Rice growth adapting to deepwater

Flooding Tolerance of Rice: Regulatory Pathways and Adaptive Mechanisms

Rice is a major food crop for more than half of the world's population, while its production is seriously threatened by flooding, a common environmental stress worldwide. Flooding leads to oxygen deficiency, which is a major problem for submerged plants. Over the past three decades, significant progress has been made in understanding rice adaptation and molecular regulatory mechanisms in response to flooding. At the seed germination and seedling establishment stages, the CIPK15-SnRK1A-MYBS1 signaling cascade plays a central role in determining rice submergence tolerance. However, from seedlings to mature plants for harvesting, SUB1A- and SK1/SK2-regulated pathways represent two principal and opposite regulatory mechanisms in rice. In addition, phytohormones, especially gibberellins, induce adaptive responses to flooding throughout the rice growth period. This review summarizes the significant adaptive traits observed in flooded rice varieties and updates the molecular genetics and mechanisms of submergence tolerance in rice.

A group VIIIa ethylene-responsive factor, CmERF4, negatively regulates waterlogging tolerance in chrysanthemum

Ethylene-responsive factors (ERF) play an important role in plant responses to waterlogging stress. However, the function and mechanism of action of ERFVIII in response to waterlogging stress remain poorly understood. In this study, we found that expression of the ERF VIIIa gene CmERF4 in chrysanthemum was induced by waterlogging stress. CmERF4 localized to the nucleus when expressed in tobacco leaves. Yeast two-hybrid and luciferase assays showed that CmERF4 is a transcriptional inhibitor. CmERF4 overexpression in chrysanthemum reduced plant waterlogging tolerance, whereas overexpression of the chimeric activator CmERF4-VP64 reversed its transcriptional activity, promoting higher waterlogging tolerance than that observed in wild-type plants, indicating that CmERF4 negatively regulates waterlogging tolerance. Transcriptome profiling showed that energy metabolism and reactive oxygen species (ROS) pathway-associated genes were differentially expressed between CmERF4-VP64 and wild-type plants. RT-qPCR analysis of selected energy metabolism and reactive oxygen species-related genes showed that the gene expression patterns were consistent with the expression levels obtained from RNA-seq analysis. Overall, we identified new functions of CmERF4 in negatively regulating chrysanthemum waterlogging tolerance by modulating energy metabolism and ROS pathway genes.

CiAP2/ERF65 and CiAP2/ERF106, a pair of homologous genes in pecan (Carya illinoensis), regulate plant responses during submergence in transgenic Arabidopsis thaliana

When plants are entirely submerged, photosynthesis and respiration are severely restricted, affecting plant growth and potentially even causing plant death. The AP2/ERF superfamily has been widely reported to play a vital role in plant growth, development and resistance to biotic and abiotic stresses. However, no relevant studies exist on flooding stress in pecan. In this investigation, we observed that CiAP2/ERF65 positively modulated the hypoxia response during submergence, whereas CiAP2/ERF106 was sensitive to submergence. The levels of physiological and biochemical indicators, such as POD, CAT and among others, in CiAP2/ERF65-OE lines were significantly higher than those in wild-type Arabidopsis thaliana, indicating that the antioxidant capacity of CiAP2/ERF65-OE lines was enhanced under submergence. The RNA-seq results revealed that the maintenance of the expression levels of the antenna protein gene, different signaling pathways for regulation, as well as the storage and consumption of ATP, might account for the opposite phenotypes of CiAP2/ERF65 and CiAP2/ERF106. Furthermore, the expression of some stress-related genes was altered during submergence and reoxygenation. Overall, these findings enhance our understanding of submergence stress in pecan, providing important candidate genes for the molecular design and breeding of hypoxia resistant in plants.

Introducing the halophyte Salicornia europaea to investigate combined impact of salt and tidal submergence conditions

Tolerance mechanisms to single abiotic stress events are being investigated in different plant species, but how plants deal with multiple stress factors occurring simultaneously is still poorly understood. Here, we introduce Salicornia europaea as a species with an extraordinary tolerance level to both flooding and high salt concentrations. Plants exposed to 0.5MNaCl (mimicking sea water concentrations) grew larger than plants not exposed to salt. Adding more salt reduced growth, but concentrations up to 2.5MNaCl were not lethal. Regular tidal flooding with salt water (0.5MNaCl) did not affect growth or chlorophyll fluorescence, whereas continuous flooding stopped growth while plants survived. Quantitative polymerase chain reaction (qPCR) analysis of plants exposed to 1% oxygen in air revealed induction of selected hypoxia responsive genes, but these genes were not induced during tidal flooding, suggesting that S. europaea did not experience hypoxic stress. Indeed, plants were able to transport oxygen into waterlogged soil. Interestingly, sequential exposure to salt and hypoxic air changed the expression of several but not all genes as compared to their expression upon hypoxia only, demonstrating the potential to use S . europaea to investigate signalling-crosstalk between tolerance reactions to multiple environmental perturbations.

Identification of Genomic Regions for Deep-Water Resistance in Rice for Efficient Weed Control with Reduced Herbicide Use

Deep-water (DW) management in rice fields is a promising technique for efficient control of paddy weeds with reduced herbicide use. Maintaining a water depth of 10-20 cm for several weeks can largely suppress the weed growth, though it also inhibits rice growth because the DW management is usually initiated immediately after transplanting. Improving the DW resistance of rice during the initial growth stage is essential to avoid suppressing growth. In this study, we demonstrate a large genetic variation in the above-ground biomass (AGB) after the end of DW management among 165 temperate japonica varieties developed in Japan. Because the AGB closely correlated with plant length (PL) and tiller number (TN) at the early growth stage, we analyzed genomic regions associated with PL and TN by conducting a genome-wide association study. For PL, a major peak was detected on chromosome 3 (qPL3), which includes a gene encoding gibberellin biosynthesis, OsGA20ox1. The rice varieties with increased PL had a higher expression level of OsGA20ox1 as reported previously. For TN, a major peak was detected on chromosome 4 (qTN4), which includes NAL1 gene associated with leaf morphological development and panicle number. Although there was less difference in the expression level of NAL1 between genotypes, our findings suggest that an amino acid substitution in the exon region is responsible for the phenotypic changes. We also found that the rice varieties having alternative alleles of qPL3 and qTN4 showed significantly higher AGB than the varieties with the reference alleles. Our results suggest that OsGA20ox1 and NAL1 are promising genes for improving DW resistance in rice.

Plant Adaptation to Flooding Stress under Changing Climate Conditions: Ongoing Breakthroughs and Future Challenges

Climate-change-induced variations in temperature and rainfall patterns are a serious threat across the globe. Flooding is the foremost challenge to agricultural productivity, and it is believed to become more intense under a changing climate. Flooding is a serious form of stress that significantly reduces crop yields, and future climatic anomalies are predicted to make the problem even worse in many areas of the world. To cope with the prevailing flooding stress, plants have developed different morphological and anatomical adaptations in their roots, aerenchyma cells, and leaves. Therefore, researchers are paying more attention to identifying developed and adopted molecular-based plant mechanisms with the objective of obtaining flooding-resistant cultivars. In this review, we discuss the various physiological, anatomical, and morphological adaptations (aerenchyma cells, ROL barriers (redial O2 loss), and adventitious roots) and the phytohormonal regulation in plants under flooding stress. This review comprises ongoing innovations and strategies to mitigate flooding stress, and it also provides new insights into how this knowledge can be used to improve productivity in the scenario of a rapidly changing climate and increasing flood intensity.

