Plant responses to environmental stresses-from gene to biotechnology

A data-driven genome annotation approach for cassava

Genome annotation files play a critical role in dictating the quality of downstream analyses by providing essential predictions for gene positions and structures. These files are pivotal in decoding the complex information encoded within DNA sequences. Here, we generated experimental data resolving RNA 5'- and 3'-ends as well as full-length RNAs for cassava TME12 sticklings in ambient temperature and cold. We used these data to generate genome annotation files using the TranscriptomeReconstructoR (TR) tool. A careful comparison to high-quality genome annotations suggests that our new TR genome annotations identified additional genes, resolved the transcript boundaries more accurately and identified additional RNA isoforms. We enhanced existing cassava genome annotation files with the information from TR that maintained the different transcript models as RNA isoforms. The resultant merged annotation was subsequently utilized for comprehensive analysis. To examine the effects of genome annotation files on gene expression studies, we compared the detection of differentially expressed genes during cold using the same RNA-seq data but alternative genome annotation files. We found that our merged genome annotation that included cold-specific TR gene models identified about twice as many cold-induced genes. These data indicate that environmentally induced genes may be missing in off-the-shelf genome annotation files. In conclusion, TR offers the opportunity to enhance crop genome annotations with implications for the discovery of differentially expressed candidate genes during plant-environment interactions.

Improving crop salt tolerance through soil legacy effects

Soil salinization poses a critical problem, adversely affecting plant development and sustainable agriculture. Plants can produce soil legacy effects through interactions with the soil environments. Salt tolerance of plants in saline soils is not only determined by their own stress tolerance but is also closely related to soil legacy effects. Creating positive soil legacy effects for crops, thereby alleviating crop salt stress, presents a new perspective for improving soil conditions and increasing productivity in saline farmlands. Firstly, the formation and role of soil legacy effects in natural ecosystems are summarized. Then, the processes by which plants and soil microbial assistance respond to salt stress are outlined, as well as the potential soil legacy effects they may produce. Using this as a foundation, proposed the application of salt tolerance mechanisms related to soil legacy effects in natural ecosystems to saline farmlands production. One aspect involves leveraging the soil legacy effects created by plants to cope with salt stress, including the direct use of halophytes and salt-tolerant crops and the design of cropping patterns with the specific crop functional groups. Another aspect focuses on the utilization of soil legacy effects created synergistically by soil microorganisms. This includes the inoculation of specific strains, functional microbiota, entire soil which legacy with beneficial microorganisms and tolerant substances, as well as the application of novel technologies such as direct use of rhizosphere secretions or microbial transmission mechanisms. These approaches capitalize on the characteristics of beneficial microorganisms to help crops against salinity. Consequently, we concluded that by the screening suitable salt-tolerant crops, the development rational cropping patterns, and the inoculation of safe functional soils, positive soil legacy effects could be created to enhance crop salt tolerance. It could also improve the practical significance of soil legacy effects in the application of saline farmlands.

CRF transcription factors in the trade-off between abiotic stress response and plant developmental processes

Climate change-induced environmental stress significantly affects crop yield and quality. In response to environmental stressors, plants use defence mechanisms and growth suppression, creating a resource trade-off between the stress response and development. Although stress-responsive genes have been widely engineered to enhance crop stress tolerance, there is still limited understanding of the interplay between stress signalling and plant growth, a research topic that can provide promising targets for crop genetic improvement. This review focuses on Cytokinin Response Factors (CRFs) transcription factor's role in the balance between abiotic stress adaptation and sustained growth. CRFs, known for their involvement in cytokinin signalling and abiotic stress responses, emerge as potential targets for delaying senescence and mitigating yield penalties under abiotic stress conditions. Understanding the molecular mechanisms regulated by CRFs paves the way for decoupling stress responses from growth inhibition, thus allowing the development of crops that can adapt to abiotic stress without compromising development. This review highlights the importance of unravelling CRF-mediated pathways to address the growing need for resilient crops in the face of evolving climatic conditions.

A Comparative Analysis of XGBoost and Neural Network Models for Predicting Some Tomato Fruit Quality Traits from Environmental and Meteorological Data

The tomato as a raw material for processing is globally important and is pivotal in dietary and agronomic research due to its nutritional, economic, and health significance. This study explored the potential of machine learning (ML) for predicting tomato quality, utilizing data from 48 cultivars and 28 locations in Hungary over 5 seasons. It focused on °Brix, lycopene content, and colour (a/b ratio) using extreme gradient boosting (XGBoost) and artificial neural network (ANN) models. The results revealed that XGBoost consistently outperformed ANN, achieving high accuracy in predicting °Brix (R² = 0.98, RMSE = 0.07) and lycopene content (R² = 0.87, RMSE = 0.61), and excelling in colour prediction (a/b ratio) with a R² of 0.93 and RMSE of 0.03. ANN lagged behind particularly in colour prediction, showing a negative R² value of -0.35. Shapley additive explanation's (SHAP) summary plot analysis indicated that both models are effective in predicting °Brix and lycopene content in tomatoes, highlighting different aspects of the data. SHAP analysis highlighted the models' efficiency (especially in °Brix and lycopene predictions) and underscored the significant influence of cultivar choice and environmental factors like climate and soil. These findings emphasize the importance of selecting and fine-tuning the appropriate ML model for enhancing precision agriculture, underlining XGBoost's superiority in handling complex agronomic data for quality assessment.

Enzymes Involved in Antioxidant and Detoxification Processes Present Changes in the Expression Levels of Their Coding Genes under the Stress Caused by the Presence of Antimony in Tomato

Currently, there is an increasing presence of heavy metals and metalloids in soils and water due to anthropogenic activities. However, the biggest problem caused by this increase is the difficulty in recycling these elements and their high permanence in soils. There are plants with great capacity to assimilate these elements or make them less accessible to other organisms. We analyzed the behavior of Solanum lycopersicum L., a crop with great agronomic interest, under the stress caused by antimony (Sb). We evaluated the antioxidant response throughout different exposure times to the metalloid. Our results showed that the enzymes involved in the AsA-GSH cycle show changes in their expression level under the stress caused by Sb but could not find a relationship between the NITROSOGLUTATHIONE REDUCTASE (GSNOR) expression data and nitric oxide (NO) content in tomato roots exposed to Sb. We hypothesize that a better understanding of how these enzymes work could be key to develop more tolerant varieties to this kind of abiotic stress and could explain a greater or lesser phytoremediation capacity. Moreover, we deepened our knowledge about Glutathione S-transferase (GST) and Glutathione Reductase (GR) due to their involvement in the elimination of the xenobiotic component.

Genome-wide analysis of the LAZ1 gene family in Gossypium hirsutum

BACKGROUND

As the world's leading fiber crop and a major oil-producing crop, cotton fiber yield and fiber quality are affected by environmental stresses, especially heat, drought and salinity. The LAZ1 (Lazarus 1) family genes are responsive to abscisic acid, drought, and salt treatments. Currently, mining and functional analyses of LAZ1 family genes in cotton have not been reported.

METHODS AND RESULTS

In this study, 20 GhLAZ1 genes, designated GhLAZ1-1 - GhLAZ1-20, were identified in the genome of Gossypium hirsutum through the construction of an HMM model, and their molecular properties, chromosomal localization, phylogeny, gene structure, evolutionary selection pressure, promoter cis elements and gene expression under salt stress were analyzed. With the exception of GhLAZ1-17 and GhLAZ1-20, the remaining 18 GhLAZ1 genes were unevenly localized on 13 chromosomes in G. hirsutum; evolutionary analysis showed that these genes could be divided into three subfamilies; and evolutionary selection pressure analysis demonstrated that the GhLAZ1 genes were all under purifying selection. Many elements related to light responses, hormone responses, and abiotic stresses were predicted on the GhLAZ1 family gene promoters, and real-time quantitative PCR results showed that GhLAZ1-2, GhLAZ1-8, and GhLAZ1-18 were upregulated significantly in salt-treated cotton leaves.

CONCLUSIONS

Our results suggested that GhLAZ1 genes were involved in the salt tolerance mechanism in G. hirsutum and provided a reference for further exploring the function and molecular mechanism of LAZ1 genes.

