Physiological basis of tolerance to complete submergence in rice involves genetic factors in addition to the SUB1 gene

Unraveling the genetic enigma of rice submergence tolerance: Shedding light on the role of ethylene response factor-encoding gene SUB1A-1

The world's low-lying rice (Oryza sativa) cultivation areas are under threat of submergence or flash flooding due to global warming. Rice plants manifest a variety of physiological and morphological changes to cope with submergence and hypoxia, including lowering carbohydrate consumption, inhibiting shoot elongation, and forming a thicker leaf gas film during submergence. Functional studies have revealed that submergence tolerance in rice is mainly determined by an ethylene response factor (ERF) transcription factor-encoding gene, namely SUBMERGENCE 1A-1 (SUB1A-1) located in the SUB1 quantitative trait locus. The SUB1A-1-dependent submergence tolerance is manifested through hormonal signaling involving ethylene, gibberellic acid, brassinosteroid, auxin and jasmonic acid. Considerable progress has been made toward the introduction of SUB1A-1 into rice varieties through a conventional marker-assisted backcrossing approach. Here, we review the recent advances in the physiological, biochemical and molecular dynamics of rice submergence tolerance mediated by the 'quiescence strategy'. Thus, the present review aims to provide researchers with insights into the genetics of rice submergence tolerance and future perspectives for designing submergence-resilient plants for sustainable agriculture under the uncertainties of climate change.

Multi-stress resilience in plants recovering from submergence

Submergence limits plants' access to oxygen and light, causing massive changes in metabolism; after submergence, plants experience additional stresses, including reoxygenation, dehydration, photoinhibition and accelerated senescence. Plant responses to waterlogging and partial or complete submergence have been well studied, but our understanding of plant responses during post-submergence recovery remains limited. During post-submergence recovery, whether a plant can repair the damage caused by submergence and reoxygenation and re-activate key processes to continue to grow, determines whether the plant survives. Here, we summarize the challenges plants face when recovering from submergence, primarily focusing on studies of Arabidopsis thaliana and rice (Oryza sativa). We also highlight recent progress in elucidating the interplay among various regulatory pathways, compare post-hypoxia reoxygenation between plants and animals and provide new perspectives for future studies.

Integrated Transcriptomic and Metabolomics Analysis of the Root Responses of Orchardgrass to Submergence Stress

Submergence stress can severely affect plant growth. Orchardgrass (Dactylis glomerata L.) is an important forage grass, and the molecular mechanisms of orchardgrass to submergence stress are not well understood. The roots of the flood-tolerant cultivar "Dian Bei" were harvested at 0 h, 8 h and 24 h of submergence stress. The combined transcriptomic and metabolomic analyses showed that β-alanine metabolism, flavonoid biosynthesis, and biosynthesis of amino acid pathways were significantly enriched at 8 h and 24 h of submergence stress and were more pronounced at 24 h. Most of the flavonoid biosynthesis-related genes were down-regulated for the synthesis of metabolites such as naringenin, apigenin, naringin, neohesperidin, naringenin chalcone, and liquiritigenin in response to submergence stress. Metabolites such as phenylalanine, tyrosine, and tryptophan were up-regulated under stress. The predominant response of flavonoid and amino acids biosynthesis to submergence stress suggests an important role of these pathways in the submergence tolerance of orchardgrass.

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.

QTL and Candidate Genes: Techniques and Advancement in Abiotic Stress Resistance Breeding of Major Cereals

