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In lowland rice ecosystems stagnant flooding or partial submergence has a significant negative impact on important yield attributing traits resulting in substantial grain yield reduction. Genetics of this stress is not yet studied intensively. Rashpanjor (IC 575321), a landrace from India, was identified and used as the tolerant donor for stagnant flooding and was crossed with high yielding variety Swarna to develop the RIL population for the present investigation. Yield and yield attributing traits of 180 F(2:8) lines in rainfed non-stressed and stressed (stagnant flooding with 45 ± 5 cm standing water) conditions were recorded in the wet season of 2018 and stress susceptibility and tolerance indices of yield component traits were deduced. Homo-polymorphic high-quality SNPs between two parents derived from genotyping by sequencing were employed and 17 putative QTLs for plant height, shoot elongation, panicle number, grain weight, panicle length in control and stagnant flooding conditions were identified. Tolerance and susceptibility indexes for these traits were detected in chromosomes 1, 3, 4, 5, 6, 10, 11, and 12 with PVE ranging from 6.53 to 57.89%. Two major QTLs clusters were found for stress susceptibility index of grain and panicle weight on chromosome 1 and plant height in non-stress condition and stress tolerance index of elongation ability on chromosome 3. Putative functional genes present either in associated non-synonymous SNPs or inside the QTL regions were also predicted. Some of them were directly associated with ethylene biosynthesis and encoding auxin responsive factors for better adaptation under stagnant flooding and also coded for different transcription factors viz. NAC domain-binding protein, WRKY gene family, and MYB class known for ROS scavenging and production of metabolites to enhance tolerance to stagnant flooding. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-021-01107-x.

Plant's response to fresh- and saline-water flooding and the resulting partial submergence, seems different due to the added complexities of element toxicity of salinity. We identified a few rice genotypes which can tolerate combined stresses of partial submergence and salinity during saline water flooding. To gain mechanistic insights, we compared two rice genotypes: Varshadhan (freshwater-flooding tolerant) and Rashpanjor (both fresh- and saline-water flooding tolerant). We found greater ethylene production and increased "respiratory burst oxidase homolog" (RBOH)-mediated reactive oxygen species (ROS) production led to well-developed constitutive aerenchyma formation in Rashpanjor, which makes it preadapted to withstand fresh- and saline-water flooding. On the contrary, an induced aerenchyma formation-dependent tolerance mechanism of Varshadhan worked well for freshwater flooding but failed to provide tolerance to saline-water flooding. Additional salt stress was found to significantly inhibit the induced aerenchyma formation process due to the dampening of ROS signaling by the action of metallothionein in Varshadhan. Besides, inconspicuous changes in ionic regulation processes in these two genotypes under saline-water flooding suggest preadapted constitutive aerenchyma formation plays a more significant role than elemental toxicity per se in tolerating combined stresses encountered during saline water flooding in rice. Overall, our study indicated that well-developed constitutive aerenchyma provide an adaptive advantage during partial submergence due to saline water flooding in rice as the key process of induced aerenchyma formation is hampered in the presence of salinity stress coupled with partial submergence.

Rice is highly sensitive to salt stress at flowering stage. With the objective of detection of quantitative trait loci (QTLs) in multi-environment for this stage, 180 backcross-derived lines (BC3F5) from salt tolerant donor Pokkali (AC41585) and recurrent parent IR 64 were subjected to evaluation in saline (EC = 8 dSm−1) and non-saline environments in wet season of 2014 and 2015 employing a novel phenotyping protocol. Nine multi-environmental consistent QTLs for spikelet degeneration, K+ concentration in flag leaf, stress susceptibility index for grain (SSI-Grain) and spikelet sterility (SSI-STE) on chromosomes1, 2, 3, 4 and 11 with 17–42% phenotypic variances were detected. Among several digenic epistatic interactions, one was associated with the main effect QTL (qSSI-STE-11-1) over the years. Similarly genotype × environment interaction associated with two additive QTLs, qDEG-S-2-2 and qSSI-STE-2-1 had positive effect on the resultant phenotype. Functional genes encoding calmodulin-binding protein and potassium transporter were predicted inside the consistent QTLs. Detected stable QTLs, associated markers, predicted genes and derived introgression lines with these QTLs could be utilized in future breeding programme.

In this investigation, an attempt was made to identify quantitative trait locus (QTL)/gene associated with JIP-test parameters in rice. Thirty main effect additive QTLs (M-QTLs) along with more than 500 digenic epistatic QTLs were detected using a backcross-derived population from tolerant genotype Pokkali (AC41585) and the susceptible counterpart IR64. These M-QTLs were located in almost all the chromosomes except chromosome number 6 and 8. Most of the M-QTLs showed pleiotropic effects. Positional similarity of all these overlapping additive and additive × additive interaction, QTLs indicated the substantial resemblance of the genetic basis of many JIP-test parameters which imparted salinity tolerance in rice at the seedling stage. Twenty-three potential functional genes were also delineated inside these additive QTLs regions. The identified putative QTLs for JIP-test parameters and probable functional genes lying therein are useful for imparting greater photosynthetic potential in rice under salt stress.

Stagnant flooding (SF) is a serious threat for rice production in rainfed lowland areas of Southeast Asian countries. To overview the SF effect, photosynthetic performances and productivity were studied with three landraces (Ravana, Kamini, and Rashpanjor) and four high-yielding cultivars (Savitri, Savitri-Sub1, Gayatri, and Varshadhan) of rice under medium depth (40-50 cm) of water level. Stagnant flooding significantly increased the stem elongation and decreased yield and yield attributing parameters. The chlorophyll a fluorescence rises from O- to P-step with distinct J- and I-step were noticed in all the cultivars up to 75 d of SF. Prolonged flooding (> 2 months) perturbed both donor and acceptor side of PSII. Vitality indices (PIABS and PITOT) decreased greatly under prolonged SF. Analysis of O-J-I-P transients suggests that the information is useful for agricultural planning with the purpose to enhance rice yield under lowland medium depth SF.