Algal Bio-Stimulants Enhance Salt Tolerance in Common Bean: Dissecting Morphological, Physiological, and Genetic Mechanisms for Stress Adaptation

Salinity adversely affects the plant's morphological characteristics, but the utilization of aqueous algal extracts (AE) ameliorates this negative impact. In this study, the application of AE derived from Chlorella vulgaris and Dunaliella salina strains effectively reversed the decline in biomass allocation and water relations, both in normal and salt-stressed conditions. The simultaneous application of both extracts in salt-affected soil notably enhanced key parameters, such as chlorophyll content (15%), carotene content (1%), photosynthesis (25%), stomatal conductance (7%), and transpiration rate (23%), surpassing those observed in the application of both AE in salt-affected as compared to salinity stress control. Moreover, the AE treatments effectively mitigated lipid peroxidation and electrolyte leakage induced by salinity stress. The application of AE led to an increase in GB (6%) and the total concentration of free amino acids (47%) by comparing with salt-affected control. Additionally, salinity stress resulted in an elevation of antioxidant enzyme activities, including superoxide dismutase, ascorbate peroxidase, catalase, and glutathione reductase. Notably, the AE treatments significantly boosted the activity of these antioxidant enzymes under salinity conditions. Furthermore, salinity reduced mineral contents, but the application of AE effectively counteracted this decline, leading to increased mineral levels. In conclusion, the application of aqueous algal extracts, specifically those obtained from Chlorella vulgaris and Dunaliella salina strains, demonstrated significant efficacy in alleviating salinity-induced stress in Phaseolus vulgaris plants.

Metabolic pathways engineering for drought or/and heat tolerance in cereals

Drought (D) and heat (H) are the two major abiotic stresses hindering cereal crop growth and productivity, either singly or in combination (D/+H), by imposing various negative impacts on plant physiological and biochemical processes. Consequently, this decreases overall cereal crop production and impacts global food availability and human nutrition. To achieve global food and nutrition security vis-a-vis global climate change, deployment of new strategies for enhancing crop D/+H stress tolerance and higher nutritive value in cereals is imperative. This depends on first gaining a mechanistic understanding of the mechanisms underlying D/+H stress response. Meanwhile, functional genomics has revealed several stress-related genes that have been successfully used in target-gene approach to generate stress-tolerant cultivars and sustain crop productivity over the past decades. However, the fast-changing climate, coupled with the complexity and multigenic nature of D/+H tolerance suggest that single-gene/trait targeting may not suffice in improving such traits. Hence, in this review-cum-perspective, we advance that targeted multiple-gene or metabolic pathway manipulation could represent the most effective approach for improving D/+H stress tolerance. First, we highlight the impact of D/+H stress on cereal crops, and the elaborate plant physiological and molecular responses. We then discuss how key primary metabolism- and secondary metabolism-related metabolic pathways, including carbon metabolism, starch metabolism, phenylpropanoid biosynthesis, γ-aminobutyric acid (GABA) biosynthesis, and phytohormone biosynthesis and signaling can be modified using modern molecular biotechnology approaches such as CRISPR-Cas9 system and synthetic biology (Synbio) to enhance D/+H tolerance in cereal crops. Understandably, several bottlenecks hinder metabolic pathway modification, including those related to feedback regulation, gene functional annotation, complex crosstalk between pathways, and metabolomics data and spatiotemporal gene expressions analyses. Nonetheless, recent advances in molecular biotechnology, genome-editing, single-cell metabolomics, and data annotation and analysis approaches, when integrated, offer unprecedented opportunities for pathway engineering for enhancing crop D/+H stress tolerance and improved yield. Especially, Synbio-based strategies will accelerate the development of climate resilient and nutrient-dense cereals, critical for achieving global food security and combating malnutrition.

Plant Promoters and Terminators for High-Precision Bioengineering

High-precision bioengineering and synthetic biology require fine-tuning gene expression at both transcriptional and posttranscriptional levels. Gene transcription is tightly regulated by promoters and terminators. Promoters determine the timing, tissues and cells, and levels of the expression of genes. Terminators mediate transcription termination of genes and affect mRNA levels posttranscriptionally, e.g., the 3'-end processing, stability, translation efficiency, and nuclear to cytoplasmic export of mRNAs. The promoter and terminator combination affects gene expression. In the present article, we review the function and features of plant core promoters, proximal and distal promoters, and terminators, and their effects on and benchmarking strategies for regulating gene expression.

Production of, Factors Affecting, Gene Regulations, and Challenges in Tissue Cultured Plant through Soilless Culture

Soilless culture also known as water based culture and substrate based culture has immense potential to grow tissue cultured plants in a closed and controlled environment system. This review analyzes the various factors that affect the vegetative growth, reproductive growth, metabolic processes, and gene regulatory functions of tissue cultured plants and the suitability of soilless culture for tissue culture plants. Experiments show that morphological and reproductive abnormalities are mitigated in tissue cultured plants by gene regulation in a closed and controlled environment system. Various factors of a soilless culture influence gene regulation and enhance cellular, molecular, and biochemical processes and compensate constraints in tissue cultured plants in closed and controlled environment conditions. The soilless culture can be utilized to harden and grow tissue culture plants. The tissue cultured plants counter water logging problems and are supplied with nutrients at 7 day intervals in the water based culture. It is necessary to analyze the involvement of regulatory genes in detail in combating challenges of tissue cultured plants in soilless cultures under closed systems. Detailed studies are also required to determine anatomy, genesis, and function of microtuber cells in tissue cultured plants.

Comparative and expression analyses of AP2/ERF genes reveal copy number expansion and potential functions of ERF genes in Solanaceae

BACKGROUND

The AP2/ERF gene family is a superfamily of transcription factors that are important in the response of plants to abiotic stress and development. However, comprehensive research of the AP2/ERF genes in the Solanaceae family is lacking.

RESULTS

Here, we updated the annotation of AP2/ERF genes in the genomes of eight Solanaceae species, as well as Arabidopsis thaliana and Oryza sativa. We identified 2,195 AP2/ERF genes, of which 368 (17%) were newly identified. Based on phylogenetic analyses, we observed expansion of the copy number of these genes, especially those belonging to specific Ethylene-Responsive Factor (ERF) subgroups of the Solanaceae. From the results of chromosomal location and synteny analyses, we identified that the AP2/ERF genes of the pepper (Capsicum annuum), the tomato (Solanum lycopersicum), and the potato (Solanum tuberosum) belonging to ERF subgroups form a tandem array and most of them are species-specific without orthologs in other species, which has led to differentiation of AP2/ERF gene repertory among Solanaceae. We suggest that these genes mainly emerged through recent gene duplication after the divergence of these species. Transcriptome analyses showed that the genes have a putative function in the response of the pepper and tomato to abiotic stress, especially those in ERF subgroups.

CONCLUSIONS

Our findings will provide comprehensive information on AP2/ERF genes and insights into the structural, evolutionary, and functional understanding of the role of these genes in the Solanaceae.

Air pollution in the places of Betula pendula growth and development changes the physicochemical properties and the main allergen content of its pollen

Pollen allergy becomes an increasing problem for humans, especially in the regions, where the air pollution level increases due to the traffic and urbanization. These factors may also affect the physiological activity of plants, causing changes in pollen allergenicity. The aim of the study was to estimate the influence of air pollutants on the chemical composition of birch pollen and the secondary structures of the Bet v1 protein. The research was conducted in seven locations in Malopolska region, South of Poland of a different pollution level. We have found slight fluctuations in the values of parameters describing the photosynthetic light reactions, similar spectra of leaf reflectance and the negligible differences in the discrimination values of the δ13C carbon isotope were found. The obtained results show a minor effect of a degree of pollution on the physiological condition B. pendula specimen. On the other hand, mean Bet v1 concentration measured in pollen samples collected in Kraków was significantly higher than in less polluted places (p = .03886), while FT-Raman spectra showed the most distinct variations in the wavenumbers characteristic of proteins. Pollen collected at sites of the increased NOx and PM concentration, show the highest percentage values of potential aggregated forms and antiparallel β-sheets in the expense of α-helix, presenting a substantial impact on chemical compounds of pollen, Bet v1 concentration and on formation of the secondary structure of proteins, what can influence their functions.

