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Finding solutions to mitigate the impact of salinity on crops is important for global food security because soil salinity significantly reduces plant growth and grain yield. Ethanol may play an important role in mitigating the negative salt-induced effects on crops. Soybean root growth was significantly reduced under salt stress; however, it was restored and comparable to control values by ethanol application even under stress. To study the positive mechanism of ethanol on soybean growth, a proteomic approach was carried out. The categories with the greatest changes in protein numbers were protein metabolism, transport, and cell organization in biological processes, nucleus and cytosol in cellular components, and nucleic acid binding activity in molecular functions. Proteomic data were confirmed using immunoblot analysis. Reactive oxygen species enzymes increased under salt stress; among them, mitochondrial ascorbate peroxidase was further accumulated by ethanol application. Among the cell wall and membrane-associated proteins, xyloglucan xyloglucosyl transferase and H+-ATPase increased and decreased, respectively, under salt stress; however, they were restored to control levels by ethanol application. These results suggest that soybeans were adversely affected by salt stress and recovered with ethanol application via the regulation of cell wall and membrane functions through the detoxification of reactive oxygen species.

Flooding induces low-oxygen stress, which reduces plant growth. The activity of the γ-aminobutyric acid (GABA) shunt is crucial for plant stress adaptation, in which it acts by changing cytosolic pH, limiting reactive oxygen species production, regulating nitrogen metabolism, and bypassing steps in the tricarboxylic acid cycle. GABA accumulates under osmotic stress as well as flooding stress. To clarify the dynamic roles of GABA accumulation in wheat under flooding stress, biochemical and enzymatic analyses were performed using a plant-derived smoke solution (PDSS), which rescued wheat growth from flooding stress. Alcohol dehydrogenase abundance increased under flooding stress; however, under the same conditions, pyruvic acid content increased only following PDSS application. Glutamic acid content increased under flooding stress, but decreased following the application of PDSS after 2 days of flooding. Glutamate decarboxylase abundance and GABA content increased under flooding stress, and further increased after 1 day of application of PDSS. Succinyl semialdehyde dehydrogenase accumulated after 2 days of flooding. These results suggest that flooding stress increases GABA content along with the increase and decrease of glutamate decarboxylase and succinyl semialdehyde dehydrogenase, respectively. Additionally, PDSS increased GABA content along with the increase of glutamate decarboxylase abundance at the initial stage of application.

Climate change jeopardizes soybean production by declining seed yield and quality. In this review, the morphophysiological alterations of soybean in response to abiotic stress are summarized, followed by illustrations of cellular metabolisms and regulatory mechanisms to organellar stress based on subcellular proteomics. This highlights the communications associated with reactive oxygen species scavenging, molecular chaperones, and phytohormone signals among subcellular compartments. Given the complexity of climate change and the limitations of plants in coping with multiple abiotic stresses, a generic response to environmental constraints is proposed between calcium and abscisic acid signals in subcellular organelles. This review summarizes the findings of subcellular proteomics in stressed soybean and discusses the future prospects of subcellular proteomics for promoting the improvement of climate-tolerant crops.

Higher production of secondary metabolites is one of the adaptive responses to alleviate the impact of environmental injuries. In the present investigation, the production of these metabolites with medicinal importance induced by salinity in Carum copticum was investigated. To develop a better way for the production of medicinal substances, callogenesis and plant regeneration were analyzed, and seeds, calli, and/or regenerated seedlings were exposed to different concentrations of NaCl under in vitro culture conditions. The maximum frequency of callus induction was obtained on a medium supplemented with 0.25 mg L−1 2, 4-dichlorophenoxyacetic (2,4-D) and 1 mg L−1 benzyl amino purine (BAP) from stem explants. Plant regeneration with multiple shoots was obtained from pieces of callus transferred to MS medium fortified with 0.25 mg L−1 2,4-D and 1.5 mg L−1 BAP. Four weeks after treatment, salinity induced a substantial increase in the accumulation of reducing sugars and proline as compatible osmolytes and the activity of antioxidant enzymes. Total phenolics and anthocyanin significantly increased in all samples with increasing NaCl concentrations; however, the regenerated seedlings showed a reduction in these compounds at severe NaCl concentration compared to the control. Moreover, NaCl enhanced thymol, γ-terpinene, sabinene, and myrcene in the seedlings and calli, as well as carvacrol, limonene, and α-terpinene in the regenerated seedlings. These results suggest that salinity has a marked impact on improving the content of antioxidant metabolites and essential oils in C. copticum, whose callus might be the most salt tolerant in all tested samples.

