Physio-biochemical and proteome analysis of chickpea in early phases of cold stress

Global insights into intermediate metabolites: Signaling, metabolic divergence and stress response modulation in plants

Climate change-induced environmental stresses pose significant challenges to plant survival and agricultural productivity. In response, many plants undergo genetic reprogramming, resulting in profound alterations in metabolic pathways and the production of diverse secondary metabolites. As a critical molecular junction, intermediate metabolites by targeted intensification or suppression of subpathways channel cell resources into a multifaceted array of functions such as cell signals, photosynthesis, energy metabolism, ROS homeostasis, producing defensive and protective molecules, epigenetic regulation and stress memory, phytohormones biosynthesis and cell wall architecture under stress conditions. Unlike the well-established functions of end products, intermediate metabolites are context-dependent and produce enigmatic alternatives during stress. As key components of signal transduction pathways, intermediate metabolites with relay and integration of stress signals ensure responses to stress combinations. Investigating efficient metabolic network pathways and their role in regulating unpredictable paths from upstream to downstream levels can unlock their full potential to shape the future of agriculture and ensure global food security. Here, we summarized the activity of some intermediate metabolites, from the perception step to tolerance responses to stress factors.

Integrated transcriptomic and metabolomic data reveal the cold stress responses molecular mechanisms of two coconut varieties

Among tropical fruit trees, coconut holds significant edible and economic importance. The natural growth of coconuts faces a challenge in the form of low temperatures, which is a crucial factor among adverse environmental stresses impacting their geographical distribution. Hence, it is essential to enhance our comprehension of the molecular mechanisms through which cold stress influences various coconut varieties. We employed analyses of leaf growth morphology and physiological traits to examine how coconuts respond to low temperatures over 2-hour, 8-hour, 2-day, and 7-day intervals. Additionally, we performed transcriptome and metabolome analyses to identify the molecular and physiological shifts in two coconut varieties displaying distinct sensitivities to the cold stress. As the length of cold stress extended, there was a prominent escalation within the soluble protein (SP), proline (Pro) concentrations, the activity of peroxidase (POD) and superoxide dismutase (SOD) in the leaves. Contrariwise, the activity of glutathione peroxidase (GSH) underwent a substantial reduction during this period. The widespread analysis of metabolome and transcriptome disclosed a nexus of genes and metabolites intricately cold stress were chiefly involved in pathways centered around amino acid, flavonoid, carbohydrate and lipid metabolism. We perceived several stress-responsive metabolites, such as flavonoids, carbohydrates, lipids, and amino acids, which unveiled considerably, lower in the genotype subtle to cold stress. Furthermore, we uncovered pivotal genes in the amino acid biosynthesis, antioxidant system and flavonoid biosynthesis pathway that presented down-regulation in coconut varieties sensitive to cold stress. This study broadly enriches our contemporary perception of the molecular machinery that contributes to altering levels of cold stress tolerance amid coconut genotypes. It also unlocks several unique prospects for exploration in the areas of breeding or engineering, aiming to identifying tolerant and/or sensitive coconut varieties encompassing multi-omics layers in response to cold stress conditions.

Melatonin-regulated heat shock proteins and mitochondrial ATP synthase induce drought tolerance through sustaining ROS homeostasis in H2S-dependent manner

Drought is thought to be one of the major global hazards to crop production. Understanding the role of melatonin (Mel) during plant adaptive responses to drought stress (DS) was the aim of the current investigation. Involvement of hydrogen sulfide (H2S) was also explored in Mel-regulated mechanisms of plants' tolerance to DS. A perusal of the data shows that exposure of tomato plants to DS elevated the activity of mitochondrial enzymes viz. pyruvate dehydrogenase, malate dehydrogenase, and citrate synthase. Whereas the activity of ATP synthase and ATPase was downregulated under stress conditions. Under DS, an increase in the expression level of heat shock proteins (HSPs) and activation level of antioxidant defense system was observed as well. On the other hand, an increase in the activity of NADPH oxidase and glycolate oxidase was observed along with the commencement of oxidative stress and accompanying damage. Application of 30 μM Mel to drought-stressed plants enhanced H2S accumulation and further elevated the activity of mitochondrial enzymes, activation level of the defense system, and expression of HSP17.6 and HSP70. Positive effect of Mel on these attributes was reflected by reduced level of ROS and related damage. However, application of H2S biosynthesis inhibitor DL-propargylglycine reversed the effect of Mel on the said attributes and again the damaging effects of drought were observed even in presence of Mel. This observation led us to conclude that Mel-regulated defense mechanisms operate through endogenous H2S under DS conditions.

Rethinking underutilized cereal crops: pan-omics integration and green system biology

MAIN CONCLUSION

Due to harsh lifestyle changes, in the present era, nutritional security is needed along with food security so it is necessary to include underutilized cereal crops (UCCs) in our daily diet to counteract the rising danger of human metabolic illness. We can attain both the goal of zero hunger and nutritional security by developing improved UCCs using advanced pan-omics (genomics, transcriptomics, proteomics, metabolomics, nutrigenomics, phenomics and ionomics) practices. Plant sciences research progressed profoundly since the last few decades with the introduction of advanced technologies and approaches, addressing issues of food demand of the growing population, nutritional security challenges and climate change. However, throughout the expansion and popularization of commonly consumed major cereal crops such as wheat and rice, other cereal crops such as millet, rye, sorghum, and others were impeded, despite their potential medicinal and nutraceutical qualities. Undoubtedly neglected underutilized cereal crops (UCCs) also have the capability to withstand diverse climate change. To relieve the burden of major crops, it is necessary to introduce the new crops in our diet in the way of UCCs. Introgression of agronomically and nutritionally important traits by pan-omics approaches in UCCs could be a defining moment for the population's well-being on the globe. This review discusses the importance of underutilized cereal crops, as well as the application of contemporary omics techniques and advanced bioinformatics tools that could open up new avenues for future study and be valuable assets in the development and usage of UCCs in the perspective of green system biology. The increased and improved use of UCCs is dependent on number of factors that necessitate a concerted research effort in agricultural sciences. The emergence of functional genomics with molecular genetics might gear toward the reawakening of interest in underutilized cereals crops. The need of this era is to focus on potential UCCs in advanced agriculture and breeding programmes. Hence, targeting the UCCs, might provide a bright future for better health and scientific rationale for its use.