Conditional QTL mapping for seed germination and seedling traits under salt stress and candidate gene prediction in wheat

Breeding new wheat varieties with salt resistance is one of the best ways to solve a constraint on the sustainability and expansion of wheat cultivation. Therefore, understanding the molecular components or genes related to salt tolerance must contribute to the cultivation of salt-tolerant varieties. The present study used a recombinant inbred line (RIL) population to genetically dissect the effects of different salt stress concentrations on wheat seed germination and seedling traits using two quantitative trait locus (QTL) mapping methods. A total of 31 unconditional and 11 conditional QTLs for salt tolerance were identified on 11 chromosomes explaining phenotypic variation (PVE) ranging from 2.01 to 65.76%. Of these, 15 major QTLs were found accounting for more than 10% PVE. QTL clusters were detected on chromosomes 2A and 3B in the marker intervals 'wPt-8328 and wPt-2087' and 'wPt-666008 and wPt-3620', respectively, involving more than one salt tolerance trait. QRdw3B and QSfw3B.2 were most consistent in two or more salt stress treatments. 16 candidate genes associated with salt tolerance were predicted in wheat. These results could be useful to improve salt tolerance by marker-assisted selection (MAS) and shed new light on understanding the genetic basis of salt tolerance in wheat.

Plant hormones and neurotransmitter interactions mediate antioxidant defenses under induced oxidative stress in plants

Due to global climate change, abiotic stresses are affecting plant growth, productivity, and the quality of cultivated crops. Stressful conditions disrupt physiological activities and suppress defensive mechanisms, resulting in stress-sensitive plants. Consequently, plants implement various endogenous strategies, including plant hormone biosynthesis (e.g., abscisic acid, jasmonic acid, salicylic acid, brassinosteroids, indole-3-acetic acid, cytokinins, ethylene, gibberellic acid, and strigolactones) to withstand stress conditions. Combined or single abiotic stress disrupts the normal transportation of solutes, causes electron leakage, and triggers reactive oxygen species (ROS) production, creating oxidative stress in plants. Several enzymatic and non-enzymatic defense systems marshal a plant's antioxidant defenses. While stress responses and the protective role of the antioxidant defense system have been well-documented in recent investigations, the interrelationships among plant hormones, plant neurotransmitters (NTs, such as serotonin, melatonin, dopamine, acetylcholine, and γ-aminobutyric acid), and antioxidant defenses are not well explained. Thus, this review discusses recent advances in plant hormones, transgenic and metabolic developments, and the potential interaction of plant hormones with NTs in plant stress response and tolerance mechanisms. Furthermore, we discuss current challenges and future directions (transgenic breeding and genome editing) for metabolic improvement in plants using modern molecular tools. The interaction of plant hormones and NTs involved in regulating antioxidant defense systems, molecular hormone networks, and abiotic-induced oxidative stress tolerance in plants are also discussed.

Heat stress mitigation in tomato (Solanum lycopersicum L.) through foliar application of gibberellic acid

Phytohormones mediate physiological, morphological, and enzymatic responses and are important regulators of plant growth and development at different stages. Even though temperature is one of the most important abiotic stressors for plant development and production, a spike in the temperature may have disastrous repercussions for crop performance. Physiology and growth of two tomato genotypes ('Ahmar' and 'Roma') were studied in two growth chambers (25 and 45 °C) when gibberellic acid (GA₃) was applied exogenously. After the 45 days of planting, tomato plants were sprayed with GA₃ at concentrations of 25, 50, 75, and 100 mg L⁻¹, whereas untreated plants were kept as control. Under both temperature conditions, shoot and root biomass was greatest in 'Roma' plants receiving 75 mg L⁻¹ GA₃, followed by 50 mg L⁻¹ GA₃. Maximum CO₂ index, photosynthetic rate, transpiration rate, and greenness index were recorded in 'Roma' plants cultivated at 25 °C, demonstrating good effects of GA₃ on tomato physiology. Likewise, GA₃ enhanced the proline, nitrogen, phosphorus, and potassium levels in the leaves of both genotypes at both temperatures. Foliar-sprayed GA₃ up to 100 mg L⁻¹ alleviated the oxidative stress, as inferred from the lower concentrations of MDA and H₂O_2, and boosted the activities of superoxide dismutase, peroxidase, catalase. The difference between control and GA₃-treated heat-stressed plants suggests that GA₃ may have a function in mitigating heat stress. Overall, our findings indicate that 75 mg L⁻¹ of GA₃ is the optimal dosage to reduce heat stress in tomatoes and improve their morphological, physiological, and biochemical characteristics.

In silico genome wide identification and expression analysis of the WUSCHEL-related homeobox gene family in Medicago sativa

Alfalfa (Medicago sativa) is an important food and feed crop which rich in mineral sources. The WUSCHEL-related homeobox (WOX) gene family plays important roles in plant development and identification of putative gene families, their structure, and potential functions is a primary step for not only understanding the genetic mechanisms behind various biological process but also for genetic improvement. A variety of computational tools, including MAFFT, HMMER, hidden Markov models, Pfam, SMART, MEGA, ProtTest, BLASTn, and BRAD, among others, were used. We identified 34 MsWOX genes based on a systematic analysis of the alfalfa plant genome spread in eight chromosomes. This is an expansion of the gene family which we attribute to observed chromosomal duplications. Sequence alignment analysis revealed 61 conserved proteins containing a homeodomain. Phylogenetic study sung reveal five evolutionary clades with 15 motif distributions. Gene structure analysis reveals various exon, intron, and untranslated structures which are consistent in genes from similar clades. Functional analysis prediction of promoter regions reveals various transcription binding sites containing key growth, development, and stress-responsive transcription factor families such as MYB, ERF, AP2, and NAC which are spread across the genes. Most of the genes are predicted to be in the nucleus. Also, there are duplication events in some genes which explain the expansion of the family. The present research provides a clue on the potential roles of MsWOX family genes that will be useful for further understanding their functional roles in alfalfa plants.

Biomonitoring of Soil Contaminated with Herbicides

The state of environmental pollution is of random character, and it depends on climatic conditions, landforms, development and industrialization. It is estimated that in the last decade as many pollutants have been released into the environment as in the previous 70 years, and the pollution rate still increases. Many scientific reports indicate that, in addition to metals, pesticides are the most commonly detected compounds in the environment. This situation is mainly due to the irrational use of these chemicals by humans. Mostly, soil environment changes caused by the influence of pesticides can be determined by various chemical analyses, which require the use of sophisticated and expensive equipment. However, biological methods, such as those using microbiological activity and an abundance of microorganisms, e.g., organisms responsible for the cycle of organic matter and nutrients, tend to be neglected. For this reason, the aim of the present study is not only to assess the validity of other research studies that were performed based on the available literature but to compile methods and compare them, which allows for an in depth understanding of the complexity of soil processes following herbicide application by conducting comprehensive soil biomonitoring.

The Functional Interplay between Ethylene, Hydrogen Sulfide, and Sulfur in Plant Heat Stress Tolerance

Plants encounter several abiotic stresses, among which heat stress is gaining paramount attention because of the changing climatic conditions. Severe heat stress conspicuously reduces crop productivity through changes in metabolic processes and in growth and development. Ethylene and hydrogen sulfide (H2S) are signaling molecules involved in defense against heat stress through modulation of biomolecule synthesis, the antioxidant system, and post-translational modifications. Other compounds containing the essential mineral nutrient sulfur (S) also play pivotal roles in these defense mechanisms. As biosynthesis of ethylene and H2S is connected to the S-assimilation pathway, it is logical to consider the existence of a functional interplay between ethylene, H2S, and S in relation to heat stress tolerance. The present review focuses on the crosstalk between ethylene, H2S, and S to highlight their joint involvement in heat stress tolerance.

