Botanical and biological pesticides elicit a similar Induced Systemic Response in tomato (Solanum lycopersicum) secondary metabolism

Functional characterization and structural basis of a reversible glycosyltransferase involves in plant chemical defence

Plants experience numerous biotic stresses throughout their lifespan, such as pathogens and pests, which can substantially affect crop production. In response, plants have evolved various metabolites that help them withstand these stresses. Here, we show that two specialized metabolites in the herbaceous perennial Belamcanda chinensis, tectorigenin and its glycoside tectoridin, have diverse defensive effects against phytopathogenic microorganisms and antifeeding effects against insect pest. We further functionally characterized a 7-O-uridine diphosphate glycosyltransferase Bc7OUGT, which catalyses a novel reversible glycosylation of tectorigenin and tectoridin. To elucidate the catalytic mechanisms of Bc7OUGT, we solved its crystal structure in complex with UDP and UDP/tectorigenin respectively. Structural analysis revealed the Bc7OUGT possesses a narrow but novel substrate-binding pocket made up by plentiful aromatic residues. Further structure-guided mutagenesis of these residues increased both glycosylation and deglycosylation activities. The catalytic reversibility of Bc7OUGT was also successfully applied in an one-pot aglycon exchange reaction. Our findings demonstrated the promising biopesticide activity of tectorigenin and its glycosides, and the characterization and mechanistic study of Bc7OUGT could facilitate the design of novel reversible UGTs to produce valuable glycosides with health benefits for both plants and humans.

Effect of nanopesticides (azoxystrobin and bifenthrin) on the phenolic content and metabolic profiles of strawberries (Fragaria × ananassa)

BACKGROUND

Nanoencapsulation has opened promising fields of innovation for pesticides. Conventional pesticides can cause side effects on plant metabolism. To date, the effect of nanoencapsulated pesticides on plant phenolic contents has not been reported.

RESULTS

In this study, a comparative evaluation of the phenolic contents and metabolic profiles of strawberries was performed for plants grown under controlled field conditions and treated with two separate active ingredients, azoxystrobin and bifenthrin, loaded into two different types of nanocarriers (Allosperse® polymeric nanoparticles and SiO2 nanoparticles). There were small but significant decreases of the total phenolic content (9%) and pelargonidin 3-glucoside content (6%) in strawberries treated with the nanopesticides. An increase of 31% to 125% was observed in the levels of gallic acid, quercetin, and kaempferol in the strawberries treated with the nanoencapsulated pesticides compared with the conventional treatments. The effects of the nanocarriers on the metabolite and phenolic profiles was identified by principal component analysis.

CONCLUSION

Overall, even though the effects of nanopesticides on the phenological parameters of strawberry plants were not obvious, there were significant changes to the plants at a molecular level. In particular, nanocarriers had some subtle effects on plant health and fruit quality through variations in total and individual phenolics in the fruits. Further research will be needed to assess the impact of diverse nanopesticides on other groups of plant metabolites. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Metabolomics-Based Mechanistic Insights into Revealing the Adverse Effects of Pesticides on Plants: An Interactive Review

In plant biology, metabolomics is often used to quantitatively assess small molecules, metabolites, and their intermediates in plants. Metabolomics has frequently been applied to detect metabolic alterations in plants exposed to various biotic and abiotic stresses, including pesticides. The widespread use of pesticides and agrochemicals in intensive crop production systems is a serious threat to the functionality and sustainability of agroecosystems. Pesticide accumulation in soil may disrupt soil-plant relationships, thereby posing a pollution risk to agricultural output. Application of metabolomic techniques in the assessment of the biological consequences of pesticides at the molecular level has emerged as a crucial technique in exposome investigations. State-of-the-art metabolomic approaches such as GC-MS, LC-MS/MS UHPLC, UPLC-IMS-QToF, GC/EI/MS, MALDI-TOF MS, and ¹H-HR-MAS NMR, etc., investigating the harmful effects of agricultural pesticides have been reviewed. This updated review seeks to outline the key uses of metabolomics related to the evaluation of the toxicological impacts of pesticides on agronomically important crops in exposome assays as well as bench-scale studies. Overall, this review describes the potential uses of metabolomics as a method for evaluating the safety of agricultural chemicals for regulatory applications. Additionally, the most recent developments in metabolomic tools applied to pesticide toxicology and also the difficulties in utilizing this approach are discussed.

Reactive oxygen species signaling is involved in melatonin-induced reduction of chlorothalonil residue in tomato leaves

Pesticide overuse has led to serious global concerns regarding food safety and environmental pollution. Although the reduction of pesticide residue is critical, our knowledge about induced pesticide metabolism in plants remains fragmentary. Melatonin (N-acetyl-5-methoxytryptamine) is an effective stress-relieving agent in both animals and plants, but little is known about the melatonin signaling mechanism and its effect on pesticide metabolism in plants. Here, we found that exogenous melatonin treatment significantly reduced chlorothalonil residue by 41 % but suppression of endogenous melatonin accumulation increased chlorothalonil residue in tomato leaves. Moreover, melatonin increased photosynthesis, Fv/Fm, Calvin cycle enzyme activity, antioxidant enzyme activity, glutathione pool, and RESPIRATORY BURST HOMOLOG1 (RBOH1) expression in tomato leaves. However, the upregulation of RBOH1, CYP724B2, GST1, GST2, GSH and ABC, the increased glutathione concentrations and the activity of detoxification enzymes due to melatonin treatment were all significantly attenuated by the treatment with an NADPH oxidase inhibitor and a ROS scavenger, indicating a clear relationship between the reduction of pesticide residue and induction in detoxifying enzymes and genes upon melatonin treatment in an apoplastic H₂O₂-dependent manner. These results reveal that melatonin-induced reduction in chlorothalonil residue is mediated by H₂O₂ signaling in tomato leaves.

