Submergence research using Rumex palustris as a model; looking back and going forward

Strong plastic responses in aerenchyma formation in F1 hybrids of Imperata cylindrica under different soil moisture conditions

Hybrids can express traits plastically, enabling them to occupy environments that differ from parental environments. However, there is insufficient evidence demonstrating how phenotypic plasticity in specific traits mediates hybrid performance. Two parental ecotypes of Imperata cylindrica produce F1 hybrids. The E-type in wet habitats has larger internal aerenchyma than the C-type in dry habitats. This study evaluated relationships between habitat utilisation, aerenchyma plasticity, and growth of I. cylindrica accessions. We hypothesize that plasticity in expressing parental traits explains hybrid establishment in habitats with various soil moisture conditions. Aerenchyma formation was examined in the leaf midribs, rhizomes and roots of two parental ecotypes and their F1 hybrids in their natural habitats. In common garden experiments, we examined plastic aerenchyma formation in leaf midribs, rhizomes and roots of natural and artificial F1 hybrids and parental ecotypes and quantified vegetative growth performance. In the natural habitats where soil moisture content varied widely, the F1 hybrids showed larger variation in aerenchyma formation in rhizomes than their parental ecotypes. In the common garden experiments, F1 hybrids showed high plasticity of aerenchyma formation in rhizomes, and their growth was similar to that of C-type and E-type under drained and flooded conditions, respectively. The results demonstrate that F1 hybrids of I. cylindrica exhibit plasticity in aerenchyma development in response to varying local soil moisture content. This characteristic allows the hybrids to thrive in diverse soil moisture conditions.

A quantitative trait locus conferring flood tolerance to deepwater rice regulates the formation of two distinct types of aquatic adventitious roots

A key trait conferring flood tolerance is the ability to grow adventitious roots as a response to submergence. The genetic traits of deepwater rice determining the development and characteristics of aquatic adventitious roots (AAR) had not been evaluated. We used near-isogenic lines introgressed to test the hypothesis that the impressive shoot elongation ability of deepwater rice linked to quantitative trait loci 1 and 12 also promote the development of AAR. The deepwater rice genotype NIL-12 possessed expanded regions at the stem nodes where numerous AAR developed as a response to submergence. Two types (AR1 and AR2) of roots with distinct timing of emergence and large differences in morphological and anatomical traits formed within 3 (AR1) to 7 (AR2) d of submergence. The mechanical impedance provided by the leaf sheath caused AR2 to emerge later promoting thicker roots, higher elongation capacity and higher desiccation tolerance. Upregulation of key genes suggests a joint contribution in activating the meristem in AAR enhancing the development of these in response to submergence. The morphological and anatomical traits suggested that AR2 is better adapted to long-term flooding than AR1. We therefore propose that AR2 in deepwater rice functions as an evolutionary defence strategy to tackle periodic submergence.

The Role of Aquaporins in Plant Growth under Conditions of Oxygen Deficiency

Plants frequently experience hypoxia due to flooding caused by intensive rainfall or irrigation, when they are partially or completely submerged under a layer of water. In the latter case, some resistant plants implement a hypoxia avoidance strategy by accelerating shoot elongation, which allows lifting their leaves above the water surface. This strategy is achieved due to increased water uptake by shoot cells through water channels (aquaporins, AQPs). It remains a puzzle how an increased flow of water through aquaporins into the cells of submerged shoots can be achieved, while it is well known that hypoxia inhibits the activity of aquaporins. In this review, we summarize the literature data on the mechanisms that are likely to compensate for the decline in aquaporin activity under hypoxic conditions, providing increased water entry into cells and accelerated shoot elongation. These mechanisms include changes in the expression of genes encoding aquaporins, as well as processes that occur at the post-transcriptional level. We also discuss the involvement of hormones, whose concentration changes in submerged plants, in the control of aquaporin activity.

Dimorphic Leaf Development of the Aquatic Plant Callitriche palustris L. Through Differential Cell Division and Expansion

Heterophylly, or phenotypic plasticity in leaf form, is a remarkable feature of amphibious plants. When the shoots of these plants grow underwater, they often develop surprisingly different leaves from those that emerge in air. Among aquatic plants, it is typical for two or more distinct leaf development processes to be observed in the same individual exposed to different environments. Here, we analyze the developmental processes of heterophylly in the amphibious plant Callitriche palustris L. (Plantaginaceae). First, we reliably cultured this species under laboratory conditions and established a laboratory strain. We also established a framework for molecular-based developmental analyses, such as whole-mount in situ hybridization. We observed several developmental features of aerial and submerged leaves, including changes in form, stomata and vein formation, and transition of the meristematic zone. Then we defined developmental stages for C. palustris leaves. We found that in early stages, aerial and submerged leaf primordia had similar forms, but became discriminable through cell divisions with differential direction, and later became highly distinct via extensive cell elongation in submerged leaf primordia.

Sub1 Rice: Engineering Rice for Climate Change

By the year 2100, the number of people on Earth is expected to increase by ∼50%, placing increasing demands on food production in a time when a changing climate is predicted to compromise crop yields. Feeding this future world requires scientifically informed innovations in agriculture. Here, we describe how a rice gene conferring tolerance to prolonged submergence has helped farmers in South and Southeast Asia mitigate rice crop failure during floods. We discuss how planting of this new variety benefited socially disadvantaged groups. This example indicates that investment in agricultural improvement can protect farmers from risks associated with a changing climate.