Repeatome Analyses and Satellite DNA Chromosome Patterns in Deschampsia sukatschewii, D. cespitosa, and D. antarctica (Poaceae)

Subpolar and polar ecotypes of Deschampsia sukatschewii (Popl.) Roshev, D. cespitosa (L.) P. Beauv, and D. antarctica E. Desv. are well adapted to stressful environmental conditions, which make them useful model plants for genetic research and breeding. For the first time, the comparative repeatome analyses of subpolar and polar D. sukatschewii, D. cespitosa, and D. antarctica was performed using RepeatExplorer/TAREAN pipelines and FISH-based chromosomal mapping of the identified satellite DNA families (satDNAs). In the studied species, mobile genetic elements of class 1 made up the majority of their repetitive DNA; interspecific variations in the total amount of Ty3/Gypsy and Ty1/Copia retroelements, DNA transposons, ribosomal, and satellite DNA were revealed; 12–18 high confident and 7–9 low confident putative satDNAs were identified. According to BLAST, most D. sukatschewii satDNAs demonstrated sequence similarity with satDNAs of D. antarctica and D. cespitosa indicating their common origin. Chromosomal mapping of 45S rDNA, 5S rDNA, and satDNAs of D. sukatschewii allowed us to construct the species karyograms and detect new molecular chromosome markers important for Deschampsia species. Our findings confirmed that genomes of D. sukatschewii and D. cespitosa were more closely related compared to D. antarctica according to repeatome composition and patterns of satDNA chromosomal distribution.

Rhizosphere Tripartite Interactions and PGPR-Mediated Metabolic Reprogramming towards ISR and Plant Priming: A Metabolomics Review

Plant growth-promoting rhizobacteria (PGPR) are beneficial microorganisms colonising the rhizosphere. PGPR are involved in plant growth promotion and plant priming against biotic and abiotic stresses. Plant-microbe interactions occur through chemical communications in the rhizosphere and a tripartite interaction mechanism between plants, pathogenic microbes and plant-beneficial microbes has been defined. However, comprehensive information on the rhizosphere communications between plants and microbes, the tripartite interactions and the biochemical implications of these interactions on the plant metabolome is minimal and not yet widely available nor well understood. Furthermore, the mechanistic nature of PGPR effects on induced systemic resistance (ISR) and priming in plants at the molecular and metabolic levels is yet to be fully elucidated. As such, research investigating chemical communication in the rhizosphere is currently underway. Over the past decades, metabolomics approaches have been extensively used in describing the detailed metabolome of organisms and have allowed the understanding of metabolic reprogramming in plants due to tripartite interactions. Here, we review communication systems between plants and microorganisms in the rhizosphere that lead to plant growth stimulation and priming/induced resistance and the applications of metabolomics in understanding these complex tripartite interactions.

The Impact of Bio-Stimulants on Cd-Stressed Wheat (Triticum aestivum L.): Insights Into Growth, Chlorophyll Fluorescence, Cd Accumulation, and Osmolyte Regulation

It has been established that wheat (Triticum aestivum L.) has a higher Cd absorption capacity than other cereal crops causing an excess daily Cd intake and a huge threat for public health. Therefore, the reduction of Cd accumulation in wheat from the soil is a crucial food-security issue. A pot trial was performed on Cd-stressed wheat seedlings to evaluate the morphological and physio-biochemical responses via foliage spray of two different bio-stimulants, i.e., ascorbic acid (AsA) and moringa leaf extract (MLE). Two wheat cultivars (Fsd-08 and Glxy-13) were exposed to cadmium (CdCl₂.5H₂O) stress (0, 500, and 1,000 μM), along with foliar spray of AsA (0 and 50 mM) and MLE (0 and 3%). The most observable growth reduction was documented in plants that are exposed to a higher Cd concentration (1,000 μM), followed by the lower Cd level (500 μM). The wheat growth attributes, such as number of leaves per plant, number of tillers per plant, biomass yield, shoot/root length, and leaf area, were greatly depressed under the Cd stress, irrespective of the cultivar. Under the increasing Cd stress, a significant diminution was observed in maximum photochemical efficiency (Fv/Fm), photochemical quenching (qP), and electron transport rate (ETR) accompanied with reduced gas exchange attributes. However, Cd-induced phytotoxicity enhanced the non-photochemical quenching (NPQ) and internal carbon dioxide concentration (Ci), which was confirmed by their significant positive correlation with Cd contents in shoot and root tissues of both cultivars. The contents of proline, AsA, glycine betaine (GB), tocopherol, total free amino acid (TFAA), and total soluble sugar (TSS) were greatly decreased with Cd stress (1,000 μM), while MLE and AsA significantly enhanced the osmolytes accumulation under both Cd levels (especially 500 μM level). The Cd accumulation was predominantly found in the root as compared to shoots in both cultivars, which has declined after the application of MLE and AsA. Conclusively, MLE was found to be more effective to mitigate Cd-induced phytotoxicity up to 500 μM Cd concentration, compared with the AsA amendment.

Physiological Responses to Drought, Salinity, and Heat Stress in Plants: A Review

On the world stage, the increase in temperatures due to global warming is already a reality that has become one of the main challenges faced by the scientific community. Since agriculture is highly dependent on climatic conditions, it may suffer a great impact in the short term if no measures are taken to adapt and mitigate the agricultural system. Plant responses to abiotic stresses have been the subject of research by numerous groups worldwide. Initially, these studies were concentrated on model plants, and, later, they expanded their studies in several economically important crops such as rice, corn, soybeans, coffee, and others. However, agronomic evaluations for the launching of cultivars and the classical genetic improvement process focus, above all, on productivity, historically leaving factors such as tolerance to abiotic stresses in the background. Considering the importance of the impact that abiotic stresses can have on agriculture in the short term, new strategies are currently being sought and adopted in breeding programs to understand the physiological, biochemical, and molecular responses to environmental disturbances in plants of agronomic interest, thus ensuring the world food security. Moreover, integration of these approaches is bringing new insights on breeding. We will discuss how water deficit, high temperatures, and salinity exert effects on plants.

Defense interplay of the zinc-oxide nanoparticles and melatonin in alleviating the arsenic stress in soybean (Glycine max L.)

Present study showed the successful application of the modified hydrothermal method for synthesizing the zinc oxide nanoparticles (ZnO-NPs) efficiently. Well as-synthesized ZnO-NPs are analyzed for various techniques viz., X-ray diffraction (XRD), SEM micrographs, EDAX/Mapping pattern, Raman Spectroscopy Pattern, UV, Photoluminescence (PL) and X-ray photoemission spectroscopy (XPS) analysis. All these measurements showed that ZnO-NPs are highly pure with no internal defects, and can be potentially used in the plant applications. Hence, we further determined the effect of these nanoparticles and melatonin for the modulation of the As tolerance in soybean plants by examining the various growth attributes and metabolic parameters. Our results demonstrated that As-stress inhibited growth (∼34%), photosynthesis-related parameters (∼18-28%) and induced ROS accumulation; however, all these attributes are substantially reversed by the ZnO-NPs and melatonin treatments. Moreover, the As stress induced malondialdehyde (MDA; 71%) and hydrogen peroxide (H2O2; 82%) are partially reversed by the ZnO-NPs and melatonin in the As-stressed plants. This might have resulted due to the ZnO-NPs and melatonin induced activities of the antioxidants plant defense. Overall, the ZnO-NPs and melatonin supplementation separately and in combination positively regulated the As tolerance in soybean; however, the effect of their combined application on the As tolerance was more profound relative to the individual application. These results suggested the synergetic effect of the ZnO-NPs and melatonin on the As tolerance in soybean. However, the in-depth mechanism underlying the defense crosstalk between the ZnO-NPs and melatonin needs to be further explored.