The present study shows that salt tolerance in the reproductive stage of rice is primarily governed by the selective Na+ and K+ transport from the root to upper plant parts. Ionic discrimination at the flag leaf, governed by differential expression of Na+- and K+-specific transporters/ion pumps, is associated with reduced spikelet sterility and reproductive stage salt tolerance. Reproductive stage salt tolerance is crucial in rice to guarantee yield under saline condition. In the present study, differential ionic selectivity and the coordinated transport (from root to flag leaf) of Na+ and K+ were investigated to assess their impact on reproductive stage salt tolerance. Four rice genotypes having differential salt sensitivity were subjected to reproductive stage salinity stress in pots. The selective Na+ and K+ transport from the root to upper plant parts was observed in tolerant genotypes. We noticed that prolonged salt exposure did not alter flag leaf greenness even up to 6 weeks; however, it had a detrimental effect on panicle development especially in the salt-susceptible genotype Sabita. But more precise chlorophyll fluorescence imaging analysis revealed salinity-induced damages in Sabita. The salt-tolerant genotype Pokkali (AC41585), a potential Na+ excluder, managed to sequester higher Na+ load in the roots with little upward transport as evident from greater expression of HKT1 and HKT2 transporters. In contrast, the moderately salt-tolerant Lunidhan was less selective in Na+ transport, but possessed a higher capacity to Na+ sequestration in leaves. Higher K+ uptake and tissue-specific redistribution mediated by HAK and AKT transporters showed robust control in selective K+ movement from the root to flag leaf and developing panicles. On the contrary, expressions of Na+-specific transporters in developing panicles were either down-regulated or unaffected in tolerant and moderately tolerant genotypes. Yet, in the panicles of the susceptible genotype Sabita, some of the Na+-specific transporter genes (SOS1, HKT1;5, HKT2;4) were upregulated. Apart from the ionic regulation strategy, cellular energy balance mediated by different plasma-membrane and tonoplastic H+-pumps were also associated with the reproductive stage salt tolerance in rice.

Background and Aims Submergence tolerance in rice is primarily attributed to the action of the SUB1 gene, but other associated traits such as leaf gas film (LGF) thickness, leaf hydrophobicity, porosity and leaf density have been known to aid submergence tolerance in rice. However, association of these traits with SUB1 quantitative trait locus (QTL) has not been demonstrated. In this study, we aim to investigate (1) whether the presence of the SUB1 QTL in the genetic background has any influence on the thickness of the LGF and (ii) whether its removal has any impact on stress perception and submergence tolerance in Sub1 and non-Sub1 rice. Methods We examined 12 genotypes (including both Sub1 and non-Sub1 types) for different leaf traits such as initial LGF thickness, leaf hydrophobicity, tissue porosity and leaf density in order to work out the relatioship of these traits to the SUB1 QTL in rice. Furthermore, we investigated the changes in the gene expression profile and different metabolic processes in selected genotypes in the presence and absence of their LGF to study its impact on stress perception and adaptation. Key Results The initial thickness of the LGF and hydrophobicity seemed to have a highly positive correlation with the presence of the SUB1 QTL in the genetic background of rice; however, other leaf traits such as porosity and density seemed to be independent of it. Artificial removal of the LGF resulted in partial loss of tolerance, showing increased ethylene production and early induction of anoxia-related genes (SUB1A-1, ACS5, Ramy3D and ADH1) which manifested symptoms such as increased stem elongation, faster chlorophyll and starch breakdown, and partial loss of quiescence in SUB1-containing rice genotypes. Stripping of the LGF resulted in early and enhanced induction of SUB1A-1, indicating a quicker perception of stress. Conclusions The presence of SUB1 in the genetic background positively influences surface hydrophobicity and the concomitant LGF thickness of rice. Furthermore, LGF helps in terms of providing better ethylene dissipation and reduced in planta accumulation, owing to the slowing down of ethylene-induced leaf senescence under submergence stress.

Salinity is one of the major constraints in rice production. To date, development of salt-tolerant rice cultivar is primarily focused on salt-exclusion strategies, which incur greater energy cost. The present study aimed to evaluate a balancing strategy of ionic discrimination vis-a-vis tissue tolerance, which could potentially minimize the energy cost of salt tolerance in rice. Four rice genotypes, viz., FL478, IR29, Kamini, and AC847, were grown hydroponically and subjected to salt stress equivalent to 12 dS m-1 at early vegetative stage. Different physiological observations (leaf chlorophyll content, chlorophyll fluorescence traits, and tissue Na+ and K+ content) and visual scoring suggested a superior Na+-partitioning strategy operating in FL478. A very low tissue Na+/K+ ratio in the leaves of FL478 after 7 days of stress hinted the existence of selective ion transport mechanism in this genotype. On the contrary, Kamini, an equally salt-tolerant genotype, was found to possess a higher leaf Na+/K+ ratio than does FL478 under similar stress condition. Salt-induced expression of different Na+ and K+ transporters indicated significant upregulation of SOS, HKT, NHX, and HAK groups of transporters in both leaves and roots of FL478, followed by Kamini. The expression of plasma membrane and vacuolar H+ pumps (OsAHA1, OsAHA7, and OsV-ATPase) were also upregulated in these two genotypes. On the other hand, IR29 and AC847 showed greater salt susceptibility owing to excess upward transport of Na+ and eventually died within a few days of stress imposition. But in the "leaf clip" assay, it was found that both IR29 and Kamini had high tissue-tolerance and chlorophyll-retention abilities. On the contrary, FL478, although having higher ionic-discrimination ability, showed the least degree of tissue tolerance as evident from the LC50 score (amount of Na+ required to reduce the initial chlorophyll content to half) of 336 mmol g-1 as against 459 and 424 mmol g-1 for IR29 and Kamini, respectively. Overall, the present study indicated that two components (ionic selectivity and tissue tolerance) of salt tolerance mechanism are distinct in rice. Unique genotypes like Kamini could effectively balance both of these strategies to achieve considerable salt tolerance, perhaps with lesser energy cost.

