Proteome analysis of soybean roots under waterlogging stress at an early vegetative stage

Genome-wide identification and analyses of ZmAPY genes reveal their roles involved in maize development and abiotic stress responses

Apyrase is a class of enzyme that catalyzes the hydrolysis of nucleoside triphosphates/diphosphates (NTP/NDP), which widely involved in regulation of plant growth and stress responses. However, apyrase family genes in maize have not been identified, and their characteristics and functions are largely unknown. In this study, we identified 16 apyrases (named as ZmAPY1-ZmAPY16) in maize genome, and analyzed their phylogenetic relationships, gene structures, chromosomal distribution, upstream regulatory transcription factors and expression patterns. Analysis of the transcriptome database unveiled tissue-specific and abiotic stress-responsive expression of ZmAPY genes in maize. qPCR analysis further confirmed their responsiveness to drought, heat, and cold stresses. Association analyses indicated that variations of ZmAPY5 and ZmAPY16 may regulate maize agronomic traits and drought responses. Our findings shed light on the molecular characteristics and evolutionary history of maize apyrase genes, highlighting their roles in various biological processes and stress responses. This study forms a basis for further exploration of apyrase functions in maize.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01474-9.

Transcriptomic and Metabolomic Analyses Reveal the Response Mechanism of Ophiopogon japonicus to Waterlogging Stress

Ophiopogon japonicus, a plant that thrives in river alluvial dams, often faces waterlogging stress due to sustained rainfall and flood seasons, which significantly impacts its growth and development. Currently, the mechanisms of waterlogging tolerance in Ophiopogon japonicus are still unclear. This study analyzed the transcriptome and metabolome data for Ophiopogon japonicus in the Sichuan region (referred to as CMD) under varying degrees of waterlogging stress: mild, moderate, and severe. The results indicate that the group exposed to flooding stress exhibited a higher number of differentially expressed genes (DEGs) compared to the control group. Notably, most DEGs were downregulated and primarily enriched in phenylpropanoid biosynthesis, starch and sucrose metabolism, and plant hormone signal transduction pathways. A total of 5151 differentially accumulated metabolites (DAMs) were identified, with significantly upregulated DAMs annotated to two clusters, namely flavonoids such as apiin, pelargonin, and others. Furthermore, our study revealed significant upregulation in the expression of C2H2 (C2H2 zinc finger proteins) and AP2/ERF-ERF (the subfamily ERF proteins of APETALA2/ethylene-responsive element binding factors) transcription factors in CMD under flooding stress, suggesting their critical roles in enabling CMD to adapt to these conditions. In conclusion, this research provides insights into the intricate molecular mechanisms underlying CMD's response to flooding stress and reports valuable genetic data for the development of transgenic plants with improved waterlogging tolerance.

Effects of drought, subsequent waterlogging and redrying on growth, physiology and metabolism of wheat

With climate change, longer periods without precipitation but also heavy rains will become more frequent. Thus, understanding and predicting the implications of drought-waterlogging-redrying cycles for plants is essential. We examined the effects of such events on wheat (Triticum aestivum). We measured the impacts of subsequent water treatments (drought-waterlogging-redrying) on plant shoot and root biomass, photosynthesis and transpiration, as well as on primary metabolites and transcripts of leaves. Drought and drought followed by waterlogging severely reduced shoot and root biomass. Chlorophyll fluorescence parameters and the CO2 assimilation rate per unit leaf area were not affected by the treatments but, after the redrying phase, plants grown under the stress treatments showed a higher transpiration rate per unit leaf area and a lower instantaneous water use efficiency. Many organic acids of the citrate cycle were less concentrated in leaves of stressed plants, while most amino acids were more concentrated. Transcript analysis of genes involved in signalling and metabolism revealed different expression patterns. While some genes responded only to drought or drought followed by waterlogging, several genes were induced upon both treatments and some were still upregulated at the end of the redrying phase. We provide insights into how wheat responds to changes in water regimes, with some of the changes probably allowing the plants to cope with these stressors, at least to a certain degree.

Genome-Wide Investigation of Apyrase (APY) Genes in Peanut (Arachis hypogaea L.) and Functional Characterization of a Pod-Abundant Expression Promoter AhAPY2-1p

Peanut (Arachis hypogaea L.) is an important food and feed crop worldwide and is affected by various biotic and abiotic stresses. The cellular ATP levels decrease significantly during stress as ATP molecules move to extracellular spaces, resulting in increased ROS production and cell apoptosis. Apyrases (APYs) are the nucleoside phosphatase (NPTs) superfamily members and play an important role in regulating cellular ATP levels under stress. We identified 17 APY homologs in A. hypogaea (AhAPYs), and their phylogenetic relationships, conserved motifs, putative miRNAs targeting different AhAPYs, cis-regulatory elements, etc., were studied in detail. The transcriptome expression data were used to observe the expression patterns in different tissues and under stress conditions. We found that the AhAPY2-1 gene showed abundant expression in the pericarp. As the pericarp is a key defense organ against environmental stress and promoters are the key elements regulating gene expression, we functionally characterized the AhAPY2-1 promoter for its possible use in future breeding programs. The functional characterization of AhAPY2-1P in transgenic Arabidopsis plants showed that it effectively regulated GUS gene expression in the pericarp. GUS expression was also detected in flowers of transgenic Arabidopsis plants. Overall, these results strongly suggest that APYs are an important future research subject for peanut and other crops, and AhPAY2-1P can be used to drive the resistance-related genes in a pericarp-specific manner to enhance the defensive abilities of the pericarp.

Critical water contents at leaf, stem and root level leading to irreversible drought-induced damage in two woody and one herbaceous species

Plant water content is a simple and promising parameter for monitoring drought-driven plant mortality risk. However, critical water content thresholds leading to cell damage and plant failure are still unknown. Moreover, it is unclear whether whole-plant or a specific organ water content is the most reliable indicator of mortality risk. We assessed differences in dehydration thresholds in leaf, stem and root samples, hampering the organ-specific rehydration capacity and increasing the mortality risk. We also tested eventual differences between a fast experimental dehydration of uprooted plants, compared to long-term water stress induced by withholding irrigation in potted plants. We investigated three species with different growth forms and leaf habits i.e., Helianthus annuus (herbaceous), Populus nigra (deciduous tree) and Quercus ilex (evergreen tree). Results obtained by the two dehydration treatments largely overlapped, thus validating bench dehydration as a fast but reliable method to assess species-specific critical water content thresholds. Regardless of the organ considered, a relative water content value of 60% induced significant cell membrane damage and loss of rehydration capacity, thus leading to irreversible plant failure and death.

Identification, characterization of Apyrase (APY) gene family in rice (Oryza sativa) and analysis of the expression pattern under various stress conditions

Apyrase (APY) is a nucleoside triphosphate (NTP) diphosphohydrolase (NTPDase) which is a member of the superfamily of guanosine diphosphatase 1 (GDA1)-cluster of differentiation 39 (CD39) nucleoside phosphatase. Under various circumstances like stress, cell growth, the extracellular adenosine triphosphate (eATP) level increases, causing a detrimental influence on cells such as cell growth retardation, ROS production, NO burst, and apoptosis. Apyrase hydrolyses eATP accumulated in the extracellular membrane during stress, wounds, into adenosine diphosphate (ADP) and adenosine monophosphate (AMP) and regulates the stress-responsive pathway in plants. This study was designed for the identification, characterization, and for analysis of APY gene expression in Oryza sativa. This investigation discovered nine APYs in rice, including both endo- and ecto-apyrase. According to duplication event analysis, in the evolution of OsAPYs, a significant role is performed by segmental duplication. Their role in stress control, hormonal responsiveness, and the development of cells is supported by the corresponding cis-elements present in their promoter regions. According to expression profiling by RNA-seq data, the genes were expressed in various tissues. Upon exposure to a variety of biotic as well as abiotic stimuli, including anoxia, drought, submergence, alkali, heat, dehydration, salt, and cold, they showed a differential expression pattern. The expression analysis from the RT-qPCR data also showed expression under various abiotic stress conditions, comprising cold, salinity, cadmium, drought, submergence, and especially heat stress. This finding will pave the way for future in-vivo analysis, unveil the molecular mechanisms of APY genes in stress response, and contribute to the development of stress-tolerant rice varieties.