At least 75% of the world's grain production comes from the three most important cereal crops: rice (Oryza sativa), wheat (Triticum aestivum), and maize (Zea mays). However, abiotic stressors such as heavy metal toxicity, salinity, low temperatures, and drought are all significant hazards to the growth and development of these grains. Quantitative trait locus (QTL) discovery and mapping have enhanced agricultural production and output by enabling plant breeders to better comprehend abiotic stress tolerance processes in cereals. Molecular markers and stable QTL are important for molecular breeding and candidate gene discovery, which may be utilized in transgenic or molecular introgression. Researchers can now study synteny between rice, maize, and wheat to gain a better understanding of the relationships between the QTL or genes that are important for a particular stress adaptation and phenotypic improvement in these cereals from analyzing reports on QTL and candidate genes. An overview of constitutive QTL, adaptive QTL, and significant stable multi-environment and multi-trait QTL is provided in this article as a solid framework for use and knowledge in genetic enhancement. Several QTL, such as DRO1 and Saltol, and other significant success cases are discussed in this review. We have highlighted techniques and advancements for abiotic stress tolerance breeding programs in cereals, the challenges encountered in introgressing beneficial QTL using traditional breeding techniques such as mutation breeding and marker-assisted selection (MAS), and the in roads made by new breeding methods such as genome-wide association studies (GWASs), the clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 system, and meta-QTL (MQTL) analysis. A combination of these conventional and modern breeding approaches can be used to apply the QTL and candidate gene information in genetic improvement of cereals against abiotic stresses.

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.

The influence of endophytes on rice fitness under environmental stresses

KEY MESSAGE

Endophytes are crucial for the promotion of rice growth and stress tolerance and can be used to increase rice crop yield. Endophytes can thus be exploited in biotechnology and genetic engineering as eco-friendly and cost-effective means for the development of high-yielding and stress-tolerant rice plants. Rice (Oryza sativa) crop is continuously subjected to biotic and abiotic stresses, compromising growth and consequently yield. The situation is exacerbated by climate change impacting on ecosystems and biodiversity. Genetic engineering has been used to develop stress-tolerant rice, alongside physical and chemical methods to mitigate the effect of these stresses. However, the success of these strategies has been hindered by short-lived field success and public concern on adverse effects associated. The limited success in the field of stress-tolerant cultivars developed through breeding or transgenic approaches is due to the complex nature of stress tolerance as well as to the resistance breakdown caused by accelerated evolution of pathogens. It is therefore necessary to develop novel and acceptable strategies to enhance rice stress tolerance and durable resistance and consequently improve yield. In the last decade, plant growth promoting (PGP) microbes, especially endophytes, have drawn the attention of agricultural scientists worldwide, due to their ability to mitigate environmental stresses in crops, without causing adverse effects. Increasing evidence indicates that endophytes effectively confer fitness benefits also to rice under biotic and abiotic stress conditions. Endophyte-produced metabolites can control the expression of stress-responsive genes and improve the physiological performance and growth of rice plants. This review highlights the current evidence available for PGP microbe-promoted tolerance of rice to abiotic stresses such as salinity and drought and to biotic ones, with special emphasis on endophytes. Associated molecular mechanisms are illustrated, and prospects for sustainable rice production also in the light of the impending climate change, discussed.

Gene regulatory networks shape developmental plasticity of root cell types under water extremes in rice

Understanding how roots modulate development under varied irrigation or rainfall is crucial for development of climate-resilient crops. We established a toolbox of tagged rice lines to profile translating mRNAs and chromatin accessibility within specific cell populations. We used these to study roots in a range of environments: plates in the lab, controlled greenhouse stress and recovery conditions, and outdoors in a paddy. Integration of chromatin and mRNA data resolves regulatory networks of the following: cycle genes in proliferating cells that attenuate DNA synthesis under submergence; genes involved in auxin signaling, the circadian clock, and small RNA regulation in ground tissue; and suberin biosynthesis, iron transporters, and nitrogen assimilation in endodermal/exodermal cells modulated with water availability. By applying a systems approach, we identify known and candidate driver transcription factors of water-deficit responses and xylem development plasticity. Collectively, this resource will facilitate genetic improvements in root systems for optimal climate resilience.