Submergence during germination imposes germination stage oxygen deficiency (GSOD). Natural variation in anaerobic germination potential (AGP), manifested by their differences in GSOD tolerance, is available in rice. Present study was performed to understand differential responses of two rice cultivars, Naveen and AC41620 (susceptible and tolerant to GSOD, respectively) subjecting them to 48-h continuous submergence during germination. Transcriptome analysis revealed more elaborate regulation of gene expression in AC41620 compared to Naveen. Validation of transcriptome data through q-PCR of selected genes and biochemical analysis related to carbohydrate metabolism, anaerobic respiration and oxidative stress tolerance were more significant in AC41620, than Naveen. The time-course enzyme assays for continued submergence suggested that the activity of α-amylase, pyruvate decarboxylase and alcohol dehydrogenase increased under continuous submergence. Efficient nitrogen metabolism supported by increased nitrate and nitrite reductase activities and better handling of reactive oxygen species (ROS) because of increased antioxidant enzyme activities were found to be associated with GSOD in AC41620. Increased ethylene production along with action of ABA, GA and G-proteins aided in GSOD tolerance of AC41620. The differentially expressed genes identified in the present study will serve as a useful genomic resource for extending our understanding of molecular mechanism of anaerobic germination vis-a-vis GSOD tolerance in rice.

The activities of starch hydrolyzing enzymes and phosphatases were studied in seedlings of three Indica rice (Oryza sativa L.) cultivars, namely Panikekoa & T 1471 that showed good capacity for seedling establishment under submergence (tolerant) and IR 42 which had poor under water seedling establishment capacity (susceptible). Under submergence the total amylolytic activities were significantly higher in susceptible cultivars compared to the tolerant cultivars. Likely, the activities of α-amylase, debranching enzymes and α-glucosidase were also higher in susceptible cultivar IR 42. The activities of starch phosphorylase were comparatively higher in tolerant cultivars than susceptible cultivars. Susceptible cultivars maintained higher activities of both acid and alkaline phosphatase as well as phytase activities. Tolerant cultivars with higher seed biomass and low activity of hydrolytic enzymes might sustain the supply of food materials for longer period and hence, survived and established themselves under water.

Stagnant flooding (SF) is an important constraint which prolonges partial submergence damages of rice plants and reduces grain yield. Due to the heterogeneity in flood-prone ecosystem, many different types of traditional rice varieties are being grown by the farmers. The local landraces adapted to extreme in water availability could be the sources of new gene(s) which would be utilized to improve the adaptability of rice to SF with high yield. The main goal of this study is to identify new genetic resources tolerant to SF based on morpho-physiological traits. A total of 16 rice varieties were selected after initial screening from more than 400 rice varieties which were collected from eastern states of India. The increase rate of plant height was higher under SF compared to control, whereas no such trend was observed in the increment rate of aboveground total dry weight and culm dry weight. Area of aerenchyma gas spaces per tiller increased whereas root oxidase activity decreased under SF. The reduction of root oxidase activity, leaf area, and leaf dry weight was higher in susceptible varieties under SF compared to control. Stability index for different grain yield and yield attributes revealed that the impact of SF differed among different varieties. Correlation coefficient studies among different parameters taking stability index showed significant association with the grain yield. Based on the findings, it was concluded that maintenance of equivalent panicle weight and panicle number, plant height and harvest index at the maturity stage, leaf area, leaf and culm dry weights, root oxidase activity and tiller numbers at the flowering stage under SF compared to control help the plant to counteract the adverse effects of SF.

Plants experience multiple abiotic stresses during the same growing season. The implications of submergence with and without saline water on growth and survival were investigated using four contrasting rice cultivars, FR13A (submergence-tolerant, salinity-susceptible), IR42 (susceptible to salinity and submergence), and Rashpanjor and AC39416 (salinity-tolerant, submergence-susceptible). Though both FR13A and IR42 showed sensitivity to salinity, FR13A exhibited higher initial biomass as well as maintained greater dry mass under saline condition. Greater reduction of chlorophyll (Chl) contents due to salinity was observed in the susceptible cultivars, including FR13A, compared to the salinity-tolerant cultivars. Exposure of plants to salinity before submergence decreased the survival chance under submergence. Yet, survival percentage under submergence was greater in FR13A compared to other cultivars. Generally, the reduction in the Chl content and damage to PSII were higher under the submergence compared to salinity conditions. The submergence-tolerant cultivar, FR13A, maintained greater quantities of Chl during submergence compared to other cultivars. Quantification of the Chl a fluorescence transients (JIP-test) revealed large cultivar differences in the response of PSII to submergence in saline and nonsaline water. The submergence-tolerant cultivar maintained greater chloroplast structural integrity and functional ability irrespective of the quality of flooding water.

Bacterial leaf blight (BLB) is a serious threat for rice (Oryza sativa L.) cultivation caused by the bacterial pathogen Xanthomonas oryzae pv. oryzae. The pathogen mainly damages the leaf chlorophyllous tissue, resulting in poor photosynthesis and causing up to 50% reductions in grain yield. In the present work, we have compared the structural and functional ability of the chloroplast of three varieties of rice with different degrees of susceptibility (TN1, highly susceptible; IR-20, moderately resistant; DV-85, resistant to BLB) treated with riboflavin (1 and 2 mM) and infected with BLB, with chlorophyll fluorescence as a tool. As indicated by the chlorophyll fluorescence technique, the disease progress curve and yield data, riboflavin acted as an effective vitamin for inducing resistance against BLB. Plants treated with riboflavin showed improved PSII activity, more chlorophyll content and higher yield than the diseased plants.