Waterlogging priming alleviates the oxidative damage, carbohydrate consumption, and yield loss in soybean (Glycine max) plants exposed to waterlogging

In this study, we tested whether waterlogging priming at the vegetative stage would mitigate a subsequent waterlogging event at the reproductive stage in soybean [Glycine max (L.) Merr.]. Plants (V3 stage) were subjected to priming for 7days and then exposed to waterlogging stress for 5days (R2 stage) with non-primed plants. Roots and leaves were sampled on the fifth day of waterlogging and the second and fifth days of reoxygenation. Overall, priming decreased the H2 O2 concentration and lipid peroxidation in roots and leaves during waterlogging and reoxygenation. Priming also decreased the activity of antioxidative enzymes in roots and leaves and increased the foliar concentration of phenols and photosynthetic pigments. Additionally, priming decreased fermentation and alanine aminotransferase activity during waterlogging and reoxygenation. Finally, priming increased the concentration of amino acids, sucrose, and total soluble sugars in roots and leaves during waterlogging and reoxygenation. Thus, primed plants were higher and more productive than non-primed plants. Our study shows that priming alleviates oxidative stress, fermentation, and carbohydrate consumption in parallel to increase the yield of soybean plants exposed to waterlogging and reoxygenation.

Phenotyping for waterlogging tolerance in crops: current trends and future prospects

Yield losses to waterlogging are expected to become an increasingly costly and frequent issue in some regions of the world. Despite the extensive work that has been carried out examining the molecular and physiological responses to waterlogging, phenotyping for waterlogging tolerance has proven difficult. This difficulty is largely due to the high variability of waterlogging conditions such as duration, temperature, soil type, and growth stage of the crop. In this review, we highlight use of phenotyping to assess and improve waterlogging tolerance in temperate crop species. We start by outlining the experimental methods that have been utilized to impose waterlogging stress, ranging from highly controlled conditions of hydroponic systems to large-scale screenings in the field. We also describe the phenotyping traits used to assess tolerance ranging from survival rates and visual scoring to precise photosynthetic measurements. Finally, we present an overview of the challenges faced in attempting to improve waterlogging tolerance, the trade-offs associated with phenotyping in controlled conditions, limitations of classic phenotyping methods, and future trends using plant-imaging methods. If effectively utilized to increase crop resilience to changing climates, crop phenotyping has a major role to play in global food security.

Crosstalk between H2 S and NO: an emerging signalling pathway during waterlogging stress in legume crops

In legumes, waterlogging is a major detrimental factor leading to huge yield losses. Generally, legumes lack tolerance to submergence, and conventional breeding to develop tolerant varieties are limited due to the lack of tolerant germplasm and potential target genes. Moreover, our understanding of the various signalling cascades, their interactions and key pathways induced during waterlogging is limited. Here, we focus on the role of two important plant signalling molecules, viz. hydrogen sulphide (H₂ S) and nitric oxide (NO), during waterlogging stress in legumes. Plants and soil microbes produce these signalling molecules both endogenously and exogenously under various stresses, including waterlogging. NO and H₂ S are known to regulate key physiological pathways, such as stomatal closure, leaf senescence and regulation of numerous stress signalling pathways, while NO plays a pivotal role in adventitious root formation during waterlogging. The crosstalk between H₂ S and NO is synergistic because of the resemblance of their physiological effects and proteomic functions, which mainly operate through cysteine-dependent post-translational modifications via S-nitrosation and persulfidation. Such knowledge has provided novel platforms for researchers to unravel the complexity associated with H₂ S-NO signalling and interactions with plant stress hormones. This review provides an overall summary on H₂ S and NO, including biosynthesis, biological importance, crosstalk, transporter regulation as well as understanding their role during waterlogging using 'multi-omics' approach. Understanding H₂ S and NO signalling will help in deciphering the metabolic interactions and identifying key regulatory genes that could be used for developing waterlogging tolerance in legumes.

Using the Knowledge of Post-transcriptional Regulations to Guide Gene Selections for Molecular Breeding in Soybean

The omics approaches allow the scientific community to successfully identify genomic regions associated with traits of interest for marker-assisted breeding. Agronomic traits such as seed color, yield, growth habit, and stress tolerance have been the targets for soybean molecular breeding. Genes governing these traits often undergo post-transcriptional modifications, which should be taken into consideration when choosing elite genes for molecular breeding. Post-transcriptional regulations of genes include transcript regulations, protein modifications, and even the regulation of the translational machinery. Transcript regulations involve elements such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) for the maintenance of transcript stability or regulation of translation efficiency. Protein modifications involve molecular modifications of target proteins and the alterations of their interacting partners. Regulations of the translational machinery include those on translation factors and the ribosomal protein complex. Post-transcriptional regulations usually involve a set of genes instead of a single gene. Such a property may facilitate molecular breeding. In this review, we will discuss the post-transcriptional modifications of genes related to favorable agronomic traits such as stress tolerance, growth, and nutrient uptake, using examples from soybean as well as other crops. The examples from other crops may guide the selection of genes for marker-assisted breeding in soybean.

iTRAQ Proteomic Analysis of Wheat (Triticum aestivum L.) Genotypes Differing in Waterlogging Tolerance

Transient and chronic waterlogging constrains crop production in many regions of the world. Here, we invoke a novel iTRAQ-based proteomic strategy to elicit protein synthesis and regulation responses to waterlogging in tolerant (XM 55) and sensitive genotypes (YM 158). Of the 7,710 proteins identified, 16 were distinct between the two genotypes under waterlogging, partially defining a proteomic basis for waterlogging tolerance (and sensitivity). We found that 11 proteins were up-regulated and 5 proteins were down-regulated; the former included an Fe-S cluster assembly factor, heat shock cognate 70, GTP-binding protein SAR1A-like and CBS domain-containing protein. Down-regulated proteins contained photosystem II reaction center protein H, carotenoid 9, 10 (9', 10')-cleavage dioxygenase-like, psbP-like protein 1 and mitochondrial ATPase inhibitor. We showed that nine proteins responded to waterlogging with non-cultivar specificity: these included 3-isopropylmalate dehydratase large subunit, solanesyl-diphosphate synthase 2, DEAD-box ATP-dependent RNA helicase 3, and 3 predicted or uncharacterized proteins. Sixteen of the 28 selected proteins showed consistent expression patterns between mRNA and protein levels. We conclude that waterlogging stress may redirect protein synthesis, reduce chlorophyll synthesis and enzyme abundance involved in photorespiration, thus influencing synthesis of other metabolic enzymes. Collectively, these factors accelerate the accumulation of harmful metabolites in leaves in waterlogging-susceptible genotypes. The differentially expressed proteins enumerated here could be used as biological markers for enhancing waterlogging tolerance as part of future crop breeding programs.

