The influence of salt stress on ABA and auxin concentrations in two maize cultivars differing in salt resistance

The regulating mechanism of salt tolerance of black walnut seedlings was revealed by the physiological and biochemical integration analysis

Salt stress is an important abiotic stress that seriously affects plant growth. In order to research the salt tolerance of walnut rootstocks so as to provide scientific basis for screening salt-tolerant walnut rootstocks, two kinds of black walnut seedlings, Juglans microcarpa L. (JM) and Juglans nigra L. (JN), were treated under salt stress with different concentrations of NaCl (0, 50, 100, and 200 mM) and the growth situation of seedlings were observed. The physiological indexes of JM and JN seedlings were also measured in different days after treatment. Our study showed salt stress inhibited seedlings growth and limited biomass accumulation. Walnut mainly increased osmotic adjustment ability by accumulation Pro and SS. Furthermore, with the duration of treatment time increased, SOD and APX activities decreased, TPC and TFC contents increased. Walnut accumulated Na mostly in roots and transported more K and Ca to aboveground parts. The growth and physiological response performance differed between JM and JN, specifically, the differences occurred in the ability to absorb minerals, regulate osmotic stress, and scavenge ROS. Salt tolerance of JM and JN was assessed by principal component analysis (PCA) and resulted in JN > JM. In conclusion, our results indicated that JN has higher salt tolerance than JM, and JN might be used as a potential germplasm resource for the genetic breeding of walnuts.

Plant Metabolomics: Current Initiatives and Future Prospects

Plant metabolomics is a rapidly advancing field of plant sciences and systems biology. It involves comprehensive analyses of small molecules (metabolites) in plant tissues and cells. These metabolites include a wide range of compounds, such as sugars, amino acids, organic acids, secondary metabolites (e.g., alkaloids and flavonoids), lipids, and more. Metabolomics allows an understanding of the functional roles of specific metabolites in plants' physiology, development, and responses to biotic and abiotic stresses. It can lead to the identification of metabolites linked with specific traits or functions. Plant metabolic networks and pathways can be better understood with the help of metabolomics. Researchers can determine how plants react to environmental cues or genetic modifications by examining how metabolite profiles change under various crop stages. Metabolomics plays a major role in crop improvement and biotechnology. Integrating metabolomics data with other omics data (genomics, transcriptomics, and proteomics) provides a more comprehensive perspective of plant biology. This systems biology approach enables researchers to understand the complex interactions within organisms.

Multi-Omics Revealed Peanut Root Metabolism Regulated by Exogenous Calcium under Salt Stress

High salinity severely inhibits plant seedling root development and metabolism. Although plant salt tolerance can be improved by exogenous calcium supplementation, the metabolism molecular mechanisms involved remain unclear. In this study, we integrated three types of omics data (transcriptome, metabolome, and phytohormone absolute quantification) to analyze the metabolic profiles of peanut seedling roots as regulated by exogenous calcium under salt stress. (1) exogenous calcium supplementation enhanced the allocation of carbohydrates to the TCA cycle and plant cell wall biosynthesis rather than the shikimate pathway influenced by up-regulating the gene expression of antioxidant enzymes under salt stress; (2) exogenous calcium induced further ABA accumulation under salt stress by up-regulating the gene expression of ABA biosynthesis key enzymes AAO2 and AAO3 while down-regulating ABA glycosylation enzyme UGT71C5 expression; (3) exogenous calcium supplementation under salt stress restored the trans-zeatin absolute content to unstressed levels while inhibiting the root cis-zeatin biosynthesis.

A Review of Potato Salt Tolerance

Potato is the world's fourth largest food crop. Due to limited arable land and an ever-increasing demand for food from a growing population, it is critical to increase crop yields on existing acreage. Soil salinization is an increasing problem that dramatically impacts crop yields and restricts the growing area of potato. One possible solution to this problem is the development of salt-tolerant transgenic potato cultivars. In this work, we review the current potato planting distribution and the ways in which it overlaps with salinized land, in addition to covering the development and utilization of potato salt-tolerant cultivars. We also provide an overview of the current progress toward identifying potato salt tolerance genes and how they may be deployed to overcome the current challenges facing potato growers.

Exploration of plant growth promoting traits and regulatory mechanisms of Bacillus anthracis PM21 in enhancing salt stress tolerance in maize

Bacillus species have been reported to reduce the negative effects of salt stress on plants; the involvement of Bacillus anthracis PM21 and the internal mechanisms involved in this process are unclear. The effects of PM21 inoculation on maize plants under salt stress were investigated in this study. The study aimed to assess the ability of Bacillus anthracis PM21 to endure high levels of salinity stress while preserving the concentration of plant growth regulators. The biomass, photosynthetic pigments, relative water content (RWC), antioxidants, osmoprotectants, inorganic ion contents, regulation of plant hormones and expression of antioxidants enzyme encoded genes were investigated under normal and salinity stress conditions. Bacillus anthracis PM21 produced a significant amount of 1-aminocyclopropane-1-carboxylate deaminase enzyme (ACC deaminase) and exopolysaccharides (EPS) under salt stress and normal conditions. PM21 also produced plant growth stimulants including indole acetic acid, gibberellic acid (GA3), kinetin, and siderophore under salinity stress and normal conditions. Under salt stress, PM21 inoculation markedly increased plant growth indices, stimulate antioxidant enzyme mechanisms, osmoprotectants, and chlorophyll content. The use of qRT-PCR to analyze the transcription of targeted genes indicated greater expression of antioxidant-encoded genes and inferred their possible function in salinity stress tolerance. Our findings shed light on the functions of PM21 and its regulatory mechanisms in plant salt stress tolerance, as well as the importance of PM21 in this process. This study will provide a thorough analysis of the theoretical framework for adopting PM21 in agricultural production as an eco-friendly method to enhance crop growth and yield under salinity stress.

Insights into Adaptive Regulation of the Leaf-Petiole System: Strategies for Survival of Water Lily Plants under Salt Stress

The water lily (Nymphaea tetragona) is an ancient angiosperm that belongs to the Nymphaeaceae family. As a rooted floating-leaf plant, water lilies are generally cultivated in fresh water, therefore, little is known about their survival strategies under salt stress. Long-term salt stress causes morphological changes, such as the rapid regeneration of floating leaves and a significant decrease in leaf number and surface area. We demonstrate that salt stress induces toxicity soon after treatment, but plants can adapt by regenerating floating leaves that are photosynthetically active. Transcriptome profiling revealed that ion binding was one of the most-enriched GO terms in leaf-petiole systems under salt stress. Sodium-transporter-related genes were downregulated, whereas K+ transporter genes were both up- and downregulated. These results suggest that restricting intracellular Na+ importing while maintaining balanced K+ homeostasis is an adaptive strategy for tolerating long-term salt stress. ICP-MS analysis identified the petioles and leaves as Na-hyperaccumulators, with a maximum content of over 80 g kg−1 DW under salt stress. Mapping of the Na-hyperaccumulation trait onto the phylogenetic relationships revealed that water lily plants might have a long evolutionary history from ancient marine plants, or may have undergone historical ecological events from salt to fresh water. Ammonium transporter genes involved in nitrogen metabolism were downregulated, whereas NO3−-related transporters were upregulated in both the leaves and petioles, suggesting a selective bias toward NO3− uptake under salt stress. The morphological changes we observed may be due to the reduced expression of genes related to auxin signal transduction. In conclusion, the floating leaves and submerged petioles of the water lily use a series of adaptive strategies to survive salt stress. These include the absorption and transport of ions and nutrients from the surrounding environments, and the ability to hyperaccumulate Na+. These adaptations may serve as the physiological basis for salt tolerance in water lily plants.

