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Rice is the staple food for more than 3.5 billion people worldwide. The sensitivity of rice to heat, drought, and salinity is well documented. However, rice response to combinations of these stresses is not well understood. A contrasting set of rice genotypes for heat (N22, Gharib), drought (Moroberekan, Pusa 1121) and salinity (Pokkali, IR64) were selected to characterize their response under drought, and combination of drought with heat and salinity at the sensitive seedling stage. Sensitive genotypes (IR64, Pusa 1121, Gharib) recorded higher reactive oxygen species accumulation (20–40%), membrane damage (8–65%) and reduction in photosynthetic efficiency (10–23%) across the stress and stress combinations as compared to stress tolerant checks. On the contrary, N22 and Pokkali performed best under drought + heat, and drought + salinity combination, respectively. Moreover, gene expression pattern revealed the highest expression of catalase (CAT), ascorbate peroxidase (APX) and GATA28a in N22 under heat + drought, whereas the highest expression of CAT, APX, superoxide dismutase (SOD), DEHYDRIN, GATA28a and GATA28b in Pokkali under drought + salinity. Interestingly, the phenotypic variation and expression level of genes highlighted the role of different set of physiological traits and genes under drought and drought combination with heat and salinity stress. This study reveals that rice response to stress combinations was unique with rapid readjustment at physiological and molecular levels. Moreover, phenotypic changes under stress combinations showed substantial adaptive plasticity in rice, which warrant further investigations at molecular level. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-022-01162-y.

Abiotic stress tolerance has been weakened during the domestication of all major staple crops. Soil salinity is a major environmental constraint that impacts over half of the world population; however, given the increasing reliance on irrigation and the lack of available freshwater, agriculture in the 21st century will increasingly become saline. Therefore, global food security is critically dependent on the ability of plant breeders to create high-yielding staple crop varieties that will incorporate salinity tolerance traits and account for future climate scenarios. Previously, we have argued that the current agricultural practices and reliance on crops that exclude salt from uptake is counterproductive and environmentally unsustainable, and thus called for a need for a major shift in a breeding paradigm to incorporate some halophytic traits that were present in wild relatives but were lost in modern crops during domestication. In this review, we provide a comprehensive physiological and molecular analysis of the key traits conferring crop halophytism, such as vacuolar Na

Mutation breeding has a long track record in the development of crop cultivars with improved tolerance to abiotic stresses such as heat, salinity and drought. Oryza sativa L. cv IR64 is a very popular high yielding rice, but susceptible to major abiotic stresses, such as low and high temperatures, salinity and drought. We subjected IR64 to gamma irradiation and generated a mutant population (M3) with ~2,000 families. These were screened at the seedling stage for tolerance to high-temperature stress using hydroponics and controlled-environment chambers, resulting in the identification of three mutant lines showing a robust seedling phenotype. Under heat stress, higher CO2 assimilation (10-30%), higher spikelet fertility (40-45%) and higher antioxidant activity (15-20% catalase activity) confirmed superiority of the selected mutant lines over wild type plants at seedling and flowering stages. Upon exposure to salinity and drought stress, the three selected lines also exhibited better tolerance than wild type in terms of higher CO2 assimilation, stomatal conductance, transpiration and chlorophyll fluorescence. Transcript and protein abundance analyses confirmed higher constitutive levels of heat shock proteins and antioxidant enzymes in the mutant lines relative to wild type. Tolerance to multiple abiotic stresses was reflected in higher (25-30%) grain yield than wild type. It is anticipated that the mutant lines identified will be useful for developing new improved cultivars for dry and saline areas and may be exploited to dissect the molecular basis of multiple stress tolerance in crop plants

Plants are exposed to various environmental challenges that can hamper their growth, development, and productivity. Being sedentary, plants cannot escape from these unfavorable environmental conditions and have evolved various signaling cascades to endure them. The two-component signaling (TCS) system is one such essential signaling circuitry present in plants regulating responses against multiple abiotic and biotic stresses. It is among the most ancient and evolutionary conserved signaling pathways in plants, which include membrane-bound histidine kinases (HKs), cytoplasmic histidine phosphotransfer proteins (Hpts), and nuclear or cytoplasmic response regulators (RRs). At the same time, TCS also involved in many signaling circuitries operative in plants in response to diverse hormones. These plant growth hormones play a significant role in diverse physiological and developmental processes, and their contribution to plant stress responses is coming up in a big way. Therefore, it is intriguing to know how TCS and various plant growth regulators, along with the key transcription factors, directly or indirectly control the responses of plants towards diverse stresses. The present review attempts to explore this relationship, hoping that this knowledge will contribute towards developing crop plants with enhanced climate resilience.

Glyoxalase (GLY) system, comprising of GLYI and GLYII enzymes, has emerged as one of the primary methylglyoxal (MG) detoxification pathways with an indispensable role during abiotic and biotic stresses. MG homeostasis is indeed very closely guarded by the cell as its higher levels are cytotoxic for the organism. The dynamic responsiveness of MG-metabolizing GLY pathway to both endogenous cues such as, phytohormones, nutrient status, etc., as well as external environmental fluctuations (abiotic and biotic stresses) indicates that a tight regulation occurs in the cell to maintain physiological levels of MG in the system. Interestingly, GLY pathway is also manipulated by its substrates and reaction products. Hence, an investigation of signalling and regulatory aspects of GLY pathway would be worthwhile. Herein, we have attempted to converge all known factors acting as signals or directly regulating GLYI/II enzymes in plants. Further, we also discuss how crosstalk between these different signal molecules might facilitate the regulation of glyoxalase pathway. We believe that MG detoxification is controlled by intricate mechanisms involving a plethora of signal molecules.

