Regulatory Gene Networks in Drought Stress Responses and Resistance in Plants

Comparative physiological and transcriptomic analyses reveal genotype specific response to drought stress in Siberian wildrye (Elymus sibiricus)

Siberian wildrye (Elymus sibiricus) is a xero-mesophytic forage grass with high nutritional quality and stress tolerance. Among its numerous germplasm resources, some possess superior drought resistance. In this study, we firstly investigated the physiological differences between the leaves of drought-tolerant (DT) and drought-sensitive (DS) genotypes under different field water contents (FWC) in soil culture. The results showed that, under drought stress, DT maintained a lower leaf water potential for water absorption, sustained higher photosynthetic efficiency, and reduced oxidative damage in leaves by efficiently maintaining the ascorbic acid-glutathione (ASA-GSH) cycle to scavenge reactive oxygen species (ROS) compared to DS. Secondly, using RNA sequencing (RNA-seq), we analyzed the gene expression profiles of DT and DS leaves under osmotic stress of hydroponics induced by PEG-6000. Through differential analysis, we identified 1226 candidate unigenes, from which we subsequently screened out 115/212 differentially expressed genes (DEGs) that were more quickly induced/reduced in DT than in DS under osmotic stress. Among them, Unigene0005863 (EsSnRK2), Unigene0053902 (EsLRK10) and Unigene0031985 (EsCIPK5) may be involved in stomatal closure induced by abscisic acid (ABA) signaling pathway. Unigene0047636 (EsCER1) may positively regulates the synthesis of very-long-chain (VLC) alkanes in cuticular wax biosynthesis, influencing plant responses to abiotic stresses. Finally, the contents of wax and cutin were measured by GC-MS under osmotic stress of hydroponics induced by PEG-6000. Corresponding to RNA-seq, contents of wax monomers, especially alkanes and alcohols, showed significant induction by osmotic stress in DT but not in DS. It is suggested that limiting stomatal and cuticle transpiration under drought stress to maintain higher photosynthetic efficiency and water use efficiency (WUE) is one of the critical mechanisms that confer stronger drought resistance to DT. This study provides some insights into the molecular mechanisms underlying drought tolerance in E. sibiricus. The identified genes may provide a foundation for the selection and breeding of drought-tolerant crops.

A novel plant growth regulator B2 mediates drought resistance by regulating reactive oxygen species, phytohormone signaling, phenylpropanoid biosynthesis, and starch metabolism pathways in Carex breviculmis

Drought is one of the most common environmental stressors that severely threatens plant growth, development, and productivity. B2 (2,4-dichloroformamide cyclopropane acid), a novel plant growth regulator, plays an essential role in drought adaptation, significantly enhancing the tolerance of Carex breviculmis seedlings. Its beneficial effects include improved ornamental value, sustained chlorophyll content, increased leaf dry weight, elevated relative water content, and enhanced root activity under drought conditions. B2 also directly scavenges hydrogen peroxide and superoxide anion contents while indirectly enhancing the activities of antioxidant enzymes (superoxide dismutase, peroxidase, catalase, and ascorbate peroxidase) to detoxify reactive oxygen species (ROS) oxidative damage. Transcriptome analysis demonstrated that B2 activates drought-responsive transcription factors (AP2/ERF-ERF, WRKY, and mTERF), leading to significant upregulation of genes associated with phenylpropanoid biosynthesis (HCT, POD, and COMT). Additionally, these transcription factors were found to suppress the degradation of starch. B2 regulates phytohormone signaling related-genes, leading to an increase in abscisic acid contents in drought-stressed plants. Collectively, these findings offer new insights into the intricate mechanisms underlying C. breviculmis' resistance to drought damage, highlighting the potential application of B2 for future turfgrass establishment and management with enhanced drought tolerance.

The potential of proline as a key metabolite to design real-time plant water deficit and low-light stress detector in ornamental plants

Nowadays, people are interested to use plants, especially air-purifying plants, in residential and other indoor settings to purify indoor air and increase the green area in the building. In this study, we investigated the effect of water deficit and low light intensity on the physiology and biochemistry of popular ornamental plants, including Sansevieria trifasciata, Episcia cupreata and Epipremnum aureum. Plants were grown under low light intensity in the range of 10-15 μmol quantum m-2 s-1 and 3 days of water deficit. The results showed that these three ornamental plants responded to water deficit with different pathways. Metabolomic analysis indicated that water deficit affected Episcia cupreata and Epipremnum aureum by inducing a 1.5- to 3-fold increase of proline and a 1.1- to 1.6-fold increase in abscisic acid compared to well-watered conditions, which led to hydrogen peroxide accumulation. This resulted in a reduction of stomatal conductance, photosynthesis rate and transpiration. Sansevieria trifasciata responded to water deficit by significantly increasing gibberellin by around 2.8-fold compared to well-watered plants and proline contents by around 4-fold, while stomatal conductance, photosynthesis rate and transpiration were maintained. Notably, proline accumulation under water deficit stress could be attributed to both gibberellic acid and abscisic acid, depending on plant species. Therefore, the enhancement of proline accumulation in ornamental plants under water deficit could be detected early from day 3 after water deficit conditions, and this compound can be used as a key compound for real-time biosensor development in detecting plant stress under water deficit in a future study.

Mutation in Arabidopsis mitochondrial Pentatricopeptide repeat 40 gene affects tolerance to water deficit

MAIN CONCLUSION

The Arabidopsis Pentatricopeptide repeat 40 (PPR40) insertion mutants have increased tolerance to water deficit compared to wild-type plants. Tolerance is likely the consequence of ABA hypersensitivity of the mutants. Plant growth and development depend on multiple environmental factors whose alterations can disrupt plant homeostasis and trigger complex molecular and physiological responses. Water deficit is one of the factors which can seriously restrict plant growth and viability. Mitochondria play an important role in cellular metabolism, energy production, and redox homeostasis. During drought and salinity stress, mitochondrial dysfunction can lead to ROS overproduction and oxidative stress, affecting plant growth and survival. Alternative oxidases (AOXs) and stabilization of mitochondrial electron transport chain help mitigate ROS damage. The mitochondrial Pentatricopeptide repeat 40 (PPR40) protein was implicated in stress regulation as ppr40 mutants were found to be hypersensitive to ABA and high salinity during germination. This study investigated the tolerance of the knockout ppr40-1 and knockdown ppr40-2 mutants to water deprivation. Our results show that these mutants display an enhanced tolerance to water deficit. The mutants had higher relative water content, reduced level of oxidative damage, and better photosynthetic parameters in water-limited conditions compared to wild-type plants. ppr40 mutants had considerable differences in metabolic profiles and expression of a number of stress-related genes, suggesting important metabolic reprogramming. Tolerance to water deficit was also manifested in higher survival rates and alleviated growth reduction when watering was suspended. Enhanced sensitivity to ABA and fast stomata closure was suggested to lead to improved capacity for water conservation in such environment. Overall, this study highlights the importance of mitochondrial functions and in particular PPR40 in plant responses to abiotic stress, particularly drought.

Potential of UV-B radiation in drought stress resilience: A multidimensional approach to plant adaptation and future implications

The escalating impact of climate change and ultraviolet (UV) radiation is subjecting plants to unique combinations of UV-B and drought stress. These combined stressors could have additive, synergistic, or antagonistic effects, but the precise nature of these impacts remains uncertain, hampering our ability to predict plant adaptations approach towards stressors. Our analysis of various studies shows that UV-B or drought conditions detrimentally influence plant growth and health metrics by the enhanced generation of reactive oxygen species causing damage to lipids, proteins, carbohydrates and DNA. Further reducing biomass accumulation, plant height, photosynthetic efficiency, leaf area, and water transpiration, while enhancing stress-related symptoms. In response to UV-B radiation and drought stress, plants exhibit a notable up-regulation of specific acclimation-associated metabolites, including proline, flavonoids, anthocyanins, unsaturated fatty acids, and antioxidants. These metabolites play a pivotal role in conferring protection against environmental stresses. Their biosynthesis and functional roles are potentially modulated by signalling molecules such as hydrogen peroxide, abscisic acid, jasmonic acid, salicylic acid, and ethylene, all of which have associated genetic markers that further elucidate their involvement in stress response pathways. In comparison to single stress, the combination of UV-B and drought induces the plant defence responses and growth retardation which are less-than-additive. This sub-additive response, consistent across different study environments, suggests the possibility of a cross-resistance mechanism. Our outlines imply that the adverse effects of increased drought and UV-B could potentially be mitigated by cross-talk between UV-B and drought regimes utilizing a multidimensional approach. This crucial insight could contribute significantly to refining our understanding of stress tolerance in the face of ongoing global climate change.