Potential use of a novel actinobacterial species to ameliorate tungsten nanoparticles induced oxidative damage in cereal crops

Tungsten nanoparticles (WNPs) could induce hazard impact on plant growth and development; however, no study investigated their phytotoxicity. On the other hand, plant growth-promoting bacteria (PGPB) can effectively reduce WNPs toxicity. To this end, Nocardiopsis sp. was isolated and employed to mitigate the phytotoxic effect of WNPs on three crops (wheat, barley, and oat). Soil contamination with WPNs induced the W accumulation in all tested crops, inhibited both growth and photosynthesis and induced oxidative damage. On the other hand, pre-inoculation with Nocardiopsis sp. significantly reduced W level in treated plants. Concomitantly, Nocardiopsis sp. strikingly mitigated the inhibitory effect of WNPs by augmenting both growth and reactive oxygen species (ROS) homeostasis. To cope with heavy metal stress, all the tested species orchestrated their antioxidant homeostasis through enhancing the production of antioxidant metabolites (e.g., phenolics, flavonoids and tocopherols) and elevated the activities of ROS-scavenging enzymes (e.g., APX, POX, CAT, as well as the enzymes involved in AsA/GSH cycle). Moreover, pre-inoculation with Nocardiopsis sp. improved the detoxification metabolism by enhancing the accumulation of phytochelatins (PCs), metallothionein (MTC) and glutathione-S-transferase (GST) in grasses grown in WNPs-contaminated soils. Overall, restrained ROS homeostasis and improved WNPs detoxification systems were the bases underlie the WNPs stress mitigating impact of Nocardiopsis sp treatment.

Seed and seedling diversity delimitation and differentiation of Indian populations of Melia dubia cav

Melia dubia is one of the most important industrial tree species in the South East Asia. In last few decades, the populations of M. dubia has rapidly expanded in the Indian sub-continents, leading to an increase in the genetic diversity of species. However, very less information is available on intra-specific variation in Melia under the Indian subcontinent. Therefore, a present investigation was undertaken, to assess the level of diversity in seed and saplings of the Melia populations (ecotypes) collected from three agro-ecological regions of India. Results revealed that the seed and saplings of all the ecotypes are significantly different for all the traits, except for number of branches per plant, and the maximum variability was recorded in germination percentage, seed weight, internodal length, and sapling height of the species. The high heritability for seed weight (0.99), length (0.99), and width (0.97), and germination percentage (0.99) indicated that selection and genetic gain for these traits would be effective during the commencement of improvement program. Trait association analysis explained that higher seed weight significantly reduced sapling height, collar diameter, number of leaves per plant, internodal length, petiole length, and germination percentage (r = −0.86; p < 0.001) that ultimately reduced the seedling vigor in Melia dubia. Interestingly, the number of branches per plant were not associated with any of the morphological traits. The first principal component explained 50.09% of the entire variation and all the traits contributed greatly to the variation for this principal component, except for number of branches, leaf width and seed length. The clustering approach assorted geographic variation of M. dubia populations into three main sub-clusters i.e. South, North, and North East populations each consisting of five, seven and one populations (including cultivar), respectively. Among different ecotypes, Bahumukhi, Varsha and US Nagar seed sources outperformed all others in seedling vigour (sapling height) and rest of the growth parameters. Overall, findings explained that considerable scope exists for the development of superior planting material of M. dubia through exploration of seeds and selection at the early seedling stage.

Why flowers close at noon? A case study of an alpine species Gentianopsis paludosa (Gentianaceae)

Repeatable floral closure with diurnal rhythms, that is, flower opening in the morning and closing in the evening, was widely reported. However, the rhythm of flower opening in the morning but closing in the midday received much less attention. Gentianopsis paludosa, Gentianaceae, has an obvious petal movement rhythm opening in the morning and closing at noon at northeast of the Qinghai-Tibetan Plateau. In this study, we examined the effects of temperature (T), relative humidity (RH), and illumination intensity (II) on G. paludosa's flower closure. Furthermore, we monitored the environmental changes inside and outside of the flowers, aiming to test the effect of floral closure on the stability of microenvironment inside the flower. Finally, we artificially interrupted temporal petal closure and investigated its effects on reproductive fitness. The results showed that high/low temperature contributed more to the flower closure than low RH, while illumination intensity had no significant effect on it. The medium temperature, relative humidity and illumination intensity (environmental conditions at 10:00) did not delay flower closure when flowers at pre-closing period or stimulate reopen when flowers full closed. Floral closure provided a stable temperature condition and a higher RH condition inside the flower. Meanwhile, compulsive opening and delayed closure of flowers decreased the seed-set ratio while no effect was found when flowers were forced to close. We conclude that endogenous rhythm regulates floral closure. The rhythm of petal movement providing a stable microenvironment for G. paludosa, increasing the seed production and saving energy from flower opening maintenance, which might be an adaptive strategy to against unfavorable environmental conditions.

Melatonin confers fenugreek tolerance to salinity stress by stimulating the biosynthesis processes of enzymatic, non-enzymatic antioxidants, and diosgenin content

Salinity-induced stress is widely considered a main plant-growth-limiting factor. The positive effects of melatonin in modulating abiotic stresses have led this hormone to be referred to as a growth regulator in plants. This study aims to show how melatonin protects fenugreek against the negative effects of salt stress. Different amounts of melatonin (30, 60, and 90 ppm), salinity stress (150 mM and 300 mM), and the use of both salinity and melatonin were used as treatments. The results showed that applying different melatonin levels to salinity-treated fenugreek plants effectively prevented the degradation of chlorophyll a, chlorophyll b, total chlorophyll, and carotenoid contents compared with salinity treatment without melatonin application. Besides, melatonin increases the biosynthesis of enzymatic and non-enzymatic antioxidants, thereby adjusting the content of reactive oxygen species, free radicals, electrolyte leakage, and malondialdehyde content. It was observed that applying melatonin increased the activity of potassium-carrying channels leading to the maintenance of ionic homeostasis and increased intracellular water content under salinity stress. The results revealed that melatonin activates the defense signaling pathways in fenugreek through the nitric oxide, auxin, and abscisic acid-dependent pathways. Melatonin, in a similar vein, increased the expression of genes involved in the biosynthesis pathway of diosgenin, a highly important steroidal sapogenin in medical and food industries, and hence the diosgenin content. When 150 mM salinity stress and 60 ppm melatonin were coupled, the diosgenin concentration rose by more than 5.5 times compared to the control condition. In conclusion, our findings demonstrate the potential of melatonin to enhance the plant tolerance to salinity stress by stimulating biochemical and physiological changes.

Characterization of RBPome in Oxidative Stress Conditions

Cellular redox signaling is triggered by accumulation of various reactive oxygen species (ROS) that integrate with other signaling cascades to enable plants to ultimately respond to (a)biotic stresses. The identification of key regulators underlying redox signaling networks is therefore of high priority. This chapter describes an improved mRNA interactome capture method that allows to systematically detect oxidative stress responsive regulators in the post-transcriptional gene regulation (PTGR) pathway. The protocol includes PSB-D suspension cell culture preparation, setup of oxidative stress conditions, short-term exposure to UV irradiation, cell lysis, pull-down and purification of crosslinked messenger ribonucleoproteins, their mass spectrometric analyses, and identification of proteome by statistical analyses. As result, a comprehensive inventory of the functional oxidative stress responsive RBPome (OxRBPome) is generated, which paves the way toward new insights into PTGR processes in redox signaling.

Multifaceted roles of silicon in mitigating environmental stresses in plants

Food security relies on plant productivity and plant's resilience to climate change driven environmental stresses. Plants employ diverse adaptive mechanisms of stress-signalling pathways, antioxidant defense, osmotic adjustment, nutrient homeostasis and phytohormones. Over the last few decades, silicon has emerged as a beneficial element for enhancing plant growth productivity. Silicon ameliorates biotic and abiotic stress conditions by regulating the physiological, biochemical and molecular responses. Si-uptake and transport are facilitated by specialized Si-transporters (Lsi1, Lsi2, Lsi3, and Lsi6) and, the differential root anatomy has been shown to reflect in the varying Si-uptake in monocot and dicot plants. Silicon mediates a number of plant processes including osmotic, ionic stress responses, metabolic processes, stomatal physiology, phytohormones, nutrients and source-sink relationship. Further studies on the transcriptional and post-transcriptional regulation of the Si transporter genes are required for better uptake and transport in spatial mode and under different stress conditions. In this article, we present an account of the availability, uptake, Si transporters and, the role of Silicon to alleviate environmental stress and improve plant productivity.