Proteomic analysis of drought stress response mechanism in soybean (Glycine max L.) leaves

Knowledge of the physiological and molecular mechanisms of drought responses is fundamental for developing genetically drought tolerant and high yielding crops. To understand molecular mechanism of drought tolerance of soybean (Glycine max L.), we compared leaf proteome patterns of in two genotypes GN-3074 (drought tolerant) and GN-2032 (drought-sensitive) under drought stress during vegetative stage. Proteins were extracted from leaves of well-watered and drought-treated plants by using the trichloroacetic acid (TCA)-acetone precipitation method and analyzed by two-dimensional polyacrylamide gel electrophoresis. Out 488 reproducibly detected and analyzed on two-dimensional electrophoresis gels, 26 proteins showed significant changes in at least one genotype. The identification of 20 differentially expressed proteins using mass spectrometry revealed a coordinated expression of proteins involved in cellular metabolisms including photosynthesis, oxidative stress defense, respiration, metabolism process, signal transduction, phosphorus transduction, and methyl transduction which enable plant to cope with drought conditions. The most identified proteins involved in photosynthesis and oxidative stress defense system. The up-regulation of several photosynthetic proteins and also high abundance of oxidative stress defense proteins in GN-3074 genotypes as compare to GN-2032 genotypes might reflect the fact that drought tolerance of GN-3074 is due to effective photosynthetic machinery and more defense against oxidative stress. Our results suggest that soybean plant might response to drought stress by applying efficiently stay-green mechanism through coordinated gene expression during vegetative stage.

Metabolic Responses to Waterlogging Differ between Roots and Shoots and Reflect Phloem Transport Alteration in Medicago truncatula

Root oxygen deficiency that is induced by flooding (waterlogging) is a common situation in many agricultural areas, causing considerable loss in yield and productivity. Physiological and metabolic acclimation to hypoxia has mostly been studied on roots or whole seedlings under full submergence. The metabolic difference between shoots and roots during waterlogging, and how roots and shoots communicate in such a situation is much less known. In particular, the metabolic acclimation in shoots and how this, in turn, impacts on roots metabolism is not well documented. Here, we monitored changes in the metabolome of roots and shoots of barrel clover (Medicago truncatula), growth, and gas-exchange, and analyzed phloem sap exudate composition. Roots exhibited a typical response to hypoxia, such as γ-aminobutyrate and alanine accumulation, as well as a strong decline in raffinose, sucrose, hexoses, and pentoses. Leaves exhibited a strong increase in starch, sugars, sugar derivatives, and phenolics (tyrosine, tryptophan, phenylalanine, benzoate, ferulate), suggesting an inhibition of sugar export and their alternative utilization by aromatic compounds production via pentose phosphates and phosphoenolpyruvate. Accordingly, there was an enrichment in sugars and a decline in organic acids in phloem sap exudates under waterlogging. Mass-balance calculations further suggest an increased imbalance between loading by shoots and unloading by roots under waterlogging. Taken as a whole, our results are consistent with the inhibition of sugar import by waterlogged roots, leading to an increase in phloem sugar pool, which, in turn, exert negative feedback on sugar metabolism and utilization in shoots.

Review: Proteomic Techniques for the Development of Flood-Tolerant Soybean

Soybean, which is rich in protein and oil as well as phytochemicals, is cultivated in several climatic zones. However, its growth is markedly decreased by flooding stress, which is caused by climate change. Proteomic techniques were used for understanding the flood-response and -tolerant mechanisms in soybean. Subcellular proteomics has potential to elucidate localized cellular responses and investigate communications among subcellular components during plant growth and under stress stimuli. Furthermore, post-translational modifications play important roles in stress response and tolerance to flooding stress. Although many flood-response mechanisms have been reported, flood-tolerant mechanisms have not been fully clarified for soybean because of limitations in germplasm with flooding tolerance. This review provides an update on current biochemical and molecular networks involved in soybean tolerance against flooding stress, as well as recent developments in the area of functional genomics in terms of developing flood-tolerant soybeans. This work will expedite marker-assisted genetic enhancement studies in crops for developing high-yielding stress-tolerant lines or varieties under abiotic stress.

Physiological approach to decipher the drought tolerance of a soybean genotype from Brazilian savana

Drought is one of the major constraints for soybean production in Brazil. In this study we investigated the physiological traits of two soybean parental genotypes under progressive soil drying and rewetting. The plants were evaluated under full irrigation (control) conditions and under water deficit imposed by suspending irrigation until the plants reached predawn leaf water potentials (Ψam) of -1.0 MPa (moderate) and -1.5 MPa (severe). Physiological analyses showed that these genotypes exhibit different responses to water deficit. The Embrapa 48 genotype reached moderate and severe water potential two days after the BR16 genotype and was able to maintain higher levels of A, ETR and ΦPSII even under deficit conditions. This result was not related to changes in gs, 13C isotopic composition and presence of a more efficient antioxidant system. In addition, Fv/Fm values did not decrease in Embrapa 48 genotype in relation to irrigated condition showing that stress was not causing photochemical inhibition of photosynthesis. The greater reduction in the relative growth of the shoots, with concomitant greater growth of the root system under drought, indicates that the tolerant genotype is able to preferentially allocated carbon to the roots, presenting less damage to photosynthesis. Therefore, the physiological responses revealed that the tolerant genotype postponed leaf dehydration by a mechanism involving a more efficient use and translocation of water from root to shoot to maintain cell homeostasis and photosynthetic metabolism under stress.

Genome-wide identification, characterization and expression pattern analysis of APYRASE family members in response to abiotic and biotic stresses in wheat

APYRASEs, which directly regulate intra- and extra-cellular ATP homeostasis, play a pivotal role in the regulation of various stress adaptations in mammals, bacteria and plants. In the present study, we identified and characterized wheat APYRASE family members at the genomic level in wheat. The results identified a total of nine APY homologs with conserved ACR domains. The sequence alignments, phylogenetic relations and conserved motifs of wheat APYs were bioinformatically analyzed. Although they share highly conserved secondary and tertiary structures, the wheat APYs could be mainly categorized into three groups, according to phylogenetic and structural analysis. Additionally, these APYs exhibited similar expression patterns in the root and shoot, among which TaAPY3-1, TaAPY3-3 and TaAPY3-4 had the highest expression levels. The time-course expression patterns of the eight APYs in response to biotic and abiotic stress in the wheat seedlings were also investigated. TaAPY3-2, TaAPY3-3, TaAPY3-4 and TaAPY6 exhibited strong sensitivity to all kinds of stresses in the leaves. Some APYs showed specific expression responses, such as TaAPY6 to heavy metal stress, and TaAPY7 to heat and salt stress. These results suggest that the stress-inducible APYs could have potential roles in the regulation of environmental stress adaptations. Moreover, the catalytic activity of TaAPY3-1 was further analyzed in the in vitro system. The results showed that TaAPY3-1 protein exhibited high catalytic activity in the degradation of ATP and ADP, but with low activity in degradation of TTP and GTP. It also has an extensive range of temperature adaptability, but preferred relatively acidic pH conditions. In this study, the genome-wide identification and characterization of APYs in wheat were suggested to be useful for further genetic modifications in the generation of high-stress-tolerant wheat cultivars.

