Comparative metabolomics in Glycine max and Glycine soja under salt stress to reveal the phenotypes of their offspring

Transcriptome and metabolome analyses reveal the regulatory role of MdPYL9 in drought resistance in apple

BACKGROUND

The mechanisms by which the apple MdPYL9 gene mediates the response to drought stress remain unclear. Here, transcriptome and metabolome analyses of apple plants under drought were used to investigate the mechanisms by which MdPYL9 regulates the response to drought stress in apple. MdPYL9-overexpressed transgenic and non-transgenic apple histoculture seedlings were rooted, transplanted, and subjected to drought treatments to clarify the mechanisms underlying the responses of apples to drought stress through phenotypic observations, physiological and biochemical index measurements, and transcriptomic and metabolomic analyses.

RESULTS

Under drought stress treatment, transgenic plants were less affected by drought stress than non-transgenic plants. Decreases in the net photosynthetic rate, stomatal conductance, and transpiration rate of transgenic apple plants were less pronounced in transgenic plants than in non-transgenic plants, and increases in the intercellular CO2 concentration were less pronounced in transgenic plants than in non-transgenic plants. The relative electrical conductivity and content of malondialdehyde, superoxide anion, and hydrogen peroxide were significantly lower in transgenic plants than in non-transgenic plants, and the chlorophyll content and activities of antioxidant enzymes (superoxide dismutase, peroxidase, and catalase) were significantly higher in transgenic plants than in non-transgenic plants. The number of differentially expressed genes (DEGs) involved in the response to drought stress was lower in transgenic plants than in non-transgenic plants, and the most significant and highly annotated DEGs in the transgenic plants were involved in the flavonoid biosynthesis pathway, and the most significant and highly annotated DEGs in control plants were involved in the phytohormone signal transduction pathway. The number of differentially accumulated metabolites involved in the response to drought stress was lower in transgenic plants than in non-transgenic plants, and up-regulated metabolites were significantly enriched in apigenin-7-O-glucoside in transgenic plants and in abscisic acid in non-transgenic plants. In the flavonoid biosynthetic pathway, the expression of genes encoding chalcone synthase (CHS) and chalcone isomerase (CHI) was more significantly down-regulated in non-transgenic plants than in transgenic plants, and the expression of the gene encoding 4-coumarate-CoA ligase (4CL) was more significantly up-regulated in transgenic plants than in non-transgenic plants, which resulted in the significant up-regulation of apigenin-7-O-glucoside in transgenic plants.

CONCLUSIONS

The above results indicated that the over-expression of MdPYL9 increased the drought resistance of plants under drought stress by attenuating the down-regulation of the expression of genes encoding CHS and CHI and enhancing the up-regulated expression of the gene encoding 4CL, which enhanced the content of apigenin-7-O-glucoside.

Comparative study of leaf nutrient reabsorption by two different ecotypes of wild soybean under low-nitrogen stress

Wild soybean (Glycine soja), the ancestor of cultivated soybean, has evolved into many ecotypes with different adaptations to adversity under the action of divergent evolution. Barren-tolerant wild soybean has developed adaptation to most nutrient-stress environments, especially with respect to low nitrogen (LN) conditions. This study describes the differences in physiological and metabolomic changes between common wild soybean (GS1) and barren-tolerant wild soybean(GS2) under LN stress. Compared with plants grown under the unstressed control (CK) conditions, the young leaves of barren-tolerant wild soybean under LN conditions maintained relatively stable chlorophyll, concentration and rates of photosynthesis and transpiration, as well as increased carotenoid content, whereas the net photosynthetic rate (P_N) of GS1 decreased significantly 0.64-fold (p < 0.05) in the young leaves of GS1. The ratio of internal to atmospheric CO₂ concentrations increased significantly 0.07-fold (p < 0.05), 0.09-fold (p < 0.05) in the young leaves of GS1 and GS2, respectively, and increased significantly 0.05-fold (p < 0.05) and 0.07-fold (p < 0.05) in the old leaves of GS1 and GS2, respectively, relative to the CK. The concentration of chlorophylls a and b decreased significantly 0.45-fold (p < 0.05), 0.13-fold (p > 0.05) in the young leaves of GS1 and GS2, respectively, and decreased significantly 0.74-fold (p < 0.01) and 0.60-fold (p < 0.01) in the old leaves of GS1 and GS2, respectively. Under LN stress, nitrate concentration in the young leaves of GS1 and GS2 decreased significantly 0.69- and 0.50-fold (p < 0.01), respectively, relative to CK, and decreased significantly 2.10-fold and 1.77-fold (p < 0.01) in the old leaves of GS1 and GS2, respectively. Barren-tolerant wild soybean increased the concentration of beneficial ion pairs. Under LN stress, Zn²⁺ significantly increased by 1.06- and 1.35-fold (p < 0.01) in the young and old leaves of GS2 (p < 0.01), but there was no significant change in GS1. The metabolism of amino acids and organic acids was high in GS2 young and old leaves, and the metabolites related to the TCA cycle were significantly increased. The 4-aminobutyric acid (GABA) concertation decreased significantly 0.70-fold (p < 0.05) in the young leaves of GS1 but increased 0.21-fold (p < 0.05) significantly in GS2. The relative concentration of proline increased significantly 1.21-fold (p < 0.01) and 2.85-fold (p < 0.01) in the young and old leaves of GS2. Under LN stress, GS2 could maintain photosynthesis rate and enhance the reabsorption of nitrate and magnesium in young leaves, compared to GS1. More importantly, GS2 exhibited increased amino acid and TCA cycle metabolism in young and old leaves. Adequate reabsorption of mineral and organic nutrients is an important strategy for barren-tolerant wild soybeans to survive under LN stress. Our research provides a new perspective on the exploitation and utilization of wild soybean resources.

Overexpression of LjPLT3 Enhances Salt Tolerance in Lotus japonicus

Intracellular polyols are used as osmoprotectants by many plants under environmental stress. However, few studies have shown the role of polyol transporters in the tolerance of plants to abiotic stresses. Here, we describe the expression characteristics and potential functions of Lotus japonicus polyol transporter LjPLT3 under salt stress. Using LjPLT3 promoter-reporter gene plants showed that LjPLT3 was expressed in the vascular tissue of L. japonicus leaf, stem, root, and nodule. The expression was also induced by NaCl treatment. Overexpression of LjPLT3 in L. japonicus modified the growth rate and saline tolerance of the transgenic plants. The OELjPLT3 seedlings displayed reduced plant height under both nitrogen-sufficient and symbiotic nitrogen fixation conditions when 4 weeks old. The nodule number of OELjPLT3 plants was reduced by 6.7–27.4% when 4 weeks old. After exposure to a NaCl treatment in Petri dishes for 10 days, OELjPLT3 seedlings had a higher chlorophyll concentration, fresh weight, and survival rate than those in the wild type. For symbiotic nitrogen fixation conditions, the decrease in nitrogenase activity of OELjPLT3 plants was slower than that of the wild type after salt treatment. Compared to the wild type, both the accumulation of small organic molecules and the activity of antioxidant enzymes were higher under salt stress. Considering the concentration of lower reactive oxygen species (ROS) in transgenic lines, we speculate that overexpression of LjPLT3 in L. japonicus might improve the ROS scavenging system to alleviate the oxidative damage caused by salt stress, thereby increasing plant salinity tolerance. Our results will direct the breeding of forage legumes in saline land and also provide an opportunity for the improvement of poor and saline soils.

Plant Metabolomics: An Overview of the Role of Primary and Secondary Metabolites against Different Environmental Stress Factors

Several environmental stresses, including biotic and abiotic factors, adversely affect the growth and development of crops, thereby lowering their yield. However, abiotic factors, e.g., drought, salinity, cold, heat, ultraviolet radiations (UVr), reactive oxygen species (ROS), trace metals (TM), and soil pH, are extremely destructive and decrease crop yield worldwide. It is expected that more than 50% of crop production losses are due to abiotic stresses. Moreover, these factors are responsible for physiological and biochemical changes in plants. The response of different plant species to such stresses is a complex phenomenon with individual features for several species. In addition, it has been shown that abiotic factors stimulate multi-gene responses by making modifications in the accumulation of the primary and secondary metabolites. Metabolomics is a promising way to interpret biotic and abiotic stress tolerance in plants. The study of metabolic profiling revealed different types of metabolites, e.g., amino acids, carbohydrates, phenols, polyamines, terpenes, etc, which are accumulated in plants. Among all, primary metabolites, such as amino acids, carbohydrates, lipids polyamines, and glycine betaine, are considered the major contributing factors that work as osmolytes and osmoprotectants for plants from various environmental stress factors. In contrast, plant-derived secondary metabolites, e.g., phenolics, terpenoids, and nitrogen-containing compounds (alkaloids), have no direct role in the growth and development of plants. Nevertheless, such metabolites could play a significant role as a defense by protecting plants from biotic factors such as herbivores, insects, and pathogens. In addition, they can enhance the resistance against abiotic factors. Therefore, metabolomics practices are becoming essential and influential in plants by identifying different phytochemicals that are part of the acclimation responses to various stimuli. Hence, an accurate metabolome analysis is important to understand the basics of stress physiology and biochemistry. This review provides insight into the current information related to the impact of biotic and abiotic factors on variations of various sets of metabolite levels and explores how primary and secondary metabolites help plants in response to these stresses.

