Natural variation in specialised metabolites production in the leafy vegetable spider plant (Gynandropsis gynandra L. (Briq.)) in Africa and Asia
Sogbohossou, E.O.D. ; Achigan Dako, Enoch ; Mumm, R. ; Vos, C.H. de; Schranz, M.E. - \ 2020
Phytochemistry 178 (2020). - ISSN 0031-9422
The improvement and promotion of leafy vegetables, used for both food and medicine, benefits greatly from detailed knowledge of their health-promoting specialised metabolites. In the present study, we investigated the global metabolite variation in the leaves of 48 accessions of the leafy vegetable Gynandropsis gynandra using two complementary analytical platforms: liquid-chromatography mass spectrometry (LC-MS) for an untargeted comparison of non-volatile semi-polar metabolites and gas-chromatography mass spectrometry (GC-MS) for an untargeted comparison of volatile metabolites. Our results revealed large variation in 936 semi-polar compounds including flavonoids, terpene glycosides, glucosinolates and various phenolic compounds. Unsupervised multivariate analysis indicated the variation in levels of the semi-polar metabolites was mainly driven by geography, with accessions from both West Africa and Asia forming a group clearly separated from East African accessions.
Detected volatile metabolites included various sesquiterpenes, aldehydes, ketones, and sulphur-containing isothiocyanates.
Variation in these compounds was however not geographically specific, but most likely linked to the taste and aroma of the leaves. The relative abundance in glucosinolates and isothiocyanates in the leaves allowed the clustering of accessions into two main groups that could be used for further plant-herbivore interaction studies. This study revealed both the broad spectrum of phytochemicals present in Gynandropsis gynandra leaves and the substantial variation in metabolite profiles among accessions from different regions of the world.
Our results provide a basis for the development of breeding programs aiming at improving the levels of specialised
metabolites in this tropical leafy vegetable for increased resistance against pests and diseases and improved human health.
Modulation of the Tomato Fruit Metabolome by LED Light
Ntagkas, N. ; Vos, C.H. de; Woltering, E.J. ; Nicole, Celine ; Labrie, C.W. ; Marcelis, L.F.M. - \ 2020
Metabolites 10 (2020)266. - ISSN 2218-1989 - 19 p.
Metabolic profiles of tomatoes change during ripening and light can modulate the activity of relevant biochemical pathways. We investigated the effects of light directly supplied to the fruits on the metabolome of the fruit pericarp during ripening. Mature green tomatoes were exposed to well-controlled conditions with light as the only varying factor; control fruits were kept in darkness. In experiment 1 the fruits were exposed to either white light or darkness for 15 days.
In experiment 2, fruits were exposed to different light spectra (blue, green, red, far-red, white) added to white background light for seven days. Changes in the global metabolome of the fruit pericarp were monitored using LCMS and GCMS (554 compounds in total). Health-beneficial compounds (carotenoids, flavonoids, tocopherols and phenolic acids) accumulated faster under white light compared to darkness, while alkaloids and chlorophylls decreased faster. Light also changed the levels of taste-related metabolites including glutamate and malate. The light spectrum treatments indicated that the addition of blue light was the most effective treatment in altering the fruit metabolome. We conclude that light during ripening of tomatoes can have various effects on the metabolome and may help with shaping the levels of key compounds involved in various fruit quality characteristics.
MYB5-like and bHLH influence flavonoid composition in pomegranate
Arlotta, Carmen ; Puglia, Giuseppe D. ; Genovese, Claudia ; Toscano, Valeria ; Karlova, R.B. ; Beekwilder, M.J. ; Vos, C.H. de; Raccuia, Salvatore A. - \ 2020
Plant Science 298 (2020). - ISSN 0168-9452
The fruit of the pomegranate (Punica granatum L.) is an important nutraceutical food rich in polyphenolic compounds, including hydrolysable tannins, anthocyanins and flavonols. Their composition varies according to cultivar, tissue and fruit development stage and is probably regulated by a combination of MYB and bHLH type
transcription factors (TFs). In this study, metabolomics analysis during fruit developmental stages in the main pomegranate cultivars, Wonderful and Valenciana with contrasting colour of their ripe fruits, showed that flavonols were mostly present in flowers while catechins were highest in unripe fruits and anthocyanins in late fruit
maturation stages. A novel MYB TF, PgMYB5-like, was identified, which differs from previously isolated pomegranate TFs by unique C-terminal protein motifs and lack of the amino-acid residues conserved among anthocyanins promoting MYBs. In both pomegranate cultivars the expression of PgMYB5-like was high at flowering stage, while it decreased during fruit ripening. A previously identified bHLH-type TF, PgbHLH, also showed high transcript levels at flowering stage in both cultivars, while it showed a decrease in expression during fruit ripening in cv. Valenciana, but not in cv. Wonderful. Functional analysis of both TFs was performed by agroinfiltration into Nicotiana benthamiana leaves. Plants infiltrated with the PgMYB5-like+PgbHLH combined construct showed a specific and significant accumulation of intermediates of the flavonoid pathway, especially dihydroflavonols, while anthocyanins were not produced. Thus, we propose a role for PgMYB5-like and PgbHLH in the first steps of flavonoid production in flowers and in unripe fruits. The expression patterns of these two TFs may be key in determining the differential flavonoid composition in both flowers and fruits of the pomegranate varieties Wonderful and Valenciana.