Nitrogen application improves salt tolerance of grape seedlings via regulating hormone metabolism

Salt stress is a dominant environmental factor that restricts the growth and yield of crops. Nitrogen is an essential mineral element for plants, regulates various physiological and biochemical processes, and has been reported to enhance salt tolerance in plants. However, the crosstalk between salt and nitrogen in grapes is not well understood. In this study, we found that nitrogen supplementation (0.01 and 0.1 mol L-1 NH4 NO3 ) significantly increased the accumulation of proline, chlorophyll, Na+ , NH4 + , and NO3 - , while it reduced the malondialdehyde content and inhibited photosynthetic performance under salt stress conditions (200 mmol L-1 NaCl). Further transcriptome and metabolome analyses showed that a total of 4890 differentially expressed genes (DEGs) and 753 differently accumulated metabolites (DAMs) were identified. Joint omics results revealed that plant hormone signal transduction pathway connected the DEGs and DAMs. In-depth analysis revealed that nitrogen supplementation increased the levels of endogenous abscisic acid, salicylic acid, and jasmonic acid by inducing the expression of 11, 4, and 13 genes related to their respective biosynthesis pathway. In contrast, endogenous indoleacetic acid content was significantly reduced due to the remarkable regulation of seven genes of its biosynthetic pathway. The modulation in hormone contents subsequently activated the differential expression of 13, 10, 12, and 29 genes of the respective downstream hormone signaling transduction pathways. Overall, all results indicate that moderate nitrogen supplementation could improve salt tolerance by regulating grape physiology and endogenous hormone homeostasis, as well as the expression of key genes in signaling pathways, which provides new insights into the interactions between mineral elements and salt stress.

The Biocontrol Potential of Endophytic Trichoderma Fungi Isolated from Hungarian Grapevines, Part II, Grapevine Stimulation

In the first part of this two-piece publication, the isolation, identification and in vitro characterization of ten endophytic Trichoderma isolates were reported. Here we report the ability of two different mixes of some of these isolates (Trichoderma simmonsii, Trichoderma orientale and Trichoderma gamsii as well as of Trichoderma afroharzianum and T. simmonsii) to colonize and stimulate the growth of grapevines. Two commercial vineyards about 400 km away from the site of isolation were used as experimental fields, from which the strains of three Trichoderma species were re-isolated up to four years after rootstock soaking treatment with conidiospores, performed before planting. The treatments decreased the overall percentage of lost plants of about 30%, although a low number of lost plants (about 5%) were observed also in the control plot. For all cultivars and clones, the Trichoderma treatments significantly increased both the bud burst ratio and bud burst vigor index. In addition, the grape must parameters such as the Brix degrees, as well as the extract, the D-glucose and the D-fructose concentrations all appeared to be improved, suggesting a potentially higher ethanol content of the produced wine. We conclude that grapevine-endophytic Trichoderma isolates promote plant growth, which could be a useful feature for sustainable agriculture in general and integrated plant production in particular.

De novo transcriptome analysis of high-salinity stress-induced antioxidant activity and plant phytohormone alterations in Sesuvium portulacastrum

Sesuvium portulacastrum has a strong salt tolerance and can grow in saline and alkaline coastal and inland habitats. This study investigated the physiological and molecular responses of S. portulacastrum to high salinity by analyzing the changes in plant phytohormones and antioxidant activity, including their differentially expressed genes (DEGs) under similar high-salinity conditions. High salinity significantly affected proline (Pro) and hydrogen peroxide (H2O2) in S. portulacastrum seedlings, increasing Pro and H2O2 contents by 290.56 and 83.36%, respectively, compared to the control. Antioxidant activities, including superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), significantly increased by 83.05, 205.14, and 751.87%, respectively, under high salinity. Meanwhile, abscisic acid (ABA) and gibberellic acid (GA3) contents showed the reverse trend of high salt treatment. De novo transcriptome analysis showed that 36,676 unigenes were matched, and 3,622 salt stress-induced DEGs were identified as being associated with the metabolic and biological regulation processes of antioxidant activity and plant phytohormones. POD and SOD were upregulated under high-salinity conditions. In addition, the transcription levels of genes involved in auxin (SAURs and GH3), ethylene (ERF1, ERF3, ERF114, and ABR1), ABA (PP2C), and GA3 (PIF3) transport or signaling were altered. This study identified key metabolic and biological processes and putative genes involved in the high salt tolerance of S. portulacastrum and it is of great significance for identifying new salt-tolerant genes to promote ecological restoration of the coastal strand.

Pseudomonas and Curtobacterium Strains from Olive Rhizosphere Characterized and Evaluated for Plant Growth Promoting Traits

Plant growth promoting (PGP) bacteria are known to enhance plant growth and protect them from environmental stresses through different pathways. The rhizosphere of perennial plants, including olive, may represent a relevant reservoir of PGP bacteria. Here, seven bacterial strains isolated from olive rhizosphere have been characterized taxonomically by 16S sequencing and biochemically, to evaluate their PGP potential. Most strains were identified as Pseudomonas or Bacillus spp., while the most promising ones belonged to genera Pseudomonas and Curtobacterium. Those strains have been tested for their capacity to grow under osmotic or salinity stress and to improve the germination and early development of Triticum durum subjected or not to those stresses. The selected strains had the ability to grow under severe stress, and a positive effect has been observed in non-stressed seedlings inoculated with one of the Pseudomonas strains, which showed promising characteristics that should be further evaluated. The biochemical and taxonomical characterization of bacterial strains isolated from different niches and the evaluation of their interaction with plants under varying conditions will help to increase our knowledge on PGP microorganisms and their use in agriculture.

The root apoplastic pH as an integrator of plant signaling

Plant nutrition, growth, and response to environmental stresses are pH-dependent processes that are regulated at the apoplastic and subcellular levels. The root apoplastic pH is especially sensitive to external cues and can also be modified by intracellular inputs, such as hormonal signaling. Optimal crosstalk of the mechanisms involved in the extent and span of the apoplast pH fluctuations promotes plant resilience to detrimental biotic and abiotic factors. The fact that variations in local pHs are a standard mechanism in different signaling pathways indicates that the pH itself can be the pivotal element to provide a physiological context to plant cell regions, allowing a proportional reaction to different situations. This review brings a collective vision of the causes that initiate root apoplastic pHs variations, their interaction, and how they influence root response outcomes.

An Insight into Abiotic Stress and Influx Tolerance Mechanisms in Plants to Cope in Saline Environments

Simple Summary

This review focuses on plant growth and development harmed by abiotic stress, primarily salt stress. Salt stress raises the intracellular osmotic pressure, leading to hazardous sodium buildup. Plants react to salt stress signals by regulating ion homeostasis, activating the osmotic stress pathway, modulating plant hormone signaling, and altering cytoskeleton dynamics and cell wall composition. Understanding the processes underlying these physiological and biochemical responses to salt stress could lead to more effective agricultural crop yield measures. In this review, researchers outline recent advances in plant salt stress control. The study of plant salt tolerance processes is essential, both theoretically and practically, to improve agricultural output, produce novel salt-tolerant cultivars, and make full use of saline soil. Based on past research, this paper discusses the adverse effects of salt stress on plants, including photosynthesis suppression, ion homeostasis disturbance, and membrane peroxidation. The authors have also covered the physiological mechanisms of salt tolerance, such as the scavenging of reactive oxygen species and osmotic adjustment. This study further identifies specific salt stress-responsive mechanisms linked to physiological systems. Based on previous studies, this article reviews the current methodologies and techniques for improving plant salt tolerance. Overall, it is hoped that the above-mentioned points will impart helpful background information for future agricultural and crop plant production.

Abstract

Salinity is significant abiotic stress that affects the majority of agricultural, irrigated, and cultivated land. It is an issue of global importance, causing many socio-economic problems. Salt stress mainly occurs due to two factors: (1) soil type and (2) irrigation water. It is a major environmental constraint, limiting crop growth, plant productivity, and agricultural yield. Soil salinity is a major problem that considerably distorts ecological habitats in arid and semi-arid regions. Excess salts in the soil affect plant nutrient uptake and osmotic balance, leading to osmotic and ionic stress. Plant adaptation or tolerance to salinity stress involves complex physiological traits, metabolic pathways, the production of enzymes, compatible solutes, metabolites, and molecular or genetic networks. Different plant species have different salt overly sensitive pathways and high-affinity K⁺ channel transporters that maintain ion homeostasis. However, little progress has been made in developing salt-tolerant crop varieties using different breeding approaches. This review highlights the interlinking of plant morpho-physiological, molecular, biochemical, and genetic approaches to produce salt-tolerant plant species. Most of the research emphasizes the significance of plant growth-promoting rhizobacteria in protecting plants from biotic and abiotic stressors. Plant growth, survival, and yield can be stabilized by utilizing this knowledge using different breeding and agronomical techniques. This information marks existing research areas and future gaps that require more attention to reveal new salt tolerance determinants in plants—in the future, creating genetically modified plants could help increase crop growth and the toleration of saline environments.

