Effect of short-term cold stress on oxidative damage and transcript accumulation of defense-related genes in chickpea seedlings

Physio-biochemical and DNA methylation analysis of the defense response network of wheat to drought stress

In the present work, physio-biochemical and DNA methylation analysis were conducted in wheat (Triticum aestivum L.) cultivars "Bolani" (drought-tolerant) and "Sistan" (drought-sensitive) during drought treatments: well-watered (at 90% field capacity (FC)), mild stress (at 50% FC, and severe stress (at 25% FC). During severe stress, O2•- and H2O2 content in cultivar Sistan showed significant increase (by 1.3 and 2.5-fold, respectively) relative to cultivar Bolani. In Bolani, the increased levels of radical scavenging activity (by 32%), glycine betaine (GB) (by 11.44%), proline (4-fold), abscisic acid (by 63.76%), and more stability of relative water content (RWC) (2-fold) were observed against drought-induced oxidative stress. Methylation level significantly decreased from 70.26% to 60.64% in Bolani and from 69.06% to 59.85% in Sistan during stress, and higher decreased tendency was related to CG and CHG in Bolani but CG in Sistan under severe stress. Methylation patterns showed that the highest polymorphism in Bolani was mainly as CG. As the intensity of stress increased, the enhanced physio-biochemical responses of Bolani cultivar were accompanied by a more decrease in the number of unchanged bands. According to heat map analysis, the highest difference (84.38%) in methylation patterns was observed between control and severe stress. Multivariate analysis using principal component analysis (PCA) showed a cultivar-specific methylation during stress and that methylation changes between cultivars are much higher than that of within a cultivar. Higher methylation to demethylation in Bolani (30.06 vs. 22.12%) compared to that of cultivar Sistan (23.21 vs. 30.15%) indicated more demethylation did not induce tolerance responses in Sistan. Sequencing differentially methylated fragments along with qRT-PCR analysis showed the efficient role of various DNA fragments, including demethylated fragments such as phosphoenol pyruvate carboxylase (PEPC), beta-glucosidase (BGlu), glycosyltransferase (GT), glutathione S-transferase (GST) and lysine demethylase (LSD) genes and methylated fragments like ubiquitin E2 enzyme genes in the development of drought tolerance. These results suggested the specific roles of DNA methylation in development of drought tolerance in wheat landrace.

Low-temperature acclimation related with developmental regulations of polyamines and ethylene metabolism in wheat recombinant inbred lines

Winter survival is determined by complicated developmental regulations enabling wheat to adjust their transcriptome and metabolome to develop low temperature (LT) tolerance. The aim of the study was to clarify the metabolic responses developmentally regulated in six F6 recombinant inbred lines from a cross between Pishtaz (spring parent) and Mironovskaya 808 (winter parent). Spring genotypes, including pishtaz, RILs 4006 and 4014 showed lower LT tolerance, PAs (except the spermin), GABA and proline contents and DPPH• scavenging capacity. In these genotypes, genes and enzymes involved in the pathways of PAs and GABA degradation and ethylene biosynthesis were more active than other genotypes. RILs 4012 and 4016 with short vernalization displayed higher tolerance and lower H2O2 content compared to Pishtaz. Strong vernalization requirements in winter and facultative genotypes (Mironovskaya 808 parent and RILs 4003 and 4005) results in up-regulation of the metabolites and genes involved in PAs and GABA biosynthesis pathways (particularly when vernalization fulfillment occurred) to establish high tolerance as compared to genotypes without vernalization requirement. LT tolerance in all genotypes significantly decreased after vernalization fulfillment in February. Results indicated that LT tolerance was partly validated from developmental regulation of PAs, GABA, and ethylene metabolism during venalization and LT acclimation.