Coping with the cold: unveiling cryoprotectants, molecular signaling pathways, and strategies for cold stress resilience

Low temperature stress significantly threatens crop productivity and economic sustainability. Plants counter this by deploying advanced molecular mechanisms to perceive and respond to cold stress. Transmembrane proteins initiate these responses, triggering a series of events involving secondary messengers such as calcium ions (Ca2+), reactive oxygen species (ROS), and inositol phosphates. Of these, calcium signaling is paramount, activating downstream phosphorylation cascades and the transcription of cold-responsive genes, including cold-regulated (COR) genes. This review focuses on how plants manage freeze-induced damage through dual strategies: cold tolerance and cold avoidance. Tolerance mechanisms involve acclimatization to decreasing temperatures, fostering gradual accumulation of cold resistance. In contrast, avoidance mechanisms rely on cryoprotectant molecules like potassium ions (K+), proline, glycerol, and antifreeze proteins (AFPs). Cryoprotectants modulate intracellular solute concentration, lower the freezing point, inhibit ice formation, and preserve plasma membrane fluidity. Additionally, these molecules demonstrate antioxidant activity, scavenging ROS, preventing protein denaturation, and subsequently mitigating cellular damage. By forming extensive hydrogen bonds with water molecules, cryoprotectants also limit intercellular water movement, minimizing extracellular ice crystal formation, and cell dehydration. The deployment of cryoprotectants is a key adaptive strategy that bolsters plant resilience to cold stress and promotes survival in freezing environments. However, the specific physiological and molecular mechanisms underlying these protective effects remain insufficiently understood. Therefore, this review underscores the need for further research to elucidate these mechanisms and assess their potential impact on crop productivity and sustainability, contributing to the progressive discourse in plant biology and environmental science.

Foliar application of putrescine, salicylic acid, and ascorbic acid mitigates frost stress damage in Vitis vinifera cv. ̒Giziluzum̕

BACKGROUND

Cold stress is an effective factor in reducing production and injuring fruit trees. Various materials, such as salicylic acid, ascorbic acid, and putrescine, are used to alleviate the damage of abiotic stress.

RESULTS

The effect of different treatments of putrescine, salicylic acid, and ascorbic acid on alleviating the damage of frost stress (- 3 °C) to grapes 'Giziluzum' was investigated. Frost stress increased the amount of H₂O₂, MDA, proline, and MSI. On the other hand, it decreased the concentration of chlorophyll and carotenoids in the leaves. Putrescine, salicylic acid and ascorbic acid significantly increased the activities of catalase, guaiacol peroxidase, ascorbate peroxidase, and superoxide dismutase under frost stress. Following frost stress, the grapes treated with putrescine, salicylic acid, and ascorbic acid showed higher levels of DHA, AsA, and AsA/DHA than the untreated grapes. Our results showed that the treatment with ascorbic acid outperformed the other treatments in adjusting frost stress damages.

CONCLUSION

The use of compounds, such as ascorbic ac id, salicylic acid, and putrescine, modulates the effects of frost stress, thereby increasing the antioxidant defense system of cells, reducing its damage, and stabilizing stable cell conditions, so it can be used to reduce frost damage to different grape cultivars.

Estimation of genetic diversity using seed storage protein (SSP) profiling in wild and cultivated species of Cicer L

BACKGROUND

The narrow genetic diversity of chickpea is a serious impediment to modern cultivar creation. Seed storage proteins (SSPs) are stable and have minimal or no degradation when subjected to isolation and SDS-PAGE.

METHODS AND RESULTS

We have characterized SSPs of 436 chickpea genotypes, belonging to nine annual Cicer species, originated from 47 countries by SDS-PAGE and determined the extent of genetic diversity in chickpea through clustering. Based on scoring, a total of 44 bands (10 to 170 kDa) were identified, which were all polymorphic. The least appeared protein bands were 11, 160 and 170 kDa where band of 11 and 160 kDa was present exclusively in wild type. Five bands were present in < 10% of genotypes. Bands appeared in 200-300 genotypes were suggested less polymorphic, on contrary bands present in 10-150 genotypes were suggested more polymorphic. Polymorphism of protein bands in context to their potential functions reported in literature were explored and suggested that the glubulins were most and glutelins were least abundant, whereas albumins with their known role in stress tolerance can be used as marker in chickpea breeding. Cluster analysis produced 14 clusters, interestingly three clusters contained only Pakistani genotypes and thus Pakistani genotypes appeared as a separate entity from the rest of the genotypes.

CONCLUSION

Our results indicate that SDS-PAGE of SSPs is a powerful technique in determining the genetic diversity plus it is easily adaptable, due to its cost effectiveness in comparison to other genomics tools.

Proteomics for abiotic stresses in legumes: present status and future directions

Legumes are the most important crop plants in agriculture, contributing 27% of the world's primary food production. However, productivity and production of Legumes is reduced due to increasing environmental stress. Hence, there is a pressing need to understand the molecular mechanism involved in stress response and legumes adaptation. Proteomics provides an important molecular approach to investigate proteins involved in stress response. Both the gel-based and gel-free-based techniques have significantly contributed to understanding the proteome regulatory network in leguminous plants. In the present review, we have discussed the role of different proteomic approaches (2-DE, 2 D-DIGE, ICAT, iTRAQ, etc.) in the identification of various stress-responsive proteins in important leguminous crops, including soybean, chickpea, cowpea, pigeon pea, groundnut, and common bean under variable abiotic stresses including heat, drought, salinity, waterlogging, frost, chilling and metal toxicity. The proteomic analysis has revealed that most of the identified differentially expressed proteins in legumes are involved in photosynthesis, carbohydrate metabolism, signal transduction, protein metabolism, defense, and stress adaptation. The proteomic approaches provide insights in understanding the molecular mechanism of stress tolerance in legumes and have resulted in the identification of candidate genes used for the genetic improvement of plants against various environmental stresses. Identifying novel proteins and determining their expression under different stress conditions provide the basis for effective engineering strategies to improve stress tolerance in crop plants through marker-assisted breeding.