Genome-wide characterization, evolution, and expression profiling of FBA gene family in response to light treatments and abiotic stress in Nicotiana tabacum

Fructose 1,6-bisphosphate aldolase (FBA) as a key enzyme play crucial roles in glycolysis, gluconeogenesis and Calvin cycle processes in plants. However, limited information is known regarding FBA genes in Nicotiana tabacum. In this study, 16 FBAs were identified and characterized in Nicotiana tabacum. Phylogenetic analysis revealed that these genes can be categorized as type I (NtFBA1-10 located in chloroplast) and type II (NtFBA11-16 located in cytoplasm) subfamilies. According to the conserved motifs and gene structure analysis, NtFBA protein sequences had the highly homologous to FBAs in other species. Most members of the NtFBA gene family responded positively to NaHCO3 stress, especially the expression of NtFBA13/14 increased by 642%. In addition, the expression results of NtFBAs under five abiotic stress (light, NaCl, NaHCO3, drought, and cold) conditions were showed that NtFBA13/14 were highly up-regulated. qRT-PCR results showed that most of the NtFBAs expressed higher in leaves. NtFBA7/8 and NtFBA13/14 have important significance in photosynthesis and abiotic stress, respectively. This study provides a basis foundation for further elucidating the function of NtFBAs and the N. tabacum mechanism of resistance under abiotic stress.

Omics for the Improvement of Abiotic, Biotic, and Agronomic Traits in Major Cereal Crops: Applications, Challenges, and Prospects

Omics technologies, namely genomics, transcriptomics, proteomics, metabolomics, and phenomics, are becoming an integral part of virtually every commercial cereal crop breeding program, as they provide substantial dividends per unit time in both pre-breeding and breeding phases. Continuous advances in omics assure time efficiency and cost benefits to improve cereal crops. This review provides a comprehensive overview of the established omics methods in five major cereals, namely rice, sorghum, maize, barley, and bread wheat. We cover the evolution of technologies in each omics section independently and concentrate on their use to improve economically important agronomic as well as biotic and abiotic stress-related traits. Advancements in the (1) identification, mapping, and sequencing of molecular/structural variants; (2) high-density transcriptomics data to study gene expression patterns; (3) global and targeted proteome profiling to study protein structure and interaction; (4) metabolomic profiling to quantify organ-level, small-density metabolites, and their composition; and (5) high-resolution, high-throughput, image-based phenomics approaches are surveyed in this review.

Drought and Heat Stress in Cool-Season Food Legumes in Sub-Tropical Regions: Consequences, Adaptation, and Mitigation Strategies

Drought and heat stress are two major abiotic stresses that challenge the sustainability of agriculture to a larger extend. The changing and unpredictable climate further aggravates the efforts made by researchers as well as farmers. The stresses during the terminal stage of cool-season food legumes may affect numerous physiological and biochemical reactions that may result in poor yield. The plants possess a good number of adaptative and avoiding mechanisms to sustain the adverse situation. The various agronomic and breeding approaches may help in stress-induced alteration. The physiological and biochemical response of crops to any adverse situation is very important to understand to develop mechanisms and approaches for tolerance in plants. Agronomic approaches like altering the planting time, seed priming, foliar application of various macro and micro nutrients, and the application of rhizobacteria may help in mitigating the adverse effect of heat and drought stress to some extent. Breeding approaches like trait-based selection, inheritance studies of marker-based selection, genetic approaches using the transcriptome and metabolome may further pave the way to select and develop crops with better heat and drought stress adaptation and mitigation.

Delineation of mechanistic approaches employed by plant growth promoting microorganisms for improving drought stress tolerance in plants

Drought stress is expected to increase in intensity, frequency, and duration in many parts of the world, with potential negative impacts on plant growth and productivity. The plants have evolved complex physiological and biochemical mechanisms to respond and adjust to water-deficient environments. The physiological and biochemical mechanisms associated with water-stress tolerance and water-use efficiency have been extensively studied. Besides these adaptive and mitigating strategies, the plant growth-promoting rhizobacteria (PGPR) play a significant role in alleviating plant drought stress. These beneficial microorganisms colonize the endo-rhizosphere/rhizosphere of plants and enhance drought tolerance. The common mechanism by which these microorganisms improve drought tolerance included the production of volatile compounds, phytohormones, siderophores, exopolysaccharides, 1-aminocyclopropane-1-carboxylate deaminase (ACC deaminase), accumulation of antioxidant, stress-induced metabolites such as osmotic solutes proline, alternation in leaf and root morphology and regulation of the stress-responsive genes. The PGPR is an easy and efficient alternative approach to genetic manipulation and crop enhancement practices because plant breeding and genetic modification are time-consuming and expensive processes for obtaining stress-tolerant varieties. In this review, we will elaborate on PGPR's mechanistic approaches in enhancing the plant stress tolerance to cope with the drought stress.

Functional Characteristics Analysis of Dehydrins in Larix kaempferi under Osmotic Stress

Dehydrins (DHN) belong to the late embryogenesis abundant II family and have been found to enhance plant tolerance to abiotic stress. In the present study, we reported four DHNs in Larix kaempferi (LkDHN) which were identified from the published transcriptome. Alignment analysis showed that these four LkDHNs shared close relationships and belonged to SK3-type DHNs. The electrophoretic mobility shift assay indicated that these four LkDHNs all possess sequence-independent binding capacity for double-strands DNAs. The subcellular localizations of the four LkDHNs were in both the nucleus and cytoplasm, indicating that these LkDHNs enter the nucleus to exert the ability to bind DNA. The preparation of tobacco protoplasts with different concentrations of mannitol showed that LkDHNs enhanced the tolerance of plant cells under osmotic stress. The overexpression of LkDHNs in yeasts enhanced their tolerance to osmotic stress and helped the yeasts to survive severe stress. In addition, LkDHNs in the nucleus of salt treated tobacco increased. All of these results indicated that the four LkDHNs help plants survive from heavy stress by participating in DNA protection. These four LKDHNs played similar roles in the response to osmotic stress and assisted in the adaptation of L. kaempferi to the arid and cold winter of northern China.

Alleviation of Heat Stress in Tomato by Exogenous Application of Sulfur

Temperature is a key factor influencing plant growth and productivity, however sudden increases in temperature can cause severe consequences in terms of crop performance. We evaluated the influence of elementary sulfur application on the physiology and growth of two tomato genotypes (“Ahmar” and “Roma”) grown in two growth chambers (at 25 and 45 °C). Plants were sprayed with 2, 4, 6, and 8 ppm sulfur 45 days after sowing (untreated plants were kept as control). Plants of the “Roma” cultivar receiving 6 ppm sulfur exhibited maximal shoot and root biomass values followed by those receiving 4 ppm under both temperature conditions. Maximal CO2 index, photosynthetic rate, transpiration rate, and greenness index values (188.1 µmol mol−1, 36.3 µmol CO2 m−2 s−1, 1.8 µmol H2O m−2 s−1, and 95 SPAD, respectively) were observed in plants of “Roma” cultivar grown at 25 °C, indicating positive influences of sulfur on tomato physiology. Similarly, sulfur maximized proline, nitrogen, phosphorus, and potassium contents in leaves of both genotypes at both temperatures. The differences between control and sulfur-treated plants grown under heat stress indicate a possible role of sulfur in mitigating heat stress. Overall, our results suggest that 6 ppm of sulfur is the best dose to alleviate tomato heat stress and enhance the morphological, physiological, and biochemical attributes of tomato plants.

Effect of sodium chloride on the expression of genes involved in the salt tolerance of Bacillus sp. strain “SX4” isolated from salinized greenhouse soil

Salt stress is one of the important adverse conditions affecting bacterium growth. How bacteria isolated from greenhouse soil cope with salt stress and regulate the genes responsible for salt tolerance are still unclear. We conducted RNA transcriptome profiling of genes contributing to the salt tolerance of a Bacillus sp. strain (“SX4”) obtained from salinized soil. Results showed that NaCl effectively regulated the growth of “SX4” in terms of cell length and colony-forming unit number decrease. A total of 121 upregulated and 346 downregulated genes were detected under salt stress with reference to the control. The largest numbers of differential expression genes were 17 in carbon metabolism, 13 in the biosynthesis of amino acids, 10 in a two-component system, and 10 in ABC transporter pathways for adapting to salt stress. Our data revealed that cation, electron and transmembrane transport, and catalytic activity play important roles in the resistance of bacterial cells to salt ions. Single-nucleotide polymorphism and the mutation of base pair T:A to C:G play potential roles in the adaptation of “SX4” to high NaCl concentrations. The findings from this study provide new insights into the molecular mechanisms of strain “SX4” and will be helpful in promoting the application of salt-tolerant bacteria.