Metabolic and biochemical responses of Potamogeton anguillanus Koidz. (Potamogetonaceae) to low oxygen conditions

Oxygen availability in water is considered one of the most important factors for growth and productivity in aquatic submerged macrophytes. In the present study, the growth, stress responses, and metabolic changes in Potamogeton anguillanus Koidz. (Potamogetonaceae) were assessed after a 21-day exposure to low (hypoxia; dissolved oxygen, DO < 1 mg/L) or null (anoxia) oxygen concentrations in water. High growth rates and an increased indole acetic acid (IAA) content in P. anguillanus were observed under the hypoxic conditions (4-fold to control) compared to the anoxic conditions. In addition, the activation of glycolysis and fermentation processes was further recorded, given the increase in alcohol dehydrogenase activity and pyruvate concentration on the studied plants that were exposed to low oxygen concentrations. Moreover, the positive correlations of antioxidative enzyme activities, catalase (CAT) and guaiacol peroxidase (POD) with hydrogen peroxide (H₂O₂) confirmed the species ability to scavenge excess H₂O₂ under low oxygen stress. The capillary electrophoresis-mass spectrometry (CE-MS) analysis of the metabolome identified metabolite accumulations (e.g., glutamate, glutamine, aspartate, asparagine, valine, malate, lactate, citrate, isocitrate, proline and γ-amino butyric acid) in response to the anoxia.

PhERF2, an ethylene-responsive element binding factor, plays an essential role in waterlogging tolerance of petunia

Ethylene-responsive element binding factors (ERFs) are involved in regulation of various stress responses in plants, but their biological functions in waterlogging stress are largely unclear. In this study, we identified a petunia (Petunia × hybrida) ERF gene, PhERF2, that was significantly induced by waterlogging in wild-type (WT). To study the regulatory role of PhERF2 in waterlogging responses, transgenic petunia plants with RNAi silencing and overexpression of PhERF2 were generated. Compared with WT plants, PhERF2 silencing compromised the tolerance of petunia seedlings to waterlogging, shown as 96% mortality after 4 days waterlogging and 14 days recovery, while overexpression of PhERF2 improved the survival of seedlings subjected to waterlogging. PhERF2-RNAi lines exhibited earlier and more severe leaf chlorosis and necrosis than WT, whereas plants overexpressing PhERF2 showed promoted growth vigor under waterlogging. Chlorophyll content was dramatically lower in PhERF2-silenced plants than WT or overexpression plants. Typical characteristics of programmed cell death (PCD), DNA condensation, and moon-shaped nuclei were only observed in PhERF2-overexpressing lines but not in PhERF2-RNAi or control lines. Furthermore, transcript abundances of the alcoholic fermentation-related genes ADH1-1, ADH1-2, ADH1-3, PDC1, and PDC2 were reduced in PhERF2-silenced plants, but increased in PhERF2-overexpressing plants following exposure to 12-h waterlogging. In contrast, expression of the lactate fermentation-related gene LDH was up-regulated in PhERF2-silenced plants, but down-regulated in its overexpressing plants. Moreover, PhERF2 was observed to directly bind to the ADH1-2 promoter bearing ATCTA motifs. Our results demonstrate that PhERF2 contributes to petunia waterlogging tolerance through modulation of PCD and alcoholic fermentation system.

Physiological and morphological responses to permanent and intermittent waterlogging in seedlings of four evergreen trees of temperate swamp forests

Waterlogging decreases a plant's metabolism, stomatal conductance (gs) and photosynthetic rate (A); however, some evergreen species show acclimation to waterlogging. By studying both the physiological and morphological responses to waterlogging, the objective of this study was to assess the acclimation capacity of four swamp forest species that reside in different microhabitats. We proposed that species (Luma apiculata [D.C.] Burret. and Drimys winteri J.R. et G. Forster.) abundant in seasonally and intermittently waterlogged areas (SIWA) would have a higher acclimation capacity than species abundant in the inner swamp (Blepharocalyx cruckshanksii [H et A.] Mied. and Myrceugenia exsucca [D.C.] Berg.) where permanent waterlogging occurs (PWA); it was expected that the species from SIWA would maintain leaf expansion and gas exchange rates during intermittent waterlogging treatments. Conversely, we expected that PWA species would have higher constitutive waterlogging tolerance, and this would be reflected in the formation of lenticels and adventitious roots. Over the course of 2 months, we subjected seedlings to different waterlogging treatments: (i) permanent (sudden, SW), (ii) intermittent (gradual) or (iii) control (field capacity, C). Survival after waterlogging was high (≥80%) for all species and treatments, and only the growth rate of D. winteri subjected to SW was affected. Drimys winteri plants had low, but constant A and g during both waterlogging treatments. Conversely, L. apiculata had the highest A and g values, and g increased significantly during the first several days of waterlogging. In general, seedlings of all species subjected to waterlogging produced more adventitious roots and fully expanded leaves and had higher specific leaf area (SLA) and stomatal density (StD) than seedlings in the C treatment. From the results gathered here, we partially accept our hypothesis as all species showed high tolerance to waterlogging, maintained growth, and had increased A or g during different time points of waterlogging. Differences in leaf (SLA) and stomata functioning (gs, StD) plasticity likely allows plants to maintain positive carbon gains when waterlogging occurs. The species-specific differences found here were not entirely related to microhabitat distribution.

Transcriptome profiling of the floating-leaved aquatic plant Nymphoides peltata in response to flooding stress

BACKGROUND

Waterlogging or flooding is one of the most challenging abiotic stresses experienced by plants. Unlike many flooding-tolerant plants, floating-leaved aquatic plants respond actively to flooding stress by fast growth and elongation of its petioles to make leaves re-floating. However, the molecular mechanisms of this plant group responding to flood have not been investigated before. Here, we investigated the genetic basis of this adaptive response by characterizing the petiole transcriptomes of a floating-leaved species Nymphoides peltata under normal and flooding conditions.