Adoption Trend of Climate-Resilient Rice Varieties in Bangladesh

Rice is a major crop in Bangladesh that supports both food security and livelihoods. However, a need remains for improved productivity and adaptation to the risks associated with climate change. To accomplish this, the increased adoption of climate-resilient and high-yielding rice varieties can be beneficial. Therefore, we conducted a study in Bangladesh over three consecutive years: 2016, 2017, and 2018. The scope of the study included the major cropping season (wet), Aman. The yield advantages of climate-resilient rice varieties were evaluated and compared with those of the varieties popular with farmers. We included new stress-tolerant varieties, such as submergence-tolerant rice (BRRI dhan51 and BRRI dhan52) and drought-tolerant rice (BRRI dhan56 and BRRI dhan71), along with farmer-chosen controls, in the study. We conducted the evaluation through on-farm trials to compare the varieties in both submergence- and drought-affected environments. The seasonal trials provided measured results of yield advantages. The participating farmers were also studied over the three-year-period to capture their varietal adoption rates. We calculated both the location estimated yield advantages (LEYA) and the location observed yield advantages (LOYA). The results revealed that, under non-stress conditions, the grain yields of climate-resilient varieties were either statistically similar to or higher than those of the farmer-chosen controls. Our study also revealed a year-to-year progressive adoption rate for the introduced varieties. The study suggests that the wide-scale introduction and popularization of climate-resilient varieties can ensure higher productivity and climate risk adaptation. The close similarity between LOYA and LEYA indicated that the observational and experiential conclusions of the host farmers were similar to the scientific performance of the varieties. We also found that comparison performed through on-farm trials was a critical method for enhancing experiential learning and obtaining an accurate estimation of yield advantages.

The submergence tolerance regulator SUB1A differentially coordinates molecular adaptation to submergence in mature and growing leaves of rice (Oryza sativa L.)

A typical adaptive response to submergence regulated by SUB1A, the ethylene-responsive transcription factor gene, is the restricted elongation of the uppermost leaves. However, the molecular and physiological functions of SUB1A have been characterized using entire shoot tissues, most of which are mature leaves that do not elongate under submergence. We aimed to identify leaf-type-specific and overlapping adaptations coordinated in SUB1A-dependent and -independent manners. To this end, we compared the transcriptomic and hormonal responses to submergence between mature and growing leaves using rice genotypes with and without SUB1A. Monosaccharide, branched-chain amino acid, and nucleoside metabolism, associated with ATP synthesis, were commonly activated in both leaf types regardless of genotype. In both leaf types, pathways involved in carbohydrate and nitrogen metabolism were suppressed by SUB1A, with more severe restriction in growing leaves that have a greater energy demand if SUB1A is absent. In growing leaves, accumulation of and responsiveness to growth-regulating hormones were properly modulated by SUB1A, which correlated with restricted elongation. In mature leaves, submergence-induced auxin accumulation was suppressed by SUB1A. This study demonstrates that different sets of hormonal pathways, both of which are modulated by SUB1A, contribute to distinct adaptive responses to submergence in mature and growing rice leaves.

Finding a breather for Oryza sativa: Understanding hormone signalling pathways involved in rice plants to submergence stress

During the course of evolution, different ecotypes of rice (Oryza sativa L.) have evolved distinct strategies to cope with submergence stress. Such contrasting responses are mediated by plant hormones that are principle regulators of growth, development and responses to various biotic and abiotic stresses. These hormones act cooperatively and show extensive crosstalk which is mediated by key regulatory genes that serve as nodes of molecular communication. The presence or absence of such genes leads to significant changes in hormone signalling pathways and hence, governs the type of response that the plant will exhibit. As flooding is one of the leading causes of crop loss across all the major rice-producing countries, it is crucial to deeply understand the molecular nexus governing the response to submergence to produce flood resilient varieties. This review focuses on the hormonal signalling pathways that mediate two contrasting responses of the rice plant to submergence stress namely, rapid internode elongation to escape flood waters and quiescence response that enables the plant to survive under complete submergence. The significance of several key genes such as Sub1A-1, SLR1, SD1 and SK1/SK2, in defining the ultimate response to submergence has also been discussed.

Physiological and molecular implications of multiple abiotic stresses on yield and quality of rice

Abiotic stresses adversely affect rice yield and productivity, especially under the changing climatic scenario. Exposure to multiple abiotic stresses acting together aggravates these effects. The projected increase in global temperatures, rainfall variability, and salinity will increase the frequency and intensity of multiple abiotic stresses. These abiotic stresses affect paddy physiology and deteriorate grain quality, especially milling quality and cooking characteristics. Understanding the molecular and physiological mechanisms behind grain quality reduction under multiple abiotic stresses is needed to breed cultivars that can tolerate multiple abiotic stresses. This review summarizes the combined effect of various stresses on rice physiology, focusing on grain quality parameters and yield traits, and discusses strategies for improving grain quality parameters using high-throughput phenotyping with omics approaches.