Exploring the Effects of Selenium and Brassinosteroids on Photosynthesis and Protein Expression Patterns in Tomato Plants under Low Temperatures

This study aimed to assess the effects of low-temperature stress on two tomato cultivars (S-22 and PKM-1) treated with 24-epibrassinolide (EBL) and selenium (Se) by determining the changes in the proteomics profiles, growth biomarkers, biochemical parameters, and physiological functions. The growth parameters, photosynthetic traits, and activity of nitrate reductase in the S-22 and PKM-1 plants were markedly reduced by exposure to low temperatures. However, the combined application of EBL and Se under different modes significantly enhanced the aforementioned parameters under stress and non-stress conditions. Exposure to low temperatures increased the activities of the antioxidant enzymes (catalase, peroxidase, and superoxide dismutase) and the proline content of leaves, which were further enhanced by treatment with Se and EBL in both varieties. This research sheds light on the potential for employing exogenous EBL and Se as crucial biochemical tactics to assist tomato plants in surviving low-temperature stress. Moreover, the differentially expressed proteins that were involved in plant metabolism following the combined application of EBL and Se under low-temperature stress were additionally identified. Functional analysis revealed that the Q54YH4 protein plays an active role against plant stressors. The conserved regions in the protein sequences were analyzed for assessing the reliability of plant responses against the external application of EBL and Se under low temperatures.

Comprehensive Identification and Expression Profiling of the VQ Motif-Containing Gene Family in Brassica juncea

Valine-glutamine (VQ) motif-containing proteins are a class of highly conserved transcriptional regulators in plants and play key roles in plant growth, development, and response to various stresses. However, the VQ family genes in mustard have not yet been comprehensively identified and analyzed. In this study, a total of 120 VQ family genes (BjuVQ1 to BjuVQ120), which were unevenly distributed on 18 chromosomes (AA_Chr01 to BB_Chr08), were characterized in mustard. A phylogenetic tree analysis revealed that the BjuVQ proteins were clustered into nine distinct groups (groups I to IX), and members in the same group shared a highly conserved motif composition. A gene structure analysis suggested that most BjuVQ genes were intronless. A gene duplication analysis revealed that 254 pairs of BjuVQ genes were segmentally duplicated and one pair was tandemly duplicated. Expression profiles obtained from RNA-seq data demonstrated that most BjuVQ genes have different gene expression profiles in different organs, including leaf, stem, root, flower bud, pod, and seed. In addition, over half of the BjuVQ genes were differentially expressed at some time points under low temperature treatment. The qRT-PCR data revealed that BjuVQ23, BjuVQ55, BjuVQ57, BjuVQ67, BjuVQ100, and BjuVQ117 were upregulated in response to cold stress. Taken together, our study provides new insights into the roles of different BjuVQ genes in mustard and their possible roles in growth and development, as well as in response to cold stress.

Cold stress-induced changes in metabolism of carbonyl compounds and membrane fatty acid composition in chickpea

In this study, changes in membrane fatty acid (FA) composition and damage indices contents as well as the transcript patterns of carbonyl-detoxifying genes were evaluated in two chickpea (Cicer arietinum L.) genotypes, cold-tolerant Sel96th11439 and cold-sensitive ILC533 under cold stress (CS; 4 °C). During CS, H2O2 and malondialdehyde (MDA) contents increased (by 47% and 57%, respectively) in the sensitive genotype, while these contents remained unchanged in the tolerant genotype. In tolerant plants, higher content of linoleic, linolenic, unsaturated FAs (UFAs), total FAs and double bond index (DBI) (by 23, 21, 19, 17 and 9%, respectively) was observed at 6 days after stress (DAS) compared to sensitive plants, which, along with alterations of the damage indices, indicate their enhanced tolerance to CS. Compared with the sensitive genotype, less lipoxygenase (LOX) activity (by 59%) in the tolerant genotype was accompanied by decreased MDA and increased levels of UFAs and DBI during CS, particularly at 6 DAS. Upregulation of aldehyde dehydrogenase and aldo-keto reductase genes (by 9- and 10-fold, respectively) at 1 DAS, along with the enhanced transcript levels of aldehyde reductase and 2-alkenal reductase (by 3- and 14.7-fold, respectively) at 6 DAS were accompanied by increased UFAs and reduced MDA contents in the tolerant genotype. Overall, the results suggest that cold tolerance in chickpea was partly associated with regulation of membrane FA compositions and the potential metabolic networks involved in synthesis and degradation of carbonyl compounds.