Ecotype Division and Chemical Diversity of Cynomorium songaricum from Different Geographical Regions

Cynomorium songaricum is an important endangered plant with significant medicinal and edible values. However, the lack of resources and quality variation have limited the comprehensive developments and sustainable utilization of C. songaricum. Here, we evaluated the chemical and genetic traits of C. songaricum from the highly suitable habitat regions simulated with species distribution models. The PCA and NJ tree analyses displayed intraspecific variation in C. songaricum, which could be divided into two ecotypes: ecotype I and ecotype II. Furthermore, the LC-MS/MS-based metabolomic was used to identify and analyze the metabolites of two ecotypes. The results indicated that a total of 589 compounds were detected, 236 of which were significantly different between the two ecotypes. Specifically, the relative content and the kind of flavonoids were more abundant in ecotype I, which were closely associated with the medicinal activities. In contrast, amino acids and organic acids were more enriched in ecotype II, which may provide better nutritional quality and unique flavor. In summary, our findings demonstrate the ecotype division and chemical diversity of C. songaricum in China from different geographical regions and provide a reference for the development of germplasm and directed plant breeding of endangered medicinal plants.

Metabolite Profiling of Soy By-Products: A Comprehensive Approach

Soy is the major oilseed crop as soybeans are widely used to produce biofuel, food, and feed. Other parts of the plant are left on the ground after harvest. The accumulation of such by-products on the soil can cause environmental problems. This work presents for the first time a comprehensive metabolite profiling of soy by-products collected directly from the ground just after mechanical harvesting. A two-liquid-phase extraction using n-heptane and EtOH-H2O 7:3 (v/v) provided extracts with complete characterization by gas chromatography and ultra-high-performance liquid chromatography both coupled to time-of-flight mass spectrometry. A total of 146 metabolites, including flavones, flavonols, isoflavonoids, fatty acids, steroids, mono-, sesqui-, di-, and triterpenoids, were tentatively identified in soy by-products and soybeans. These proved to be sources of a wide range of bioactive metabolites, thus suggesting that they could be valorized while reducing potential environmental damage in line with a circular economy model.

Reprogramming of Plant Central Metabolism in Response to Abiotic Stresses: A Metabolomics View

Abiotic stresses rewire plant central metabolism to maintain metabolic and energy homeostasis. Metabolites involved in the plant central metabolic network serve as a hub for regulating carbon and energy metabolism under various stress conditions. In this review, we introduce recent metabolomics techniques used to investigate the dynamics of metabolic responses to abiotic stresses and analyze the trend of publications in this field. We provide an updated overview of the changing patterns in central metabolic pathways related to the metabolic responses to common stresses, including flooding, drought, cold, heat, and salinity. We extensively review the common and unique metabolic changes in central metabolism in response to major abiotic stresses. Finally, we discuss the challenges and some emerging insights in the future application of metabolomics to study plant responses to abiotic stresses.

Enhanced reactive oxygen detoxification occurs in salt-stressed soybean roots expressing GmSALT3

Soybean (Glycine max) is an important crop globally for food and edible oil production. Soybean plants are sensitive to salinity (NaCl), with significant yield decreases reported under saline conditions. GmSALT3 is the dominant gene underlying a major QTL for salt tolerance in soybean. GmSALT3 encodes a transmembrane protein belonging to the plant cation/proton exchanger (CHX) family, and is predominately expressed in root phloem and xylem associated cells under both saline and non-saline conditions. It is currently unknown through which molecular mechanism(s) the ER-localised GmSALT3 contributes to salinity tolerance, as its localisation excludes direct involvement in ion exclusion. In order to gain insights into potential molecular mechanism(s), we used RNA-seq analysis of roots from two soybean NILs (near isogenic lines); NIL-S (salt-sensitive, Gmsalt3), and NIL-T (salt-tolerant, GmSALT3), grown under control and saline conditions (200 mM NaCl) at three time points (0 h, 6 h, and 3 days). Gene ontology (GO) analysis showed that NIL-T has greater responses aligned to oxidation reduction. ROS were less abundant and scavenging enzyme activity was greater in NIL-T, consistent with the RNA-seq data. Further analysis indicated that genes related to calcium signalling, vesicle trafficking and Casparian strip (CS) development were upregulated in NIL-T following salt treatment. We propose that GmSALT3 improves the ability of NIL-T to cope with saline stress through preventing ROS overaccumulation in roots, and potentially modulating Ca2+ signalling, vesicle trafficking and formation of diffusion barriers.

Metabolite Profiles Provide Insights into Underlying Mechanism in Bupleurum (Apiaceae) in Response to Three Levels of Phosphorus Fertilization

Phosphorus (P) deficiency affects plant yield and quality, yet at the same time, excessive phosphorus application does not necessarily promote the growth of plants. How to maintain a balance between biomass accumulation and phosphorus application is a problem. Therefore, the purpose of this research was to explore the relationship between yield and quality of Bupleurum and phosphorus fertilization, based on three phosphorus fertilization levels (20 kg∙ha^-1; 10 kg∙ha^-1; and 0 kg∙ha^-1). We adopted gas chromatography-mass spectrometry to assess the response of primary metabolites of different plant tissues (flowers, main shoots, lateral shoots and roots) to phosphorus fertilization. At the same time, high-performance liquid chromatography was used to quantify saikosaponin A and saikosaponin D, the main active ingredients of Bupleurum. Our research showed that low phosphorus level application has a positive impact on the yield and quality of Bupleurum, especially the above-ground parts increasing the fresh weight of flowers and lateral shoots and the length of main shoots, and moreover, increasing the saikosaponins content in all above-ground parts while decreasing the content in roots which show no significance increase in fresh weight and length. However, high phosphorus level showed a negative impact as it decreases the saikosaponins content significantly in flowers and roots. Furthermore, phosphorus application changed the proportion of saikosaponins, promoting the content of saikosaponin A and inhibiting the content of saikosaponin D in most organs of Bupleurum. Therefore, we can say that high phosphorus application is not preferable to the yield and quality of Bupleurum. To identify the metabolic pathways and special key metabolites, a total of 73 metabolites were discovered, and four differential metabolites-ether, glycerol, chlorogenic and L-rhamnose-were considered to be the key metabolites of Bupleurum's response to phosphorus fertilization. Furthermore, Bupleurum's response to phosphorus fertilization was mainly related to metabolic pathways, such as starch and sucrose metabolism and galactose metabolism. Under the phosphorus level, the content of sugars, organic acids and their derivatives, polyols and their derivatives and alkyl were upregulated in flowers. Furthermore, the contents of compounds in the main shoot and lateral shoots showed the same upward trend, except glycosides and polyols and their derivatives.

Metabolomic Variability of Different Soybean Genotypes: β-Carotene-Enhanced (Glycine max), Wild (Glycine soja), and Hybrid (Glycine max × Glycine soja) Soybeans

We obtained a new hybrid soybean (Hybrid) by hybridizing β-carotene-enhanced soybean (BCE; Glycine max L.) containing the phytoene synthase-2A-carotene desaturase gene and wild-type soybean (Wild; Glycine soja). To investigate metabolic changes between variants, we performed metabolic profiling of leaves (three growth stages) and seeds. Multivariate analyses revealed significant metabolic differences between genotypes in seeds and leaves, with seeds showing accumulation of phytosterols, tocopherols, and carotenoids (BCE only), indicating co-induction of the methylerythritol 4-phosphate and mevalonic acid pathways. Additionally, Hybrid produced intermediate levels of carotenoids and high levels of amino acids. Principal component analysis revealed metabolic discrimination between growth stages of soybean leaves and identified differences in leaf groups according to different genotypes at 8, 12, and 16 weeks, with Wild showing higher levels of environmental stress-related compounds relative to BCE and Hybrid leaves. The metabolic profiling approach could be a useful tool to identify metabolic links in various soybean cultivars.