Life-Cycle Multiomics of Rice Shoots Reveals Growth Stage-Specific Effects of Drought Stress and Time-Lag Drought Responses

Field-grown rice plants are exposed to various stresses at different stages of their life cycle, but little is known about the effects of stage-specific stresses on phenomes and transcriptomes. In this study, we performed integrated time-course multiomics on rice at 3-d intervals from seedling to heading stage under six drought conditions in a well-controlled growth chamber. Drought stress at seedling and reproductive stages reduced yield performance by reducing seed number and setting rate, respectively. High temporal resolution analysis revealed that drought response occurred in two steps: a rapid response via the abscisic acid (ABA) signaling pathway and a slightly delayed DEHYDRATION-RESPONSIVE ELEMENT-BINDING PROTEIN (DREB) pathway, allowing plants to respond flexibly to deteriorating soil water conditions. Our long-term time-course multiomics showed that temporary drought stress delayed flowering due to prolonged expression of the flowering repressor gene GRAIN NUMBER, PLANT HEIGHT AND HEADING DATE 7 (Ghd7) and delayed expression of the florigen genes HEADING DATE 3a (Hd3a) and RICE FLOWERING LOCUS T 1 (RFT1). Our life-cycle multiomics dataset on rice shoots under drought conditions provides a valuable resource for further functional genomic studies to improve crop resilience to drought stress.

Asparagine-rich protein (NRP) mediates stress response by regulating biosynthesis of plant secondary metabolites in Arabidopsis

The plant-specific stress response protein NRP (asparagine-rich protein) is characterized by an asparagine-rich domain at its N-terminus and a conserved development and cell death (DCD) domain at its C-terminus. Previous transcriptional studies and phenotypic analyses have demonstrated the involvement of NRP in response to severe stress conditions, such as high salt and ER Endoplasmic reticulum-stress. We have recently identified distinct roles for NRP in biotic- and abiotic-stress signaling pathways, in which NRP interacts with different signaling proteins to change their subcellular localizations and stability. Here, to further explore the function of NRP, a transcriptome analysis was carried out on nrp1nrp2 knock-out lines at different life stages or under different growing conditions. The most significant changes in the transcriptome at both stages and conditions turned out to be the induction of the synthesis of secondary metabolites (SMs). Such an observation implicates that NRP is a general stress-responsive protein involved in various challenges faced by plants during their life cycle, which might involve a broad alteration in the distribution of SMs.

Comparative transcriptomic analyses of two sugarcane Saccharum L. cultivars differing in drought tolerance

Sugarcane (Saccharum spp.) is an important cash crop, and drought is an important factors limiting its yield. To study the drought resistance mechanism of sugarcane, the transcriptomes of two sugarcane varieties with different levels of drought resistance were compared under different water shortage levels. The results showed that the transcriptomes of the two varieties were significantly different. The differentially expressed genes were enriched in starch and sucrose metabolism, linoleic acid metabolism, glycolysis/gluconeogenesis, and glyoxylate and dicarboxylate metabolic pathways. Unique trend genes of the variety with strong drought resistance (F172) were significantly enriched in photosynthesis, mitogen-activated protein kinases signaling pathway, biosynthesis of various plant secondary metabolites, and cyanoamino acid metabolism pathways. Weighted correlation network analysis indicated that the blue4 and plum1 modules correlated with drought conditions, whereas the tan and salmon4 modules correlated with variety. The unique trend genes expressed in F172 and mapped to the blue4 module were enriched in photosynthesis, purine metabolism, starch and sucrose metabolism, beta-alanine metabolism, photosynthesis-antenna proteins, and plant hormone signal transduction pathways. The expression of genes involved in the photosynthesis-antenna protein and photosynthesis pathways decreased in response to water deficit, indicating that reducing photosynthesis might be a means for sugarcane to respond to drought stress. The results of this study provide insights into drought resistance mechanisms in plants, and the related genes and metabolic pathways identified may be helpful for sugarcane breeding in the future.

Genome-Wide Analysis of Strictosidine Synthase-like Gene Family Revealed Their Response to Biotic/Abiotic Stress in Poplar

The strictosidine synthase-like (SSL) gene family is a small plant immune-regulated gene family that plays a critical role in plant resistance to biotic/abiotic stresses. To date, very little has been reported on the SSL gene in plants. In this study, a total of thirteen SSLs genes were identified from poplar, and these were classified into four subgroups based on multiple sequence alignment and phylogenetic tree analysis, and members of the same subgroup were found to have similar gene structures and motifs. The results of the collinearity analysis showed that poplar SSLs had more collinear genes in the woody plants Salix purpurea and Eucalyptus grandis. The promoter analysis revealed that the promoter region of PtrSSLs contains a large number of biotic/abiotic stress response elements. Subsequently, we examined the expression patterns of PtrSSLs following drought, salt, and leaf blight stress, using RT-qPCR to validate the response of PtrSSLs to biotic/abiotic stresses. In addition, the prediction of transcription factor (TF) regulatory networks identified several TFs, such as ATMYB46, ATMYB15, AGL20, STOP1, ATWRKY65, and so on, that may be induced in the expression of PtrSSLs in response to adversity stress. In conclusion, this study provides a solid basis for a functional analysis of the SSL gene family in response to biotic/abiotic stresses in poplar.

Transcriptional and Post-Translational Regulation of Plant bHLH Transcription Factors during the Response to Environmental Stresses

Over the past decades, extensive research has been conducted to identify and characterize various plant transcription factors involved in abiotic stress responses. Therefore, numerous efforts have been made to improve plant stress tolerance by engineering these transcription factor genes. The plant basic Helix-Loop-Helix (bHLH) transcription factor family represents one of the most prominent gene families and contains a bHLH motif that is highly conserved in eukaryotic organisms. By binding to specific positions in promoters, they activate or repress the transcription of specific response genes and thus affect multiple variables in plant physiology such as the response to abiotic stresses, which include drought, climatic variations, mineral deficiencies, excessive salinity, and water stress. The regulation of bHLH transcription factors is crucial to better control their activity. On the one hand, they are regulated at the transcriptional level by other upstream components; on the other hand, they undergo various modifications such as ubiquitination, phosphorylation, and glycosylation at the post-translational level. Modified bHLH transcription factors can form a complex regulatory network to regulate the expression of stress response genes and thus determine the activation of physiological and metabolic reactions. This review article focuses on the structural characteristics, classification, function, and regulatory mechanism of bHLH transcription factor expression at the transcriptional and post-translational levels during their responses to various abiotic stress conditions.

Advances in the study of the function and mechanism of the action of flavonoids in plants under environmental stresses

MAIN CONCLUSION

This review summarizes the anti-stress effects of flavonoids in plants and highlights its role in the regulation of polar auxin transport and free radical scavenging mechanism. As secondary metabolites widely present in plants, flavonoids play a vital function in plant growth, but also in resistance to stresses. This review introduces the classification, structure and synthetic pathways of flavonoids. The effects of flavonoids in plant stress resistance were enumerated, and the mechanism of flavonoids in plant stress resistance was discussed in detail. It is clarified that plants under stress accumulate flavonoids by regulating the expression of flavonoid synthase genes. It was also determined that the synthesized flavonoids are transported in plants through three pathways: membrane transport proteins, vesicles, and bound to glutathione S-transferase (GST). At the same time, the paper explores that flavonoids regulate polar auxin transport (PAT) by acting on the auxin export carrier PIN-FORMED (PIN) in the form of ATP-binding cassette subfamily B/P-glycoprotein (ABCB/PGP) transporter, which can help plants to respond in a more dominant form to stress. We have demonstrated that the number and location of hydroxyl groups in the structure of flavonoids can determine their free radical scavenging ability and also elucidated the mechanism by which flavonoids exert free radical removal in cells. We also identified flavonoids as signaling molecules to promote rhizobial nodulation and colonization of arbuscular mycorrhizal fungi (AMF) to enhance plant-microbial symbiosis in defense to stresses. Given all this knowledge, we can foresee that the in-depth study of flavonoids will be an essential way to reveal plant tolerance and enhance plant stress resistance.

Highlight Induced Transcriptional Priming against a Subsequent Drought Stress in Arabidopsis thaliana

In plants, priming allows a more rapid and robust response to recurring stresses. However, while the nature of plant response to a single stress can affect the subsequent response to the same stress has been deeply studied, considerably less is known on how the priming effect due to one stress can help plants cope with subsequent different stresses, a situation that can be found in natural ecosystems. Here, we investigate the potential priming effects in Arabidopsis plants subjected to a high light (HL) stress followed by a drought (D) stress. The cross-stress tolerance was assessed at the physiological and molecular levels. Our data demonstrated that HL mediated transcriptional priming on the expression of specific stress response genes. Furthermore, this priming effect involves both ABA-dependent and ABA-independent responses, as also supported by reduced expression of these genes in the aba1-3 mutant compared to the wild type. We have also assessed several physiological parameters with the aim of seeing if gene expression coincides with any physiological changes. Overall, the results from the physiological measurements suggested that these physiological processes did not experience metabolic changes in response to the stresses. In addition, we show that the H3K4me3 epigenetic mark could be a good candidate as an epigenetic mark in priming response. Overall, our results help to elucidate how HL-mediated priming can limit D-stress and enhance plant responses to stress.