Genomics, Proteomics, and Metabolomics Approaches to Improve Abiotic Stress Tolerance in Tomato Plant

To explore changes in proteins and metabolites under stress circumstances, genomics, proteomics, and metabolomics methods are used. In-depth research over the previous ten years has gradually revealed the fundamental processes of plants' responses to environmental stress. Abiotic stresses, which include temperature extremes, water scarcity, and metal toxicity brought on by human activity and urbanization, are a major cause for concern, since they can result in unsustainable warming trends and drastically lower crop yields. Furthermore, there is an emerging reliance on agrochemicals. Stress is responsible for physiological transformations such as the formation of reactive oxygen, stomatal opening and closure, cytosolic calcium ion concentrations, metabolite profiles and their dynamic changes, expression of stress-responsive genes, activation of potassium channels, etc. Research regarding abiotic stresses is lacking because defense feedbacks to abiotic factors necessitate regulating the changes that activate multiple genes and pathways that are not properly explored. It is clear from the involvement of these genes that plant stress response and adaptation are complicated processes. Targeting the multigenicity of plant abiotic stress responses caused by genomic sequences, transcripts, protein organization and interactions, stress-specific and cellular transcriptome collections, and mutant screens can be the first step in an integrative approach. Therefore, in this review, we focused on the genomes, proteomics, and metabolomics of tomatoes under abiotic stress.

The differential modulation of secondary metabolism induced by a protein hydrolysate and a seaweed extract in tomato plants under salinity

Climate change and abiotic stress challenges in crops are threatening world food production. Among others, salinity affects the agricultural sector by significantly impacting yield losses. Plant biostimulants have received increasing attention in the agricultural industry due to their ability to improve health and resilience in crops. The main driving force of these products lies in their ability to modulate plant metabolic processes involved in the stress response. This study's purpose was to investigate the effect of two biostimulant products, including a protein hydrolysate (Clever HX^®) and a seaweed extract with high amino acids content (Ascovip^®), and their combination, on the metabolomics profile of tomato crops grown under salt stress (150 mM NaCl). Several stress indicators (leaf relative water content, membrane stability index, and photosynthesis activity) and leaf mineral composition after salinity stress exposure were assessed to evaluate stress mitigation, together with growth parameters (shoot and root biomasses). After that, an untargeted metabolomics approach was used to investigate the mechanism of action of the biostimulants and their link with the increased resilience to stress. The application of the biostimulants used reduced the detrimental effect of salinity. In saline conditions, protein hydrolysate improved shoot dry weight while seaweed extracts improved root dry weight. Regarding stress indicators, the application of the protein hydrolysate was found to alleviate the membrane damage caused by salinity stress compared to untreated plants. Surprisingly, photosynthetic activity significantly improved after treatment with seaweed extracts, suggesting a close correlation between root development, root water assimilation capacity and photosynthetic activity. Considering the metabolic reprogramming after plant biostimulants application, protein hydrolysates and their combination with seaweed extracts reported a distinctive metabolic profile modulation, mainly in secondary metabolite, lipids and fatty acids, and phytohormones biosynthetic pathways. However, treatment with seaweed extract reported a similar metabolic reprogramming trend compared to salinity stress. Our findings indicate a different mechanism of action modulated by protein hydrolysate and seaweed extract, suggesting stronger activity as a stress mitigator of protein hydrolysate in tomato crops under salinity stress.

Role of foliar biostimulants (of plant origin) on grapevine adaptation to climate change

Heat waves and drought stress are typical aspects of current climate change, significantly affecting the grapevine physiology in many world growing areas. Biostimulants can play an important role in reducing the negative effects of climate change; that’s why this experiment was set up in order to test two new foliar biostimulants (protein hydrolysates of plant origin). The field experiment was carried out in 2017 and 2018 in Oltrepo pavese area (Lombardia region, northwest Italy, 270 m asl), on a six-year-old vineyard of V. vinifera L. cv. Merlot clone 181 grafted on Gravesac, Guyot trellis, 4,000 vines/ha and not irrigated. Two new protein hydrolysates of plant origin were sprayed twice, just after fruit set and 15 days later, by using 2.5 L/ha. Leaf proteomics and metabolomics were studied in 2017, while productive and qualitative data were recorded in both years at harvest (September 1st, 2017 and August 28th 2018). The most significant findings were: (a) the treatments slowed down the grape ripening, by stimulating vegetative activity and reducing sugar accumulation; (b) less heat and drought stress symptoms were observed in the canopies of treated vines, as compared to the control ones.

Bensulfuron-Methyl, Terbutylazine, and 2,4-D Butylate Disturb Plant Growth and Resistance by Deteriorating Rhizosphere Environment and Plant Secondary Metabolism in Wheat Seedlings

Frequent and improper use of herbicides disrupts a plant's metabolism, causing oxidative stress that degrades crop quality. However, few studies have examined the inhibitory effects of herbicides on plant growth and defense mechanisms in terms of their impact on soil quality and crop rhizosphere. Therefore, the current study investigated the detrimental impacts of six typical and multilevel herbicides on the microbial community and signal molecules in the soil as well as on the levels of hormones and secondary metabolites in wheat seedlings. Interestingly, bensulfuron-methyl, terbutylazine (TBA), and 2,4-D butylate significantly induced oxidative damage while reducing the number of phytohormones (salicylic acid and jasmonic acid) and secondary metabolites (tricin, quercetin, and caffeic acid) in the roots and leaves compared with the controls, isoproturon, fenoxaprop-p-ethyl, and pretilachlor. At twice the recommended levels (2×), they also decreased the microbial α diversity and, in particular, the abundance of Gammaproteobacteria, Alphaproteobacteria, Actinobacteria, Bacteroidia, Verrucomicrobia, Bacilli, Acidimicrobiia, Deltaproteobacteria, and Gemmatimonadetes by disrupting the level of enzymes (e.g., urease and sucrase) and metabolites (indole-3-acetic acid, salicylic acid, apigenin, 4-hydroxybenzoic acid, DIMBOA, and melatonin) in the rhizosphere soil. Overall, significant exposure to herbicides may inhibit wheat growth by disturbing the microbial composition in the rhizosphere soil and the distribution of secondary metabolites in wheat seedlings.

Integration of Phenomics and Metabolomics Datasets Reveals Different Mode of Action of Biostimulants Based on Protein Hydrolysates in Lactuca sativa L. and Solanum lycopersicum L. Under Salinity

Plant phenomics is becoming a common tool employed to characterize the mode of action of biostimulants. A combination of this technique with other omics such as metabolomics can offer a deeper understanding of a biostimulant effect in planta. However, the most challenging part then is the data analysis and the interpretation of the omics datasets. In this work, we present an example of how different tools, based on multivariate statistical analysis, can help to simplify the omics data and extract the relevant information. We demonstrate this by studying the effect of protein hydrolysate (PH)-based biostimulants derived from different natural sources in lettuce and tomato plants grown in controlled conditions and under salinity. The biostimulants induced different phenotypic and metabolomic responses in both crops. In general, they improved growth and photosynthesis performance under control and salt stress conditions, with better performance in lettuce. To identify the most significant traits for each treatment, a random forest classifier was used. Using this approach, we found out that, in lettuce, biomass-related parameters were the most relevant traits to evaluate the biostimulant mode of action, with a better response mainly connected to plant hormone regulation. However, in tomatoes, the relevant traits were related to chlorophyll fluorescence parameters in combination with certain antistress metabolites that benefit the electron transport chain, such as 4-hydroxycoumarin and vitamin K1 (phylloquinone). Altogether, we show that to go further in the understanding of the use of biostimulants as plant growth promotors and/or stress alleviators, it is highly beneficial to integrate more advanced statistical tools to deal with the huge datasets obtained from the -omics to extract the relevant information.