Physiological and antioxidant responses associated with Sub1 gene introgressed rice (Oryza sativa L.) lines under complete submergence

Rice is the only crop which is well adapted to aquatic environment but, it is unable to survive if completely submerged for several weeks. Breeding rice varieties with submergence tolerance is one of the best approaches to alleviate the adverse effect of submergence which requires the introgression of Sub1 gene into elite rice varieties. Hence, the study was undertaken to introgress submergence tolerant gene into the rice variety Jaya through Marker-Assisted Backcross Breeding. Also the physiological and biochemical responses like survival percentage, underwater shoot elongation, total carbohydrate content and superoxide dismutase activity were also studied in Sub1 introgressed lines. We could develop twenty Sub1 introgressed lines with Sub1 region of 3.1-5.1mb and with 80.0- 95.3% recurrent parent genome recovery. Sub1 introgressed Jaya lines and the tolerant checks FR13A and Swarna Sub1 had lower shoot elongation under water, higher superoxide dismutase activity (about 5 times) upto 4 h after de-submergence which resulted in higher survival percentage. The reduced shoot elongation of tolerant varieties reduced the utilization of stored carbohydrate. Through our research we introgressed Sub1 gene into rice variety Jaya through Marker-Assisted Backcross Breeding and could study the physiological responses under submergence by which we confirmed the presence of Sub1 gene in these lines. These lines could be field evaluated and could be released as a new variety thus helping the farmers of flood prone areas of Kerala.

Beneficial Root-Associated Microbiome during Drought and Flooding Stress in Plants

Crop productivity is seriously threatened by the rise in the frequency and severity of drought and flood events around the world. Reduced drought and flooding stress in vulnerable species and ecosystems depends on our ability to comprehend how drought and flooding affect plant physiology and plant-associated microbes. Involvement of both abscisic acid ABA-dependent and ABA-independent pathways has been noted during drought. Hypoxic conditions impede hydraulic conductance, nutrient uptake and plant growth and development, as well as root aerobic respiration. The root microbiome, which works with the roots during drought and flood, is made up of plant growth-promoting rhizosphere, endophytes and mycorrhizas. A large number of phytohormones, primarily auxins, cytokinin and ethylene, as well as enzymes like 1-Aminocyclopropane-1-Carboxylate deaminase (ACC deaminase) and metabolites like exopolysaccharides are produced by rhizospheric microbes. These phytohormones, enzymes and metabolites have role in the induction of systemic drought tolerance in plants. Under hypoxia, anaerobic microbes with the potential to harm the plant due to their pathogenic behavior or soil denitrification ability are more likely to be present in the rhizosphere and roots. This review concentrates on the primary mechanisms of plant-microbe interactions under drought and flood stress as well as the importance of flood and drought-tolerant microbes in maintaining and increasing crop plant productivity under stress.

Identification of a Major Locus for Lodging Resistance to Typhoons Using QTL Analysis in Rice

We detected a new target quantitative trait locus (QTL) for lodging resistance in rice by analyzing lodging resistance to typhoons (Maysak and Haishen) using a scale from 0 (no prostrating) to 1 (little prostrating or prostrating) to record the resistance score in a Cheongcheong/Nagdong double haploid rice population. Five quantitative trait loci for lodging resistance to typhoons were detected. Among them, qTyM6 and qTyH6 exhibited crucial effects of locus RM3343-RM20318 on chromosome 6, which overlaps with our previous rice lodging studies for the loci qPSLSA6-2, qPSLSB6-5, and qLTI6-2. Within the target locus RM3343-RM20318, 12 related genes belonging to the cytochrome P450 protein family were screened through annotation. Os06g0599200 (OsTyM/Hq6) was selected for further analysis. We observed that the culm and panicle lengths were positively correlated with lodging resistance to typhoons. However, the yield was negatively correlated with lodging resistance to typhoons. The findings of this study improve an understanding of rice breeding, particularly the culm length, early maturing, and heavy panicle varieties, and the mechanisms by which the plant's architecture can resist natural disasters such as typhoons to ensure food safety. These results also provide the insight that lodging resistance in rice may be associated with major traits such as panicle length, culm length, tiller number, and heading date, and thereby improvements in these traits can increase lodging resistance to typhoons. Moreover, rice breeding should focus on maintaining suitable varieties that can withstand the adverse effects of climate change in the future and provide better food security.

The Effects of Submergence on Selected Malaysian Rice Varieties

Various varieties have been developed in Malaysia, mainly to improve rice response to environmental changes, pests, and diseases, as well as to increase rice productivity under stressful conditions. Despite being semi-aquatic plants, rice is intolerant to complete submergence for a long period. This study was conducted to evaluate the response of seven Malaysian rice varieties at the vegetative stage under submergence stress. Two-week-old rice seedlings were submerged for 14 days, and the changes in plant height, chlorophyll content, and soluble sugar content were determined. The survival percentage of these varieties was observed after 14 days of de-submergence, where UKMRC2 and MR220CL possessed high survivability (90% & 60%, respectively). After submergence, all varieties showed height increment and reduced chlorophyll and soluble sugar contents. Based on our analyses, UKMRC2 performed better than other varieties, although slightly less than IR64-Sub1. It was confirmed that UKMRC2 is the submergence-tolerant variety, and its response to underwater germination was also determined. Our result showed that UKMRC2 might possess tolerance to anaerobic germination conditions, and more studies are needed to understand its molecular mechanism for submergence. In conclusion, many varieties used were susceptible to submergence, and the development of more submergence-tolerant varieties is crucial for Malaysia’s food security sustainability.

Different survival strategies involve carbon translocation rather than de novo C assimilation under complete submergence in rice plant

This study investigated the effect of transient submergence on the recovery of photosynthetic activity and translocation of photosynthate in IR67520 (Sub1A genotype) and IR72442 (non-Sub1A genotype) using ¹³C-labeled tracer, coupled with some photosynthetic physiological assessments. Plant growth, photosynthetic capacity, and photosynthetic recovery were studied by treating the two rice genotypes without or completely submerged for 7 days in transparent acrylic tanks filled with water to a depth of 80 cm, followed by 7 days of reaeration. Results revealed that the IR67520 was able to obtain new carbon source for assimilation during at 7 days of recovery periods. The IR72442 genotype partitioned ¹³C to the newly developed upper leaves more than the IR67520 genotype did. This was due to its inability to obtain CO₂ from other source during post submergence. Recovery of chlorophyll content, ability to retain higher biomass, and ability to grow faster at 7 days of recovery periods also indicated the ability of Sub1A genotype to reactivate its photosynthetic capacity.

Beneficial and pathogenic plant-microbe interactions during flooding stress

The number and intensity of flood events will likely increase in the future, raising the risk of flooding stress in terrestrial plants. Understanding flood effects on plant physiology and plant-associated microbes is key to alleviate flooding stress in sensitive species and ecosystems. Reduced oxygen supply is the main constrain to the plant and its associated microbiome. Hypoxic conditions hamper root aerobic respiration and, consequently, hydraulic conductance, nutrient uptake, and plant growth and development. Hypoxia favours the presence of anaerobic microbes in the rhizosphere and roots with potential negative effects to the plant due to their pathogenic behaviour or their soil denitrification ability. Moreover, plant physiological and metabolic changes induced by flooding stress may also cause dysbiotic changes in endosphere and rhizosphere microbial composition. The negative effects of flooding stress on the holobiont (i.e., the host plant and its associated microbiome) can be mitigated once the plant displays adaptive responses to increase oxygen uptake. Stress relief could also arise from the positive effect of certain beneficial microbes, such as mycorrhiza or dark septate endophytes. More research is needed to explore the spiralling, feedback flood responses of plant and microbes if we want to promote plant flood tolerance from a holobiont perspective.