The present study reports an unequivocal and improved protocol for efficient screening of salt tolerance at flowering stage in rice, which can aid phenotyping of population for subsequent identification of QTLs associated with salinity stress, particularly at reproductive stage. To validate the new method, the selection criteria, level and time of imposition of stress; plant growth medium were standardized using three rice genotypes. The setup was established with a piezometer placed in a perforated pot for continuous monitoring of soil EC and pH throughout the period of study. Further, fertilizer enriched soil was partially substituted by gravels for stabilization and maintaining the uniformity of soil EC in pots without hindering its buffering capacity. The protocol including modified medium (Soil:Stone, 4:1) at 8 dS m(−1) salinity level was validated using seven different genotypes possessing differential salt sensitivity. Based on the important selection traits such as high stability index for plant yield, harvest index and number of grains/panicle and also high K(+) concentration and low Na(+)– K(+) ratio in flag leaf at grain filling stage were validated and employed in the evaluation of a mapping population in the modified screening medium. The method was found significantly efficient for easy maintenance of desired level of soil salinity and identification of genotypes tolerant to salinity at reproductive stage. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12298-018-0591-7) contains supplementary material, which is available to authorized users.

Chlorophyll a fluorescence (ChlF) parameters measured with fluorescence imaging techniques were used to investigate the combined effect of salt and partial submergence stress to understand photosynthetic performance in rice (Oryza sativa L.). ChlF parameters such as maximal fluorescence (Fm), variable fluorescence (Fv=Fm –F0), the maximal photochemical efficiency of PSII (Fv/Fm) and the quantum yield of nonregulated energy dissipation of PSII (Y(NO)) were able to distinguish genotypes precisely based on their sensitivity to stress. Upon analysis, we found the images of F0 were indistinguishable among the genotypes, irrespective of their tolerance to salt and partial submergence stress. On the contrary, the images of Fm and Fv/Fm showed marked differences between the tolerant and susceptible genotypes in terms of tissue greenness and the appearance of dark spots as stress symptoms. The images of effective PSII quantum yield, the coefficient of nonphotochemical quenching (qN) and the coefficient of photochemical quenching (qP) captured under different PAR were able to distinguish the tolerant and susceptible genotypes, and were also quite effective for differentiating the tolerant and moderately tolerant ones. Similarly, the values of electron transport rate, qN, qP and Y(NO) were also able to distinguish the genotypes based on their sensitivity to stress. Overall, this investigation indicates the suitability of chlorophyll fluorescence imaging technique for precise phenotyping of rice based on their sensitivity to the combined effect of salt and partial submergence.

The impact of submergence on the photosynthesis and antioxidant capacities in three Indica rice cultivars namely FR 13A, IR 42, and Sabita having differential response to flooding were examined under 8 days (d) of complete submergence and subsequent re-aeration for 24 h. All upon three genotypes showed inhibition of CO2 photosynthetic rate due to complete submergence; this was accompanied with the decrease in the Rubisco activity, stomatal conductance (gs), and leaf chlorophyll (Chl) content. These parameters decreased further after 24 h of re-aeration. The decrease was more pronounced in sensitive cultivar, IR 42, and elongating type cultivar, Sabita. Sensitivity of elongating type cultivar under complete submergence was alike to submergence sensitive type cultivar. The activities of antioxidant enzymes such as superoxide dismutase, catalase, guaiacol peroxidase, ascorbate peroxidase, dehydroascorbate reductase, and glutathione reductase and levels of ascorbate were found to be significantly high in tolerant cv. FR 13A during submergence and subsequent re-aeration period. This study indicates that the suppression of CO2 photo-assimilation under submergence was not only due to decrease of gs and leaf chlorophyll content but mainly due to the inhibition of rubisco activity. A greater protection of the photosynthetic system was observed through antioxidant system, since the degree of protection was more, when the levels of ascorbate and the activities of antioxidant enzymes were high.

To keep pace with ever growing global population, progressive and sustained increase in rice production is necessary, especially in areas with extremely variable climatic conditions, where rice crop suffers from numerous abiotic stresses including salinity. Designing an effective phenotyping strategy requires thorough understanding of plant survival under stress. The investigation was carried out with four rice cultivars namely FR13A, IR42, Rashpanjor, and Pokkali that differed in salinity tolerance. The study showed that a genotype with initial vigour had some advantage in preserving shoot biomass under salt stress. Though both FR13A and IR42 showed sensitivity to salinity, FR13A with higher initial biomass maintained greater dry weight under saline condition. Increase of Na+:K+ ratio under salinity, due to accelerated absorption of Na+ and lesser absorption of K+ compared to control, was considerably higher in susceptible (118–200 %) than in tolerant (33–48 %) genotypes. While Na+ concentration in shoot increased significantly in both tolerant and susceptible genotypes, decrease in shoot K+ content was noticed only in susceptible genotypes. The imbalance of Na+ and K+ contents led to increased H2O2 production, causing greater peroxidation of membrane lipids and reduction in chlorophyll content and CO2 photosynthetic rate. Certain chlorophyll fluorescence parameters could distinguish between salinity tolerant and sensitive genotypes. To protect the plant from oxidative damage, several enzymatic and nonenzymatic antioxidants such as ascorbate were involved. The genotypes with capacity to assemble antioxidant enzymes in time could detoxify the reactive oxygen species more efficiently, leading to greater protection and reduced impact of salt stress.