Integrative analysis of the pharmaceutical active ingredient and transcriptome of the aerial parts of Glycyrrhiza uralensis under salt stress reveals liquiritin accumulation via ABA-mediated signaling

The aerial parts of Glycyrrhiza uralensis supply substantial raw material for the extraction of active pharmaceutical ingredients comprehensively utilized in many industries. Our previous study indicated that salt stress increased the content of active ingredients. However, the regulatory mechanism remains unclear. In this study, RNA-sequencing (RNA-seq) of the aerial parts of G. uralensis treated with 150 mM NaCl for 0, 2, 6, and 12 h was performed to identify the key genes and metabolic pathways regulating pharmacological active component accumulation. The main active component detection showed that liquiritin was the major ingredient and exhibited more than a ten-fold significant increase in the 6 h NaCl treatment. Temporal expression analysis of the obtained 4245 differentially expressed genes (DEGs) obtained by RNA-seq revealed two screened profiles that included the significant up-regulated DEGs (UDEGs) at different treatment points. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of these UDEGs identified phenylpropanoid metabolism and flavonoid biosynthesis as the most significantly enriched pathways in 2 h treated materials. Interestingly, the carotenoid biosynthesis pathway that is related to ABA synthesis was also discovered, and the ABA content was significantly promoted after 6 h NaCl treatment. Following ABA stimulation, the content of liquiritin demonstrated a significant and immediate increase after 2 h treatment, with the corresponding consistent expression of genes involved in the pathways of ABA signal transduction and flavonoid biosynthesis, but not in the pathway of glycyrrhizic acid biosynthesis. Our study concludes that salt stress might promote liquiritin accumulation through the ABA-mediated signaling pathway, and provides effective reference for genetic improvement and comprehensive utilization of G. uralensis.

The Caucasian Clover Gene TaMYC2 Responds to Abiotic Stress and Improves Tolerance by Increasing the Activity of Antioxidant Enzymes

Abiotic stress affects metabolic processes in plants and restricts plant growth and development. In this experiment, Caucasian clover (Trifolium ambiguum M. Bieb.) was used as a material, and the CDS of TaMYC2, which is involved in regulating the response to abiotic stress, was cloned. The CDS of TaMYC2 was 726 bp in length and encoded 241 amino acids. The protein encoded by TaMYC2 was determined to be unstable, be highly hydrophilic, and contain 23 phosphorylation sites. Subcellular localization results showed that TaMYC2 was localized in the nucleus. TaMYC2 responded to salt, alkali, cold, and drought stress and could be induced by IAA, GA3, and MeJA. By analyzing the gene expression and antioxidant enzyme activity in plants before and after stress, we found that drought and cold stress could induce the expression of TaMYC2 and increase the antioxidant enzyme activity. TaMYC2 could also induce the expression of ROS scavenging-related and stress-responsive genes and increase the activity of antioxidant enzymes, thus improving the ability of plants to resist stress. The results of this experiment provide references for subsequent in-depth exploration of both the function of TaMYC2 in and the molecular mechanism underlying the resistance of Caucasian clover.

Insight Between the Epigenetics and Transcription Responding of Cotton Hypocotyl Cellular Elongation Under Salt-Alkaline Stress

Gossypium barbadense is a cultivated cotton not only known for producing superior fiber but also for its salt and alkaline resistance. Here, we used Whole Genome Bisulfite Sequencing (WGBS) technology to map the cytosine methylation of the whole genome of the G. barbadense hypocotyl at single base resolution. The methylation sequencing results showed that the mapping rates of the three samples were 75.32, 77.54, and 77.94%, respectively. In addition, the Bisulfite Sequence (BS) conversion rate was 99.78%. Approximately 71.03, 53.87, and 6.26% of the cytosine were methylated at CG, CHG, and CHH sequence contexts, respectively. A comprehensive analysis of DNA methylation and transcriptome data showed that the methylation level of the promoter region was a positive correlation in the CHH context. Saline-alkaline stress was related to the methylation changes of many genes, transcription factors (TFs) and transposable elements (TEs), respectively. We explored the regulatory mechanism of DNA methylation in response to salt and alkaline stress during cotton hypocotyl elongation. Our data shed light into the relationship of methylation regulation at the germination stage of G. barbadense hypocotyl cell elongation and salt-alkali treatment. The results of this research help understand the early growth regulation mechanism of G. barbadense in response to abiotic stress.

Phytohormone profiles in non-transformed and AtCKX transgenic centaury (Centaurium erythraea Rafn) shoots and roots in response to salinity stress in vitro

Plant hormones regulate numerous developmental and physiological processes. Abiotic stresses considerably affect production and distribution of phytohormones as the stress signal triggers. The homeostasis of plant hormones is controlled by their de novo synthesis and catabolism. The aim of this work was to analyse the contents of total and individual groups of endogenous cytokinins (CKs) as well as indole-3-acetic acid (IAA) in AtCKX overexpressing centaury plants grown in vitro on graded NaCl concentrations (0, 50, 100, 150, 200 mM). The levels of endogenous stress hormones including abscisic acid (ABA), salicylic acid (SA) and jasmonic acid (JA) were also detected. The elevated contents of total CKs were found in all analysed centaury shoots. Furthermore, increased amounts of all five CK groups, as well as enhanced total CKs were revealed on graded NaCl concentrations in non-transformed and AtCKX roots. All analysed AtCKX centaury lines exhibited decreased amounts of endogenous IAA in shoots and roots. Consequently, the IAA/bioactive CK forms ratios showed a significant variation in the shoots and roots of all AtCKX lines. In shoots and roots of both non-transformed and AtCKX transgenic centaury plants, salinity was associated with an increase of ABA and JA and a decrease of SA content.

OsCYP714D1 improves plant growth and salt tolerance through regulating gibberellin and ion homeostasis in transgenic poplar

Cytochrome P450 monooxygenases (CYP450s) play crucial roles in the regulation of plant growth and response to abiotic stress. However, their functions in woody trees are still largely unknown. Previously, we reported that expression of the rice cytochrome P450 monooxygenase gene OsCYP714D1 increased gibberellic acid (GA) accumulation and shoot growth in transgenic poplar. In this work, we demonstrate that expression of OsCYP714D1 improved the salt tolerance of transgenic poplar plants. Compared to wild type, plant height and K⁺ content were significantly higher, whereas plant growth inhibition and Na⁺ content were significantly lower, in transgenic plants grown under high salt stress condition. Transcriptomic analyses revealed that OsCYP714D1 expression up-regulated the expressions of GA biosynthesis, signaling and stress responsive genes in transgenic plants under both normal and high salt stress conditions. Further gene ontology (GO) analyses indicated that genes involved in plant hormone and ion metabolic activities were significantly enriched in transgenic plants. Our findings imply that OsCYP714D1 participated in the regulation of both shoot growth and salt resistance through regulating gibberellin and ion homeostasis in transgenic poplar, and it can be used as a candidate gene for the engineering of new tree varieties with improved biomass production and salt stress resistance.

Crucial Cell Signaling Compounds Crosstalk and Integrative Multi-Omics Techniques for Salinity Stress Tolerance in Plants

In the era of rapid climate change, abiotic stresses are the primary cause for yield gap in major agricultural crops. Among them, salinity is considered a calamitous stress due to its global distribution and consequences. Salinity affects plant processes and growth by imposing osmotic stress and destroys ionic and redox signaling. It also affects phytohormone homeostasis, which leads to oxidative stress and eventually imbalances metabolic activity. In this situation, signaling compound crosstalk such as gasotransmitters [nitric oxide (NO), hydrogen sulfide (H2S), hydrogen peroxide (H2O2), calcium (Ca), reactive oxygen species (ROS)] and plant growth regulators (auxin, ethylene, abscisic acid, and salicylic acid) have a decisive role in regulating plant stress signaling and administer unfavorable circumstances including salinity stress. Moreover, recent significant progress in omics techniques (transcriptomics, genomics, proteomics, and metabolomics) have helped to reinforce the deep understanding of molecular insight in multiple stress tolerance. Currently, there is very little information on gasotransmitters and plant growth regulator crosstalk and inadequacy of information regarding the integration of multi-omics technology during salinity stress. Therefore, there is an urgent need to understand the crucial cell signaling crosstalk mechanisms and integrative multi-omics techniques to provide a more direct approach for salinity stress tolerance. To address the above-mentioned words, this review covers the common mechanisms of signaling compounds and role of different signaling crosstalk under salinity stress tolerance. Thereafter, we mention the integration of different omics technology and compile recent information with respect to salinity stress tolerance.