Identification of drought-responsive phenolic compounds and their biosynthetic regulation under drought stress in Ligularia fischeri

Ligularia fischeri, a leafy edible plant found in damp shady regions, has been used as an herbal medicine and is also consumed as a horticultural crop. In this study, we investigated the physiological and transcriptomic changes, especially those involved in phenylpropanoid biosynthesis, induced by severe drought stress in L. fischeri plants. A distinguishing characteristic of L. fischeri is a color change from green to purple due to anthocyanin biosynthesis. We chromatographically isolated and identified two anthocyanins and two flavones upregulated by drought stress using liquid chromatography-mass spectrometry and nuclear magnetic resonance analyses in this plant for the first time. In contrast, all types of caffeoylquinic acids (CQAs) and flavonol contents were decreased under drought stress. Further, we performed RNA sequencing to examine the molecular changes in these phenolic compounds at the transcriptome level. In an overview of drought-inducible responses, we identified 2,105 hits for 516 distinct transcripts as drought-responsive genes. Moreover, differentially expressed genes (DEGs) associated with phenylpropanoid biosynthesis accounted for the greatest number of both up- and downregulated DEGs by Kyoto Encyclopedia of Genes and Genomes enrichment analysis. We identified 24 meaningful DEGs based on the regulation of phenylpropanoid biosynthetic genes. Potential drought-responsive genes included upregulated flavone synthase (LfFNS, TRINITY DN31661 c0 g1 i1) and anthocyanin 5-O-glucosyltransferase (LfA5GT1, TRINITY DN782 c0 g1 i1), which could contribute to the high levels of flavones and anthocyanins under drought stress in L. fischeri. In addition, the downregulated shikimate O-hydroxycinnamolytransferase (LfHCT, TRINITY DN31661 c0 g1 i1) and hydroxycinnamoyl-CoA quinate/shikimate transferase (LfHQT4, TRINITY DN15180 c0 g1 i1) genes led to a reduction in CQAs. Only one or two BLASTP hits for LfHCT were obtained for six different Asteraceae species. It is possible that the HCT gene plays a crucial role in CQAs biosynthesis in these species. These findings expand our knowledge of the response mechanisms to drought stress, particularly regarding the regulation of key phenylpropanoid biosynthetic genes in L. fischeri.

Molecular characterization reveals that OsSAPK3 improves drought tolerance and grain yield in rice

BACKGROUND

Many data suggest that the sucrose non-fermenting 1-related kinases 2 (SnRK2s) are very important to abiotic stress for plants. In rice, these kinases are known as osmotic stress/ABA-activated protein kinases (SAPKs). Osmotic stress/ABA-activated protein kinase 3 (OsSAPK3) is a member of SnRK2II in rice, but its function is still unclear.

RESULTS

The expression of OsSAPK3 was up regulated by drought, NaCl, PEG and ABA. OsSAPK3 mutated seedings (sapk3-1 and sapk3-2) showed reduced hypersensitivity to exogenous ABA. In addition, under drought conditions, sapk3-1 and sapk3-2 showed more intolerance to drought, including decreased survival rate, increased water loss rate, increased stomatal conductance and significantly decreased expression levels of SLAC1 and SLAC7. Physiological and metabolic analyses showed that OsSAPK3 might play an important role in drought stress signaling pathway by affecting osmotic adjustment and osmolytes, ROS detoxification and expression of ABA dependent and independent dehydration-responsive genes. All gronomic traits analyses demonstrated that OsSAPK3 could improve rice yield by affecting the regulation of tiller numbers and grain size.

CONCLUSION

OsSAPK3 plays an important role in both ABA-dependent and ABA-independent drought stress responses. More interestingly, OsSAPK3 could improve rice yield by indirectly regulating tiller number and grain size. These findings provide new insight for the development of drought-resistant rice.

Transcriptomic and metabolic regulatory network characterization of drought responses in tobacco

Drought stress usually causes huge economic losses for tobacco industries. Drought stress exhibits multifaceted impacts on tobacco systems through inducing changes at different levels, such as physiological and chemical changes, changes of gene transcription and metabolic changes. Understanding how plants respond and adapt to drought stress helps generate engineered plants with enhanced drought resistance. In this study, we conducted multiple time point-related physiological, biochemical,transcriptomic and metabolic assays using K326 and its derived mutant 28 (M28) with contrasting drought tolerance. Through integrative analyses of transcriptome and metabolome,we observed dramatic changes of gene expression and metabolic profiles between M28 and K326 before and after drought treatment. we found that some of DEGs function as key enzymes responsible for ABA biosynthesis and metabolic pathway, thereby mitigating impairment of drought stress through ABA signaling dependent pathways. Four DEGs were involved in nitrogen metabolism, leading to synthesis of glutamate (Glu) starting from NO-3 /NO-2 that serves as an indicator for stress responses. Importantly, through regulatory network analyses, we detected several drought induced TFs that regulate expression of genes responsible for ABA biosynthesis through network, indicating direct and indirect involvement of TFs in drought responses in tobacco. Thus, our study sheds some mechanistic insights into how plant responding to drought stress through transcriptomic and metabolic changes in tobacco. It also provides some key TF or non-TF gene candidates for engineering manipulation for breeding new tobacco varieties with enhanced drought tolerance.

The intertwining of Zn-finger motifs and abiotic stress tolerance in plants: Current status and future prospects

Environmental stresses such as drought, high salinity, and low temperature can adversely modulate the field crop's ability by altering the morphological, physiological, and biochemical processes of the plants. It is estimated that about 50% + of the productivity of several crops is limited due to various types of abiotic stresses either presence alone or in combination (s). However, there are two ways plants can survive against these abiotic stresses; a) through management practices and b) through adaptive mechanisms to tolerate plants. These adaptive mechanisms of tolerant plants are mostly linked to their signalling transduction pathway, triggering the action of plant transcription factors and controlling the expression of various stress-regulated genes. In recent times, several studies found that Zn-finger motifs have a significant function during abiotic stress response in plants. In the first report, a wide range of Zn-binding motifs has been recognized and termed Zn-fingers. Since the zinc finger motifs regulate the function of stress-responsive genes. The Zn-finger was first reported as a repeated Zn-binding motif, comprising conserved cysteine (Cys) and histidine (His) ligands, in Xenopus laevis oocytes as a transcription factor (TF) IIIA (or TFIIIA). In the proteins where Zn²⁺ is mainly attached to amino acid residues and thus espousing a tetrahedral coordination geometry. The physical nature of Zn-proteins, defining the attraction of Zn-proteins for Zn²⁺, is crucial for having an in-depth knowledge of how a Zn²⁺ facilitates their characteristic function and how proteins control its mobility (intra and intercellular) as well as cellular availability. The current review summarized the concept, importance and mechanisms of Zn-finger motifs during abiotic stress response in plants.

The cassava (Manihot-esculenta Crantz)'s nitrate transporter NPF4.5, expressed in seedling roots, involved in nitrate flux and osmotic stress

AtNPF4.5/AIT2, which was predicted to be a low-affinity transporter capable for nitrate uptake, was screened by ABA receptor complex in Arabidopsis ten years ago. However, the molecular and biochemical characterizations of AtNPF4.5 in plants remained largely unclear. In this study, the function of a plasma-membrane-localized and root-specifically-expressed gene MeNPF4.5 (Manihot-esculenta NITRATE TRANSPORTER 1 PTR FAMILY4.5), an ortholog of the Arabidopsis thaliana NPF4.5, was investigated in cassava roots as a nitrate efflux transporter on low nitrate medium and an influx transporter following exposure to high concentration of external nitrates. Moreover, RNA interference (RNAi) of MeNPF4.5 reduced the nitrate efflux capacity but the overexpressing cassava seedlings increased the ability of efflux from the elongation to the mature zone of root under low nitrate treatments. Besides, MeNPF4.5-RNAi expression reduced the nitrate influx capacity but enhanced nitrate absorption in parts of overexpressing plants from the meristem, elongation to mature zone of roots under high nitrate conditions. Furthermore, MeNPF4.5-RNAi seedlings survived owing to roots that could grow normally, but the MeNPF4.5-over-expressors showed adverse growth under 7% PEG6000 stress, suggesting that MeNPF4.5 negatively regulated the osmotic stress and was involved in nitrate flux through cassava seedlings.