Identification of Functional Genetic Variations Underlying Flooding Tolerance in Brazilian Soybean Genotypes

Flooding is a frequent environmental stress that reduces soybean (Glycine max) growth and grain yield in many producing areas in the world, such as, e.g., in the United States, Southeast Asia and Southern Brazil. In these regions, soybean is frequently cultivated in lowland areas by rotating with rice (Oryza sativa), which provides numerous technical, economic and environmental benefits. Given these realities, this work aimed to characterize physiological responses, identify genes differentially expressed under flooding stress in Brazilian soybean genotypes with contrasting flooding tolerance, and select SNPs with potential use for marker-assisted selection. Soybean cultivars TECIRGA 6070 (flooding tolerant) and FUNDACEP 62 (flooding sensitive) were grown up to the V6 growth stage and then flooding stress was imposed. Total RNA was extracted from leaves 24 h after the stress was imposed and sequenced. In total, 421 induced and 291 repressed genes were identified in both genotypes. TECIRGA 6070 presented 284 and 460 genes up- and down-regulated, respectively, under flooding conditions. Of those, 100 and 148 genes were exclusively up- and down-regulated, respectively, in the tolerant genotype. Based on the RNA sequencing data, SNPs in differentially expressed genes in response to flooding stress were identified. Finally, 38 SNPs, located in genes with functional annotation for response to abiotic stresses, were found in TECIRGA 6070 and absent in FUNDACEP 62. To validate them, 22 SNPs were selected for designing KASP assays that were used to genotype a panel of 11 contrasting genotypes with known phenotypes. In addition, the phenotypic and grain yield impacts were analyzed in four field experiments using a panel of 166 Brazilian soybean genotypes. Five SNPs possibly related to flooding tolerance in Brazilian soybean genotypes were identified. The information generated from this research will be useful to develop soybean genotypes adapted to poorly drained soils or areas subject to flooding.

A super pan-genomic landscape of rice

Pan-genomes from large natural populations can capture genetic diversity and reveal genomic complexity. Using de novo long-read assembly, we generated a graph-based super pan-genome of rice consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African rice. Our pan-genome reveals extensive structural variations (SVs) and gene presence/absence variations. Additionally, our pan-genome enables the accurate identification of nucleotide-binding leucine-rich repeat genes and characterization of their inter- and intraspecific diversity. Moreover, we uncovered grain weight-associated SVs which specify traits by affecting the expression of their nearby genes. We characterized genetic variants associated with submergence tolerance, seed shattering and plant architecture and found independent selection for a common set of genes that drove adaptation and domestication in Asian and African rice. This super pan-genome facilitates pinpointing of lineage-specific haplotypes for trait-associated genes and provides insights into the evolutionary events that have shaped the genomic architecture of various rice species.

Silicon enhances the submergence tolerance of rice by regulating quiescence strategy and alleviating oxidative damage

The safety of rice production under submergence is one of the research hotspots worldwide. Although the effects of silicon (Si) on enhancing plant stress tolerance have been widely investigated, the underlying mechanisms mediated by Si under submergence remains poorly understood. In this study, wild type (WT) and Si-defective mutant (lsi1) rice were chosen to investigate the mechanisms of Si-mediated rice resistance to submergence. Our results showed that Si addition effectively mitigated oxidative damages under submergence by reducing the content of hydrogen peroxide (H₂O₂) and superoxide (O₂^.-) in WT rice plants. Moreover, Si treatment increased rice yield by 21.5% for WT rice under submergence. The application of Si significantly inhibited the elongation and internode length in WT rice under submergence, through the synergistic regulation of endogenous hormones ethylene (ET), gibberellic acid (GA) and jasmonic acid (JA). Further investigation showed that the ethylene-responsive factor (ERF) SUB1A gene was expressed under submergence in WT and lsi1 rice, but Si addition did not influence the expression of SUB1A. Interestingly, exogenous Si down-regulated the relative expression levels of Si transporter genes Lsi1 and Lsi2 in WT rice roots by 51.7% and 48.0%, respectively. However, the physiological characteristics and genes expression of lsi1 rice were not affected by Si application regardless of submergence. The present study indicated that Si enhances the submergence tolerance and reduce the adverse effects of yield loss through the removal of reactive oxygen species and the adjustment of quiescence strategy.

Identification and analysis of miRNAs-lncRNAs-mRNAs modules involved in stem-elongation of deepwater rice (Oryza sativa L.)

Deepwater is an abiotic stress that limits rice cultivation worldwide due to recurrent floods. The miRNAs and lncRNAs are two non-coding RNAs emerging as major regulators of gene expressions under different abiotic stresses. However, the regulation of these two non-coding RNAs under deepwater stress in rice is still unexplored. In this study, small RNA-seq and RNA-seq from internode and node tissues were analyzed to predict deepwater stress responsive miRNAs and lncRNAs, respectively. Additionally, a competitive endogenous RNA (ceRNA) study revealed about 69 and 25 lncRNAs acting as endogenous target mimics (eTM) with the internode and node miRNAs, respectively. In ceRNA analyses, some of the key miRNAs such as miR1850.1, miR1848, and IN-nov-miR145 were upregulated while miR159e was downregulated, and their respective eTM lncRNAs and targets were found to have opposite expressions. Moreover, we have transiently expressed one module (IN-nov-miR145-Cc-TCONS_00011544-Os11g36430.3) in tobacco leaves. The integrated analysis has identified differentially expressed (DE) miRNAs, lncRNAs and their target genes, and the complex regulatory network, which might lead to stem elongation under deepwater stress. In this novel attempt to identify and characterize miRNAs and lncRNAs under deepwater stress in rice, we have provided, probably for the first time, a reference platform to study the interactions of these two non-coding RNAs with respective target genes through transient expression analyses.

Time-course analysis and transcriptomic identification of key response strategies to complete submergence in Nelumbo nucifera

Water submergence is an environmental stress with detrimental effects on plant growth and survival. As a wetland plant species, lotus (Nelumbo nucifera) is widely cultivated in flood-prone lowlands throughout Asian countries, but little is known about its endurance and acclimation mechanisms to complete submergence. Here, we combined a time-course submergence experiment and an RNA-sequencing transcriptome analysis on two lotus varieties of "Qiuxing" and "China Antique". Both varieties showed a low submergence tolerance, with a median lethal time of around 10 days. Differentially expressed gene (DEG) analysis and weighted gene co-expression network analysis (WGCNA) identified a number of key genes putatively involved in lotus submergence responses. Lotus plants under complete submergence developed thinned leaves and elongated petioles containing high density of aerenchyma. All four lotus submergence responsive ERF-VII genes and gene sets corresponding to the low oxygen "escape" strategy (LOES) were elevated. In addition, a number of lotus innate immunity genes were rapidly induced by submergence, likely to confer resistance to possible pathogen infections. Our data also reveals the likely involvement of jasmonic acid in modulating lotus submergence responses, but to a lesser extent than the gaseous ethylene hormone. These results suggest that lotus plants primarily take the LOES strategy in coping with submergence-induced complex stresses, and will be valuable for people understanding the molecular basis underlying the plant submergence acclimations.

Opportunities for Improving Waterlogging Tolerance in Cereal Crops-Physiological Traits and Genetic Mechanisms

Waterlogging occurs when soil is saturated with water, leading to anaerobic conditions in the root zone of plants. Climate change is increasing the frequency of waterlogging events, resulting in considerable crop losses. Plants respond to waterlogging stress by adventitious root growth, aerenchyma formation, energy metabolism, and phytohormone signalling. Genotypes differ in biomass reduction, photosynthesis rate, adventitious roots development, and aerenchyma formation in response to waterlogging. We reviewed the detrimental effects of waterlogging on physiological and genetic mechanisms in four major cereal crops (rice, maize, wheat, and barley). The review covers current knowledge on waterlogging tolerance mechanism, genes, and quantitative trait loci (QTL) associated with waterlogging tolerance-related traits, the conventional and modern breeding methods used in developing waterlogging tolerant germplasm. Lastly, we describe candidate genes controlling waterlogging tolerance identified in model plants Arabidopsis and rice to identify homologous genes in the less waterlogging-tolerant maize, wheat, and barley.

