Autonomous Greenhouse Challenge, Second Edition (2019)
Hemming, Silke ; Zwart, Feije de; Elings, Anne ; Petropoulou, Anna ; Righini, Isabella - \ 2020
Wageningen University & Research
artificial intelligence - autonomous greenhouse - horticulture - tomato - sensors - Greenhouse climate - Resource consumption
The dataset contains data on outdoor and indoor greenhouse climate, irrigation, status of actuators, requested and realized climate setpoints, resource consumption, harvest, crop-related parameters, tomato quality, analysis of irrigation and drain samples and root-zone/slab information. Data were collected during a 6-month cherry tomato production (cv. Axiany) in 6 high-tech glasshouse compartments, located at the Wageningen Research Centre in Bleiswijk (The Netherlands). The dataset was produced during the second edition of Autonomous Greenhouse Challenge. This competition sees five international teams - consisting of scientists, professionals and students with multi-disciplinary expertise - challenging themselves in order to make a large step towards the Autonomous Greenhouse. The teams' names are: The Automators, AICU, IUA.CAAS, Digilog and Automatoes. The teams developed their own intelligent algorithms and used them to determine the set points for climate, irrigation and a number of cultivation-related parameters and control the production of cherry tomato crop remotely. The teams objective was to maximize net profit, by minimizing use of resources (e.g. water, nutrients, energy -heating and electricity- CO2) while optimizing income as a function of production and fruit quality. The achievements in AI-controlled compartments were compared with a reference compartment, operated manually by three Dutch commercial growers (named Reference). The dataset contains raw and processed data. Raw data were collected via climate measuring boxes and sensors, climate and irrigation process computer, weather station, manual registrations (performed by the greenhouse staff).
Salt stress and fluctuating light have separate effects on photosynthetic acclimation, but interactively affect biomass
Zhang, Yuqi ; Kaiser, Elias ; Marcelis, Leo F.M. ; Yang, Qichang ; Li, Tao - \ 2020
Plant, Cell & Environment 43 (2020)9. - ISSN 0140-7791 - p. 2192 - 2206.
fluctuating light - light acclimation - photosynthesis - salt stress - stomatal conductance - tomato
In nature, soil salinity and fluctuating light (FL) often occur concomitantly. However, it is unknown whether salt stress interacts with FL on leaf photosynthesis, architecture, biochemistry, pigmentation, mineral concentrations, as well as whole-plant biomass. To elucidate this, tomato (Solanum lycopersicum) seedlings were grown under constant light (C, 200 μmol m−2 s−1) or FL (5–650 μmol m−2 s−1), in combination with no (0 mM NaCl) or moderate (80 mM NaCl) salinity, for 14 days, at identical photoperiods and daily light integrals. FL and salt stress had separate effects on leaf anatomy, biochemistry and photosynthetic capacity: FL reduced leaf thickness as well as nitrogen, chlorophyll and carotenoid contents per unit leaf area, but rarely affected steady-state and dynamic photosynthetic properties along with abundance of key proteins in the electron transport chain. Salt stress, meanwhile, mainly disorganized chloroplast grana stacking, reduced stomatal density, size and aperture as well as photosynthetic capacity. Plant biomass was affected interactively by light regime and salt stress: FL reduced biomass in salt stressed plants by 17%, but it did not affect biomass of non-stressed plants. Our results stress the importance of considering FL when inferring effects of salt-stress on photosynthesis and productivity under fluctuating light intensities.