Two Auxinic Herbicides Affect Brassica napus Plant Hormone Levels and Induce Molecular Changes in Transcription

With the introduction of the new auxinic herbicide halauxifen-methyl into the oilseed rape (Brassica napus) market, there is a need to understand how this new molecule interacts with indigenous plant hormones (e.g., IAA) in terms of crop response. The aim of this study was to investigate the molecular background by using different growth conditions under which three different auxinic herbicides were administered. These were halauxifen-methyl (Hal), alone and together with aminopyralid (AP) as well as picloram (Pic). Three different hormone classes were determined, free and conjugated indole-3-acetic acid (IAA), aminocyclopropane carboxylic acid (ACC) as a precursor for ethylene, and abscisic acid (ABA) at two different temperatures and growth stages as well as over time (2–168 h after treatment). At 15 °C growth temperature, the effect was more pronounced than at 9 °C, and generally, the younger leaves independent of the developmental stage showed a larger effect on the alterations of hormones. IAA and ACC showed reproducible alterations after auxinic herbicide treatments over time, while ABA did not. Finally, a transcriptome analysis after treatment with two auxinic herbicides, Hal and Pic, showed different expression patterns. Hal treatment leads to the upregulation of auxin and hormone responses at 48 h and 96 h. Pic treatment induced the hormone/auxin response already after 2 h, and this continued for the other time points. The more detailed analysis of the auxin response in the datasets indicate a role for GH3 genes and genes encoding auxin efflux proteins. The upregulation of the GH3 genes correlates with the increase in conjugated IAA at the same time points and treatments. Also, genes for were found that confirm the upregulation of the ethylene pathway.

Morphological Analysis, Protein Profiling and Expression Analysis of Auxin Homeostasis Genes of Roots of Two Contrasting Cultivars of Rice Provide Inputs on Mechanisms Involved in Rice Adaptation towards Salinity Stress

Plants remodel their root architecture in response to a salinity stress stimulus. This process is regulated by an array of factors including phytohormones, particularly auxin. In the present study, in order to better understand the mechanisms involved in salinity stress adaptation in rice, we compared two contrasting rice cultivars—Luna Suvarna, a salt tolerant, and IR64, a salt sensitive cultivar. Phenotypic investigations suggested that Luna Suvarna in comparison with IR64 presented stress adaptive root traits which correlated with a higher accumulation of auxin in its roots. The expression level investigation of auxin signaling pathway genes revealed an increase in several auxin homeostasis genes transcript levels in Luna Suvarna compared with IR64 under salinity stress. Furthermore, protein profiling showed 18 proteins that were differentially regulated between the roots of two cultivars, and some of them were salinity stress responsive proteins found exclusively in the proteome of Luna Suvarna roots, revealing the critical role of these proteins in imparting salinity stress tolerance. This included proteins related to the salt overly sensitive pathway, root growth, the reactive oxygen species scavenging system, and abscisic acid activation. Taken together, our results highlight that Luna Suvarna involves a combination of morphological and molecular traits of the root system that could prime the plant to better tolerate salinity stress.

Improving Performance of Salt-Grown Crops by Exogenous Application of Plant Growth Regulators

Soil salinity is one of the major abiotic stresses restricting plant growth and development. Application of plant growth regulators (PGRs) is a possible practical means for minimizing salinity-induced yield losses, and can be used in addition to or as an alternative to crop breeding for enhancing salinity tolerance. The PGRs auxin, cytokinin, nitric oxide, brassinosteroid, gibberellin, salicylic acid, abscisic acid, jasmonate, and ethylene have been advocated for practical use to improve crop performance and yield under saline conditions. This review summarizes the current knowledge of the effectiveness of various PGRs in ameliorating the detrimental effects of salinity on plant growth and development, and elucidates the physiological and genetic mechanisms underlying this process by linking PGRs with their downstream targets and signal transduction pathways. It is shown that, while each of these PGRs possesses an ability to alter plant ionic and redox homeostasis, the complexity of interactions between various PGRs and their involvement in numerous signaling pathways makes it difficult to establish an unequivocal causal link between PGRs and their downstream effectors mediating plants' adaptation to salinity. The beneficial effects of PGRs are also strongly dependent on genotype, the timing of application, and the concentration used. The action spectrum of PGRs is also strongly dependent on salinity levels. Taken together, this results in a rather narrow "window" in which the beneficial effects of PGR are observed, hence limiting their practical application (especially under field conditions). It is concluded that, in the light of the above complexity, and also in the context of the cost-benefit analysis, crop breeding for salinity tolerance remains a more reliable avenue for minimizing the impact of salinity on plant growth and yield. Further progress in the field requires more studies on the underlying cell-based mechanisms of interaction between PGRs and membrane transporters mediating plant ion homeostasis.

One-time abscisic acid priming induces long-term salinity resistance in Vicia faba: Changes in key transcripts, metabolites, and ionic relations

Abscisic acid (ABA) priming is known to enhance plant growth and survival under salinity. However, the mechanisms mediating this long-term acclimatization to salt stress are still obscure. Specifically, the long-term transcriptional changes and their effects on ion relations were never investigated. This motivated us to study the long-term (8 days) effect of one-time 24 h root priming treatment with 10 μM ABA on transcription levels of relevant regulated key genes, osmotically relevant metabolites, and ionic concentrations in Vicia faba grown under 50 mM NaCl salinity. The novelty of this study is that we could demonstrate long-term effects of a one-time ABA application. ABA-priming was found to prevent the salt-induced decline in root and shoot dry matter, improved photosynthesis, and inhibited terminal wilting of plants. It substantially increased the mRNA level of AAPK and 14-3-3 ABA inducible kinases and ion transporters (PM H⁺ -ATPase, VFK1, KUP7, SOS1, and CLC1). These ABA-induced transcriptional changes went along with altered tissue ion patterns. Primed plants accumulated less Na⁺ and Cl^- but more K⁺ , Ca²⁺ , Zn²⁺ , Fe²⁺ , Mn²⁺ , NO₃ ^- , and SO₄ ^2- . Priming changed the composition pattern of organic osmolytes under salinity, with glucose and fructose being dominant in unprimed, whereas sucrose was dominant in the primed plants. We conclude that one-time ABA priming mitigates salt stress in Vicia faba by persistently changing transcription patterns of key genes, stabilizing the ionic and osmotic balance, and improving photosynthesis and growth.

Short-term drought triggers defence mechanisms faster than ABA accumulation in the epiphytic bromeliad Acanthostachys strobilacea

Epiphytic bromeliads might experience drought after a few hours without water, which is especially critical during early life stages. Consequently, juvenile epiphytic bromeliads probably rely on short-term activation of drought tolerance strategies, although the biochemical processes involved are still poorly understood. In this study, we aimed to evaluate the short-term drought response of juvenile plants of the epiphytic bromeliad Acanthostachys strobilacea (Schult. & Schult. f.) Klotzsch. We hypothesized that short-term drought would induce the accumulation of abscisic acid (ABA) and secondary messengers such as reactive oxygen and nitrogen species (ROS and RNS, respectively) before the activation of defence mechanisms. Three-month-old plants were transferred from well-watered to dry substrates and stress markers were assessed at 0, 2, 5, 10, 24, 48, and 72 h. Drought caused a 27.3% decrease in relative water content compared to the well-watered control at 72 h. A nearly 5-fold increment in the ABA content occurred at 72 h of stress, which was about two days after the first detection of peaks in RNS levels and defence mechanisms activation. Indeed, ascorbate peroxidase (EC 1.11.1.11) activities and proline content increased after 10 h, whereas after 24 h a higher catalase (EC 1.11.1.6) activity and osmotic adjustment occurred. Oxidative stress markers and photochemical efficiency of photosystem II indicated no significant damage induced by drought. We concluded that defence mechanisms activation during early drought in juvenile A. strobilacea might be regulated initially by ABA-independent pathways and RNS, while ABA-induced responses are triggered at subsequent stages of stress.

Metabolomic and Biochemical Analysis of Two Potato (Solanum tuberosum L.) Cultivars Exposed to In Vitro Osmotic and Salt Stresses

Globally, many crop production areas are threatened by drought and salinity. Potato (Solanum tuberosum L.) is susceptible to these challenging environmental conditions. In this study, an in vitro approach was employed to compare the tolerance of potato cultivars ‘BARI-401’ (red skin) and ‘Spunta’ (yellow skin). To simulate ionic and osmotic stress, MS media was supplemented with lithium chloride (LiCl 20 mM) and mannitol (150 mM). GC-MS and spectrophotometry techniques were used to determine metabolite accumulation. Other biochemical properties, such as total phenols concentration (TPC), total flavonoids concentration (TFC), antioxidant capacity (DPPH free radical scavenging capacity), polyphenol oxidase (PPO), and peroxidase (POD) activities, were also measured. The two cultivars respond differently to ionic and osmotic stress treatments, with Spunta accumulating more defensive metabolites in response, indicating a higher level of tolerance. While further investigation of the physiological and biochemical responses of these varieties to drought and salinity is required, the approach taken in this paper provides useful information prior to open field evaluation.