Low Temperature Stress Tolerance: An Insight Into the Omics Approaches for Legume Crops

The change in climatic conditions is the major cause for decline in crop production worldwide. Decreasing crop productivity will further lead to increase in global hunger rate. Climate change results in environmental stress which has negative impact on plant-like deficiencies in growth, crop yield, permanent damage, or death if the plant remains in the stress conditions for prolonged period. Cold stress is one of the main abiotic stresses which have already affected the global crop production. Cold stress adversely affects the plants leading to necrosis, chlorosis, and growth retardation. Various physiological, biochemical, and molecular responses under cold stress have revealed that the cold resistance is more complex than perceived which involves multiple pathways. Like other crops, legumes are also affected by cold stress and therefore, an effective technique to mitigate cold-mediated damage is critical for long-term legume production. Earlier, crop improvement for any stress was challenging for scientific community as conventional breeding approaches like inter-specific or inter-generic hybridization had limited success in crop improvement. The availability of genome sequence, transcriptome, and proteome data provides in-depth sight into different complex mechanisms under cold stress. Identification of QTLs, genes, and proteins responsible for cold stress tolerance will help in improving or developing stress-tolerant legume crop. Cold stress can alter gene expression which further leads to increases in stress protecting metabolites to cope up the plant against the temperature fluctuations. Moreover, genetic engineering can help in development of new cold stress-tolerant varieties of legume crop. This paper provides a general insight into the "omics" approaches for cold stress in legume crops.

Salicylic acid: A key regulator of redox signalling and plant immunity

In plants, the reactive oxygen species (ROS) formed during normal conditions are essential in regulating several processes, like stomatal physiology, pathogen immunity and developmental signaling. However, biotic and abiotic stresses can cause ROS over-accumulation leading to oxidative stress. Therefore, a suitable equilibrium is vital for redox homeostasis in plants, and there have been major advances in this research arena. Salicylic acid (SA) is known as a chief regulator of ROS; however, the underlying mechanisms remain largely unexplored. SA plays an important role in establishing the hypersensitive response (HR) and systemic acquired resistance (SAR). This is underpinned by a robust and complex network of SA with Non-Expressor of Pathogenesis Related protein-1 (NPR1), ROS, calcium ions (Ca²⁺), nitric oxide (NO) and mitogen-activated protein kinase (MAPK) cascades. In this review, we summarize the recent advances in the regulation of ROS and antioxidant defense system signalling by SA at the physiological and molecular levels. Understanding the molecular mechanisms of how SA controls redox homeostasis would provide a fundamental framework to develop approaches that will improve plant growth and fitness, in order to meet the increasing global demand for food and bioenergy.

Cold Tolerance during the Reproductive Phase in Chickpea (Cicer arietinum L.) Is Associated with Superior Cold Acclimation Ability Involving Antioxidants and Cryoprotective Solutes in Anthers and Ovules