The genetic and functional analysis of flavor in commercial tomato: the FLORAL4 gene underlies a QTL for floral aroma volatiles in tomato fruit
Tikunov, Yury M. ; Roohanitaziani, Raana ; Meijer-Dekens, Fien ; Molthoff, Jos ; Paulo, Joao ; Finkers, Richard ; Capel, Iris ; Carvajal Moreno, Fatima ; Maliepaard, Chris ; Nijenhuis-de Vries, Mariska ; Labrie, Caroline W. ; Verkerke, Wouter ; Heusden, Adriaan W. van; Eeuwijk, Fred van; Visser, Richard G.F. ; Bovy, Arnaud G. - \ 2020
The Plant Journal 103 (2020)3. - ISSN 0960-7412
2-phenylethanol - aroma - flavor - quantitative trait loci - Solanum lycopersicum - tomato - volatiles
Tomato (Solanum lycopersicum L.) has become a popular model for genetic studies of fruit flavor in the last two decades. In this article we present a study of tomato fruit flavor, including an analysis of the genetic, metabolic and sensorial variation of a collection of contemporary commercial glasshouse tomato cultivars, followed by a validation of the associations found by quantitative trait locus (QTL) analysis of representative biparental segregating populations. This led to the identification of the major sensorial and chemical components determining fruit flavor variation and detection of the underlying QTLs. The high representation of QTL haplotypes in the breeders’ germplasm suggests that there is great potential for applying these QTLs in current breeding programs aimed at improving tomato flavor. A QTL on chromosome 4 was found to affect the levels of the phenylalanine-derived volatiles (PHEVs) 2-phenylethanol, phenylacetaldehyde and 1-nitro-2-phenylethane. Fruits of near-isogenic lines contrasting for this locus and in the composition of PHEVs significantly differed in the perception of fruity and rose-hip-like aroma. The PHEV locus was fine mapped, which allowed for the identification of FLORAL4 as a candidate gene for PHEV regulation. Using a gene-editing-based (CRISPR-CAS9) reverse-genetics approach, FLORAL4 was demonstrated to be the key factor in this QTL affecting PHEV accumulation in tomato fruit.
Detection of QTLs for genotype × environment interactions in tomato seeds and seedlings
Geshnizjani, Nafiseh ; Snoek, Basten L. ; Willems, Leo A.J. ; Rienstra, Juriaan A. ; Nijveen, Harm ; Hilhorst, Henk W.M. ; Ligterink, Wilco - \ 2020
Plant, Cell & Environment 43 (2020)8. - ISSN 0140-7791 - p. 1973 - 1988.
high phosphate - low nitrogen - maternal environment - QTL × E - seed quality - seedling establishment - tomato
Seed quality and seedling establishment are the most important factors affecting successful crop development. They depend on the genetic background and are acquired during seed maturation and therefor, affected by the maternal environment under which the seeds develop. There is little knowledge about the genetic and environmental factors that affect seed quality and seedling establishment. The aim of this study is to identify the loci and possible molecular mechanisms involved in acquisition of seed quality and how these are controlled by adverse maternal conditions. For this, we used a tomato recombinant inbred line (RIL) population consisting of 100 lines which were grown under two different nutritional environmental conditions, high phosphate and low nitrate. Most of the seed germination traits such as maximum germination percentage (Gmax), germination rate (t50) and uniformity (U8416) showed ample variation between genotypes and under different germination conditions. This phenotypic variation leads to identification of quantitative trait loci (QTLs) which were dependent on genetic factors, but also on the interaction with the maternal environment (QTL × E). Further studies of these QTLs may ultimately help to predict the effect of different maternal environmental conditions on seed quality and seedling establishment which will be very useful to improve the production of high-performance seeds.
Revisiting the Role of Master Regulators in Tomato Ripening
Wang, Rufang ; Angenent, Gerco C. ; Seymour, Graham ; Maagd, Ruud A. de - \ 2020
Trends in Plant Science 25 (2020)3. - ISSN 1360-1385 - p. 291 - 301.
CRISPR- mutagenesis - gain-of-function - mutants - ripening - tomato - transcription factors
The study of transcriptional regulation of tomato ripening has been led by spontaneous mutations in transcription factor (TF) genes that completely inhibit normal ripening, suggesting that they are ‘master regulators’. Studies using CRISPR/Cas9 mutagenesis to produce knockouts of the underlying genes indicate a different picture, suggesting that the regulation is more robust than previously thought. This requires us to revisit our model of the regulation of ripening and replace it with one involving a network of partially redundant components. At the same time, the fast rise of CRISPR/Cas mutagenesis, resulting in unexpectedly weak phenotypes, compared with knockdown technology, suggests that compensatory mechanisms may obscure protein functions. This emphasises the need for assessment of these mechanisms in plants and for the careful design of mutagenesis experiments.