Age-Dependent Abiotic Stress Resilience in Plants

Developmental age is a strong determinant of stress responses in plants. Differential susceptibility to various environmental stresses is widely observed at both the organ and whole-plant level. While it is clear that age determines stress susceptibility, the causes, regulatory mechanisms, and functions are only now beginning to emerge. Compared with concepts on age-related biotic stress resilience, advancements in the abiotic stress field are relatively limited. In this review, we focus on current knowledge of ontogenic resistance to abiotic stresses, highlighting examples at the organ (leaf) and plant level, preceded by an overview of the relevant concepts in plant aging. We also discuss age-related abiotic stress resilience mechanisms, speculate on their functional relevance, and outline outstanding questions.

Recent Advances of Genetic Resources, Genes and Genetic Approaches for Flooding Tolerance in Rice

Flooding is one of the most hazardous natural disasters and a major stress constraint to rice production throughout the world, which results in huge economic losses. The frequency and duration of flooding is predicted to increase in near future as a result of global climate change. Breeding of flooding tolerance in rice is a challenging task because of the complexity of the component traits, screening technique, environmental factors and genetic interactions. A great progress has been made during last two decades to find out the flooding tolerance mechanism in rice. An important breakthrough in submergence research was achieved by the identification of major quantitative trait locus (QTL) SUB1 in rice chromosomes that acts as the primary contributor for tolerance. This enabled the use of marker-assisted backcrossing (MABC) to transfer SUB1 QTL into popular varieties which showed yield advantages in flood prone areas. However, SUB1 varieties are not always tolerant to stagnant flooding and flooding during germination stage. So, gene pyramiding approach can be used by combining several important traits to develop new breeding rice lines that confer tolerances to different types of flooding. This review highlights the important germplasm/genetic resources of rice to different types of flooding stress. A brief discussion on the genes and genetic mechanism in rice exhibited to different types of flooding tolerance was discussed for the development of flood tolerant rice variety. Further research on developing multiple stresses tolerant rice can be achieved by combining SUB1 with other tolerance traits/genes for wider adaptation in the rain-fed rice ecosystems.

Interéaction of submergence tolerance and drought yield QTLs (Sub1 and qDTYs) enhances morpho‐physiological traits and survival of rice (Oryza sativa L.) under submergence

Climate change has caused increasing incidences of the extreme flooding around the world, which has impacted rice production, especially in rainfed ecosystems. Breeding for submergence tolerant rice varieties has been conducted to mitigate the adverse effects and help farmers to reduce yield loss. The present study was carried out to introgress the submergence tolerance QTL (Sub1) from IR64‐Sub1 into drought‐tolerant lines; UKM5 and UKM91 possessing the drought yield quantitative trait loci (qDTYs), viz. qDTY12.1 and qDTY3.1, and to evaluate the effects of the combination of these QTLs in improving the morpho‐physiological traits and survival under submergence. UKM5 and UKM91 were selected as the recipient of the Sub1 locus because of the intermediate submergence tolerance they possessed even though they only have qDTY/s. Therefore, the introgression of Sub1 into these lines was hypothesised to enhance survival. Submergence stress was given for 14 days to BC1F4 lines from the two breeding populations. Lines with better survival than the tolerant check, IR64‐Sub1 were selected and evaluated under 18 days of submergence stress. Generally, lines with Sub1 and qDTYs from UKM5*/IR64‐Sub1 and UKM91*/IR64‐Sub1 populations had higher survival rate (SR) of 90–100%, lower shoot elongation percentage (EP) and a smaller percentage of chlorophyll content change (CCC) than IR64‐Sub1. The selected lines also showed a low percentage of non‐structural carbohydrate change (NSCC) which related to the ability to recover after submergence. In both populations, the interaction of qDTY3.1 with Sub1 proved to give the best improvement on EP and CCC. This experiment provides novel findings; that is, the combinations of Sub1 + qDTY12.1 + qDTY3.1 showed high survival rate in the population of UKM5*/IR64‐Sub1, while qDTY3.1 improved SR of the lines from UKM91*/IR64‐Sub1 population to 100%. These results proved that the action of Sub1, qDTY/s and their interaction differ in contrasting population or background. The QTL combinations showed a consistent effect in both submergence experiments and proved the effectiveness of Sub1 and qDTYs combinations in enhancing the morpho‐physiological traits and survival.

Identification of QTLs associated with the anaerobic germination potential using a set of Oryza nivara introgression lines

BACKGROUND

Rice (Oryza sativa L.) is an important crop and a staple food for half of the population around the world. The recent water and labor shortages are encouraging farmers to shift from traditional transplanting to direct-seeding. However, poor germination and slow elongation of the coleoptile constrains large-scale application of direct-seeding.

OBJECTIVE

This study was aimed to investigate the genetic basis of the anaerobic germination (AG) potential using a set of Oryza nivara (O. nivara) introgression lines (ILs).

METHODS

In this study, a total of 131 ILs were developed by introducing O. nivara chromosome segments into the elite indica rice variety 93-11 through advanced backcrossing and repeated selfing. A high-density genetic map has been previously constructed with 1,070 bin-markers. The seeds of ILs were germinated and used to measure coleoptile length under normal and anaerobic conditions. QTLs associated with AG potential were determined in rice.

RESULTS

Based on the high-density genetic map of the IL population, two QTLs, qAGP1 and qAGP3 associated with AG tolerance were characterized and located on chromosomes 1 and 3, respectively. Each QTL explained 15% of the phenotypic variance. Specifically, the O. nivara-derived chromosome segments of the two QTLs were positively tolerance to anaerobic condition by increasing coleoptile length. In a further analysis of public transcriptome data, a total of 26 and 36 genes within qAGP1 and qAGP3 were transcriptionally induced by anaerobic stress, respectively.

CONCLUSIONS

Utilization of O. nivara-derived alleles at qAGP1 and qAGP3 can potentially enhance tolerance to anaerobic stress at the germination stage in rice, thereby accelerating breeding of rice varieties to be more adaptative for direct-seeding.

Plant Morphological, Physiological and Anatomical Adaption to Flooding Stress and the Underlying Molecular Mechanisms

Globally, flooding is a major threat causing substantial yield decline of cereal crops, and is expected to be even more serious in many parts of the world due to climatic anomaly in the future. Understanding the mechanisms of plants coping with unanticipated flooding will be crucial for developing new flooding-tolerance crop varieties. Here we describe survival strategies of plants adaptation to flooding stress at the morphological, physiological and anatomical scale systemically, such as the formation of adventitious roots (ARs), aerenchyma and radial O₂ loss (ROL) barriers. Then molecular mechanisms underlying the adaptive strategies are summarized, and more than thirty identified functional genes or proteins associated with flooding-tolerance are searched out and expounded. Moreover, we elaborated the regulatory roles of phytohormones in plant against flooding stress, especially ethylene and its relevant transcription factors from the group VII Ethylene Response Factor (ERF-VII) family. ERF-VIIs of main crops and several reported ERF-VIIs involving plant tolerance to flooding stress were collected and analyzed according to sequence similarity, which can provide references for screening flooding-tolerant genes more precisely. Finally, the potential research directions in the future were summarized and discussed. Through this review, we aim to provide references for the studies of plant acclimation to flooding stress and breeding new flooding-resistant crops in the future.

Abscisic Acid as an Emerging Modulator of the Responses of Plants to Low Oxygen Conditions

Different environmental and developmental cues involve low oxygen conditions, particularly those associated to abiotic stress conditions. It is widely accepted that plant responses to low oxygen conditions are mainly regulated by ethylene (ET). However, interaction with other hormonal signaling pathways as gibberellins (GAs), auxin (IAA), or nitric oxide (NO) has been well-documented. In this network of interactions, abscisic acid (ABA) has always been present and regarded to as a negative regulator of the development of morphological adaptations to soil flooding: hyponastic growth, adventitious root emergence, or formation of secondary aerenchyma in different plant species. However, recent evidence points toward a positive role of this plant hormone on the modulation of plant responses to hypoxia and, more importantly, on the ability to recover during the post-hypoxic period. In this work, the involvement of ABA as an emerging regulator of plant responses to low oxygen conditions alone or in interaction with other hormones is reviewed and discussed.