Screening of Salt Stress Responsive Genes in Brachypodium distachyon (L.) Beauv. by Transcriptome Analysis

As one of the most common abiotic stresses, salt stress seriously impairs crop yield. Brachypodium distachyon (L.) Beauv. is a model species for studying wheat and other grasses. In the present investigation, the physiological responses of B. distachyon treated with different concentrations of NaCl for 24 h were measured. Therefore, the control and the seedlings of B. distachyon treated with 200 mM NaCl for 24 h were selected for transcriptome analysis. Transcriptome differential analysis showed that a total of 4116 differentially expressed genes (DEGs) were recognized, including 3120 upregulated and 996 downregulated ones. GO enrichment assay indicated that some subsets of genes related to the active oxygen scavenging system, osmoregulatory substance metabolism, and abscisic-acid (ABA)-induced stomatal closure were significantly upregulated under salt stress. The MapMan analysis revealed that the upregulated genes were dramatically enriched in wax metabolic pathways. The expressions of transcription factor (TF) family members such as MYB, bHLH, and AP2/ERF were increased under salt stress, regulating the response of plants to salt stress. Collectively, these findings provided valuable insights into the mechanisms underlying the responses of grass crops to salt stress.

A Survey of Mycoviral Infection in Fusarium spp. Isolated from Maize and Sorghum in Argentina Identifies the First Mycovirus from Fusarium verticillioides

Mycoviruses appear to be widespread in Fusarium species worldwide. The aim of this work was to identify mycoviral infections in Fusarium spp., isolated from maize and sorghum grown in Argentina, and to estimate their potential effects on the pathogenicity and toxigenesis of the host fungus towards maize. Mycoviruses were identified in 2 out of 105 isolates analyzed; Fusarium verticillioides strain Sec505 and Fusarium andiyazi strain 162. They were characterized as members of the genus Mitovirus by high-throughput sequencing and sequence analysis. The F. verticillioides mitovirus was a novel mycovirus whereas the F. andiyazi mitovirus was found to be a new strain of a previously identified mitovirus. We have named these mitoviruses, Fusarium verticillioides mitovirus 1 (FvMV1) and Fusarium andiyazi mitovirus 1 strain 162 (FaMV1-162). To our knowledge, FvMV1 is the first mycovirus reported as naturally infecting F. verticillioides, the major causal agent of ear rot and fumonisin producer in corn. Both mitoviruses exhibited 100% vertical transmission rate to microconidia. The Fa162 strain infected with FaMV1-162 did not show phenotypic alterations. In contract, F. verticillioides Sec505 infected with FvMV1 showed increased virulence as well as microconidia and fumonisin-B1 production, compared with two uninfected strains. These results suggest that FvMV1 could have a role in modulating F. verticillioides pathogenicity and toxin production worth further exploring.

Brown gold of marginal soil: Plant growth promoting bacteria to overcome plant abiotic stress for agriculture, biofuels and carbon sequestration

Marginal land is defined as land with poor soil characteristics and low crop productivity with no potential for profit. Poor soil quality due to the presence of xenobiotics or climate change is of great concern. Sustainable food production with increasing population is a challenge which becomes more difficult due to poor soil quality. Marginal soil can be made productive with the use of Plant Growth Promoting Bacteria (PGPB). This review outlines how PGPB can be used to improve marginal soil quality and its implications on agriculture, rhizoremediation, abiotic stress (drought, salinity and heavy metals) tolerance, carbon sequestration and production of biofuels. The feasibility of the idea is supported by several studies which showed maximal increase in the growth of plants inoculated with PGPB than to uninoculated plants grown in marginal soil when compared to the growth of plants inoculated with PGPB in healthy soil. The combination of PGPB and plants grown in marginal soil will serve as a green technology leading to the next green revolution, reduction in soil pollution and fossil fuel use, neutralizing abiotic stress and climate change effects.

Auxin acts as a downstream signaling molecule involved in hydrogen sulfide-induced chilling tolerance in cucumber

This report proves a cross talk between H₂S and IAA in cold stress response, which has presented strong evidence that IAA acts as a downstream signal mediating the H₂S-induced stress tolerance in cucumber seedlings. We evaluated changes in endogenous hydrogen sulfide (H₂S) and indole-3-acetic acid (IAA) emission systems, and the interactive effect of exogenous H₂S and IAA on chilling tolerance in cucumber seedlings. The results showed that chilling stress increased the activity and relative mRNA expression of L-/D-cysteine desulfhydrase (L-/D-CD), which in turn induced the accumulation of endogenous H₂S. Similarly, the endogenous IAA system was triggered by chilling stress. We found that 1.0 mM sodium hydrosulfide (NaHS, an H₂S donor) significantly enhanced the activity of flavin monooxygenase (FMO) and relative expression of FMO-like proteins (YUCCA2), which in turn elevated endogenous IAA levels in cucumber seedlings. However, IAA had little effects on activities of L-/D-CD and endogenous H₂S levels. H₂S-induced IAA production accompanied by increase in chilling tolerance, as shown by the decrease in stress-induced electrolyte leakage (EL) and reactive oxygen species (ROS) accumulation, and increase in gene expressions and enzyme activities of photosynthesis. 1-naphthylphthalamic acid (NPA, an IAA polar transport inhibitor) declined H₂S-induced chilling tolerance and defense genes' expression. However, scavenging of H₂S had a little effect on IAA-induced chilling tolerance. These results suggest that IAA acting as a downstream signaling molecule is involved in the H₂S-induced chilling tolerance in cucumber seedlings.

Metabolomics: A Way Forward for Crop Improvement

Metabolomics is an emerging branch of "omics" and it involves identification and quantification of metabolites and chemical footprints of cellular regulatory processes in different biological species. The metabolome is the total metabolite pool in an organism, which can be measured to characterize genetic or environmental variations. Metabolomics plays a significant role in exploring environment-gene interactions, mutant characterization, phenotyping, identification of biomarkers, and drug discovery. Metabolomics is a promising approach to decipher various metabolic networks that are linked with biotic and abiotic stress tolerance in plants. In this context, metabolomics-assisted breeding enables efficient screening for yield and stress tolerance of crops at the metabolic level. Advanced metabolomics analytical tools, like non-destructive nuclear magnetic resonance spectroscopy (NMR), liquid chromatography mass-spectroscopy (LC-MS), gas chromatography-mass spectrometry (GC-MS), high performance liquid chromatography (HPLC), and direct flow injection (DFI) mass spectrometry, have sped up metabolic profiling. Presently, integrating metabolomics with post-genomics tools has enabled efficient dissection of genetic and phenotypic association in crop plants. This review provides insight into the state-of-the-art plant metabolomics tools for crop improvement. Here, we describe the workflow of plant metabolomics research focusing on the elucidation of biotic and abiotic stress tolerance mechanisms in plants. Furthermore, the potential of metabolomics-assisted breeding for crop improvement and its future applications in speed breeding are also discussed. Mention has also been made of possible bottlenecks and future prospects of plant metabolomics.

Grafting Cucumber Onto Pumpkin Induced Early Stomatal Closure by Increasing ABA Sensitivity Under Salinity Conditions

During early periods of salt stress, reduced stomatal opening can prevent water loss and wilting. Abscisic acid (ABA) signal plays an important role in this process. Here, we show that cucumber grafted onto pumpkin exhibits rapid stomatal closure, which helps plants to adapt to osmotic stress caused by salinity. Increased ABA contents in the roots, xylem sap, and leaves were evaluated in two grafting combinations (self-grafted cucumber and cucumber grafted onto pumpkin rootstock). The expression levels of ABA biosynthetic or signaling related genes NCED2 (9-cis-epoxycarotenoid dioxygenase gene 2), ABCG22 (ATP-binding cassette transporter genes 22), PP2C (type-2C protein phosphatases), and SnRK2.1 (sucrose non-fermenting 1-related protein kinases 2) were investigated. Results showed that a root-sourced ABA signal led to decreased stomatal opening and transpiration in the plants grafted onto pumpkin. Furthermore, plants grafted onto pumpkin had increased sensitivity to ABA, compared with self-grafted cucumbers. The inhibition of ABA biosynthesis with fluridon in roots increased the transpiration rate (Tr) and stomatal conductance (Gs) in the leaves. Our study demonstrated that the roots of pumpkin increases the sensitivity of the scion to ABA delivered from the roots to the shoots, and enhances osmotic tolerance under NaCl stress. Such a mechanism can be greatly exploited to benefit vegetable production particularly in semiarid saline regions.