Biostimulants in Viticulture: A Sustainable Approach against Biotic and Abiotic Stresses

Climate change and disproportionate anthropogenic interventions, such as the excess of phytopharmaceutical products and continuous soil tillage, are jeopardizing viticulture by subjecting plants to continuous abiotic stress. One of the main physiological repercussions of abiotic stress is represented by the unbalanced redox homeostasis due to the overproduction of reactive oxygen species (ROS), ultimately leading to a state of oxidative stress (detrimental to grape quality). To these are added the direct and indirect damages caused by pathogens (biotic stresses). In light of this scenario, it is inevitable that sustainable techniques and sensitivity approaches for environmental and human health have to be applied in viticulture. Sustainable viticulture can only be made with the aid of sustainable products. Biostimulant (PB) applications (including resistance inducers or elicitors) in the vineyard have become interesting maneuvers for counteracting vine diseases and improving grape quality. These also represent a partial alternative to soil fertilization by improving nutrient absorption and avoiding its leaching into the groundwater. Their role as elicitors has important repercussions in the stimulation of the phenylpropanoid pathway by triggering the activation of several enzymes, such as polyphenol oxidase, lipoxygenase, phenylalanine ammonia-lyase, and peroxidase (with the accumulation of phenolic compounds). The present review paper summarizes the PBs' implications in viticulture, gathering historical, functional, and applicative information. This work aims to highlight the innumerable beneficial effects on vines brought by these products. It also serves to spur the scientific community to a greater contribution in investigating the response mechanisms of the plant to positive inductions.

Omics technologies used in pesticide residue detection and mitigation in crop

In agriculture, the convenience and efficacy of chemical pesticides have become inevitable to manage cultivated crop production. Here, we review the worldwide use of pesticides based on their categories, mode of actions and toxicity. Excessive use of pesticides may lead to hazardous pesticide residues in crops, causing adverse effects on human health and the environment. A wide range of high-tech-analytical methods are available to analyse pesticide residues. However, they are mostly time-consuming and inconvenient for on-site detection, calling for the development of biosensors that detect cellular changes in crops. Such new detection methods that combine biological and physicochemical knowledge may overcome the shortage in current farming to develop sustainable systems that support environmental and human health. This review also comprehensively compiles domestic pesticide residues removal tips from vegetables and fruits. Synthetic pesticide alternatives such as biopesticide and nanopesticide are greener to the environment. However, its safety assessment for large-scale application needs careful evaluation. Lastly, we strongly call for reversions of pesticide application trends based on the changing climate, which is lacking in the current scenario.

The hidden effects of agrochemicals on plant metabolism and root-associated microorganisms

Agrochemicals are commonly used in agriculture to protect crops and ensure yields. Several of them are mobile within the plant and, being perceived as xenobiotics regardless of their protective/curative roles, they induce a reprogramming of secondary metabolism linked to the detoxification processes even in the absence of phenotype symptoms. Moreover, it is well documented that plants are able to shape the microbial population at the rhizosphere and to significantly affect the processes occurring therein thanks to the root exudation of different metabolites. Here we show that plant metabolic response to foliarly-applied pesticides is much broader than what previously thought and includes diverse and compound-specific hidden processes. Among others, stress-related metabolism and phytohormones profile underwent a considerable reorganization. Moreover, a distinctive microbial rearrangement of the rhizosphere was recorded following foliar application of pesticides. Such effects have unavoidably energetic and metabolic costs for the plant paving the way to both positive and negative aspects. The understanding of these effects is crucial for an increasingly sustainable use of pesticides in agriculture.

Brassinosteroids as a multidimensional regulator of plant physiological and molecular responses under various environmental stresses

Biotic and abiotic stresses, especially heavy metal toxicity, are becoming a big problem in agriculture, which pose serious threats to crop production. Plant hormones have recently been used to develop stress tolerance in a variety of plants. Brassinosteroids (BRs) are the sixth class of plant steroid hormones, with pleiotropic effects on plants. Exogenous application of BRs to boost plant tolerance mechanisms to various stresses has been a major research focus. Numerous studies have revealed the role of these steroidal hormones in the up-regulation of stress-related resistance genes, as well as their interactions with other metabolic pathways. BRs interact with other phytohormones such as auxin, cytokinin, ethylene, gibberellin, jasmonic acid, abscisic acid, salicylic acid, and polyamines to regulate a variety of physiological and developmental processes in plants. BRs regulate expressions of many BR-inducible genes by activating the brassinazole-resistant 1 (BZR1)/BRI1-EMS suppressor 1 (BES1) complex. Moreover, to improve plant development under a variety of stresses, BRs regulate antioxidant enzyme activity, chlorophyll concentration, photosynthetic capability, and glucose metabolism. This review will provide insights into the mechanistic role and actions of brassinosteroids in plants in response to various stresses.