Over-expression of spermidine synthase 2 (SlSPDS2) in tomato plants improves saline-alkali stress tolerance by increasing endogenous polyamines content to regulate antioxidant enzyme system and ionic homeostasis

Endogenous spermidine can improve the resistance of plants to saline-alkali stress. SlSPDS1 and SlSPDS2 are the main spermidine synthase (SPDS) genes in tomatoes. In comparison with SlSPDS1, SlSPDS2 plays an important role in wild-type tomato seedling under saline-alkali stress. However, limited research has focused on the role of SlSPDS2 in saline-alkali stress. Wild-type (WT) and SPDS gene (SlSPDS2) transgenic over-expression tomato seedlings were used to explore the function of endogenous spermidine on the saline-alkali resistance of tomato seedlings. The results show that SlSPDS2 overexpression under normal conditions and saline-alkali stress increased the content of endogenous free polyamines and the expression levels of polyamine synthesis-related genes in tomato seedlings. Under saline-alkali stress, SlSPDS2 overexpression significantly reduced Na+/K+ ratio, relative electrical conductivity, O2·-, H2O2, and malondialdehyde content, increased Seedling index, relative water content, antioxidant enzyme activities (peroxidase, superoxide dismutase, and catalase), and the contents of proline and soluble sugar in tomato leaf, and mitigated the adverse effect of saline-alkali stress on tomato seedlings. In summary, the overexpression of SlSPDS2 tomato seedlings regulated the ionic homeostasis, antioxidant enzyme system, and osmotic regulatory substances of tomato seedlings living in saline-alkali environment by increasing endogenous free polyamine content, thereby improving the resistance of tomato seedlings against saline-alkali 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.

Outcomes of Low-Temperature Stress on Biological Alterations within Pothos (Epipremnum aureum) Leaves

Pothos (Epipremnum aureum) is a commonly used indoor ornamental foliage, particularly in the middle and lower regions of the Yangtze River in China. It typically grows in the tropical area, and it is yet unclear whether prolonged winter temperatures cause plant damage and impact its development. In this study, the E. aureum chilling injury response was explored by maintaining it at 1 °C. Based on the acquired results, low-temperature stress (LTS) induced wilting and yellowing of leaves and diminished chloroplast pigment concentrations, particularly the chlorophyll b content. LTS also induced overproduction of reactive oxygen species (ROS) within E. aureum and enhanced the relative electrical conductivity and superoxide dismutase activity. In addition, with prolonged LTS, the anatomical structure of E. aureum was severely damaged, resulting in a marked reduction in the photochemical activity of the photosystem Ⅱ reaction center and suppressed photosynthesis. Moreover, results of the transcriptomic analysis revealed that LTS induced the expression of genes involved in the α-linolenic acid metabolic pathway, plant hormone network, host plant–pathogen association, and MAPK axis, suggesting that LTS would activate its resistant response to cold stress. These results unraveled the physiological and transcriptomical response of E. aureum to chilling injury, which would lay a theoretical foundation for the cultivation of low-temperature-tolerant varieties of E. aureum.

Synthesis of magnetic nanoparticles and their effects on growth and physiological parameters of Calotropis procera seedlings

The present study was carried out to elucidate effects of synthesized magnetic nanoparticles (MNPs) on morphological and physiological parameters and main essential oil components of Calotropis procera seedlings. For this purpose, 21-day-old seedlings grown under hydroponic conditions were treated by the different MNP concentrations (0, 50, 100, 150, and 200 mg L^-1). The results showed that the growth parameters, chlorophyll pigments, soluble sugars, and total proteins significantly increased in leaf under MNP treatment, except for the root length. As compared to the control, MNPs induced a substantial change in the activities of antioxidant enzymes, H₂O₂, and malondialdehyde contents. Ascorbate peroxidase activity showed a meaningful increase in leaf treated with 200 mg L^-1 MNPs, while superoxide dismutase activity and concentration of H₂O₂ conspicuously decreased relative to the control. Moreover, MNPs enhanced geranial, 1,8-cineol, a-phellandrene, citronellal, camphor, and terpinen-4-ol contents as major components. These results suggest that MNPs could be a promising method of iron application in agricultural systems. Regarding the effects of MNPs, 200-mg L^-1 MNPs were most effective on the production of main essential oils and plant growth that could serve as a favorable elicitor for plant improvement.

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.

Unraveling Cadmium Toxicity in Trifolium repens L. Seedling: Insight into Regulatory Mechanisms Using Comparative Transcriptomics Combined with Physiological Analyses

Trifolium repens (T. repens) can accumulate significant amounts of heavy metal ions, and has strong adaptability to wide environmental conditions, and relatively large biomass, which is considered a potential plant for phytoremediation. However, the molecular mechanisms of T. repens involved in Cd tolerance have not yet been studied in detail. This study was conducted to examine the integrative responses of T. repens exposed to a high-level CdCl₂ by investigating the physiological and transcriptomic analyses. The results suggested that T. repens seedlings had a high degree of tolerance to Cd treatment. The roots accumulated higher Cd concentration than leaves and were mainly distributed in the cell wall. The content of MDA, soluble protein, the relative electrolyte leakage, and three antioxidant enzymes (POD, SOD, and APX) was increased with the Cd treatment time increasing, but the CAT enzymes contents were decreased in roots. Furthermore, the transcriptome analysis demonstrated that the differentially expressed genes (DEGs) mainly enriched in the glutathione (GSH) metabolism pathway and the phenylpropanoid biosynthesis in the roots. Overexpressed genes in the lignin biosynthesis in the roots might improve Cd accumulation in cell walls. Moreover, the DEGs were also enriched in photosynthesis in the leaves, transferase activity, oxidoreductase activity, and ABA signal transduction, which might also play roles in reducing Cd toxicity in the plants. All the above, clearly suggest that T. repens employ several different mechanisms to protect itself against Cd stress, while the cell wall biosynthesis and GSH metabolism could be considered the most important specific mechanisms for Cd retention in the roots of T. repens.

Transcriptome sequencing and gene expression profiling of Pinus sibirica under different cold stresses

Cold stress is a major abiotic factor that affects plant growth and geographical distribution. Pinus sibirica is extremely frigostable tree species. To understand the molecular mechanisms of cold tolerance by P. sibirica, physiological responses were analyzed and transcriptome profiling was conducted to the plants treated by cold stress. The physiological data showed that membrane permeability relative conductivity (REC), reactive oxygen species (ROS), malonaldehyde (MDA) content, peroxidase (POD) and catalase (CAT) activity, soluble sugar, soluble protein and proline contents were increased significantly (p < 0.05) in response to cold stress. Transcriptome analysis identified a total of 871, 1397 and 872 differentially expressed genes (DEGs) after cold treatment for 6 h, 24 h and 48 h at -20°C, respectively. The signaling pathway mediated by Ca²⁺ as a signaling molecule and abscisic acid pathways were the main cold signal transduction pathways in P. sibirica. The APETALA2/Ethylene-Responsive Factor (AP2/ERF) and MYB transcription factor families also play an important role in the transcriptional regulation of P. sibirica. In addition, many genes related to photosynthesis were differentially expressed under cold stress. We also validated the reliability of transcriptome data with quantitative real-time PCR. This study lays the foundation for understanding the molecular mechanisms related to cold responses in P. sibirica.