Green Challenges: plant en bodemweerbaarheidtegen ondergrondse ziekten
Streminska, Marta ; Breeuwsma, Suzanne ; Huisman, Huei Ming ; Vos, Ric de; Eekelen, Henriette van; Stevens, Luc ; Salm, Caroline van der - \ 2020
Bleiswijk : Stichting Wageningen Research, Wageningen Plant Research, Business unit Glastuinbouw (Rapport WPR 943) - 61
Crops in soil-based and soilless greenhouse cultivation systems are susceptible to various soilborne diseases, such as foot and root rot and wilting, caused by pathogens as Fusarium and Pythium. The Grºeen Challenges project aims to reduce the use of chemical plant protection products and to develop new measures and strategies for disease and pest control through a system approach. This project investigated which measures can be taken to promote soil disease suppression and induced plant resistance against soilborne pathogens (Fusarium and Pythium) in different horticultural crops: vegetable crops (tomato and cucumber) and ornamental crop (lisianthus).
Comparative Metabolomics and Molecular Phylogenetics of Melon (Cucumis melo, Cucurbitaceae) Biodiversity
Moing, Annick ; Allwood, J.W. ; Aharoni, Asaph ; Baker, John ; Beale, M.H. ; Ben-Dor, Shifra ; Biais, B. ; Brigante, Federico ; Burger, Yosef ; Deborde, C. ; Erban, A. ; Doron-Faigenboim, Adi ; Gur, Amit ; Goodacre, R. ; Hansen, T. ; Jacob, Daniel ; Katzir, Nurit ; Kopka, Joachim ; Lewinsohn, Efraim ; Maucourt, Mickael ; Meir, Sagit ; Miller, Sonia ; Mumm, R. ; Oren, Elad ; Paris, Harry S. ; Rogachev, Ilana ; Rollin, Dominique ; Saar, Uzi ; Schjoerring, Jan K. ; Tadmor, Y. ; Tzuri, Galil ; Vos, C.H. de; Ward, J. ; Yeselson, Elena ; Hall, R.D. ; Schaffer, A. - \ 2020
Metabolites 10 (2020)3. - ISSN 2218-1989 - 26 p.
The broad variability of Cucumis melo (melon, Cucurbitaceae) presents a challenge to conventional classification and organization within the species. To shed further light on the infraspecific relationships within C. melo, we compared genotypic and metabolomic similarities among 44 accessions representative of most of the cultivar-groups. Genotyping-by-sequencing (GBS) provided
over 20,000 single-nucleotide polymorphisms (SNPs). Metabolomics data of the mature fruit flesh and rind provided over 80,000 metabolomic and elemental features via an orchestra of six complementary metabolomic platforms. These technologies probed polar, semi-polar, and non-polar metabolite
fractions as well as a set of mineral elements and included both flavor- and taste-relevant volatile and non-volatile metabolites. Together these results enabled an estimate of “metabolomic/elemental distance” and its correlation with the genetic GBS distance of melon accessions. This study indicates
that extensive and non-targeted metabolomics/elemental characterization produced classifications that strongly, but not completely, reflect the current and extensive genetic classification. Certain melon Groups, such as Inodorous, clustered in parallel with the genetic classifications while other genome
to metabolome/element associations proved less clear. We suggest that the combined genomic, metabolic, and element data reflect the extensive sexual compatibility among melon accessions and the breeding history that has, for example, targeted metabolic quality traits, such as taste and flavor.