Analysis and Functional Verification of PlPM19L Gene Associated with Drought-Resistance in Paeonia lactiflora Pall

The herbaceous peony (Paeonia lactiflora Pall.) is widely cultivated as an ornamental, medicinal and edible plant in China. Drought stress can seriously affect the growth of herbaceous peony and reduce its quality. In our previous research, a significantly differentially expressed gene, PM19L, was obtained in herbaceous peony under drought stress based on transcriptome analysis, but little is known about its function. In this study, the first PM19L that was isolated in herbaceous peony was comprised of 910 bp, and was designated as PlPM19L (OP480984). It had a complete open reading frame of 537 bp and encoded a 178-amino acid protein with a molecular weight of 18.95 kDa, which was located in the membrane. When PlPM19L was transferred into tobacco, the transgenic plants had enhanced tolerance to drought stress, potentially due to the increase in the abscisic acid (ABA) content and the reduction in the level of hydrogen peroxide (H₂O₂). In addition, the enhanced ability to scavenge H₂O₂ under drought stress led to improvements in the enzyme activity and the potential photosynthetic capacity. These results combined suggest that PlPM19L is a key factor to conferring drought stress tolerance in herbaceous peony and provide a scientific theoretical basis for the following improvement in the drought resistance of herbaceous peony and other plants through genetic engineering technology.

Nanoparticles: The Plant Saviour under Abiotic Stresses

Climate change significantly affects plant growth and productivity by causing different biotic and abiotic stresses to plants. Among the different abiotic stresses, at the top of the list are salinity, drought, temperature extremes, heavy metals and nutrient imbalances, which contribute to large yield losses of crops in various parts of the world, thereby leading to food insecurity issues. In the quest to improve plants' abiotic stress tolerance, many promising techniques are being investigated. These include the use of nanoparticles, which have been shown to have a positive effect on plant performance under stress conditions. Nanoparticles can be used to deliver nutrients to plants, overcome plant diseases and pathogens, and sense and monitor trace elements that are present in soil by absorbing their signals. A better understanding of the mechanisms of nanoparticles that assist plants to cope with abiotic stresses will help towards the development of more long-term strategies against these stresses. However, the intensity of the challenge also warrants more immediate approaches to mitigate these stresses and enhance crop production in the short term. Therefore, this review provides an update of the responses (physiological, biochemical and molecular) of plants affected by nanoparticles under abiotic stress, and potentially effective strategies to enhance production. Taking into consideration all aspects, this review is intended to help researchers from different fields, such as plant science and nanoscience, to better understand possible innovative approaches to deal with abiotic stresses in agriculture.

Abscisic acid-controlled redox proteome of Arabidopsis and its regulation by heterotrimeric Gβ protein

The plant hormone abscisic acid (ABA) plays crucial roles in regulation of stress responses and growth modulation. Heterotrimeric G-proteins are key mediators of ABA responses. Both ABA and G-proteins have also been implicated in intracellular redox regulation; however, the extent to which reversible protein oxidation manipulates ABA and/or G-protein signaling remains uncharacterized. To probe the role of reversible protein oxidation in plant stress response and its dependence on G-proteins, we determined the ABA-dependent reversible redoxome of wild-type and Gβ-protein null mutant agb1 of Arabidopsis. We quantified 6891 uniquely oxidized cysteine-containing peptides, 923 of which show significant changes in oxidation following ABA treatment. The majority of these changes required the presence of G-proteins. Divergent pathways including primary metabolism, reactive oxygen species response, translation and photosynthesis exhibited both ABA- and G-protein-dependent redox changes, many of which occurred on proteins not previously linked to them. We report the most comprehensive ABA-dependent plant redoxome and uncover a complex network of reversible oxidations that allow ABA and G-proteins to rapidly adjust cellular signaling to adapt to changing environments. Physiological validation of a subset of these observations suggests that functional G-proteins are required to maintain intracellular redox homeostasis and fully execute plant stress responses.

Regulatory mechanisms behind the phenotypic plasticity associated with Setaria italica water deficit tolerance

Drought is one of the main environmental stresses that negatively impacts vegetative and reproductive yield. Water deficit responses are determined by the duration and intensity of the stress, which, together with plant genotype, will define the chances of plant survival. The metabolic adjustments in response to water deficit are complex and involve gene expression modulation regulated by DNA-binding proteins and epigenetic modifications. This last mechanism may also regulate the activity of transposable elements, which in turn impact the expression of nearby loci. Setaria italica plants submitted to five water deficit regimes were analyzed through a phenotypical approach, including growth, physiological, RNA-seq and sRNA-seq analyses. The results showed a progressive reduction in yield as a function of water deficit intensity associated with signaling pathway modulation and metabolic adjustments. We identified a group of loci that were consistently associated with drought responses, some of which were related to water deficit perception, signaling and regulation. Finally, an analysis of the transcriptome and sRNAome allowed us to identify genes putatively regulated by TE- and sRNA-related mechanisms and an intriguing positive correlation between transcript levels and sRNA accumulation in gene body regions. These findings shed light on the processes that allow S. italica to overcome drought and survive under water restrictive conditions.

Regulatory network established by transcription factors transmits drought stress signals in plant

Plants are sessile organisms that evolve with a flexible signal transduction system in order to rapidly respond to environmental changes. Drought, a common abiotic stress, affects multiple plant developmental processes especially growth. In response to drought stress, an intricate hierarchical regulatory network is established in plant to survive from the extreme environment. The transcriptional regulation carried out by transcription factors (TFs) is the most important step for the establishment of the network. In this review, we summarized almost all the TFs that have been reported to participate in drought tolerance (DT) in plant. Totally 466 TFs from 86 plant species that mostly belong to 11 families are collected here. This demonstrates that TFs in these 11 families are the main transcriptional regulators of plant DT. The regulatory network is built by direct protein-protein interaction or mutual regulation of TFs. TFs receive upstream signals possibly via post-transcriptional regulation and output signals to downstream targets via direct binding to their promoters to regulate gene expression.

Transcriptome Approach Reveals the Response Mechanism of Heimia myrtifolia (Lythraceae, Myrtales) to Drought Stress

Drought is a major environmental condition that inhibits the development and cultivation of Heimia myrtifolia. The molecular processes of drought resistance in H. myrtifolia remain unknown, which has limited its application. In our study, transcriptome analyzes were compared across three treatment groups (CK, T1, and T2), to investigate the molecular mechanism of drought resistance. Plant leaves wilted and drooped as the duration of drought stress increased. The relative water content of the leaves declined dramatically, and relative electrolyte leakage rose progressively. Using an RNA-Seq approach, a total of 62,015 unigenes with an average length of 1730 bp were found, with 86.61% of them annotated to seven databases, and 14,272 differentially expressed genes (DEGs) were identified in drought stress. GO and KEGG enrichment analyzes of the DEGs revealed significantly enriched KEGG pathways, including photosynthesis, photosynthetic antenna proteins, plant hormone signal transduction, glutathione metabolism, and ascorbate and aldarate metabolism. Abscisic acid signal transduction was the most prevalent in the plant hormone signal transduction pathway, and other plant hormone signal transductions were also involved in the drought stress response. The transcription factors (including MYB, NAC, WRKY, and bHLH) and related differential genes on significantly enriched pathways all played important roles in the drought process, such as photosynthesis-related genes and antioxidant enzyme genes. In conclusion, this study will provide several genetic resources for further investigation of the molecular processes that will be beneficial to H. myrtifolia cultivation and breeding.

Multienvironment QTL analysis delineates a major locus associated with homoeologous exchanges for water-use efficiency and seed yield in canola

Canola varieties exhibit variation in drought avoidance and drought escape traits, reflecting adaptation to water-deficit environments. Our understanding of underlying genes and their interaction across environments in improving crop productivity is limited. A doubled haploid population was analysed to identify quantitative trait loci (QTL) associated with water-use efficiency (WUE) related traits. High WUE in the vegetative phase was associated with low seed yield. Based on the resequenced parental genome data, we developed sequence-capture-based markers and validated their linkage with carbon isotope discrimination (Δ¹³ C) in an F₂ population. RNA sequencing was performed to determine the expression of candidate genes underlying Δ¹³ C QTL. QTL contributing to main and QTL × environment interaction effects for Δ¹³ C and yield were identified. One multiple-trait QTL for Δ¹³ C, days to flower, plant height, and seed yield was identified on chromosome A09. Interestingly, this QTL region overlapped with a homoeologous exchange (HE) event, suggesting its association with the multiple traits. Transcriptome analysis revealed 121 significantly differentially expressed genes underlying Δ¹³ C QTL on A09 and C09, including in HE regions. Sorting out the negative relationship between vegetative WUE and seed yield is a priority. Genetic and genomic resources and knowledge so developed could improve canola WUE and yield.