Background: The two-component signaling (TCS) system is an important signal transduction machinery in prokaryotes and eukaryotes, excluding animals, that uses a protein phosphorylation mechanism for signal transmission. Conclusion: Prokaryotes have a primitive type of TCS machinery, which mainly comprises a membrane- bound sensory histidine kinase (HK) and its cognate cytoplasmic response regulator (RR). Hence, it is sometimes referred to as two-step phosphorelay (TSP). Eukaryotes have more sophisticated signaling machinery, with an extra component - a histidine-containing phosphotransfer (HPT) protein that shuttles between HK and RR to communicate signal baggage. As a result, the TSP has evolved from a two-step phosphorelay (His–Asp) in simple prokaryotes to a multi-step phosphorelay (MSP) cascade (His–Asp–His–Asp) in complex eukaryotic organisms, such as plants, to mediate the signaling network. This molecular evolution is also reflected in the form of considerable structural modifications in the domain architecture of the individual components of the TCS system. In this review, we present TCS system's evolutionary journey from the primitive TSP to advanced MSP type across the genera. This information will be highly useful in designing the future strategies of crop improvement based on the individual members of the TCS machinery.

Heat stress, owing to the recent climate change events, has emerged as one of the major environmental factors posing a grave threat to plant survival and crop productivity. Oxidative damage due to increased generation of reactive oxygen and dicarbonyl species in response to heat, is one of the serious consequences of high temperature stress. Methylglyoxal (MG), is one such cytotoxic dicarbonyl metabolite whose levels are known to increase in response to high temperature and various other stress conditions in plants. In fact, it is considered as a general consequence of stress in plants. The synergistic co-activation of reactive oxygen species scavenging and the MG detoxification pathways thus, plays a key role in regulation of stress responses for plant acclimation. Glyoxalase enzymes are the major MG detoxifying proteins in the living organisms. In plants, glyoxalases are encoded as multigenic families, known to be involved in plant growth and development, although, chiefly associated with multiple stress inducible behaviour and tolerance. While their role in salinity, drought and heavy metal stresses has been well-studied, their significance under high temperature stress has received limited coverage. In this review, we emphasize on the dynamic role of glyoxalases under high temperature stress for conferring thermotolerance. Through analysis of heat responsive transcriptomes and proteomes of various plants, we provide evidence for a hitherto, unexplored role of glyoxalases as a mechanism of mounting thermotolerance responses. We also, show that ‘priming’ induced stress/cross stress tolerance in plants involves the activation of glyoxalase pathway.

Chloride channels (CLCs), member of anion transporting proteins, are present ubiquitously in all life forms. Diverging from its name, the CLC family includes both channel and exchanger (proton-coupled) proteins; nevertheless, they share conserved structural organization. They are engaged in diverse indispensable functions such as acid and fluoride tolerance in prokaryotes to muscle stabilization, transepithelial transport, and neuronal development in mammals. Mutations in genes encoding CLCs lead to several physiological disorders in different organisms, including severe diseases in humans. Even in plants, loss of CLC protein function severely impairs various cellular processes critical for normal growth and development. These proteins sequester Cl- into the vacuole, thus, making them an attractive target for improving salinity tolerance in plants caused by high abundance of salts, primarily NaCl. Besides, some CLCs are involved in NO3 - transport and storage function in plants, thus, influencing their nitrogen use efficiency. However, despite their high significance, not many studies have been carried out in plants. Here, we have attempted to concisely highlight the basic structure of CLC proteins and critical residues essential for their function and classification. We also present the diverse functions of CLCs in plants from their first cloning back in 1996 to the knowledge acquired as of now. We stress the need for carrying out more in-depth studies on CLCs in plants, for they may have future applications towards crop improvement.

Rice, one of the most important staple food crops in the world, is highly sensitive to soil salinity at the seedling stage. The ultimate yield of this crop is a function of the number of seedlings surviving after transplantation in saline water. Oryza sativa cv. IR64 is a high-yielding salinity-sensitive variety, while Pokkali is a landrace traditionally cultivated by the local farmers in the coastal regions in India. However, the machinery responsible for the seedling-stage tolerance in Pokkali is not understood. To bridge this gap, we subjected young seedlings of these contrasting genotypes to salinity and performed detailed investigations about their growth parameters, ion homeostasis, biochemical composition, and photosynthetic parameters after every 24 h of salinity for three days. Taken together, all the physiological and biochemical indicators, such as proline accumulation, K+/Na+ ratio, lipid peroxidation, and electrolyte leakage, clearly revealed significant differences between IR64 and Pokkali under salinity, establishing their contrasting nature at this stage. In response to salinity, the Fv/Fm ratio (maximum quantum efficiency of Photosystem II as inferred from Chl a fluorescence) and the energy conserved for the electron transport after the reduction of QA (the primary electron acceptor of PSII), to QA−, and reduction of the end electron acceptor molecules towards the PSI (Photosystem I) electron acceptor side was higher in Pokkali than IR64 plants. These observations reflect a direct contribution of photosynthesis towards seedling-stage salinity tolerance in rice. These findings will help to breed high-yielding crops for salinity prone agricultural lands.