Chickpea is sensitive to cold stress, especially at reproductive stage, resulting in flower and pod abortion that significantly reduces seed yield. In the present study, we evaluated (a) whether cold acclimation imparts reproductive cold tolerance in chickpea; (b) how genotypes with contrasting sensitivity respond to cold acclimation; and (c) the involvement of cryoprotective solutes and antioxidants in anthers and ovules in cold acclimation. Four chickpea genotypes with contrasting cold sensitivity (cold-tolerant: ICC 17258, ICC 16349; cold-sensitive: ICC 15567, GPF 2) were grown in an outdoor environment for 40 days in November (average maximum/minimum temperature 24.9/15.9 °C) before being subjected to cold stress (13/7 °C), with or without cold acclimation in a controlled environment of walk-in-growth chambers. The 42-d cold acclimation involved 7 d exposure at each temperature beginning with 23/15 °C, 21/13 °C, 20/12 °C, 20/10 °C, 18/8 °C, 15/8 °C (12 h/12 h day/night), prior to exposing the plants to cold stress (13/7 °C, 12 h/12 h day/night; 700 μmol m⁻² s⁻¹ light intensity; 65–70% relative humidity). Cold acclimation remarkably reduced low temperature-induced leaf damage (as membrane integrity, leaf water status, stomatal conductance, photosynthetic pigments, and chlorophyll fluorescence) under cold stress in all four genotypes. It only reduced anther and ovule damage in cold-tolerant genotypes due to improved antioxidative ability, measured as enzymatic (superoxide dismutase, catalase, ascorbate peroxidase, and glutathione reductase) and non-enzymatic (ascorbate and reduced glutathione), solutes (particularly sucrose and γ-aminobutyric acid) leading to improving reproductive function and yield traits, whereas cold-sensitive genotypes were not responsive. The study concluded that cold tolerance in chickpea appears to be related to the better ability of anthers and ovules to acclimate, involving various antioxidants and cryoprotective solutes. This information will be useful in directing efforts toward increasing cold tolerance in chickpea.

The Impact of Far-Red Light Supplementation on Hormonal Responses to Cold Acclimation in Barley

Cold acclimation, the necessary prerequisite for promotion of freezing tolerance, is affected by both low temperature and enhanced far-red/red light (FR/R) ratio. The impact of FR supplementation to white light, created by artificial LED light sources, on the hormone levels, metabolism, and expression of the key hormone metabolism-related genes was determined in winter barley at moderate (15 °C) and low (5 °C) temperature. FR-enhanced freezing tolerance at 15 °C was associated with promotion of abscisic acid (ABA) levels, and accompanied by a moderate increase in indole-3-acetic acid (IAA) and cis-zeatin levels. The most prominent impact on the plants’ freezing tolerance was found after FR pre-treatment at 15 °C (for 10 days) followed by cold treatment at FR supplementation (7 days). The response of ABA was diminished in comparison with white light treatment, probably due to the elevation of stress tolerance during FR pre-treatment. Jasmonic acid (JA) and salicylic acid (SA) were transiently reduced. When the plants were exposed directly to a combination of cold (5 °C) and FR supplementation, ABA increase was higher than in white light, and was associated with enhanced elevation of JA and, in the longer term (after 7 days), with IAA and cis-zeatin increase, which indicates a stronger stress response and better acclimation. Cold hardening was more efficient when FR light was applied in the early developmental stage of the barley plants (three-leaf stage, 18 days), rather than in later stages (28-days). The dynamics of the phytohormone changes are well supported by the expression profiles of the key hormone metabolism-related genes. This series of treatments serves as evidence for the close relationship between plant hormones, light quality, and low temperature at the beginning of cold acclimation. Besides the timing of the FR treatments, plant age also represents a key factor during light spectrum-dependent cold acclimation.

Effect of cold stress on polyamine metabolism and antioxidant responses in chickpea