Food security is a major challenge in the present world due to erratic weather and climatic changes. Environmental stress negatively affects plant growth and development which leads to reduced crop yields. Technological advancements have caused remarkable improvements in crop-breeding programs. Proteins have an indispensable role in developing stress resilience and tolerance in crops. Genomic and biotechnological advancements have made the process of crop improvement more accurate and targeted. Proteomic studies provide the information required for such targeted approaches. The crosstalk among cellular components is being analyzed by subcellular proteomics. Additionally, the functional diversity of proteins is being unraveled by post-translational modifications during abiotic stress. The exploration of precise cellular responses and the networking among different cellular organelles help in the prediction of signaling pathways and protein–protein interactions. High-throughput mass-spectrometry-based protein studies are now possible due to incremental advancements in mass-spectrometry techniques, sample protocols, and bioinformatic tools as well as the increasing availability of plant genome sequence information for multiple species. In this review, the key role of proteomic analysis in identifying the abiotic-stress-responsive mechanisms in various crops was summarized. The development and availability of advanced computational tools were discussed in detail. The highly variable protein responses among different crops have provided a wide avenue for molecular-marker-assisted genetic buildup studies to develop smart, high-yielding, and stress-tolerant varieties to cope with food-security challenges.

Does climate change influence on genetic regulatory systems? Previous studies on genetic regulatory systems have focused on specific systems and environmental stimuli. We elucidate a causal relationship for a ‘minimal’ genetic regulatory system in environmental changes. This model is independent of the types of signal transmitting molecules, kinetics, and environmental stimuli. Novel inequalities based on the model indicate: (i) an information-theoretic quantity mutual information between the number of catalytic molecules and product molecules catalyzed decreases in the genetic regulatory system in response to climate change; (ii) the genetic regulatory system is degraded from the level of closed-to open-loop control systems in response to climate change. We relate the relationships suggested by the inequalities to interpretation of soybean omics data collected under an experimental condition of flooding. We manifest a mathematical framework for designing genetic modification strategy to mitigate the effect of the climate change on genetic regulatory systems. Our model suggests genetic regulatory system degradation, which is unavoidable, in the progression of climatic change.

Drought is one of the severe environmental stresses threatening agriculture around the globe. Nitric oxide plays diverse roles in plant growth and defensive responses. Despite a few studies supporting the role of nitric oxide in plants under drought responses, little is known about its pivotal molecular amendment in the regulation of stress signaling. In this study, a label-free nano-liquid chromatography-mass spectrometry approach was used to determine the effects of sodium nitroprusside (SNP) on polyethylene glycol (PEG)-induced osmotic stress in banana roots. Plant treatment with SNP improved plant growth and reduced the percentage of yellow leaves. A total of 30 and 90 proteins were differentially identified in PEG+SNP against PEG and PEG+SNP against the control, respectively. The majority of proteins differing between them were related to carbohydrate and energy metabolisms. Antioxidant enzyme activities, such as superoxide dismutase and ascorbate peroxidase, decreased in SNP-treated banana roots compared to PEG-treated banana. These results suggest that the nitric oxide-induced osmotic stress tolerance could be associated with improved carbohydrate and energy metabolism capability in higher plants.