RESULTS

Clean reads under normal and flooding conditions with pooled sampling strategy were assembled into 124,302 unigenes. A total of 8883 unigenes were revealed to be differentially expressed between normal and flooding conditions. Among them, top ranked differentially expressed genes were mainly involved in antioxidant process, photosynthesis process and carbohydrate metabolism, including the glycolysis and a modified tricarboxylic acid cycle - alanine metabolism. Eight selected unigenes with significantly differentiated expression changes between normal and flooding conditions were validated by qRT-PCR.

CONCLUSIONS

Among these processes, antioxidant process and glycolysis are commonly induced by waterlogging or flooding environment in plants, whereas photosynthesis and alanine metabolism are rarely occurred in other flooding-tolerant plants, suggesting the significant contributions of the two processes in the active response of N. peltata to flooding stress. Our results provide a valuable genomic resource for future studies on N. peltata and deepen our understanding of the genetic basis underlying the response to flooding stress in aquatic plants.

Differentially Expressed microRNAs and Target Genes Associated with Plastic Internode Elongation in Alternanthera philoxeroides in Contrasting Hydrological Habitats

Phenotypic plasticity is crucial for plants to survive in changing environments. Discovering microRNAs, identifying their targets and further inferring microRNA functions in mediating plastic developmental responses to environmental changes have been a critical strategy for understanding the underlying molecular mechanisms of phenotypic plasticity. In this study, the dynamic expression patterns of microRNAs under contrasting hydrological habitats in the amphibious species Alternanthera philoxeroides were identified by time course expression profiling using high-throughput sequencing technology. A total of 128 known and 18 novel microRNAs were found to be differentially expressed under contrasting hydrological habitats. The microRNA:mRNA pairs potentially associated with plastic internode elongation were identified by integrative analysis of microRNA and mRNA expression profiles, and were validated by qRT-PCR and 5' RLM-RACE. The results showed that both the universal microRNAs conserved across different plants and the unique microRNAs novelly identified in A. philoxeroides were involved in the responses to varied water regimes. The results also showed that most of the differentially expressed microRNAs were transiently up-/down-regulated at certain time points during the treatments. The fine-scale temporal changes in microRNA expression highlighted the importance of time-series sampling in identifying stress-responsive microRNAs and analyzing their role in stress response/tolerance.

Hydrogen cyanamide breaks grapevine bud dormancy in the summer through transient activation of gene expression and accumulation of reactive oxygen and nitrogen species

BACKGROUND

Hydrogen cyanamide (HC) and pruning (P) have frequently been used to break dormancy in grapevine floral buds. However, the exact underlying mechanism remains elusive. This study aimed to address the early mode of action of these treatments on accumulation of reactive oxygen species (ROS) and reactive nitrogen species (RNS) and expression of related genes in the dormancy breaking buds of grapevine in the summer.

RESULTS

The budbreak rates induced by pruning (P), hydrogen cyanamide (HC), pruning plus hydrogen cyanamide (PHC) and water (control) after 8 days were 33, 53, 95, and 0 %, respectively. Clearly, HC was more effective in stimulating grapevine budbreak and P further enhanced its potency. In situ staining of longitudinal bud sections after 12 h of treatments detected high levels of ROS and nitric oxide (NO) accumulated in the buds treated with PHC, compared with HC or P alone. The amounts of ROS and NO accumulated were highly correlated with the rates of budbreak among these treatments, highlighting the importance of a rapid, transient accumulation of sublethal levels of ROS and RNS in dormancy breaking. Microarray analysis revealed specific alterations in gene expression in dormancy breaking buds induced by P, HC and PHC after 24 h of treatment. Relative to control, PHC altered the expression of the largest number of genes, while P affected the expression of the least number of genes. PHC also exerted a greater intensity in transcriptional activation of these genes. Gene ontology (GO) analysis suggests that alteration in expression of ROS related genes is the major factor responsible for budbreak. qRT-PCR analysis revealed the transient expression dynamics of 12 specific genes related to ROS generation and scavenge during the 48 h treatment with PHC.

CONCLUSION

Our results suggest that rapid accumulation of ROS and NO at early stage is important for dormancy release in grapevine in the summer, and the identification of the commonly expressed specific genes among the treatments allowed the construction of the signal transduction pathway related to ROS/RNS metabolism during dormancy release. The rapid accumulation of a sublethal level of ROS/RNS subsequently induces cell wall loosening and expansion for bud sprouting.

Growth promotion and inhibition of the Amazonian wild rice species Oryza grandiglumis to survive flooding

In Asian cultivated rice (Oryza sativa), distinct mechanisms to survive flooding are activated in two groups of varieties. Submergence-tolerant rice varieties possessing the SUBMERGENCE1A (SUB1A) gene display reduced growth during flash floods at the seedling stage and resume growth after the flood recedes, whereas deepwater rice varieties possessing the SNORKEL1 (SK1) and SNORKEL2 (SK2) genes display enhanced growth based on internodal elongation during prolonged submergence at the mature stage. In this study, we investigated the occurrence of these growth responses to submergence in the wild rice species Oryza grandiglumis, which is native to the Amazon floodplains. When subjected to gradual submergence, adult plants of O. grandiglumis accessions showed enhanced internodal elongation with rising water level and their growth response closely resembled that of deepwater varieties of O. sativa with high floating capacity. On the other hand, when subjected to complete submergence, seedlings of O. grandiglumis accessions displayed reduced shoot growth and resumed normal growth after desubmergence, similar to the response of submergence-tolerant varieties of O. sativa. Neither SUB1A nor the SK genes were detected in the O. grandiglumis accessions. These results indicate that the O. grandiglumis accessions are capable of adapting successfully to flooding by activating two contrasting mechanisms as the situation demands and that each mechanism of adaptation to flooding is not mediated by SUB1A or the SK genes.