Metabolic and genomic characteristics of polyamines (PAs) may be associated with the induction of cold tolerance (CT) responses in plants. Characteristics of PAs encoding genes in chickpea (Cicer arietinum L.) and their function under cold stress (CS) are currently unknown. In this study, the potential role of PAs along with the antioxidative defense systems were assessed in two chickpea genotypes (Sel96th11439, cold-tolerant and ILC533, cold-sensitive) under CS conditions. Six days after exposure to CS, the leaf H₂O₂ content and electrolyte leakage index increased in the sensitive genotype by 47.7 and 59 %, respectively, while these values decreased or remained unchanged, respectively, in the tolerant genotype. In tolerant genotype, the enhanced activity of superoxide dismutase (SOD) (by 50 %) was accompanied by unchanged activities of ascorbate peroxidase (APX), guaiacol peroxidase (GPX) and catalase (CAT) as well as the accumulation of glutathione (GSH) (by 43 %) on the sixth day of CS. Higher levels of putrescine (Put) (322 %), spermidine (Spd) (45 %), spermine (Spm) (69 %) and the highest ratio of Put/(Spd + Spm) were observed in tolerant genotype compared to the sensitive one on the sixth day of CS. Gamma-aminobutyric acid (GABA) accumulation was 74 % higher in tolerant genotype compared to the sensitive one on the sixth day of CS. During CS, the activity of diamine oxidase (DAO) and polyamine oxidase (PAO) increased in tolerant (by 3.02- and 2.46-fold) and sensitive (by 2.51- and 2.8-fold) genotypes, respectively, in comparison with the respective non-stressed plants (normal conditions). The highest activity of DAO and PAO in the tolerant genotype was accompanied by PAs decomposition and a peak in GABA content on the sixth day of CS. The analysis of chickpea genome revealed the presence of five PAs biosynthetic genes, their chromosomal locations, and cis-regulatory elements. A significant increase in transcript levels of arginine decarboxylase (ADC) (24.26- and 7.96-fold), spermidine synthase 1 (SPDS1) (3.03- and 1.53-fold), SPDS2 (5.5- and 1.62-fold) and spermine synthase (SPMS) (3.92- and 1.65-fold) genes was detected in tolerant and sensitive genotypes, respectively, whereas the expression of ornithine decarboxylase (ODC) genes decreased significantly under CS conditions in both genotypes. Leaf chlorophyll and carotenoid contents exhibited declining trends in the sensitive genotype, while these photosynthetic pigments were stable in the tolerant genotype due to the superior performance of defensive processes under CS conditions. Overall, these results suggested the specific roles of putative PAs genes and PAs metabolism in development of effective CT responses in chickpea.

Developing Climate-Resilient Chickpea Involving Physiological and Molecular Approaches With a Focus on Temperature and Drought Stresses

Chickpea is one of the most economically important food legumes, and a significant source of proteins. It is cultivated in more than 50 countries across Asia, Africa, Europe, Australia, North America, and South America. Chickpea production is limited by various abiotic stresses (cold, heat, drought, salt, etc.). Being a winter-season crop in northern south Asia and some parts of the Australia, chickpea faces low-temperature stress (0-15°C) during the reproductive stage that causes substantial loss of flowers, and thus pods, to inhibit its yield potential by 30-40%. The winter-sown chickpea in the Mediterranean, however, faces cold stress at vegetative stage. In late-sown environments, chickpea faces high-temperature stress during reproductive and pod filling stages, causing considerable yield losses. Both the low and the high temperatures reduce pollen viability, pollen germination on the stigma, and pollen tube growth resulting in poor pod set. Chickpea also experiences drought stress at various growth stages; terminal drought, along with heat stress at flowering and seed filling can reduce yields by 40-45%. In southern Australia and northern regions of south Asia, lack of chilling tolerance in cultivars delays flowering and pod set, and the crop is usually exposed to terminal drought. The incidences of temperature extremes (cold and heat) as well as inconsistent rainfall patterns are expected to increase in near future owing to climate change thereby necessitating the development of stress-tolerant and climate-resilient chickpea cultivars having region specific traits, which perform well under drought, heat, and/or low-temperature stress. Different approaches, such as genetic variability, genomic selection, molecular markers involving quantitative trait loci (QTLs), whole genome sequencing, and transcriptomics analysis have been exploited to improve chickpea production in extreme environments. Biotechnological tools have broadened our understanding of genetic basis as well as plants' responses to abiotic stresses in chickpea, and have opened opportunities to develop stress tolerant chickpea.