Methylglyoxal (MG), a reactive carbonyl compound, is generated during metabolism in living systems. However, under stress, its levels increase rapidly leading to cellular toxicity. Although the generation of MG is spontaneous in a cell, its detoxification is essentially catalyzed by the glyoxalase enzymes. In plants, modulation of MG content via glyoxalases influences diverse physiological functions ranging from regulating growth and development to conferring stress tolerance. Interestingly, there has been a preferred expansion in the number of isoforms of these enzymes in plants, giving them high plasticity in their actions for accomplishing diverse roles. Future studies need to focus on unraveling the interplay of these multiple isoforms of glyoxalases possibly contributing towards the unique adaptability of plants to diverse environments.

Methylglyoxal (MG) is a metabolically generated highly cytotoxic compound that accumulates in all living organisms, from Escherichia coli to humans, under stress conditions. To detoxify MG, nature has evolved reduced glutathione (GSH)-dependent glyoxalase and NADPH-dependent aldo-keto reductase systems. But both GSH and NADPH have been reported to be limiting in plants under stress conditions, and thus detoxification might not be performed efficiently. Recently, glyoxalase III (GLY III)-like enzyme activity has been reported from various species, which can detoxify MG without any cofactor. In the present study, we have tested whether an E. coli gene, hchA, encoding a functional GLY III, could provide abiotic stress tolerance to living systems. Overexpression of this gene showed improved tolerance in E. coli and Saccharomyces cerevisiae cells against salinity, dicarbonyl, and oxidative stresses. Ectopic expression of the E. coli GLY III gene (EcGLY-III) in transgenic tobacco plants confers tolerance against salinity at both seedling and reproductive stages as indicated by their height, weight, membrane stability index, and total yield potential. Transgenic plants showed significantly increased glyoxalase and antioxidant enzyme activity that resisted the accumulation of excess MG and reactive oxygen species (ROS) during stress. Moreover, transgenic plants showed more anti-glycation activity to inhibit the formation of advanced glycation end product (AGE) that might prevent transgenic plants from stress-induced senescence. Taken together, all these observations indicate that overexpression of EcGLYIII confers salinity stress tolerance in plants and should be explored further for the generation of stress-tolerant plants.

Rice is an important staple food crop that feeds over half of the human population, particularly in developing countries. Increasing salinity is a major challenge for continuing rice production. Though rice is affected by salinity at all the developmental stages, it is most sensitive at the early seedling stage. The yield thus depends on how many seedlings can withstand saline water at the stage of transplantation, especially in coastal farms. The rapid development of "omics" approaches has assisted researchers in identifying biological molecules that are responsive to salt stress. Several salinity-responsive quantitative trait loci (QTL) contributing to salinity tolerance have been identified and validated, making it essential to narrow down the search for the key genes within QTLs. Owing to the impressive progress of molecular tools, it is now clear that the response of plants toward salinity is highly complex, involving multiple genes, with a specific role assigned to the repertoire of transcription factors (TF). Targeting the TFs for improving salinity tolerance can have an inbuilt advantage of influencing multiple downstream genes, which in turn can contribute toward tolerance to multiple stresses. This is the first comparative study for TF-driven salinity tolerance in contrasting rice cultivars at the seedling stage that shows how tolerant genotypes behave differently than sensitive ones in terms of stress tolerance. Understanding the complexity of salt-responsive TF networks at the seedling stage will be helpful to alleviate crop resilience and prevent crop damage at an early growth stage in rice.

Root system architecture plays an important role in plant adaptation to drought stress. The root system architecture (RSA) consists of several structural features, which includes number and length of main and lateral roots along with the density and length of root hairs. These features exhibit plasticity under water-limited environments and could be critical to developing crops with efficient root systems for adaptation under drought. Recent advances in the omics approaches have significantly improved our understanding of the regulatory mechanisms of RSA remodeling under drought and the identification of genes and other regulatory elements. Plant response to drought stress at physiological, morphological, biochemical, and molecular levels in root cells is regulated by various phytohormones and their crosstalk. Stress-induced reactive oxygen species play a significant role in regulating root growth and development under drought stress. Several transcription factors responsible for the regulation of RSA under drought have proven to be beneficial for developing drought tolerant crops. Molecular breeding programs for developing drought-tolerant crops have been greatly benefitted by the availability of quantitative trait loci (QTLs) associated with the RSA regulation. In the present review, we have discussed the role of various QTLs, signaling components, transcription factors, microRNAs and crosstalk among various phytohormones in shaping RSA and present future research directions to better understand various factors involved in RSA remodeling for adaptation to drought stress. We believe that the information provided herein may be helpful in devising strategies to develop crops with better RSA for efficient uptake and utilization of water and nutrients under drought conditions.