Examination of the leaf proteome during flooding stress and the induction of programmed cell death in maize

BACKGROUND

Maize is a major economic crop worldwide, with substantial crop loss attributed to flooding. During a stress response, programmed cell death (PCD) can be an effective way for plants better adapt. To identify flooding stress related PCD proteins in maize leaves, proteomic analysis was performed using two-dimensional fluorescence difference gel electrophoresis (2D-DIGE) and mass spectrometry.

RESULTS

Comparative proteomics was combined with physiological and biochemical analysis of maize leaves under flooding stress. Fv/Fm, qP, qN and relative water content (RWC) were found to be altered in response to flooding stress, with an increase in H2O2 content noted in vivo. Furthermore, DNA ladder detection indicated that PCD had occurred under flooding treatment. The maize leaf proteome was analyzed via 2D-DIGE gel, with a total of 32 differentially expressed spots isolated, 31 spots were successfully identified via MALDI-TOF/TOF MS which represent 28 proteins. The identified proteins were related to energy metabolism and photosynthesis, PCD, phytohormones and polyamines. To better characterize the role of translationally controlled tumor protein (TCTP) in PCD during a stress response, mRNA expression was examined in different plants by stress-induced PCD. These included heat stress induced rice protoplasts, Tobacco Mosaic Virus infected tobacco leaves and dark induced rice and Arabidopsis thaliana leaves, all of which showed active PCD, and TCTP expression was increased in different degrees. Moreover, S-adenosylmethionine synthase 2 (SAMS2) and S-adenosylmethionine decarboxylase (SAMDC) mRNA expression were also increased, but ACC synthase (ACS) and ACC oxidase (ACO) mRNA expression were not found in maize leaves following flooding. Lastly, ethylene and polyamine concentrations were increased in response to flooding treatment in maize leaves.

CONCLUSIONS

Following flooding stress, the photosynthetic systems were damaged, resulting in a disruption in energy metabolism, with the noted photosynthetic decline also possibly attributed to ROS production. The observed PCD could be regulated by TCTP with a possible role for H2O2 in TCTP induction under flooding stress. Additionally, increased SAMS2 expression was closely associated with an increased polyamine synthesis during flooding treatment.

Isolation of an alcohol dehydrogenase cDNA from and characterization of its expression in chrysanthemum under waterlogging

A PCR strategy was used to isolate a full-length CgADH (alcohol dehydrogenase) cDNA from chrysanthemum. The gene putatively encodes a 378 residue polypeptides, which shares 95% homology with tomato alcohol dehydrogenase class III. Endogenous ethylene generated in waterlogged Chrysanthemum zawadskii was enhanced by exogenous ethylene but decreased by 1-methylcyclopropene (1-MCP), an inhibitor of ethylene action. In waterlogged roots, the transcription of the gene encoding alcohol dehydrogenase (ADH, EC 1.1.1.1) increased rapidly but transiently, peaking at 7.5 fold the non-waterlogged level after 2h of stress. Waterlogging elevated ADH activity after a prolonged episode of stress. The exogenous supply of 40μLL(-1) ethylene suppressed the production of ethanol, while that of 4μLL(-1) 1-MCP enhanced it. Ethylene appeared to suppress an acceleration of both CgADH expression and fermentation, and alleviates ethanolic fermentation probably through by as a signal to acceleration of waterlogging-induced aerenchyma formation. This supports the previously observed phenomenon that the expression level of ADH gene is regulated by the local level of physiologically active ethylene. The relevance of the CgADH gene in relation to chrysanthemum waterlogging was discussed as well.

Post-embryonic root organogenesis in cereals: branching out from model plants

The root architecture of higher plants is amazingly diverse. In this review, we compare the lateral root developmental programme in cereals and Arabidopsis thaliana. In cereals, cells in the endodermis are recruited to form the new root cap and overlying cortical cells divide to facilitate the emergence of the lateral root primordium. The TIR1/ABF2 auxin receptors and the AUX/IAA, ARF, and LBD transcriptional regulatory proteins are conserved in cereals and Arabidopsis. Several elements of this regulatory network are common to lateral and crown roots in cereals. Also, the ground meristem from which crown roots differentiate shows similarities with the root pericycle. Studies in cereals promise to give complementary insights into the mechanisms regulating the development of post-embryonic roots in plants.

Ethylene-induced differential petiole growth in Arabidopsis thaliana involves local microtubule reorientation and cell expansion

• Hyponastic growth is an upward petiole movement induced by plants in response to various external stimuli. It is caused by unequal growth rates between adaxial and abaxial sides of the petiole, which bring rosette leaves to a more vertical position. The volatile hormone ethylene is a key regulator inducing hyponasty in Arabidopsis thaliana. Here, we studied whether ethylene-mediated hyponasty occurs through local stimulation of cell expansion and whether this involves the reorientation of cortical microtubules (CMTs). • To study cell size differences between the two sides of a petiole in ethylene and control conditions, we analyzed epidermal imprints. We studied the involvement of CMT orientation in epidermal cells using the tubulin marker line as well as genetic and pharmacological means of CMT manipulation. • Our results demonstrate that ethylene induces cell expansion at the abaxial side of the- petiole and that this can account for the observed differential growth. At the abaxial side, ethylene induces CMT reorientation from longitudinal to transverse, whereas, at the adaxial side, it has an opposite effect. The inhibition of CMTs disturbed ethylene-induced hyponastic growth. • This work provides evidence that ethylene stimulates cell expansion in a tissue-specific manner and that it is associated with tissue-specific changes in the arrangement of CMTs along the petiole.