Stimulated biosynthesis of delphinidin-related anthocyanins in tea shoots reducing the quality of green tea in summer
Zhang, Qunfeng ; Hu, Jianhui ; Liu, Meiya ; Shi, Yuanzhi ; Vos, C.H. de; Ruan, Jianyun - \ 2020
Journal of the Science of Food and Agriculture 100 (2020)4. - ISSN 0022-5142 - p. 1505 - 1514.
BACKGROUND: Greater proportions of purple tea buds and leaves usually appear in the summer, which seriously affects the
color and taste quality of green tea products, yet the metabolism of purple tea shoots in summer remains unclear. Here, the metabolomic profiles and gene expression of related flavonoid metabolic pathways in the purple and normal green shoots of ‘Longjing 43’, and the quality of green teamade with these two phenotypes, were analyzed and compared.
RESULTS: Differential metabolites identified using high-performance liquid chromatography–Orbitrap/mass spectrometry indicated that anthocyanin biosynthesis in purple leaves was enriched, with higher levels of anthocyanidins
(delphinidin-hexose-coumaroyl showed the greatest increase), proanthocyanidins (oligomers of catechins) and kaempferol
glycoside. Expression patterns of the genes ANR, ANS, FLS, LAR, C4H, PAL, CHI, CHS and DFR revealed that the metabolism of
anthocyanin is positively regulated by high temperature and/or light levels in summer. Gas chromatography–mass spectrometry
results showed that, in purple tea shoots, themetabolism of carbohydrates was enriched whereas that of amino acids was
diminished, while their mannose, fructose, D-galactose, sorbose and D-glucose contents were more than double those found in green leaves. A sensory evaluation confirmed that a greater quantity of purple shoots had a greater negative impact on green tea quality because of a bitter taste and dark color (leaves and infusions were tested).
CONCLUSIONS: These results highlight the need for and possibility of improving commercial tea quality via cultivation that
controls the temperature or light of tea gardens during the summer.
© 2019 Society of Chemical Industry
Supporting information may be found in the
Variation in secondary metabolites in a unique set of tomato accessions collected in Turkey
Bakir, Sena ; Capanoglu, Esra ; Hall, Robert D. ; Vos, Ric C.H. de - \ 2020
Food Chemistry 317 (2020). - ISSN 0308-8146
Acetonitrile (Pubchem CID: 6342) - Formic acid (Pubchem CID: 284) provided by Merck (Frankfurter, Germany) - LC-MS grade methanol (Pubchem CID: 887) - Metabolomics - Multivariate analysis - Semi-polar phytochemicals - Tomato
In this study, 50 tomato landraces grown in Turkey were investigated in terms of their secondary metabolite profiles. Each accession was planted in 2016 and 2017 in 3 replicates in an open field. In this study, color, pH and brix of the fruit samples were measured and an unbiased LCMS-based metabolomics approach was applied. Based on Principal Components Analysis (PCA) and Hierarchical Cluster Analysis (HCA) of the relative abundance levels of >250 metabolites, it could be concluded that fruit size was the most influential to the biochemical composition, rather than the geographical origin of accessions. Results indicated substantial biodiversity in various metabolites generally regarded as key to fruit quality aspects, including sugars; phenolic compounds like phenylpropanoids and flavonoids; alkaloids and glycosides of flavour-related volatile compounds. The phytochemical data provides insight into which Turkish accessions might be most promising as starting materials for the tomato processing and breeding industries.
Identification of bioactive phytochemicals in mulberries
D’urso, Gilda ; Mes, Jurriaan J. ; Montoro, Paola ; Hall, Robert D. ; Vos, Ric C.H. de - \ 2020
Metabolites 10 (2020)1. - ISSN 2218-1989
Antioxidant activity - High resolution mass spectrometry - In vitro gastrointestinal digestion - Mulberry - α-glucosidase inhibitory activity
Mulberries are consumed either freshly or as processed fruits and are traditionally used to tackle several diseases, especially type II diabetes. Here, we investigated the metabolite compositions of ripe fruits of both white (Morus alba) and black (Morus nigra) mulberries, using reversed-phase HPLC coupled to high resolution mass spectrometry (LC-MS), and related these to their in vitro antioxidant and α-glucosidase inhibitory activities. Based on accurate masses, fragmentation data, UV/Vis light absorbance spectra and retention times, 35 metabolites, mainly comprising phenolic compounds and amino sugar acids, were identified. While the antioxidant activity was highest in M. nigra, the α-glucosidase inhibitory activities were similar between species. Both bioactivities were mostly resistant to in vitro gastrointestinal digestion. To identify the bioactive compounds, we combined LC-MS with 96-well-format fractionation followed by testing the individual fractions for α-glucosidase inhibition, while compounds responsible for the antioxidant activity were identified using HPLC with an online antioxidant detection system. We thus determined iminosugars and phenolic compounds in both M. alba and M. nigra, and anthocyanins in M. nigra as being the key α-glucosidase inhibitors, while anthocyanins in M. nigra and both phenylpropanoids and flavonols in M. alba were identified as key antioxidants in their ripe berries.