Alleviation of the effect of salinity on growth and yield of strawberry by foliar spray of selenium-nanoparticles

The present study investigated the beneficial role of selenium-nanoparticles (Se-NPs) in mitigating the adverse effects of soil-salinity on growth and yield of strawberry (Fragaria × ananassa Duch.) plants by maneuvering physiological and biochemical mechanisms. The foliar spray of Se-NPs (10 and 20 mg L^-1) improved the growth and yield parameters of strawberry plants grown on non-saline and different saline soils (0, 25, 50 and 75 mM NaCl), which was attributed to their ability to protect photosynthetic pigments. Se-NPs-treated strawberry plants exhibited higher levels of key osmolytes, including total soluble carbohydrates and free proline, compared with untreated plants under saline conditions. Foliar application of Se-NPs improved salinity tolerance in strawberry by reducing stress-induced lipid peroxidation and H₂O₂ content through enhancing activities of antioxidant enzymes like superoxide dismutase and peroxidase. Additionally, Se-NPs-treated strawberry plants showed accumulation of indole-3-acetic acid and abscisic acid, the vital stress signaling molecules, which are involved in regulating different morphological, physiological and molecular responses of plants to salinity. Moreover, the enhanced levels of organic acids (e.g., malic, citric and succinic acids) and sugars (e.g., glucose, fructose and sucrose) in the fruits of Se-NPs-treated strawberry plants under saline conditions indicated the positive impacts of Se-NPs on the improvement of fruit quality and nutritional values. Our results collectively demonstrate the definite roles of Se-NPs in management of soil salinity-induced adverse effects on not only strawberry plants but also other crops.

Implication of salt stress induces changes in pigment production, antioxidant enzyme activity, and qRT-PCR expression of genes involved in the biosynthetic pathway of Bixa orellana L

The effect of salt stress on pigment synthesis and antioxidant enzyme activity as well as in the genes involved in the biosynthetic pathway of bixin was studied. The 14-day germinated seedlings of Bixa orellana were induced into the various NaCl concentration (0, 25, 50, 75, 100 mM). After 45 days, leaves were taken for pigment analysis, antioxidant assays, and gene expression analysis to study the response of salt stress. The pigment content such as chlorophyll level was increased upon salt stress with a reduction in total carotenoid clearly indicating the adaptability of plants towards the stressed state. The level of β-carotene was increased in the highest concentration of salt stress treatment. The secondary metabolites such as bixin and abscisic acid (ABA) content were also high in elevated concentration of salt-treated seedling than control. The antioxidant enzyme activity was increased with the highest dose of salt stress suggesting the antioxidant enzymes to protect the plant from the deleterious effects. The mRNA transcript gene of the carotenoid biosynthetic pathway such as phytoene synthase (PSY), 1-deoxyxylulose-5-phosphate synthase (DXS), phytoene desaturase (PDS), beta-lycopene cyclase (LCY-β), epsilon lycopene cyclase (LCY-ε), carboxyl methyl transferase (CMT), aldehyde dehydrogenase (ADH), lycopene cleavage dioxygenase (LCD), and carotenoid cleavage dioxygenase (CCD) showed differential expression pattern under salt stress. In addendum, we studied the co-expression network analysis of gene to assess the co-related genes associated in the biosynthesis pathway of carotenoid. From the co-expression analysis result showed, the LCY, PDS, and PSY genes were closely correlated with other genes. These finding may provide insight to the plants to exist in the stress condition and to improve the industrially important pigment production.

Early response to salt ions in maize (Zea mays L.)

Abscisic acid (ABA) regulates leaf growth and transpiration rate of plants exposed to salt stress. Despite the known fact that cell dehydration is instrumental for the modulation of ABA concentrations when NaCl is high in the external environment, it was never tested as to whether sodium (Na) or chlorine (Cl) also modulate ABA concentrations. To answer this question, a hydroponic study on maize (Zea mays) was established, by exposing plants to 50mM of sodium glucosamide or glucosamine chloride. The effect of both ions on ABA was investigated in an early stage before (i) the salt ions accumulated to toxic tissue concentrations and before (ii) cells dehydrated. This allowed studying early responses to Na and Cl separately, well before plants were stressed by these ions. Gas chromatography-mass spectrometry analysis was used to quantify ABA concentrations in roots and in leaves after a period of 2h after ion application. The transcript abundance of the key regulatory enzyme of the biosynthesis of ABA in maize, the 9-cis-epoxycarotenoid dioxygenase gene viviparous 14, was quantified via real-time quantitative-reverse-transcriptase-polymerase-chain-reaction. The results reveal that Cl and Na induce the increase of leaf tissue ABA concentrations at two hours after plants were exposed to 50mM of the ions. Surprisingly, this effect was more pronounced in response to the Cl component. The increase in the guard-cell regulating ABA concentration correlated with a reduced transpiration. Mainly because of this result we suggest that the early accumulation of ABA is useful in maintaining cell turgor.

The pH of the Apoplast: Dynamic Factor with Functional Impact Under Stress

The apoplast is an interconnected compartment with a thin water-film that alkalinizes under stress. This systemic pH increase may be a secondary effect without functional implications, arising from ion movements or proton-pump regulations. On the other hand, there are increasing indications that it is part of a mechanism to withstand stress. Regardless of this controversy, alkalinization of the apoplast has received little attention. The apoplastic pH (pH_apo) increases not only during plant-pathogen interactions but also in response to salinity or drought. Not much is known about the mechanisms that cause the leaf apoplast to alkalinize, nor whether, and if so, how functional impact is conveyed. Controversial explanations have been given, and the unusual complexity of pH_apo regulation is considered as the primary reason behind this lack of knowledge. A gathering of scattered information revealed that changes in pH_apo convey functionality by regulating stomatal aperture via the effects exerted on abscisic acid. Moreover, apoplastic alkalinization may regulate growth under stress, whereas this needs to be verified. In this review, a comprehensive survey about several physiological mechanisms that alkalize the apoplast under stress is given, and the suitability of apoplastic alkalinization as transducing element for the transmission of sensory information is discussed.

Study of phytohormone profile and oxidative metabolism as key process to identification of salinity response in tomato commercial genotypes

Climatic change, intensive agriculture, and worsening water quality induce abiotic stress conditions for plants. Among these factors, salinity stress is a limit factor for plant growth. Therefore, the purpose of this study was to analyze the phytohormones role and oxidative metabolism in response to salt stress of two genotypes of tomato cv. Grand Brix and cv. Marmande RAF, the crops were carried out in a growth chamber. Salinity stress reduces biomass and relative growth rate (RGR) in both genotypes, this effect being greater in cv. Marmande RAF. These results, together with main stress indicator response, the O₂^.-, indicate that cv. Marmande RAF is more sensitive to Saline stress. Grand Brix showed less oxidative stress, because it presented greater detoxification of the O₂^-, due to SOD enzyme activity induction and greater antioxidant capacity. Furthermore, Grand Brix has a better hormonal profile adapted to salt stress resistance, the accumulation of IAA, GA4 and CKs and their beneficial role against oxidative stress could make the difference between resistance and sensitivity to salt stress. On the other hand, a lower ACC concentration, ethylene precursor, combined with a greater O₂^.- detoxification in the cv. Grand Brix could play a fundamental role in tolerance to saline stress. Besides, an increase in ABA levels promotes better stomatal closure, better photosynthesis control and a lower rate of water loss. This data could be essential to select plants with greater resistance to saline stress.

A genome-wide transcriptome map of pistachio (Pistacia vera L.) provides novel insights into salinity-related genes and marker discovery

Background

Pistachio (Pistacia vera L.) is one of the most important commercial nut crops worldwide. It is a salt-tolerant and long-lived tree, with the largest cultivation area in Iran. Climate change and subsequent increased soil salt content have adversely affected the pistachio yield in recent years. However, the lack of genomic/global transcriptomic sequences on P. vera impedes comprehensive researches at the molecular level. Hence, whole transcriptome sequencing is required to gain insight into functional genes and pathways in response to salt stress.