Abiotic stresses are emerging as a potential threat to sustainable agriculture worldwide. Soil salinity and drought will be the major limiting factors for rice productivity in years to come. The Salt Overly Sensitive (SOS) pathway plays a key role in salinity tolerance by maintaining the cellular ion homeostasis, with SOS2, a S/T kinase, being a vital component. The present study investigated the role of the OsSOS2, a SOS2 homolog from rice, in improving salinity and drought tolerance. Transgenic plants with either overexpression (OE) or knockdown (KD) of OsSOS2 were raised in one of the high-yielding cultivars of rice-IR64. Using a combined approach based on physiological, biochemical, anatomical, microscopic, molecular, and agronomic assessment, the evidence presented in this study advocates the role of OsSOS2 in improving salinity and drought tolerance in rice. The OE plants were found to have favorable ion and redox homeostasis when grown in the presence of salinity, while the KD plants showed the reverse pattern. Several key stress-responsive genes were found to work in an orchestrated manner to contribute to this phenotype. Notably, the OE plants showed tolerance to stress at both the seedling and the reproductive stages, addressing the two most sensitive stages of the plant. Keeping in mind the importance of developing crops plants with tolerance to multiple stresses, the present study established the potential of OsSOS2 for biotechnological applications to improve salinity and drought stress tolerance in diverse cultivars of rice.

OsCYP2-P is an active cyclophilin (having peptidyl-prolyl cis/trans-isomerase activity, PPIase) isolated from the wild rice Pokkali having a natural capacity to grow and yield seeds in coastal saline regions of India. Transcript abundance analysis in rice seedlings showed the gene is inducible by multiple stresses, including salinity, drought, high temperature, and heavy metals. To dissect the role of OsCYP2-P gene in stress response, we raised overexpression (OE) and knockdown (KD) transgenic rice plants with2-3 folds higher and approximately 2-fold lower PPIase activity, respectively. Plants overexpressing this gene had more favorable physiological and biochemical parameters (K

Serotonin (Ser) and melatonin (Mel) serve as master regulators of plant growth and development by influencing diverse cellular processes. The enzymes namely, tryptophan decarboxylase (TDC) and tryptamine 5-hydroxylase (T5H) catalyse the formation of Ser from tryptophan. Subsequently, serotonin N-acetyl transferase (SNAT) and acetyl-serotonin methyltransferase (ASMT) form Mel from Ser. Plant genomes harbour multiple genes for each of these four enzymes, all of which have not been identified. Therefore, to delineate information regarding these four gene families, we carried out a genome-wide analysis of the genes involved in Ser and Mel biosynthesis in Arabidopsis, tomato, rice and sorghum. Phylogenetic analysis unravelled distinct evolutionary relationships among these genes from different plants. Interestingly, no gene family except ASMTs showed monocot- or dicot-specific clustering of respective proteins. Further, we observed tissue-specific, developmental and stress/hormone-mediated variations in the expression of the four gene families. The light/dark cycle also affected their expression in agreement with our quantitative reverse transcriptase-PCR (qRT-PCR) analysis. Importantly, we found that miRNAs (miR6249a and miR-1846e) regulated the expression of Ser and Mel biosynthesis under light and stress by influencing the expression of OsTDC5 and OsASMT18, respectively. Thus, this study may provide opportunities for functional characterization of suitable target genes of the Ser and Mel pathway to decipher their exact roles in plant physiology.

Marker-free transgenic lines of rice are developed with enhanced trehalose accumulation that is associated with improved grain yield under salinity, sodicity, and drought stresses., Edaphic factors such as salinity, sodicity, and drought adversely affect crop productivity, either alone or in combination. Despite soil sodicity being reported as an increasing problem worldwide, limited efforts have been made to address this issue. In the present study, we aimed to generate rice with tolerance to sodicity in conjunction with tolerance to salinity and drought. Using a fusion gene from E. coli coding for trehalose-6-phosphate synthase/phosphatase (TPSP) under the control of an ABA-inducible promoter, we generated marker-free, high-yielding transgenic rice (in the IR64 background) that can tolerate high pH (~9.9), high EC (~10.0 dS m–1), and severe drought (30–35% soil moisture content). The transgenic plants retained higher relative water content (RWC), chlorophyll content, K+/Na+ ratio, stomatal conductance, and photosynthetic efficiency compared to the wild-type under these stresses. Positive correlations between trehalose overproduction and high-yield parameters were observed under drought, saline, and sodic conditions. Metabolic profiling using GC-MS indicated that overproduction of trehalose in leaves differently modulated other metabolic switches, leading to significant changes in the levels of sugars, amino acids, and organic acids in transgenic plants under control and stress conditions. Our findings reveal a novel potential technological solution to tackle multiple stresses under changing climatic conditions.

Reductions in crop yields as a consequence of global climate change threaten worldwide food security. It is therefore imperative to develop high-yielding crop plants that show sustainable production under stress conditions. In order to achieve this aim through breeding or genetic engineering, it is crucial to have a complete and comprehensive understanding of the molecular basis of plant architecture and the regulation of its sub-components that contribute to yield under stress. Rice is one of the most widely consumed crops and is adversely affected by abiotic stresses such as drought and salinity. Using it as a model system, in this review we present a summary of our current knowledge of the physiological and molecular mechanisms that determine yield traits in rice under optimal growth conditions and under conditions of environmental stress. Based on physiological functioning, we also consider the best possible combination of genes that may improve grain yield under optimal as well as environmentally stressed conditions. The principles that we present here for rice will also be useful for similar studies in other grain crops.