PYR/PYL/RCAR Receptors Play a Vital Role in the Abscisic-Acid-Dependent Responses of Plants to External or Internal Stimuli

Abscisic acid (ABA) is a phytohormone that plays a key role in regulating several developmental processes as well as in response to stressful conditions such as drought. Activation of the ABA signaling cascade allows the induction of an appropriate physiological response. The basic components of the ABA signaling pathway have been recognized and characterized in recent years. Pyrabactin resistance, pyrabactin resistance-like, and the regulatory component of ABA receptors (PYR/PYL/RCAR) are the major components responsible for the regulation of the ABA signaling pathway. Here, we review recent findings concerning the PYR/PYL/RCAR receptor structure, function, and interaction with other components of the ABA signaling pathway as well as the termination mechanism of ABA signals in plant cells. Since ABA is one of the basic elements related to abiotic stress, which is increasingly common in the era of climate changes, understanding the perception and transduction of the signal related to this phytohormone is of paramount importance in further increasing crop tolerance to various stress factors.

Metabolic adjustment and regulation of gene expression are essential for increased resistance to severe water deficit and resilience post-stress in soybean

Background

Soybean is the main oilseed crop grown in the world; however, drought stress affects its growth and physiology, reducing its yield. The objective of this study was to characterize the physiological, metabolic, and genetic aspects that determine differential resistance to water deficit in soybean genotypes.

Methods

Three soybean genotypes were used in this study, two lineages (L11644 and L13241), and one cultivar (EMBRAPA 48-C48). Plants were grown in pots containing 8 kg of a mixture of soil and sand (2:1) in a greenhouse under sunlight. Soil moisture in the pots was maintained at field capacity until the plants reached the stage of development V4 (third fully expanded leaf). At this time, plants were subjected to three water treatments: Well-Watered (WW) (plants kept under daily irrigation); Water Deficit (WD) (withholding irrigation until plants reached the leaf water potential at predawn of -1.5 ± 0.2 MPa); Rewatered (RW) (plants rehydrated for three days after reached the water deficit). The WW and WD water treatments were evaluated on the eighth day for genotypes L11644 and C48, and on the tenth day for L13241, after interruption of irrigation. For the three genotypes, the treatment RW was evaluated after three days of resumption of irrigation. Physiological, metabolic and gene expression analyses were performed.

Results

Water deficit inhibited growth and gas exchange in all genotypes. The accumulation of osmolytes and the concentrations of chlorophylls and abscisic acid (ABA) were higher in L13241 under stress. The metabolic adjustment of lineages in response to WD occurred in order to accumulate amino acids, carbohydrates, and polyamines in leaves. The expression of genes involved in drought resistance responses was more strongly induced in L13241. In general, rehydration provided recovery of plants to similar conditions of control treatment. Although the C48 and L11644 genotypes have shown some tolerance and resilience responses to severe water deficit, greater efficiency was observed in the L13241 genotype through adjustments in morphological, physiological, genetic and metabolic characteristics that are combined in the same plant. This study contributes to the advancement in the knowledge about the resistance to drought in cultivated plants and provides bases for the genetic improvement of the soybean culture.

C2H2 Zinc Finger Proteins Response to Abiotic Stress in Plants

Abiotic stresses have already exhibited the negative effects on crop growth and development, thereby influencing crop quality and yield. Therefore, plants have developed regulatory mechanisms to adopt against such harsh changing environmental conditions. Recent studies have shown that zinc finger protein transcription factors play a crucial role in plant growth and development as well as in stress response. C2H2 zinc finger proteins are one of the best-studied types and have been shown to play diverse roles in the plant abiotic stress responses. However, the C2H2 zinc finger network in plants is complex and needs to be further studied in abiotic stress responses. Here in this review, we mainly focus on recent findings on the regulatory mechanisms, summarize the structural and functional characterization of C2H2 zinc finger proteins, and discuss the C2H2 zinc finger proteins involved in the different signal pathways in plant responses to abiotic stress.

Transcript profiles of wild and domesticated sorghum under water-stressed conditions and the differential impact on dhurrin metabolism

MAIN CONCLUSION

Australian native species of sorghum contain negligible amounts of dhurrin in their leaves and the cyanogenesis process is regulated differently under water-stress in comparison to domesticated sorghum species. Cyanogenesis in forage sorghum is a major concern in agriculture as the leaves of domesticated sorghum are potentially toxic to livestock, especially at times of drought which induces increased production of the cyanogenic glucoside dhurrin. The wild sorghum species endemic to Australia have a negligible content of dhurrin in the above ground tissues and thus represent a potential resource for key agricultural traits like low toxicity. In this study we investigated the differential expression of cyanogenesis related genes in the leaf tissue of the domesticated species Sorghum bicolor and the Australian native wild species Sorghum macrospermum grown in glasshouse-controlled water-stress conditions using RNA-Seq analysis to analyse gene expression. The study identified genes, including those in the cyanogenesis pathway, that were differentially regulated in response to water-stress in domesticated and wild sorghum. In the domesticated sorghum, dhurrin content was significantly higher compared to that in the wild sorghum and increased with stress and decreased with age whereas in wild sorghum the dhurrin content remained negligible. The key genes in dhurrin biosynthesis, CYP79A1, CYP71E1 and UGT85B1, were shown to be highly expressed in S. bicolor. DHR and HNL encoding the dhurrinase and α-hydroxynitrilase catalysing bio-activation of dhurrin were also highly expressed in S. bicolor. Analysis of the differences in expression of cyanogenesis related genes between domesticated and wild sorghum species may allow the use of these genetic resources to produce more acyanogenic varieties in the future.

Meta-Analysis as a Tool to Identify Candidate Genes Involved in the Fagus sylvatica L. Abiotic Stress Response

In this study, we aimed to evaluate whether candidate genes for abiotic stresses in Fagus sylvatica L. are also candidate genes for herbaceous plants, with the purpose of better defining the abiotic stress response model of F. sylvatica. Therefore, a meta-analysis was performed on published papers related to abiotic stress. Firstly, we carried out a systematic review regarding the activity of 24 candidate genes selected for F. sylvatica under abiotic stress reported in 503 articles. After choosing the inclusion criteria, 73 articles out of 503, regarding 12 candidate genes, were included in this analysis. We performed an exploratory meta-analysis based on the random-effect model and the combined effect-size approach (Cohen’s d). The results obtained through Forest and Funnel plots indicate that the candidate genes for F. sylvatica are considered to be candidate genes in other herbaceous species. These results allowed us to set up models of plants’ response to abiotic stresses implementing the stress models in forest species. The results of this study will serve to bridge knowledge gaps regarding the pathways of response to abiotic stresses in trees based on the meta-analysis. The study approach used could be extended to observe larger gene databases and different species.

A Novel WRKY Transcription Factor from Ipomoea trifida, ItfWRKY70, Confers Drought Tolerance in Sweet Potato

WRKY transcription factors are one of the important families in plants, and have important roles in plant growth, abiotic stress responses, and defense regulation. In this study, we isolated a WRKY gene, ItfWRKY70, from the wild relative of sweet potato Ipomoea trifida (H.B.K.) G. Don. This gene was highly expressed in leaf tissue and strongly induced by 20% PEG6000 and 100 μM abscisic acid (ABA). Subcellar localization analyses indicated that ItfWRKY70 was localized in the nucleus. Overexpression of ItfWRKY70 significantly increased drought tolerance in transgenic sweet potato plants. The content of ABA and proline, and the activity of SOD and POD were significantly increased, whereas the content of malondialdehyde (MDA) and H2O2 were decreased in transgenic plants under drought stress. Overexpression of ItfWRKY70 up-regulated the genes involved in ABA biosynthesis, stress-response, ROS-scavenging system, and stomatal aperture in transgenic plants under drought stress. Taken together, these results demonstrated that ItfWRKY70 plays a positive role in drought tolerance by accumulating the content of ABA, regulating stomatal aperture and activating the ROS scavenging system in sweet potato.

Gene Co-Expression Analysis Reveals Transcriptome Divergence between Wild and Cultivated Sugarcane under Drought Stress

Drought is the main abiotic stress that constrains sugarcane growth and production. To understand the molecular mechanisms that govern drought stress, we performed a comprehensive comparative analysis of physiological changes and transcriptome dynamics related to drought stress of highly drought-resistant (ROC22, cultivated genotype) and weakly drought-resistant (Badila, wild genotype) sugarcane, in a time-course experiment (0 h, 4 h, 8 h, 16 h and 32 h). Physiological examination reviewed that ROC22, which shows superior drought tolerance relative to Badila, has high performance photosynthesis and better anti-oxidation defenses under drought conditions. The time series dataset enabled the identification of important hubs and connections of gene expression networks. We identified 36,956 differentially expressed genes (DEGs) in response to drought stress. Of these, 15,871 DEGs were shared by the two genotypes, and 16,662 and 4423 DEGs were unique to ROC22 and Badila, respectively. Abscisic acid (ABA)-activated signaling pathway, response to water deprivation, response to salt stress and photosynthesis-related processes showed significant enrichment in the two genotypes under drought stress. At 4 h of drought stress, ROC22 had earlier stress signal transduction and specific up-regulation of the processes response to ABA, L-proline biosynthesis and MAPK signaling pathway–plant than Badila. WGCNA analysis used to compile a gene regulatory network for ROC22 and Badila leaves exposed to drought stress revealed important candidate genes, including several classical transcription factors: NAC87, JAMYB, bHLH84, NAC21/22, HOX24 and MYB102, which are related to some antioxidants and trehalose, and other genes. These results provide new insights and resources for future research and cultivation of drought-tolerant sugarcane varieties.