Green and White Asparagus (Asparagus officinalis): A Source of Developmental, Chemical and Urinary Intrigue
Pegiou, Irini ; Mumm, R. ; Acharya, Parag ; Vos, C.H. de; Hall, R.D. - \ 2020
Metabolites 10 (2020)1. - ISSN 2218-1989
asparagus; secondary metabolites; asparagus aroma; flavour; phytonutrients; plant metabolomics
Asparagus (Asparagus officinalis) is one of the world’s top 20 vegetable crops. Both green and white shoots (spears) are produced; the latter being harvested before becoming exposed to light. The crop is grown in nearly all areas of the world, with the largest production regions being China, Western Europe, North America and Peru. Successful production demands high farmer input and specific environmental conditions and cultivation practices. Asparagus materials have also been used for centuries as herbal medicine. Despite this widespread cultivation and consumption, we still know relatively little about the biochemistry of this crop and how this relates to the nutritional, flavour, and neutra-pharmaceutical properties of the materials used. To date, no-one has directly compared the contrasting compositions of the green and white crops. In this short review, we have summarised most of the literature to illustrate the chemical richness of the crop and how this might relate to key quality parameters. Asparagus has excellent nutritional properties and its flavour/fragrance is attributed to a set of volatile components including pyrazines and sulphur-containing compounds. More detailed research, however, is needed and we propose that (untargeted) metabolomics should have a more prominent role to play in these investigations.
A genetical metabolomics approach for bioprospecting plant biosynthetic gene clusters
Witjes, Lotte ; Kooke, Rik ; Hooft, Justin van der; Vos, Ric de; Keurentjes, Joost ; Medema, Marnix ; Nijveen, Harm - \ 2019
Wageningen University & Research
Bioinformatics - Specialized metabolism - Natural products - Gene cluster - Genetics - GWAS - QTL - Metabolomics - Mass spectrometry - Comparative genomics
Coupling DAD and MS data in untargeted metabolomics
Wehrens, H.R.M.J. ; Engel, J. ; Treuren, R. van; Vos, R. de; Haug, Kenneth ; Rocca-Serra, Philippe - \ 2019
Influence of foliar kaolin application and irrigation on photosynthetic activity of grape berries
Garrido, Andreia ; Serôdio, João ; Vos, Ric De ; Conde, Artur ; Cunha, Ana - \ 2019
Agronomy 9 (2019)11. - ISSN 2073-4395
Grape berry tissues - Irrigation - Kaolin - Light micro-climates - Mitigation strategies - Photosynthesis - Photosynthetic pigments - Pulse amplitude modulated (PAM) fluorometry - Vitis vinifera L
Climate changes may cause severe impacts both on grapevine and berry development. Foliar application of kaolin has been suggested as a mitigation strategy to cope with stress caused by excessive heat/radiation absorbed by leaves and grape berry clusters. However, its effect on the light micro-environment inside the canopy and clusters, as well as on the acclimation status and physiological responses of the grape berries, is unclear. The main objective of this work was to evaluate the effect of foliar kaolin application on the photosynthetic activity of the exocarp and seeds, which are the main photosynthetically active berry tissues. For this purpose, berries from high light (HL) and low light (LL) microclimates in the canopy, from kaolin-treated and non-treated, irrigated and non-irrigated plants, were collected at three developmental stages. Photochemical and non-photochemical efficiencies of both tissues were obtained by a pulse amplitude modulated chlorophyll fluorescence imaging analysis. The maximum quantum efficiency (Fv/Fm) data for green HL-grown berries suggest that kaolin application can protect the berry exocarp from light stress. At the mature stage, exocarps of LL grapes from irrigated plants treated with kaolin presented higher Fv/Fm and relative electron transport rates (rETR200) than those without kaolin. However, for the seeds, a negative interaction between kaolin and irrigation were observed especially in HL grapes. These results highlight the impact of foliar kaolin application on the photosynthetic performance of grape berries growing under different light microclimates and irrigation regimes, throughout the season. This provides insights for a more case-oriented application of this mitigation strategy on grapevines.