Comparative Transcriptome Combined with Proteome Analyses Revealed Key Factors Involved in Alfalfa (Medicago sativa) Response to Waterlogging Stress

Alfalfa (Medicago sativa) is the most widely grown and most important forage crop in the world. However, alfalfa is susceptible to waterlogging stress, which is the major constraint for its cultivation area and crop production. So far, the molecular mechanism of alfalfa response to the waterlogging is largely unknown. Here, comparative transcriptome combined with proteomic analyses of two cultivars (M12, tolerant; M25, sensitive) of alfalfa showing contrasting tolerance to waterlogging were performed to understand the mechanism of alfalfa in response to waterlogging stress. Totally, 748 (581 up- and 167 down-regulated) genes were differentially expressed in leaves of waterlogging-stressed alfalfa compared with the control (M12_W vs. M12_CK), whereas 1193 (740 up- and 453 down-regulated) differentially abundant transcripts (DATs) were detected in the leaves of waterlogging-stressed plants in comparison with the control plants (M25_W vs. M25_CK). Furthermore, a total of 187 (122 up- and 65 down-regulated) and 190 (105 up- and 85 down-regulated) differentially abundant proteins (DAPs) were identified via isobaric tags for relative and absolute quantification (iTRAQ) method in M12_W vs. M12_CK and M25_W vs. M25_CK comparison, respectively. Compared dataset analysis of proteomics and transcriptomics revealed that 27 and eight genes displayed jointly up-regulated or down-regulated expression profiles at both mRNA and protein levels in M12_W vs. M12_CK comparison, whereas 30 and 27 genes were found to be co-up-regulated or co-down-regulated in M25_W vs. M25_CK comparison, respectively. The strongly enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways for co-up-regulated genes at mRNA and protein levels in M12_W vs. M12_CK comparison were 'Amino sugar and nucleotide sugar metabolism', 'Arginine and proline metabolism' and 'Starch and sucrose metabolism', whereas co-up-regulated protein-related pathways including 'Arginine and proline metabolism' and 'Valine, leucine and isoleucine degradation' were largely enriched in M25_W vs. M25_CK comparison. Importantly, the identified genes related to beta-amylase, Ethylene response Factor (ERF), Calcineurin B-like (CBL) interacting protein kinases (CIPKs), Glutathione peroxidase (GPX), and Glutathione-S-transferase (GST) may play key roles in conferring alfalfa tolerance to waterlogging stress. The present study may contribute to our understanding the molecular mechanism underlying the responses of alfalfa to waterlogging stress, and also provide important clues for further study and in-depth characterization of waterlogging-resistance breeding candidate genes in alfalfa.

Proteomic analysis reveals response of differential wheat (Triticum aestivum L.) genotypes to oxygen deficiency stress

BACKGROUND

Waterlogging is one of the main abiotic stresses that limit wheat production. Quantitative proteomics analysis has been applied in the study of crop abiotic stress as an effective way in recent years (e.g. salt stress, drought stress, heat stress and waterlogging stress). However, only a few proteins related to primary metabolism and signal transduction, such as UDP - glucose dehydrogenase, UGP, beta glucosidases, were reported to response to waterlogging stress in wheat. The differentially expressed proteins between genotypes of wheat in response to waterlogging are less-defined. In this study, two wheat genotypes, one is sensitive to waterlogging stress (Seri M82, named as S) and the other is tolerant to waterlogging (CIGM90.863, named as T), were compared in seedling roots under hypoxia conditions to evaluate the different responses at proteomic level.

RESULTS

A total of 4560 proteins were identified and the number of differentially expressed proteins (DEPs) were 361, 640, 788 in S and 33, 207, 279 in T in 1, 2, 3 days, respectively. These DEPs included 270 common proteins, 681 S-specific and 50 T-specific proteins, most of which were misc., protein processing, DNA and RNA processing, amino acid metabolism and stress related proteins induced by hypoxia. Some specific proteins related to waterlogging stress, including acid phosphatase, oxidant protective enzyme, S-adenosylmethionine synthetase 1, were significantly different between S and T. A total of 20 representative genes encoding DEPs, including 7 shared DEPs and 13 cultivar-specific DEPs, were selected for further RT-qPCR analysis. Fourteen genes showed consistent dynamic expression patterns at mRNA and protein levels.

CONCLUSIONS

Proteins involved in primary metabolisms and protein processing were inclined to be affected under hypoxia stress. The negative effects were more severe in the sensitive genotype. The expression patterns of some specific proteins, such as alcohol dehydrogenases and S-adenosylmethionine synthetase 1, could be applied as indexes for improving the waterlogging tolerance in wheat. Some specific proteins identified in this study will facilitate the subsequent protein function validation and biomarker development.

Differential accumulation of proteins in oil palms affected by fatal yellowing disease

There is still no consensus on the true origin of fatal yellowing, one of the most important diseases affecting oil palm (Elaeis guineensis Jacq.) plantations. This study involved two-dimensional liquid chromatography coupled with tandem mass spectrometry (2D-UPLC-MSE) analyses to identify changes in protein profiles of oil palms affected by FY disease. Oil palm roots were sampled from two growing areas. Differential accumulation of proteins was assessed by comparing plants with and without symptoms and between plants at different stages of FY development. Most of the proteins identified with differential accumulation were those related to stress response and energy metabolism. The latter proteins include the enzymes alcohol dehydrogenase and aldehyde dehydrogenase, related to alcohol fermentation, which were identified in plants with and without symptoms. The presence of these enzymes suggests an anaerobic condition before or during FY. Transketolase, isoflavone reductase, cinnamyl alcohol dehydrogenase, caffeic acid 3-O-methyltransferase, S-adenosylmethionine synthase, aldehyde dehydrogenase and ferritin, among others, were identified as potential marker proteins and could be used to guide selection of FY-tolerant oil palm genotypes or to understand the source of this anomaly. When comparing different stages of FY, we observed high accumulation of alcohol dehydrogenase and other abiotic stress related-proteins at all disease stages. On the other hand, biological stress-related proteins were more accumulated at later stages of the disease. These results suggest that changes in abiotic factors can trigger FY development, creating conditions for the establishment of opportunistic pathogens.

Proteomic analysis by iTRAQ-MRM of soybean resistance to Lamprosema Indicate

BACKGROUND

Lamprosema indicate is a major leaf feeding insect pest to soybean, which has caused serious yield losses in central and southern China. To explore the defense mechanisms of soybean resistance to Lamprosema indicate, a highly resistant line (Gantai-2-2) and a highly susceptible line (Wan 82-178) were exposed to Lamprosema indicate larval feedings for 0 h and 48 h, and the differential proteomic analyses of these two lines were carried out.

RESULTS

The results showed that 31 differentially expressed proteins (DEPs) were identified in the Gantai-2-2 when comparing 48 h feeding with 0 h feeding, and 53 DEPs were identified in the Wan 82-178. 28 DEPs were identified when comparing Gantai-2-2 with Wan 82-178 at 0 h feeding. The bioinformatic analysis results showed that most of the DEPs were associated with ribosome, linoleic acid metabolism, flavonoid biosynthesis, phenylpropanoid biosynthesis, peroxisome, stilbenoid, diarylheptanoid and gingerol biosynthesis, glutathione metabolism, pant hormone signal transduction, and flavone and flavonol biosynthesis, as well as other resistance related metabolic pathways. The MRM analysis showed that the iTRAQ results were reliable.

CONCLUSIONS

According to the analysis of the DEPs results, the soybean defended or resisted the Lamprosema indicate damage by the induction of a synthesis of anti-digestive proteins which inhibit the growth and development of insects, reactive oxygen species scavenging, signaling pathways, secondary metabolites synthesis, and so on.

Biochemical and proteomics analyses of antioxidant enzymes reveal the potential stress tolerance in Rhododendron chrysanthum Pall

Background

Rhododendron chrysanthum Pall., an endangered species with significant ornamental and medicinal value, is endemic to the Changbai Mountain of China and can also serve as a significant plant resource for investigating the stress tolerance in plants. Proteomics is an effective analytical tool that provides significant information about plant metabolism and gene expression. However, no proteomics data have been reported for R. chrysanthum previously. In alpine tundra, the abiotic stress will lead to a severe over-accumulation of reactive oxygen species (ROS). Many alpine plants overcome the severe stresses and protect themselves from the oxidative damage by increasing the ratio and activity of antioxidant enzymes.