Inter-tissue and inter-organ signaling in drought stress response and phenotyping of drought tolerance

Plant response to drought stress includes systems for intracellular regulation of gene expression and signaling, as well as inter-tissue and inter-organ signaling, which helps entire plants acquire stress resistance. Plants sense water-deficit conditions both via the stomata of leaves and roots, and transfer water-deficit signals from roots to shoots via inter-organ signaling. Abscisic acid is an important phytohormone involved in the drought stress response and adaptation, and is synthesized mainly in vascular tissues and guard cells of leaves. In leaves, stress-induced abscisic acid is distributed to various tissues by transporters, which activates stomatal closure and expression of stress-related genes to acquire drought stress resistance. Moreover, the stepwise stress response at the whole-plant level is important for proper understanding of the physiological response to drought conditions. Drought stress is sensed by multiple types of sensors as molecular patterns of abiotic stress signals, which are transmitted via separate parallel signaling networks to induce downstream responses, including stomatal closure and synthesis of stress-related proteins and metabolites. Peptide molecules play important roles in the inter-organ signaling of dehydration from roots to shoots, as well as signaling of osmotic changes and reactive oxygen species/Ca²⁺ . In this review, we have summarized recent advances in research on complex plant drought stress responses, focusing on inter-tissue signaling in leaves and inter-organ signaling from roots to shoots. We have discussed the mechanisms via which drought stress adaptations and resistance are acquired at the whole-plant level, and have proposed the importance of quantitative phenotyping for measuring plant growth under drought conditions.

Serendipita indica alleviates drought stress responses in walnut (Juglans regia L.) seedlings by stimulating osmotic adjustment and antioxidant defense system

Juglans regia L. is a good host for Serendipita indica. Under drought condition, seedlings colonized with S. indica showed higher values in plant height, total fresh biomass, root/shoot ratio, relative growth rate, leaf relative water content and chlorophyll content, gas exchange parameters, maximal photochemical efficiency, photochemical quenching, and effective photosystem II quantum yield than the uncolonized seedlings. It suggested beneficial effects of S. indica on host plants' growth and physiological parameters in response to drought. In comparison with the uncolonized seedlings, S. indica-colonized seedlings showed lower levels in hydrogen peroxide, superoxide anion, malondialdehyde, and relative electrical conductivity under drought condition, suggesting the ability of S. indica to prevent or retard the accumulation of reactive oxygen species and to diminish the oxidative injure. Furthermore, walnut seedlings responded to drought by actively accumulating osmotic regulation substances including soluble protein, soluble sugar, and proline. Root colonization with S. indica was more conductive to the accumulation. Moreover, in response to drought stress, walnut seedlings, regardless of colonization, increased activities of superoxide dismutase, catalase, peroxidase, ascorbate peroxidase, dehydroascorbate reductase, monodehydroascorbate reductase, and glutathione reductase, levels of ascorbate and glutathione, and ratios of reduced ascorbate/dehydroascorbic acid and reduced glutathione/oxidized glutathione in leaves and roots. S. indica colonization induced much more increase in the abovementioned indicators as compared to the uncolonized seedlings. Overall, S. indica colonization alleviated the detrimental effects of drought stress by altering root system, enhancing osmotic adjustment, and repressing the accumulation of reactive oxygen species via stimulating antioxidant system including enzymatic and nonenzymatic components. KEY POINTS: • S. indica stimulated root growth of walnut seedlings under drought condition. • S. indica accelerated osmotic adjustment under drought condition. • S. indica activated antioxidant defense mechanism under drought condition.

Prioritization of biological processes based on the reconstruction and analysis of associative gene networks describing the response of plants to adverse environmental factors

Methods for prioritizing or ranking candidate genes according to their importance based on specif ic criteria via the analysis of gene networks are widely used in biomedicine to search for genes associated with diseases and to predict biomarkers, pharmacological targets and other clinically relevant molecules. These methods have also been used in other f ields, particularly in crop production. This is largely due to the development of technologies to solve problems in marker-oriented and genomic selection, which requires knowledge of the molecular genetic mechanisms underlying the formation of agriculturally valuable traits. A new direction for the study of molecular genetic mechanisms is the prioritization of biological processes based on the analysis of associative gene networks. Associative gene networks are heterogeneous networks whose vertices can depict both molecular genetic objects (genes, proteins, metabolites, etc.) and the higher-level factors (biological processes, diseases, external environmental factors, etc.) related to regulatory, physicochemical or associative interactions. Using a previously developed method, biological processes involved in plant responses to increased cadmium content, saline stress and drought conditions were prioritized according to their degree of connection with the gene networks in the SOLANUM TUBEROSUM knowledge base. The prioritization results indicate that fundamental processes, such as gene expression, post-translational modif ications, protein degradation, programmed cell death, photosynthesis, signal transmission and stress response play important roles in the common molecular genetic mechanisms for plant response to various adverse factors. On the other hand, a group of processes related to the development of seeds (“seeding development”) was revealed to be drought specif ic, while processes associated with ion transport (“ion transport”) were included in the list of responses specif ic to salt stress and processes associated with the metabolism of lipids were found to be involved specif ically in the response to cadmium.

BASIC PENTACYSTEINE2 negatively regulates osmotic stress tolerance by modulating LEA4-5 expression in Arabidopsis thaliana

Osmotic stress substantially affects plant growth and development. Study of plant transcription factors involved in osmotic stress can enhance our understanding of the mechanisms of plant osmotic stress tolerance and how the tolerance of plants to osmotic stress can be improved. Here, we identified the specific function of Arabidopsis thaliana BARLEY B RECOMBINANT/BASIC PENTACYSTEINE transcription factor, BPC2, in the osmotic stress response. Phenotypic analysis showed that loss-of-function of BPC2 led to an increase in osmotic stress tolerance in the seedling growth stage. Physiological analysis showed that mutation of BPC2 in Arabidopsis alleviated osmotic-induced increases in H₂O₂ accumulation, the malondialdehyde (MDA) content, and percent electrolyte leakage. BPC2 was localized in the nucleus. RNA-seq and qRT-PCR analysis showed that BPC2 could negatively regulate the expression of late embryogenesis abundant (LEA) genes (LEA3, LEA4-2, and LEA4-5). Further analysis showed that BPC2 could directly bind to the promoter of LEA4-5 in vitro and in vivo. Overexpression of BPC2 enhanced hypersensitivity to osmotic stress in the seedling growth stage. Overexpression of BPC2 led to decreases in LEA4-5 expression and aggravated osmotic-induced increases in H₂O₂ accumulation, the MDA content, and percent electrolyte leakage. Overall, our results indicate that BPC2 negatively regulates LEA4-5 expression to modulate osmotic-induced H₂O₂ accumulation, the MDA content, and percent electrolyte leakage, all of which affect the osmotic stress response in Arabidopsis thaliana.

A draft genome provides hypotheses on drought tolerance in a keystone plant species in Western North America threatened by climate change

Climate change presents distinct ecological and physiological challenges to plants as extreme climate events become more common. Understanding how species have adapted to drought, especially ecologically important nonmodel organisms, will be crucial to elucidate potential biological pathways for drought adaptation and inform conservation strategies. To aid in genome-to-phenome research, a draft genome was assembled for a diploid individual of Artemisia tridentata subsp. tridentata, a threatened keystone shrub in western North America. While this taxon has few genetic resources available and genetic/genomics work has proven difficult due to genetic heterozygosity in the past, a draft genome was successfully assembled. Aquaporin (AQP) genes and their promoter sequences were mined from the draft genome to predict mechanisms regulating gene expression and generate hypotheses on key genes underpinning drought response. Fifty-one AQP genes were fully assembled within the draft genome. Promoter and phylogenetic analyses revealed putative duplicates of A. tridentata subsp. tridentata AQPs which have experienced differentiation in promoter elements, potentially supporting novel biological pathways. Comparison with nondrought-tolerant congener supports enrichments of AQP genes in this taxon during adaptation to drought stress. Differentiation of promoter elements revealed that paralogues of some genes have evolved to function in different pathways, highlighting these genes as potential candidates for future research and providing critical hypotheses for future genome-to-phenome work.