Wheat is an important staple food crop for one-third of the global population; however, its growth is reduced by flooding. On the other hand, a plant-derived smoke solution enhances plant growth; however, its mechanism is not fully understood. To reveal the effects of the plant-derived smoke solution on wheat under flooding, morphological, biochemical, and proteomic analyses were conducted. The plant-derived smoke solution improved wheat-leaf growth, even under flooding. According to the functional categorization of proteomic results, oppositely changed proteins were correlated with photosynthesis, glycolysis, biotic stress, and amino-acid metabolism with or without the plant-derived smoke solution under flooding. Immunoblot analysis confirmed that RuBisCO activase and RuBisCO large/small subunits, which decreased under flooding, were recovered by the application of the plant-derived smoke solution. Furthermore, the contents of chlorophylls a and b significantly decreased by flooding stress; however, they were recovered by the application of the plant-derived smoke solution. In glycolysis, fructose-bisphosphate aldolase and glyceraldehyde-3-phosphate dehydrogenase decreased with the application of the plant-derived smoke solution under flooding as compared with flooding alone. Additionally, glutamine, glutamic acid, aspartic acid, and serine decreased under flooding; however, they were recovered by the plant-derived smoke solution. These results suggest that the application of the plant-derived smoke solution improves the recovery of wheat growth through the regulation of photosynthesis and glycolysis even under flooding conditions. Furthermore, the plant-derived smoke solution might promote wheat tolerance against flooding stress through the regulation of amino-acid metabolism.

Wheat is vulnerable to numerous diseases; on the other hand, silver nanoparticles (AgNPs) exhibit a sterilizing action. To understand the combined effects of AgNPs with nicotinate and potassium nitrate (KNO3) for plant growth and sterilization, a gel- and label-free proteomics was performed. Root weight was promoted by the treatment of AgNPs mixed with nicotinate and KNO3. From a total of 5557 detected proteins, 90 proteins were changed by the mixture of AgNPs, nicotinate, and KNO3; among them, 25 and 65 proteins increased and decreased, respectively. The changed proteins were mainly associated with redox and biotic stress in the functional categorization. By immunoblot analysis, the abundance of glutathione reductase/peroxiredoxin and pathogen-related protein three significantly decreased with the mixture. Furthermore, from the changed proteins, the abundance of starch synthase and lipoxygenase significantly increased and decreased, respectively. Through biochemical analysis, the starch contents increased with the mixture. The application of esculetin, which is a lipoxygenase inhibitor, increased the weight and length of the root. These results suggest that the AgNPs mixed with nicotinate and KNO3 cause positive effects on wheat seedlings by regulating pathogen-related protein and reactive-oxygen species scavenging. Furthermore, increasing starch and decreasing lipoxygenase might improve wheat growth.

Plant-derived smoke solution enhances soybean root growth; however, its mechanism is not clearly understood. Subcellular proteomics techniques were used for underlying roles of plant-derived smoke solution on soybean root growth. The fractions of membrane and nucleus were purified and evaluated for purity. ATPase and histone were enriched in the fractions of membrane and nucleus, respectively. Principal component analysis of proteomic results indicated that the plant-derived smoke solution affected the proteins in the membrane and nucleus. The proteins in the membrane and nucleus mainly increased and decreased, respectively, by the treatment of plant-derived smoke solution compared with control. In the proteins in the plasma membrane, ATPase increased, which was confirmed by immunoblot analysis, and ATP contents increased through the treatment of plant-derived smoke solution. Additionally, although the nuclear proteins mainly decreased, the expression of RNA polymerase II was up-regulated through the treatment of plant-derived smoke solution. These results indicate that plant-derived smoke solution enhanced soybean root growth through the transcriptional promotion with RNA polymerase II expression and the energy production with ATPase accumulation.