Metabolic Model of the Phytophthora infestans-Tomato Interaction Reveals Metabolic Switches during Host Colonization
Rodenburg, Sander Y.A. ; Seidl, Michael F. ; Judelson, Howard S. ; Vu, Andrea L. ; Govers, Francine ; Ridder, Dick de - \ 2019
mBio 10 (2019)4. - ISSN 2150-7511
metabolic modeling - metabolism - oomycetes - Phytophthora infestans - tomato
The oomycete pathogen Phytophthora infestans causes potato and tomato late blight, a disease that is a serious threat to agriculture. P. infestans is a hemibiotrophic pathogen, and during infection, it scavenges nutrients from living host cells for its own proliferation. To date, the nutrient flux from host to pathogen during infection has hardly been studied, and the interlinked metabolisms of the pathogen and host remain poorly understood. Here, we reconstructed an integrated metabolic model of P. infestans and tomato (Solanum lycopersicum) by integrating two previously published models for both species. We used this integrated model to simulate metabolic fluxes from host to pathogen and explored the topology of the model to study the dependencies of the metabolism of P. infestans on that of tomato. This showed, for example, that P. infestans, a thiamine auxotroph, depends on certain metabolic reactions of the tomato thiamine biosynthesis. We also exploited dual-transcriptome data of a time course of a full late blight infection cycle on tomato leaves and integrated the expression of metabolic enzymes in the model. This revealed profound changes in pathogen-host metabolism during infection. As infection progresses, P. infestans performs less de novo synthesis of metabolites and scavenges more metabolites from tomato. This integrated metabolic model for the P. infestans-tomato interaction provides a framework to integrate data and generate hypotheses about in planta nutrition of P. infestans throughout its infection cycle.IMPORTANCE Late blight disease caused by the oomycete pathogen Phytophthora infestans leads to extensive yield losses in tomato and potato cultivation worldwide. To effectively control this pathogen, a thorough understanding of the mechanisms shaping the interaction with its hosts is paramount. While considerable work has focused on exploring host defense mechanisms and identifying P. infestans proteins contributing to virulence and pathogenicity, the nutritional strategies of the pathogen are mostly unresolved. Genome-scale metabolic models (GEMs) can be used to simulate metabolic fluxes and help in unravelling the complex nature of metabolism. We integrated a GEM of tomato with a GEM of P. infestans to simulate the metabolic fluxes that occur during infection. This yields insights into the nutrients that P. infestans obtains during different phases of the infection cycle and helps in generating hypotheses about nutrition in planta.
Development of an in vitro protocol to screen Clavibacter michiganensis subsp. michiganensis pathogenicity in different Solanum species.
Mohd Nadzir, M.M. ; Vieira Lelis, Flavia ; Thapa, B. ; Ali, Afrida ; Visser, R.G.F. ; Heusden, A.W. van; Wolf, J.M. van der - \ 2019
Plant Pathology 68 (2019)1. - ISSN 0032-0862 - p. 42 - 48.
Clavibacter - Cmm - disease screening - in vitro - PathoScreen - tomato
Clavibacter michiganensis subsp. michiganensis (Cmm) is a quarantine organism in Europe and in many other countries. It is one of the most severe bacterial pathogens affecting tomato. Screening tomato plants for their resistance level
to Cmm requires a large amount of space under quarantine conditions and is therefore costly. This project developed a new inoculation protocol on in vitro tomato plants to facilitate a more economic and higher throughput disease screening. A new method using the PathoScreen system was tested to localize green fluorescent protein-tagged Cmm in planta and to quantify the pathogen based on the percentage of corrected GFP (cGFP%). The system was sensitive in detecting the GFP-tagged Cmm in the shoots, but in the roots a high autofluorescence masked detection and thus sensitivity of the assay. The in vitro protocol was tested on several wild relatives of tomato, which were previously screened in a greenhouse assay. The correlation between wilt symptoms in vitro and wilt symptoms in the greenhouse was overall moderate (r = 0.6462). The protocol worked well in differentiating the two parents that were used in the mapping studies. This study shows that the in vitro protocol can be efficiently used for resistance breeding in many tomato genotypes.