Physiological and comparative transcriptome analysis of leaf response and physiological adaption to saline alkali stress across pH values in alfalfa (Medicago sativa)

Soil salinization is a critical factor limiting growth and causing physiological dysfunction in plants. The damage from alkaline salt in most plants is significantly greater than that from neutral salt. However, there is still a lack of research on the action mechanism by which saline alkali stress on plants under the same salt concentration across different pH values. The present study examined the effects of different pH values (7.0, 8.0, 9.0, and 10.0) under the same salt concentration (200 mmolL^-1) on photosynthetic function, photoprotective mechanism, nitrogen metabolism, and osmotic regulation in alfalfa (Medicago sativa) leaves, including a transcriptomic analysis of changes in gene expression related to the above metabolic processes. The results showed that low pH saline alkali stress (pH 7.0 and 8.0) promoted chlorophyll synthesis in alfalfa leaves, and non-photochemical quenching (NPQ) and cyclic electron transfer (CEF) were promoted. There was no significant effect on plant growth or photochemical activity. The soluble sugar, proline, and soluble protein contents did not change significantly, and there was no obvious oxidative damage in alfalfa leaves. However, when pH increased to 9.0 and 10.0, KEGG enrichment analysis showed that photosynthesis (map00195) and nitrogen metabolism (map00910) were significantly enriched (P < 0.05), and PSII antenna protein coding genes were down-regulated under pH 9.0 and 10.0 treatments. The activities of PSII and PSI were decreased under high pH saline alkali stress, and the expression levels of the photosynthetic electron transporter-related genes PetA, PetB, petE, and petF were also significantly down-regulated. PSII was more sensitive to high pH saline alkali stress than PSI, and the PSII receptor side was more sensitive to high pH saline alkali stress than the PSII donor side. The activities of the oxygen-evolving complex (OEC) and PSI were significantly damaged only at pH 10.0. The activities of nitrate reductase (NR) and nitrite reductase (NiR), the expression levels of their genes, and the content of soluble protein were also decreased under pH 9.0 and 10.0 treatments. The inhibition of plant growth and oxidative damage to alfalfa leaves caused by high pH saline alkali stress were mainly related to the inhibition of photosynthesis (light energy absorption, electron transfer) and nitrogen metabolism (NO₃^- reduction). Under high pH saline alkali stress (pH 10.0), the photoprotection mechanisms such as CEF and NPQ were inhibited, which was also one of the important reasons for photoinhibition in alfalfa leaves. The accumulation of osmotic adjustment substances, such as soluble sugar and proline, was an important mechanism by which alfalfa physiologically adapted to high pH alkaline salt stress.

Integrated transcriptomics and metabolomics analysis to characterize alkali stress responses in canola (Brassica napus L.)

BACKGROUND

Soil salinization is a major constraint limiting agricultural development and affecting crop growth and productivity, especially in arid and semi-arid regions. Understanding the molecular mechanism of the adaptability of canola to salt stress is very important to improve the salt tolerance of canola and promote its cultivation in saline alkali soil.

RESULTS

To identify the metabolomic and transcriptomic mechanisms of canola under alkaline salt stress, we collected roots of control (no salt treatment) and 72 h Na₂CO₃-stressed canola seedlings (hydroponics) for metabolic profiling of metabolites, supplemented with RNA-Seq analysis and real-time quantitative PCR validation. Metabolomic analysis showed that the metabolites of amino acids and fatty acids were higher accumulated under alkaline salt stress, including L-proline, L-glutamate, L-histidine, L-phenylalanine, L-citrulline, L-tyrosine, L-saccharopine, L-tryptophan, linoleic acid, dihomo gamma linolenic acid, alpha linolenic acid, Eric acid, oleic acid and neuronic acid, while the metabolism of carbohydrate (sucrase, alpha, alpha trehalose), polyol (ribitol), UDP-D-galactose, D-mannose, D-fructose and D-glucose 6-phosphate decreased. Transcriptomic and metabolomic pathway analysis indicated that carbohydrate metabolism may not play an important role in the resistance of canola to alkaline salt stress. Organic acid metabolism (fatty acid accumulation) and amino acid metabolism are important metabolic pathways in the root of canola under alkaline salt stress.

CONCLUSIONS

These results suggest that the genes and metabolites involved in fatty acid metabolism and amino acids metabolism in roots of canola may regulate salt tolerance of canola seedlings under alkaline salt stress, which improves our understanding of the molecular mechanisms of salt tolerance in canola.

Integrated Metabolomic and Transcriptomic Analysis Reveals the Flavonoid Regulatory Network by Eutrema EsMYB90

Flavonoids are representative secondary metabolites with different metabolic functions in plants. Previous study found that ectopic expression of EsMYB90 from Eutremasalsugineum could strongly increase anthocyanin content in transgenic tobacco via regulating the expression of anthocyanin biosynthesis genes. In the present research, metabolome analysis showed that there existed 130 significantly differential metabolites, of which 23 metabolites enhanced more than 1000 times in EsMYB90 transgenic tobacco leaves relative to the control, and the top 10 of the increased metabolites included caffeic acid, cyanidin O-syringic acid, myricetin and naringin. A total of 50 markedly differential flavonoids including flavones (14), flavonols (13), flavone C-glycosides (9), flavanones (7), catechin derivatives (5), anthocyanins (1) and isoflavone (1) were identified, of which 46 metabolites were at a significantly enhanced level. Integrated analysis of metabolome and transcriptome revealed that ectopic expression of EsMYB90 in transgenic tobacco leaves is highly associated with the prominent up-regulation of 16 flavonoid metabolites and the corresponding 42 flavonoid biosynthesis structure genes in phenylpropanoid/flavonoid pathways. Dual luciferase assay documented that EsMYB90 strongly activated the transcription of NtANS and NtDFR genes via improving their promoter activity in transiently expressed tobacco leaves, suggesting that EsMYB90 functions as a key regulator on anthocyanin and flavonoid biosynthesis. Taken together, the crucial regulatory role of EsMYB90 on enhancing many flavonoid metabolite levels is clearly demonstrated via modulating flavonoid biosynthesis gene expression in the leaves of transgenic tobacco, which extends our understanding of the regulating mechanism of MYB transcription factor in the phenylpropanoid/flavonoid pathways and provides a new clue and tool for further investigation and genetic engineering of flavonoid metabolism in plants.

Crucial Cell Signaling Compounds Crosstalk and Integrative Multi-Omics Techniques for Salinity Stress Tolerance in Plants

In the era of rapid climate change, abiotic stresses are the primary cause for yield gap in major agricultural crops. Among them, salinity is considered a calamitous stress due to its global distribution and consequences. Salinity affects plant processes and growth by imposing osmotic stress and destroys ionic and redox signaling. It also affects phytohormone homeostasis, which leads to oxidative stress and eventually imbalances metabolic activity. In this situation, signaling compound crosstalk such as gasotransmitters [nitric oxide (NO), hydrogen sulfide (H2S), hydrogen peroxide (H2O2), calcium (Ca), reactive oxygen species (ROS)] and plant growth regulators (auxin, ethylene, abscisic acid, and salicylic acid) have a decisive role in regulating plant stress signaling and administer unfavorable circumstances including salinity stress. Moreover, recent significant progress in omics techniques (transcriptomics, genomics, proteomics, and metabolomics) have helped to reinforce the deep understanding of molecular insight in multiple stress tolerance. Currently, there is very little information on gasotransmitters and plant growth regulator crosstalk and inadequacy of information regarding the integration of multi-omics technology during salinity stress. Therefore, there is an urgent need to understand the crucial cell signaling crosstalk mechanisms and integrative multi-omics techniques to provide a more direct approach for salinity stress tolerance. To address the above-mentioned words, this review covers the common mechanisms of signaling compounds and role of different signaling crosstalk under salinity stress tolerance. Thereafter, we mention the integration of different omics technology and compile recent information with respect to salinity stress tolerance.

Effect of salt stress on the growth, mineral contents, and metabolite profiles of spinach

BACKGROUND

Increased soil salt concentration decreases productivity and changes the physiological and chemical properties of plants. Various omics technologies have been used to understand the salt response in plants but overall changes in the metabolite profiles of spinach (Spinacia oleracea L.) under salt stress have not been studied. In this article, therefore, the changes in mineral and metabolite profiles of spinach plants cultivated with different NaCl concentrations of 0-200 mmol L^-1 in the irrigation water were analyzed to investigate the effect of salt stress on nutritional quality.