Plants produce a wide array of nutrients that exert synergistic interaction among whole combinations of nutrients. Therefore comprehensive nutrient profiling is required to evaluate their nutritional/nutraceutical value and health promoting effect. In order to obtain such datasets for mung bean, which is known as a medicinal plant with heat alleviating effect, proteomic and metabolomic analyses were performed using four cultivars from China, Thailand, and Myanmar. In total, 449 proteins and 210 metabolic compounds were identified in seed coat; whereas 480 proteins and 217 metabolic compounds were detected in seed flesh, establishing the first comprehensive dataset of mung bean for nutraceutical evaluation. Keywords: Mung bean, Health-promoting food, Nutritional/nutraceutical value, Metabolic network, Metabolomics, Proteomics

High level of UV-B irradiation followed by dark treatment accumulates secondary metabolites in Clematis terniflora DC. To investigate the response mechanism under high level of UV-B irradiation followed by dark treatment, transcriptomic and proteomic analyses were performed in leaves of Clematis terniflora DC. The experimental design for the transcriptomic and proteomic analyses in leaves of C. terniflora under stresses was organized into a picture. For transcriptomics, mRNA-sequencing technology was used. Genes identified in leaves of C. terniflora at starting point, high level of UV-B irradiation, and high level of UV-B irradiation followed by dark treatment were listed; genes with different expression levels at starting point, high level of UV-B irradiation, and high level of UV-B irradiation followed by dark treatment were also presented in this DiB article. For proteomics, a gel-free/label-free proteomic technique was used. Proteins with different abundances in leaves at starting point, high level of UV-B irradiation, and high level of UV-B irradiation followed by dark treatment were presented in this DiB article. In order to monitor the expression levels of genes under the stress, quantitative reverse transcription polymerase chain reaction was performed. The primer sequences of genes selected for quantitative reverse transcription polymerase chain reaction was presented in this DiB article.

In flooded hypocotyl of soybean (Glycine max), cell division in phellogen and the elongation of these cells are enhanced, and thereby a secondary aerenchyma with high porosity is produced. Auxin controls cell division and cell elongation in many plants, so we studied its role in secondary aerenchyma development. Soybean plants with fully expanded unifoliolate leaves were flooded for 6 d with solutions (100 μM each) of seven anti-auxins. TIBA, NPA, HFCA, 1-NOA, or CHPAA did not restrict the secondary aerenchyma formation, while MH moderately suppressed the aerenchyma development, and PCIB strongly inhibited the development of phellogen and secondary aerenchyma. However, the endogenous IAA concentrations in the flooded hypocotyls did not increase or decrease relative to the controls until 72 h, when a secondary aerenchyma was observed. From these results, it is unclear whether auxin plays an important role in the process of secondary aerenchyma formation under flooding.

Once candidate genes are available, the application of genetic transformation plays a major part to study their function in plants for adaptation to respective environmental stresses, including waterlogging (WL). The introduction of stress-inducible genes into wheat remains difficult because of low transformation and plant regeneration efficiencies and expression variability and instability. Earlier, we found two cDNAs encoding WL stress-responsive wheat pathogenesis-related proteins 1.2 (TaBWPR-1.2), TaBWPR-1.2#2 and TaBWPR-1.2#13. Using microprojectile bombardment, both cDNAs were introduced into “Bobwhite”. Despite low transformation efficiency, four independent T2 homozygous lines for each gene were isolated, where transgenes were ubiquitously and variously expressed. The highest transgene expression was obtained in Ubi:TaBWPR-1.2#2 L#11a and Ubi:TaBWPR-1.2#13 L#4a. Using quantitative proteomics, the root proteins of L#11a were analyzed to explore possible physiological pathways regulated by TaBWPR-1.2 under normal and waterlogged conditions. In L#11a, the abundance of proteasome subunit alpha type-3 decreased under normal conditions, whereas that of ferredoxin precursor and elongation factor-2 increased under waterlogged conditions in comparison with normal plants. Proteomic results suggest that L#11a is one of the engineered wheat plants where TaBWPR-1.2#2 is most probably involved in proteolysis, protein synthesis and alteration in the energy pathway in root tissues via the above proteins in order to gain metabolic adjustment to WL.

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.