Crop yield and production responses to climate disasters in China

In recent decades, climate disasters, especially droughts and floods, have disrupted food production and caused yield losses. Crop models cannot identify quantitative changes of crop yield and production caused by climate disasters directly, and empirical approaches possibly underestimate the effects due to the use of the entire world or an individual nation as the unit of study. Here, we quantified the losses of crop yield and production resulting from droughts and floods across China during 1982-2012 using the superposed epoch analysis (SEA) method. We defined the actual-occurred and control composited series using provincial-level data in China, i.e., covered area (CA), affected area (AA), and sown area (SA) from 1982 to 2012, and crop yields and production of maize, rice, soybean, and wheat from 1979 to 2015. The results showed that maize and soybean in China suffered serious damage from droughts, with reductions in yields and production ranging from 7.8% to 11.6% between 1982 and 2012. Droughts and floods significantly decreased wheat yield by 5.8% and 6.1%, respectively. Moreover, rice yield and production were sensitive to both droughts and floods, with reductions of 4.5-6.3%. Among the MGPA, crops cultivated in NEC and the Huang-Huai-Hai Plain (HHH) were more easily affected by droughts. Among the four main crops and the three types of rice in the mid-lower reaches of the Yangtze River (MLYR), the yield and production of only early rice were sensitive to floods. The quantitative identification of the spatial responses of crop yields and production to droughts and floods can help us better understand the impacts of climate disasters on food security in China and the whole world, which is essential for addressing potential adaptation strategies.

The Seedlings of Different Japonica Rice Varieties Exhibit Differ Physiological Properties to Modulate Plant Survival Rates under Submergence Stress

Oryza sativa is a major food crop in Asia. In recent years, typhoons and sudden downpours have caused field flooding, which has resulted in serious harm to the production of rice. In this study, our data revealed that the plant heights of the five Japonica varieties increased during submergence. The elongation rates of TN14, KH139, and TK9 increased significantly during submergence. Chlorophyll contents of the five varieties significantly decreased after submergence and increased after recovery. Moreover, the chlorophyll content of KH139 was significantly higher than those of the other four varieties after recovery. The plant survival rates of the five varieties were higher than 50% after four-day submergence. After eight-day submergence, the survival rate of KH139 remained at 90%, which was the highest among the different varieties. The KH139 presented lower accumulation of hydrogen peroxide and the catalase activity than those of the other four varieties under submergence. The sucrose synthase 1 and alcohol dehydrogenase 1 were induced in KH139 under submergence. The results presented that different varieties of japonica rice have different flood tolerances, especially KH139 under submergence was superior to that of the other four varieties. These results can provide crucial information for future research on japonica rice under flooding stress.

The Many Facets of Hypoxia in Plants

Plants are aerobic organisms that require oxygen for their respiration. Hypoxia arises due to the insufficient availability of oxygen, and is sensed by plants, which adapt their growth and metabolism accordingly. Plant hypoxia can occur as a result of excessive rain and soil waterlogging, thus constraining plant growth. Increasing research on hypoxia has led to the discovery of the mechanisms that enable rice to be productive even when partly submerged. The identification of Ethylene Response Factors (ERFs) as the transcription factors that enable rice to survive submergence has paved the way to the discovery of oxygen sensing in plants. This, in turn has extended the study of hypoxia to plant development and plant–microbe interaction. In this review, we highlight the many facets of plant hypoxia, encompassing stress physiology, developmental biology and plant pathology.

Submergence tolerance and recovery in Lotus: Variation among fifteen accessions in response to partial and complete submergence

Several Lotus species are perennial forage legumes which tolerate waterlogging, but knowledge of responses to partial or complete shoot submergence is scant. We evaluated the responses of 15 Lotus accessions to partial and complete shoot submergence and variations in traits associated with tolerance and recovery after de-submergence. Accessions of Lotus tenuis, L. corniculatus, L. pedunculatus and L. japonicus were raised for 43 d and then subjected to aerated root zone (control), deoxygenated stagnant root zone with shoots in air (stagnant), stagnant root zone with partial (75 %) and complete submergence of shoots, for 7 d. The recovery ability from complete submergence was also assessed. We found inter- and intra-specific variations in the stem extension responses (i.e. promoted or restricted compared to controls) depending on water depth. Eight of 15 accessions promoted the stem extension when in partial submergence, while three of those eight (all L. tenuis accessions) had a restricted stem extension when under complete submergence. Two accessions (belonging to L. corniculatus and L. penduculatus species) also promoted the stem extension under complete submergence. The accessions that attained better recovery in terms of leaves produced after de-submergence, were those that had high leaf and root sugar concentration at de-submergence, and high thickness and persistence of gas films on leaves during submergence (all L. tenuis accessions). We conclude that all Lotus accessions were able to tolerate 7 d of partial and complete shoot submergence, despite adopting different stem extension responses.

Tolerant mechanisms to O2 deficiency under submergence conditions in plants

Wetland plants can tolerate long-term strict hypoxia and anoxic conditions and the subsequent re-oxidative stress compared to terrestrial plants. During O2 deficiency, both wetland and terrestrial plants use NAD(P)+ and ATP that are produced during ethanol fermentation, sucrose degradation, and major amino acid metabolisms. The oxidation of NADH by non-phosphorylating pathways in the mitochondrial respiratory chain is common in both terrestrial and wetland plants. As the wetland plants enhance and combine these traits especially in their roots, they can survive under long-term hypoxic and anoxic stresses. Wetland plants show two contrasting strategies, low O2 escape and low O2 quiescence strategies (LOES and LOQS, respectively). Differences between two strategies are ascribed to the different signaling networks related to phytohormones. During O2 deficiency, LOES-type plants show several unique traits such as shoot elongation, aerenchyma formation and leaf acclimation, whereas the LOQS-type plants cease their growth and save carbohydrate reserves. Many wetland plants utilize NH4+ as the nitrogen (N) source without NH4+-dependent respiratory increase, leading to efficient respiratory O2 consumption in roots. In contrast, some wetland plants with high O2 supply system efficiently use NO3- from the soil where nitrification occurs. The differences in the N utilization strategies relate to the different systems of anaerobic ATP production, the NO2--driven ATP production and fermentation. The different N utilization strategies are functionally related to the hypoxia or anoxia tolerance in the wetland plants.

Eco-Physiological Traits Related to Recovery from Complete Submergence in the Model Legume Lotus japonicus

Submergence is a severe form of stress for most plants. Lotus japonicus is a model legume with potential use in assisting breeding programs of closely related forage Lotus species. Twelve L. japonicus genotypes (10 recombinant inbred lines (RILs) and 2 parental accessions) with different constitutive shoot to root dry mass ratios (S:R) were subjected to 7 days of submergence in clear water and allowed to recover for two weeks post-submergence; a set of non-submerged plants served as controls. Relative growth rate (RGR) was used to indicate the recovery ability of the plants. Leaf relative water content (RWC), stomatal conductance (gs), greenness of basal and apical leaves, and chlorophyll fluorescence (Fv/Fm, as a measure of photoinhibition) were monitored during recovery, and relationships among these variables and RGR were explored across genotypes. The main results showed (i) variation in recovery ability (RGR) from short-term complete submergence among genotypes, (ii) a trade-off between growth during vs. after the stress indicated by a negative correlation between RGR during submergence and RGR post-submergence, (iii) an inverse relationship between RGR during recovery and S:R upon de-submergence, (iv) positive relationships between RGR at early recovery and RWC and gs, which were negatively related to S:R, suggesting this parameter as a good estimator of plant water balance post-submergence, (v) chlorophyll retention allowed fast recovery as revealed by the positive relationship between greenness of basal and apical leaves and RGR during the first recovery week, and (vi) full repair of the submergence-damaged photosynthetic apparatus occurred more slowly (second recovery week) than full recovery of plant water relations. The inclusion of these traits contributing to submergence recovery in L. japonicus should be considered to speed up the breeding process of the closely related forage Lotus spp. used in current agriculture.