Integration of Gas Exchange With Metabolomics: High-Throughput Phenotyping Methods for Screening Biostimulant-Elicited Beneficial Responses to Short-Term Water Deficit

Biostimulants are emerging as a feasible tool for counteracting reduction in climate change-related yield and quality under water scarcity. As they are gaining attention, the necessity for accurately assessing phenotypic variables in their evaluation is emerging as a critical issue. In light of this, high-throughput phenotyping techniques have been more widely adopted. The main bottleneck of these techniques is represented by data management, which needs to be tailored to the complex, often multifactorial, data. This calls for the adoption of non-linear regression models capable of capturing dynamic data and also the interaction and effects between multiple factors. In this framework, a commercial glycinebetaine- (GB-) based biostimulant (Vegetal B60, ED&F Man) was tested and distributed at a rate of 6 kg/ha. Exogenous application of GB, a widely accumulated and documented stress adaptor molecule in plants, has been demonstrated to enhance the plant abiotic stress tolerance, including drought. Trials were conducted on tomato plants during the flowering stage in a greenhouse. The experiment was designed as a factorial combination of irrigation (water-stressed and well-watered) and biostimulant treatment (treated and control) and adopted a mixed phenotyping-omics approach. The efficacy of a continuous whole-canopy multichamber system coupled with generalized additive mixed modeling (GAMM) was evaluated to discriminate between water-stressed plants under the biostimulant treatment. Photosynthetic performance was evaluated by using GAMM, and was then correlated to metabolic profile. The results confirmed a higher photosynthetic efficiency of the treated plants, which is correlated to biostimulant-mediated drought tolerance. Furthermore, metabolomic analyses demonstrated the priming effect of the biostimulant for stress tolerance and detoxification and stabilization of photosynthetic machinery. In support of this, the overaccumulation of carotenoids was particularly relevant, given their photoprotective role in preventing the overexcitation of photosystem II. Metabolic profile and photosynthetic performance findings suggest an increased effective use of water (EUW) through the overaccumulation of lipids and leaf thickening. The positive effect of GB on water stress resistance could be attributed to both the delayed onset of stress and the elicitation of stress priming through the induction of H₂O₂-mediated antioxidant mechanisms. Overall, the mixed approach supported by a GAMM analysis could prove a valuable contribution to high-throughput biostimulant testing.

Plant growth-promoting bacterial endophytes as biocontrol agents of pre- and post-harvest diseases: Fundamentals, methods of application and future perspectives

Sustainable agriculture requires the recruitment of bacterial agents to control diverse plant diseases such as bacterial endophytes. Bacterial endophytes colonize and inhabit internal plant tissues without causing any apparent damage. Within the plant, these bacteria exert multiple beneficiary effects, including direct stimulation of plant growth by the action of phytohormones or the production of metabolites. However, bacterial endophytes also protect their plant host through biocontrol pathogens or by inducing plant innate immune system. The present work makes a systematic and in-depth review on the current state of endophytic bacterial diversity, their plant colonization strategies, and their potential roles as protective agents against plant diseases during pre- and post-harvest stages of crop productivity. In addition, an exploration of their beneficial effects on sustainable agriculture by reducing/eliminating the use of toxic agrochemicals was conducted. Finally, we propose diverse effective strategies for the application of endophytic bacteria as biological agents during both pre- and post-harvest stages, with the aim of protecting crop plants and their agricultural products.

Combining Molecular Weight Fractionation and Metabolomics to Elucidate the Bioactivity of Vegetal Protein Hydrolysates in Tomato Plants

The comprehension of the bioactive fractions involved in the biostimulant activity of plant derived protein hydrolysates (PH) is a complex task, but it can also lead to significant improvements in the production of more effective plant biostimulants. The aim of this work is to shed light onto the bioactivity of different PH dialysis fractions (PH1 < 0.5-1 kDa; PH2 > 0.5-1 kDa; PH3 < 8-10 kDa; PH4 > 8-10 kDa) of a commercial PH-based biostimulant through a combined in vivo bioassay and metabolomics approach. A first tomato rooting bioassay investigated the auxin-like activity of PH and its fractions, each of them at three nitrogen levels (3, 30, and 300 mg L^-1 of N) in comparison with a negative control (water) and a positive control (indole-3-butyric acid, IBA). Thereafter, a second experiment was carried out where metabolomics was applied to elucidate the biochemical changes imposed by the PH and its best performing fraction (both at 300 mg L^-1 of N) in comparison to water and IBA. Overall, both the PH and its fractions increased the root length of tomato cuttings, compared to negative control. Moreover, the highest root length was obtained in the treatment PH1 following foliar application. Metabolomics allowed highlighting a response to PH1 that involved changes at phytohormones and secondary metabolite level. Notably, such metabolic reprogramming supported the effect on rooting of tomato cuttings, being shared with the response induced by the positive control IBA. Taken together, the outcome of in vivo assays and metabolomics indicate an auxin-like activity of the selected PH1 fraction.

Metabolomic Responses of Maize Shoots and Roots Elicited by Combinatorial Seed Treatments With Microbial and Non-microbial Biostimulants

Microbial and non-microbial plant biostimulants have been successfully used to improve agriculture productivity in a more sustainable manner. Since the mode of action of biostimulants is still largely unknown, the present work aimed at elucidating the morpho-physiological and metabolomic changes occurring in maize (Zea mays L.) leaves and roots following seed treatment with (i) a consortium of two beneficial fungi [arbuscular mycorrhizal fungi (AMF) and Trichoderma koningii TK7] and rhizobacteria, (ii) a protein hydrolyzate-based biostimulant (PH) alone, or (iii) in combination with a consortium of T. koningii TK7 and rhizobacteria. The application of PH alone or in combination with Trichoderma elicited significant increases (+16.6%) in the shoot biomass compared to untreated maize plants, whereas inoculation with AMF + Trichoderma elicited significant increases in root dry biomass (+48.0%) compared to untreated plants. Distinctive metabolomic signatures were achieved from the different treatments, hence suggesting that different molecular processes were involved in the plants response to the biostimulants. The metabolic reprogramming triggered by the treatments including the protein hydrolyzate was hierarchically more pronounced than the application of microorganisms alone. Most of the differential metabolites could be ascribed to the secondary metabolism, with phenylpropanoids and terpenes being the most represented compounds. The application of PH triggered an accumulation of secondary metabolites, whereas the opposite trend of accumulation was seen in the case of microorganisms alone. The increase in biomass could be related to two processes, namely the modulation of the multilayer phytohormone interaction network and a possible increase in nitrogen use efficiency via the GS-GOGAT system.