Background Rice productivity is adversely affected by environmental stresses. Transcription factors (TFs), as the regulators of gene expression, are the key players contributing to stress tolerance and crop yield. Histone gene binding protein-1b (OsHBP1b) is a TF localized within the Saltol QTL in rice. Recently, we have reported the characterization of OsHBP1b in relation to salinity and drought tolerance in a model system tobacco. In the present study, we over-express the full-length gene encoding OsHBP1b in the homologous system (rice) to assess its contribution towards multiple stress tolerance and grain yield. Results We provide evidence to show that transgenic rice plants over-expressing OsHBP1b exhibit better survival and favourable osmotic parameters under salinity stress than the wild type counterparts. These transgenic plants restricted reactive oxygen species accumulation by exhibiting high antioxidant enzyme activity (ascorbate peroxidase and superoxide dismutase), under salinity conditions. Additionally, these transgenic plants maintained the chlorophyll concentration, organellar structure, photosynthesis and expression of photosynthesis and stress-related genes even when subjected to salinity stress. Experiments conducted for other abiotic stresses such as drought and high temperature revealed improved tolerance in these transgenic plants with better root and shoot growth, better photosynthetic parameters, and enhanced antioxidant enzyme activity, in comparison with WT. Further, the roots of transgenic lines showed large cortical cells and accumulated a good amount of callose, unlike the WT roots, thus enabling them to penetrate hard soil and prevent the entry of harmful ions in the cell. Conclusion Collectively, our results show that rice HBP1b gene contributes to multiple abiotic stress tolerance through several molecular and physiological pathways and hence, may serve as an important gene for providing multiple stress tolerance and improving crop yield in rice. Electronic supplementary material The online version of this article (10.1186/s12284-019-0316-8) contains supplementary material, which is available to authorized users.

Although only 2–4% of absorbed light is emitted as chlorophyll (Chl) a fluorescence, its measurement provides valuable information on photosynthesis of the plant, particularly of Photosystem II (PSII) and Photosystem I (PSI). In this paper, we have examined photosynthetic parameters of Suaeda fruticosa L. (family: Amaranthaceae), surviving under extreme xerohalophytic conditions, as influenced by diurnal rhythm or continuous dark condition. We report here CO2 gas exchange and the kinetics of Chl a fluorescence of S. fruticosa, made every 3 hours (hrs) for 3 days, using a portable infra-red gas analyzer and a Handy PEA fluorimeter. Our measurements on CO2 gas exchange show the maximum rate of photosynthesis to be at 08:00 hrs under diurnal condition and at 05:00 hrs under continuous dark. From the OJIP phase of Chl a fluorescence transient, we have inferred that the maximum quantum yield of PSII photochemistry must have increased during the night under diurnal rhythm, and between 11:00 and 17:00 hrs under constant dark. Overall, our study has revealed novel insights into how photosynthetic reactions are affected by the photoperiodic cycles in S. fruticosa under high salinity. This study has further revealed a unique strategy operating in this xero-halophyte where the repair mechanism for damaged PSII operates during the dark, which, we suggest, contributes to its ecological adaptation and ability to survive and reproduce under extreme saline, high light, and drought conditions. We expect these investigations to help in identifying key genes and pathways for raising crops for saline and dry areas.

Osmotic stress has severe effects on crop productivity. Since climate change is predicted to exacerbate this problem, the development of new crops that are tolerant to osmotic stresses, especially drought and salinity stress, is required. However, only limited success has been achieved to date, primarily because of the lack of a clear understanding of the mechanisms that facilitate osmosensing. Here, we discuss the potential mechanisms of osmosensing in plants. We highlight the roles of proteins such as receptor-like kinases, which sense stress-induced cell wall damage, mechanosensitive calcium channels, which initiate a calcium-induced stress response, and phospholipase C, a membrane-bound enzyme that is integral to osmotic stress perception. We also discuss the roles of aquaporins and membrane-bound histidine kinases, which could potentially detect changes in extracellular osmolarity in plants, as they do in prokaryotes and lower eukaryotes. These putative osmosensors have the potential to serve as master regulators of the osmotic stress response in plants and could prove to be useful targets for the selection of osmotic stress-tolerant crops.

Plant growth promotion by microbes is a cumulative phenomenon involving multiple traits, many of which are not explored yet. Hence, to unravel microbial mechanisms underlying growth promotion, we have analyzed the genomes of two potential growth-promoting microbes, viz. Pseudomonas sp. CK-NBRI-02 (P2) and Bacillus marisflavi CK-NBRI-03 (P3) for the presence plant-beneficial traits. Besides known traits, we found that microbes differ in their ability to metabolize methylglyoxal (MG), a ubiquitous cytotoxin regarded as general consequence of stress in plants. P2 exhibited greater tolerance to MG and possessed better ability to sustain plant growth under dicarbonyl stress. Whereas under salinity, only P3 showed a dose-dependent induction in MG detoxification activity in accordance with concomitant increase in MG levels, contributing to enhanced salt tolerance. Further, salt-stressed transcriptomes of both the strains showed differences with respect to MG, ion and osmolyte homeostasis, with P3 being more responsive to stress. Importantly, application of either strain altered MG levels and subsequently MG detoxification machinery in Arabidopsis, probably to strengthen plant defense response and growth. We therefore, suggest a crucial role of microbial MG resistance in plant growth promotion and that it should be considered as a beneficial trait while screening microbes for stress mitigation in plants. This article is protected by copyright. All rights reserved.