Nonstructural carbohydrate (NSC) accumulation in submergence tolerant rice cultivars (cv) was studied in six Indica rice [Oryza sativa (L.)] cv under control and simulated submerged conditions. Tolerant cultivars accumulated greater contents of NSC compared to the susceptible cultivars. Starch and total NSC content showed significant positive association with survival percentage. On the other hand, elongation due to submergence was significantly a negative association with survival. The CO2 photosynthetic rate, chlorophyll content, maximum photochemical efficiency of PS II (Fv/Fm), and activities of Rubisco were not significantly different between tolerant and susceptible cv under control condition. The ADP glucose pyrophosphorylase (AGPPase) activity was significantly higher in the tolerant cv and was a positive association with starch/NSC, whereas Fructose 1,6-diphosphatase (FDPase) activity was significantly higher in susceptible cv compared to tolerant cv and was a negative association with starch/NSC...

Rice (Oryza sativa) is probably the most important crop to ensure world's food security. Adapted to semi-aquatic ecology, it has got an innate ability to tolerate submergence to some extent. Nevertheless, long period of submergence invites unavoidable negative consequences starting from yield and quality reduction of the produce to complete crop failure. Under submergence plants are deprived of oxygen either completely (anoxia) or partially (hypoxia) which is well-recognized as a potent abiotic stress factor. Significant research efforts have been directed globally toward understanding the mechanism of submergence tolerance particularly during vegetative stage of rice; as the crop frequently encounters flash flood or water stagnation after transplanting and during its initial growth stage. Thanks to these scientific endeavors which resulted in identification, cloning, characterization, and deployment of genes like SUB1 (Xu et al., 2006; imparts quiescence during submergence) and SNORKEL1 and SNORKEL2 (Hattori et al., 2009; induce quick elongation of internodes) which help rice plants either to tolerate or to escape submergence during its vegetative growth stage. However these genes, unfortunately, have little or no consequences when seed germination under submergence is concerned. Seed germination under oxygen deprived condition is gradually becoming an area of active research owing to the shifting trend of direct seeding by abandoning traditional transplanting method, in order to intensify as well as economize rice cultivation (Kumar and Ladha, 2011). Though, direct seeding can potentially reduce cultivation cost, it also makes the crop vulnerable to the fluctuations of monsoon rains which are quite frequent in South and South-East Asia (the rice bowl of the world) dominated by low land rain-fed ecosystem. Unpredicted heavy downpour immediately after direct seeding can call upon flash flood. Low land situation can also result in continuous water stagnation for several days. Stagnant water can condition typical stress situation by restricting free diffusion of oxygen from air to germinating seeds (Narsai et al., 2015). But grossly being adapted to aquatic ecology, rice has developed the unique mechanism to germinate and elongate its coleoptile under water (nearly at the rate of 1 mm h−1) even in complete absence of oxygen (Magneschi and Perata, 2009; Narsai et al., 2015)—a phenomenon termed as anaerobic germination (AG). However, anaerobic germination potential (AGP) varies greatly among different rice cultivars which ultimately provide an edge to a few cultivars to perform better under oxygen deprived conditions over others. In recent literatures, the rice cultivars having better germination potential under oxygen deprived condition and hence are capable of withstanding the stress have been deemed as anaerobic germination tolerant, while the cultivars having the contrasting character have been termed as anaerobic germination susceptible (Angaji et al., 2010; Baltazar et al., 2014; Kretzschmar et al., 2015). Since, this is an upcoming area of research, it is necessary to set the terminologies right at the very beginning as once established these terminologies will stand for future and can even percolate and perpetuate in related field of studies. In this article, we would try to critically analyze the aptness of the terminologies used so far by logical arguments and present our view where we feel a need for change/rectification.

The influence of submergence on photosynthesis and antioxidant capacities in rice varieties Swarna and Swarna-Sub1 with or without Sub1 QTL were evaluated under control, simulated complete submergence and subsequent re-aeration. The leaf photosynthetic rate and stomatal conductance decreased in the both varieties during the progression of submergence as compared to the control plants, but significant varietal differences were observed after 1 d of submergence. Submergence also altered the PSII activity, as reflected in a decrease in the values of Fo, Fm and Fv/Fm and degradation of chlorophyll, more in Swarna than in Swarna-Sub1. During early submergence period, the activities of superoxide dismutase (SOD), ascorbate peroxidase (APX), dehydroascorbate reductase (DHAR), glutathione reductase (GR) against reactive oxygen species were increased in the both varieties. However, with the progress of submergence period (after 7 d), the activities of SOD, catalase (CAT), APX, guaiacol peroxidase (GPX), GR and DHAR declined, more in Swarna than in Swarna-Sub1. During re-aeration, Swarna-Sub1 showed significant increase of above antioxidant enzymes but not in Swarna. Swarna-Sub1 improves photosynthetic activity, showing higher photosynthetic rate compared to Swarna under submergence and subsequent re-aeration because of less degradation of chlorophyll, higher stomatal conductance, and efficient PSII activity along with better antioxidant protection from oxidative damage.

Flash floods adversely affect rice productivity in vast areas of rainfed lowlands in South and Southeast Asia and tropical Africa. Tolerant landraces that withstand submergence for 1–2 weeks were identified; however, incorporation of tolerance into modern high-yielding varieties through conventional breeding methods has been slow because of the complexity of both the tolerance phenotype and floodwater conditions, and the ensuing discrepancies encountered upon phenotyping in different environments. Designing an effective phenotyping strategy requires a thorough understanding of the specific floodwater characteristics that most likely affect survival during flooding. We investigated the implications of floodwater temperature and light penetration, caused by artificial shading, seasonal variation, or water turbidity, for seedling survival after submergence. Three field experiments were conducted using rice genotypes contrasting in their tolerance of submergence: FR13A and Kusuma (tolerant); Gangasiuli (intermediate); Sabita, CRK-2-6 and Raghukunwar (elongating/avoiding types); and IR42 (sensitive). We tested the hypotheses that warmer floodwater decreases plant survival and that turbid water augment plant mortality by causing effects similar to those caused by shading, by reducing light penetration. Plants survive better when water is cooler, and survival decreased at about 8% per unit increase in water temperature above 26 °C. Lower intensity of light and warmer temperatures seem to reduce biomass and increase mortality under flooding. An increase in the concentrations of O2 and CO2 and a decrease in water pH did not improve survival in clear unshaded water. Turbid floodwater was more damaging to rice as plant mortality increased as the percentage of silt increased, and the effects of water turbidity cannot be explained by the reduction in light penetration alone. Even the most tolerant rice cultivar, FR13A, experienced higher mortality when flooded with turbid floodwater. Correlation studies revealed that cultivars with the capacity to maintain higher biomass, higher chlorophyll, and non-structural carbohydrate concentrations after submergence had higher survival. These findings help to understand the variation observed in submergence tolerance when screening is done under different environments. The study could have implications for designing proper screening strategies and assessing the damage submergence causes across different rice-growing regions.