Evaluation of physiological and biochemical responses of pistachio plants (Pistacia vera L.) exposed to pesticides

Pesticides may manipulate plant physiology as non-target organisms. In this study, we examined biochemical responses of pistachio plants (Pistacia vera L.) to imidacloprid and phosalone as common pesticides used to control pistachio psyllids. Enzymatic characterization in treated plants with pesticides showed greater specific activities of superoxide dismutase, catalase, ascorbate peroxidase, guaiacol peroxidase, phenylalanine ammonia-lyase, glutathione reductase, and glutathione S-transferase compared with untreated plants during 14 days after treatment. Further experiments displayed elevated levels of total phenols and total proteins coupled with significant increases in proline and total soluble carbohydrate contents in treated plants in comparison to untreated plants. Moreover, pesticide treatment leads to a significant decrease in polyphenol oxidase activity. Nevertheless, no significant changes in contents of hydrogen peroxide, malondialdehyde, total chlorophyll, and electrolyte leakage index were obtained in treated plants. Pesticides' impacts on host plant physiology resulted in similar responses between two pesticides with differences in peak days. Overall, the findings of this study provide an insight into the side effects of phosalone and imidacloprid, chemicals with no specific target site in plants, on the physiology and biochemistry of pistachio plants at recommended rates.

Comparative transcriptomic analysis reveals the coordinated mechanisms of Populus × canadensis 'Neva' leaves in response to cadmium stress

Cadmium (Cd), a heavy metal element has strong toxicity to living organisms. Excessive Cd accumulation directly affects the absorption of mineral elements, inhibits plant tissue development, and even induces mortality. Populus × canadensis 'Neva', the main afforestation variety planted widely in northern China, was a candidate variety for phytoremediation. However, the genes relieving Cd toxicity and increasing Cd tolerance of this species were still unclear. In this study, we employed transcriptome sequencing on two Cd-treated cuttings to identify the key genes involved in Cd stress responses of P. × canadensis 'Neva' induced by 0 (CK), 10 (C10), and 20 (C20) mg/L Cd(NO3)2 4H2O. We discovered a total of 2,656 (1,488 up-regulated and 1,168 down-regulated) and 2,816 DEGs (1,470 up-regulated and 1,346 down-regulated) differentially expressed genes (DEGs) between the CK vs C10 and CK vs C20, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses in response to the Cd stress indicated that many DEGs identified were involved in the catalytic activity, the oxidoreductase activity, the transferase activity, and the biosynthesis of secondary metabolites. Based on the enrichment results, potential candidate genes were identified related to the calcium ion signal transduction, transcription factors, the antioxidant defense system, and transporters and showed divergent expression patterns under the Cd stress. We also validated the reliability of transcriptome data with the real-time PCR. Our findings deeper the understanding of the molecular responsive mechanisms of P. × canadensis 'Neva' on Cd tolerance and further provide critical resources for phytoremediation applications.

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.

Omics and CRISPR-Cas9 Approaches for Molecular Insight, Functional Gene Analysis, and Stress Tolerance Development in Crops

Plants are regularly exposed to biotic and abiotic stresses that adversely affect agricultural production. Omics has gained momentum in the last two decades, fueled by statistical methodologies, computational capabilities, mass spectrometry, nucleic-acid sequencing, and peptide-sequencing platforms. Functional genomics—especially metabolomics, transcriptomics, and proteomics—have contributed substantially to plant molecular responses to stress. Recent progress in reverse and forward genetics approaches have mediated high-throughput techniques for identifying stress-related genes. Furthermore, web-based genetic databases have mediated bioinformatics techniques for detecting families of stress-tolerant genes. Gene ontology (GO) databases provide information on the gene product’s functional features and help with the computational estimation of gene function. Functional omics data from multiple platforms are useful for positional cloning. Stress-tolerant plants have been engineered using stress response genes, regulatory networks, and pathways. The genome-editing tool, CRISPR-Cas9, reveals the functional features of several parts of the plant genome. Current developments in CRISPR, such as de novo meristem induction genome-engineering in dicots and temperature-tolerant LbCas12a/CRISPR, enable greater DNA insertion precision. This review discusses functional omics for molecular insight and CRISPR-Cas9-based validation of gene function in crop plants. Omics and CRISPR-Cas9 are expected to garner knowledge on molecular systems and gene function and stress-tolerant crop production.

Cold Stress Response: An Overview in Chlamydomonas

Low temperature (or cold) is one of the major environmental factors that limit the growth and development of many plants. Various plant species have evolved complex mechanisms to adjust to decreased temperature. Mesophilic chlorophytes are a widely distributed group of eukaryotic photosynthetic organisms, but there is insufficient information about the key molecular processes of their cold acclimation. The best available model for studying how chlorophytes respond to and cope with variations in temperature is the unicellular green alga Chlamydomonas reinhardtii. Chlamydomonas has been widely used for decades as a model system for studying the fundamental mechanisms of the plant heat stress response. At present, unraveling novel cold-regulated events in Chlamydomonas has attracted increasing research attention. This mini-review summarizes recent progress on low-temperature-dependent processes in the model alga, while information on other photosynthetic organisms (cyanobacteria and land plants) was used to strengthen generalizations or specializations of cold-induced mechanisms in plant evolution. Here, we describe recent advances in our understanding of cold stress response in Chlamydomonas, discuss areas of controversy, and highlight potential future directions in cold acclimation research.

A comparative metabolomic study on desi and kabuli chickpea (Cicer arietinum L.) genotypes under rainfed and irrigated field conditions

Chickpea is considered among the most important leguminous crops in the world. However, in recent years drought conditions and/or limited availability of water have significantly reduced the production of chickpea. The current study was aimed to understand the legume stress response at the metabolic level for the determination of chickpea genotypes which can resist yield losses and could be cultivated with limited water availability. Here, we have analyzed two genotypes of chickpea, desi and kabuli under rainfed condition using a GC–MS based untargeted metabolomics approach. Results revealed significant differences in several metabolite features including oxalic acid, threonic acid, inositol, maltose and l-proline between studied groups. Accumulation of plant osmoprotectants such as l-proline, sugars and sugar alcohols was higher in desi genotype than kabuli genotype of chickpea when grown under the rainfed condition. Metabolic pathway analysis suggests that the inositol phosphate metabolism was involved in plant defense mechanisms against the limited water availability.