In nature, plants are exposed to an ever-changing environment with increasing frequencies of multiple abiotic stresses. These abiotic stresses act either in combination or sequentially, thereby driving vegetation dynamics and limiting plant growth and productivity worldwide. Plants’ responses against these combined and sequential stresses clearly differ from that triggered by an individual stress. Until now, experimental studies were mainly focused on plant responses to individual stress, but have overlooked the complex stress response generated in plants against combined or sequential abiotic stresses, as well as their interaction with each other. However, recent studies have demonstrated that the combined and sequential abiotic stresses overlap with respect to the central nodes of their interacting signaling pathways, and their impact cannot be modelled by swimming in an individual extreme event. Taken together, deciphering the regulatory networks operative between various abiotic stresses in agronomically important crops will contribute towards designing strategies for the development of plants with tolerance to multiple stress combinations. This review provides a brief overview of the recent developments in the interactive effects of combined and sequentially occurring stresses on crop plants. We believe that this study may improve our understanding of the molecular and physiological mechanisms in untangling the combined stress tolerance in plants, and may also provide a promising venue for agronomists, physiologists, as well as molecular biologists.

Methylglyoxal (MG) is ubiquitously produced in all living organisms as a byproduct of glycolysis, higher levels of which are cytotoxic, leading to oxidative stress and apoptosis in the living systems. Though its generation is spontaneous but its detoxification involves glyoxalase pathway genes. Based on this understanding, the present study describes the possible role of MG as a novel non-antibiotic-based selection agent in rice. Further, by metabolizing MG, the glyoxalase pathway genes viz. glyoxalase I (GLYI) and glyoxalase II (GLYII), may serve as selection markers. Therefore, herein, transgenic rice harboring GLYI-GLYII genes (as selection markers) were developed and the effect of MG as a selection agent was assessed. The 3 mM MG concentration was observed as optimum for the selection of transformed calli, allowing efficient callus induction and proliferation along with high regeneration frequency (55 ± 2%) of the transgenic calli. Since the transformed calli exhibited constitutively higher activity of GLYI and GLYII enzymes compared to the wild type calli, the rise in MG levels was restricted even upon exogenous addition of MG during the selection process, resulting in efficient selection of the transformed calli. Therefore, MG-based selection method is a useful and efficient system for selection of transformed plants without significantly compromising the transformation efficiency. Further, this MG-based selection system is bio-safe and can pave way towards better public acceptance of transgenic plants.

In rice (Oryza sativa), Si nutrition is known to improve salinity tolerance; however, limited efforts have been made to elucidate the underlying mechanism. Salt-Overly Sensitive (SOS) pathway contributes to salinity tolerance in plants in a major way which works primarily through Na+ exclusion from the cytosol. SOS1, a vital component of SOS pathway is a Na+/H+ antiporter that maintains ion homeostasis. In this study, we evaluated the effect of overexpression of Oryza sativa SOS1 (OsSOS1) in tobacco (cv. Petit Havana) and rice (cv. IR64) for modulating its response towards salinity further exploring its correlation with Si nutrition. OsSOS1 transgenic tobacco plants showed enhanced tolerance to salinity as evident by its high chlorophyll content and maintaining favorable ion homeostasis under salinity stress. Similarly, transgenic rice overexpressing OsSOS1 also showed improved salinity stress tolerance as shown by higher seed germination percentage, seedling survival and low Na+ accumulation under salinity stress. At their mature stage, compared with the non-transgenic plants, the transgenic rice plants showed better growth and maintained better photosynthetic efficiency with reduced chlorophyll loss under stress. Also, roots of transgenic rice plants showed reduced accumulation of Na+ leading to reduced oxidative damage and cell death under salinity stress which ultimately resulted in improved agronomic traits such as higher number of panicles and fertile spikelets per panicle. Si nutrition was found to improve the growth of salinity stressed OsSOS1 rice by upregulating the expression of Si transporters (Lsi1 and Lsi2) that leads to more uptake and accumulation of Si in the rice shoots. Metabolite profiling showed better stress regulatory machinery in the transgenic rice, since they maintained higher abundance of most of the osmolytes and free amino acids.

Leaves are the primary food‐producing organs for a plant that carry out photosynthesis and contribute to biomass and grain yield. Leaf senescence is a developmentally regulated physiological process but early leaf senescence is known to negatively affect plant yield. The cuticle is an outer waxy protective layer on the leaf surface which protects plants from pathogens attack as well as dehydration. Our understanding of the molecular mechanisms underlying cuticle development and leaf senescence is still immature. The present study reports the role of the DEGENERATED PANICLE AND PARTIAL STERILITY 1 (DPS1) gene encoding a cystathionine β‐synthase (CBS) domain‐containing protein in cuticle development and leaf senescence in rice. The dps1 loss‐of‐function mutant showed leaf senescence phenotype with twisted leaves, significantly reduced chlorophyll content and degenerated chloroplasts characterized by a reduced number of starch granules and an abundance of osmiophilic bodies. Furthermore, dps1 leaves displayed defective cuticle development, reduced wax and cutin compounds, and lower relative water content as compared with wild type. Physiological assays showed significantly higher accumulation of reactive oxygen species (ROS) accompanied by enhanced DNA fragmentation in dps1 leaves, which could be associated with chloroplast degeneration and defective cuticle development. Transcriptome analysis revealed altered expression of several critical genes related to photosynthesis and wax/cutin pathway. This study revealed a crucial role of DPS1 in regulating leaf cuticle development and senescence by affecting the expression of several genes. Thus, a moderate expression of DPS1 is necessary for better plant growth and productivity.