Results

In our study, wild type and domesticated Rhododendron chrysanthum Pall. were used as experimental and control groups, respectively. Proteomics method combined with biochemical approach were applied for the stress tolerance investigation of R. chrysanthum at both protein and molecular level. A total of 1,395 proteins were identified, among which 137 proteins were up-regulate in the experimental group. The activities of superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidases (APXs), and glutathione peroxidase (GPX) were significantly higher and the expression of APXs and GPX were also increased in the experimental group. Moreover, the interaction network analysis of these enzymes also reveals that the antioxidant enzymes play important roles in the stress resistance in plants.

Conclusions

This is the first report of the proteome of Rhododendron chrysanthum Pall., and the data reinforce the notion that the antioxidant system plays a significant role in plant stress survival. Our results also verified that R. chrysanthum is highly resistant to abiotic stress and can serve as a significant resource for investigating stress tolerance in plants.

Reviewers

This article was reviewed by George V. (Yura) Shpakovski and Ramanathan Sowdhamini.

Electronic supplementary material

The online version of this article (doi:10.1186/s13062-017-0181-6) contains supplementary material, which is available to authorized users.

Genetic variation and association mapping of waterlogging tolerance in chrysanthemum

Forty-five molecular markers were detected significantly associated with chrysanthemum' waterlogging tolerance, and four favorable parental lines were identified as potential donors for improving waterlogging tolerance in chrysanthemum. The productivity of chrysanthemum is downgraded by waterlogging soils, which has driven a search for germplasm showing an enhanced level of waterlogging tolerance (WT). As yet little is known regarding the mode of inheritance of WT in chrysanthemum. The study set out to characterize the extent of genetic variation for WT represented in a collection of one hundred chrysanthemum accessions by testing them under both greenhouse and field conditions. A membership function value of waterlogging (MFVW), which integrated a wilting index, a chlorosis score and the proportion of dead leaf in waterlogged plants, was used as a measure of WT. The variation for MFVW among plants grown in the greenhouse (two experiments) was generally higher than that generated in field-grown (one experiment) plants. The MFVW broad sense heritability was 0.82, and the phenotypic coefficient of variation (31.8 %) was larger than the genetic one (28.8 %). Association mapping (AM) identified 45 markers related to WT: 25 by applying the general linear model (GLM) + principal component (PC) model, 16 by applying the mixed linear model (MLM), 31 by applying the MLM + Q matrix model and 12 by applying the MLM + PC model. Of the associated markers, eight and two were predictive in two and three experiments within all models, respectively; the proportion of the phenotypic variance explained by the eight associations ranged from 6.3 to 16.4 %. On the basis of their harboring all four of the leading markers E2M16-2, SSR150-6, E19M16-1 and E10M10-12, the varieties 'Nannong Xuefeng', 'Qx097', 'Nannong Xunzhang' and 'Finch' were identified as potential donors for future improvement of WT in chrysanthemum.

Molecular approaches for genetic improvement of seed quality and characterization of genetic diversity in soybean: a critical review

Soybean is an economically important leguminous crop. Genetic improvements of soybeans have focused on enhancement of seed and oil yield, development of varieties suited to different cropping systems, and breeding resistant/tolerant varieties for various biotic and abiotic stresses. Plant breeders have used conventional breeding techniques for the improvement of these traits in soybean. The conventional breeding process can be greatly accelerated through the application of molecular and genomic approaches. Molecular markers have proved to be a new tool in soybean breeding by enhancing selection efficiency in a rapid and time-bound manner. An overview of molecular approaches for the genetic improvement of soybean seed quality parameters, considering recent applications of marker-assisted selection and 'omics' research, is provided in this article.

Isobaric Tags for Relative and Absolute Quantitation (iTRAQ)-Based Comparative Proteome Analysis of the Response of Ramie under Drought Stress

In this study, we conducted the first isobaric tags for relative and absolute quantitation (isobaric tags for relative and absolute quantitation (iTRAQ))-based comparative proteomic analysis of ramie plantlets after 0 (minor drought stress), 24 (moderate drought stress), and 72 h (severe drought stress) of treatment with 15% (w/v) poly (ethylene glycol)6000 (PEG6000) to simulate drought stress. In our study, the association analysis of proteins and transcript expression revealed 1244 and 968 associated proteins identified in leaves and roots, respectively. L1, L2, and L3 are leaf samples which were harvested at 0, 24, and 72 h after being treated with 15% PEG6000, respectively. Among those treatment groups, a total of 118, 216, and 433 unique proteins were identified as differentially expressed during L1 vs. L2, L2 vs. L3, and L1 vs. L3, respectively. R1, R2, and R3 are root samples which were harvested at 0, 24, and 72 h after being treated with 15% PEG6000, respectively. Among those treatment groups，a total of 124, 27, and 240 unique proteins were identified as differentially expressed during R1 vs. R2, R2 vs. R3, and R1 vs. R3, respectively. Bioinformatics analysis indicated that glycolysis/gluconeogenesis was significantly upregulated in roots in response to drought stress. This enhancement may result in more glycolytically generated adenosine triphosphate (ATP) in roots to adapt to adverse environmental conditions. To obtain complementary information related to iTRAQ data, the mRNA levels of 12 proteins related to glycolysis/gluconeogenesis in leaves and 7 in roots were further analyzed by qPCR. Most of their expression levels were higher in R3 than R1 and R2, suggesting that these compounds may promote drought tolerance by modulating the production of available energy.

Role of Proteomics in Crop Stress Tolerance

Plants often experience various biotic and abiotic stresses during their life cycle. The abiotic stresses include mainly drought, salt, temperature (low/high), flooding and nutritional deficiency/excess which hamper crop growth and yield to a great extent. In view of a projection 50% of the crop loss is attributable to abiotic stresses. However, abiotic stresses cause a myriad of changes in physiological, molecular and biochemical processes operating in plants. It is now widely reported that several proteins respond to these stresses at pre- and post-transcriptional and translational levels. By knowing the role of these stress inducible proteins, it would be easy to comprehensively expound the processes of stress tolerance in plants. The proteomics study offers a new approach to discover proteins and pathways associated with crop physiological and stress responses. Thus, studying the plants at proteomic levels could help understand the pathways involved in stress tolerance. Furthermore, improving the understanding of the identified key metabolic proteins involved in tolerance can be implemented into biotechnological applications, regarding recombinant/transgenic formation. Additionally, the investigation of identified metabolic processes ultimately supports the development of antistress strategies. In this review, we discussed the role of proteomics in crop stress tolerance. We also discussed different abiotic stresses and their effects on plants, particularly with reference to stress-induced expression of proteins, and how proteomics could act as vital biotechnological tools for improving stress tolerance in plants.