DNA sequence and shape are predictive for meiotic crossovers throughout the plant kingdom
Demirci, Sevgin ; Peters, Sander A. ; Ridder, Dick de; Dijk, Aalt D.J. van - \ 2018
The Plant Journal 95 (2018)4. - ISSN 0960-7412 - p. 686 - 699.
Arabidopsis thaliana - crossover - DNA shape - genome accessibility - machine learning - maize - meiotic recombination - prediction - rice - tomato
A better understanding of genomic features influencing the location of meiotic crossovers (COs) in plant species is both of fundamental importance and of practical relevance for plant breeding. Using CO positions with sufficiently high resolution from four plant species [Arabidopsis thaliana, Solanum lycopersicum (tomato), Zea mays (maize) and Oryza sativa (rice)] we have trained machine-learning models to predict the susceptibility to CO formation. Our results show that CO occurrence within various plant genomes can be predicted by DNA sequence and shape features. Several features related to genome content and to genomic accessibility were consistently either positively or negatively related to COs in all four species. Other features were found as predictive only in specific species. Gene annotation-related features were especially predictive for maize, whereas in tomato and Arabidopsis propeller twist and helical twist (DNA shape features) and AT/TA dinucleotides were found to be the most important. In rice, high roll (another DNA shape feature) and low CA dinucleotide frequency in particular were found to be associated with CO occurrence. The accuracy of our models was sufficient for Arabidopsis and rice (area under receiver operating characteristic curve, AUROC > 0.5), and was high for tomato and maize (AUROC ≫ 0.5), demonstrating that DNA sequence and shape are predictive for meiotic COs throughout the plant kingdom.
Quantitative Trait Loci in Solanaceae species
Kuzniar, Arnold ; Singh, G. - \ 2018
Wageningen University & Research
plant breeding - plant genetics - quantitative trait locus - QTL - genetic marker - trait - Solanaceae - tomato - potato - FAIR data - RDF - SQLite - csv
This tar archive contains experimental data on Quantitative Trait Loci (QTLs) mapped in Solanacea species. In particular, the QTL data were extracted from tomato- and potato-specific literature using the QTL TableMiner++ tool, and the resulting data were made available in machine-readable and semantically-interoperable formats: SQLite database (.db); comma-separated value file (.csv); RDF/Turle file (.ttl).
The battle in the apoplast: further insights into the roles of proteases and their inhibitors in plant-pathogen interactions
Karimi Jashni, M. ; Mehrabi, R. ; Collemare, J. ; Mesarich, C.H. ; Wit, P.J.G.M. de - \ 2015
Frontiers in Plant Science 6 (2015). - ISSN 1664-462X - 7 p.
cf-2-dependent disease resistance - extracellular serine-protease - l. enhances resistance - class iv chitinases - phytophthora-infestans - cladosporium-fulvum - proteolytic-enzymes - antifungal activity - gene-expression - tomato
Upon host penetration, fungal pathogens secrete a plethora of effectors to promote disease, including proteases that degrade plant antimicrobial proteins, and protease inhibitors (PIs) that inhibit plant proteases with antimicrobial activity. Conversely, plants secrete proteases and PIs to protect themselves against pathogens or to mediate recognition of pathogen proteases and PIs, which leads to induction of defense responses. Many examples of proteases and PIs mediating effector-triggered immunity in host plants have been reported in the literature, but little is known about their role in compromising basal defense responses induced by microbe-associated molecular patterns. Recently, several reports appeared in literature on secreted fungal proteases that modify or degrade pathogenesis-related proteins, including plant chitinases or PIs that compromise their activities. This prompted us to review the recent advances on proteases and PIs involved in fungal virulence and plant defense. Proteases and PIs from plants and their fungal pathogens play an important role in the arms race between plants and pathogens, which has resulted in co-evolutionary diversification and adaptation shaping pathogen lifestyles.