Petiole hyponasty: an ethylene-driven, adaptive response to changes in the environment

BACKGROUND

Many plant species can actively reorient their organs in response to dynamic environmental conditions. Organ movement can be an integral part of plant development or can occur in response to unfavourable external circumstances. These active reactions take place with or without a directional stimulus and can be driven either by changes in turgor pressure or by asymmetric growth. Petiole hyponasty is upward movement driven by a higher rate of cell expansion on the lower (abaxial) compared with the upper (adaxial) side. Hyponasty is common among rosette species facing environmental stresses such as flooding, proximity of neighbours or elevated ambient temperature. The complex regulatory mechanism of hyponasty involves activation of pathways at molecular and developmental levels, with ethylene playing a crucial role.

SCOPE

We present current knowledge on the mechanisms that promote hyponasty in the context of other organ movements, including tropic and nastic reactions together with circumnutation. We describe major environmental cues resulting in hyponasty and briefly discuss their perception and signal transduction. Since ethylene is a central agent triggering hyponasty, we focus on ethylene in controlling different stages during plant development and summarize current knowledge on the relationship between ethylene and cell growth.

Hormonal interplay during adventitious root formation in flooded tomato plants

Soil flooding, which results in a decline in the availability of oxygen to submerged organs, negatively affects the growth and productivity of most crops. Although tomato (Solanum lycopersicum) is known for its sensitivity to waterlogging, its ability to produce adventitious roots (ARs) increases plant survival when the level of oxygen is decreased in the root zone. Ethylene entrapment by water may represent the first warning signal to the plant indicating waterlogging. We found that treatment with the ethylene biosynthesis inhibitor aminoethoxyvinylglycine (AVG) and the auxin transport inhibitor 1-naphthylphthalamic acid (NPA) resulted in a reduction of AR formation in waterlogged plants. We observed that ethylene, perceived by the Never Ripe receptor, stimulated auxin transport. In a process requiring the Diageotropica gene, auxin accumulation in the stem triggered additional ethylene synthesis, which further stimulated a flux of auxin towards to the flooded parts of the plant. Auxin accumulation in the base of the plant induces growth of pre-formed root initials. This response of tomato plants results in a new root system that is capable of replacing the original one when it has been damaged by submergence.

Intraspecific variation in the magnitude and pattern of flooding-induced shoot elongation in Rumex palustris

BACKGROUND AND AIMS

Intraspecific variation in flooding tolerance is the basic pre-condition for adaptive flooding tolerance to evolve, and flooding-induced shoot elongation is an important trait that enables plants to survive shallow, prolonged flooding. Here an investigation was conducted to determine to what extent variation in flooding-induced leaf elongation exists among and within populations of the wetland species Rumex palustris, and whether the magnitude of elongation can be linked to habitat characteristics.

METHODS

Offspring of eight genotypes collected in each of 12 populations from different sites (ranging from river mudflats with dynamic flooding regimes to areas with stagnant water) were submerged, and petioles, laminas and roots were harvested separately to measure traits related to elongation and plant growth.

KEY RESULTS

We found strong elongation of petioles upon submergence, and both among- and within-population variation in this trait, not only in final length, but also in the timing of the elongation response. However, the variation in elongation responses could not be linked to habitat type.

CONCLUSIONS

Spatio-temporal variation in the duration and depth of flooding in combination with a presumably weak selection against flooding-induced elongation may have contributed to the maintenance of large genetic variation in flooding-related traits among and within populations.

Gene-expression profiling of grape bud response to two alternative dormancy-release stimuli expose possible links between impaired mitochondrial activity, hypoxia, ethylene-ABA interplay and cell enlargement

A grape-bud-oriented genomic platform was produced for a large-scale comparative analysis of bud responses to two stimuli of grape-bud dormancy release, hydrogen cyanamide (HC) and heat shock (HS). The results suggested considerable similarity in bud response to the stimuli, both in the repertoire of responding genes and in the temporary nature of the transcriptome reprogramming. Nevertheless, the bud response to HC was delayed, more condensed and stronger, as reflected by a higher number of regulated genes and a higher intensity of regulation compared to the response to HS. Integrating the changes occurring in response to both stimuli suggested perturbation of mitochondrial activity, development of oxidative stress and establishment of a situation that resembles hypoxia, which coincides with induction of glycolysis and fermentation, as well as changes in the interplay between ABA and ethylene metabolism. The latter is known to induce various growth responses in submerged plants and the possibility of a similar mechanism operating in the bud meristem during dormancy release is raised. The new link suggested between sub lethal stress, mitochondrial activity, hypoxic conditions, ethylene metabolism and cell enlargement during bud dormancy release may be instrumental in understanding the dormancy-release mechanism. Temporary increase of acetaldehyde, ethanol and ethylene in response to dormancy release stimuli demonstrated the predictive power of the working model, and its relevance to dormancy release was demonstrated by enhancement of bud break by exogenous ethylene and its inhibition by an ethylene signal inhibitor.

Effects of cell number and cell size on petiole length variation in a stoloniferous herb

In stoloniferous species, the length of petioles is of pivotal importance because it determines the position of leaf blades within the canopy. From a mechanistic perspective, two developmental processes, cell division and cell elongation, are responsible for the length of a given petiole. This study aimed at quantifying the relative contributions of cell division and cell elongation to genotypic and plastic variation in petiole length of the stoloniferous herb Trifolium repens. Thirty-four genotypes of T. repens were grown under high light conditions and simulated canopy shade. Cells were counted and their lengths measured on epidermal prints from fully grown petioles of leaves that had been initiated in the experimental light conditions. Cell number was the main trait explaining petiole length differences among genotypes grown under high light, while both cell number and length changed in response to shading. Our study revealed a strong negative correlation between shade-induced changes in cell number and cell length: genotypes that responded to shading by increasing cell numbers hardly changed in cell length, and vice versa. Our results suggest that genotypic and phenotypic variation in petiole length results from a complex interplay between the developmental processes of cell elongation and cell division.