Close relationship between the state of the oxygen evolving complex and rice cold stress tolerance

The results of the present work suggested a relationship between the growth stability and functional/structural parameters associated to the primary photochemistry and oxygen evolving complex (OEC) in tolerant rice plants under suboptimal low temperatures (SLT) stress. This was concluded from the absence of changes in net photosynthetic rate and in fraction of reaction centers to reduce quinone A, and very small changes in P680 efficiency to trap and donate electrons to quinone A and in fraction of active OEC in tolerant plants under cold stress but not in sensitive plants. The SLT stress also induced OEC activity limitations in both genotypes, but in a greater extent in sensitive plants. However, an assay using an artificial electron donor to replace OEC indicated that the P680⁺ capacity to accept electrons was not altered in both genotypes under SLT stress from the beginning of the stress treatment, suggesting that the OEC structure stability is related to rice SLT tolerance to sustain the photosynthesis. This hypothesis was also supported by the fact that tolerant plants but not sensitive plants did not alter the gene expression and protein content of PsbP under SLT stress, an OEC subunit with a role in stabilizing of OEC structure.

Comparative transcriptome profiling reveals cold stress responsiveness in two contrasting Chinese jujube cultivars

BACKGROUND

Low temperature is a major factor influencing the growth and development of Chinese jujube (Ziziphus jujuba Mill.) in cold winter and spring. Little is known about the molecular mechanisms enabling jujube to cope with different freezing stress conditions. To elucidate the freezing-related molecular mechanism, we conducted comparative transcriptome analysis between 'Dongzao' (low freezing tolerance cultivar) and 'Jinsixiaozao' (high freezing tolerance cultivar) using RNA-Seq.

RESULTS

More than 20,000 genes were detected at chilling (4 °C) and freezing (- 10 °C, - 20 °C, - 30 °C and - 40 °C) stress between the two cultivars. The numbers of differentially expressed genes (DEGs) between the two cultivars were 1831, 2030, 1993, 1845 and 2137 under the five treatments. Functional enrichment analysis suggested that the metabolic pathway, response to stimulus and catalytic activity were significantly enriched under stronger freezing stress. Among the DEGs, nine participated in the Ca²⁺ signal pathway, thirty-two were identified to participate in sucrose metabolism, and others were identified to participate in the regulation of ROS, plant hormones and antifreeze proteins. In addition, important transcription factors (WRKY, AP2/ERF, NAC and bZIP) participating in freezing stress were activated under different degrees of freezing stress.

CONCLUSIONS

Our research first provides a more comprehensive understanding of DEGs involved in freezing stress at the transcriptome level in two Z. jujuba cultivars with different freezing tolerances. These results may help to elucidate the molecular mechanism of freezing tolerance in jujube and also provides new insights and candidate genes for genetically enhancing freezing stress tolerance.

Legume genomics and transcriptomics: From classic breeding to modern technologies

Legumes are essential and play a significant role in maintaining food standards and augmenting physiochemical soil properties through the biological nitrogen fixation process. Biotic and abiotic factors are the main factors limiting legume production. Classical breeding methodologies have been explored extensively about the problem of truncated yield in legumes but have not succeeded at the desired rate. Conventional breeding improved legume genotypes but with more resources and time. Recently, the invention of next-generation sequencing (NGS) and high-throughput methods for genotyping have opened new avenues for research and developments in legume studies. During the last decade, genome sequencing for many legume crops documented. Sequencing and re-sequencing of important legume species have made structural variation and functional genomics conceivable. NGS and other molecular techniques such as the development of markers; genotyping; high density genetic linkage maps; quantitative trait loci (QTLs) identification, expressed sequence tags (ESTs), single nucleotide polymorphisms (SNPs); and transcription factors incorporated into existing breeding technologies have made possible the accurate and accelerated delivery of information for researchers. The application of genome sequencing, RNA sequencing (transcriptome sequencing), and DNA sequencing (re-sequencing) provide considerable insights for legume development and improvement programs.

Moreover, RNA-Seq helps to characterize genes, including differentially expressed genes, and can be applied for functional genomics studies, especially when there is limited information available for the studied genomes. Genome-based crop development studies and the availability of genomics data as well as decision-making gears look be specific for breeding programs. This review mainly presents an overview of the path from classical breeding to new emerging genomics tools, which will trigger and accelerate genomics-assisted breeding for recognition of novel genes for yield and quality characters for sustainable legume crop production.

Melatonin-related mitochondrial respiration responses are associated with growth promotion and cold tolerance in plants

Melatonin has the ability to improve plant growth and strengthened plant tolerance to environmental stresses; however, the effects of melatonin on mitochondrial respiration in plants and the underlying biochemical and molecular mechanisms are still unclear. The objective of the study is to determine possible effects of melatonin on mitochondrial respiration and energy efficiency in maize leaves grown under optimum temperature and cold stress and to reveal the relationship between melatonin-induced possible alterations in mitochondrial respiration and cold tolerance. Melatonin and cold stress, alone and in combination, caused significant increases in activities and gene expressions of pyruvate dehydrogenase, citrate synthase, and malate dehydrogenase, indicating an acceleration in the rate of tricarboxylic acid cycle. Total mitochondrial respiration rate, cytochrome pathway rate, and alternative respiration rate were increased by the application of melatonin and/or cold stress. Similarly, gene expression and protein levels of cytochrome oxidase and alternative oxidase were also enhanced by melatonin and/or cold stress. The highest values for all these parameters were obtained from the seedlings treated with the combined application of melatonin and cold stress. The activity and gene expression of ATP synthase and ATP concentration were augmented by melatonin under control and cold stress. On the other hand, cold stress reduced markedly plant growth parameters, including root length, plant height, leaf surface area, and chlorophyll content and increased the content of reactive oxygen species (ROS), including superoxide anion and hydrogen peroxide and oxidative damage, including malondialdehyde content and electrolyte leakage level; however, melatonin significantly promoted the plant growth parameters and reduced ROS content and oxidative damage under control and cold stress. These data revealed that melatonin-induced growth promotion and cold tolerance in maize is associated with its modulating effect on mitochondrial respiration.

Advances and challenges in uncovering cold tolerance regulatory mechanisms in plants

Contents Summary I. Introduction II. Cold stress and physiological responses in plants III. Sensing of cold signals in plants IV. Messenger molecules involved in cold signal transduction V. Cold signal transduction in plants VI. Conclusions and perspectives Acknowledgements References SUMMARY: Cold stress is a major environmental factor that seriously affects plant growth and development, and influences crop productivity. Plants have evolved a series of mechanisms that allow them to adapt to cold stress at both the physiological and molecular levels. Over the past two decades, much progress has been made in identifying crucial components involved in cold-stress tolerance and dissecting their regulatory mechanisms. In this review, we summarize recent major advances in our understanding of cold signalling and put forward open questions in the field of plant cold-stress responses. Answering these questions should help elucidate the molecular mechanisms underlying plant tolerance to cold stress.