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.

Phenotypic, Nutritional, and Antioxidant Characterization of Blanched Oenanthe javanica for Preferable Cultivar

Blanching is a technique used in blocking sunlight for the production of tender, sweet, and delicious stems in the field. This technique is also used in water dropwort (Oenanthe javanica), an important vegetable in East Asia. In China, the steamed stems of water dropwort are prepared with boiled rice. However, the effect of blanching on the nutritional level and antioxidant capacity of water dropwort has not been explored yet. The current study aims to determine the nutrient contents and antioxidant capacities of five cultivars and select the best cultivar. They were mainly compared in terms of phenotypic, physiological, nutritional, and antioxidant levels after blanch cultivation. Results indicate that blanching significantly influenced the phenotype, physiology, and nutritional level of water dropwort in all cultivars. Although few parameters decreased with blanching, starch, sugars, vitamins, minerals, and antioxidant activities increased significantly in the blanched stems in mid- and post-blanching periods. The most noticeable changes were detected in post-blanching samples. Furthermore, the best cultivar (V11E0012) was identified among them. Therefore, blanched water dropwort could be consumed for achieving more nutraceuticals and antioxidants, and cultivar V11E0012 could be recommend for blanching cultivation.

Introgression of Sub1 (SUB1) QTL in mega rice cultivars increases ethylene production to the detriment of grain- filling under stagnant flooding

In the recent time, Submergence1 (Sub1)QTL, responsible for imparting tolerance to flash flooding, has been introduced in many rice cultivars, but resilience of the QTL to stagnant flooding (SF) is not known. The response of Sub1-introgression has been tested on physiology, molecular biology and yield of two popular rice cultivars (Swarna and Savitri) by comparison of the parental and Sub1-introgression lines (SwarnaSub1 and SavitriSub1) under SF. Compared to control condition SF reduced grain yield and tiller number and increased plant height and Sub1- introgression mostly matched these effects. SF increased ethylene production by over-expression of ACC-synthase and ACC-oxidase enzyme genes of panicle before anthesis in the parental lines. Expression of the genes changed with Sub1-introgression, where some enzyme isoform genes over-expressed after anthesis under SF. Activities of endosperm starch synthesizing enzymes SUS and AGPase declined concomitantly with rise ethylene production in the Sub1-introgressed lines resulting in low starch synthesis and accumulation of soluble carbohydrates in the developing spikelets. In conclusion, Sub1-introgression into the cultivars increased susceptibility to SF. Subjected to SF, the QTL promoted genesis of ethylene in the panicle at anthesis to the detriment of grain yield, while compromising with morphological features like tiller production and stem elongation.

Comprehensive metabolomic, proteomic and physiological analyses of grain yield reduction in rice under abrupt drought-flood alternation stress

Abrupt drought-flood alternation (T1) is a meteorological disaster that frequently occurs during summer in southern China and the Yangtze river basin, often causing a significant loss of rice production. In this study, the response mechanism of yield decline under abrupt drought-flood alternation stress at the panicle differentiation stage was analyzed by looking at the metabolome, proteome as well as yield and physiological and biochemical indexes. The results showed that drought and flood stress caused a decrease in the yield of rice at the panicle differentiation stage, and abrupt drought-flood alternation stress created a synergistic effect for the reduction of yield. The main reason for the decrease of yield per plant under abrupt drought-flood alternation was the decrease of seed setting rate. Compared with CK0 (no drought and no flood), the net photosynthetic rate and soluble sugar content of T1 decreased significantly and its hydrogen peroxidase, superoxide dismutase, peroxidase activity increased significantly. The identified differential metabolites and differentially expressed proteins indicated that photosynthesis metabolism, energy metabolism pathway and reactive oxygen species response have changed strongly under abrupt drought-flood alteration stress, which are factors that leads to the rice grain yield reduction.