Proteomic responses of drought-tolerant and drought-sensitive cotton varieties to drought stress

Drought, one of the most widespread factors reducing agricultural crop productivity, affects biological processes such as development, architecture, flowering and senescence. Although protein analysis techniques and genome sequencing have made facilitated the proteomic study of cotton, information on genetic differences associated with proteomic changes in response to drought between different cotton genotypes is lacking. To determine the effects of drought stress on cotton seedlings, we used two-dimensional polyacrylamide gel electrophoresis (2-DE) and matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry to comparatively analyze proteome of drought-responsive proteins during the seedling stage in two cotton (Gossypium hirsutum L.) cultivars, drought-tolerant KK1543 and drought-sensitive Xinluzao26. A total of 110 protein spots were detected on 2-DE maps, of which 56 were identified by MALDI-TOF and MALDI-TOF/TOF mass spectrometry. The identified proteins were mainly associated with metabolism (46.4 %), antioxidants (14.2 %), and transport and cellular structure (23.2 %). Some key proteins had significantly different expression patterns between the two genotypes. In particular, 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase, UDP-D-glucose pyrophosphorylase and ascorbate peroxidase were up-regulated in KK1543 compared with Xinluzao26. Under drought stress conditions, the vacuolar H(+)-ATPase catalytic subunit, a 14-3-3g protein, translation initiation factor 5A and pathogenesis-related protein 10 were up-regulated in KK1543, whereas ribosomal protein S12, actin, cytosolic copper/zinc superoxide dismutase, protein disulfide isomerase, S-adenosylmethionine synthase and cysteine synthase were down-regulated in Xinluzao26. This work represents the first characterization of proteomic changes that occur in response to drought in roots of cotton plants. These differentially expressed proteins may be related to biochemical pathways responsible for drought tolerance in KK1543. Although further studies are needed, this proteomic analysis underlines the role of post-translational events. The differentially expressed proteins and their corresponding genes may be used as markers for the breeding of drought tolerance in cotton.

Proteins involved in biophoton emission and flooding-stress responses in soybean under light and dark conditions

To know the molecular systems basically flooding conditions in soybean, biophoton emission measurements and proteomic analyses were carried out for flooding-stressed roots under light and dark conditions. Photon emission was analyzed using a photon counter. Gel-free quantitative proteomics were performed to identify significant changes proteins using the nano LC-MS along with SIEVE software. Biophoton emissions were significantly increased in both light and dark conditions after flooding stress, but gradually decreased with continued flooding exposure compared to the control plants. Among the 120 significantly identified proteins in the roots of soybean plants, 73 and 19 proteins were decreased and increased in the light condition, respectively, and 4 and 24 proteins were increased and decreased, respectively, in the dark condition. The proteins were mainly functionally grouped into cell organization, protein degradation/synthesis, and glycolysis. The highly abundant lactate/malate dehydrogenase proteins were decreased in flooding-stressed roots exposed to light, whereas the lysine ketoglutarate reductase/saccharopine dehydrogenase bifunctional enzyme was increased in both light and dark conditions. Notably, however, specific enzyme assays revealed that the activities of these enzymes and biophoton emission were sharply increased after 3 days of flooding stress. This finding suggests that the source of biophoton emission in roots might involve the chemical excitation of electron or proton through enzymatic or non-enzymatic oxidation and reduction reactions. Moreover, the lysine ketoglutarate reductase/saccharopine dehydrogenase bifunctional enzyme may play important roles in responses in flooding stress of soybean under the light condition and as a contributing factor to biophoton emission.

Ectopic expression of Pokkali phosphoglycerate kinase-2 (OsPGK2-P) improves yield in tobacco plants under salinity stress

KEY MESSAGE

Our results indicate that OsPGK2a-P gene is differentially regulated in contrasting rice cultivars under stress and its overexpression confers salt stress tolerance in transgenic tobacco. Phosphoglycerate kinase (PGK; EC = 2.7.2.3) plays a major role for ATP production during glycolysis and 1, 3-bisphosphoglycerate production to participate in the Calvin cycle for carbon fixation in plants. Whole genome analysis of rice reveals the presence of four PGK genes (OsPgks) on different chromosomes. Comparative expression analysis of OsPgks in rice revealed highest level of transcripts for OsPgk2 at most of its developmental stages. Detailed characterization of OsPgk2 transcript and protein showed that it is strongly induced by salinity stress in two contrasting genotypes of rice, i.e., cv IR64 (salt sensitive) and landrace Pokkali (salt tolerant). Ectopic expression of OsPgk2a-P (isolated from Pokkali) in transgenic tobacco improved its salinity stress tolerance by higher chlorophyll retention and enhanced proline accumulation, besides maintaining better ion homeostasis. Ectopically expressing OsPgk2a-P transgenic tobacco plants showed tall phenotype with more number of pods than wild-type plants. Therefore, OsPgk2a-P appears to be a potential candidate for increasing salinity stress tolerance and enhanced yield in crop plants.

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.

Comparative analysis of endogenous hormones level in two soybean (Glycine max L.) lines differing in waterlogging tolerance

Waterlogged condition due to flooding is one of the major abiotic stresses that drastically affect the soybean growth and yield around the world. As a result, many breeders have focused on the development of waterlogging tolerance in soybean varieties, and thus, several tolerant varieties were developed. However, the physiological mechanism of waterlogging tolerance is not yet fully understood. We particularly studied the endogenous hormones regulation during waterlogging in two contrasting soybean genotypes. According to our results, adventitious roots were better developed in the waterlogging tolerant line (WTL) than in the waterlogging susceptible line (WSL). Endogenous hormones also showed significant differences between WTL and WSL. The ethylene production ratio was higher in WTL than in WSL, and methionine was higher in WTL than in WSL. Other endogenous abscisic acid (ABA) contents were lower in WTL than in WSL. Conversely, gibberellic acid (GA) showed a tendency to be high in WTL, especially the levels of the bioactive GA4. The ratio of total GA and ABA was significantly higher in WTL than in WSL. Anatomical study of the root revealed that aerenchyma cells in the stele were better developed in WTL than in WSL.

Analysis of gene expression and proteomic profiles of clonal genotypes from Theobroma cacao subjected to soil flooding

Soil flooding causes changes in gene transcription, synthesis and degradation of proteins and cell metabolism. The main objective of this study was to understand the biological events of Theobroma cacao during soil flooding-induced stress, using the analyses of gene expression and activity of key enzymes involved in fermentation, as well as the identification of differentially expressed proteins by mass spectrometry in two contrasting genotypes for flooding tolerance (tolerant - TSA-792 and susceptible - TSH-774). Soil anoxia caused by flooding has led to changes in the expression pattern of genes associated with the biosynthesis of alcohol dehydrogenase (ADH), pyruvate decarboxylase (PDC) and lactate dehydrogenase (LDH) in leaves and roots of the two evaluated genotypes. Significant differences were observed between the enzyme activities of the two genotypes. Leaves and roots of the TSA-792 genotype showed higher ADH activity as compared to the TSH-774 genotype, whereas the activities of PDC and LDH have varied over the 96 h of soil flooding, being higher for TSA-792 genotype, at the initial stage, and TSH-774 genotype, at the final stage. Some of the identified proteins are those typical of the anaerobic metabolism-involved in glycolysis and alcoholic fermentation-and different proteins associated with photosynthesis, protein metabolism and oxidative stress. The ability to maintain glycolysis and induce fermentation was observed to play an important role in anoxia tolerance in cacao and may also serve to distinguish tolerant and susceptible genotypes in relation to this stressor.

Breakthroughs spotlighting roles for extracellular nucleotides and apyrases in stress responses and growth and development

Animal and plant cells release nucleotides into their extracellular matrix when touched, wounded, and when their plasma membranes are stretched during delivery of secretory vesicles and growth. These released nucleotides then function as signaling agents that induce rapid increases in the concentration of cytosolic calcium, nitric oxide and superoxide. These, in turn, are transduced into downstream physiological changes. These changes in plants include changes in the growth of diverse tissues, in gravitropism, and in the opening and closing of stomates. The concentration of extracellular nucleotides is controlled by various phosphatases, prominent among which are apyrases EC 3.6.1.5 (nucleoside triphosphate diphosphohydrolases, NTPDases). This review provides phylogenetic and pHMM analyses of plant apyrases as well as analysis of predicted post-translational modifications for Arabidopsis apyrases. This review also summarizes and discusses recent advances in research on the roles of apyrases and extracellular nucleotides in controlling plant growth and development. These include new findings that document how apyrases and extracellular nucleotides control auxin transport, modulate stomatal aperture, and mediate biotic and abiotic stress responses, and on how apyrase suppression leads to growth inhibition.