RESULTS

Increasing NaCl concentration decreased plant growth due to mineral imbalance. The amounts of minerals (K⁺ , Ca²⁺ , and Fe²⁺ ) were reduced with increasing NaCl concentration, resulting in altered ratios of Na⁺ :K⁺ and Na⁺ :Ca²⁺ . The change in the mineral ratios due to NaCl irrigation led to a decrease in the height and an increase in the weight of spinach. Moreover, the profiles of 32 metabolites, including flavonoids, amino acids, acidic compounds, sugars, and lipid-related compounds, were altered by NaCl irrigation; most of them showed decreased levels. In particular, at 200 mmol L^-1 NaCl, the levels of sucrose, glutamic acid, hexose sugars, and acidic compounds significantly decreased upon NaCl irrigation. Based on these metabolites, a salt-stress-related spinach metabolomic pathway was proposed.

CONCLUSION

Sodium chloride irrigation increased mineral imbalance, resulting in decreased plant growth, and the levels of most metabolites involved in energy production, sensory quality, and health benefits decreased with NaCl irrigation. The results suggest that NaCl irrigation negatively affects the nutritional quality of spinach. © 2020 Society of Chemical Industry.

A Balance between the Activities of Chloroplasts and Mitochondria Is Crucial for Optimal Plant Growth

Energy metabolism in plant cells requires a balance between the activities of chloroplasts and mitochondria, as they are the producers and consumers of carbohydrates and reducing equivalents, respectively. Recently, we showed that the overexpression of Arabidopsis thaliana purple acid phosphatase 2 (AtPAP2), a phosphatase dually anchored on the outer membranes of chloroplasts and mitochondria, can boost the plant growth and seed yield of Arabidopsis thaliana by coordinating the activities of both organelles. However, when AtPAP2 is solely overexpressed in chloroplasts, the growth-promoting effects are less optimal, indicating that active mitochondria are required for dissipating excess reducing equivalents from chloroplasts to maintain the optimal growth of plants. It is even more detrimental to plant productivity when AtPAP2 is solely overexpressed in mitochondria. Although these lines contain high level of adenosine triphosphate (ATP), they exhibit low leaf sucrose, low seed yield, and early senescence. These transgenic lines can be useful tools for studying how hyperactive chloroplasts or mitochondria affect the physiology of their counterparts and how they modify cellular metabolism and plant physiology.

Metabolomics as a Tool to Study Underused Soy Parts: In Search of Bioactive Compounds

The valorization of agri-food by-products is essential from both economic and sustainability perspectives. The large quantity of such materials causes problems for the environment; however, they can also generate new valuable ingredients and products which promote beneficial effects on human health. It is estimated that soybean production, the major oilseed crop worldwide, will leave about 597 million metric tons of branches, leaves, pods, and roots on the ground post-harvesting in 2020/21. An alternative for the use of soy-related by-products arises from the several bioactive compounds found in this plant. Metabolomics studies have already identified isoflavonoids, saponins, and organic and fatty acids, among other metabolites, in all soy organs. The present review aims to show the application of metabolomics for identifying high-added-value compounds in underused parts of the soy plant, listing the main bioactive metabolites identified up to now, as well as the factors affecting their production.

Widely targeted metabolomics analysis reveals new biomarkers and mechanistic insights on chestnut (Castanea mollissima Bl.) calcification process

Chestnut calcification is a quality deterioration due to fast water loss, which has been of deep concern for chestnut quality control because its mechanism is unclear. In order to find out the different key metabolites and metabolic pathways related to the occurrence of chestnut calcification, in this study, liquid chromatography-tandem mass spectrometry (LC-MS/MS) based widely targeted metabolomics analysis was performed on chestnuts that were stored at 50%-55% (low relative humidity, LRH) at 25 °C and 85%-90% (high relative humidity, HRH) at 25 °C. A total of 611 metabolites were detected, and 55 differentially accumulated metabolites were identified as key metabolites involved in chestnut calcification process. The decrease in some monosaccharides accompanied with the increase in some unsaturated fatty acids indicated the degradation of chestnut cell wall and cell membrane during calcification process. As a stress response, amino acid metabolism related to membrane stability was significantly activated. In addition, the enhancement of phenylpropanoid biosynthesis pathway and flavonoid biosynthesis pathway characterized by the accumulation of lignin precursors and antioxidants suggested that lignification process was triggered in calcified chestnut. Therefore, the degradation and hardening of the cell wall and membrane damage were proposed to be associated with the calcification occurrence of chestnut. The metabolic profile of chestnut characterized in this study provided new insights into chestnut calcification process and laid a foundation for further chestnut quality control.

Plant metabolomics for studying the effect of two insecticides on comprehensive constituents of Lonicerae Japonicae Flos

Pesticides' overuse and misuse have been reported to induce ingredient variations in herbal medicine, which is now gaining attention in the medicinal field as a form of alternative medicine. To date, available studies on pesticide-induced ingredient variations of herbal medicine are limited only on a few compounds and remain most others unexamined. In this study, a plant metabolomics-based strategy was performed to systematically explore the effects of two frequently used insecticides on the comprehensive constituents of Lonicerae Japonicae Flos (LJF), the flower buds of Lonicera japonica Thunb. Field trials were designed on a cultivating plot of L. japonica with controls and treatments of imidacloprid (IMI) and compound flonicamid and acetamiprid (CFA). Unbiased metabolite profiling was conducted by ultra-high performance liquid chromatography/quadrupole-Orbitrap mass spectrometer. After data pretreatment by automatic extraction and screening, a data matrix of metabolite features was submitted for statistical analyses. Consequently, 29 metabolic markers, including chlorogenic acids, iridoids and organic acid-glucosides were obtained and characterized. The relative quantitative assay was subsequently performed to monitor their variations across flowering developments. This is the first study that systematically explored the insecticide-induced metabolite variations of LJF while taking into account the inherent variability of flowering development. The results were beneficial for holistic quality assessment of LJF and significant for guiding scientific use of pesticides in the large-scale cultivation.

Metabolomic Profiling of Drought-Tolerant and Susceptible Peanut (Arachis hypogaea L.) Genotypes in Response to Drought Stress

Peanut is frequently constrained by extreme environmental conditions such as drought. To reveal the involvement of metabolites, TAG 24 (drought-tolerant) and JL 24 (drought-sensitive) peanut genotypes were investigated under control and 20% PEG 6000-mediated water scarcity conditions at the seedling stage. Samples were analyzed by gas chromatography-mass spectrometry (GC-MS) to identify untargeted metabolites and targeted metabolites, i.e., polyamines and polyphenols by high-performance liquid chromatography (HPLC) and ultrahigh-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS), respectively. The principal component analysis (PCA), partial least-squares discriminant analysis (PLS-DA), heat map, and cluster analysis were applied to the metabolomics data obtained by the GC-MS technique to determine the important metabolites for drought tolerance. Among 46 resulting metabolites, pentitol, phytol, xylonic acid, d-xylopyranose, stearic acid, and d-ribose were important drought-responsive metabolites. Agmatine and cadaverine were present in TAG 24 leaves and roots, respectively, during water-deficit conditions and believed to be the potential polyamines for drought tolerance. Polyphenols such as syringic acid and vanillic acid were produced more in the leaves of TAG 24, while catechin production was high in JL 24 during stress conditions. Seven metabolic pathways, namely, galactose metabolism, starch and sucrose metabolism, fructose and mannose metabolism, pentose and glucuronate interconversion, propanoate metabolism, amino sugar and nucleotide sugar metabolism, and biosynthesis of unsaturated fatty acids were significantly affected by water-deficit conditions. This study provides valuable information about the metabolic response of peanut to drought stress and metabolites identified, which encourages further study by transcriptome and proteomics to improve drought tolerance in peanut.

1H NMR-based metabolomic study of the effects of flavonoids on citrinin production by Monascus

Monascus comprises purple-red molds. Various compounds can be obtained from these species, including statins and food-safe yellow, red, and orange pigments. However, the secondary metabolite citrinin, a mycotoxin, is produced during the late stages of growth. Citrinin biosynthesis should be reduced to apply Monascus pigments safely. Fortunately, this can be achieved by the addition of flavonoids (genistein, daidzein, apigenin, and kaempferol). However, the effects of these flavonoids on other metabolites remain unknown. Here, we report a ¹H NMR-based multivariate metabolomic analysis of the effects of flavonoids on mycotoxin citrinin production by Monascus. Fifteen metabolites involved in lysine and arginine biosynthesis and alanine, aspartate, glutamate, biotin, arginine, proline, and glutathione metabolism were detected. The reduction in glutamate, aspartate, biotin, and 2-phosphoglycerate content suggested their association with the citrinin reduction mechanism. This study identifies the citrinin production pathway in Monascus and will aid in the development of citrinin-control methods.