Genetic strategies for improving crop yields

The current trajectory for crop yields is insufficient to nourish the world's population by 20501. Greater and more consistent crop production must be achieved against a backdrop of climatic stress that limits yields, owing to shifts in pests and pathogens, precipitation, heat-waves and other weather extremes. Here we consider the potential of plant sciences to address post-Green Revolution challenges in agriculture and explore emerging strategies for enhancing sustainable crop production and resilience in a changing climate. Accelerated crop improvement must leverage naturally evolved traits and transformative engineering driven by mechanistic understanding, to yield the resilient production systems that are needed to ensure future harvests.

Genetic strategies for improving crop yields

The current trajectory for crop yields is insufficient to nourish the world's population by 2050¹. Greater and more consistent crop production must be achieved against a backdrop of climatic stress that limits yields, owing to shifts in pests and pathogens, precipitation, heat-waves and other weather extremes. Here we consider the potential of plant sciences to address post-Green Revolution challenges in agriculture and explore emerging strategies for enhancing sustainable crop production and resilience in a changing climate. Accelerated crop improvement must leverage naturally evolved traits and transformative engineering driven by mechanistic understanding, to yield the resilient production systems that are needed to ensure future harvests.

Marker Assisted Breeding to Develop Multiple Stress Tolerant Varieties for Flood and Drought Prone Areas

BACKGROUND

Climate extremes such as drought and flood have become major constraints to the sustainable rice crop productivity in rainfed environments. Availability of suitable climate-resilient varieties could help farmers to reduce the grain yield losses resulting from the climatic extremities. The present study was undertaken with an aim to develop high-yielding drought and submergence tolerant rice varieties using marker assisted introgression of qDTY1.1, qDTY2.1, qDTY3.1 and Sub1. Performance of near isogenic lines (NILs) developed in the background of Swarna was evaluated across 60 multi-locations trials (MLTs). The selected promising lines from MLTs were nominated and evaluated in national trials across 18 locations in India and 6 locations in Nepal.

RESULTS

Grain yield advantage of the NILs with qDTY1.1 + qDTY2.1 + qDTY3.1 + Sub1 and qDTY2.1 + qDTY3.1 + Sub1 ranged from 76 to 2479 kg ha- 1 and 396 to 2376 kg ha- 1 under non-stress (NS) respectively and 292 to 1118 kg ha- 1 and 284 to 2086 kg ha- 1 under reproductive drought stress (RS), respectively. The NIL, IR96322-34-223-B-1-1-1-1 having qDTY1.1 + qDTY2.1 + qDTY3.1 + Sub1 has been released as variety CR dhan 801 in India. IR 96321-1447-651-B-1-1-2 having qDTY1.1 + qDTY3.1 + Sub 1 and IR 94391-131-358-19-B-1-1-1 having qDTY3.1 + Sub1 have been released as varieties Bahuguni dhan-1' and 'Bahuguni dhan-2' respectively in Nepal. Background recovery of 94%, 93% and 98% was observed for IR 96322-34-223-B-1-1-1-1, IR 96321-1447-651-B-1-1-2 and IR 94391-131-358-19-B-1-1-1 respectively on 6 K SNP Infinium chip.

CONCLUSION

The drought and submergence tolerant rice varieties with pyramided multiple QTLs can ensure 0.2 to 1.7 t ha- 1 under reproductive stage drought stress and 0.1 to 1.0 t ha- 1 under submergence conditions with no yield penalty under non-stress to farmers irrespective of occurrence of drought and/or flood in the same or different seasons.

Rice SUB1A constrains remodelling of the transcriptome and metabolome during submergence to facilitate post-submergence recovery

The rice (Oryza sativa L.) ethylene-responsive transcription factor gene SUB1A-1 confers tolerance to prolonged, complete submergence by limiting underwater elongation growth. Upon desubmergence, SUB1A-1 genotypes rapidly recover photosynthetic function and recommence development towards flowering. The underpinnings of the transition from stress amelioration to the return to homeostasis are not well known. Here, transcriptomic and metabolomic analyses were conducted to identify mechanisms by which SUB1A improves physiological function over the 24 hr following a sublethal submergence event. Evaluation of near-isogenic genotypes after submergence and over a day of reaeration demonstrated that SUB1A transiently constrains the remodelling of cellular activities associated with growth. SUB1A influenced the abundance of ca. 1,400 transcripts and had a continued impact on metabolite content, particularly free amino acids, glucose, and sucrose, throughout the recovery period. SUB1A promoted recovery of metabolic homeostasis but had limited influence on mRNAs associated with growth processes and photosynthesis. The involvement of low energy sensing during submergence and recovery was supported by dynamics in trehalose-6-phosphate and mRNAs encoding key enzymes and signalling proteins, which were modulated by SUB1A. This study provides new evidence of convergent signalling pathways critical to the rapidly reversible management of carbon and nitrogen metabolism in submergence resilient rice.