ADPglucose pyrophosphorylase (AGP) and sucrose synthase (SS) are important enzymes in starch biosynthesis pathway of rice endosperm. In this work we test the hypothesis that difference in individual grain weight among rice cultivars or within a cultivar is directly related to the variation in activities of these enzymes and hormonal manipulation of enzyme activity can enhance grain yield. One potential mechanism for yield increases is that reduction of ethylene concentration at anthesis may improve assimilates partitioning to grains and increases its weight. In the experiment, three indica rice cultivars differing in grain size and weight were grown in the field conditions during the dry season of 2007. Dry matter growth, rate of division of endosperm cells, starch and sugar concentrations as well as AGP and SS activities of endosperm and ethylene evolution of spatially separated developing spikelets of panicle of the three cultivars were measured during the early part of grain filling period. Growth and cell division rates as well as activities of enzymes were higher in a big sized seed compared to a small sized seed in sequel to the difference in either cultivars or position on the panicle axis. Growth and enzyme activities correlated negatively with ethylene concentration. It is concluded that seed weight of inferior spikelets can be improved in rice panicle by increasing activities of starch synthesizing enzymes through manipulation of ethylene production, while cultivar difference in seed weight remains beyond the purview of such manipulations.

Regeneration capacity of submerged rice (Oryza sativa) seedlings in terms of CO2 photosynthetic rate, chlorophyll a fluorescence and chlorophyll and carbohydrate content were investigated in three Indica rice cultivars namely FR 13A, Kalaputia and IR 42 that differed in submergence tolerance. Twenty-one day old plants were completely submerged under water for 8 days. Subsequently, plants were kept under normal conditions with 5–10 cm of stagnant water above soil surface for a further period of 15 days. After complete submergence, all genotypes showed inhibition of CO2 photosynthetic rate. Submergence treatment resulted in a significant reduction of Rubisco activity. Maximal photochemical efficiency (Fv/Fm) of PS II and area above the fluorescence curve between Fo and Fm decreased more under submergence especially in susceptible cultivar IR 42. When re-aerated, the plants recovered to various degrees. The carbohydrate content of plants was found to be significantly and positively associated with submergence tolerance and regeneration growth. The tolerant cultivar (FR 13A) could survive submergence apparently because it possessed 1.9–2.0 and 3.2–3.7-fold more non-structural carbohydrate content before and after submergence compared to the susceptible cultivar (IR 42) and it had a better capability to restore its photosynthetic capacity during post-submergence periods.

The effects of submergence on chlorophyll (Chl) a fluorescence were compared in seven Oryza sativa (L.) cultivars, namely FR 13A, Khoda, Khadara, Kalaputia (tolerant), Sabita, and Hatipanjari (avoiding type), and IR 42 (susceptible). Seedlings were submerged for 4 d under complete darkness. Oxygen concentration of flood water decreased with the period of submergence with concomitant increase in concentration of carbon dioxide. Submergence caused diminution in the amount of total Chl. Genotypic differences were observed for Chl content and survival percentage. Quantification of the Chl a fluorescence transients (JIP-test) revealed large cultivar differences in the response of photosystem 2 (PS2) to submergence. The kinetics of Chl a fluorescence rise showed complex changes in the magnitudes and rise of O-J, J-I, and I-P phases caused by submergence. The selective suppression of the J-I phase of fluorescence especially after 2 d of submergence provided evidence for weakened electron donation from the oxygen evolving complex whereas under severe submergence stress (4 d) both O-J and J-I steps were suppressed greatly with highly suppressed P-step, which resulted in lowering of variable fluorescence. Grouping probability or energetic connectivity between PS2 obtained through JIP-test from the data after 2 d of submergence showed a direct relation with survival percentage, i.e. fluorescence measurements contained the information of the survival chance of a plant under submerged conditions. The information could be used in identifying the submergence tolerant cultivars when the damage is not very severe.

Flash flooding adversely affects rice productivity in vast areas of rainfed lowlands in South and Southeast Asia. Tolerant genotypes were identified and key traits such as high levels of non-structural carbohydrates (NSC, starch and soluble sugars) and limited underwater elongation were found to be associated with tolerance. In this study, we evaluated the role of NSC before and after submergence and shoot elongation during submergence in submergence tolerance using genotypes that contrast in initial NSC content and elongation ability during submergence. The traits were further manipulated using a growth promoter, GA3, and a potent gibberellin synthesis inhibitor, paclobutrazol (PB). Submergence for 10 days resulted in higher mortality of IR42 (intolerant), followed by Sabita and Hatipanjari. The latter two cultivars have a high initial NSC similar to that of the tolerant cultivar, FR13A, but elongated to higher extent under water. Exogenous GA3 enhanced underwater elongation and depletion of NSC and reduced survival. Conversely, PB suppressed elongation, improved the retention of NSC and enhanced survival. FR13A is less responsive to PB but more responsive to GA, suggesting its inherently low GA concentration under submergence. Underwater elongation is associated with NSC consumed during submergence but not with NSC level before submergence. Seedling survival showed a stronger association with NSC maintained after submergence (r2 = 0.74) than with NSC before submergence (r2 = 0.27). This suggests that carbohydrates maintained after submergence, being the result of both initial level, and the level used during submergence, is more important for survival.