Enhancing Salt Tolerance of Plants: From Metabolic Reprogramming to Exogenous Chemical Treatments and Molecular Approaches

Plants grow on soils that not only provide support for root anchorage but also act as a reservoir of water and nutrients important for plant growth and development. However, environmental factors, such as high salinity, hinder the uptake of nutrients and water from the soil and reduce the quality and productivity of plants. Under high salinity, plants attempt to maintain cellular homeostasis through the production of numerous stress-associated endogenous metabolites that can help mitigate the stress. Both primary and secondary metabolites can significantly contribute to survival and the maintenance of growth and development of plants on saline soils. Existing studies have suggested that seed/plant-priming with exogenous metabolites is a promising approach to increase crop tolerance to salt stress without manipulation of the genome. Recent advancements have also been made in genetic engineering of various metabolic genes involved in regulation of plant responses and protection of the cells during salinity, which have therefore resulted in many more basic and applied studies in both model and crop plants. In this review, we discuss the recent findings of metabolic reprogramming, exogenous treatments with metabolites and genetic engineering of metabolic genes for the improvement of plant salt tolerance.

Metabotyping of different soybean genotypes and distinct metabolism in their seeds and leaves

The metabolome of three soybean genotypes, Glycine max Hwangkeum (elite or domesticated cultivar), Glycine max Napjakong (landrace or semi-wild cultivar) and Glycine soja Dolkong (wild cultivar), were characterized in seeds and leaves using a 1H NMR-based metabolomics approach. Expression of primary and secondary metabolites were different in seeds and leaves as well as amongst soybean genotypes. Different kaempferol glycosides were observed in the leaves but not in the seeds, and quercetin derivatives were found only in G. max Napjakong and G. soja Dolkong. Moreover, epicatechin was found only in the seeds of G. max Napjakong and G. soja Dolkong. These results demonstrate distinct adaptations of different soybean genotypes to given environmental conditions. The current study, therefore, provides useful information on global metabolic compositions that might be used to develop soybean-based products through better understanding of the metabolic phenotypes of existing soybean genotypes.

Comparative metabolic profiling of cultivated and wild black soybeans reveals distinct metabolic alterations associated with their domestication

Generally, cultivated black soybean (CBS) has been used as a major source of various nutrients for humans and animals. To assess the metabolic alterations induced by domestication in soybean, we performed a comprehensive metabolite profiling of 56 soybean varieties, including 28 CBS and 28 wild black soybean (WBS) varieties. A total of 48 metabolites were characterized, including 45 primary and 3 secondary metabolites, from CBS and WBS. The results of principal component analysis and hierarchical cluster analysis (HCA) revealed significant metabolic differences between CBS and WBS that were closely related to metabolic pathways. The results indicate that flavonoids correlated positively with phenylalanine, a precursor for phenylpropanoid biosynthesis; the contents of flavonoids and phenylpropanoids were higher in WBS. Pathway analysis revealed that CBS contained large amounts of TCA cycle intermediates, amino acids, and fatty acids as a result of increased energy metabolism, amino acid metabolism, and seed filling. The projection to latent structure method, using the partial least squares method, was applied to predict the flavonoid content in soybean seed, which indicated that sucrose, threonic acid, citric acid, and fatty acids are important in predicting the antioxidant content of samples. This work will provide important information for designing new soybean cultivars with enhanced nutritional and agricultural traits.

Applications of metabolomics in the research of soybean plant under abiotic stress

Qualitative and quantitative metabolomics analysis of all small-molecule metabolites in organisms is an emerging omics technology alongside genomics and proteomics. Plant metabolites are extremely diverse both within species and in terms of their physiological function. Plant metabolomics studies use mainly liquid/gas chromatography-mass spectrometry (LC/GC-MS) and nuclear magnetic resonance (NMR) techniques combined with chemometrics and multivariate statistical analysis to analyze plant metabolites, and metabolomics plays a key role in agricultural and food science research. In this review, we discuss the status of metabolomics in soybean in response to abiotic stresses such as drought, heat, salinity, flooding, chilling and heavy metal stresses and analyze the challenges and opportunities. Furthermore, the notable metabolites detected in response to different stresses are summarized to provide a reference for applications of metabolomics in soybean research.

Enhanced Salt Tolerance of Rhizobia-inoculated Soybean Correlates with Decreased Phosphorylation of the Transcription Factor GmMYB183 and Altered Flavonoid Biosynthesis

Soybean (Glycine max (L.) Merrill) is an important component of the human diet and animal feed, but soybean production is limited by abiotic stresses especially salinity. We recently found that rhizobia inoculation enhances soybean tolerance to salt stress, but the underlying mechanisms are unaddressed. Here, we used quantitative phosphoproteomic and metabonomic approaches to identify changes in phosphoproteins and metabolites in soybean roots treated with rhizobia inoculation and salt. Results revealed differential regulation of 800 phosphopeptides, at least 32 of these phosphoproteins or their homologous were reported be involved in flavonoid synthesis or trafficking, and 27 out of 32 are transcription factors. We surveyed the functional impacts of all these 27 transcription factors by expressing their phospho-mimetic/ablative mutants in the roots of composite soybean plants and found that phosphorylation of GmMYB183 could affect the salt tolerance of the transgenic roots. Using data mining, ChIP and EMSA, we found that GmMYB183 binds to the promoter of the soybean GmCYP81E11 gene encoding for a Cytochrome P450 monooxygenase which contributes to the accumulation of ononin, a monohydroxy B-ring flavonoid that negatively regulates soybean tolerance to salinity. Phosphorylation of GmMYB183 was inhibited by rhizobia inoculation; overexpression of GmMYB183 enhanced the expression of GmCYP81E11 and rendered salt sensitivity to the transgenic roots; plants deficient in GmMYB183 function are more tolerant to salt stress as compared with wild-type soybean plants, these results correlate with the transcriptional induction of GmCYP81E11 by GmMYB183 and the subsequent accumulation of ononin. Our findings provide molecular insights into how rhizobia enhance salt tolerance of soybean plants.

Comparative non-targeted metabolomic analysis reveals insights into the mechanism of rice yellowing

Yellowing of rice during storage is a highly concerned issue for managing rice quality whereas the yellowing mechanism is not clearly elucidated so far. Thus, the comparative untargeted metabolomic analysis was performed in this study. The results revealed that glycolysis pathway and tricarboxylic acid cycle (TCA) were significantly enhanced in yellowed rice, indicating the activated energy metabolism was trigged during the yellowing process. In addition, the increased aromatic compounds (4-hydroxycinnamic acid and benzoic acid) and their precursors (phenylalanine, tyrosine) suggested the activation of shikimate-phenylpropanoid biosynthesis in yellowed rice, which is an antioxidant defense related pathway. In particular, the pathways involved in the metabolism of glutamate and arginine also significantly altered in yellowed rice. Therefore, the enriched pathways of increased amino acids, sugars, sugar alcohols, and intermediates of the TCA cycle during yellowing process are proposed to be associated with the response of heat and dry induced by the yellowing process.

Comparative Metabolomic Analysis of Rapeseeds from Three Countries

Rapeseed is an important oilseed with proper fatty acid composition and abundant bioactive components. Canada and China are the two major rapeseed-producing countries all over the world. Meanwhile, Canada and Mongolia are major importers of rapeseed due to the great demand for rapeseed in China. To investigate the metabolites in rapeseeds from three countries, ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MS)-based metabolomics was employed to analyze rapeseeds from China, Canada, and Mongolia. As results, 67, 53, and 68 metabolites showed significant differences between Chinese and Canadian, Chinese and Mongolian, and Canadian and Mongolian rapeseeds, respectively. Differential metabolites were mainly distributed in the metabolic pathways including phenylpropanoid biosynthesis, flavone and flavonol biosynthesis, and ubiquinone and other terpenoid-quinone biosynthesis. Among the differential metabolites, contents of sinapate and sinapine were higher in Chinese rapeseeds, while the contents of brassicasterol, stigmasterol, and campestanol were higher in Canadian rapeseeds. These findings might provide insight into the metabolic characteristics of rapeseeds from three countries to guide processing and consumption of the products of rapeseed.

Identifying the metabolomics and physiological differences among Soja in the early flowering stage

Wild soybean (Glycine soja) and cultivated soybean (Glycine max) belong to the subgenus Soja. We investigated the photosynthetic activity, mineral nutrition and metabolomics of the salt-tolerant wild soybean (W2), salt-sensitive wild soybean (W1) and cultivated soybean (C) in the early flowering stage, with a focus on the physiological and cellular metabolism-related differences among Soja to reveal the adaptive mechanisms. The photosynthetic activity of W2 was greater than that of W1 and the Mg, Zn, Mo, Mn and B contents showed the same trend. Carbohydrate, polyol, organic acid and fatty acid contents, as well as the secondary metabolism, were greater in W2 than W1, while the amino acid metabolism was lower in W2 than W1. These levels could minimize damage and maximize survival and growth, which might be the mechanisms that W2 adapts under adverse environmental conditions. The photosynthetic activity of C was greater than that of W1 and C also contained more K, Zn and B. The metabolomics study indicated that carbohydrate and organic acid metabolism were relatively greater, while the amino acid content and secondary metabolism level were lower in C than W1. These were presumably the result of long-term breeding and domestication. This comparative study among Soja will help in increasing the understanding and protection of wild soybean resources, as well as the improvement and utilization of cultivated soybean.