Identification of QTLs for yield and agronomic traits in rice under stagnant flooding conditions

BACKGROUND

Stagnant flooding, where water of 25-50 cm remains until harvest time, is a major problem in rainfed lowland areas. Most of the Sub1 varieties, which can withstand around 2 weeks of complete submergence, perform poorly in these conditions. Hence, varieties tolerant of stagnant flooding are essential.

RESULTS

This paper presents the first study to map QTLs associated with tolerance to stagnant flooding, along with a parallel study under normal irrigation, using an F₇ mapping population consisting of 148 RILs derived from a cross of Ciherang-Sub1 and the stagnant-flooding tolerant line IR10F365. Phenotypic data was collected for 15 key traits under both environments. Additionally, survival rate was measured under stress conditions. Genotyping was performed using the Illumina Infinium genotyping platform with a 6 K SNP chip, resulting in 469 polymorphic SNPs. Under stress and irrigated conditions, 38 and 46 QTLs were identified, respectively. Clusters of QTLs were detected in both stress and normal conditions, especially on chromosomes 3 and 5.

CONCLUSIONS

Unique and common QTLs were identified and their physiological consequences are discussed. These beneficial QTLs can be used as targets for molecular breeding and can be further investigated to understand the underlying molecular mechanisms involved in stagnant flooding tolerance in rice.

Evolutionary analysis of the SUB1 locus across the Oryza genomes

BACKGROUND

Tolerance to complete submergence is recognized in a limited number of Asian rice (Oryza sativa L.) varieties, most of which contain submergence-inducible SUB1A on the polygenic SUBMERGENCE-1 (SUB1) locus. It has been shown that the SUB1 locus encodes two Ethylene-Responsive Factor (ERF) genes, SUB1B and SUB1C, in all O. sativa varieties. These genes were also found in O rufipogon and O nivara, wild relatives of O. sativa. However, detailed analysis of the polygenic locus in other Oryza species has not yet been made.

FINDINGS

Chromosomal location, phylogenetic, and gene structure analyses have revealed that the SUB1 locus is conserved in the long arm of chromosome 9 in most Oryza species. We also show that the SUB1A-like gene of O. nivara is on chromosome 1 and that Leersia perrieri, a grass-tolerant to deep-flooding, presents three ERF genes in the SUB1 locus.

CONCLUSION

We provide here a deeper insight into the evolutionary origin and variation of the SUB1 locus and raise the possibility that an association of these genes with flooding tolerance in L. perrieri may exist.

Transcriptomic Analysis of Gibberellin- and Paclobutrazol-Treated Rice Seedlings under Submergence

Submergence stress is a limiting factor for rice growing in rainfed lowland areas of the world. It is known that the phytohormone gibberellin (GA) has negative effects on submergence tolerance in rice, while its inhibitor paclobutrazol (PB) does the opposite. However, the physiological and molecular basis underlying the GA- and PB-regulated submergence response remains largely unknown. In this study, we reveal that PB could significantly enhance rice seedling survival by retaining a higher level of chlorophyll content and alcohol dehydrogenase activity, and decelerating the consumption of non-structure carbohydrate when compared with the control and GA-treated samples. Further transcriptomic analysis identified 3936 differentially expressed genes (DEGs) among the GA- and PB-treated samples and control, which are extensively involved in the submergence and other abiotic stress responses, phytohormone biosynthesis and signaling, photosynthesis, and nutrient metabolism. The results suggested that PB enhances rice survival under submergence through maintaining the photosynthesis capacity and reducing nutrient metabolism. Taken together, the current study provided new insight into the mechanism of phytohormone-regulated submergence response in rice.