Extracts of Common Pesticidal Plants Increase Plant Growth and Yield in Common Bean Plants

Common bean (Phaseolus vulgaris) is an important food and cash crop in many countries. Bean crop yields in sub-Saharan Africa are on average 50% lower than the global average, which is largely due to severe problems with pests and diseases as well as poor soil fertility exacerbated by low-input smallholder production systems. Recent on-farm research in eastern Africa has shown that commonly available plants with pesticidal properties can successfully manage arthropod pests. However, reducing common bean yield gaps still requires further sustainable solutions to other crop provisioning services such as soil fertility and plant nutrition. Smallholder farmers using pesticidal plants have claimed that the application of pesticidal plant extracts boosts plant growth, potentially through working as a foliar fertiliser. Thus, the aims of the research presented here were to determine whether plant growth and yield could be enhanced and which metabolic processes were induced through the application of plant extracts commonly used for pest control in eastern Africa. Extracts from Tephrosia vogelii and Tithonia diversifolia were prepared at a concentration of 10% w/v and applied to potted bean plants in a pest-free screen house as foliar sprays as well as directly to the soil around bean plants to evaluate their contribution to growth, yield and potential changes in primary or secondary metabolites. Outcomes of this study showed that the plant extracts significantly increased chlorophyll content, the number of pods per plant and overall seed yield. Other increases in metabolites were observed, including of rutin, phenylalanine and tryptophan. The plant extracts had a similar effect to a commercially available foliar fertiliser whilst the application as a foliar spray was better than applying the extract to the soil. These results suggest that pesticidal plant extracts can help overcome multiple limitations in crop provisioning services, enhancing plant nutrition in addition to their established uses for crop pest management.

Biostimulants for Plant Growth Promotion and Sustainable Management of Phytoparasitic Nematodes in Vegetable Crops

The parasitism of root-knot nematodes, Meloidogyne spp., can cause heavy yield losses to vegetable crops. Plant biostimulants are often reported for a side-suppressive effect on these pests and many commercial products are increasingly included in sustainable nematode control strategies. Source materials of most biostimulants derived from plant or seaweed raw materials were documented for a reliable suppression of root-knot nematode species, whereas the suppressiveness of microbial biostimulants was found largely variable, as related to the crop and to environmental factors. Chitosan-based biostimulants were also stated for a variable phytonematode suppression, though clearly demonstrated only by a few number of studies. In a preliminary experimental case study, four commercial biostimulants based on quillay extract (QE), sesame oil (SO), seaweeds (SE), or neem seed cake (NC) were comparatively investigated for their effects against the root-knot nematode M. incognita on potted tomato. Soil treatments with all the four biostimulants resulted in a significant reduction of nematode eggs and galls on tomato roots, though NC and SO were significantly more suppressive than QE or SE. In addition, almost all biostimulant treatments also resulted in a significant improvement of tomato growth compared to the non-treated control. These preliminary results seem to confirm the literature data and clearly indicate the potential role of biostimulants for a safe nematode management both in organic and integrated crop systems.

Thiamethoxam Metabolism and Metabolic Effects in Cell Suspension Culture of Tea ( Camellia sinensis L.)

Thiamethoxam (TMX) has already been proven to have a physiological effect in plant tissue or cell expect for the insecticidal activity. In our previous study, TMX was verified to be metabolized by tea cells in either a suspension culture or tea plant into several metabolites. Here, tea cell suspension cultures were treated for 45 days to investigate the metabolite effects in both the tea cells and the culture supernatants by nontargeted metabolomics. Using multivariate analysis (PCA and OPLS-DA), all treatment and control groups could be clearly separated. Inside the cells, 113 metabolites were found to be up-regulated while 122 were down-regulated, when compared with untreated cells. In the culture supernatant, there were 128 up-regulated and 35 down-regulated metabolites, compared to untreated cultures. KEGG searches revealed that the alanine, aspartate, and glutamate metabolic pathways were strongly affected by TMX metabolism within the tea cell. Molecular docking models showed that (i) 4-aminobutyrate aminotransferase may be related to the formation of 2-chloro-thiazole-5-carboxylic acid and (ii) 3'(2'),5'-bisphosphate nucleotidase may be able to interact with TMX. This study can help us to understand the interaction mechanism of pesticides with plant cells.

Transformation of polyphenols found in pigmented gluten-free flours during in vitro large intestinal fermentation

In this work, 18 gluten-free flours (prepared from cereals, pseudocereals and legumes), differing in pigmentation, were screened for their phenolic profiles, cooked and, then, subjected to digestion and large intestinal fermentation in vitro. A combined targeted/untargeted metabolomic approach was used to elucidate the microbial biotransformation processes of polyphenols following digestion. This preliminary work demonstrated an increase in 3,5-dihydroxybenzoic acid (on average from 0.67 up to 1.30 μmol/g dry matter) throughout large intestinal fermentation of pseudocereals (esp. quinoa), due to their high alkylresorcinol contents. Isoflavones were converted into equol- or O-desmethylangolensin- derivatives, whereas anthocyanins were degraded into lower-molecular-weight phenolics (i.e., protocatechuic aldehyde and 4-hydroxybenzoic acid, with the latter exhibiting the highest increase over time). A decreasing trend was observed for antioxidant activities (i.e., FRAP and ORAC values) moving from digested to faecal fermented samples. These findings highlight that gluten-free flours are able to deliver bioaccessible polyphenols to the colon.

Metabolomic responses triggered by arbuscular mycorrhiza enhance tolerance to water stress in wheat cultivars

Under global climate change forecasts, the pressure of environmental stressors (and in particular drought) on crop productivity is expected to rise and challenge further global food security. The application of beneficial microorganisms may represent an environment friendly tool to secure improved crop performance and yield stability. Accordingly, this current study aimed at elucidating the metabolomic responses triggered by mycorrhizal (Funneliformis mosseae) inoculation of durum (Triticum durum Desf.; cv. 'Mongibello') and bread wheat cultivars (Triticum aestivum L.; cv. 'Chinese Spring') under full irrigation and water deficit regimes. Metabolomics indicated a similar regulation of secondary metabolism in both bread and durum wheat cultivars following water limiting conditions. Nonetheless, a mycorrhizal fungi (AMF) x cultivar interaction could be observed, with the bread wheat cultivar being more affected by arbuscular colonization under water limiting conditions. Discriminant compounds could be mostly related to sugars and lipids, both being positively modulated by AMF colonization under water stress. Moreover, a regulation of metabolites related to oxidative stress and a tuning of crosstalk between phytohormones were also evidenced. Among the latter, the stimulation of the brassinosteroids biosynthetic pathway was particularly evident in inoculated wheat roots, supporting the hypothesis of their involvement in enhancing plant response to water stress and modulation of oxidative stress conditions. This study proposes new insights on the modulation of the tripartite interaction plant-AMF-environmental stress.