Metabolite and Phytohormone Profiling Illustrates Metabolic Reprogramming as an Escape Strategy of Deepwater Rice during Partially Submerged Stress

Rice varieties that can survive under submergence conditions respond to flooding either by enhancing internode elongation or by quiescence of shoot elongation. Despite extensive efforts to identify key metabolites triggered by complete submergence of rice possessing SUBMERGENCE 1 (SUB1) locus, metabolic responses of internode elongation of deepwater rice governed by the SNORKEL 1 and 2 genes remain elusive. This study investigated specific metabolomic responses under partial submergence (PS) to deepwater- (C9285) and non-deepwater rice cultivars (Taichung 65 (T65)). In addition, we examined the response in a near-isogenic line (NIL-12) that has a C9285 genomic fragment on chromosome 12 introgressed into the genetic background of T65. Under short-term submergence (0-24 h), metabolite profiles of C9285, NIL-12, and T65 were compared to extract significantly changed metabolites in deepwater rice under PS conditions. Comprehensive metabolite and phytohormone profiling revealed increases in metabolite levels in the glycolysis pathway in NIL-12 plants. Under long-term submergence (0-288 h), we found decreased amino acid levels. These metabolomic changes were opposite when compared to those in flood-tolerant rice with SUB1 locus. Auxin conjugate levels related to stress response decreased in NIL-12 lines relative to T65. Our analysis helped clarify the complex metabolic reprogramming in deepwater rice as an escape strategy.

Diel O2 Dynamics in Partially and Completely Submerged Deepwater Rice: Leaf Gas Films Enhance Internodal O2 Status, Influence Gene Expression and Accelerate Stem Elongation for 'Snorkelling' during Submergence

Deepwater rice has a remarkable shoot elongation response to partial submergence. Shoot elongation to maintain air-contact enables 'snorkelling' of O2 to submerged organs. Previous research has focused on partial submergence of deepwater rice. We tested the hypothesis that leaf gas films enhance internode O2 status and stem elongation of deepwater rice when completely submerged. Diel patterns of O2 partial pressure (pO2) were measured in internodes of deepwater rice when partially or completely submerged, and with or without gas films on leaves, for the completely submerged plants. We also took measurements for paddy rice. Deepwater rice elongated during complete submergence and the shoot tops emerged. Leaf gas films improved O2 entry during the night, preventing anoxia in stems, which is of importance for elongation of the submerged shoots. Expressions of O2 deprivation inducible genes were upregulated in completely submerged plants during the night, and more so when gas films were removed from the leaves. Diel O2 dynamics showed similar patterns in paddy and deepwater rice. We demonstrated that shoot tops in air enabled 'snorkelling' and increased O2 in internodes of both rice ecotypes; however, 'snorkelling' was achieved only by rapid shoot elongation by deepwater rice, but not by paddy rice.

Partial Submergence Tolerance in Rice (<i>Oryza sativa</i> L.) Cultivated in North Sulawesi at the Vegetative Phase

BACKGROUND AND OBJECTIVE

The partial-submergence-tolerant crop plants, including rice are required for fulfilling food needs when a flooding disaster occurs in Indonesia. The information of effective selection method for obtaining submergence tolerant rice is required for increasing the North Sulawesi capacity as a pillar of national food security. This study evaluated the partial-submergence-tolerance in 10 rice cultivars that are cultivated in North Sulawesi Province based on the morphological characters (plant height, shoot dry mass, shoot length, root dry mass, root length, root volume, shoot:root ratio and leaf number) at the vegetative phase.

MATERIAL AND METHODS

This experiment was conducted in the greenhouse using 10 rice cultivars (cv. Cigeulis, Seruni, Mekongga, Ciherang, TB, Ombong, Inpari 13, Burungan, Temo and Superwin). These cultivars were grown at the vegetative phase in partial submergence condition (the entire root system and 30 cm of above-ground shoot was under water) for 20 days, with 8 replicates, in a randomized block design.

RESULTS

The longer duration of partial-submergence treatment resulted in the decrease of leaf number, the increase of plant height and the increase of shoot elongation. There were three categories of partial-submergence tolerance, i.e., tolerant for Cigeulis and TB, semi tolerant for Seruni, Mekongga, Inpari 13, Burungan, Temo and Superwin and non-tolerant for Ciherang and Ombong.

CONCLUSION

Rice cv. TB as tolerant cultivar showed better growth response under partial submergence rather than other rice cultivars at the vegetative phase.

Ethylene signaling involves in seeds germination upon submergence and antioxidant response elicited confers submergence tolerance to rice seedlings

BACKGROUND

Flooding has negative impact on agriculture. The plant hormone ethylene is involved in plant growth and stress responses, which are important role in tolerance and adaptation regulatory mechanisms during submergence stress. Ethylene signaling crosstalk with gibberellin signaling enhances tolerance in lowland rice (Flood Resistant 13A) through a quiescence strategy or in deepwater rice through an escape strategy when rice is submerged. Information regarding ethylene-mediated priming in submergence stress tolerance in rice is scant. Here, we used 1-aminocyclopropane-1-carboxylic acid, an ethylene precursor, to evaluate the response in submerged rice seedlings.

RESULTS

The germination rate and mean germination times of rice seeds was higher in seedlings under submergence only when ethylene signaling was inhibited by supplemented with silver nitrate (AgNO₃). Reduced leaf chlorophyll contents and induced senescence-associated genes in rice seedlings under submergence were relieved by pretreatment with an ethylene precursor. The ethylene-mediated priming by pretreatment with an ethylene precursor enhanced the survival rate and hydrogen peroxide (H₂O₂) and superoxide (O₂^-) anion accumulation and affected antioxidant response in rice seedlings.

CONCLUSIONS

Pretreatment with an ethylene precursor leads to reactive oxygen species generation, which in turn triggered the antioxidant response system, thus improving the tolerance of rice seedlings to complete submergence stress. Thus, H₂O₂ signaling may contribute to ethylene-mediated priming to submergence stress tolerance in rice seedlings.

Root phenotypes of dwarf and "overgrowth" SLN1 barley mutants, and implications for hypoxic stress tolerance

Gibberellins are central to the regulation of plant development and growth. Action of gibberellins involves the degradation of DELLA proteins, which are negative regulators of growth. In barley (Hordeum vulgare), certain mutations affecting genes involved in gibberellin synthesis or coding for the barley DELLA protein (Sln1) confer dwarfism. Recent studies have identified new alleles of Sln1 with the capacity to revert the dwarf phenotype back to the taller phenotypes. While the effect of these overgrowth alleles on shoot phenotypes has been explored, no information is available for roots. Here, we examined aspects of the root phenotypes displayed by plants with various Sln1 gene alleles, and tested responses to growth in an O₂-deficient root-zone as occurs during soil waterlogging. One overgrowth line, bearing the Sln1d.8 allele carrying two amino acid substitutions (one in the amino terminus and one in the GRAS domain of the encoded DELLA protein), displays profound and opposite effects on shoot height and root length. While it stimulates shoot height, it severely compromises root length by a reduction of cell size in zones distal to the root apex. In addition, Sln1d.8 plants counteract the negative effect of the original mutation on the formation of adventitious roots. Interestingly, plants bearing this allele display enhanced resistance to flooding stress in a way non-related with increased root porosity. Thus, various Sln1 gene alleles contribute to root phenotypes and can also influence plant responses to root-zone O₂-deficiency stress.

Exo-ethylene application mitigates waterlogging stress in soybean (Glycine max L.)

BACKGROUND

Waterlogging (WL) is a key factor hindering soybean crop productivity worldwide. Plants utilize various hormones to avoid various stress conditions, including WL stress; however, the physiological mechanisms are still not fully understood.