How ethylene works in the reproductive organs of higher plants: a signaling update from the third millennium

Ethylene (ET) is a notable signaling molecule in higher plants. In the year 1993 the ET receptor gene, ETR1, was identified; this ETR1 receptor protein being the first plant hormone receptor to be isolated. It is striking that there are six ET receptors in tomato instead of five in Arabidopsis, the two best-known signaling-model systems. Even though over the last few years great progress has been made in elucidating the genes and proteins involved in ET signaling, the complete pathway remains to be established. The present review examines the most representative successive advances that have taken place in this millennium in terms of the signaling pathway of ET, as well as the implications of the signaling in the reproductive organs of plants (i.e., flowers, fruits, seeds and pollen grains). A detailed comparative study is made on the advances in knowledge in the last decade, showing how the characterization of ET signaling provides clues for understanding how higher plants regulate their ET sensitivity. Also, it is indicated that ET signaling is at present sparking interest within phytohormonal molecular physiology and biology, and it is explained why several socio-economic aspects (flowering and fruit ripening) are undoubtedly involved in ET physiology.

A variable cluster of ethylene response factor-like genes regulates metabolic and developmental acclimation responses to submergence in rice

Submergence-1 (Sub1), a major quantitative trait locus affecting tolerance to complete submergence in lowland rice (Oryza sativa), contains two or three ethylene response factor (ERF)-like genes whose transcripts are regulated by submergence. In the submergence-intolerant japonica cultivar M202, this locus encodes two ERF genes, Sub1B and Sub1C. In the tolerant near-isogenic line containing the Sub1 locus from the indica FR13A, M202(Sub1), the locus additionally encodes the ERF gene Sub1A. During submergence, the tolerant M202(Sub1) displayed restrained leaf and internode elongation, chlorophyll degradation, and carbohydrate consumption, whereas the enzymatic activities of pyruvate decarboxylase and alcohol dehydrogenase were increased significantly compared with the intolerant M202. Transcript levels of genes associated with carbohydrate consumption, ethanolic fermentation, and cell expansion were distinctly regulated in the two lines. Sub1A and Sub1C transcript levels were shown to be upregulated by submergence and ethylene, with the Sub1C allele in M202 also upregulated by treatment with gibberellic acid (GA). These findings demonstrate that the Sub1 region haplotype determines ethylene- and GA-mediated metabolic and developmental responses to submergence through differential expression of Sub1A and Sub1C. Submergence tolerance in lowland rice is conferred by a specific allele variant of Sub1A that dampens ethylene production and GA responsiveness, causing quiescence in growth that correlates with the capacity for regrowth upon desubmergence.

The stimulating effects of ethylene and auxin on petiole elongation and on hyponastic curvature are independent processes in submerged Rumex palustris

The flooding-tolerant plant species Rumex palustris (Sm.) responds to complete submergence with stimulation of petiole elongation mediated by the gaseous hormone ethylene. We examined the involvement of auxin in petiole elongation. The manipulation of petiolar auxin levels by removing the leaf blade, or by addition of synthetic auxins or auxin transport inhibitors, led to the finding that auxin plays an important role in submergence-induced petiole elongation in R. palustris. A detailed kinetic analysis revealed a transient effect of removing the auxin source (leaf blade), explaining why earlier studies in which less frequent measurements were taken failed to identify any role for auxin in petiole elongation. We previously showed that the onset of stimulated petiole elongation depends on a more upright petiole angle being reached by means of hyponastic (upward) curvature, a differential growth process that is also regulated by ethylene and auxin. This raised the possibility that both ethylene and auxin stimulate elongation only indirectly by influencing hyponastic growth. We show here that the action of ethylene and auxin in promoting petiole elongation in submerged R. palustris is independent of the promoting effect that these hormones also exert on the hyponastic curvature of the same petiole.

Interactions between ethylene, gibberellin and abscisic acid regulate emergence and growth rate of adventitious roots in deepwater rice

Growth of adventitious roots is induced in deepwater rice (Oryza sativa L.) when plants become submerged. Ethylene which accumulates in flooded plant parts is responsible for root growth induction. Gibberellin (GA) is ineffective on its own but acts in a synergistic manner together with ethylene to promote the number of penetrating roots and the growth rate of emerged roots. Studies with the GA biosynthesis inhibitor paclobutrazol revealed that root emergence was dependent on GA activity. Abscisic acid (ABA) acted as a competitive inhibitor of GA activity. Root growth rate on the other hand was dependent on GA concentration and ABA acted as a potent inhibitor possibly of GA but also of ethylene signaling. The results indicated that root emergence and elongation are distinct phases of adventitious root growth that are regulated through different networking between ethylene, GA and ABA signaling pathways. Adventitious root emergence must be coordinated with programmed death of epidermal cells which cover root primordia. Epidermal cell death is also controlled by ethylene, GA and ABA albeit with cell-type specific cross-talk. Different interactions between the same hormones may be a means to ensure proper timing of cell death and root emergence and to adjust the growth rate of emerged adventitious roots.

How plants cope with complete submergence

Flooding is a widespread phenomenon that drastically reduces the growth and survival of terrestrial plants. The dramatic decrease of gas diffusion in water compared with in air is a major problem for terrestrial plants and limits the entry of CO(2) for photosynthesis and of O(2) for respiration. Responses to avoid the adverse effects of submergence are the central theme in this review. These include underwater photosynthesis, aerenchyma formation and enhanced shoot elongation. Aerenchyma facilitates gas diffusion inside plants so that shoot-derived O(2) can diffuse to O(2)-deprived plant parts, such as the roots. The underwater gas-exchange capacity of leaves can be greatly enhanced by a thinner cuticle, reorientation of the chloroplasts towards the epidermis and increased specific leaf area (i.e. thinner leaves). At the same time, plants can outgrow the water through increased shoot elongation, which in some species is preceded by an adjustment of leaf angle to a more vertical position. The molecular regulatory networks involved in these responses, including the putative signals to sense submergence, are discussed and suggestions made on how to unravel the mechanistic basis of the induced expression of various adaptations that alleviate O(2) shortage underwater.

