deepwater rice under deepwater-flood conditions. Because of space considerations, details of the function of SK genes have not been included in this review, but they have been summarized by and.

12Formation of aerenchyma is essential to the survival and functioning of plants subjected to waterlogging. The aerenchyma contributes to O2 supply from shoots to roots and to the ventilation of gases (e.g. CO2 and methane) from roots to shoots. The ventilation of gases in aerenchyma is mainly caused by gas diffusion in rice, but in some wetland species with 'through-flow pathways' (e.g. along rhizomes), gas flows can also occur by humidity- and Venturi-induced pressure flows (e.g. Phragmites australis; ). The aerenchyma may provide a photosynthetic benefit by concentrating CO2 from root respiration and transporting it to the leaf intercellular spaces in some wetland plant species.

13In general, aerenchyma can be classified into two types: (i) schizogenous aerenchyma, which develops by cell separation and differential cell expansion that creates spaces between cells, in e.g. Rumex palustris; and (ii) lysigenous aerenchyma, formed by the death and subsequent lysis of some cells, e.g., in rice, maize, wheat, and barley. In the roots, lysigenous aerenchyma forms in the cortex (Figure 2), whereas in the stems it can form in the cortex and pith cavity.

14In some wetland plant species such as rice, root lysigenous aerenchyma is constitutively formed under drained soil conditions (i.e., aerobic conditions; ), and its formation can be further enhanced during soil waterlogging (Figure 2;;;; ). In rice, aerenchyma formation is initiated at the apical parts of the roots and gradually expands to the basal parts of the roots (Figure 2; ). Fully developed aerenchyma, which is observed on the basal parts of roots, separates the inner stele from the outer cell layers (i.e., sclerenchyma, hypodermis/exodermis, and epidermis) of the roots (Figure 2;;; ). Strands of remaining cells and cell walls separate gas spaces in the cortex, forming radial bridges, which are important for the structural integrity of the root and for both apoplastic and symplastic transport of nutrients (Figure 2; ). During aerenchyma formation in rice root, cell death begins at the cells in the mid-cortex and then spreads out radially to the surrounding cortical cells. The epidermis, hypodermis/exodermis, endodermis, and stele are unaffected, indicating that lysigenous aerenchyma formation occurs by closely controlled mechanisms.

15By contrast, in non-wetland plant species such as maize, wheat, and barley, root lysigenous aerenchyma does not form under well-drained soil conditions, but it may be induced by poor aeration. Generally, induction of aerenchyma formation takes 24-72 hours after the start of anaerobic treatment. In addition, aerenchyma formation is less extensive in non-wetland plant species than in wetland plant species. Thus, non-wetland plants are less tolerant to waterlogging than wetland plants, such as rice.

16In rice and maize, ethylene is implicated in the induction of lysigenous aerenchyma formation. Rice roots form lysigenous aerenchyma constitutively even under well-aerated conditions. Lysigenous aerenchyma formation in rice roots can be further increased by ethylene treatment under aerated conditions and decreased by treatment with an ethylene perception inhibitor (e.g. silver ions) under stagnant (0.1% agar) deoxygenated conditions (which mimics hypoxic/anoxic conditions in waterlogged soils; ), although cultivars (e.g. Norin 36 and RB3) differ in their sensitivity to ethylene. also pointed out that consideration of the lengths of the roots sampled was important for comparison of aerenchyma formations between treatments. More recently, ethylene has been shown to increase root aerenchyma formation in another rice cultivar, Calrose. In maize roots, ethylene biosynthesis is stimulated by enhancing the activity of 1-aminocyclopropene-1-carboxylic acid (ACC) synthase and ACC oxidase at the beginning of aerenchyma formation. Thus, treatment of maize roots with inhibitors of ethylene biosynthesis (e.g. aminoethoxyvinylglycine, aminooxyacetic acid (AOA), and cobalt chloride) or action (e.g. silver ions) effectively blocks aerenchyma formation under hypoxic conditions. These observations indicate that ethylene works as a trigger for the induction of aerenchyma formation in rice and maize. On the other hand, in the roots of another wetland species (Juncus effusus), lysigenous aerenchyma formation is not affected by treatment with ethylene or the ethylene perception inhibitor 1-methylcyclopropene (1-MCP; ). To determine whether ethylene is (or is not) a common factor in regulation of the induction of lysigenous aerenchyma formation in the roots of wetland species, the effect of ethylene on aerenchyma formation should be studied by treatment of a wider range of wetland species while considering the possible influences of root length and tissue age along the root axes.