Phellogen (cork cambium) usually produces cork tissue, but when flooded it produces secondary aerenchyma, comprising living cells with non-suberized walls in the stems, roots, and root nodules of some Fabaceae. In the cell walls of cork tissues, the plant hormone abscisic acid (ABA), promotes suberin deposition. Thus, ABA may decrease in flooded tissues, where secondary aerenchyma cells are developing. Here, we investigated whether ABA is involved in the formation of aerenchyma in soybean (Glycine max) hypocotyls when flooded. Hypocotyls flooded with water produced a large amount of secondary aerenchyma, and were highly porous. On the other hand, application of 1.0 μM ABA suppressed the enlargement of phellogen-derived cells, thereby suppressing subsequent gas space formation, and then almost completely inhibited aerenchyma development. Berberine-aniline blue staining indicated that not only elongated cells in the secondary aerenchyma but also packed cells, which were formed under flooding with ABA, contained no suberized cell walls. Compared to non-flooded plants, the endogenous ABA concentration in the flooded hypocotyls was decreased to 50% within 24 hr, and the low level was maintained for at least 72 hr. In addition, phellogen developed at 48 hr after flooding and secondary aerenchyma was observed at 72 hr. These results indicate that secondary aerenchyma formation requires a decrease in negative regulator ABA in soybean plants, that is, ABA inhibits elongation of cells derived from phellogen in secondary aerenchyma formation such as internodal cell elongation of floating rice stems.

The aims of this study were to detect plasma-membrane intrinsic protein type 2 (PIP2) genes of soybean (cv. Enrei) and to analyze mRNA levels of these genes under normoxic (control) and hypoxic conditions. A sequence similarity search with cDNA sequences in soybean genome revealed three putative aquaporin genes with high homology to GmPIP2;2. The genes were designated GmPIP2 genes. The mRNA levels in roots of soybean seedlings were measured at 3, 6, 12, and 27 hr after hypoxic stress onset. The mRNA levels of all GmPIP2s showed clear diurnal changes in the control, meanwhile, those under hypoxic conditions were significantly down-regulated even at 3 hr after stress onset. These results suggest that the four GmPIP2 genes are transcriptionally co-regulated by the diurnal change and oxygen concentration in the surrounding environment, and the transcriptional regulation may be involved in adjustment of water-transport in roots of soybean seedlings.

Here, we present the data from a comparative physiology and proteomics approach used to analyze the response of two wheat genotypes (SERI M 82 (SE) and SW89.5193/kAu2 (SW)) with contrasting responses to drought stress. Proteomic analysis resulted in identification of 49 unique proteins with significant change in abundance (2-fold) under water shortage in roots and leaves. Gene ontology analysis of drought-responsive proteins (DRPs) suggested an induction of proteins related to cell wall biogenesis, ATP synthesis, photosynthesis, and carbohydrate/energy metabolism in leaves under stress condition. A large fraction of root proteins were identified to be involved in defense and oxidative stress response. In addition, a significant change was detected in proteins related to protein synthesis, ATP synthesis, and germin-like proteins in response to drought stress. A detailed analysis of this data may be obtained from Ref. [1].

The supernodulating variety “Sakukei 4”, which has improved growth and yield, was recently developed. To evaluate its physiological traits related to the high productivity, we compared dry matter production, nitrogen (N) accumulation and N utilization in Sakukei 4 with those in the parental normally nodulating varieties, Enrei and Tamahomare, and a nonnodulating line, En1282, in pot experiments. The seed yield of Sakukei 4 was similar to that of Enrei and Tamahomare.Leaf area and relative ureide abundance in xylem sap were maintained for longer growth period in Sakukei 4 and Tamahomare than in Enrei. The total amount of nodule N2fixation at maturity was also larger in Sakukei 4 andTamahomare than in Enrei and En1282. In En1282 and Enrei, a larger part of N accumulated in leaves and stems before seed maturation was translocated to seeds during seed filling. However, Sakukei 4 and Tamahomare, more N tended to remain in leaves and stems at maturity. These observations suggested that the physiological traits of dry-matter accumulation and N utilization in Sakukei 4 were quite similar to those in Tamahomare, despite the difference in nodulation. N use efficiency for dry matter production (NUED) was lower in Sakukei 4 than in Enrei and Tamahomare, probably due to the energy cost for sustaining a greater number and mass of nodules. This observation indicated that the low NUED of Sakukei 4 impairs its productivity and seed yield, and therefore Sakukei 4 could not exceed Enrei or Tamahomare in seed productivity.