New perspectives in flooding research: the use of shade avoidance and Arabidopsis thaliana

BACKGROUND

Complete submergence of Rumex palustris leads to hyponastic (upward) petiole growth followed by enhanced petiole elongation. Previous pharmacological experiments have provided insights into the signal transduction pathway leading to this combined 'escape' response. It will, however, be difficult to gain further knowledge using these methods. Consequently, new approaches are required.

SCOPE

Here we propose that different environmental signals resulting in similar phenotypes can help to understand better the submergence response. In this review, we show that both ethylene and shade induce similar growth responses in R. palustris and Arabidopsis thaliana. We illustrate how this can be exploited to unravel novel signalling components in submergence-induced elongation growth. Furthermore, we illustrate the potential of arabidopsis as a useful model in submergence research based on similarities with submergence-tolerant species such as R. palustris and the molecular opportunities it presents. This is illustrated by examples of current work exploring this concept.

CONCLUSIONS

Incorporating different model systems, such as arabidopsis and shade avoidance, into submergence research can be expected to create powerful tools to unravel signal transduction routes determining submergence tolerance.

Ethylene regulates fast apoplastic acidification and expansin A transcription during submergence-induced petiole elongation in Rumex palustris

The semi-aquatic dicot Rumex palustris responds to complete submergence by enhanced elongation of young petioles. This elongation of petiole cells brings leaf blades above the water surface, thus reinstating gas exchange with the atmosphere and increasing survival in flood-prone environments. We already know that an enhanced internal level of the gaseous hormone ethylene is the primary signal for underwater escape in R. palustris. Further downstream, concentration changes in abscisic acid (ABA), gibberellin (GA) and auxin are required to gain fast cell elongation under water. A prerequisite for cell elongation in general is cell wall loosening mediated by proteins such as expansins. Expansin genes might, therefore, be important target genes in submergence-induced and plant hormone-mediated petiole elongation. To test this hypothesis we have studied the identity, kinetics and regulation of expansin A mRNA abundance and protein activity, as well as examined pH changes in cell walls associated with this adaptive growth. We found a novel role of ethylene in triggering two processes affecting cell wall loosening during submergence-induced petiole elongation. First, ethylene was shown to promote fast net H(+) extrusion, leading to apoplastic acidification. Secondly, ethylene upregulates one expansin A gene (RpEXPA1), as measured with real-time RT-PCR, out of a group of 13 R. palustris expansin A genes tested. Furthermore, a significant accumulation of expansin proteins belonging to the same size class as RpEXPA1, as well as a strong increase in expansin activity, were apparent within 4-6 h of submergence. Regulation of RpEXPA1 transcript levels depends on ethylene action and not on GA and ABA, demonstrating that ethylene evokes at least three, parallel operating pathways that, when integrated at the whole petiole level, lead to coordinated underwater elongation. The first pathway involves ethylene-modulated changes in ABA and GA, these acting on as yet unknown downstream components, whereas the second and third routes encompass ethylene-induced apoplastic acidification and ethylene-induced RpEXPA1 upregulation.

Gibberellin-regulated XET is differentially induced by auxin in rice leaf sheath bases during gravitropic bending

The asymmetric distribution of auxin plays a fundamental role in plant gravitropism, yet little is understood about how its lateral distribution stimulates growth. In the present work, the asymmetric distribution not only of auxin, but also that of gibberellins (GAs), was observed in rice leaf sheath bases following gravistimulation. Gravistimulation induced the transient accumulation of greater amounts of both IAA and GA in the lower halves of the leaf sheath bases of rice seedlings. OsGA3ox1, a gene of active GA synthesis, was differentially induced by gravistimulation. Furthermore, 2,3,5-tri-iodobenzoic acid (TIBA), an inhibitor of auxin transport, substantially decreased the asymmetric distribution of IAA and the gradient of OsGA3ox1 expression. Externally applied GA(3) restored the gravitropic curvature of rice leaf sheaths inhibited by either TIBA or by ancymidol, a GA synthesis inhibitor. The expression of XET (encoding xyloglucan endotransglycosylase) was differentially induced in the lower halves of gravistimulated leaf sheath bases and was also up-regulated by exogenous IAA and GA(3). Both ancymidol and TIBA decreased the gradient of XET expression. These data suggest that the asymmetric distribution of auxin effected by gravistimulation induced a gradient of GAs via asymmetric expression of OsGA3ox1 in rice leaf sheath bases, and hence caused the asymmetric expression of XET. Cell wall loosening in the curvature site of the leaf sheath triggered by the expression of XET would contribute to gravitropic growth.

Ethylene-induced differential growth of petioles in Arabidopsis. Analyzing natural variation, response kinetics, and regulation

Plants can reorient their organs in response to changes in environmental conditions. In some species, ethylene can induce resource-directed growth by stimulating a more vertical orientation of the petioles (hyponasty) and enhanced elongation. In this study on Arabidopsis (Arabidopsis thaliana), we show significant natural variation in ethylene-induced petiole elongation and hyponastic growth. This hyponastic growth was rapidly induced and also reversible because the petioles returned to normal after ethylene withdrawal. To unravel the mechanisms behind the natural variation, two contrasting accessions in ethylene-induced hyponasty were studied in detail. Columbia-0 showed a strong hyponastic response to ethylene, whereas this response was almost absent in Landsberg erecta (Ler). To test whether Ler is capable of showing hyponastic growth at all, several signals were applied. From all the signals applied, only spectrally neutral shade (20 micromol m(-2) s(-1)) could induce a strong hyponastic response in Ler. Therefore, Ler has the capacity for hyponastic growth. Furthermore, the lack of ethylene-induced hyponastic growth in Ler is not the result of already-saturating ethylene production rates or insensitivity to ethylene, as an ethylene-responsive gene was up-regulated upon ethylene treatment in the petioles. Therefore, we conclude that Ler is missing an essential component between the primary ethylene signal transduction chain and a downstream part of the hyponastic growth signal transduction pathway.