Direct and Indirect Transcriptional Effects of Abiotic Stress in Zea mays Plants Defective in RNA-Directed DNA Methylation

Plants respond to abiotic stress stimuli, such as water deprivation, through a hierarchical cascade that includes detection and signaling to mediate transcriptional and physiological changes. The phytohormone abscisic acid (ABA) is well-characterized for its regulatory role in these processes in response to specific environmental cues. ABA-mediated changes in gene expression have been demonstrated to be temporally-dependent, however, the genome-wide timing of these responses are not well-characterized in the agronomically important crop plant Zea mays (maize). ABA-mediated responses are synergistic with other regulatory mechanisms, including the plant-specific RNA-directed DNA methylation (RdDM) epigenetic pathway. Our prior work demonstrated that after relatively long-term ABA induction (8 h), maize plants homozygous for the mop1-1 mutation, defective in a component of the RdDM pathway, exhibit enhanced transcriptional sensitivity to the phytohormone. At this time-point, many hierarchically positioned transcription factors are differentially expressed resulting in primary (direct) and secondary (indirect) transcriptional outcomes. To identify more immediate and direct MOP1-dependent responses to ABA, we conducted a transcriptomic analysis using mop1-1 mutant and wild type plants treated with ABA for 1 h. One h of ABA treatment was sufficient to induce unique categories of differentially expressed genes (DEGs) in mop1-1. A comparative analysis between the two time-points revealed that distinct epigenetically-regulated changes in gene expression occur within the early stages of ABA induction, and that these changes are predicted to influence less immediate, indirect transcriptional responses. Homology with MOP1-dependent siRNAs and a gene regulatory network (GRN) were used to identify putative immediate and indirect targets, respectively. By manipulating two key regulatory networks in a temporal dependent manner, we identified genes and biological processes regulated by RdDM and ABA-mediated stress responses. Consistent with mis-regulation of gene expression, mop1-1 homozygous plants are compromised in their ability to recover from water deprivation. Collectively, these results indicate transcriptionally and physiologically relevant roles for MOP1-mediated regulation of gene expression of plant responses to environmental stress.

Isotopically Dimethyl Labeling-Based Quantitative Proteomic Analysis of Phosphoproteomes of Soybean Cultivars

Isotopically dimethyl labeling was applied in a quantitative post-translational modification (PTM) proteomic study of phosphoproteomic changes in the drought responses of two contrasting soybean cultivars. A total of 9457 phosphopeptides were identified subsequently, corresponding to 4571 phosphoprotein groups and 3889 leading phosphoproteins, which contained nine kinase families consisting of 279 kinases. These phosphoproteins contained a total of 8087 phosphosites, 6106 of which were newly identified and constituted 54% of the current soybean phosphosite repository. These phosphosites were converted into the highly conserved kinase docking sites by bioinformatics analysis, which predicted six kinase families that matched with those newly found nine kinase families. The overly post-translationally modified proteins (OPP) occupies 2.1% of these leading phosphoproteins. Most of these OPPs are photoreceptors, mRNA-, histone-, and phospholipid-binding proteins, as well as protein kinase/phosphatases. The subgroup population distribution of phosphoproteins over the number of phosphosites of phosphoproteins follows the exponential decay law, Y = 4.13e-0.098X - 0.04. Out of 218 significantly regulated unique phosphopeptide groups, 188 phosphoproteins were regulated by the drought-tolerant cultivar under the water loss condition. These significantly regulated phosphoproteins (SRP) are mainly enriched in the biological functions of water transport and deprivation, methionine metabolic processes, photosynthesis/light reaction, and response to cadmium ion, osmotic stress, and ABA response. Seventeen and 15 SRPs are protein kinases/phosphatases and transcription factors, respectively. Bioinformatics analysis again revealed that three members of the calcium dependent protein kinase family (CAMK family), GmSRK2I, GmCIPK25, and GmAKINβ1 kinases, constitute a phosphor-relay-mediated signal transduction network, regulating ion channel activities and many nuclear events in this drought-tolerant cultivar, which presumably contributes to the development of the soybean drought tolerance under water deprivation process.

Detecting drought regulators using stochastic inference in Bayesian networks

Drought is a natural hazard that affects crops by inducing water stress. Water stress, induced by drought accounts for more loss in crop yield than all the other causes combined. With the increasing frequency and intensity of droughts worldwide, it is essential to develop drought-resistant crops to ensure food security. In this paper, we model multiple drought signaling pathways in Arabidopsis using Bayesian networks to identify potential regulators of drought-responsive reporter genes. Genetically intervening at these regulators can help develop drought-resistant crops. We create the Bayesian network model from the biological literature and determine its parameters from publicly available data. We conduct inference on this model using a stochastic simulation technique known as likelihood weighting to determine the best regulators of drought-responsive reporter genes. Our analysis reveals that activating MYC2 or inhibiting ATAF1 are the best single node intervention strategies to regulate the drought-responsive reporter genes. Additionally, we observe simultaneously activating MYC2 and inhibiting ATAF1 is a better strategy. The Bayesian network model indicated that MYC2 and ATAF1 are possible regulators of the drought response. Validation experiments showed that ATAF1 negatively regulated the drought response. Thus intervening at ATAF1 has the potential to create drought-resistant crops.

Potato Response to Drought Stress: Physiological and Growth Basis

Drought poses a major challenge to the production of potatoes worldwide. Climate change is predicted to further aggravate this challenge by intensifying potato crop exposure to increased drought severity and frequency. There is an ongoing effort to adapt our production systems of potatoes through the development of drought-tolerant cultivars that are appropriately engineered for the changing environment. The breeding of drought-tolerant cultivars can be approached through the identification of drought-related physiological and biochemical traits and their deployment in new potato cultivars. Thus, the main objective of this study was to develop a method to identify and characterize the drought-tolerant potato genotypes and the related key traits. To achieve this objective, first we studied 56 potato genotypes including 54 cultivars and 2 advanced breeding lines to assess drought tolerance in terms of tuber yield in the greenhouse experiment. Drought differentially reduced tuber yield in all genotypes. Based on their capacity to maintain percent tuber yield under drought relative to their well-watered controls, potato genotypes differed in their ability to tolerate drought. We then selected six genotypes, Bannock Russet, Nipigon, Onaway, Denali, Fundy, and Russet Norkotah, with distinct yield responses to drought to further examine the physiological and biochemical traits governing drought tolerance. The drought-induced reduction in tuber yield was only 15-20% for Bannock Russet and Nipigon, 44-47% for Onaway and Denali, and 83-91% for Fundy and Russet Norkotah. The tolerant genotypes, Bannock Russet and Nipigon, exhibited about a 2-3-fold increase in instantaneous water-use efficiency (WUE) under drought as compared with their well-watered controls. This stimulation was about 1.8-2-fold for moderately tolerant genotypes, Onaway and Denali, and only 1.5-fold for sensitive genotypes, Fundy, and Russet Norkotah. The differential stimulation of instantaneous WUE of tolerant and moderately tolerant genotypes vs. sensitive genotypes was accounted for by the differential suppression of the rates of photosynthesis, stomatal conductance, and transpiration rates across genotypes. Potato genotypes varied in their response to leaf protein content under drought. We suggest that the rates of photosynthesis, instantaneous WUE, and leaf protein content can be used as the selection criteria for the drought-tolerant potato genotypes.

Cellular Phosphorylation Signaling and Gene Expression in Drought Stress Responses: ABA-Dependent and ABA-Independent Regulatory Systems

Drought is a severe and complex abiotic stress that negatively affects plant growth and crop yields. Numerous genes with various functions are induced in response to drought stress to acquire drought stress tolerance. The phytohormone abscisic acid (ABA) accumulates mainly in the leaves in response to drought stress and then activates subclass III SNF1-related protein kinases 2 (SnRK2s), which are key phosphoregulators of ABA signaling. ABA mediates a wide variety of gene expression processes through stress-responsive transcription factors, including ABA-RESPONSIVE ELEMENT BINDING PROTEINS (AREBs)/ABRE-BINDING FACTORS (ABFs) and several other transcription factors. Seed plants have another type of SnRK2s, ABA-unresponsive subclass I SnRK2s, that mediates the stability of gene expression through the mRNA decay pathway and plant growth under drought stress in an ABA-independent manner. Recent research has elucidated the upstream regulators of SnRK2s, RAF-like protein kinases, involved in early responses to drought stress. ABA-independent transcriptional regulatory systems and ABA-responsive regulation function in drought-responsive gene expression. DEHYDRATION RESPONSIVE ELEMENT (DRE) is an important cis-acting element in ABA-independent transcription, whereas ABA-RESPONSIVE ELEMENT (ABRE) cis-acting element functions in ABA-responsive transcription. In this review article, we summarize recent advances in research on cellular and molecular drought stress responses and focus on phosphorylation signaling and transcription networks in Arabidopsis and crops. We also highlight gene networks of transcriptional regulation through two major regulatory pathways, ABA-dependent and ABA-independent pathways, that ABA-responsive subclass III SnRK2s and ABA-unresponsive subclass I SnRK2s mediate, respectively. We also discuss crosstalk in these regulatory systems under drought stress.