Changes in the expression of some genes involved in the biosynthesis of secondary metabolites in Cuminum cyminum L. under UV stress

Biotic and abiotic stresses cause special defense reactions in plant organs, which after a series of reactions, these stresses produce secondary metabolites. The effect of ultraviolet radiation on the expression of key genes involved in the biosynthesis of secondary metabolites (Phenylalanine ammonia lyase (PAL), Hydroxymethylglutaryl-CoA reductase (HMG-CoA reductase), GPP synthases, Deoxyribonino heptulosinate 7-phosphate synthase (DAHP), and Deoxy Xylose Phosphate Synthase (DXS)), and the association of these genes with different amounts of secondary metabolites (phenol, terpene, flavonoids, anthocyanins, alkaloids, lycopene, and beta-carotene) was investigated in this study. The results of this study showed that the application of UV-B stress significantly increased the expression of GPPs, HMG-CoA reductase, DXS, DAHPs, and PAL genes compared to the control plants. The expression of two key genes involved in the biosynthesis of phenylpropanoids, including DAHPs and PAL, increased with UV-B stress, and the highest expression was related to the PAL gene. The results revealed that UV-B stress caused a significant increase in total levels of terpenoids, phenols, flavonoids, anthocyanins, alkaloids, beta-carotene, and lycopene. The highest relative expression of all genes was obtained in treatment A (UV-B radiation for 1 h), while in treatment B (UV-B radiation for 2 h), no significant changes were observed in the expression of the genes.

Physiological studies and genome-wide microRNA profiling of cold-stressed Brassica napus

Temperature extremes, including cold, adversely impact plant growth and development. Plant responses to cold stress (CS) are regulated at both transcriptional and post-transcriptional levels. MicroRNAs (miRNAs), small non-coding RNAs, are known to be involved in post-transcriptional regulation of various developmental processes and metal stress in Brassica napus L. (canola), however, their role in response to CS is largely unknown. In this study, changes in various physiological parameters and endogenous abundance of miRNAs were characterized in spring canola seedlings (DH12075) exposed to 4 °C for 0-48 h. Cold stress induced electrolyte leakage, increased the levels of malondialdheyde and antioxidant enzymes and reduced photosynthetic efficiency. Using small RNA sequencing, 70 known and 126 novel miRNAs were identified in CS leaf tissues and among these, 25 known and 104 novel miRNAs were differentially expressed. Quantitative real-time (qRT) PCR analysis of eight selected miRNAs confirmed their CS responsiveness. Furthermore, the expression of six out of eight miRNAs exhibited an opposite trend in a winter variety of canola, 'Mendel', when compared to 'DH12075'. This first study on the B. napus miRNAome provides a framework for further functional analysis of these miRNAs and their targets in response to CS which may contribute towards the future development of cold resilient crops.

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.

Proteomic and Biochemical Changes during Senescence of Phalaenopsis 'Red Dragon' Petals

Phalaenopsis flowers are some of the most popular ornamental flowers in the world. For most ornamental plants, petal longevity determines postharvest quality and garden performance. Therefore, it is important to have insight into the senescence mechanism of Phalaenopsis. In the present study, a proteomic approach combined with ultrastructural observation and activity analysis of antioxidant enzymes was used to profile the molecular and biochemical changes during pollination-induced petal senescence in Phalaenopsis “Red Dragon”. Petals appeared to be visibly wilting at 24 h after pollination, accompanied by the mass degradation of macromolecules and organelles during senescence. In addition, 48 protein spots with significant differences in abundance were found by two-dimensional electrophoresis (2-DE) and subjected to matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF/TOF-MS). There were 42 protein spots successfully identified and homologous to known functional protein species involved in key biological processes, including antioxidant pathways, stress response, protein metabolism, cell wall component metabolism, energy metabolism, cell structure, and signal transduction. The activity of all reactive oxygen species (ROS)-scavenging enzymes was increased, keeping the content of ROS at a low level at the early stage of senescence. These results suggest that two processes, a counteraction against increased levels of ROS and the degradation of cellular constituents for maintaining nutrient recycling, are activated during pollination-induced petal senescence in Phalaenopsis. The information provides a basis for understanding the mechanism regulating petal senescence and prolonging the florescence of Phalaenopsis.

Cold and Heat Stress Diversely Alter Both Cauliflower Respiration and Distinct Mitochondrial Proteins Including OXPHOS Components and Matrix Enzymes

Complex proteomic and physiological approaches for studying cold and heat stress responses in plant mitochondria are still limited. Variations in the mitochondrial proteome of cauliflower (Brassica oleracea var. botrytis) curds after cold and heat and after stress recovery were assayed by two-dimensional polyacrylamide gel electrophoresis (2D PAGE) in relation to mRNA abundance and respiratory parameters. Quantitative analysis of the mitochondrial proteome revealed numerous stress-affected protein spots. In cold, major downregulations in the level of photorespiratory enzymes, porine isoforms, oxidative phosphorylation (OXPHOS) and some low-abundant proteins were observed. In contrast, carbohydrate metabolism enzymes, heat-shock proteins, translation, protein import, and OXPHOS components were involved in heat response and recovery. Several transcriptomic and metabolic regulation mechanisms are also suggested. Cauliflower plants appeared less susceptible to heat; closed stomata in heat stress resulted in moderate photosynthetic, but only minor respiratory impairments, however, photosystem II performance was unaffected. Decreased photorespiration corresponded with proteomic alterations in cold. Our results show that cold and heat stress not only operate in diverse modes (exemplified by cold-specific accumulation of some heat shock proteins), but exert some associations at molecular and physiological levels. This implies a more complex model of action of investigated stresses on plant mitochondria.

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.

Proteomics in commercial crops: An overview

Proteomics is a rapidly growing area of biological research that is positively affecting plant science. Recent advances in proteomic technology, such as mass spectrometry, can now identify a broad range of proteins and monitor their modulation during plant growth and development, as well as during responses to abiotic and biotic stresses. In this review, we highlight recent proteomic studies of commercial crops and discuss the advances in understanding of the proteomes of these crops. We anticipate that proteomic-based research will continue to expand and contribute to crop improvement.

SIGNIFICANCE

Plant proteomics study is a rapidly growing area of biological research that is positively impacting plant science. With the recent advances in new technologies, proteomics not only allows us to comprehensively analyses crop proteins, but also help us to understand the functions of the genes. In this review, we highlighted recent proteomic studies in commercial crops and updated the advances in our understanding of the proteomes of these crops. We believe that proteomic-based research will continue to grow and contribute to the improvement of crops.