Potentiality of Soybean Proteomics in Untying the Mechanism of Flood and Drought Stress Tolerance

Dissecting molecular pathways at protein level is essential for comprehensive understanding of plant stress response mechanism. Like other legume crops, soybean, the world's most widely grown seed legume and an inexpensive source of protein and vegetable oil, is also extremely sensitive to abiotic stressors including flood and drought. Irrespective of the kind and severity of the water stress, soybean exhibits a tight control over the carbon metabolism to meet the cells required energy demand for alleviating stress effects. The present review summarizes the major proteomic findings related to changes in soybean proteomes in response to flood and drought stresses to get a clear insight into the complex mechanisms of stress tolerance. Furthermore, advantages and disadvantages of different protein extraction protocols and challenges and future prospects of soybean proteome study are discussed in detail to comprehend the underlying mechanism of water stress acclimation.

Analysis of flooding-responsive proteins localized in the nucleus of soybean root tips

Flooding stress has negative impact on soybean cultivation as it severely impairs plant growth and development. To examine whether nuclear function is affected in soybean under flooding stress, abundance of nuclear proteins and their mRNA expression were analyzed. Two-day-old soybean seedlings were treated with flooding for 2 days, and nuclear proteins were purified from root tips. Gel-free proteomics analysis identified a total of 39 flooding-responsive proteins, of which abundance of 8 and 31 was increased and decreased, respectively, in soybean root tips. Among these differentially regulated proteins, the mRNA expression levels of five nuclear-localized proteins were further analyzed. The mRNA levels of four proteins, which are splicing factor PWI domain-containing protein, epsilon2-COP, beta-catenin, and clathrin heavy chain decreased under flooding stress, were also down-regulated. In addition, mRNA level of a receptor for activated protein kinase C1(RACK1) was down-regulated, though its protein was accumulated in the soybean nucleus in response to flooding stress. These results suggest that several nuclear-related proteins are decreased at both the protein and mRNA level in the root tips of soybean under flooding stress. Furthermore, RACK1 might have an important role with accumulation in the soybean nucleus under flooding-stress conditions.

Soybean proteomics

Soybean, the world's most widely grown seed legume, is an important global source of vegetable oil and protein. Though, complete draft genome sequence of soybean is now available, but functional genomics studies remain in their infancy, as this agricultural legume species exhibits genetic constrains like genome duplications and self-incompatibilities. The techniques of proteomics provide much powerful tool for functional analysis of soybean. In the present review, an attempt has been made to summarize all significant contributions in the field of soybean proteomics. Special emphasis is given to subcellular proteomics in response to abiotic stresses for better understanding molecular basis of acquisition of stress tolerance mechanism. Detailed protocols of protein extraction, solubilization, fractionation of subcellular organelle, and proteins identification are explained for soybean proteomics. All this information would not only enrich us in understanding the plants response to environmental stressors but would also enable us to design genetically engineered stress tolerant soybean.

Dynamic QTL analysis and candidate gene mapping for waterlogging tolerance at maize seedling stage

Soil waterlogging is one of the major abiotic stresses adversely affecting maize growth and yield. To identify dynamic expression of genes or quantitative trait loci (QTL), QTL associated with plant height, root length, root dry weight, shoot dry weight and total dry weight were identified via conditional analysis in a mixed linear model and inclusive composite interval mapping method at three respective periods under waterlogging and control conditions. A total of 13, 19 and 23 QTL were detected at stages 3D|0D (the period during 0-3 d of waterlogging), 6D|3D and 9D|6D, respectively. The effects of each QTL were moderate and distributed over nine chromosomes, singly explaining 4.14-18.88% of the phenotypic variation. Six QTL (ph6-1, rl1-2, sdw4-1, sdw7-1, tdw4-1 and tdw7-1) were identified at two consistent stages of seedling development, which could reflect a continuous expression of genes; the remaining QTL were detected at only one stage. Thus, expression of most QTL was influenced by the developmental status. In order to provide additional evidence regarding the role of corresponding genes in waterlogging tolerance, mapping of Expressed Sequence Tags markers and microRNAs were conducted. Seven candidate genes were observed to co-localize with the identified QTL on chromosomes 1, 4, 6, 7 and 9, and may be important candidate genes for waterlogging tolerance. These results are a good starting point for understanding the genetic basis for selectively expressing of QTL in different stress periods and the common genetic control mechanism of the co-localized traits.

Soybean proteomics for unraveling abiotic stress response mechanism

Plant response to abiotic stresses depends upon the fast activation of molecular cascades involving stress perception, signal transduction, changes in gene and protein expression and post-translational modification of stress-induced proteins. Legumes are extremely sensitive to flooding, drought, salinity and heavy metal stresses, and soybean is not an exception of that. Invention of immobilized pH gradient strips followed by advancement in mass spectrometry has made proteomics a fast, sensitive and reliable technique for separation, identification and characterization of stress-induced proteins. As the functional translated portion of the genome plays an essential role in plant stress response, proteomic studies provide us a finer picture of protein networks and metabolic pathways primarily involved in stress tolerance mechanism. Identifying master regulator proteins that play key roles in the abiotic stress response pathway is fundamental in providing opportunities for developing genetically engineered stress-tolerant crop plants. This review highlights recent contributions in the field of soybean biology to comprehend the complex mechanism of abiotic stress acclimation. Furthermore, strengths and weaknesses of different proteomic methodologies of extracting complete proteome and challenges and future prospects of soybean proteome study both at organ and whole plant levels are discussed in detail to get new insights into the plant abiotic stress response mechanism.

Influence of stress hormones on the auxin homeostasis in Brassica rapa seedlings

KEY MESSAGE : Stress hormones, particularly jasmonic acid, influenced root growth, auxin levels, and transcription of auxin amidohydrolase BrIAR3 in Brassica rapa seedlings, while auxin conjugate synthetases BrGH3.1 and BrGH3.9 were down-regulated by all treatments. The influence of stress hormones: jasmonic acid (JA), salicylic acid (SA), and abscisic acid (ABA) on 1-day-old seedlings of Chinese cabbage (Brassica rapa L. ssp. pekinensis) was investigated with particular focus on auxin levels and the regulation of reversible auxin conjugation as a mechanism of auxin homeostasis. At the physiological level, stress hormones inhibited root growth, where JA was the most prominent inhibitor with an IC50 value 3.1 μM, which is one and two orders of magnitude lower than that found for ABA and SA, respectively. JA treatment significantly increased the total auxin content, by induction of free and conjugated forms. Also, the stress hormones affected the transcription of genes involved in the process of the reversible auxin conjugation: auxin amidohydrolases BrIAR3 and BrILL2, and auxin conjugate synthetases BrGH3.1 and BrGH3.9. JA treatment increased the transcript level of BrIAR3 two-fold, while it did not affect the transcription of BrILL2. SA and ABA down-regulated the transcription of both auxin amidohydrolase genes by 30 %. Transcription of both auxin conjugate synthetases was significantly down-regulated by all treatments by 30-70 %. Among the investigated biochemical stress markers, glutathione along with protein carbonylation appeared the most affected upon treatments. The redox status of the seedlings was shifted to the more oxidized state upon JA and ABA treatments, whereas SA caused more reduced redox state in comparison to the control. The principal component analysis visualized relationship among auxin and stress parameters upon treatments. Accordingly, the role of auxin in stress response of Brassica seedlings was discussed.