Threat at One End of the Plant: What Travels to Inform the Other Parts?

Adaptation and response to environmental changes require dynamic and fast information distribution within the plant body. If one part of a plant is exposed to stress, attacked by other organisms or exposed to any other kind of threat, the information travels to neighboring organs and even neighboring plants and activates appropriate responses. The information flow is mediated by fast-traveling small metabolites, hormones, proteins/peptides, RNAs or volatiles. Electric and hydraulic waves also participate in signal propagation. The signaling molecules move from one cell to the neighboring cell, via the plasmodesmata, through the apoplast, within the vascular tissue or-as volatiles-through the air. A threat-specific response in a systemic tissue probably requires a combination of different traveling compounds. The propagating signals must travel over long distances and multiple barriers, and the signal intensity declines with increasing distance. This requires permanent amplification processes, feedback loops and cross-talks among the different traveling molecules and probably a short-term memory, to refresh the propagation process. Recent studies show that volatiles activate defense responses in systemic tissues but also play important roles in the maintenance of the propagation of traveling signals within the plant. The distal organs can respond immediately to the systemic signals or memorize the threat information and respond faster and stronger when they are exposed again to the same or even another threat. Transmission and storage of information is accompanied by loss of specificity about the threat that activated the process. I summarize our knowledge about the proposed long-distance traveling compounds and discuss their possible connections.

Identification and Characterization of the APX Gene Family and Its Expression Pattern under Phytohormone Treatment and Abiotic Stress in Populus trichocarpa

Ascorbate peroxidase (APX) is a member of class I of the heme-containing peroxidase family. The enzyme plays important roles in scavenging reactive oxygen species for protection against oxidative damage and maintaining normal plant growth and development, as well as in biotic stress responses. In this study, we identified 11 APX genes in the Populus trichocarpa genome using bioinformatic methods. Phylogenetic analysis revealed that the PtrAPX proteins were classifiable into three clades and the members of each clade shared similar gene structures and motifs. The PtrAPX genes were distributed on six chromosomes and four segmental-duplicated gene pairs were identified. Promoter cis-elements analysis showed that the majority of PtrAPX genes contained a variety of phytohormone- and abiotic stress-related cis-elements. Tissue-specific expression profiles indicated that the PtrAPX genes primarily function in roots and leaves. Real-time quantitative PCR (RT-qPCR) analysis indicated that PtrAPX transcription was induced in response to drought, salinity, high ammonium concentration, and exogenous abscisic acid treatment. These results provide important information on the phylogenetic relationships and functions of the APX gene family in P. trichocarpa.

Priming with a Seaweed Extract Strongly Improves Drought Tolerance in Arabidopsis

Drought represents a major threat to plants in natural ecosystems and agricultural settings. The biostimulant Super Fifty (SF), produced from the brown alga Ascophyllum nodosum, enables ecologically friendly stress mitigation. We investigated the physiological and whole-genome transcriptome responses of Arabidopsis thaliana to drought stress after a treatment with SF. SF strongly decreased drought-induced damage. Accumulation of reactive oxygen species (ROS), which typically stifle plant growth during drought, was reduced in SF-primed plants. Relative water content remained high in SF-treated plants, whilst ion leakage, a measure of cell damage, was reduced compared to controls. Plant growth requires a functional shoot apical meristem (SAM). Expression of a stress-responsive negative growth regulator, RESPONSIVE TO DESICCATION 26 (RD26), was repressed by SF treatment at the SAM, consistent with the model that SF priming maintains the function of the SAM during drought stress. Accordingly, expression of the cell cycle marker gene HISTONE H4 (HIS4) was maintained at the SAMs of SF-primed plants, revealing active cell cycle progression after SF priming during drought. In accordance with this, CYCP2;1, which promotes meristem cell division, was repressed by drought but enhanced by SF. SF also positively affected stomatal behavior to support the tolerance to drought stress. Collectively, our data show that SF priming mitigates multiple cellular processes that otherwise impair plant growth under drought stress, thereby providing a knowledge basis for future research on crops.

Transcriptional Regulation of Drought Response in Arabidopsis and Woody Plants

Within the context of global warming, long-living plants such as perennial woody species endure adverse conditions. Among all of the abiotic stresses, drought stress is one of the most detrimental stresses that inhibit plant growth and productivity. Plants have evolved multiple mechanisms to respond to drought stress, among which transcriptional regulation is one of the key mechanisms. In this review, we summarize recent progress on the regulation of drought response by transcription factor (TF) families, which include abscisic acid (ABA)-dependent ABA-responsive element/ABRE-binding factors (ABRE/ABF), WRKY, and Nuclear Factor Y families, as well as ABA-independent AP2/ERF and NAC families, in the model plant Arabidopsis. We also review what is known in woody species, particularly Populus, due to its importance and relevance in economic and ecological processes. We discuss opportunities for a deeper understanding of drought response in woody plants with the development of high-throughput omics analyses and advanced genome editing techniques.

Drought Stress Responses and Resistance in Plants: From Cellular Responses to Long-Distance Intercellular Communication

The drought stress responses of vascular plants are complex regulatory mechanisms because they include various physiological responses from signal perception under water deficit conditions to the acquisition of drought stress resistance at the whole-plant level. It is thought that plants first recognize water deficit conditions in roots and that several molecular signals then move from roots to shoots. Finally, a phytohormone, abscisic acid (ABA) is synthesized mainly in leaves. However, the detailed molecular mechanisms of stress sensors and the regulators that initiate ABA biosynthesis in response to drought stress conditions are still unclear. Another important issue is how plants adjust ABA propagation, stress-mediated gene expression and metabolite composition to acquire drought stress resistance in different tissues throughout the whole plant. In this review, we summarize recent advances in research on drought stress responses, focusing on long-distance signaling from roots to shoots, ABA synthesis and transport, and metabolic regulation in both cellular and whole-plant levels of Arabidopsis and crops. We also discuss coordinated mechanisms for acquiring drought stress adaptations and resistance via tissue-to-tissue communication and long-distance signaling.

Elevated CO2-induced changes in photosynthesis, antioxidant enzymes and signal transduction enzyme of soybean under drought stress

Rising atmospheric [CO2] influences plant growth, development, productivity and stress responses. Soybean is a major oil crop. At present, it is unclear how elevated [CO2] affects the physiological and biochemical pathways of soybean under drought stress. In this study, changes in the photosynthetic capacity, photosynthetic pigment and antioxidant level were evaluated in soybean at flowering stages under different [CO2] (400 μmol mol-1 and 600 μmol mol-1) and water level (the relative water content of the soil was 75-85% soil capacity, and the relative water content of the soil was 35-45% soil capacity under drought stress). Changes in levels of osmolytes, hormones and signal transduction enzymes were also determined. The results showed that under drought stress, increasing [CO2] significantly reduced leaf transpiration rate (E), net photosynthetic rate (PN) and chlorophyll b content. Elevated [CO2] significantly decreased the content of malondialdehyde (MDA) and proline (PRO), while significantly increased superoxide dismutase (SOD) and abscisic acid (ABA) under drought stress. Elevated [CO2] significantly increased the transcript and protein levels of calcium-dependent protein kinase (CDPK), and Glutathione S- transferase (GST). The content of HSP-70 and the corresponding gene expression level were significantly reduced by elevated [CO2], irrespective of water treatments. Taken together, these results suggest that elevated [CO2] does not alleviate the negative impacts of drought stress on photosynthesis. ABA, CDPK and GST may play an important role in elevated CO2-induced drought stress responses.

Phenotyping in Arabidopsis and Crops-Are We Addressing the Same Traits? A Case Study in Tomato

The convenient model Arabidopsis thaliana has allowed tremendous advances in plant genetics and physiology, in spite of only being a weed. It has also unveiled the main molecular networks governing, among others, abiotic stress responses. Through the use of the latest genomic tools, Arabidopsis research is nowadays being translated to agronomically interesting crop models such as tomato, but at a lagging pace. Knowledge transfer has been hindered by invariable differences in plant architecture and behaviour, as well as the divergent direct objectives of research in Arabidopsis versus crops compromise transferability. In this sense, phenotype translation is still a very complex matter. Here, we point out the challenges of "translational phenotyping" in the case study of drought stress phenotyping in Arabidopsis and tomato. After briefly defining and describing drought stress and survival strategies, we compare drought stress protocols and phenotyping techniques most commonly used in the two species, and discuss their potential to gain insights, which are truly transferable between species. This review is intended to be a starting point for discussion about translational phenotyping approaches among plant scientists, and provides a useful compendium of methods and techniques used in modern phenotyping for this specific plant pair as a case study.