Results

RNA sequencing of a pooled sample representing 24 different tissues of two pistachio cultivars with contrasting salinity tolerance under control and salt treatment by Illumina Hiseq 2000 platform resulted in 368,953,262 clean 100 bp paired-ends reads (90 Gb). Following creating several assemblies and assessing their quality from multiple perspectives, we found that using the annotation-based metrics together with the length-based parameters allows an improved assessment of the transcriptome assembly quality, compared to the solely use of the length-based parameters. The generated assembly by Trinity was adopted for functional annotation and subsequent analyses. In total, 29,119 contigs annotated against all of five public databases, including NR, UniProt, TAIR10, KOG and InterProScan. Among 279 KEGG pathways supported by our assembly, we further examined the pathways involved in the plant hormone biosynthesis and signaling as well as those to be contributed to secondary metabolite biosynthesis due to their importance under salinity stress. In total, 11,337 SSRs were also identified, which the most abundant being dinucleotide repeats. Besides, 13,097 transcripts as candidate stress-responsive genes were identified. Expression of some of these genes experimentally validated through quantitative real-time PCR (qRT-PCR) that further confirmed the accuracy of the assembly. From this analysis, the contrasting expression pattern of NCED3 and SOS1 genes were observed between salt-sensitive and salt-tolerant cultivars.

Conclusion

This study, as the first report on the whole transcriptome survey of P. vera, provides important resources and paves the way for functional and comparative genomic studies on this major tree to discover the salinity tolerance-related markers and stress response mechanisms for breeding of new pistachio cultivars with more salinity tolerance.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3989-7) contains supplementary material, which is available to authorized users.

Trichoderma for climate resilient agriculture

Climate change is one of the biggest challenges of the twenty-first century for sustainable agricultural production. Several reports highlighted the need for better agricultural practices and use of eco-friendly methods for sustainable crop production under such situations. In this context, Trichoderma species could be a model fungus to sustain crop productivity. Currently, these are widely used as inoculants for biocontrol, biofertilization, and phytostimulation. They are reported to improve photosynthetic efficiency, enhance nutrient uptake and increase nitrogen use efficiency in crops. Moreover, they can be used to produce bio-energy, facilitate plants for adaptation and mitigate adverse effect of climate change. The technological advancement in high throughput DNA sequencing and biotechnology provided deep insight into the complex and diverse biotic interactions established in nature by Trichoderma spp. and efforts are being made to translate this knowledge to enhance crop growth, resistance to disease and tolerance to abiotic stresses under field conditions. The discovery of several traits and genes that are involved in the beneficial effects of Trichoderma spp. has resulted in better understanding of the performance of bioinoculants in the field, and will lead to more efficient use of these strains and possibly to their improvement by genetic modification. The present mini-review is an effort to elucidate the molecular basis of plant growth promotion and defence activation by Trichoderma spp. to garner broad perspectives regarding their functioning and applicability for climate resilient agriculture.

Thiourea priming enhances salt tolerance through co-ordinated regulation of microRNAs and hormones in Brassica juncea

Activation of stress tolerance mechanisms demands transcriptional reprogramming. Salt stress, a major threat to plant growth, enhances ROS production and affects transcription through modulation of miRNAs and hormones. The present study delineates salt stress ameliorating action of thiourea (TU, a ROS scavenger) in Brassica juncea and provides mechanistic link between redox, microRNA and hormones. The ameliorative potential of TU towards NaCl stress was related with its ability to decrease ROS accumulation in roots and increase Na+ accumulation in shoots. Small RNA sequencing revealed enrichment of down-regulated miRNAs in NaCl + TU treated roots, indicating transcriptional activation. Ranking analysis identified three key genes including BRX4, CBL10 and PHO1, showing inverse relationship with corresponding miRNA expression, which were responsible for TU mediated stress mitigation. Additionally, ABA level was consistently higher till 24 h in NaCl, while NaCl + TU treated roots showed only transient increase at 4 h suggesting an effective stress management. Jasmonate and auxin levels were also increased, which prioritized defence and facilitated root growth, respectively. Thus, the study highlights redox as one of the "core" components regulating miRNA and hormone levels, and also strengthens the use of TU as a redox priming agent for imparting crop resilience to salt stress.

Expression profiles and hormonal regulation of tobacco NtEXGT gene and its involvement in abiotic stress response

Despite the intensive study of xyloglucan endotransglucosylases/hydrolases, their multifaceted role in plant growth regulation in changing environmental conditions is not yet clarified. The functional role of the large number of genes encoding this group of enzymes is also still unclear. NtEXGT gene encodes one of xyloglucan endotransglucosylases/hydrolases (XTHs) of Nicotiana tabacum L. The highest level of NtEXGT gene expression was detected in young flowers and leaves near the shoot apex. Expression of the NtEXGT gene in leaves was induced by cytokinins, auxins, brassinosteroids and gibberellins. NtEXGT gene was also up-regulated by salinity, drought, cold, cadmium and 10 μM abscisic acid treatments and down-regulated in response to 0 °C and 100 μM abscisic acid. Pretreatment of leaves with fluridone contributed to smaller increase in the level of NtEXGT transcripts in response to drought stress. These data suggest that NtEXGT gene is ABA-regulated and probably implicated in ABA-dependent signaling in response to stress factors. 35S::NtEXGT plants of tobacco showed higher rate of root growth under salt-stress conditions, greater frost and heat tolerance as compared with the wild type tobacco plants.

A Quantitative Profiling Method of Phytohormones and Other Metabolites Applied to Barley Roots Subjected to Salinity Stress

As integral parts of plant signaling networks, phytohormones are involved in the regulation of plant metabolism and growth under adverse environmental conditions, including salinity. Globally, salinity is one of the most severe abiotic stressors with an estimated 800 million hectares of arable land affected. Roots are the first plant organ to sense salinity in the soil, and are the initial site of sodium (Na+) exposure. However, the quantification of phytohormones in roots is challenging, as they are often present at extremely low levels compared to other plant tissues. To overcome this challenge, we developed a high-throughput LC-MS method to quantify ten endogenous phytohormones and their metabolites of diverse chemical classes in roots of barley. This method was validated in a salinity stress experiment with six barley varieties grown hydroponically with and without salinity. In addition to phytohormones, we quantified 52 polar primary metabolites, including some phytohormone precursors, using established GC-MS and LC-MS methods. Phytohormone and metabolite data were correlated with physiological measurements including biomass, plant size and chlorophyll content. Root and leaf elemental analysis was performed to determine Na+ exclusion and K+ retention ability in the studied barley varieties. We identified distinct phytohormone and metabolite signatures as a response to salinity stress in different barley varieties. Abscisic acid increased in the roots of all varieties under salinity stress, and elevated root salicylic acid levels were associated with an increase in leaf chlorophyll content. Furthermore, the landrace Sahara maintained better growth, had lower Na+ levels and maintained high levels of the salinity stress linked metabolite putrescine as well as the phytohormone metabolite cinnamic acid, which has been shown to increase putrescine concentrations in previous studies. This study highlights the importance of root phytohormones under salinity stress and the multi-variety analysis provides an important update to analytical methodology, and adds to the current knowledge of salinity stress responses in plants at the molecular level.

Transcriptome Analysis of the Response to NaCl in Suaeda maritima Provides an Insight into Salt Tolerance Mechanisms in Halophytes

Although salt tolerance is a feature representative of halophytes, most studies on this topic in plants have been conducted on glycophytes. Transcriptome profiles are also available for only a limited number of halophytes. Hence, the present study was conducted to understand the molecular basis of salt tolerance through the transcriptome profiling of the halophyte Suaeda maritima, which is an emerging plant model for research on salt tolerance. Illumina sequencing revealed 72,588 clustered transcripts, including 27,434 that were annotated using BLASTX. Salt application resulted in the 2-fold or greater upregulation of 647 genes and downregulation of 735 genes. Of these, 391 proteins were homologous to proteins in the COGs (cluster of orthologous groups) database, and the majorities were grouped into the poorly characterized category. Approximately 50% of the genes assigned to MapMan pathways showed homology to S. maritima. The majority of such genes represented transcription factors. Several genes also contributed to cell wall and carbohydrate metabolism, ion relation, redox responses and G protein, phosphoinositide and hormone signaling. Real-time PCR was used to validate the results of the deep sequencing for the most of the genes. This study demonstrates the expression of protein kinase C, the target of diacylglycerol in phosphoinositide signaling, for the first time in plants. This study further reveals that the biochemical and molecular responses occurring at several levels are associated with salt tolerance in S. maritima. At the structural level, adaptations to high salinity levels include the remodeling of cell walls and the modification of membrane lipids. At the cellular level, the accumulation of glycinebetaine and the sequestration and exclusion of Na+ appear to be important. Moreover, this study also shows that the processes related to salt tolerance might be highly complex, as reflected by the salt-induced enhancement of transcription factor expression, including hormone-responsive factors, and that this process might be initially triggered by G protein and phosphoinositide signaling.