Rice is a staple food consumed by almost half of the world’s population. However, in a natural environment, like any other plant, rice is exposed to various abiotic stresses such as salinity, drought, and high temperature, which in turn affect its yield. Therefore, to meet the demand of the world’s growing population, it is imperative for scientists to come up with novel strategies of combating these abiotic stresses. Over the years, transgenic rice showing improved performance under stresses such as salinity, drought, and cold have been developed using genetic engineering approaches. Additionally, scientists have also developed rice that has higher nutrient content such as, golden rice, folate-biofortified rice, iron-fortified rice, and zinc-fortified rice. In this chapter, we discuss how plants respond to heat, cold, salinity, drought, and flooding stress with an emphasis on the physiological, biochemical, and molecular mechanisms of stress tolerance. Further, we also present a few representative success stories where attempts have been made towards improving the nutritional value or for enhancing stress tolerance in rice. This information may help in promoting the interdisciplinary studies designed to assess the stress-responsive genes and their role under various abiotic stresses along with a target of improving the nutritional value in rice.

Abiotic stresses, such as drought and salinity, adversely affect rice production and cause a severe threat to food security. Conventional crop breeding techniques alone are inadequate for achieving drought stress tolerance in crop plants. Using transgenic technology, incremental improvements in tolerance to drought and salinity have been successfully attained via manipulation of gene(s) in several crop species. However, achieving the goal via pyramiding multiple genes from the same or different tolerance mechanisms has received little attention. Pyramiding of multiple genes can be achieved either through breeding, by using marker-assisted selection, or by genetic engineering through molecular stacking co-transformation or re-transformation. Transgene stacking into a single locus has added advantages over breeding or re-transformation since the former assures co-inheritance of genes, contributing to more effective tolerance in transgenic plants for generations. Drought, being a polygenic trait, the potential candidate genes for gene stacking are those contributing to cellular detoxification, osmolyte accumulation, antioxidant machinery, and signaling pathways. Since cellular dehydration is inbuilt in salinity stress, manipulation of these genes results in improving tolerance to salinity along with drought in most of the cases. In this review, attempts have been made to provide a critical assessment of transgenic plants developed through transgene stacking and approaches to achieve the same. Identification and functional validation of more such candidate genes is needed for research programs targeting the gene stacking for developing crop plants with high precision in the shortest possible time to ensure sustainable crop productivity under marginal lands.

Ensuring the sustainability of agriculture under climate change has led to a surge in alternative strategies for crop improvement. Advances in integrated crop breeding, social acceptance, and farm-level adoption are crucial to address future challenges to food security. Societal acceptance can be slow when consumers do not see the need for innovation or immediate benefits. We consider how best to address the issue of social licence and harmonised governance for novel gene technologies in plant breeding. In addition, we highlight optimised breeding strategies that will enable long-term genetic gains to be achieved. Promoted by harmonised global policy change, innovative plant breeding can realise high and sustainable productivity together with enhanced nutritional traits.

Prions can be considered as molecular memory devices, generating reproducible memory of a conformational change. Prion-like proteins (PrLPs) have been demonstrated to be present in plants, but their role in plant stress and memory remains largely unexplored. In this work, we report the widespread presence of PrLPs in plants through a comprehensive analysis of 39 genomes representing major taxonomic groups. We find diverse functional roles associated with plant ‘prionomes’. Investigation of the rice transcriptome further delineated the role of PrLPs in stress and developmental responses, leading us to explore whether and to what extent PrLPs may build stress memory. The rice prionome is significantly enriched for Transposons/Retrotransposons (Ts/RTRs), and we derived transcriptional regulatory inferences from diurnal gene expression revealing a complex regulatory network between PrLPs, transcription factors and genes known to be involved in stress priming, as well as transient and trans-generational plant memory. Overall, our data suggest that plant memory mechanisms may rely upon protein-based signals embedded in PrLPs, in addition to chromatin-based epigenetic signals and provides important insights into the anticipated role of prions in stress and memory.

Drought is a critical factor limiting the productivity of legumes worldwide. Legumes can enter into a unique tripartite symbiotic relationship with root-nodulating bacteria of genera Rhizobium, Bradyrhizobium, or Sinorhizobium and colonization by arbuscular mycorrhizal fungi (AMF). Rhizobial symbiosis provides nitrogen necessary for growth. AMF symbiosis enhances uptake of diffusion-limited nutrients such as P, Zn, Cu, etc., and also water from the soil via plant-associated fungal hyphae. Rhizobial and AMF symbioses can act synergistically in promoting plant growth and fitness, resulting in overall yield benefits under drought stress. One of the approaches that rhizobia use to survive under stress is the accumulation of compatible solutes, or osmolytes, such as trehalose. Trehalose is a non-reducing disaccharide and an osmolyte reported to accumulate in a range of organisms. High accumulation of trehalose in bacteroids during nodulation protects cells and proteins from osmotic shock, desiccation, and heat under drought stress. Manipulation of trehalose cell concentrations has been directly correlated with stress response in plants and other organisms, including AMF. However, the role of this compound in the tripartite symbiotic relationship is not fully explored. This review describes the biological importance and the role of trehalose in the tripartite symbiosis between plants, rhizobia, and AMF. In particular, we review the physiological functions and the molecular investigations of trehalose carried out using omics-based approaches. This review will pave the way for future studies investigating possible metabolic engineering of this biomolecule for enhancing abiotic stress tolerance in plants.