Host plant resistance towards the cabbage whitefly in Brassica oleracea and its wild relatives
Pelgrom, K.T.B. ; Broekgaarden, C. ; Voorrips, R.E. ; Bas, N. ; Visser, R.G.F. ; Vosman, B.J. - \ 2015
Euphytica 202 (2015)2. - ISSN 0014-2336 - p. 297 - 306.
aleyrodes-proletella homoptera - glucosinolate polymorphism - insect-resistance - cultivars - populations - fruticulosa - tomato - tabaci
The cabbage whitefly (Aleyrodes proletella) is a phloem-feeding insect that is a serious problem in Brassica oleracea crops like Brussels sprouts, kale and savoy cabbage. In order to develop whitefly-resistant varieties it is essential to identify effective sources of resistance. In this study, we screened a large collection of 432 accessions, including wild material and landraces of Brassica oleracea as well as crop wild relatives, to determine whitefly performance in a no-choice field experiment. Putatively resistant accessions were further tested under greenhouse conditions. Resistant accessions were identified among B. oleracea var. capitata (cabbage) landraces and in the species B. villosa, B. incana and B. montana. Whereas resistance in cabbage is only expressed in plants of at least 12 weeks old, some wild relatives were already starting to express resistance at 6 weeks. This could open up possibilities for breeding cabbages that are resistant at a young(er) plant age. Our research also shows again the importance of crop wild relatives for finding pest resistances.
Introgression Browser: High throughput whole-genome SNP visualization
Aflitos, S.A. ; Sanchez Perez, G.F. ; Ridder, D. de; Fransz, P. ; Schranz, M.E. ; Jong, J.H.S.G.M. de; Peters, S.A. - \ 2015
The Plant Journal 82 (2015)1. - ISSN 0960-7412 - p. 174 - 182.
in-situ hybridization - alien chromosomes - recombination - tomato - markers - thaliana - potato - identification - organization - improvement
Breeding by introgressive hybridization is a pivotal strategy to broaden the genetic basis of crops. Usually, the desired traits are monitored in consecutive crossing generations by marker-assisted selection, but their analyses fail in chromosome regions where crossover recombinants are rare or not viable. Here, we present the Introgression Browser (IBROWSER), a bioinformatics tool aimed at visualizing introgressions at nucleotide or SNP accuracy. The software selects homozygous SNPs from Variant Call Format (VCF) information and filters out heterozygous SNPs, Multi-Nucleotide Polymorphisms (MNPs) and insertion-deletions (InDels). For data analysis IBROWSER makes use of sliding windows, but if needed it can generate any desired fragmentation pattern through General Feature Format (GFF) information. In an example of tomato (Solanum lycopersicum) accessions we visualize SNP patterns and elucidate both position and boundaries of the introgressions. We also show that our tool is capable of identifying alien DNA in a panel of the closely related S. pimpinellifolium by examining phylogenetic relationships of the introgressed segments in tomato. In a third example, we demonstrate the power of the IBROWSER in a panel of 597 Arabidopsis accessions, detecting the boundaries of a SNP-free region around a polymorphic 1.17 Mbp inverted segment on the short arm of chromosome 4. The architecture and functionality of IBROWSER makes the software appropriate for a broad set of analyses including SNP mining, genome structure analysis, and pedigree analysis. Its functionality, together with the capability to process large data sets and efficient visualization of sequence variation, makes IBROWSER a valuable breeding tool.