RESULTS

To identify physiological mechanisms during WL stress, different phytohormones, such as ethephon (ETP; donor source of ethylene), abscisic acid, gibberellins, indole-3-acetic acid, kinetin, jasmonic acid, and salicylic acid were exogenously applied to soybean plants. Through this experiment, we confirmed the beneficial effects of ETP treatment. Thus, we selected ETP as a candidate hormone to mitigate WL. Further mechanistic investigation of the role of ETP in waterlogging tolerance was carried out. Results showed that ETP application mitigated WL stress, significantly improved the photosynthesis pigment, and increased the contents of endogenous GAs compared to those in untreated plants. The amino acid contents during WL stress were significantly activated by EPT treatments. The amino acid contents were significantly higher in the 100 μM ETP-treated soybean plants than in the control. ETP application induced adventitious root initiation, increased root surface area, and significantly increased the expressions of glutathione transferases and relative glutathione activity compared to those of non-ETP-treated plants. ETP-treated soybeans produced a higher up-regulation of protein content and glutathione S-transferase (GSTs) than did soybeans under the WL only treatment.

CONCLUSIONS

In conclusion, the current results suggest that ETP application enabled various biochemical and transcriptional modulations. In particular, ETP application could stimulate the higher expression of GST3 and GST8. Thus, increased GST3 and GST8 induced 1) increased GSH activity, 2) decreased reactive oxygen species (ROS), 3) mitigation of cell damage in photosynthetic apparatus, and 4) improved phenotype consecutively.

Effects of Exogenous Application of Protocatechuic Acid and Vanillic Acid to Chlorophylls, Phenolics and Antioxidant Enzymes of Rice (Oryza sativa L.) in Submergence

In this study, effects from application of protocatechuic acid (PA) and vanillic acid (VA) and their mixture on the submergence tolerance of rice were examined. The treatment of 0.01 mM PA and VA did not show significant increase of rice growth as compared to the controls. However, at higher concentrations (0.1-1.0 mM), rice shoot was elevated in submergence by 20.8-22.4%. The survival percentage of rice seedlings at any dose of PA, VA and their mixture was significantly higher than the controls. In general, the mixture of PA and VA was more active to promote shoot elongation and survival in submergence than sole treatment of either PA or VA. The amount of chlorophyll b by PA was significantly increased, while no change in chlorophyll a content was observed. VA remarkably reduced malondialdehyde quantity at three days of submergence, while no significant difference among treatment was observed in PA, the mixture, and respective controls. The two phenolic acids promoted contents of phenolics and flavonoids in rice leaves and roots, however the quantities of endogenous PA and VA in rice were not markedly differed after PA and VA treated on roots of rice seedlings. The ascorbate peroxidase and superoxide dismutase activities were enhanced, while the expression of genes encoding antioxidant enzymes was favored. VA increased the expression level of ascorbate peroxidase genes in higher levels than PA and their mixture, while no significant difference was observed in the other genes including superoxide dismutase, catalase, glutathione reductase, and peroxidase. Findings of this study showed that PA and VA increased the submergence tolerance of rice by promoting the photosynthetic and anti-oxidative processes in rice seedlings. The treatment of PA and VA mixture on seedling roots was potent to promote the submergence tolerance in rice.

Nitric oxide is essential for the development of aerenchyma in wheat roots under hypoxic stress

In response to flooding/waterlogging, plants develop various anatomical changes including the formation of lysigenous aerenchyma for the delivery of oxygen to roots. Under hypoxia, plants produce high levels of nitric oxide (NO) but the role of this molecule in plant-adaptive response to hypoxia is not known. Here, we investigated whether ethylene-induced aerenchyma requires hypoxia-induced NO. Under hypoxic conditions, wheat roots produced NO apparently via nitrate reductase and scavenging of NO led to a marked reduction in aerenchyma formation. Interestingly, we found that hypoxically induced NO is important for induction of the ethylene biosynthetic genes encoding ACC synthase and ACC oxidase. Hypoxia-induced NO accelerated production of reactive oxygen species, lipid peroxidation, and protein tyrosine nitration. Other events related to cell death such as increased conductivity, increased cellulase activity, DNA fragmentation, and cytoplasmic streaming occurred under hypoxia, and opposing effects were observed by scavenging NO. The NO scavenger cPTIO (2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide potassium salt) and ethylene biosynthetic inhibitor CoCl₂ both led to reduced induction of genes involved in signal transduction such as phospholipase C, G protein alpha subunit, calcium-dependent protein kinase family genes CDPK, CDPK2, CDPK 4, Ca-CAMK, inositol 1,4,5-trisphosphate 5-phosphatase 1, and protein kinase suggesting that hypoxically induced NO is essential for the development of aerenchyma.

Molecular and physiological characterization of AtHIGD1 in Arabidopsis

Flooding is a principal stress that limits plant productivity. The sensing of low oxygen levels (hypoxia) plays a critical role in the signaling pathway that functions in plants in flooded environments. In this study, to investigate hypoxia response mechanisms in Arabidopsis, we identified three hypoxia-related genes and subjected one of these genes, Arabidopsis thaliana HYPOXIA-INDUCED GENE DOMAIN 1 (AtHIGD1), to molecular characterization including gene expression analysis and intracellular localization of the encoded protein. AtHIGD1 was expressed in various organs but was preferentially expressed in developing siliques. Confocal microscopy of transgenic plants harboring eGFP-tagged AtHIGD1 indicated that AtHIGD1 is localized to mitochondria. Importantly, plants overexpressing AtHIGD1 exhibited increased resistance to hypoxia compared to wild type. Our results represent the first report of a biological function for an HIGD protein in plants and indicate that AtHIGD1 is a mitochondrial protein that plays an active role in mitigating the effects of hypoxia on plants.

eQTLs Regulating Transcript Variations Associated with Rapid Internode Elongation in Deepwater Rice

To avoid low oxygen, oxygen deficiency or oxygen deprivation, deepwater rice cultivated in flood planes can develop elongated internodes in response to submergence. Knowledge of the gene regulatory networks underlying rapid internode elongation is important for an understanding of the evolution and adaptation of major crops in response to flooding. To elucidate the genetic and molecular basis controlling their deepwater response we used microarrays and performed expression quantitative trait loci (eQTL) and phenotypic QTL (phQTL) analyses of internode samples of 85 recombinant inbred line (RIL) populations of non-deepwater (Taichung 65)- and deepwater rice (Bhadua). After evaluating the phenotypic response of the RILs exposed to submergence, confirming the genotypes of the populations, and generating 188 genetic markers, we identified 10,047 significant eQTLs comprised of 2,902 cis-eQTLs and 7,145 trans-eQTLs and three significant eQTL hotspots on chromosomes 1, 4, and 12 that affect the expression of many genes. The hotspots on chromosomes 1 and 4 located at different position from phQTLs detected in this study and other previous studies. We then regarded the eQTL hotspots as key regulatory points to infer causal regulatory networks of deepwater response including rapid internode elongation. Our results suggest that the downstream regulation of the eQTL hotspots on chromosomes 1 and 4 is independent, and that the target genes are partially regulated by SNORKEL1 and SNORKEL2 genes (SK1/2), key ethylene response factors. Subsequent bioinformatic analyses, including gene ontology-based annotation and functional enrichment analysis and promoter enrichment analysis, contribute to enhance our understanding of SK1/2-dependent and independent pathways. One remarkable observation is that the functional categories related to photosynthesis and light signaling are significantly over-represented in the candidate target genes of SK1/2. The combined results of these investigations together with genetical genomics approaches using structured populations with a deepwater response are also discussed in the context of current molecular models concerning the rapid internode elongation in deepwater rice. This study provides new insights into the underlying genetic architecture of gene expression regulating the response to flooding in deepwater rice and will be an important community resource for analyses on the genetic basis of deepwater responses.