Proteomic response of oat leaves to long-term salinity stress

Salinity adversely affects plant growth and production. Oat is a moderately salt-tolerant crop and can contribute to improving saline soil. The physiological and molecular responses of the oat plant to long-term salinity were studied. After a 16-day salt treatment (150 mmol L^-1NaCl in Hoagland's solution), photosynthetic rate, maximum photosystem II photochemical efficiency, and actual efficiency of photosystem II decreased. The activities of superoxide dismutase, peroxidase, and catalase significantly increased. We also investigated the protein profiles of oat leaves in response to salinity and detected 30 reproducible protein spots by two-dimensional gel electrophoresis that were differentially abundant. Specifically, one protein was up-regulated and 29 proteins were down-regulated compared with the control. These 29 proteins were identified using MALDI-TOF mass spectrometry, and 19 corresponding genes were further investigated by quantitative real-time PCR. These proteins were involved in four types of biological processes: photosynthesis, carbohydrate metabolism and energy, protein biosynthesis, and folding and detoxification. This study indicates that the lower levels of Calvin cycle-related proteins, 50S ribosomal protein L10 and adenosine-triphosphate regulation-related proteins, and the high levels of antioxidant enzymes play important roles in the response of oat to long-term salinity stress.

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.

Proteomic analysis of common bean stem under drought stress using in-gel stable isotope labeling

Drought is an abiotic stress that strongly influences plant growth, development and productivity. Proteome changes in the stem of the drought-tolerant common bean (Phaseolus vulgaris L.) cultivar Tiber have were when the plants were exposed to drought. Five-week-old plants were subjected to water deficit by withholding irrigation for 7, 12 and 17days, whereas control plants were regularly irrigated. Relative water content (RWC) of leaves, as an indicator of the degree of cell and tissue hydration, showed the highest statistically significant differences between control and drought-stressed plants after 17days of treatment, where RWC remained at 90% for control and declined to 45% for stressed plants. Plants exposed to drought for 17days and control plants at the same developmental stage were included in quantitative proteomic analysis using in-gel stable isotope labeling of proteins in combination with mass spectrometry. The quantified proteins were grouped into several functional groups, mainly into energy metabolism, photosynthesis, proteolysis, protein synthesis and proteins related to defense and stress. 70kDa heat shock protein showed the greatest increase in abundance under drought of all the proteins, suggesting its role in protecting plants against stress by re-establishing normal protein conformations and thus cellular homeostasis. The abundance of proteins involved in protein synthesis also increased under drought stress, important for recovery of damaged proteins involved in the plant cell's metabolic activities. Other important proteins in this study were related to proteolysis and folding, which are necessary for maintaining proper cellular protein homeostasis. Taken together, these results reveal the complexity of pathways involved in the drought stress response in common bean stems and enable comparison with the results of proteomic analysis of leaves, thus providing important information to further understand the biochemical and molecular mechanisms of drought response in this important legume.

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.

Emerging Genomic Tools for Legume Breeding: Current Status and Future Prospects

Legumes play a vital role in ensuring global nutritional food security and improving soil quality through nitrogen fixation. Accelerated higher genetic gains is required to meet the demand of ever increasing global population. In recent years, speedy developments have been witnessed in legume genomics due to advancements in next-generation sequencing (NGS) and high-throughput genotyping technologies. Reference genome sequences for many legume crops have been reported in the last 5 years. The availability of the draft genome sequences and re-sequencing of elite genotypes for several important legume crops have made it possible to identify structural variations at large scale. Availability of large-scale genomic resources and low-cost and high-throughput genotyping technologies are enhancing the efficiency and resolution of genetic mapping and marker-trait association studies. Most importantly, deployment of molecular breeding approaches has resulted in development of improved lines in some legume crops such as chickpea and groundnut. In order to support genomics-driven crop improvement at a fast pace, the deployment of breeder-friendly genomics and decision support tools seems appear to be critical in breeding programs in developing countries. This review provides an overview of emerging genomics and informatics tools/approaches that will be the key driving force for accelerating genomics-assisted breeding and ultimately ensuring nutritional and food security in developing countries.

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.

Phytochrome B Negatively Affects Cold Tolerance by Regulating OsDREB1 Gene Expression through Phytochrome Interacting Factor-Like Protein OsPIL16 in Rice

Cross talk between light signaling and cold signaling has been elucidated in the model plant Arabidopsis and tomato, but little is known about their relationship in rice. Here, we report that phytochrome B (phyB) mutants exhibit improved cold tolerance compared with wild type (WT) rice (Oryza sativa L. cv. Nipponbare). The phyB mutants had a lower electrolyte leakage index and malondialdehyde concentration than the WT, suggesting that they had greater cell membrane integrity and less lipid peroxidation. Real-time PCR analysis revealed that the expression levels of dehydration-responsive element binding protein 1 (OsDREB1) family genes, which functions in the cold stress response in rice, were increased in the phyB mutant under normal and cold stress conditions. PIFs are central players in phytochrome-mediated light signaling networks. To explore the relationship between rice PIFs and OsDREB1 gene expression, we produced overexpression lines of rice PIF genes. OsDREB1 family genes were up-regulated in OsPIL16-overexpression lines, which had improved cold tolerance relative to the WT. Chromatin immunoprecipitation (ChIP)-qPCR assay revealed that OsPIL16 can bind to the N-box region of OsDREB1B promoter. Expression pattern analyses revealed that OsPIL16 transcripts were induced by cold stress and was significantly higher in the phyB mutant than in the WT. Moreover, yeast two-hybrid assay showed that OsPIL16 can bind to rice PHYB. Based on these results, we propose that phyB deficiency positively regulates OsDREB1 expression through OsPIL16 to enhance cell membrane integrity and to reduce the malondialdehyde concentration, resulting in the improved cold tolerance of the phyB mutants.