Glucosinolate variability between turnip organs during development
Bonnema, Guusje ; Lee, Jun Gu ; Shuhang, Wang ; Lagarrigue, David ; Bucher, Johan ; Wehrens, Ron ; Vos, Ric De; Beekwilder, Jules - \ 2019
PLoS ONE 14 (2019)6. - ISSN 1932-6203
Turnip (Brassica rapa spp. rapa) is an important vegetable species, with a unique physiology. Several plant parts, including both the turnip tubers and leaves, are important for human consumption. During the development of turnip plants, the leaves function as metabolic source tissues, while the tuber first functions as a sink, while later the tuber turns into a source for development of flowers and seeds. In the present study, chemical changes were determined for two genotypes with different genetic background, and included seedling, young leaves, mature leaves, tuber surface, tuber core, stalk, flower and seed tissues, at seven different time points during plant development. As a basis for understanding changes in glucosinolates during plant development, the profile of glucosinolates was analysed using liquid chromatography (LC) coupled to mass spectrometry (MS). This analysis was complemented by a gene expression analysis, focussed on GLS biosynthesis, which could explain part of the observed variation, pointing to important roles of specific gene orthologues for defining the chemical differences. Substantial differences in glucosinolate profiles were observed between above-ground tissues and turnip tuber, reflecting the differences in physiological role. In addition, differences between the two genotypes and between tissues that were harvested early or late during the plant lifecycle. The importance of the observed differences in glucosinolate profile for the ecophysiology of the turnip and for breeding turnips with optimal chemical profiles is discussed.
Metabolomics of Thrips Resistance in Pepper (Capsicum spp.) Reveals Monomer and Dimer Acyclic Diterpene Glycosides as Potential Chemical Defenses
Macel, Mirka ; Visschers, I.S.G. ; Peters, Janny ; Kappers, I.F. ; Vos, C.H. de; Dam, Nicole M. van - \ 2019
Journal of Chemical Ecology 45 (2019)5-6. - ISSN 0098-0331 - p. 490 - 501.
Capsianosides . Frankliniella occidentalis . Liquid chromatography-mass spectrometry . Insects . Solanaceae . Thrips
The development of pesticide resistance in insects and recent bans on pesticides call for the identification of natural sources of
resistance in crops. Here, we used natural variation in pepper (Capsicum spp.) resistance combined with an untargeted metabolomics
approach to detect secondary metabolites related to thrips (Frankliniella occidentalis) resistance. Using leaf disc choice
assays, we tested 11 Capsicum accessions of C. annuum and C. chinense in both vegetative and flowering stages for thrips
resistance. Metabolites in the leaves of these 11 accessions were analyzed using LC-MS based untargeted metabolomics. The
choice assays showed significant differences among the accessions in thrips feeding damage. The level of resistance depended on
plant developmental stage. Metabolomics analyses showed differences in metabolomes among the Capsicum species and plant
developmental stages. Moreover, metabolomic profiles of resistant and susceptible accessions differed. Monomer and dimer
acyclic diterpene glycosides (capsianosides) were pinpointed as metabolites that were related to thrips resistance. Sucrose and
malonylated flavone glycosides were related to susceptibility. To our knowledge, this is the first time that dimer capsianosides of
pepper have been linked to insect resistance. Our results show the potential of untargeted metabolomics as a tool for discovering
metabolites that are important in plant – insect interactions.
Keywords Capsianosides . Frankliniella occidentalis . Liquid chromatography-mass spectrometry . Insects . Solanaceae . Thrips
Association between vitamin content, plant morphology and geographical origin in a worldwide collection of the orphan crop Gynandropsis gynandra (Cleomaceae)
Sogbohossou, E.O.D. ; Kortekaas, Dieke ; Achigan-Dako, Enoch G. ; Maundu, Patrick ; Stoilova, Tsvetilina ; Deynze, Allen Van; Vos, C.H. de; Schranz, M.E. - \ 2019
Planta 250 (2019)3. - ISSN 0032-0935 - p. 933 - 947.