A novel rice protein family of OsHIGDs may be involved in early signalling of hypoxia-promoted stem growth in deepwater rice

OsHIGDs was identified as a novel hypoxia-responsive protein family. Among them, OsHIGD2 is characterized as a mitochondrial protein and is related to hypoxia signalling through interacting with mitochondrial proteins of critical functions in reducing cell damages caused by hypoxia. Recent evidence supports ethylene as a key factor in modulating plant responses to submergence stress. Meanwhile, there has been general consent that ethylene is not the only signal for the submergence-induced stem growth. In this study, we confirmed that hypoxia also promotes stem elongation in deepwater rice even in the absence of ethylene. As components of ethylene-independent hypoxia signalling, five HIGD (hypoxia-induced gene domain) protein genes were identified. Among the genes, OsHIGD2 showed the fastest and strongest induction by hypoxia as well as submergence. Co-expression analysis indicated that OsHIGD2 had a simultaneous expression pattern with fermentation-related genes, such as ADH1 (alcohol dehydrogenase 1) and PDC2 (pyruvate decarboxylase 2). Transient expression of OsHIGD2 in leaf epidermal cells of Nicotiana benthamiana provided evidence that the protein is localized to mitochondria. We further identified OsHIGD2-interacting proteins through the yeast two-hybrid assay using OsHIGD2 as bait. As a result, three mitochondrial proteins were discovered that function in the regulation of redox potential or reduction of protein damages caused by reactive oxygen species. In this report, we propose that OsHIGD2 is a mitochondrial protein which takes part in the early stage of hypoxia signalling by interacting with proteins that are related to oxygen utilization.

The sunflower transcription factor HaWRKY76 confers drought and flood tolerance to Arabidopsis thaliana plants without yield penalty

Arabidopsis transgenic plants expressing the sunflower transcription factor HaWRKY76 exhibit increased yield and tolerance to drought and flood stresses. The genetic construct containing HaWRKY76 is proposed as a potential biotechnological tool to improve crops. Water deficit and water excess are abiotic stress factors that seriously affect crops worldwide. To increase the tolerance to such stresses without causing yield penalty constitutes a major goal for biotechnologists. In this survey, we report that HaWRKY76, a divergent sunflower WRKY transcription factor, is able to confer both dehydration and submergence tolerance to Arabidopsis transgenic plants without yield penalty. The expression pattern of HaWRKY76 was analyzed in plants grown in standard conditions and under different watering regimes indicating a regulation by water availability. The corresponding cDNA was isolated and cloned under the control of a constitutive promoter and Arabidopsis plants were transformed with this construct. These transgenic plants presented higher biomass, seed production and sucrose content than controls in standard growth conditions. Moreover, they exhibited tolerance to mild drought or flood (complete submergence/waterlogging) stresses as well as the same or increased yield, depending on the stress severity and plant developmental stage, compared with controls. Drought tolerance occurred via an ABA-independent mechanism and induction of stomatal closure. Submergence tolerance can be explained by the carbohydrate (sucrose and starch) preservation achieved through the repression of fermentation pathways. Higher cell membrane stability and chlorenchyma maintenance could be the nexus between tolerance responses in front of both stresses. Altogether, the obtained results indicated that HaWRKY76 can be a potential biotechnological tool to improve crops yield as well as drought and flood tolerances.

Metabolic adaptation to sugar/O2 deficiency for anaerobic germination and seedling growth in rice

Rice is characterized by a broad range of metabolic and morphological adaptations to flooding, such as germination and mobilization of stored nutrients under submergence until seedlings reach the water surface to carry out photosynthesis, and sustainable growth of mature plants for long durations under partial submergence. The underlying mechanisms of the molecular basis of adaptation to anaerobic germination and seedling growth in rice are being uncovered. Induction of an ensemble of hydrolases to mobilize endosperm nutrient reserves is one of the key factors for successful germination and coleoptile elongation in rice under submergence. To compensate for reduced efficiency of Tricarboxylic Acid cycle and oxidative respiration in mitochondria under O2 deficient conditions, α-amylases play a central role in the hydrolysis of starch to provide sugar substrates for glycolysis and alcohol fermentation for generating ATP. We review the progress on the molecular mechanism regulating α-amylase expression that involves the integration of signals generated by the hormone gibberellin (GA), sugar starvation and O2 deprivation that results in germination and sustainable seedling growth in rice under anaerobic conditions. Comparisons are also made between dicots and monocots for the molecular mechanism of induction of genes involved in alcohol fermentation and sugar/O2 deficiency sensing system.

Oxygen deficit alleviates phosphate overaccumulation toxicity in OsPHR2 overexpression plants

Overexpression of OsPHR2 increases phosphate (Pi) uptake and causes overaccumulation of Pi in rice plants, which is toxic to rice plants when they are grown in media with a sufficient Pi supply. The toxicity that results from OsPHR2 overexpression can be significantly relieved by growing the plants in a waterlogged paddy field. A comparison of the Pi uptake and growth status of OsPHR2-overexpression plants (PHR2-Oe plants) grown in paddy fields or in a laboratory setting in aerated or stagnant hydroponic conditions indicated that the oxygen limitation that is present in paddy fields and in stagnant rice culture solutions inhibits the Pi overaccumulation toxicity of PHR2-Oe plants by reducing their Pi uptake. Quantitative RT-PCR demonstrated that the expression of Pi-starvation-induced (PSI) genes was induced by oxygen limitation in both wild-type and PHR2-Oe plants. The induction of PSI genes is the consequence of reducing the Pi concentration in stagnant plants. Thus, when evaluating the efficiency of Pi use in rice germplasm or transgenic materials under hydroponic conditions, the impact of the low oxygen condition that exists in waterlogged paddies should be considered.

Soil abiotic factors influence interactions between belowground herbivores and plant roots

Root herbivores are important ecosystem drivers and agricultural pests, and, possibly as a consequence, plants protect their roots using a variety of defensive strategies. One aspect that distinguishes belowground from aboveground plant-insect interactions is that roots are constantly exposed to a set of soil-specific abiotic factors. These factors can profoundly influence root resistance, and, consequently, the outcome of the interaction with belowground feeders. In this review, we synthesize the current literature on the impact of soil moisture, nutrients, and texture on root-herbivore interactions. We show that soil abiotic factors influence the interaction by modulating herbivore abundance and behaviour, root growth and resistance, beneficial microorganisms, as well as natural enemies of the herbivores. We suggest that abiotic heterogeneity may explain the high variability that is often encountered in root-herbivore systems. We also propose that under abiotic stress, the relative fitness value of the roots and the potential negative impact of herbivory increases, which may lead to a higher defensive investment and an increased recruitment of beneficial microorganisms by the plant. At the same time, both root-feeding herbivores and natural enemies are likely to decrease in abundance under extreme environmental conditions, leading to a context- and species-specific impact on plant fitness. Only by using tightly controlled experiments that include soil abiotic heterogeneity will it be possible to understand the impact of root feeders on an ecosystem scale and to develop predictive models for pest occurrence and impact.

Mechanisms for coping with submergence and waterlogging in rice

Rice (Oryza sativa L.), unlike other cereals, can grow well in paddy fields and is highly tolerant of excess water stress, from either submergence (in which part or all of the plant is under water) or waterlogging (in which excess water in soil limits gas diffusion). Rice handles submergence stress by internal aeration and growth controls. A quiescence strategy based on Submergence-1A (SUB1A) or an escape strategy based on SNORKEL1 (SK1) and SNORKEL2 (SK2) is used for the growth controls. On the other hand, rice handles waterlogging stress by forming lysigenous aerenchyma and a barrier to radial O2 loss (ROL) in roots in order to supply O2 to the root tip. In this article, we summarize recent advances in understanding the mechanisms of responding to excess water stresses (i.e., submergence and waterlogging) in rice and other gramineous plants.