The prolific ATL family of RING-H2 ubiquitin ligases

An abundant class of E3 ubiquitin ligases encodes the RING-finger domain. The RING finger binds to the E2 ubiquitin-conjugating enzyme and brings together both the E2 and substrate. It is predicted that 477 RING finger E3 ligases exist in Arabidopsis thaliana. A particular family among them, named Arabidopsis Tóxicos en Levadura (ATL), consists of 91 members that contain the RING-H2 variation and a hydrophobic domain located at the N-terminal end. Transmembrane E3 ligases are important in several biological processes. For instance, some transmembrane RING finger E3 ligases are main participants in the endoplasmic reticulum-associated degradation pathway that targets misfolded proteins. Functional analysis of a number of ATLs has shown that some of them regulate distinct pathways in plants. Several ATLs have been shown to participate in defense responses, while others play a role in the regulation of the carbon/nitrogen response during post-germinative seedling growth transition, in the regulation of cell death during root development, in endosperm development, or in the transition to flowering under short day conditions. The ATL family has also been instrumental in evolution studies for showing how gene families are expanded in plant genomes.

Chromium-induced physiological and proteomic alterations in roots of Miscanthus sinensis

Despite the widespread occurrence of chromium toxicity, its molecular mechanism is poorly documented in plants compared to other heavy metals. To investigate the molecular mechanisms that regulate the response of Miscanthus sinensis roots to elevated level of chromium, seedlings were grown for 4 weeks and exposed to potassium dichromate for 3 days. Physiological, biochemical and proteomic changes in roots were investigated. Lipid peroxidation and H₂O₂ content in roots were significantly increased. Protein profiles analyzed by two-dimensional gel electrophoresis revealed that 36 protein spots were differentially expressed in chromium-treated root samples. Of these, 13 protein spots were up-regulated, 21 protein spots were down-regulated and 2 spots were newly induced. These differentially displayed proteins were identified by MALDI-TOF and MALDI-TOF/TOF mass spectrometry. The identified proteins included known heavy metal-inducible proteins such as carbohydrate and nitrogen metabolism, molecular chaperone proteins and novel proteins such as inositol monophosphatase, nitrate reductase, adenine phosphoribosyl transferase, formate dehydrogenase and a putative dihydrolipoamide dehydrogenase that were not known previously as chromium-responsive. Taken together, these results suggest that Cr toxicity is linked to heavy metal tolerance and senescence pathways, and associated with altered vacuole sequestration, nitrogen metabolism and lipid peroxidation in Miscanthus roots.

Comparative proteomic analysis of seedling leaves of different salt tolerant soybean genotypes

Salinity is one of the major environmental constraints limiting yield of crop plants in many semi-arid and arid regions around the world. To understand responses in soybean seedling to salt stress at proteomic level, the extracted proteins from seedling leaves of salt-sensitive genotype Jackson and salt-tolerant genotype Lee 68 under 150 mM NaCl stress for 1, 12, 72 and 144 h, respectively, were analyzed by 2-DE. Approximately 800 protein spots were detected on 2-DE gels. Among them, 91 were found to be differently expressed, with 78 being successfully identified by MALDI-TOF-TOF. The identified proteins were involved in 14 metabolic pathways and cellular processes. Based on most of the 78 salt-responsive proteins, a salt stress-responsive protein network was proposed. This network consisted of several functional components, including balancing between ROS production and scavenging, accelerated proteolysis and reduced biosynthesis of proteins, impaired photosynthesis, abundant energy supply and enhanced biosynthesis of ethylene. Salt-tolerant genotype Lee 68 possessed the ability of higher ROS scavenging, more abundant energy supply and ethylene production, and stronger photosynthesis than salt-sensitive genotype Jackson under salt stress, which may be the major reasons why it is more salt-tolerant than Jackson.

Proteomic response of wheat embryos to fosthiazate stress in a protected vegetable soil

A proteomic analysis of wheat defense response induced by the widely used organophosphorus nematicide fosthiazate is reported. Seed germination and two-dimensional gel electrophoresis (2-DE) experiments were performed using a Chinese wheat cultivar, Zhenmai No. 5. Root and shoot elongation decreased but thiobarbituric acid reactive substances (TBARS) content in embryos increased with increasing pesticide concentration. More than 1000 protein spots were reproducibly detected in each silver-stained gel. Thirty-seven protein spots with at least 2-fold changes were identified using MALDI-TOF MS/MS analysis. Of these, 24 spots were up-regulated and 13 were down-regulated. Proteins identified included some well-known classical stress responsive proteins under abiotic or biotic stresses as well as some unusual responsive proteins. Ten responsive proteins were reported for the first time at the proteomic level, including fatty acyl CoA reductase, dihydrodipicolinate synthase, DEAD-box ATPase-RNA-helicase, fimbriata-like protein, waxy B1, rust resistance kinase Lr10, putative In2.1 protein, retinoblastoma-related protein 1, pollen allergen-like protein and S-adenosyl-L-methionine:phosphoethanolamine N-methyltransferase. The proteins identified were involved in several processes such as metabolism, defense/detoxification, cell structure/cell growth, signal transduction/transcription, photosynthesis and energy. Seven candidate proteins were further analyzed at the mRNA level by RT-PCR to compare transcript and protein accumulation patterns, revealing that not all the genes were correlated well with the protein level. Identification of these responsive proteins may provide new insight into the molecular basis of the fosthiazate-stress response in the early developmental stages of plants and may be useful in stress monitoring or stress-tolerant crop breeding for environmentally friendly agricultural production.

Proteomics techniques for the development of flood tolerant crops

Proteomics is a useful analytical approach for investigating crop responses to stress. Recent remarkable advances in proteomic techniques allow for the identification of a wider range of proteins than was previously possible. The application of proteomic techniques to clarify the molecular mechanisms underlying crop responses to flooding stress may facilitate the development of flood tolerant crops. Flooding is an environmental stress found worldwide and may increase in frequency due to changes in global climate. Waterlogging resulting from flooding causes significant reductions in the growth and yield of several crops. Transient flooding displaces gases in soil pores and often causes hypoxia in plants grown on land with poor drainage. Changes in protein expression and post-translational modification of proteins occur as plants activate their defense system in response to flooding stress. In this review, we discuss the contributions that proteomic studies have made toward increasing our understanding of the well-organized cellular response to flooding in soybean and other crops. The biological relevance of the proteins identified using proteomic techniques in regard to crop stress tolerance will be discussed as well.

New insights on proteomics of transgenic soybean seeds: evaluation of differential expressions of enzymes and proteins

This work reports the evaluation of differentially expressed enzymes and proteins from transgenic and nontransgenic soybean seeds. Analysis of malondialdehyde, ascorbate peroxidase (EC 1.11.1.11), glutathione reductase (EC 1.6.4.2), and catalase (EC 1.11.1.6) revealed higher levels (29.8, 30.6, 71.4, and 35.3%, respectively) in transgenic seeds than in nontransgenic seeds. Separation of soybean seed proteins was done by two-dimensional polyacrylamide gel electrophoresis, and 192 proteins were identified by matrix-assisted laser desorption/ionization (MALDI) quadrupole time-of-flight (QTOF) mass spectrometry (MS) and electrospray ionization (ESI) QTOF MS. Additionally, the enzyme CP4 EPSPS, involved in the genetic modification, was identified by enzymatic digestions using either trypsin or chymotrypsin and ESI-QTOF MS/MS for identification. From the proteins identified, actin fragment, cytosolic glutamine synthetase, glycinin subunit G1, and glycine-rich RNA-binding protein were shown to be differentially expressed after analysis using the two-dimensional difference gel electrophoresis technique, and applying a regulator factor of 1.5 or greater.