Physiological and molecular responses of seedlings of an upland rice ('Tung Lu 3') to total submergence compared to those of a submergence-tolerant lowland rice ('FR13A')

BACKGROUND

Understanding the responses of rice to environmental stresses such as unscheduled submergence is of pressing important owing to increasing severity of weather thought to arise from global climate change. When rice is completely submerged, different types adopt either a quiescence survival strategy (i.e., minimal shoot elongation) or an escape strategy (i.e., enhanced shoot elongation). Each strategy can prolong survival depending on the circumstances. While submergence responses have been studied in rice typical of lowland and flood-prone areas, few studies have explored the physiological and molecular properties of upland rice under submergence. Here, we use seedlings of the upland rice 'Tung Lu 3' ('TL3') to analyze physiological and molecular responses to submergence. We compare them with those of 'FR13A', a lowland rice that tolerates submergence by adopting the quiescence strategy.

RESULTS

Plant height and distance between leaf sheaths, increased rapidly in 'TL3' under submergence. Although this indicated a strong escape strategy the seedlings remained totally underwater for the duration of the experiments. In contrast, 'FR13A' elongated much less. Consequently, after 4 days complete submergence followed by drainage, 'TL3' lodged much more severely than 'FR13A'. After 10 d complete submergence, 55% of 'TL3' seedlings survived compared to 100% in 'FR13A'. Chlorophyll a, b and total chlorophyll concentrations of the 2nd oldest leaves of 'TL3' were also significantly above those of 'FR13A' (but were lower than 'FR13A' in the 3rd oldest leaves) and less hydrogen peroxide accumulated in 'TL3'. Peroxidase activity in submerged 'TL3' was also greater than in 'FR13A' 1 day after submergence. Quantitative RT-PCR showed increased expression of sucrose synthase 1 and alcohol dehydrogenases 1 after 2 days complete submergence with significantly higher levels in 'TL3' compared to 'FR13A'. Expression was also higher in 'TL3' under non-submerged conditions.

CONCLUSIONS

The upland rice line 'TL3' gave a stronger elongation response than 'FR13A' to complete submergence. This escape strategy is widely considered to prejudice survival when the plant remains totally submerged. However, contrary to expectations, 'TL3' survival rates were substantial although below those for 'FR13A' while physiological, biochemical and molecular parameters linked to adaptation differed in detail but appeared to be broadly comparable. These findings highlight that submergence tolerance is determine not only by the adoption of quiescence or escape strategies but maybe by metabolic and physiological properties unrelated to the underwater elongation rate.

The buffering capacity of stems: genetic architecture of nonstructural carbohydrates in cultivated Asian rice, Oryza sativa

Harnessing stem carbohydrate dynamics in grasses offers an opportunity to help meet future demands for plant-based food, fiber and fuel production, but requires a greater understanding of the genetic controls that govern the synthesis, interconversion and transport of such energy reserves. We map out a blueprint of the genetic architecture of rice (Oryza sativa) stem nonstructural carbohydrates (NSC) at two critical developmental time-points using a subpopulation-specific genome-wide association approach on two diverse germplasm panels followed by quantitative trait loci (QTL) mapping in a biparental population. Overall, 26 QTL are identified; three are detected in multiple panels and are associated with starch-at-maturity, sucrose-at-maturity and NSC-at-heading. They tag OsHXK6 (rice hexokinase), ISA2 (rice isoamylase) and a tandem array of sugar transporters. This study provides the foundation for more in-depth molecular investigation to validate candidate genes underlying rice stem NSC and informs future comparative studies in other agronomically vital grass species.