17Ethylene-responsive lysigenous aerenchyma formation is affected by chemical inhibitors or stimulators of programmed cell death (PCD) and other signaling pathways. Heterotrimeric G-protein-, phospholipase C (PLC)-, inositol 1,4,5-trisphosphate (IP3)-, or Ca2+-dependent signaling pathways are involved in the process of lysigenous aerenchyma formation in maize roots. It has been proposed that, under oxygen deprivation, Ca2+ is released from mitochondria into the cytosol; the elevated cytosolic Ca2+ may provoke subsequent activation of kinases and phosphatases during aerenchyma formation. Lysigenous aerenchyma formation is also induced by okadaic acid, an inhibitor of protein phosphatases, and is repressed by K252a, an inhibitor of protein kinases. These calcium-dependent signalings may result in activation of expression of the genes responsible for aerenchyma formation. PCD is a tightly regulated pathway that accompanies the activation of specific biochemical pathways. PCD is distinguished from necrosis, which occurs by uncontrolled, accidental cell death without activation of signaling pathways. Cell death during lysigenous aerenchyma formation is similar to apoptosis in animal cells, which includes DNA fragmentation, nuclear condensation, and nuclear and plasma membrane blebbing.

18One of the final steps in lysigenous aerenchyma formation is degradation of the cell wall, which is mediated by cell-wall modification or degradation enzymes. Changes in esterified and de-esterified pectins in the cell wall of the maize cortex are observed during cell death. Subsequently, the cell wall is degraded by the combined action of pectolytic, xylanolytic, and cellulosolytic enzymes. The activity of cellulase (CEL) is increased by treatment with ethylene, okadaic acids, and reagents that increase intracellular Ca2+ levels, whereas CEL activity is decreased by treatment with K252a and inhibitors of Ca2+ increase. In maize roots, expression of a gene encoding xyloglucan endotransglycosylase (XET) is induced by waterlogging, and its induction is inhibited by treatment with the ethylene biosynthesis inhibitor AOA. Treatment with AOA prevents the formation of lysigenous aerenchyma, suggesting that induction of XET production in response to ethylene is involved in aerenchyma formation through cell-wall modification.

19On the basis of this evidence, proposed that cell death in the root cortex during lysigenous aerenchyma formation can be classified into five steps: (1) perception of hypoxia and initiation of ethylene biosynthesis; (2) perception of ethylene signaling by cells of the mid-cortex; (3) initiation of cell death with loss of ions to the surrounding environment, plasma membrane invagination, and formation of small vesicles; (4) chromatin condensation, increased activity of cell-wall hydrolytic enzymes, and the surrounding of organelles by membranes; and (5) cell-wall degradation, cell lysis, and absorption of the cell contents and water by the surrounding cells.

20So far, studies of lysigenous aerenchyma formation have been done mainly from a physiological perspective. However, the genes involved in lysigenous aerenchyma formation in the root have not been identified. Recently, identified genes associated with lysigenous aerenchyma formation in maize roots by using a microarray analysis combined with laser microdissection. They found that Ca2+ signaling-related genes encoding Calcineurin B-like protein and Calmodulin-like protein were upregulated under waterlogged conditions, and their expression levels were higher in the cortical cells than in the stelar cells. Waterlogging also induces the expression of cell-wall modification-related genes (e.g. XET and CEL). Induction of the expressions of calcium signaling- and cell wall modification-related genes is suppressed by treatment with 1-MCP. These results support the previously proposed mechanism of ethylene-mediated lysigenous aerenchyma formation.

21A gene encoding respiratory burst oxidase homolog (RBOH; a plant homolog of gp91phox in mammalian NADPH oxidase), which has a role in ROS generation, is upregulated strongly in the cortical cells and slightly less strongly in the stelar cells and the outer cell layers of maize roots (Figure 3;; ). On the other hand, a gene encoding metallothionein (MT), which has a role in ROS scavenging, is constitutively expressed in all of the cortical cells, the stelar cells, and the outer cell layers of maize roots under aerobic conditions. By contrast, under waterlogged conditions the MT gene is hardly expressed at all in the cortical cells but is still highly expressed in the stelar cells and the outer cell layers (Figure 3;; ). These results suggest that H2O2 and other ROS are scavenged by the constitutively expressed MT in stelar cells and the outer cell layers, whereas in the cortical cells decreased MT expression prevents ROS scavenging, thereby leading to greater ROS accumulation, which activates the subsequent processes of PCD (i.e., lysigenous aerenchyma formation) in maize roots (Figure 3). Interestingly, upregulation of RBOH and downregulation of MT also occur in rice roots during inducible aerenchyma formation under anaerobic conditions (Yamauchi and Nakazono, unpublished). Similarly, ethylene-promoted downregulation of expression of a gene encoding MT2b enhances the accumulation of H2O2 produced by NADPH oxidase and thus induces epidermal cell death in rice or aerenchyma formation in rice internodes. These results suggest that downregulation of MT genes plays an important role in tissue-specific or cell type-specific PCD in rice and maize.