The rate of water uptake by seeds is assumed to be an important factor affecting the susceptibility of seeds to flooding injury, but the traits which could contribute to restricting rapid imbibition by seeds remain undetermined in yellow-seeded soybeans. This study was conducted to determine the possible factors controlling the rate of imbibition in soybeans with yellow seed coats. The imbibition behavior of two yellow-seeded cultivars, Tamahomare and Tachinagaha, with different flooding susceptibilities was examined in relation to initial seed moisture content, the hydration location of the seed surface during imbibition, and the state of the seed coat. Low seed moisture increased the water uptake by Tamahomare intact seeds and even allowed substantially faster imbibition than occurred in its embryos, while in Tachinagaha seed moisture content had little influence on seed imbibition. This rapid imbibition by low-moisture Tamahomare seeds was not due to alterations in the permeability of the seed coat nor in water uptake by the embryo, but rather to increased movement of water along the abaxial sides of the cotyledons. The seed coat of Tamahomare loosened readily upon submergence whilst that of Tachinagaha rather tightly adhered to the embryo, suggesting that the seed coat of Tamahomare adheres very loosely to the embryo and may aid in conducting water laterally between the seed coat and embryo. The degree of adherence of the coat to the embryo and/or the ease with which the coat can be loosened upon hydration appear to play a crucial role in determining the rate of water uptake in yellow-seeded soybeans.

In vitro pollen germination experiment using agar plates showed that the growth under high nitrogen conditions enhanced the damage to pollen germination ability caused by the cooling at the young microspore stage. To clarify the physiological factors related to this damage to pollen germination, we performed the comparative proteome analysis of mature anthers and identified proteins that were changed by high nitrogen conditions or high nitrogen plus cooling conditions. Proteins were extracted from mature anther samples and separated by two-dimensional polyacrylamide gel electrophoresis. By comparing anther protein maps of the samples collected from the plants grown under standard nitrogen conditions, high nitrogen conditions and high nitrogen plus cooling conditions, we found 11 protein spots, which varied with the treatment. These protein spots were identified based on the rice proteome database and/or peptide mass fingerprinting (PMF) analysis after digestion with trypsin. Digested samples were analyzed by matrix-assisted laser desorption/ionization-time flight mass spectrometry to produce PMF data. Database searches using these PMF data revealed the identities of 9 proteins. Seven of these proteins were polypeptides involved in cell elongation, stress responses and sugar metabolism. The relation between the fluctuations of these proteins and the decrease in pollen germination are discussed.

Soybean, which is rich in protein and oil, is cultivated in several climatic zones; however, its growth is markedly decreased by flooding. Proteomics is a useful tool for understanding the flooding-response mechanism in soybean. Subcellular proteomics has the potential to elucidate localized cellular responses and investigate communications among subcellular components during plant growth and during stress. Under flooding, proteins related to signaling, stress and the antioxidative system are increased in the plasma membrane; scavenging enzymes for reactive-oxygen species are suppressed in the cell wall; protein translation is suppressed through inhibition of proteins related to preribosome biogenesis and mRNA processing in the nucleus; levels of proteins involved in the electron transport chain are reduced in the mitochondrion; and levels of proteins related to protein folding are decreased in the endoplasmic reticulum. This review discusses the advantages of a gel-free/label-free proteomic technique and methods of plant subcellular purification. It also summarizes cellular events in soybean under flooding and discusses future prospects for generation of flooding-tolerant soybean.