Significant yield reduction was recorded at flowering stage in rice varieties under salinity stress. But due to high genotype x environment interaction (GEI) the adaptability of the salt tolerant elite lines is generally poor. The identified source of tolerance, AC41585, was used in developing a backcross population. One hundred eighty BC3F4 lines were evaluated under stress (EC 8dSm−1) and non-stress conditions in net-house during the years 2012 and 2013. Under salinity stress plant yield was observed to be associated positively with the number of panicles/plant, panicle length, harvest index and negatively with the percentage of spikelet sterility and degeneration. Genotypes such as, L-41, L-45, L-112, L-171, L-192 with low IPCA and higher mean were identified with general adaptability through AMMI analysis. In addition, ‘which-won-where’ pattern of GGE Biplot detected L-192 and L-41 as highest performing genotypes in saline and non-saline environments, respectively. Both the analyses identified stable introgression line L-171 with high yield stability index having phenotypic similarity with recurrent parent, IR 64. The elite lines selected through the present study could be used in rice breeding and also to investigate the molecular basis of salt tolerance at reproductive stage.

An experiment was conducted on the three indica rice (Oryza sativa L.) cultivars IR 42, CR 383-10 and FR 13A, which are susceptible to submergence, submergence-avoiding and tolerant to submergence, respectively. A deleterious effect of submergence was noted as both above-ground dry matter accumulation and chlorophyll content decreased during submergence and subsequent re-aeration. However, the rate of reduction was lower in the tolerant cultivar. The tolerant cultivar FR 13A maintained higher dry weight during submergence and subsequent re-aeration and accumulated lower proline and malondialdehyde contents than the other cultivars. The activities of the enzymes catalase, peroxidase and superoxide dismutase, expressed on a per g fresh weight of leaves basis, were higher in FR 13A than in the other cultivars, both under water and 24 h after the initiation of re-aeration. However, ascorbic acid oxidase activity was lower in FR 13A. The cultivar CR 383-10, which has the capacity to accumulate more above-ground dry matter under normal conditions, showed a greater elongation ability under submergence and was similar to the susceptible cultivar IR 42 in terms of enzyme activities and the other parameters investigated during submergence and subsequent re-aeration. Anderungen antioxydativer Enzyme und Wachstumsparameter in Anhangigkeit von vollstandiger Uberflutung und darauf folgender Zurucknahme bei Reis-Kultivaren mit unterschiedlicher Uberflutungstoleranz Das Experiment wurde mit drei indischen Reis-Kultivaren (Oryza sativa L.), IR 42, CR 383-10 und FR 13A, die empfindlich oder tolerant gegenuber einer Uberflutung sind, durchgefuhrt. Eine schadliche Wirkung der Uberflutung wurde sowohl an der oberen Trockenmasse als auch dem Chlorophyllgehalt wahrend auch nach Beendigung der Uberflutung festgestellt. Die Reduktion war geringer bei dem toleranten Kultivar. Der tolerante Kultivar FR 13A hatte ein hoheres Trockengewicht wahrend und nach der Uberflutung und akkumulierte weniger Prolin und Malondialdehyd als die anderen Kultivare. Die Enzymaktivitaten, bestimmt auf der Basis je g Frischgewicht der Blatter zeigten fur Katalase, Peroxidase und Superoxiddismutase hohere Werte bei FR 13A sowohl unter Wasser als auch 24 Stunden nach Zurucknahme der Uberflutung. Ascorbinsaure und Oxidase Aktivitaten waren bei FR 13A dagegen geringer. Der Kultivar CR 383-10, der eine hohe Kapazitat fur die Bildung oberirdischer Trockemasse unter normalen Bedingungen aufweist, zeigte einer hohere Langenwachtumsrate unter Uberflutung, war aber empfindlich hichsichtlich der Enzymaktivitaten und anderer Parameter gegenuber Uberflutung und Zurucknahme der Uberflutung wie IR 42.

Pre-submergence reserve saccharides was found adequate to substantiate the survival of tolerant cultivar under flooding. Survival percentage declined in both tolerant and susceptible cultivars with less saccharide content. However, it was more apparent in susceptible cultivar. Plant height, fresh and dry mass of shoots, leaf mass/area ratio and starch content per plant before flooding showed significant positive association with submergence tolerance. Hence, the improved seedling vigour could be used to increase submergence tolerance.

Soil salinity is a major abiotic stress that limits rice productivity worldwide. The problem is intense – particularly in areas with extremely dry and hot climatic conditions. Designing an effective phenotyping strategy requires thorough understanding of plant survival under stress. The investigation was conducted using 12 rice cultivars differing in salinity tolerance. Among these cultivars, seedling survival on day 10 of salt treatment (12 dS m–1) was above 85% during wet season and 75% during dry season in FL478, AC39416, Pokkali and Kamini. Highly salt-tolerant cultivars maintained greater proportion of green leaf and chlorophyll content under salt stress. Unlike sensitive cultivars, tolerant cultivars taken up less Na+ and more K+, resulting in lower Na+ : K+ ratio in leaf and sheath. Normalised chlorophyll a fluorescence data revealed that the Fv/Fm and PIABS values decreased on days 3 and 7, respectively, of salt stress in susceptible rice cultivar. Salinity factor index (SFI) calculated by giving different weights to relative PIABS values after variable days of salinity stress clearly distinguished the level of tolerance among rice cultivars. The SFI can be used for grouping of moderately to highly salt-tolerant cultivars based on their tolerance level. We conclude that maintenance of greater proportion of green leaf, and restricted transport of Na+ to sheath and leaf helps the plant to counteract adverse effects of salinity on rice growth.