Salinity stress response and 'omics' approaches for improving salinity stress tolerance in major grain legumes

Sustaining yield gains of grain legume crops under growing salt-stressed conditions demands a thorough understanding of plant salinity response and more efficient breeding techniques that effectively integrate modern omics knowledge. Grain legume crops are important to global food security being an affordable source of dietary protein and essential mineral nutrients to human population, especially in the developing countries. The global productivity of grain legume crops is severely challenged by the salinity stress particularly in the face of changing climates coupled with injudicious use of irrigation water and improper agricultural land management. Plants adapt to sustain under salinity-challenged conditions through evoking complex molecular mechanisms. Elucidating the underlying complex mechanisms remains pivotal to our knowledge about plant salinity response. Improving salinity tolerance of plants demand enriching cultivated gene pool of grain legume crops through capitalizing on 'adaptive traits' that contribute to salinity stress tolerance. Here, we review the current progress in understanding the genetic makeup of salinity tolerance and highlight the role of germplasm resources and omics advances in improving salt tolerance of grain legumes. In parallel, scope of next generation phenotyping platforms that efficiently bridge the phenotyping-genotyping gap and latest research advances including epigenetics is also discussed in context to salt stress tolerance. Breeding salt-tolerant cultivars of grain legumes will require an integrated "omics-assisted" approach enabling accelerated improvement of salt-tolerance traits in crop breeding programs.

Effect of Trichoderma velutinum and Rhizoctonia solani on the Metabolome of Bean Plants (Phaseolus vulgaris L.)

The common bean (Phaseolus vulgaris L.) is one of the most important food legume crops worldwide that is affected by phytopathogenic fungi such as Rhizoctonia solani. Biological control represents an effective alternative method for the use of conventional synthetic chemical pesticides for crop protection. Trichoderma spp. have been successfully used in agriculture both to control fungal diseases and to promote plant growth. The response of the plant to the invasion of fungi activates defensive resistance responses by inducing the expression of genes and producing secondary metabolites. The purpose of this work was to analyze the changes in the bean metabolome that occur during its interaction with pathogenic (R. solani) and antagonistic (T. velutinum) fungi. In this work, 216 compounds were characterized by liquid chromatography mass spectrometry (LC-MS) analysis but only 36 were noted as significantly different in the interaction in comparison to control plants and they were tentatively characterized. These compounds were classified as: two amino acids, three peptides, one carbohydrate, one glycoside, one fatty acid, two lipids, 17 flavonoids, four phenols and four terpenes. This work is the first attempt to determine how the presence of T. velutinum and/or R. solani affect the defense response of bean plants using untargeted metabolomics analysis.

Transcriptomic reprogramming in soybean seedlings under salt stress

To obtain a comprehensive understanding of transcriptomic reprogramming under salt stress, we performed whole-transcriptome sequencing on the leaf and root of soybean seedlings subjected to salt treatment in a time-course experiment (0, 1, 2, 4, 24, and 48 hr). This time series dataset enabled us to identify important hubs and connections of gene expressions. We highlighted the analysis on phytohormone signaling pathways and their possible crosstalks. Differential expressions were also found among those genes involved in carbon and nitrogen metabolism. In general, the salt-treated seedlings slowed down their photosynthetic functions and ramped up sugar catabolism to provide extra energy for survival. Primary nitrogen assimilation was shut down whereas nitrogen resources were redistributed. Overall, the results from the transcriptomic analyses indicate that the plant uses a multipronged approach to overcome salt stress, with both fast-acting, immediate physiological responses, and longer term reactions that may involve metabolic adjustment.

Simultaneous Quantification of 22 Glucosinolates in 12 Brassicaceae Vegetables by Hydrophilic Interaction Chromatography-Tandem Mass Spectrometry

Glucosinolates, which are unique to Brassicaceae vegetables, have diverse biological activities, including antimicrobial, antioxidant, and anticancer actions. In this study, we applied hydrophilic interaction chromatography-tandem mass spectrometry (HILIC-MS/MS) to the simultaneous quantification of 22 glucosinolates in 12 Brassicaceae vegetables, including pak choi, choy sum, Chinese cabbage, cauliflower, cabbage, broccoli, Kai Lan, Brussels sprouts, rocket salad, daikon radish, red cherry radish, and watercress. Significant differences in concentration and composition of glucosinolates were observed among these vegetables. Cabbage had the highest level of total glucosinolates (μg/g dry weight: 19 551.2 ± 1317.7), whereas Kai Lan had the lowest level (7611.3 ± 868.4). Aliphatic and indole glucosinolates were the major components in the 12 vegetables ranging from 76 to 100%, except watercress (37%). On the basis of the content of glucosinolates, the 12 vegetables were well distinguishable and classified according to their morphological taxonomy. This study presents a HILIC-MS/MS approach for quantification of glucosinolates, and demonstrates the potential of glucosinolate profiles for Brassicaceae species identification.

Photosynthetic characteristics and metabolic analyses of two soybean genotypes revealed adaptive strategies to low-nitrogen stress

Nitrogen is an essential macronutrient for plants and the common limiting factor for crop productivity worldwide. An effective approach to combat N deficiency and overuse is to understand the mechanism of low-nitrogen tolerance in plants and develop low-nitrogen-tolerant crop cultivars. Wild soybean has a high tolerance to poor environmental conditions, but, until now, no study has illustrated the mechanism of low-nitrogen tolerance at a metabolomic level. In this study, the photosynthetic characteristics and metabolomics of wild and cultivated soybean seedlings were analyzed, and the mechanism of wild soybean's low-nitrogen tolerance was explained using a sand culture experiment. Wild soybean was less affected by low-nitrogen stress than cultivated soybean as assessed by plant growth parameters and photosynthesis. The root length of wild soybean increased, and a high root-shoot ratio was maintained under low-nitrogen stress. Carotenoids accumulated, which contributed to its higher low-nitrogen tolerance. A total of 48 and 60 differentially accumulated metabolites were identified in leaves and roots, respectively, between the low-nitrogen stress and control groups. The ability of wild soybean to tolerate low nitrogen also resulted from its capability to enhance the TCA cycle, synthesize key amino acids, accumulate metabolites, such as soluble sugars and organic acids, and synthesize favorable secondary metabolites under low-nitrogen stress. The current results reveal the mechanism underlying wild soybean's high low-nitrogen tolerance and provide the methodology and theoretical basis for utilizing wild soybean, improving cultivated soybean, and studying the low-nitrogen tolerance of other plants.

Large Scale Proteomic Data and Network-Based Systems Biology Approaches to Explore the Plant World

The investigation of plant organisms by means of data-derived systems biology approaches based on network modeling is mainly characterized by genomic data, while the potential of proteomics is largely unexplored. This delay is mainly caused by the paucity of plant genomic/proteomic sequences and annotations which are fundamental to perform mass-spectrometry (MS) data interpretation. However, Next Generation Sequencing (NGS) techniques are contributing to filling this gap and an increasing number of studies are focusing on plant proteome profiling and protein-protein interactions (PPIs) identification. Interesting results were obtained by evaluating the topology of PPI networks in the context of organ-associated biological processes as well as plant-pathogen relationships. These examples foreshadow well the benefits that these approaches may provide to plant research. Thus, in addition to providing an overview of the main-omic technologies recently used on plant organisms, we will focus on studies that rely on concepts of module, hub and shortest path, and how they can contribute to the plant discovery processes. In this scenario, we will also consider gene co-expression networks, and some examples of integration with metabolomic data and genome-wide association studies (GWAS) to select candidate genes will be mentioned.