The roles of ethylene, auxin, abscisic acid, and gibberellin in the hyponastic growth of submerged Rumex palustris petioles

Rumex palustris responds to complete submergence with upward movement of the younger petioles. This so-called hyponastic response, in combination with stimulated petiole elongation, brings the leaf blade above the water surface and restores contact with the atmosphere. We made a detailed study of this differential growth process, encompassing the complete range of the known signal transduction pathway: from the cellular localization of differential growth, to the hormonal regulation, and the possible involvement of a cell wall loosening protein (expansin) as a downstream target. We show that hyponastic growth is caused by differential cell elongation across the petiole base, with cells on the abaxial (lower) surface elongating faster than cells on the adaxial (upper) surface. Pharmacological studies and endogenous hormone measurements revealed that ethylene, auxin, abscisic acid (ABA), and gibberellin regulate different and sometimes overlapping stages of hyponastic growth. Initiation of hyponastic growth and (maintenance of) the maximum petiole angle are regulated by ethylene, ABA, and auxin, whereas the speed of the response is influenced by ethylene, ABA, and gibberellin. We found that a submergence-induced differential redistribution of endogenous indole-3-acetic acid in the petiole base could play a role in maintenance of the response, but not in the onset of hyponastic growth. Since submergence does not induce a differential expression of expansins across the petiole base, it is unlikely that this cell wall loosening protein is the downstream target for the hormones that regulate the differential cell elongation leading to submergence-induced hyponastic growth in R. palustris.

Expression of alpha-expansin genes during root acclimations to O2 deficiency in Rumex palustris

Thirteen alpha-expansin genes were isolated from Rumex palustris , adding to the six already documented for this species. Five alpha-expansin genes were selected for expression studies in various organs/tissues of R. palustris , with a focus on roots exposed to aerated or O2)-deficient conditions, using real-time RT-PCR. Several cases of differential expression of alpha-expansin genes in the various root types of R. palustris were documented, and the identity of the dominant transcript differed between root types (i.e., tap root vs. lateral roots vs. adventitious roots). Several genes were expressed differentially in response to low O2. In situ hybridizations showed expansin mRNA expression in the oldest region of the tap root was localized to cells near the vascular cambium; this being the first report of expansin expression associated with secondary growth in roots. In situ hybridization also showed abundant expression of expansin mRNA in the most apical 1 mm of adventitious roots. Such early expression of expansin mRNA in cells soon after being produced by the root apex presumably enables cell wall loosening in the elongation zone of roots. In addition, expression of some expansin mRNAs increased in 'mature zones' of roots; these expansins might be involved in root hair formation or in formation of lateral root primordia. The present findings support the notion that large gene families of alpha-expansins enable flexibility in expression for various organs and tissues as a normal part of plant development, as well as in response to abiotic stress.

De-submergence-induced ethylene production in Rumex palustris: regulation and ecophysiological significance

Rumex palustris responds to total submergence by increasing the elongation rate of young petioles. This favours survival by shortening the duration of submergence. Underwater elongation is stimulated by ethylene entrapped within the plant by surrounding water. However, abnormally fast extension rates were found to be maintained even when leaf tips emerged above the floodwater. This fast post-submergence growth was linked to a promotion of ethylene production that is presumed to compensate for losses brought about by ventilation. Three sources of ACC contributed to post-submergence ethylene production in R. palustris: (i) ACC that had accumulated in the roots during submergence and was transported in xylem sap to the shoot when stomata re-opened and transpiration resumed, (ii) ACC that had accumulated in the shoot during the preceding period of submergence and (iii) ACC produced de novo in the shoot following de-submergence. This new production of ethylene was associated with increased expression of an ACC synthase gene (RP-ACS1) and an ACC oxidase gene (RP-ACO1), increased ACC synthase activity and a doubling of ACC oxidase activity, measured in vitro. Out of seven species of Rumex examined, a de-submergence upsurge in ethylene production was seen only in shoots of those that had the ability to elongate fast when submerged.

Auxin regulation of the gibberellin pathway in pea

The auxin indole-3-acetic acid (IAA) has been shown to promote the biosynthesis of the active gibberellin (GA(1)) in shoots of pea (Pisum sativum). We used northern analysis to investigate the timing of IAA-induced changes in transcript levels of PsGA3ox1 (Mendel's LE), PsGA2ox1, PsGA2ox2, and PsGA20ox1, key genes for the later stages of GA(1) biosynthesis and metabolism in pea. Rapid (2-4 h) changes occurred in the transcript levels of PsGA3ox1, PsGA2ox1, and PsGA2ox2 after treatment with IAA. [(14)C]GA(1) metabolism studies in decapitated shoots indicated that IAA inhibits GA(1) deactivation, consistent with the suppression of PsGA2ox1 (SLN) transcript levels by IAA. Studies with the sln mutant also indicated that PsGA2ox1 activity is involved in GA(1) deactivation in decapitated shoots. Culture of excised internode tissue in the presence of auxin clearly demonstrated that internode tissue is a site of GA(1) biosynthesis per se. Excised internode tissue cultured in the presence/absence of cycloheximide showed that de novo protein synthesis is required for IAA-induced increases in PsGA3ox1 transcript levels. Auxin dose response studies indicated that IAA concentration is a critical determinant of GA(1) biosynthesis over 1 to 2 orders of magnitude, and a range of auxins was shown to affect the GA pathway.