Main conclusion: The variability in nutrient content and morphology in Gynandropsis gynandra is associated with the geographic origin of the accessions and provides a basis for breeding for higher levels of vitamin C, carotenoids or tocopherols in higher-yielding cultivars.We examined the variation in carotenoids, tocopherols and ascorbic acid as well as morphological traits in a worldwide germplasm of 76 accessions of the orphan leafy vegetable Gynandropsis gynandra (Cleomaceae) using greenhouse experiments and high-performance liquid chromatography analysis. The levels of carotenoids and tocopherols accumulating in the leaves varied significantly across accessions and were linked with the geographical origin and morphological variation. The main carotenoids included lutein, β-carotene, α-carotene and violaxanthin. A twofold to threefold variation was observed for these compounds. The main tocopherols detected were α-tocopherol and γ-tocopherol with a 20-fold variation. A ninefold variation in vitamin C concentration and independent of geographical origin was observed. Overall, the accessions were grouped into three clusters based on variation in nutrient content and morphology. West African accessions were short plants with small leaves and with high tocopherol contents and relatively low carotenoid contents, Asian accessions were short plants with broad leaves and with relatively low carotenoid and high tocopherol contents, while East–Southern African plants were tall with high contents of both carotenoids and chlorophylls and low tocopherol contents. Carotenoids were positively correlated with plant height as well as foliar and floral traits but negatively correlated with tocopherols. The absence of a significant correlation between vitamin C and other traits indicated that breeding for high carotenoids or tocopherols content may be coupled with improved leaf yield and vitamin C content. Our study provides baseline information on the natural variation available for traits of interest for breeding for enhanced crop yield and nutrient content in Gynandropsis gynandra.
Pyrethric acid of natural pyrethrin insecticide: complete pathway elucidation and reconstitution in Nicotiana benthamiana
Xu, H. ; Li, Wei ; Schilmiller, Anthony L. ; Eekelen, H.D.L.M. van; Vos, C.H. de; Jongsma, M.A. ; Pichersky, E. - \ 2019
New Phytologist 223 (2019)2. - ISSN 0028-646X - p. 751 - 765.
In the natural pesticides known as pyrethrins, which are esters produced in flowers of Tanacetum cinerariifolium (Asteraceae), the monoterpenoid acyl moiety is pyrethric acid or chrysanthemic acid.
We show here that pyrethric acid is produced from chrysanthemol in six steps catalyzed by four enzymes, the first five steps occurring in the trichomes covering the ovaries and the last one occurring inside the ovary tissues.
Three steps involve the successive oxidation of carbon 10 (C10) to a carboxylic group by TcCHH, a cytochrome P450 oxidoreductase. Two other steps involve the successive oxidation of the hydroxylated carbon 1 to give a carboxylic group by TcADH2 and TcALDH1, the same enzymes that catalyze these reactions in the formation of chrysanthemic acid. The ultimate result of the actions of these three enzymes is the formation of 10‐carboxychrysanthemic acid in the trichomes. Finally, the carboxyl group at C10 is methylated by TcCCMT, a member of the SABATH methyltransferase family, to give pyrethric acid. This reaction occurs mostly in the ovaries.
Expression in N. benthamiana plants of all four genes encoding aforementioned enzymes, together with TcCDS, a gene that encodes an enzyme that catalyzes the formation of chrysanthemol, led to the production of pyrethric acid.
A genetical metabolomics approach for bioprospecting plant biosynthetic gene clusters
Witjes, Lotte ; Kooke, Rik ; Hooft, Justin J.J. van der; Vos, Ric C.H. de; Keurentjes, Joost J.B. ; Medema, Marnix H. ; Nijveen, Harm - \ 2019
BMC Research Notes 12 (2019)1. - ISSN 1756-0500
Bioinformatics - Comparative genomics - Gene cluster - Genetics - GWAS - Mass spectrometry - Metabolomics - Natural products - QTL - Specialized metabolism
Objective: Plants produce a plethora of specialized metabolites to defend themselves against pathogens and insects, to attract pollinators and to communicate with other organisms. Many of these are also applied in the clinic and in agriculture. Genes encoding the enzymes that drive the biosynthesis of these metabolites are sometimes physically grouped on the chromosome, in regions called biosynthetic gene clusters (BGCs). Several algorithms have been developed to identify plant BGCs, but a large percentage of predicted gene clusters upon further inspection do not show coexpression or do not encode a single functional biosynthetic pathway. Hence, further prioritization is needed. Results: Here, we introduce a strategy to systematically evaluate potential functions of predicted BGCs by superimposing their locations on metabolite quantitative trait loci (mQTLs). We show the feasibility of such an approach by integrating automated BGC prediction with mQTL datasets originating from a recombinant inbred line (RIL) population of Oryza sativa and a genome-wide association study (GWAS) of Arabidopsis thaliana. In these data, we identified several links for which the enzyme content of the BGCs matches well with the chemical features observed in the metabolite structure, suggesting that this method can effectively guide bioprospecting of plant BGCs.