Quantitative Phosphoproteomic and Metabolomic Analyses Reveal GmMYB173 Optimizes Flavonoid Metabolism in Soybean under Salt Stress

Salinity causes osmotic stress to crops and limits their productivity. To understand the mechanism underlying soybean salt tolerance, proteomics approach was used to identify phosphoproteins altered by NaCl treatment. Results revealed that 412 of the 4698 quantitatively analyzed phosphopeptides were significantly up-regulated on salt treatment, including a phosphopeptide covering the serine 59 in the transcription factor GmMYB173. Our data showed that GmMYB173 is one of the three MYB proteins differentially phosphorylated on salt treatment, and a substrate of the casein kinase-II. MYB recognition sites exist in the promoter of flavonoid synthase gene GmCHS5 and one was found to mediate its recognition by GmMYB173, an event facilitated by phosphorylation. Because GmCHS5 catalyzes the synthesis of chalcone, flavonoids derived from chalcone were monitored using metabolomics approach. Results revealed that 24 flavonoids of 6745 metabolites were significantly up-regulated after salt treatment. We further compared the salt tolerance and flavonoid accumulation in soybean transgenic roots expressing the 35S promoter driven cds and RNAi constructs of GmMYB173 and GmCHS5, as well as phospho-mimic (GmMYB173S59D ) and phospho-ablative (GmMYB173S59A ) mutants of GmMYB173 Overexpression of GmMYB173S59D and GmCHS5 resulted in the highest increase in salt tolerance and accumulation of cyaniding-3-arabinoside chloride, a dihydroxy B-ring flavonoid. The dihydroxy B-ring flavonoids are more effective as anti-oxidative agents when compared with monohydroxy B-ring flavonoids, such as formononetin. Hence the salt-triggered phosphorylation of GmMYB173, subsequent increase in its affinity to GmCHS5 promoter and the elevated transcription of GmCHS5 likely contribute to soybean salt tolerance by enhancing the accumulation of dihydroxy B-ring flavonoids.

Metabolomics and its physiological regulation process reveal the salt-tolerant mechanism in Glycine soja seedling roots

Wild soybean (Glycine soja) is an excellent germplasm resource and has strong resistance and wide adaptability to different environments. Hence, the physiology and metabolomics characteristics of wild soybean under different types of salt stress were determined to improve understanding of salt-tolerant mechanisms of wild soybean in the field. Two types of wild soybean seedlings were exposed to two different types of salt stress for 14 d. The photosynthesis of wild soybean seedling extracts were analyzed using metabolomics based on gas chromatography-mass spectrometry. The wild soybean root extracts used metabolomics to quantify the metabolic changes and ion contents. The assimilative function of photosynthesis in salt-tolerant wild soybean was less inhibited than in common wild soybean, and it regulated accumulation of toxic ions and maintained the accumulation of K+ and Mg2+ to alleviate salt stress. Moreover, in resisting salt stress the salt-tolerant wild soybean has showed improved amino acid and carbohydrate and polyol metabolisms under neutral-salt stress and organic acid, amino acid and tricarboxylic acid metabolisms under alkali-salt stress. Our results provide valuable insights into the response of salt-tolerant wild soybean to two types of salt stress by linking stress-related physiological responses to changes in metabolites.

Discrimination of citrus fruits using FT-IR fingerprinting by quantitative prediction of bioactive compounds

High throughput screening of citrus samples containing elevated concentrations of total carotenoids, flavonoids, and phenolic compounds was accomplished using ultraviolet-visible spectroscopy and Fourier transform infrared (FT-IR) spectroscopy, combined with multivariate analysis. Principal component analysis and partial least squares discriminant analysis using FT-IR spectra were able to differentiate seven citrus fruit groups into three distinct clusters corresponding to their taxonomic relationship. Quantitative prediction modeling of total carotenoids, flavonoids, and phenolic compounds in citrus fruit was established using a partial least squares regression algorithm from the FT-IR spectra. The regression coefficients (R 2) of predicted and estimated values of total carotenoids, flavonoids, and phenolic compounds were all 0.99. The results indicated that accurate quantitative predictions of total carotenoids, flavonoids, and phenolic compounds were possible from citrus fruit FT-IR spectra, and that the resulting quantitative prediction model might be useful as a rapid selection tool for citrus fruits containing elevated carotenoids, flavonoids, and phenolic compounds.

Metabolomics analysis of Cajanus cajan L. seedlings unravelled amelioration of stress induced responses to salinity after halopriming of seeds

Soil salinity has become a major concern for agriculture. Such constraints not only reinforce the urgent need to understand the underlying mechanisms by which plants cope during salt stress but also to develop cost-effective and farmer friendly halopriming technique to alleviate the adverse effects of salinity to some extent. Metabolomics approach was used to explore different responses to physiological metabolites and pathway variations that occur during salt stress responses in Cajanus cajan L. var. Rabi and to understand the role of halopriming in ameliorating stress at the level of metabolite. Seedlings raised from non-primed and haloprimed seeds, grown in hydroponic solution, were subjected to different concentrations of NaCl. After 21 days, metabolites were extracted, derivatized and analyzed by GC-MS. The data were analysed by different multivariate analyses. Chemometric study of the identified metabolites indicated that the leaves responded most to NaCl induced stress than the stem and root with production of beta-cyano-L-alanine and also increased level of different compatible solutes. O-Acetylsalicylic was also found to increase in all the parts upon facing stress but, such upregulated metabolite production was downregulated in the leaves when the seeds were haloprimed before germination, although many of the metabolites, including beta-cyanoalanine, showed a trend of increase with increase in salt concentrations. Important metabolites produced by C. cajan seedlings in response to salinity were unravelled. Pre-germination haloprimimg of seeds resulted in amelioration of NaCl induced stress, as the levels of stress induced metabolites were lowered.

Comparison of Salt Tolerance in Soja Based on Metabolomics of Seedling Roots

Soybean is an important economic crop that is continually threatened by abiotic stresses, especially salt stress. Wild soybean is an important germplasm resource for the breeding of cultivated soybean. The root system plays a very important role in plant salt tolerance. To explore the salt tolerance-related mechanisms among Soja, we have demonstrated the seedling roots' growth and metabolomics in wild soybean, semi-wild soybean, and cultivated soybean under two types of salt stress by using gas chromatography-mass spectrometry. We characterized 47 kinds of differential metabolites under neutral salt stress, and isoleucine, serine, l-allothreonine, glutamic acid, phenylalanine, asparagines, aspartic acid, pentadecanoic acid, lignoceric acid, oleic acid, galactose, tagatose, d-arabitol, dihydroxyacetone, 3-hydroxybutyric acid, and glucuronic acid increased significantly in the roots of wild soybean seedlings. However, these metabolites were suppressed in semi-wild and cultivated soybeans. Amino acid, fatty acid, sugars, and organic acid synthesis and the secondary metabolism of antioxidants increased significantly in the roots of wild soybean seedling. Under alkaline salt stress, wild soybean contained significantly higher amounts of proline, glutamic acid, aspartic acid, l-allothreonine, isoleucine, serine, alanine, arachidic acid, oleic acid, cis-gondoic acid, fumaric acid, l-malic acid, citric acid, malonic acid, gluconic acid, 5-methoxytryptamine, salicylic acid, and fluorene than semi-wild and cultivated soybeans. Our study demonstrated that carbon and nitrogen metabolism, and the tricarboxylic acid (TCA) cycle and receiver operating characteristics (especially the metabolism of phenolic substances) of the seedling roots were important to resisting salt stress and showed a regular decreasing trend from wild soybean to cultivated soybean. The metabolomics's changes were critical factors in the evolution of salt tolerance among Soja. This study provides new insights into salt tolerance in soybean, and presents quantitative parameters for a salt tolerant soybean breeding system, which is conducive to the rational use and protection of wild soybean resources.

Metabolomic Analysis of Alfalfa (Medicago sativa L.) Root-Symbiotic Rhizobia Responses under Alkali Stress

Alkaline salts (e.g., NaHCO₃ and Na₂CO₃) causes more severe morphological and physiological damage to plants than neutral salts (e.g., NaCl and Na₂SO₄) due to differences in pH. The mechanism by which plants respond to alkali stress is not fully understood, especially in plants having symbotic relationships such as alfalfa (Medicago sativa L.). Therefore, a study was designed to evaluate the metabolic response of the root-nodule symbiosis in alfalfa under alkali stress using comparative metabolomics. Rhizobium-nodulized (RI group) and non-nodulized (NI group) alfalfa roots were treated with 200 mmol/L NaHCO₃ and, roots samples were analyzed for malondialdehydyde (MDA), proline, glutathione (GSH), superoxide dismutase (SOD), and peroxidase (POD) content. Additionally, metabolite profiling was conducted using gas chromatography combined with time-of-flight mass spectrometry (GC/TOF-MS). Phenotypically, the RI alfalfa exhibited a greater resistance to alkali stress than the NI plants examined. Physiological analysis and metabolic profiling revealed that RI plants accumulated more antioxidants (SOD, POD, GSH), osmolytes (sugar, glycols, proline), organic acids (succinic acid, fumaric acid, and alpha-ketoglutaric acid), and metabolites that are involved in nitrogen fixation. Our pairwise metabolomics comparisons revealed that RI alfalfa plants exhibited a distinct metabolic profile associated with alkali putative tolerance relative to NI alfalfa plants. Data provide new information about the relationship between non-nodulized, rhizobium-nodulized alfalfa and alkali resistance.