Fulvic acid-induced disease resistance to Botrytis cinerea in table grapes may be mediated by regulating phenylpropanoid metabolism

Gray mold caused by Botrytis cinerea is a major postharvest disease of table grapes that leads to enormous economic losses during storage and transportation. The objective of this study was to evaluate the effectiveness of fulvic acid on controlling gray mold of table grapes and explore its mechanism of action. The results showed that fulvic acid application significantly reduced downy blight severity in table grapes without exhibiting any antifungal activity in vitro. Fulvic acid induced phenylpropanoid metabolism, as evidenced by accumulation of phenolic compounds and flavonoids, higher activities of phenylalanine ammonia-lyase (PAL), cinnamate-4-hydroxylase (C4H) and 4-coumarate-CoA ligase (4CL), up-regulation of genes related to phenylpropanoid biosynthesis (PAL, C4H, 4CL, STS, ROMT and CHS). Our results suggested that fulvic acid induces resistance to B. cinerea mainly through the activation of phenylpropanoid pathway and can be used as a new activator of plant defense responses to control postharvest gray mold in table grapes.

Metabolomic insights into the mechanisms underlying tolerance to salinity in different halophytes

Salinity is among the most detrimental and diffuse environmental stresses. Halophytes are plants that developed the ability to complete their life cycle under high salinity. In this work, a mass spectrometric metabolomic approach was applied to comparatively investigate the secondary metabolism processes involved in tolerance to salinity in three halophytes, namely S. brachiata, S. maritima and S. portulacastrum. Regarding osmolytes, the level of proline was increased with NaCl concentration in S. portulacastrum and roots of S. maritima, whereas glycine betaine and polyols were accumulated in S. maritima and S. brachiata. Important differences between species were also found regarding oxidative stress balance. In S. brachiata, the amount of flavonoids and other phenolic compounds increased in presence of NaCl, whereas these metabolites were down regulated in S. portulacastrum, who accumulated carotenoids. Furthermore, distinct impairment of membrane lipids, hormones, alkaloids and terpenes was observed in our species under salinity. Finally, several other nitrogen containing compounds were involved in response to salinity, including amino acids, serotonin and polyamine conjugates. In conclusion, metabolomics highlighted that the specific mechanism each species adopted to achieve acclimation to salinity differed in the three halophytes considered, although response osmotic stress and oxidative imbalance have been confirmed as the key processes underlying NaCl tolerance.

Inoculation of Rhizoglomus irregulare or Trichoderma atroviride differentially modulates metabolite profiling of wheat root exudates

Root exudation patterns are linked to, among other things, plant growth, plant-microbe interaction and the priming effect. In this work, two complementary metabolomic approaches (both liquid and gas chromatography coupled to mass spectrometry) were applied to investigate the modulation of root exudation imposed by two beneficial fungi (substrate treatment of Trichoderma atroviride AT10, substrate application of Rhizoglomus irregulare BEG72 and seed treatment with T. atroviride AT10) on wheat (Triticum aestivum L.). The inoculation with R. irregulare elicited significant increases (by 18%, 39% and 20%) in the shoot, root dry biomass and root-to-shoot ratio compared to untreated plants, whereas inoculation with T. atroviride, as a substrate drench or as a seed coating, exhibited intermediate values for these parameters. The metabolomic approach demonstrated a broad chemical diversity, with more than 2900 compounds annotated in the root exudates. Overall, the Orthogonal Projections to Latent Structures Discriminant Analysis (OPLS-DA) supervised modelling highlighted a distinctive modulation of the metabolic profile in the root exudates as a function of both fungal inoculation and means of application. Most of the differences could be ascribed to lipids (sterols and membrane lipids), phenolic compounds and terpenoids, siderophores and chelating acids, derivatives of amino acids and phytohormones, and as such, the interaction between the wheat roots and beneficial fungi resulted in a complex response in terms of root exudates, likely involving a cascade of processes. Nonetheless, the changes imposed by plant-microbe interactions can contribute to the support of the biostimulant effects of both T. atroviride and R. irregulare.

A Combined Phenotypic and Metabolomic Approach for Elucidating the Biostimulant Action of a Plant-Derived Protein Hydrolysate on Tomato Grown Under Limited Water Availability

Plant-derived protein hydrolysates (PHs) are an important category of biostimulants able to increase plant growth and crop yield especially under environmental stress conditions. PHs can be applied as foliar spray or soil drench. Foliar spray is generally applied to achieve a relatively short-term response, whereas soil drench is used when a long-term effect is desired. The aim of the study was to elucidate the biostimulant action of PH application method (foliar spray or substrate drench) on morpho-physiological traits and metabolic profile of tomato grown under limited water availability. An untreated control was also included. A high-throughput image-based phenotyping (HTP) approach was used to non-destructively monitor the crop response under limited water availability (40% of container capacity) in a controlled environment. Moreover, metabolic profile of leaves was determined at the end of the trial. Dry biomass of shoots at the end of the trial was significantly correlated with number of green pixels (R ² = 0.90) and projected shoot area, respectively. Both drench and foliar treatments had a positive impact on the digital biomass compared to control while the photosynthetic performance of the plants was slightly influenced by treatments. Overall drench application under limited water availability more positively influenced biomass accumulation and metabolic profile than foliar application. Significantly higher transpiration use efficiency was observed with PH-drench applications indicating better stomatal conductance. The mass-spectrometry based metabolomic analysis allowed the identification of distinct biochemical signatures in PH-treated plants. Metabolomic changes involved a wide and organized range of biochemical processes that included, among others, phytohormones (notably a decrease in cytokinins and an accumulation of salicylates) and lipids (including membrane lipids, sterols, and terpenes). From a general perspective, treated tomato plants exhibited an improved tolerance to reactive oxygen species (ROS)-mediated oxidative imbalance. Such capability to cope with oxidative stress might have resulted from a coordinated action of signaling compounds (salicylic acid and hydroxycinnamic amides), radical scavengers such as carotenoids and prenyl quinones, as well as a reduced biosynthesis of tetrapyrrole coproporphyrins.

2, 3-Butanediol activated disease-resistance of creeping bentgrass by inducing phytohormone and antioxidant responses

Brown patch, caused by Rhizoctonia solani, is a serious disease in Agrostis stolonifera. 2, 3-butanediol (2, 3-BD) is the major component of volatile organic compounds and was found to initiate induced systemic resistance (ISR). To investigate the induced resistance mechanism of 2, 3-BD, we examined the effects of resistance by area affected, along with changes in the content of phytohormones (Zeatin (ZT), Abscisic Acid (ABA) and Indole-3-Acetic Acid (IAA)), the activities of three phenylpropanoid metabolic enzymes (Phenylalaninammo-Nialyase (PAL), Chalcone Isomerase (CHI) and 4-Coumarate:Coenzyme A Ligase (4CL)) and the level of secondary metabolites (total phenols, flavonoid and lignin). The result showed that 2, 3-BD treatment at 250 μmoL/L had the best induction effect with the area affected decreased from 95% of the control to 55%. Compared to the controls, treatment with 250 μmoL/L 2, 3-BD induced higher levels of PAL, CHI and 4CL activity and increased total phenols, flavonoid and lignin levels. While 2, 3-BD treatment decreased the content of ZT and ABA but increased the content of IAA compared to controls. This study provides a basis for elucidating the mechanism of 2, 3-BD as a new plant disease control agent.