Proteomic and physiological assessment of stress sensitive and tolerant variety of tomato treated with brassinosteroids and hydrogen peroxide under low-temperature stress

The aim of current investigation was to perform proteomics and physio-chemical studies to dissect the changes in contrasting varieties (S-22 and PKM-1) of Lycopersicon esculentum under low-temperature stress. Plant grown under variable low-temperature stress were analysed for their growth biomarkers, antioxidant enzyme activities, and other physiological parameters, which headed toward the determination of protein species responding to low-temperature and 24-epibrassinolide (EBL) concentrations. The plants grown under temperatures, 20/14, 12/7, and 10/3 °C recorded significantly lower growth biomarkers, SPAD chlorophyll, net photosynthetic rate and carbonic anhydrase activity in S-22 and PKM-1. Moreover, the combined effect of EBL and hydrogen peroxide (H₂O₂) significantly improved the parameters mentioned above and consecutively upgraded the different antioxidant enzymes (CAT and SOD) with higher accumulation of proline under stress and stress-free environments. Furthermore, proteomics study revealed that the maximum number of differentially expressed proteins were detected in S-22 (EBL + H₂O₂); while treatment with EBL + H₂O₂ + low temperature lost expression of 20 proteins. Overall, three proteins (O80577, Q9FJQ8, and Q9SKL2) took a substantial part in the biosynthesis of citrate cycle pathway and enhanced the growth and photosynthetic efficiency of tomato plants under low-temperature stress.

Global insights of protein responses to cold stress in plants: Signaling, defence, and degradation

Cold stress (CS) as one of the unfavorable abiotic tensions proceeds different aspects of plant responses. These responses are generated through CS effects on crucial processes such as photosynthesis, energy metabolism, ROS homeostasis, membrane fluidity and cell wall architecture. As a tolerance response, plants apply proteins in various strategies such as transferring the message of cold entrance named as signaling, producing defensive and protective molecules against the stress and degrading some unfavorable or unnecessary proteins to produce other required ones. A change in one part of these networks can irritate alternations in others. These strategies as acclimation mechanisms are conducted through gene expression reprogramming to provide a new adjusted metabolic homeostasis dependent on the stress severity and duration and plant species. Investigating protein alterations in metabolic pathways and their role in adjusting cellular components from upstream to downstream levels can provide a profound knowledge of plants tolerance mechanism against the damaging effects of CS. In this review, we summarized the activity of some cold-responsive proteins from the perception phase to tolerance response against CS.

Effect of cold stress on oxidative damage and mitochondrial respiratory properties in chickpea

The present work aimed to characterize some of the mitochondrial and defense responses involved in tolerance to cold stress (CS) in tolerant (Sel96Th11439) and sensitive (ILC533) chickpea (Cicer arietinum L.) genotypes. During CS, the tolerant genotype prevented the H₂O₂ accumulation significantly; led to a decrease in electrolyte leakage index (ELI), which was a sign of relative acclimation of this genotype compared to sensitive one. A significant positive correlation between ELI and H₂O₂ (r_0.01 = 0.86) content confirmed these results. Under cold, a significant increase in the alternative oxidase (AOX) activity was observed in tolerant genotype compared to sensitive one. In parallel, the high activity of superoxide dismutase (SOD) accompanied with catalase (CAT) and ascorbate peroxidase (APX) activities and also the extreme amounts of ascorbate and proline certified the active reactive oxygen species (ROS)-scavenging systems. There was a significant negative correlation between damage indices like H₂O₂ content and the activity of AOX (r_0.01 = -0.79) as well as significant positive correlation between AOX activity with CAT (r_0.05 = 0.61), SOD (r_0.05 = 0.51) and APX activity (r_0.05 = 0.52). The increasing succinate dehydrogenase (CaSDH), CaAOX and cytochrome c oxidase (CaCOX) gene expression showed an enhancing response of respiration under CS in tolerant plants compared to sensitive ones. The increasing trend of phosphoenol pyruvate carboxylase (PEPC) activity in tolerant genotype particularly in the sixth day of CS indicated the recovered performance of metabolism pathways. Therefore, the increase of AOX activity along with other defensive mechanisms could be coordinately related to cold tolerance mechanisms in order to alleviate cold-induced oxidative stress in chickpea.

cDNA-AFLP analysis of transcripts induced in chickpea plants by TiO2 nanoparticles during cold stress