Mitigation of NaCl Stress by Arbuscular Mycorrhizal Fungi through the Modulation of Osmolytes, Antioxidants and Secondary Metabolites in Mustard (Brassica juncea L.) Plants

Present work was carried out to investigate the possible role of arbuscular mycorrhizal fungi (AMF) in mitigating salinity-induced alterations in Brassica juncea L. Exposure to NaCl stress altered the morphological, physio-biochemical attributes, antioxidant activity, secondary metabolites and phytohormones in the mustard seedlings. The growth and biomass yield, leaf water content, and total chlorophyll content were decreased with NaCl stress. However, AMF-inoculated plants exhibited enhanced shoot and root length, elevated relative water content, enhanced chlorophyll content, and ultimately biomass yield. Lipid peroxidation and proline content were increased by 54.53 and 63.47%, respectively with 200 mM NaCl concentration. Further increase in proline content and decrease in lipid peroxidation was observed in NaCl-treated plants inoculated with AMF. The antioxidants, superoxide dismutase, ascorbate peroxidase, glutathione reductase, and reduced glutathione were increased by 48.35, 54.86, 43.85, and 44.44%, respectively, with 200 mM NaCl concentration. Further increase in these antioxidants has been observed in AMF-colonized plants indicating the alleviating role of AMF to salinity stress through antioxidant modulation. The total phenol, flavonoids, and phytohormones increase with NaCl treatment. However, NaCl-treated plants colonized with AMF showed further increase in the above parameters except ABA, which was reduced with NaCl+AMF treatment over the plants treated with NaCl alone. Our results demonstrated that NaCl caused negative effect on B. juncea seedlings; however, colonization with AMF enhances the NaCl tolerance by reforming the physio-biochemical attributes, activities of antioxidant enzymes, and production of secondary metabolites and phytohormones.

Chloride-inducible transient apoplastic alkalinizations induce stomata closure by controlling abscisic acid distribution between leaf apoplast and guard cells in salt-stressed Vicia faba

Chloride stress causes the leaf apoplast transiently to alkalize, an event that is presumed to contribute to the ability of plants to adapt to saline conditions. However, the initiation of coordinated processes downstream of the alkalinization is unknown. We hypothesize that chloride-inducible pH dynamics are a key chemical feature modulating the compartmental distribution of abscisic acid (ABA) and, as a consequence, affecting stomata aperture. Apoplastic pH and stomata aperture dynamics in intact Vicia faba leaves were monitored by microscopy-based ratio imaging and porometric measurements of stomatal conductance. ABA concentrations in leaf apoplast and guard cells were compared with pH dynamics by gas-chromatography-mass-spectrometry (GC-MS) and liquid-chromatography-tandem-mass spectrometry (LC-MS/MS). Results demonstrate that, upon chloride addition to roots, an alkalizing factor that initiates the pH dynamic propagates from root to leaf in a way similar to xylem-distributed water. In leaves, it induces a systemic transient apoplastic alkalinization that causes apoplastic ABA concentration to increase, followed by an elevation of endogenous guard cell ABA. We conclude that the transient alkalinization, which is a remote effect of chloride stress, modulates the compartmental distribution of ABA between the leaf apoplast and the guard cells and, in this way, is instrumental in inducing stomata closure during the beginning of salinity.

Expression of Brassica napus TTG2, a regulator of trichome development, increases plant sensitivity to salt stress by suppressing the expression of auxin biosynthesis genes

WRKY transcription factors (TFs) are plant specific and play important roles in regulating diverse biological processes. To identify TFs with broad-spectrum effects on various stress responses in Brassica napus, an important oil crop grown across diverse ecological regions worldwide, we functionally characterized Bna.TTG2 genes, which are homologous to the Arabidopsis AtTTG2 (WRKY44) gene. Four Bna.TTG2 genes were capable of rescuing the trichome phenotypes of Arabidopsis ttg2 mutants. Overexpressing one Bna.TTG2 family member, BnaA.TTG2.a.1, remarkably increased trichome numbers in Arabidopsis and B. napus plants. Interestingly, the BnaA.TTG2.a.1-overexpressing plants of both species exhibited increased sensitivity to salt stress. In BnaA.TTG2.a.1-overexpressing Arabidopsis under salt stress, the endogenous indole-3-acetic acid (IAA) content was reduced, and the expression of two auxin biosynthesis genes, TRYPTOPHAN BIOSYNTHESIS 5 (TRP5) and YUCCA2 (YUC2), was downregulated. The results from yeast one-hybrid, electrophoretic mobility shift, and dual-luciferase reporter assays revealed that BnaA.TTG2.a.1 is able to bind to the promoters of TRP5 and YUC2. These data indicated that BnaA.TTG2.a.1 confers salt sensitivity to overexpressing plants by suppressing the expression of IAA synthesis genes and thus lowering IAA levels. Transgenic Arabidopsis plants with an N-terminus-deleted BnaA.TTG2.a.1 no longer showed hypersensitivity to salt stress, suggesting that the N terminus of BnaA.TTG2.a.1 plays a critical role in salt stress responses. Therefore, in addition to its classical function in trichome development, our study reveals a novel role for Bna.TTG2 genes in salt stress responses.

Computed tomography scanning can monitor the effects of soil medium on root system development: an example of salt stress in corn

Seeds and young seedlings often encounter high soluble salt levels in the upmost soil layers, impeding vigorous growth by affecting root establishment. Computed tomography (CT) scanning used at low X-ray doses can help study root development in such conditions non-destructively, because plants are allowed to grow throughout the experiment. Using a high-resolution Toshiba XVision CT scanner, we studied corn (Zea mays L.) root growth under optimal and salt-stressed conditions in 3D and on a weekly basis over 3 weeks. Two groups of three corn plants were grown in the controlled environment of a growth chamber, in mid-sized plastic pots filled with sieved and autoclaved sand. Seedlings were subjected to first CT scanning 1 week after seed planting. Our main research objectives concerning root systems were: (i) to quantify structural complexity from fractal dimensions estimated on skeletal 3-D images built from CT scanning data; (ii) to measure growth from volumes and lengths and the derived relative rates and increments, after isolating primary and secondary roots from the soil medium in CT scanning data; and (iii) to assess differences in complexity and growth per week and over Weeks 1-3 for groups of corn plants. Differences between groups were present from Week 1; starting in Week 2 secondary roots were present and could be isolated, which refined the complexity and growth analyses of root systems. Besides expected Week main effects (P < 0.01 or 0.05), Week × Group interaction (P < 0.05 or 0.10), and Group main effects were observed. Graphical, quantitative, and statistical analyses of CT scanning data were thus completed at an unprecedented level, and provided new and important insights regarding root system development. Repeated CT scanning is the key to a better understanding of the establishment in the soil medium of crop plants such as corn and the assessment of salt stress effects on developing root systems, in complexity, volume, and length.

Metabolic contribution to salt stress in two maize hybrids with contrasting resistance

Salt stress reduces the growth of salt-sensitive plants such as maize. The cultivation of salt-resistant maize varieties might therefore help to reduce yield losses. For the elucidation of the underlying physiological and biochemical processes of a resistant hybrid, we used a gas chromatography mass spectrometry approach and analyzed five different salt stress levels. By comparing a salt-sensitive and a salt-resistant maize hybrid, we were able to identify an accumulation of sugars such as glucose, fructose, and sucrose in leaves as a salt-resistance adaption of the salt-sensitive hybrid. Although, both hybrids showed a strong decrease of the metabolite concentration in the tricarboxylic acid cycle. These decreases resulted in the same reduced catabolism for the salt-sensitive and even the salt-resistant maize hybrid. Surprisingly, the change of root metabolism was negligible under salt stress. Moreover, the salt-resistance mechanisms were the most effective at low salt-stress levels in the leaves of the salt-sensitive maize.