Enzymology and Regulation of δ1-Pyrroline-5-Carboxylate Synthetase 2 From Rice

Under several stress conditions, such as excess salt and drought, many plants accumulate proline inside the cell, which is believed to help counteracting the adverse effects of low water potential. This increase mainly relies upon transcriptional induction of δ¹-pyrroline-5-carboxylate synthetase (P5CS), the enzyme that catalyzes the first two steps in proline biosynthesis from glutamate. P5CS mediates both the phosphorylation of glutamate and the reduction of γ-glutamylphosphate to glutamate-5-semialdehyde, which spontaneously cyclizes to δ¹-pyrroline-5-carboxylate (P5C). In most higher plants, two isoforms of P5CS have been found, one constitutively expressed to satisfy proline demand for protein synthesis, the other stress-induced. Despite the number of papers to investigate the regulation of P5CS at the transcriptional level, to date, the properties of the enzyme have been only poorly studied. As a consequence, the descriptions of post-translational regulatory mechanisms have largely been limited to feedback-inhibition by proline. Here, we report cloning and heterologous expression of P5CS2 from Oryza sativa. The protein has been fully characterized from a functional point of view, using an assay method that allows following the physiological reaction of the enzyme. Kinetic analyses show that the activity is subjected to a wide array of regulatory mechanisms, ranging from product inhibition to feedback inhibition by proline and other amino acids. These findings confirm long-hypothesized influences of both, the redox status of the cell and nitrogen availability, on proline biosynthesis.

Silicon mediated improvement in the growth and ion homeostasis by decreasing Na+ uptake in maize (Zea mays L.) cultivars exposed to salinity stress

Silicon (Si), a major contributing constituent for plant resistance against abiotic stresses. In spite of this, the detailed mechanisms underlying the potential of Si in mitigating salt toxicity in maize (Zea mays L.) are still poorly understood. The present study deals with the response of Si application on growth, gaseous exchange, ion homeostasis and antioxidant enzyme activities in two maize cultivars (P1574 and Hycorn 11) grown under saline conditions. Salt stress remarkably reduced the plant tissue (roots and shoots) biomass, relative water contents (RWC), membrane stability index (MSI), gaseous exchange characteristics, and antioxidant enzymatic activities i.e., superoxide dismutase (SOD), peroxidase (POD), ascorbate peroxidase (APX) and catalase (CAT). However, salt-induced phytotoxicity increased the plant tissue concentration of malondialdehyde (MDA), hydrogen peroxide (H₂O₂), Na⁺/K⁺ ionic ratio, Na⁺ translocation (root to shoot), and its uptake. The detrimental effects were more prominent in Hycorn 11 cultivar than the P1574 cultivar at higher salinity level (S2; 160 mM NaCl). The addition of Si alleviated salt toxicity, which was more obvious in P1574 relative to Hycorn 11 as demonstrated by an increasing trend in RWC, MSI, and activities of SOD, POD, APX and CAT. Besides, Si-induced mitigation of salt stress was due to the depreciation in Na⁺/K⁺ ratio, Na⁺ ion uptake at the surface of maize roots, translocation in plant tissues and thereby significantly reduced Na⁺ ion accumulation. The findings showed a new dimension regarding the beneficial role of Si in maize plants grown under salt toxicity.

Role of Melatonin in Plant Tolerance to Soil Stressors: Salinity, pH and Heavy Metals

Melatonin (MT) is a pleiotropic molecule with diverse and numerous actions both in plants and animals. In plants, MT acts as an excellent promotor of tolerance against abiotic stress situations such as drought, cold, heat, salinity, and chemical pollutants. In all these situations, MT has a stimulating effect on plants, fomenting many changes in biochemical processes and stress-related gene expression. Melatonin plays vital roles as an antioxidant and can work as a free radical scavenger to protect plants from oxidative stress by stabilization cell redox status; however, MT can alleviate the toxic oxygen and nitrogen species. Beyond this, MT stimulates the antioxidant enzymes and augments antioxidants, as well as activates the ascorbate–glutathione (AsA–GSH) cycle to scavenge excess reactive oxygen species (ROS). In this review, we examine the recent data on the capacity of MT to alleviate the effects of common abiotic soil stressors, such as salinity, alkalinity, acidity, and the presence of heavy metals, reinforcing the general metabolism of plants and counteracting harmful agents. An exhaustive analysis of the latest advances in this regard is presented, and possible future applications of MT are discussed.

MAPK Enzymes: a ROS Activated Signaling Sensors Involved in Modulating Heat Stress Response, Tolerance and Grain Stability of Wheat under Heat Stress

Mitogen-activated protein kinase (MAPK) signaling cascade is highly conserved across the species triggering the self-adjustment of the cells by transmitting the external signals to the nucleus. The cascade consists of MAPK kinase kinases (MAPKKKs), MAPK kinases (MAPKKs) and MAPKs. These kinases are functionally interrelated through activation by sequential phosphorylation. MAPK cascade is involved in modulating the tolerance and regulating the growth and developmental processes in plants through transcriptional programming. The cascade has been well characterized in Arabidopsis, Tobacco and rice, but limited information is available in wheat due to complexity of genome. MAPK-based sensors have been reported to be highly specific for the external or intracellular stimuli activating specific TF, stress-associated genes (SAGs) and stress-associated proteins (SAPs) linked with heat-stress tolerance and other biological functions especially size, number and quality of grains. Even, MAPKs have been reported to influence the activity of ATP-binding cassette (ABC) transporter superfamily involved in stabilizing the quality of the grains under adverse conditions. Wheat has also diverse network of MAPKs involved in transcriptional reprogramming upon sensing the terminal HS and in turn protect the plants. Current review mainly focuses on the role of MAPKs as signaling sensor and modulator of defense mechanism for mitigating the effect of heat on plants with focus on wheat. It also indirectly protects the nutrient depletion from the grains under heat stress. MAPKs, lying at pivotal positions, can be utilized for manipulating the heat-stress response (HSR) of wheat to develop plant for future (P4F).

A single seed treatment mediated through reactive oxygen species increases germination, growth performance, and abiotic stress tolerance in Arabidopsis and rice

Hydroxyl radical (•OH) is considered to be the most damaging among reactive oxygen species. Although afew studies have reported on its effects on growth and stress adaptation of plants, no detailed studies have been performed using •OH in germination and early seedling growth under abiotic stresses. Here we report a single seed treatment with •OH on germination and seedling growth of Arabidopsis and rice under non-stressed (ambient) and various abiotic-stressed conditions (chilling, high temperature, heat, and salinity). The treatment resulted in faster seed germination and early seedling growth under non-stressed conditions, and, interestingly, these effects were more prominent under abiotic stresses. In addition, Arabidopsis seedlings from treated seeds showed faster root growth and developed more lateral roots. These results show apositive and potential practical use for •OH in model and crop plants for direct seeding in the field, as well as improvement of tolerance against emerging stresses. Abbreviations: AUC: area under curve; MGT: mean germination time; t50: time to reach 50% germination; U₇₅₂₅: time for uniform germination from 25% to 75%; ROS: reactive oxygen species; GSI: germination speed index; SI: stress index; DI: dormancy index.