We evaluated the effect of TiO₂ nanoparticles (NPs) on cold tolerance (CT) development in two chickpea (Cicer arietinum L.) genotypes (Sel96Th11439, cold tolerant, and ILC533, cold susceptible) by using cDNA-amplified fragment length polymorphism (cDNA-AFLP) technique during the first and sixth days of cold stress (CS) at 4 °C. Selective amplification by primer combinations generated 4200 transcript-derived fragments (TDFs) while 100 of them (2.62%) were differentially expressed. During CS, 60 differentially expressed TDFs of TiO₂ NPs-treated plants were cloned and 10 of them produced successfully readable sequences. These data represented different groups of genes involved in metabolism pathways, cellular defense, cell connections and signaling, transcriptional regulation and chromatin architecture. Two out of 10 TDFs were unknown genes with uncharacterized functions or sequences without homology to known ones. The network-based analysis showed a gene-gene relationship in response to CS. Quantitative reverse-transcriptase polymerase chain reaction (qPCR) confirmed differential expression of identified genes (six out of 10 TDFs) with potential functions in CT and showed similar patterns with cDNA-AFLP results. An increase in transcription level of these TDFs, particularly on the first day of CS, was crucial for developing CT through decreasing electrolyte leakage index (ELI) content in tolerant plants compared to susceptible ones, as well as in TiO₂ NPs-treated plants compared to control ones. It could also indicate probable role of TiO₂ NPs against CS-induced oxidative stress. Therefore, a new application of TiO₂ NPs in CT development is suggested for preventing or controlling the damages in field conditions and increasing crop productivity.

Metabolic acclimation of tetraploid and hexaploid wheats by cold stress-induced carbohydrate accumulation

Metabolic acclimation of plants to cold stress may be of great importance for their growth, survival and crop productivity. The accumulation carbohydrates associated with cold tolerance (CT), transcript levels for genes encoding related enzymes along with damage indices were comparatively studied in three genotypes of bread and durum wheats differing in sensitivity. Two (Norstar, bread wheat and Gerdish, durum wheat) were tolerant and the other, SRN (durum wheat), was susceptible to cold stress. During cold stress (-5°C for 24h), the contents of electrolyte leakage index (ELI) in Norstar and then Gerdish plants were lower than that of SRN plants, particularly in cold acclimated (CA) plants (4°C for 14days), confirming lethal temperature 50 (LT₅₀) under field conditions. Increased carbohydrate abundances in the cases of sucrose, glucose, fructose, hexose phosphates, fructan, raffinose, arabinose resulted in different intensities of oxidative stress in bread (Norstar) plants compared to durum plants (SRN and Gerdish) plants as well as in CA plants compared to non-acclimated (NA) ones under cold, indicating metabolic/regulatory capacity along with a decrease in ELI content and enhanced defense activities. A significant decrease in these carbohydrates, particularly sucrose, under cold in NA plants showed an elevated level of cell damage (confirmed by ELI) compared to CA plants. On the other hand, an increase in hexose phosphates, particularly in NA plants, indicated sucrose degradation along with greater production of glucose and fructose compared to CA plants. Under such conditions, a significant increase in transcript levels of sucrose synthase and acidic invertase confirmed these results. Under cold, the high ABA-containing genotypes like Norstar and then Gerdish, which were obvious in CA plants, partly induced relative acclimation of cells for acquisition of CT compared to SRN. These results reveal an important role of carbohydrate metabolism in creating CT in durum wheats (particularly in Gerdish) as well as bread wheat with possible responsive components in metabolic and transcript levels.