The key regulator of submergence tolerance, SUB1A, promotes photosynthetic and metabolic recovery from submergence damage in rice leaves

The submergence-tolerance regulator, SUBMERGENCE1A (SUB1A), of rice (Oryza sativa L.) modulates gene regulation, metabolism and elongation growth during submergence. Its benefits continue during desubmergence through protection from reactive oxygen species and dehydration, but there is limited understanding of SUB1A's role in physiological recovery from the stress. Here, we investigated the contribution of SUB1A to desubmergence recovery using the two near-isogenic lines, submergence-sensitive M202 and tolerant M202(Sub1). No visible damage was detected in the two genotypes after 3 d of submergence, but the sublethal stress differentially altered photosynthetic parameters and accumulation of energy reserves. Submergence inhibited photosystem II photochemistry and stimulated breakdown of protein and accumulation of several amino acids in both genotypes at similar levels. Upon desubmergence, however, more rapid return to homeostasis of these factors was observed in M202(Sub1). Submergence considerably restrained non-photochemical quenching (NPQ) in M202, whereas the value was unaltered in M202(Sub1) during the stress. Upon reaeration, submerged plants encounter sudden exposure to higher light. A greater capability for NPQ-mediated photoprotection can benefit the rapid recovery of photosynthetic performance and energy reserve metabolism in M202(Sub1). Our findings illuminate the significant role of SUB1A in active physiological recovery upon desubmergence, a component of enhanced tolerance to submergence.

Introduction to the Special Issue: Electrons, water and rice fields: plant response and adaptation to flooding and submergence stress

Flooding and submergence impose widespread and unpredictable environmental stresses on plants and depress the yield of most food crops. The problem is increasing, as is the need for greater food production from an expanding human population. The incompatibility of these opposing trends creates an urgent need to improve crop resilience to flooding in its multifarious forms. This Special Issue brings together research findings from diverse plant species to address the challenge of enhancing adaptation to flooding in major crops and learning from tactics of wetland plants. Here we provide an overview of the articles, with attempts to summarize how recent research results are being used to produce varieties of crop plants with greater flooding tolerance, notably in rice. The progress is considerable and based firmly on molecular and physiological research findings. The article also sets out how next-generation improvements in crop tolerance are likely to be achieved and highlights some of the new research that is guiding the development of improved varieties. The potential for non-model species from the indigenous riparian flora to uncover and explain novel adaptive mechanisms of flooding tolerance that may be introduced into crop species is also explored. The article begins by considering how, despite the essential role of water in sustaining plant life, floodwater can threaten its existence unless appropriate adaptations are present. Central to resolving the contradiction is the distinction between the essential role of cellular water as the source of electrons and protons used to build and operate the plant after combining with CO2 and O2 and the damaging role of extracellular water that, in excess, interferes with the union of these gases with photosynthetic or respiratory electrons and protons.

Molecular marker assisted gene stacking for biotic and abiotic stress resistance genes in an elite rice cultivar

Severe yield loss due to various biotic stresses like bacterial blight (BB), gall midge (insect) and Blast (disease) and abiotic stresses like submergence and salinity are a serious constraint to the rice productivity throughout the world. The most effective and reliable method of management of the stresses is the enhancement of host resistance, through an economical and environmentally friendly approach. Through the application of marker assisted selection (MAS) technique, the present study reports a successful pyramidization of genes/QTLs to confer resistance/tolerance to blast (Pi2, Pi9), gall Midge (Gm1, Gm4), submergence (Sub1), and salinity (Saltol) in a released rice variety CRMAS2621-7-1 as Improved Lalat which had already incorporated with three BB resistance genes xa5, xa13, and Xa21 to supplement the Xa4 gene present in Improved Lalat. The molecular analysis revealed clear polymorphism between the donor and recipient parents for all the markers that are tagged to the target traits. The conventional backcross breeding approach was followed till BC3F1 generation and starting from BC1F1 onwards, marker assisted selection was employed at each step to monitor the transfer of the target alleles with molecular markers. The different BC3F1s having the target genes/QTLs were inter crossed to generate hybrids with all 10 stress resistance/tolerance genes/QTLs into a single plant/line. Homozygous plants for resistance/tolerance genes in different combinations were recovered. The BC3F3 lines were characterized for their agronomic and quality traits and promising progeny lines were selected. The SSR based background selection was done. Most of the gene pyramid lines showed a high degree of similarity to the recurrent parent for both morphological, grain quality traits and in SSR based background selection. Out of all the gene pyramids tested, two lines had all the 10 resistance/tolerance genes and showed adequate levels of resistance/tolerance against the five target stresses. The study demonstrates the potential of MAS for stacking of several genes into a single line with a high degree of parental genome recovery.