Natural leaf senescence was investigated in four rainfed lowland rice cultivars, FR 13A (tolerant to submergence), Sabita and Sarala (adapted to medium depth, 0–50 cm stagnant flooding) and Dengi (conventional farmers’ cultivar). Changes in the levels of pigment content, CO2 photosynthetic rate, photosystem II photochemistry and anti-oxidant enzyme activities of flag leaves during grain-filling stage were investigated. Chlorophyll content, photochemical efficiency of photosystem II and CO2 photosynthetic rate decreased significantly with the progress of grain-filling. Likely, the activities of antioxidant enzymes namely, superoxide dismutase, catalase, guaiacol peroxidase and ascorbate peroxidase decreased with progress of grain-filling. A substantial difference was observed among the four cultivars for the sustainability index (SI) of different photosynthetic parameters and antioxidant enzyme activities; SIs of those parameters, in general, were lower in low yielding cultivar FR 13A compared to the other three cultivars. Among the four cultivars Sabita gave maximum grain yield. Yet, SI of Pn was greater in Sarala and Dengi compared to the Sabita. SIs of electron transport (ETo/CS), maximal photochemical efficiency (Fv/Fm), area above Fo and Fm, catalase and ascorbate peroxidase were also greater in Sarala and Dengi. The data showed that among the different Chl a fluorescence parameters, PI could be used with greater accuracy to distinguish slow and fast senescence rice cultivars during grain-filling period. It was concluded that maintaining the vitality of rice plants during grain-filling gave guarantee to synthesize carbohydrate, however greater yield could be realized provided superior yield attributing parameters are present.

Submergence tolerance is an important trait where short term flash flooding damages rice. Tolerant landraces that withstand submergence for 1–2 weeks were identified. Due to the heterogeneity in flood-prone ecosystem many different types of traditional rice cultivars are being grown by the farmers. The local landraces adapted to extremes in water availability could be the sources of genetic variation are to be used to improve the adaptability of rice to excess water stress. Greater genotypic variability was observed for plant height, elongation and survival %, absolute growth rate, non-structural carbohydrate retention capacity, chlorophyll content, different chlorophyll fluorescence parameters (FPs) characteristics, and re-generation growth at re-emergence. Twenty days submergence caused greater damage even in Submergence 1 (SUB1) introgressed cultivars compared to the 14 days of submergence. The FPs, carbohydrate content and dry weight at the end of submergence showed positive and highly significant association with re-generation growth. The presence of SUB1 associated primers, either SC3 or ART5, was noticed even in greater elongating types of rice genotypes. These genotypes possess one or more of the adaptive traits required for the flood-prone ecosystem, which range from temporary submergence of 1–2 weeks to long period of stagnant water tolerance. Electronic supplementary material The online version of this article (doi:10.1007/s12284-011-9065-z) contains supplementary material, which is available to authorized users.

Rice is sensitive to salinity stress at early seedling and reproductive stages. Surprisingly, major QTL/gene responsible for salinity tolerance at flowering stage is yet to be identified, mainly due to unavailability of suitable donors. In this investigation, a set of eight genotypes were phenotyped for grain yield and various yield attributing traits as influenced by salt-stress (EC= 8 dS m−1) at flowering stage and subsequently genotyped by using microsatellite markers associated with known QTLs for salt tolerance in rice. One Pokkali and two Chettivirippu accessions were found tolerant to moderately tolerant. These genotypes were genetically distant from the susceptible variety, Swarna indicating the scope of deducing novel QTLs for salttolerance at flowering stage.

Rice (Oryza sativa L.) plants experience multiple abiotic stresses when they are submerged. In addition to the effects of submergence on gas exchange, water also creates shading of submerged plants. It is believed that responses to submergence are actually responses to low light stress, although during complete submergence in addition to low light other environmental factors like reduce movement of gases affect the plant growth, and therefore, the consequences of submergence are not always alike to shade. We monitored the extent to which shade and submergence change the plant height, chlorophyll a fluorescence characteristics and CO2 photosynthetic rate in three Indica rice cultivars, namely Sarala, Kalaputia and Khoda, which differed in submergence tolerance. There were both similarities and dissimilarities between the consequence of shade and submergence on rice plants. Under shade conditions, elongation growth was greater in submergence tolerant cultivars than the sensitive cultivar, whereas elongation growth was greater under submergence in sensitive cultivar. The reduction in chlorophyll content, damage to PSII, and decrease in CO2 photosynthetic rate was more notable under submergence than the shade conditions. Our results show that several JIP-test parameters clearly distinguish between submergence tolerant and sensitive cultivars, and responses to submergence among different rice cultivars differ depending on their sensitivity to submergence. There were different interactions between cultivar and shade (~low light) and cultivar and submergence.

Germination was increasingly inhibited at concentrations above 5 and 20 mM and stopped altogether at 80 and 50 mM NaF in rice and jute respectively, whereas the inhibition of seedling growth began at much lower concentrations. Of the enzymes, RNase activity was increased by fluoride, while α-amylase, protease, phytase and ATPase activities exhibited distinct inhibition from the control.

Seeds of six rice cultivars sown in moistened soil and maintained after five days under 20±5 cm of water were compared with 30-day-old seedlings transplanted in the normal way. Compared with transplanting, the crops from anaerobic direct seeding had more plant height and above-ground dry matter, less chlorophyll and specific leaf weight, and more panicles per unit area and sterile spikelets. Panicle weight and harvest index showed highly significant positive associations with grain yield. Copyright © 2003 Whurr Publishers Ltd

Summary The submergence tolerance mechanism in respect to seedling height, carbohydrate, chlorophyll and specific leaf weight (SLW) was studied in rice. Twentyfive-day-old seedlings of 5 rice cultivars were submerged for 12 days. Submergence tolerant cultivars consumed more carbohydrates in the beginning of submergence to elongate the seedling height and later produce new carbohydrates after exposure of the leaves in the sunlight above water. Moreover, they maintained more chlorophyll and SLW as compared with susceptible cultivars during submergence.