22Oxygen molecules diffusing longitudinally through aerenchyma toward the root tips may be either consumed by respiration or diffused radially to the rhizosphere. ROL, the flux of O2 from the aerenchyma to the soil, is determined by the concentration gradient, the physical resistance to O2 diffusion in a radial direction, and consumption of O2 by cells along this radial diffusion path. ROL aerates the rhizosphere and is therefore considered to be of adaptive significance in plants growing in waterlogged soil. However, ROL reduces the supply of O2 to the root apex and thereby causes a decrease in root length in anaerobic soil.

23The roots of many wetland species, including rice, have the ability to prevent ROL to the rhizosphere by forming a barrier in the root peripheral cell layers exterior to the aerenchyma (Figure 2;; ). This adaptive trait enhances longitudinal O2 diffusion through the aerenchyma towards the root apex by diminishing losses of O2 to the rhizosphere, thereby enabling the roots to elongate into anaerobic substrates.

24The roots of some wetland species have constitutively present barriers to ROL (e.g. J. effusus; ), whereas in other species such as rice and Hordeum marinum the barrier to ROL is induced during growth under anaerobic conditions. Analysis of the spatial patterns of ROL along rice roots has revealed that O2 leakage from the basal regions of the long roots under stagnant conditions is quite low (Figure 4), but there are large amounts of O2 flux from the root apexes (Figure 4) and numerous short lateral roots that appear near the base of the main axes. The barrier to ROL, together with reoxidation of the rhizosphere around the root tips and lateral roots, enables elongation of the roots into the anoxic environment and restricts the entry of toxic compounds from highly reduced soils.

25Despite the importance of the barrier to ROL, there are few data available on the O2 permeability coefficient across the cell layers exterior to the aerenchyma. Recently, developed a gas perfusion technique to measure the O2 permeability of the outer cell layers of the roots and applied the technique to rice grown under either aerated or stagnant deoxygenated conditions. Plants grown in the stagnant O2-deficient conditions of the external growth medium showed much lower O2 permeability than plants grown in an aerated solution. The variation in O2 permeability, either by blocking apoplastic pores or killing living tissues, indicated that physical resistance is the dominating factor impeding O2 loss from rice roots, although respiratory O2 consumption may contribute to low rates of ROL. Strong physical impedance to radial O2 diffusion in rice roots has already been shown by. In this study, a barrier to ROL was evident in the adventitious roots of rice, even when respiration was inhibited by cooling the root medium to 3°C. Similar findings have been reported by and in the roots of P. australis and H. marinum, respectively. In H. marinum the physical barrier appeared to account for 84% of the reduction in O2 loss and respiratory activity for 16%.

26It seems that suberization and/or lignification of the cell walls in the root layers exterior to the aerenchyma is implicated in the development of a tight barrier to ROL (Figure 5;;;; ). In a recent study in rice, rates of ROL from the roots of plants grown under aerated or deoxygenated conditions were quantified, and the results were combined with parallel histochemistry and analytical chemistry. Deoxygenated conditions induced the early development of Casparian bands and suberin lamellae in the exodermis and of lignin in densely packed, uniseriate sclerenchymal cells located interior to the exodermis (Figure 5). In agreement with the results of the histochemical analyses, quantitative analyses using gas chromatography and mass spectrometry have shown that the levels of suberin (both aromatic and aliphatic domains), as well as lignin, released from the outer root sleeves are several times greater in plants grown in oxygen-deprived media compared with plants grown in aerated solution. Independent of the growth conditions, the total amounts of suberin and lignin increase along the roots towards the basal zones. Although these studies have shown a direct relationship between changes in O2 permeability and the formation of apoplastic barriers, the precise nature of the ROL barrier remains unclear. Namely, the relative contributions of suberin and lignin in limiting ROL are not well known; potentially, one of the two might not be needed for formation of the barrier. Function of lignin in preventing ROL may not be applied to all plant species. In Amazonian tree species, as well as in P. australis, resistance to ROL is correlated only with the deposition of suberin, but not lignin. Histochemical solute penetration studies using periodic acid have further confirmed that in the roots of P. australis the suberized exodermis--not the lignified sclerenchyma, which is easily penetrated by periodic acid--is the radial permeation barrier. found that suberin increased prior to changes in lignin in rice, suggesting that deposition of suberin is more important for the ROL barrier formation than lignin. However, the suberin and lignin deposits were not evident in the roots within the first 2 days of stagnant treatment, during which time barrier induction was already complete. In long adventitious roots (105-130 mm in length), barrier to ROL was well formed within 24 hours under stagnant deoxygenated conditions and dark granules of high-density material were observed by transmission electron microscopy in the spaces between the exodermal cells and also between the sclerenchyma cells in roots at 48 hours after the stagnant treatment. This result suggests that these microstructural changes also contribute to the diminution of ROL in the rice root. The precise nature of the barrier to ROL still needs to be more clearly elucidated (see below).