Suppression Subtractive Hybridization Versus Next-Generation Sequencing in Plant Genetic Engineering: Challenges and Perspectives

Suppression subtractive hybridization (SSH) is an effective method to identify different genes with different expression levels involved in a variety of biological processes. This method has often been used to study molecular mechanisms of plants in complex relationships with different pathogens and a variety of biotic stresses. Compared to other techniques used in gene expression profiling, SSH needs relatively smaller amounts of the initial materials, with lower costs, and fewer false positives present within the results. Extraction of total RNA from plant species rich in phenolic compounds, carbohydrates, and polysaccharides that easily bind to nucleic acids through cellular mechanisms is difficult and needs to be considered. Remarkable advancement has been achieved in the next-generation sequencing (NGS) field. As a result of progress within fields related to molecular chemistry and biology as well as specialized engineering, parallelization in the sequencing reaction has exceptionally enhanced the overall read number of generated sequences per run. Currently available sequencing platforms support an earlier unparalleled view directly into complex mixes associated with RNA in addition to DNA samples. NGS technology has demonstrated the ability to sequence DNA with remarkable swiftness, therefore allowing previously unthinkable scientific accomplishments along with novel biological purposes. However, the massive amounts of data generated by NGS impose a substantial challenge with regard to data safe-keeping and analysis. This review examines some simple but vital points involved in preparing the initial material for SSH and introduces this method as well as its associated applications to detect different novel genes from different plant species. This review evaluates general concepts, basic applications, plus the probable results of NGS technology in genomics, with unique mention of feasible potential tools as well as bioinformatics.

DNA methylation and physio-biochemical analysis of chickpea in response to cold stress

Cold stress (CS) signals are translated into physiological changes as products of direct and/or indirect of gene expression regulated by different factors like DNA methylation. In this study, some of these factors were comparatively studied in two chickpea (Cicer arietinum L.) genotypes (Sel96Th11439, cold-tolerant genotype, and ILC533, cold susceptible one) under control (23 °C) and days 1, 3, and 6 after exposing the seedlings to CS (4 °C). Under CS, tolerant genotype prevented H2O2 accumulation which led to a decrease in damage indices (malondialdehyde and electrolyte leakage index) compared to susceptible one. The significant activities of antioxidant enzymes (superoxide dismutase, catalase, ascorbate peroxidase, guaiacol peroxidase, and polyphenol oxidase) along with a significant proportion of change in DNA methylation/demethylation patterns were often effective factors in preserving cell against cold-induced oxidative stress. Chickpea cells in response to CS changed access to their genome as the number of bands without change from day 1 to day 6 of exposure to CS particularly in tolerant genotype was decreased. During CS, the methylation level was higher compared to demethylation (29.05 vs 19.79 %) in tolerant genotype and (27.92 vs 22.09 %) in susceptible one. However, for prolonged periods of CS, changes in demethylated bands in tolerant genotype were higher than that of in susceptible one (9.24 vs 4.13 %), indicating higher potential for activation of CS responsive genes. Such a status along with higher activity of antioxidants and less damage indices could be related to cold tolerance (CT) mechanisms in chickpea. Sequencing analysis confirmed the important role of some specific DNA sequences in creating CT with possible responsive components involved in CS. Thus, dynamic assessment using multi-dimensional approaches allows us to progressively fill in the gaps between physio-biochemical and molecular events in creating CT, to comprehend better the nature of the plant stress response and molecular mechanisms behind.

Salicylic acid-induced abiotic stress tolerance and underlying mechanisms in plants

Abiotic stresses (such as metals/metalloids, salinity, ozone, UV-B radiation, extreme temperatures, and drought) are among the most challenging threats to agricultural system and economic yield of crop plants. These stresses (in isolation and/or combination) induce numerous adverse effects in plants, impair biochemical/physiological and molecular processes, and eventually cause severe reductions in plant growth, development and overall productivity. Phytohormones have been recognized as a strong tool for sustainably alleviating adverse effects of abiotic stresses in crop plants. In particular, the significance of salicylic acid (SA) has been increasingly recognized in improved plant abiotic stress-tolerance via SA-mediated control of major plant-metabolic processes. However, the basic biochemical/physiological and molecular mechanisms that potentially underpin SA-induced plant-tolerance to major abiotic stresses remain least discussed. Based on recent reports, this paper: (a) overviews historical background and biosynthesis of SA under both optimal and stressful environments in plants; (b) critically appraises the role of SA in plants exposed to major abiotic stresses;