Proteomics and Metabolomics: Two Emerging Areas for Legume Improvement

The crop legumes such as chickpea, common bean, cowpea, peanut, pigeonpea, soybean, etc. are important sources of nutrition and contribute to a significant amount of biological nitrogen fixation (>20 million tons of fixed nitrogen) in agriculture. However, the production of legumes is constrained due to abiotic and biotic stresses. It is therefore imperative to understand the molecular mechanisms of plant response to different stresses and identify key candidate genes regulating tolerance which can be deployed in breeding programs. The information obtained from transcriptomics has facilitated the identification of candidate genes for the given trait of interest and utilizing them in crop breeding programs to improve stress tolerance. However, the mechanisms of stress tolerance are complex due to the influence of multi-genes and post-transcriptional regulations. Furthermore, stress conditions greatly affect gene expression which in turn causes modifications in the composition of plant proteomes and metabolomes. Therefore, functional genomics involving various proteomics and metabolomics approaches have been obligatory for understanding plant stress tolerance. These approaches have also been found useful to unravel different pathways related to plant and seed development as well as symbiosis. Proteome and metabolome profiling using high-throughput based systems have been extensively applied in the model legume species, Medicago truncatula and Lotus japonicus, as well as in the model crop legume, soybean, to examine stress signaling pathways, cellular and developmental processes and nodule symbiosis. Moreover, the availability of protein reference maps as well as proteomics and metabolomics databases greatly support research and understanding of various biological processes in legumes. Protein-protein interaction techniques, particularly the yeast two-hybrid system have been advantageous for studying symbiosis and stress signaling in legumes. In this review, several studies on proteomics and metabolomics in model and crop legumes have been discussed. Additionally, applications of advanced proteomics and metabolomics approaches have also been included in this review for future applications in legume research. The integration of these "omics" approaches will greatly support the identification of accurate biomarkers in legume smart breeding programs.

The cold responsive mechanism of the paper mulberry: decreased photosynthesis capacity and increased starch accumulation

Background

Most studies on the paper mulberry are mainly focused on the medicated and pharmacology, fiber quality, leaves feed development, little is known about its mechanism of adaptability to abiotic stress. Physiological measurement, transcriptomics and proteomic analysis were employed to understand its response to cold stress in this study.

Methods

The second to fourth fully expanded leaves from up to down were harvested at different stress time points forthe transmission electron microscope (TEM) observation. Physiological characteristics measurement included the relative electrolyte leakage (REL), SOD activity assay, soluble sugar content, and Chlorophyll fluorescence parameter measurement. For screening of differentially expressed genes, the expression level of every transcript in each sample was calculated by quantifying the number of Illumina reads. To identify the differentially expressed protein, leaves of plants under 0, 6, 12, 24, 48 and 72 h cold stress wereharvested for proteomic analysis. Finally, real time PCR was used to verify the DEG results of the RNA-seq and the proteomics data.

Results

Results showed that at the beginning of cold stress, respiratory metabolism was decreased and the transportation and hydrolysis of photosynthetic products was inhibited, leading to an accumulation of starch in the chloroplasts. Total of 5800 unigenes and 38 proteins were affected, including the repressed expression of photosynthesis and the enhanced expression in signal transduction, stress defense pathway as well as secondary metabolism. Although the transcriptional level of a large number of genes has been restored after 12 h, sustained cold stress brought more serious injury to the leaf cells, including the sharp rise of the relative electrolyte leakage, the declined Fv/Fm value, swelled chloroplast and the disintegrated membrane system.

Conclusion

The starch accumulation and the photoinhibition might be the main adaptive mechanism of the paper mulberry responded to cold stress. Most of important, enhancing the transport and hydrolysis of photosynthetic products could be the potential targets for improving the cold tolerance of the paper mulberry.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-2047-6) contains supplementary material, which is available to authorized users.

Plant mitochondrial proteomics

Mitochondrial proteomics has significantly developed since the first plant mitochondrial proteomes were published in 2001. Many studies have added to our knowledge of the protein components that make up plant mitochondria in a wide range of species. Here we present two common and one emerging quantitative proteomic techniques that can be used to study the abundance of mitochondrial proteins. For this publication, we have described the methods as an approach to determine the amount of contamination in a mitochondrial isolation to contrast historical approaches that involved the use of use of antibodies to specific marker proteins or the measurement of activity of marker enzymes. However, these approaches could easily be adapted to carry out control versus treatment studies.

Membrane fatty acid compositions and cold-induced responses in tetraploid and hexaploid wheats

Plant cells often increase cold tolerance by reprogramming their genes expression which results in adjusted metabolic alternations, a process enhanced under cold acclimation. In present study, we assessed the changes of membrane fatty acid compositions along with physio-biochemical indices like H2O2 and malondialdehyde (MDA) contents and lipoxygenase (LOX) activity during cold stress (CS) phases in acclimated and non-acclimated durum (SRN and Gerdish) and bread (Norstar) wheat genotypes. During thermal treatments, MDA was an end product of lipid peroxidation via oxidative stress (H2O2 content) rather than LOX activity. LOX activity plays a double role in mechanism of cold tolerance in wheat, particularly at severe stress. With increase in severity of CS especially in non-acclimated plants, LOX activity decreased along with an increase in MDA and other responses helped increase or maintaine unsaturated fatty acids (FAs) whereas in acclimated plants (moderate CS), increasing of LOX activity along with a decrease in MDA indicates probably its role in secondary metabolites like jasmonic acid signaling pathway. Significant increase of total FAs and particularly unsaturated FAs showed distinct cell endeavor to protect against CS in Norstar and Gerdish compared to SRN genotype. Results showed that an increase in double bond index and LOX activity and low MDA under CS could be reasons for plant cold tolerance.

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

Cold stress affects many plant physiological and biochemical components and induces cascades of alterations in metabolic pathways, amongst them the membrane fatty acid compositions, the activity of antioxidative enzymes and the regulation of gene expression. The present work aimed to characterize the changes of some of these factors in both cold acclimated (CA) and non-acclimated (NA) plants of chickpea (Cicer arietinum L.) to identify the role of the acclimation process in adjusting plant responses to severe cold stress. The results showed an increase in the unsaturated fatty acids (UFAs) ratio compared to saturated fatty acids, which was more obvious in CA plants. Defense enzymes had an important role in CA plants to create greater cold tolerance compared to NA ones in the cases of superoxide dismutase (SOD), catalase (CAT), guaiacol peroxidase (GPX) and lipoxygenase (LOX) activities. During cold stress, a high transcription level of CaCAT and CaSOD genes was detected in CA plants, but a low transcription of CaLOX gene was observed in CA plants compared to NA plants, which might have prevented the decline of UFAs (confirmed by double bond index (DBI) data). Moreover, the transcription level of the Carubisco gene, as an energy producing agent, was higher in CA plants than in NA plants and the transcription of the Catubulin gene, as a crucial substance of cell cytoskeleton, showed a decreasing trend in both CA and NA plants, but this decline was greater in NA plants. These responses showed the possible targets of cold stress as chloroplast and signal transduction to balance stress programs. The above results indicate the crucial role of FA compositions in creating cold tolerance in susceptible chickpea plants with possible responsive components and the possible interactions in protein and transcript levels even in facing extreme cold stress.