Correlation between gene expression levels under drought stress and synonymous codon usage in rice plant by in-silico study

We studied the correlation of synonymous codon usage (SCU) on gene expression levels under drought stress in rice. Sixty genes related to drought stress (with high, intermediate and low expression) were selected from rice meta-analysis data and various codon usage indices such as the effective number of codon usage (ENC), codon adaptation index (CAI) and relative synonymous codon usage (RSCU) were calculated. We found that in genes highly expressing under drought 1) GC content was higher, 2) ENC value was lower, 3) the preferred codons of some amino acids changed and 4) the RSCU ratio of GC-end codons relative to AT-end codons for 18 amino acids increased significantly compared with those in other genes. We introduce ARSCU as the Average ratio of RSCUs of GC-end codons to AT-end codons in each gene that could significantly separate high-expression genes under drought from low-expression genes. ARSCU is calculated using the program ARSCU-Calculator developed by our group to help predicting expression level of rice genes under drought. An index above ARSCU threshold is expected to indicate that the gene under study may belong to the "high expression group under drought". This information may be applied for codon optimization of genes for rice genetic engineering. To validate these findings, we further used 60 other genes (randomly selected subset of 43233 genes studied for their response to drought stress). ARSCU value was able to predict the level of expression at 88.33% of the cases. Using third set of 60 genes selected amongst high expressing genes not related to drought, only 31.65% of the genes showed ARSCU value of higher than the set threshold. This indicates that the phenomenon we described in this report may be unique for drought related genes. To justify the observed correlation between CUB and high expressing genes under drought, possible role of tRNA post transcriptional modification and tRFs was hypothesized as possible underlying biological mechanism.

Growth, Survival and Biomass Production of Barley in a Polluted Mine Soil Amended with Biochar and Animal Manure

In the present study, sheep manure (0%, 10% and 20% w/w) and biochar derived from coniferous tree woods (0%, 2.5% and 5% w/w) were incorporated into a multi-MTE contaminated soil from a former iron mine site and incubated for 10 days. A seeds of barley were grown in the amended soil and different morphological traits were measured after 30 days. Results indicated that MTE stress reduced the shoot length, stem diameter, leaf area, number of leaves and dry biomass as compared to the control. Organic amendments application increased soil pH and was found to affect significantly almost all the measured parameters. Animal manure was found effective in improvement of the morphological characteristics of barley plants comparing to biochar amendments. Our results suggested that animal manure could be used for reducing the effect of MTE on the morphological proprieties of barley grown in a former iron mine soil.

What is the Difference between the Response of Grass Pea (Lathyrus sativus L.) to Salinity and Drought Stress?—A Physiological Study

Understanding the mechanisms of plant tolerance to osmotic and chemical stress is fundamental to maintaining high crop productivity. Soil drought often occurs in combination with physiological drought, which causes chemical stress due to high concentrations of ions. Hence, it is often assumed that the acclimatization of plants to salinity and drought follows the same mechanisms. Grass pea (Lathyrus sativus L.) is a legume plant with extraordinary tolerance to severe drought and moderate salinity. The aim of the presented study was to compare acclimatization strategies of grass pea seedlings to osmotic (PEG) and chemical (NaCl) stress on a physiological level. Concentrations of NaCl and PEG were adjusted to create an osmotic potential of a medium at the level of 0.0, −0.45 and −0.65 MPa. The seedlings on the media with PEG were much smaller than those growing in the presence of NaCl, but had a significantly higher content percentage of dry weight. Moreover, the stressors triggered different accumulation patterns of phenolic compounds, soluble and insoluble sugars, proline and β-N-oxalyl-L-α,β-diamino propionic acid, as well as peroxidase and catalase activity. Our results showed that drought stress induced a resistance mechanism consisting of growth rate limitation in favor of osmotic adjustment, while salinity stress induced primarily the mechanisms of efficient compartmentation of harmful ions in the roots and shoots. Furthermore, our results indicated that grass pea plants differed in their response to drought and salinity from the very beginning of stress occurrence.

Sodium nitroprusside (SNP) improves tolerance to arsenic (As) toxicity in Vicia faba through the modifications of biochemical attributes, antioxidants, ascorbate-glutathione cycle and glyoxalase cycle

The present study was conducted to evaluate the effect of arsenic (As) toxicity and the mitigating role of nitric oxide (NO) donor sodium nitroprusside (SNP) on Vicia faba. Arsenics stress decreased the growth and biomass yield, and photosynthetic pigments, but it enhanced As accumulation. Supplementation of NO enhanced the afore-mentioned parameters except As accumulation which decreased in both shoot and root. Supplementation of NO enhanced the shoot tolerance index (Shoot TI%), root tolerance index (Root TI%) but it declined the As translocation factor (TF). Application of NO alleviated the As-induced decline in net assimilation rate, stomatal conductance, transpiration and leaf relative water content. The levels of proline and glycine betaine (GB) further increased due to NO application, whereas malondialdehyde (MDA), hydrogen peroxide (H₂O₂), electrolyte leakage (EL) and methylglyoxal (MG) declined considerably. Activities of enzymatic antioxidants such as superoxide dismutase (SOD) and catalase (CAT) increased under As stress. Supplementation of NO up-regulated the enzymes involved in Asc-Glu cycle and glyoxalase cycle under As toxicity. Another experiment was setup to authenticate whether NO was certainly able to alleviate As toxicity. For this purpose, the NO scavenger [2-(4-carboxy-2 phenyl)-4,4,5,5-tertamethylimidazoline-1-oxyl-3-oxide (cPTIO)] was added to As and NO supplemented plants. Addition of cPTIO to NO supplemented As-treated plants showed the same effect when As alone was supplied to plants. In conclusion, addition of NO to the growth medium maintained the plant performance under As toxicity through modulation of physio-biochemical attributes, antioxidant enzymes, and the Asc-Glu and glyoxalase systems.

Heliotropium thermophilum, an extreme heat tolerant species, promises plants about adaptation to high soil temperature conditions

To understand high temperature tolerance, Heliotropium thermophilum, a flowering plant thriving in a geothermal field with a soil temperature ranging between 55 and 65 °C, was grown in controlled laboratory conditions and two different soil temperatures were applied to the plants. One of them was the control group (CT 25 ± 3 °C) and the other was the high temperature group (HT 60 ± 4 °C). Water potential, dry weight, cell membrane injury (CMI), lipid peroxidation, hydrogen peroxide, chlorophylls, carotenoids, flavonoids, anthocyanins, proline and total soluble sugar contents were measured. Contents of total soluble sugars, phenolics, flavonoids, anthocyanins, proline were found to be higher in HT group than CT while CMI was opposite. Moreover, no difference was determined in water potential, dry weight, lipid peroxidation, total chlorophyll and carotenoids between CT and HT. H. thermophilum plants adapted to high temperature under laboratory conditions through changing membrane lipid saturation, accumulating osmotically active compounds to save water or increase its uptake and inducing antioxidants such as phenolic compounds to keep reactive oxygen species under control. In conclusion, this study showed that H. thermophilum plant was highly resistant to high soil temperature under optimized laboratory conditions. Moreover, a plant that can withstand 60 °C for a long period of time up to 60 days under laboratory conditions was reported for the first time.

OsNHAD is a chloroplast membrane-located transporter required for resistance to salt stress in rice (Oryza sativa)

Salt stress is one of the major environmental factors limiting crop productivity. Although physiological and molecular characterization of salt stress response in plants has been the focus for many years, research on transporters for sodium ion (Na⁺) uptake, translocation and accumulation in plants, particularly in food crops like rice is limited. In this study, we functionally identified an uncharacterized sodium ion transporter named OsNHAD which encodes a putative Na⁺ ⁄ H⁺ antiporter in rice. Homology search shows its close relation to the Arabidopsis Na⁺/H⁺ antiporter AtNHD1 with 72.74% identity of amino acids. OsNHAD transcripts mainly express in leaves and are induced by Na⁺ stress. Confocal laser scanning microscopy analysis of OsNHAD::GFP fusion in tobacco leaves shows that OsNHAD resides in the chloroplast envelop. Knock-down of OsNHAD by RNA interference led to increased rice sensitivity to Na⁺, manifested by stunted plant growth, enhanced cellular damage, reduced PSII activity and changed chloroplast morphology. Mutation of OsNHAD also resulted in accumulation of more Na⁺ in chloroplasts and in shoots as well, suggesting that OsNHAD is involved in mediating efflux and detoxification of Na⁺ but does not affect K⁺ accumulation in plant cells. Complementation test reveals that OsNHAD was able to functionally restore the Arabidopsis mutant atnhd1-1 growth phenotype. These results suggest that OsNHAD possibly mediates homeostasis of sodium ions in the subcellular compartments and tissues of the plants when challenged to salt stress.