Light-Induced Vitamin C Accumulation in Tomato Fruits is Independent of Carbohydrate Availability
Ntagkas, N. ; Woltering, E.J. ; Bouras, Sofoklis ; Vos, C.H. de; Dieleman, J.A. ; Nicole, Celine ; Labrie, C.W. ; Marcelis, L.F.M. - \ 2019
Plants 8 (2019)4. - ISSN 2223-7747
L-ascorbate (ASC) is essential for human health. Therefore, there is interest in increasing the ASC content of crops like tomato. High irradiance induces accumulation of ASC in green tomato fruits. The D-mannose/L-galactose biosynthetic pathway accounts for the most ASC in plants. The myo-inositol and galacturonate pathways have been proposed to exist but never identified in plants. The D-mannose/L-galactose starts from D-glucose. In a series of experiments, we tested the hypothesis that ASC levels depend on soluble carbohydrate content when tomato fruits ripen under irradiances that stimulate ASC biosynthesis. We show that ASC levels considerably increased when fruits ripened under light, but carbohydrate levels did not show a parallel increase. When carbohydrate levels in fruits were altered by flower pruning, no effects on
ASC levels were observed at harvest or after ripening under irradiances that induce ASC accumulation. Artificial feeding of trusses with sucrose increased carbohydrate levels, but did not affect the light-induced ASC levels. We conclude that light-induced accumulation of ASC is independent of the carbohydrate content in tomato fruits. In tomato fruit treated with light, the increase in ASC was preceded by a concomitant increase in myo-inositol.
Effects of cultivation practices on the nutritional value of crops : Wiki
Delden, S.H. van; Nijhuis, A.P. ; Talsma, E.F. ; Verdonk, J.C. ; Vos, C.H. de - \ 2019
Wageningen : Groen Kennisnet
This document was written for a Wageningen UR Knowledge Share (WURKS) programme in 2018. The aim of WURKS programmes is to keep educational content of the agronomic sector up to date and is financed by the Dutch Ministry of Agriculture, Nature and Food Quality (LNV). This specific program is targeted at “Tuin- en Akkerbouw” students at applied Universities (HBO) in the Netherlands.
Epigenetic mapping of the Arabidopsis metabolome reveals mediators of the epigenotype-phenotype map
Kooke, R. ; Morgado, L.N. ; Becker, F.F.M. ; Eekelen, H.D.L.M. van; Hazarika, Rashmi ; Zhang, Qunfeng ; Vos, C.H. de; Johannes, Frank ; Keurentjes, J.J.B. - \ 2019
Genome Research 29 (2019)1. - ISSN 1088-9051 - p. 96 - 106.
Identifying the sources of natural variation underlying metabolic differences between plants will enable a better understanding of plant metabolism and provide insights into the regulatory networks that govern plant growth and morphology. So far, however, the contribution of epigenetic variation to metabolic diversity has been largely ignored. In the present study, we utilized a panel of Arabidopsis thaliana epigenetic recombinant inbred lines (epiRILs) to assess the impact of epigenetic variation on the metabolic composition. Thirty epigenetic QTL (QTLepi) were detected, which partly overlap with QTLepi linked to growth and morphology. In an effort to identify causal candidate genes in the QTLepi regions or their putative trans-targets we performed in silico small RNA and qPCR analyses. Differentially expressed genes were further studied by phenotypic and metabolic analyses of knockout mutants. Three genes were detected that recapitulated the detected QTLepi effects, providing evidence for epigenetic regulation in cis and in trans. These results indicate that epigenetic mechanisms impact metabolic diversity, possibly via small RNAs, and thus aid in further disentangling the complex epigenotype-phenotype map.