Physiological and Metabolic Responses Triggered by Omeprazole Improve Tomato Plant Tolerance to NaCl Stress

Interest in the role of small bioactive molecules (< 500 Da) in plants is on the rise, compelled by plant scientists' attempt to unravel their mode of action implicated in stimulating growth and enhancing tolerance to environmental stressors. The current study aimed at elucidating the morphological, physiological and metabolomic changes occurring in greenhouse tomato (cv. Seny) treated with omeprazole (OMP), a benzimidazole inhibitor of animal proton pumps. The OMP was applied at three rates (0, 10, or 100 μM) as substrate drench for tomato plants grown under nonsaline (control) or saline conditions sustained by nutrient solutions of 1 or 75 mM NaCl, respectively. Increasing NaCl concentration from 1 to 75 mM decreased the tomato shoot dry weight by 49% in the 0 μM OMP treatment, whereas the reduction was not significant at 10 or 100 μM of OMP. Treatment of salinized (75 mM NaCl) tomato plants with 10 and especially 100 μM OMP decreased Na+ and Cl- while it increased Ca2+ concentration in the leaves. However, OMP was not strictly involved in ion homeostasis since the K+ to Na+ ratio did not increase under combined salinity and OMP treatment. OMP increased root dry weight, root morphological characteristics (total length and surface), transpiration, and net photosynthetic rate independently of salinity. Metabolic profiling of leaves through UHPLC liquid chromatography coupled to quadrupole-time-of-flight mass spectrometry facilitated identification of the reprogramming of a wide range of metabolites in response to OMP treatment. Hormonal changes involved an increase in ABA, decrease in auxins and cytokinin, and a tendency for GA down accumulation. Cutin biosynthesis, alteration of membrane lipids and heightened radical scavenging ability related to the accumulation of phenolics and carotenoids were observed. Several other stress-related compounds, such as polyamine conjugates, alkaloids and sesquiterpene lactones, were altered in response to OMP. Although a specific and well-defined mechanism could not be posited, the metabolic processes involved in OMP action suggest that this small bioactive molecule might have a hormone-like activity that ultimately elicits an improved tolerance to NaCl salinity stress.

Expression and functional analysis of the Propamocarb-related gene CsDIR16 in cucumbers

BACKGROUND

Cucumber downy mildew is among the most important diseases that can disrupt cucumber production. Propamocarb, also known as propyl-[3-(dimethylamino)propyl]carbamate (PM), is a systemic carbamate fungicide pesticide that is widely applied in agricultural production because of its high efficiency of pathogens control, especially cucumber downy mildew. However, residual PM can remain in cucumbers after the disease has been controlled. To explore the molecular mechanisms of PM retention, cucumber cultivars 'D9320' (with the highest residual PM content) and 'D0351' (lowest residual PM content) were studied. High-throughput tag-sequencing (Tag-Seq) results showed that the CsDIR16 gene was related to PM residue, which was verified using transgenic technology.

RESULTS

We investigated the activity of a dirigent cucumber protein encoded by the CsDIR16 in gene response to stress induced by PM treatment. Gene-expression levels of CsDIR16 were up-regulated in the fruits, leaves, and stems of 'D0351' plants in response to PM treatment. However, in cultivar 'D9320', CsDIR16 levels were down-regulated in the leaves and stems after PM treatment, with no statistically significant differences observed in the fruits. Induction by jasmonic acid, abscisic acid, polyethylene glycol 4000, NaCl, and Corynespora cassiicola Wei (Cor) resulted in CsDIR16 up-regulation in 'D0351' and 'D9320'. Expression after salicylic acid treatment was up-regulated in 'D0351', but was down-regulated in 'D9320'. CsDIR16 overexpression lowered PM residues, and these were more rapidly reduced in CsDIR16(+) transgenic 'D9320' plants than in wild-type 'D9320' and CsDIR16(-) transgenic plants.

CONCLUSIONS

Analyses of the CsDIR16-expression patterns in the cucumber cultivars with the highest and lowest levels of PM residue, and transgenic validation indicated that CsDIR16 plays a positive role in reducing PM residues. The findings of this study help understand the regulatory mechanisms occurring in response to PM stress in cucumbers and in establishing the genetic basis for developing low-pesticide residue cucumber cultivars.

A Vegetal Biopolymer-Based Biostimulant Promoted Root Growth in Melon While Triggering Brassinosteroids and Stress-Related Compounds

Plant biostimulants are receiving great interest for boosting root growth during the first phenological stages of vegetable crops. The present study aimed at elucidating the morphological, physiological, and metabolomic changes occurring in greenhouse melon treated with the biopolymer-based biostimulant Quik-link, containing lateral root promoting peptides, and lignosulphonates. The vegetal-based biopolymer was applied at five rates (0, 0.06, 0.12, 0.24, or 0.48 mL plant^-1) as substrate drench. The application of biopolymer-based biostimulant at 0.12 and 0.24 mL plant^-1 enhanced dry weight of melon leaves and total biomass by 30.5 and 27.7%, respectively, compared to biopolymer applications at 0.06 mL plant^-1 and untreated plants. The root dry biomass, total root length, and surface in biostimulant-treated plants were significantly higher at 0.24 mL plant^-1 and to a lesser extent at 0.12 and 0.48 mL plant^-1, in comparison to 0.06 mL plant^-1 and untreated melon plants. A convoluted biochemical response to the biostimulant treatment was highlighted through UHPLC/QTOF-MS metabolomics, in which brassinosteroids and their interaction with other hormones appeared to play a pivotal role. Root metabolic profile was more markedly altered than leaves, following application of the biopolymer-based biostimulant. Brassinosteroids triggered in roots could have been involved in changes of root development observed after biostimulant application. These hormones, once transported to shoots, could have caused an hormonal imbalance. Indeed, the involvement of abscisic acid, cytokinins, and gibberellin related compounds was observed in leaves following root application of the biopolymer-based biostimulant. Nonetheless, the treatment triggered an accumulation of several metabolites involved in defense mechanisms against biotic and abiotic stresses, such as flavonoids, carotenoids, and glucosinolates, thus potentially improving resistance toward plant stresses.