The plasma membrane (PM) is possibly the most diverse biological membrane of plant cells; it separates and guards the cell against its external environment. It has an extremely complex structure comprising a mosaic of lipids and proteins. The PM lipids are responsible for maintaining fluidity, permeability and integrity of the membrane and also influence the functioning of membrane proteins. However, the PM is the primary target of environmental stress, which affects its composition, conformation and properties, thereby disturbing the cellular homeostasis. Maintenance of integrity and fluidity of the PM is a prerequisite for ensuring the survival of plants during adverse environmental conditions. The ability of plants to remodel membrane lipid and protein composition plays a crucial role in adaptation towards varying abiotic environmental cues, including high or low temperature, drought, salinity and heavy metals stress. The dynamic changes in lipid composition affect the functioning of membrane transporters and ultimately regulate the physical properties of the membrane. Plant membrane-transport systems play a significant role in stress adaptation by cooperating with the membrane lipidome to maintain the membrane integrity under stressful conditions. The present review provides a holistic view of stress responses and adaptations in plants, especially the changes in the lipidome and proteome of PM under individual or combined abiotic stresses, which cause alterations in the activity of membrane transporters and modifies the fluidity of the PM. The tools to study the varying lipidome and proteome of the PM are also discussed.

Background To delineate the adaptive mechanisms operative under salinity stress, it is essential to study plant responses at the very early stages of stress which are very crucial for governing plant survival and adaptation. We believe that it is the initial perception and response phase which sets the foundation for stress adaptation in rice seedlings where plants can be considered to be in a state of osmotic shock and ion buildup. Results An isobaric Tags for Relative and Absolute Quantitation (iTRAQ) approach was used to analyze the pre-existing differences as well as the very early salt shock responsive changes in the proteome of seedlings of contrasting rice genotypes, viz salt-sensitive IR64 and salt-tolerant Pokkali. In response to a quick salt shock, shoots of IR64 exhibited hyperaccumulation of Na+, whereas in Pokkali, these ions accumulated more in roots. Interestingly, we could find 86 proteins to be differentially expressed in shoots of Pokkali seedlings under non-stress conditions whereas under stress, 63 proteins were differentially expressed in Pokkali shoots in comparison to IR64. However, only, 40 proteins under non-stress and eight proteins under stress were differentially expressed in Pokkali roots. A higher abundance of proteins involved in photosynthesis (such as, oxygen evolving enhancer proteins OEE1 & OEE3, PsbP) and stress tolerance (such as, ascorbate peroxidase, superoxide dismutase, peptidyl-prolyl cis-trans isomerases and glyoxalase II), was observed in shoots of Pokkali in comparison to IR64. In response to salinity, selected proteins such as, ribulose bisphosphate carboxylase/oxygenase activase, remained elevated in Pokkali shoots. Glutamate dehydrogenase - an enzyme which serves as an important link between Krebs cycle and metabolism of amino acids was found to be highly induced in Pokkali in response to stress. Similarly, other enzymes such as peroxidases and triose phosphate isomerase (TPI) were also altered in roots in response to stress. Conclusion We conclude that Pokkali rice seedlings are primed to face stress conditions where the proteins otherwise induced under stress in IR64, are naturally expressed in high abundance. Through specific alterations in its proteome, this proactive stress machinery contributes towards the observed salinity tolerance in this wild rice germplasm. Electronic supplementary material The online version of this article (10.1186/s12284-018-0259-5) contains supplementary material, which is available to authorized users.

Climate change impact on global agricultural food production has been evident in the past few decades. Abiotic factors such as heat, drought, and salinity share a major proportion of crop yield losses and posing a serious threat to global food security. Developing climate resilient crops has become a frontier area of basic plant science and agricultural research. Persistent efforts by scientists to understand crop responses under natural environment and progress in the field of genomics and phenomics has provided unprecedented pace to crop development programs. Rice is the most important cereal crop and staple food for more than 3 billion people worldwide. Heat, drought and salinity stress are the major constraints for global rice production. Hence, efforts are warranted to develop climate-resilient rice cultivars that can produce substantially under different abiotic stresses. Crop plants seldom face single stress in the natural environment. Indeed, heat and drought or drought and salinity are documented as very obvious combinations suggesting multiple stress tolerance as an important breeding target. Forward and reverse genetic tools could effectively contribute towards achieving the target food production to feed the future population despite limiting resources and unfavorable climatic conditions. Genetic approaches adopted for crop improvement programs categorized as forward and reverse genetics are discussed highlighting their potential benefits for tailoring stress tolerant cultivars.