The green rice leafhopper, Nephotettix cincticeps, is a vascular bundle feeder that discharges watery and gelling saliva during the feeding process. To understand the potential functions of saliva for successful and safe feeding on host plants, we analyzed the complexity of proteinaceous components in the watery saliva of N. cincticeps. Salivary proteins were collected from a sucrose diet that adult leafhoppers had fed on through a membrane of stretched parafilm. Protein concentrates were separated using SDS-PAGE under reducing and non-reducing conditions. Six proteins were identified by a gas-phase protein sequencer and two proteins were identified using LC-MS/MS analysis with reference to expressed sequence tag (EST) databases of this species. Full -length cDNAs encoding these major proteins were obtained by rapid amplification of cDNA ends-PCR (RACE-PCR) and degenerate PCR. Furthermore, gel-free proteome analysis that was performed to cover the broad range of salivary proteins with reference to the latest RNA-sequencing data from the salivary gland of N. cincticeps, yielded 63 additional protein species. Out of 71 novel proteins identified from the watery saliva, about 60 % of those were enzymes or other functional proteins, including GH5 cellulase, transferrin, carbonic anhydrases, aminopeptidase, regucalcin, and apolipoprotein. The remaining proteins appeared to be unique and species- specific. This is the first study to identify and characterize the proteins in watery saliva of Auchenorrhyncha species, especially sheath-producing, vascular bundle-feeders.

We elucidated the genome sequence of Glycine max cv. Enrei to provide a reference for characterization of Japanese domestic soybean cultivars. The whole genome sequence obtained using a next-generation sequencer was used for reference mapping into the current genome assembly of G. max cv. Williams 82 obtained by the Soybean Genome Sequencing Consortium in the USA. After sequencing and assembling the whole genome shotgun reads, we obtained a data set with about 928 Mbs total bases and 60,838 gene models. Phylogenetic analysis provided glimpses into the ancestral relationships of both cultivars and their divergence from the complex that include the wild relatives of soybean. The gene models were analyzed in relation to traits associated with anthocyanin and flavonoid biosynthesis and an overall profile of the proteome. The sequence data are made available in DAIZUbase in order to provide a comprehensive informatics resource for comparative genomics of a wide range of soybean cultivars in Japan and a reference tool for improvement of soybean cultivars worldwide.

Herbal medicine is a clinical practice of utilizing medicinal plant derivatives for therapeutic purposes. It has an enduring history worldwide and plays a significant role in the fight against various diseases. Herbal drug combinations often exhibit synergistic therapeutic action compared with single-constituent dosage, and can also enhance the cytotoxicity induced by chemotherapeutic drugs. To explore the mechanism underlying the pharmacological action of herbs, proteomic approaches have been applied to the physiology of medicinal plants and its effects on animals. This review article focuses on the existing proteomics-based medicinal plant research and discusses the following topics: (i) plant metabolic pathways that synthesize an array of bioactive compounds; (ii) pharmacological action of plants tested using in vivo and in vitro studies; and (iii) the application of proteomic approaches to indigenous plants with scarce sequence information. The accumulation of proteomic information in a biological or medicinal context may help in formulating the effective use of medicinal plants.

BACKGROUND: Flooding significantly reduces the growth and grain yield of soybean plants. Proteomic and biochemical techniques were used to determine whether the function of cotyledon and root is altered in soybean under flooding stress. RESULTS: Two-day-old soybean plants were flooded for 2 days, after which the proteins from root and cotyledon were extracted for proteomic analysis. In response to flooding stress, the abundance of 73 and 28 proteins was significantly altered in the root and cotyledon, respectively. The accumulation of only one protein, 70 kDa heat shock protein (HSP70) (Glyma17g08020.1), increased in both organs following flooding. The ratio of protein abundance of HSP70 and biophoton emission in the cotyledon was higher than those detected in the root under flooding stress. Computed tomography and elemental analyses revealed that flooding stress decreases the number of calcium oxalate crystal the cotyledon, indicating calcium ion was elevated in the cotyledon under flooding stress. CONCLUSION: These results suggest that calcium might play one role through HSP70 in the cotyledon under flooding stress.