Pesticidal Plant Extracts Improve Yield and Reduce Insect Pests on Legume Crops Without Harming Beneficial Arthropods

In the fight against arthropod crop pests using plant secondary metabolites, most research has focussed on the identification of bioactive molecules. Several hundred candidate plant species and compounds are now known to have pesticidal properties against a range of arthropod pest species. Despite this growing body of research, few natural products are commercialized for pest management whilst on-farm use of existing botanically-based pesticides remains a small, but growing, component of crop protection practice. Uptake of natural pesticides is at least partly constrained by limited data on the trade-offs of their use on farm. The research presented here assessed the potential trade-offs of using pesticidal plant extracts on legume crop yields and the regulating ecosystem services of natural pests enemies. The application of six established pesticidal plants (Bidens pilosa, Lantana camara, Lippia javanica, Tephrosia vogelii, Tithonia diversifolia, and Vernonia amygdalina) were compared to positive and negative controls for their impact on yields of bean (Phaseolus vulgaris), cowpea (Vigna unguiculata), and pigeon pea (Cajanus cajan) crops and the abundance of key indicator pest and predatory arthropod species. Analysis of field trials showed that pesticidal plant treatments often resulted in crop yields that were comparable to the use of a synthetic pesticide (lambda-cyhalothrin). The best-performing plant species were T. vogelii, T. diversifolia, and L. javanica. The abundance of pests was very low when using the synthetic pesticide, whilst the plant extracts generally had a higher number of pests than the synthetic but lower numbers than observed on the negative controls. Beneficial arthropod numbers were low with synthetic treated crops, whereas the pesticidal plant treatments appeared to have little effect on beneficials when compared to the negative controls. The outcomes of this research suggest that using extracts of pesticidal plants to control pests can be as effective as synthetic insecticides in terms of crop yields while tritrophic effects were reduced, conserving the non-target arthropods that provide important ecosystem services such as pollination and pest regulation. Thus managing crop pests using plant secondary metabolites can be more easily integrated in to agro-ecologically sustainable crop production systems.

The combination of four analytical methods to explore skeletal muscle metabolomics: Better coverage of metabolic pathways or a marketing argument?

OBJECTIVES

Metabolomics is an emerging science based on diverse high throughput methods that are rapidly evolving to improve metabolic coverage of biological fluids and tissues. Technical progress has led researchers to combine several analytical methods without reporting the impact on metabolic coverage of such a strategy. The objective of our study was to develop and validate several analytical techniques (mass spectrometry coupled to gas or liquid chromatography and nuclear magnetic resonance) for the metabolomic analysis of small muscle samples and evaluate the impact of combining methods for more exhaustive metabolite covering.

DESIGN AND METHODS

We evaluated the muscle metabolome from the same pool of mouse muscle samples after 2 metabolite extraction protocols. Four analytical methods were used: targeted flow injection analysis coupled with mass spectrometry (FIA-MS/MS), gas chromatography coupled with mass spectrometry (GC-MS), liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS), and nuclear magnetic resonance (NMR) analysis. We evaluated the global variability of each compound i.e., analytical (from quality controls) and extraction variability (from muscle extracts). We determined the best extraction method and we reported the common and distinct metabolites identified based on the number and identity of the compounds detected with low analytical variability (variation coefficient<30%) for each method. Finally, we assessed the coverage of muscle metabolic pathways obtained.

RESULTS

Methanol/chloroform/water and water/methanol were the best extraction solvent for muscle metabolome analysis by NMR and MS, respectively. We identified 38 metabolites by nuclear magnetic resonance, 37 by FIA-MS/MS, 18 by GC-MS, and 80 by LC-HRMS. The combination led us to identify a total of 132 metabolites with low variability partitioned into 58 metabolic pathways, such as amino acid, nitrogen, purine, and pyrimidine metabolism, and the citric acid cycle. This combination also showed that the contribution of GC-MS was low when used in combination with other mass spectrometry methods and nuclear magnetic resonance to explore muscle samples.

CONCLUSION

This study reports the validation of several analytical methods, based on nuclear magnetic resonance and several mass spectrometry methods, to explore the muscle metabolome from a small amount of tissue, comparable to that obtained during a clinical trial. The combination of several techniques may be relevant for the exploration of muscle metabolism, with acceptable analytical variability and overlap between methods However, the difficult and time-consuming data pre-processing, processing, and statistical analysis steps do not justify systematically combining analytical methods.

De novo transcriptome analysis of rose-scented geranium provides insights into the metabolic specificity of terpene and tartaric acid biosynthesis

Background

Rose-scented geranium (Pelargonium sp.) is a perennial herb that produces a high value essential oil of fragrant significance due to the characteristic compositional blend of rose-oxide and acyclic monoterpenoids in foliage. Recently, the plant has also been shown to produce tartaric acid in leaf tissues. Rose-scented geranium represents top-tier cash crop in terms of economic returns and significance of the plant and plant products. However, there has hardly been any study on its metabolism and functional genomics, nor any genomic expression dataset resource is available in public domain. Therefore, to begin the gains in molecular understanding of specialized metabolic pathways of the plant, de novo sequencing of rose-scented geranium leaf transcriptome, transcript assembly, annotation, expression profiling as well as their validation were carried out.

Results

De novo transcriptome analysis resulted a total of 78,943 unique contigs (average length: 623 bp, and N50 length: 752 bp) from 15.44 million high quality raw reads. In silico functional annotation led to the identification of several putative genes representing terpene, ascorbic acid and tartaric acid biosynthetic pathways, hormone metabolism, and transcription factors. Additionally, a total of 6,040 simple sequence repeat (SSR) motifs were identified in 6.8% of the expressed transcripts. The highest frequency of SSR was of tri-nucleotides (50%). Further, transcriptome assembly was validated for randomly selected putative genes by standard PCR-based approach. In silico expression profile of assembled contigs were validated by real-time PCR analysis of selected transcripts.

Conclusion

Being the first report on transcriptome analysis of rose-scented geranium the data sets and the leads and directions reflected in this investigation will serve as a foundation for pursuing and understanding molecular aspects of its biology, and specialized metabolic pathways, metabolic engineering, genetic diversity as well as molecular breeding.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3437-0) contains supplementary material, which is available to authorized users.