Metabolic Profiles Reveal Changes in Wild and Cultivated Soybean Seedling Leaves under Salt Stress

Clarification of the metabolic mechanisms underlying salt stress responses in plants will allow further optimization of crop breeding and cultivation to obtain high yields in saline-alkali land. Here, we characterized 68 differential metabolites of cultivated soybean (Glycine max) and wild soybean (Glycine soja) under neutral-salt and alkali-salt stresses using gas chromatography-mass spectrometry (GC-MS)-based metabolomics, to reveal the physiological and molecular differences in salt tolerance. According to comparisons of growth parameters under the two kinds of salt stresses, the level of inhibition in wild soybean was lower than in cultivated soybean, especially under alkali-salt stress. Moreover, wild soybean contained significantly higher amounts of phenylalanine, asparagine, citraconic acid, citramalic acid, citric acid and α-ketoglutaric acid under neutral-salt stress, and higher amounts of palmitic acid, lignoceric acid, glucose, citric acid and α-ketoglutaric acid under alkali-salt stress, than cultivated soybean. Further investigations demonstrated that the ability of wild soybean to salt tolerance was mainly based on the synthesis of organic and amino acids, and the more active tricarboxylic acid cycle under neutral-salt stress. In addition, the metabolite profiling analysis suggested that the energy generation from β-oxidation, glycolysis and the citric acid cycle plays important roles under alkali-salt stress. Our results extend the understanding of mechanisms involved in wild soybean salt tolerance and provide an important reference for increasing yields and developing salt-tolerant soybean cultivars.

Metabolic Effects of the pksCT Gene on Monascus aurantiacus Li As3.4384 Using Gas Chromatography--Time-of-Flight Mass Spectrometry-Based Metabolomics

Monascus spp. have been used for the production of natural pigments and bioactive compounds in China for several centuries. Monascus can also produce the mycotoxin citrinin, restricting its use. Disruption of the pksCT gene in Monascus aurantiacus Li AS3.4384 reduces citrinin production capacity of this strain (Monascus PHDS26) by over 98%. However, it is unclear how other metabolites of M. aurantiacus Li AS3.4384 (the wild-type strain) are affected by the pksCT gene. Here, we used metabolomic analyses to compare red yeast rice (RYR) metabolite profiles of the wild-type strain and Monascus PHDS26 at different stages of solid-state fermentation. A total of 18 metabolites forming components within the glycolysis, acetyl-CoA, amino acid, and tricarboxylic acid (TCA) cycle metabolic processes were found to be altered between the wild-type strain and Monascus PHDS26 at different stages of solid-state fermentation. Thus, these findings provide important insights into the metabolic pathways affected by the pksCT gene in M. aurantiacus.

Mechanisms of Soybean Roots' Tolerances to Salinity Revealed by Proteomic and Phosphoproteomic Comparisons Between Two Cultivars

Understanding molecular mechanisms underlying plant salinity tolerance provides valuable knowledgebase for effective crop improvement through genetic engineering. Current proteomic technologies, which support reliable and high-throughput analyses, have been broadly used for exploring sophisticated molecular networks in plants. In the current study, we compared phosphoproteomic and proteomic changes in roots of different soybean seedlings of a salt-tolerant cultivar (Wenfeng07) and a salt-sensitive cultivar (Union85140) induced by salt stress. The root samples of Wenfeng07 and Union85140 at three-trifoliate stage were collected at 0 h, 0.5 h, 1 h, 4 h, 12 h, 24 h, and 48 h after been treated with 150 mm NaCl. LC-MS/MS based phosphoproteomic analysis of these samples identified a total of 2692 phosphoproteins and 5509 phosphorylation sites. Of these, 2344 phosphoproteins containing 3744 phosphorylation sites were quantitatively analyzed. Our results showed that 1163 phosphorylation sites were differentially phosphorylated in the two compared cultivars. Among them, 10 MYB/MYB transcription factor like proteins were identified with fluctuating phosphorylation modifications at different time points, indicating that their crucial roles in regulating flavonol accumulation might be mediated by phosphorylated modifications. In addition, the protein expression profiles of these two cultivars were compared using LC MS/MS based shotgun proteomic analysis, and expression pattern of all the 89 differentially expressed proteins were independently confirmed by qRT-PCR. Interestingly, the enzymes involved in chalcone metabolic pathway exhibited positive correlations with salt tolerance. We confirmed the functional relevance of chalcone synthase, chalcone isomerase, and cytochrome P450 monooxygenase genes using soybean composites and Arabidopsis thaliana mutants, and found that their salt tolerance were positively regulated by chalcone synthase, but was negatively regulated by chalcone isomerase and cytochrome P450 monooxygenase. A novel salt tolerance pathway involving chalcone metabolism, mostly mediated by phosphorylated MYB transcription factors, was proposed based on our findings. (The mass spectrometry raw data are available via ProteomeXchange with identifier PXD002856).

Advanced development in phytochemicals analysis of medicine and food dual purposes plants used in China (2011-2014)

In 2011, we wrote a review for summarizing the phytochemical analysis (2006-2010) of medicine and food dual purposes plants used in China (Zhao et al., J. Chromatogr. A 1218 (2011) 7453-7475). Since then, more than 750 articles related to their phytochemical analysis have been published. Therefore, an updated review for the advanced development (2011-2014) in this topic is necessary for well understanding the quality control and health beneficial phytochemicals in these materials, as well as their research trends.

MET-XAlign: a metabolite cross-alignment tool for LC/MS-based comparative metabolomics

Liquid chromatography/mass spectrometry (LC/MS) metabolite profiling has been widely used in comparative metabolomics studies; however, LC/MS-based comparative metabolomics currently faces several critical challenges. One of the greatest challenges is how to effectively align metabolites across different LC/MS profiles; a single metabolite can give rise to multiple peak features, and the grouped peak features that can be used to construct a spectrum pattern of single metabolite can vary greatly between biochemical experiments and even between instrument runs. Another major challenge is that the observed retention time for a single metabolite can also be significantly affected by experimental conditions. To overcome these two key challenges, we present a novel metabolite-based alignment approach entitled MET-XAlign to align metabolites across LC/MS metabolomics profiles. MET-XAlign takes the deduced molecular mass and estimated compound retention time information that can be extracted by our previously published tool, MET-COFEA, and aligns metabolites based on this information. We demonstrate that MET-XAlign is able to cross-align metabolite compounds, either known or unknown, in LC/MS profiles not only across different samples but also across different biological experiments and different electrospray ionization modes. Therefore, our proposed metabolite-based cross-alignment approach is a great step forward and its implementation, MET-XAlign, is a very useful tool in LC/MS-based comparative metabolomics. MET-XAlign has been successfully implemented with core algorithm coding in C++, making it very efficient, and visualization interface coding in the Microsoft.NET Framework. The MET-XAlign software along with demonstrative data is freely available at http://bioinfo.noble.org/manuscript-support/met-xalign/ .

Comparative metabolic responses and adaptive strategies of wheat (Triticum aestivum) to salt and alkali stress

BACKGROUND

It is well known that salinization (high-pH) has been considered as a major environmental threat to agricultural systems. The aim of this study was to investigate the differences between salt stress and alkali stress in metabolic profiles and nutrient accumulation of wheat; these parameters were also evaluated to determine the physiological adaptive mechanisms by which wheat tolerates alkali stress.

RESULTS

The harmful effect of alkali stress on the growth and photosynthesis of wheat were stronger than those of salt stress. High-pH of alkali stress induced the most of phosphate and metal ions to precipitate; as a result, the availability of nutrients significantly declined. Under alkali stress, Ca sharply increased in roots, however, it decreased under salt stress. In addition, we detected the 75 metabolites that were different among the treatments according to GC-MS analysis, including organic acids, amino acids, sugars/polyols and others. The metabolic data showed salt stress and alkali stress caused different metabolic shifts; alkali stress has a stronger injurious effect on the distribution and accumulation of metabolites than salt stress. These outcomes correspond to specific detrimental effects of a highly pH environment.

CONCLUSIONS

Ca had a significant positive correlation with alkali tolerates, and increasing Ca concentration can immediately trigger SOS Na exclusion system and reduce the Na injury. Salt stress caused metabolic shifts toward gluconeogenesis with increased sugars to avoid osmotic stress; energy in roots and active synthesis in leaves were needed by wheat to develop salt tolerance. Alkali stress (at high pH) significantly inhibited photosynthetic rate; thus, sugar production was reduced, N metabolism was limited, amino acid production was reduced, and glycolysis was inhibited.