27Although the barrier to ROL helps wetland plants to tolerate waterlogging, it may also reduce water and nutrient uptake. For example, the rates of NH4+ and NO3- net uptake in the basal region of rice roots were about 30% of those in maize, even when the plants were grown in aerated solution and the permeability of roots to water is substantially smaller in rice than in maize. However, a recent study demonstrated that the early formation of apoplastic barriers in the endodermis and exodermis of rice roots in stagnant solutions does not significantly affect hydraulic conductivity. This is in agreement with the earlier findings of in stagnantly grown H. marinum, in which induction of the barrier to ROL did not impede the water permeability of the roots. In contrast to water flow, stagnant growth conditions markedly reduce the permeability of the rice roots to oxygen and to ions such as Fe2+, Cu2+, and NaCl. The extra suberin and lignin deposited in the roots in stagnant solutions may effectively clog the wall pores, making a barrier sufficient to block the passage of oxygen and ions, but not water, which is mainly bulk and viscous in nature. It appears that rice roots living in anaerobic media can retain oxygen in the aerenchyma while taking up sufficient water. This is achieved because of differences in the transport mechanisms of oxygen and water. When measured with heavy water, the diffusional water permeability of the outer part of the rice root was an order of magnitude smaller than that of oxygen. However, diffusional water permeability was smaller than the bulk water permeability by a factor of 600-1400. The latter parameter is the one that is important during water uptake. This suggests that rice has evolved an optimum balance between water uptake and O2 loss. Water moves predominantly through the porous apoplastic pathway by using a hydrostatic pressure gradient, whereas the movement of O2 ought to be appreciable over the whole inter-cell interface and is diffusional in nature.

28There are major uncertainties regarding the signals involved in the formation of an inducible barrier to ROL. showed that ethylene, which promotes the induction of lysigenous aerenchyma formation, did not induce a tight barrier to ROL in rice roots, indicating that these two root aeration traits, which are considered to act synergistically to enhance O2 diffusion to the root apex, appear to be differentially regulated. By contrast, a significant decline in ROL, which is correlated with suberization and lignification of the outer cell layers, is observed after the exposure of rice roots to carboxylic acids (e.g. acetic acid, propanoic acid, butyric acid, and caproic acid; ) and sulfide (in the form of phytotoxins produced by micro-organisms in waterlogged soils; ). Similar effects are found when carboxylic acids are applied to the roots of H. marinum (Kotula, Colmer, and Nakazono, unpublished). However, the reduction in ROL from the roots of rice and H. marinum exposed to toxic levels of carboxylic acids and sulfide was associated with injury, rather than with a specific signal for induction of the barrier to ROL.

29Recently, showed that Si nutrition increased suberization and lignification of rice roots, which was accompanied by silicic acid-triggered transcription of genes associated with suberin and lignin biosynthesis. As a consequence of suberization and lignification of the outer root cell layers, the oxidation power of the rice roots was reduced. Although it is suggested by that altered levels of silicic acid play a role in promoting the biosynthesis of suberin and lignin, the signal involved in inducible ROL barrier formation remains unclear.

30Although great progress has been made in our understanding of the mechanisms involved in adaptation to submergence or waterlogging, there are still gaps in our knowledge, mainly in regard to the signaling pathways and molecular processes. The genetic regulation of the formation of lysigenous aerenchyma and the barrier to ROL remains to be determined. Recently, Nakazono and his colleagues (; Shiono, Yamazaki, and Nakazono, unpublished) have been investigating the expressions of genes associated with the formation of inducible lysigenous aerenchyma and the barrier to ROL by using laser microdissection-mediated microarray analysis of the cortex in maize roots and the outer cell layers in rice roots, respectively, under anaerobic conditions. This approach should help to identify important genes involved in the formation of these two structures. Further insights into the nature of the barrier to ROL and the molecular mechanism of inducible barrier formation could be achieved from the characterization of suberin or lignin formation-affected rice mutants in comparison with the respective wild types.

31This review summarizes what is known about the physiological and molecular mechanisms used by rice to cope with submergence and waterlogging. For submergence, the mechanisms include internal aeration and growth controls (i.e., a quiescence strategy or an escape strategy). For waterlogging, the mechanisms include formation of aerenchyma and a barrier to ROL. These adaptive traits enable rice plants to have high tolerance to submergence or waterlogging compared with other dryland crops. An advantage of rice is that its genome has been fully sequenced and many tools for studying its molecular biology and genetics (e.g. oligo microarrays, mutant collections, and databases) have been developed. These resources should accelerate our understanding of the mechanisms involved in adaptation of rice to excess water stress and should lead to their introduction into dryland crops.

32The authors declare that they have no competing interests.

33All of the authors contributed equally to the drafting and revising of this paper and have read and approved the final manuscript.