Comprehensive metabolomics to evaluate the impact of industrial processing on the phytochemical composition of vegetable purees
Lopez-Sanchez, P. ; Vos, R.C.H. de; Jonker, H.H. ; Mumm, R. ; Hall, R.D. ; Bialek, L. ; Leenman, R. ; Strassburg, K. ; Vreeken, R. ; Hankemeier, T. ; Schumm, S. ; Duynhoven, J.P.M. van - \ 2015
Food Chemistry 168 (2015). - ISSN 0308-8146 - p. 348 - 355.
mass-spectrometry - plant metabolomics - thermal treatments - vitamin-c - broccoli - tomato - fruit - antioxidant - cancer - l.
The effects of conventional industrial processing steps on global phytochemical composition of broccoli, tomato and carrot purees were investigated by using a range of complementary targeted and untargeted metabolomics approaches including LC–PDA for vitamins, 1H NMR for polar metabolites, accurate mass LC–QTOF MS for semi-polar metabolites, LC–MRM for oxylipins, and headspace GC–MS for volatile compounds. An initial exploratory experiment indicated that the order of blending and thermal treatments had the highest impact on the phytochemicals in the purees. This blending-heating order effect was investigated in more depth by performing alternate blending-heating sequences in triplicate on the same batches of broccoli, tomato and carrot. For each vegetable and particularly in broccoli, a large proportion of the metabolites detected in the purees was significantly influenced by the blending-heating order, amongst which were potential health-related phytochemicals and flavour compounds like vitamins C and E, carotenoids, flavonoids, glucosinolates and oxylipins. Our metabolomics data indicates that during processing the activity of a series of endogenous plant enzymes, such as lipoxygenases, peroxidases and glycosidases, including myrosinase in broccoli, is key to the final metabolite composition and related quality of the purees.
A bead-based suspension array for the multiplexed detection of begomoviruses and their whitefly vectors
Brunschot, S.L. van; Bergervoet, J.H.W. ; Pagendam, D.E. ; Weerdt, M. de; Geering, A.D.W. ; Drenth, A. ; Vlugt, R.A.A. van der - \ 2014
Journal of Virological Methods 198 (2014). - ISSN 0166-0934 - p. 86 - 94.
leaf-curl-virus - time pcr assay - bemisia-tabaci - q biotypes - tomato - identification - geminiviruses - aleyrodidae - hemiptera - invasion
Bead-based suspension array systems enable simultaneous fluorescence-based identification of multiple nucleic acid targets in a single reaction. This study describes the development of a novel approach to plant virus and vector diagnostics, a multiplexed 7-plex array that comprises a hierarchical set of assays for the simultaneous detection of begomoviruses and Bemisia tabaci, from both plant and whitefly samples. The multiplexed array incorporates genus, species and strain-specific assays, offering a unique approach for identifying both known and unknown viruses and B. tabaci species. When tested against a large panel of sequence-characterized begomovirus and whitefly samples, the array was shown to be 100% specific to the homologous target. Additionally, the multiplexed array was highly sensitive, efficiently and concurrently determining both virus and whitefly identity from single viruliferous whitefly samples. The detection limit for one assay within the multiplexed array that specifically detects Tomato yellow leaf curl virus-Israel (TYLCV-IL) was quantified as 200 fg of TYLCV-IL DNA, directly equivalent to that of TYLCVspecific qPCR. Highly reproducible results were obtained over multiple tests. The flexible multiplexed array described in this study has great potential for use in plant quarantine, biosecurity and disease management programs worldwide. (C) 2014 Elsevier B.V. All rights reserved.
Mapping in the era of sequencing: high density genotyping and its application for mapping TYLCV resistance in Solanum pimpinellifolium
Viquez-Zamora, M. ; Caro Rios, C.M. ; Finkers, H.J. ; Tikunov, Y.M. ; Bovy, A.G. ; Visser, R.G.F. ; Bai, Y. ; Heusden, A.W. van - \ 2014
BMC Genomics 15 (2014). - ISSN 1471-2164 - 10 p.
leaf-curl-virus - recombinant inbred lines - mass-spectrometry - lycopersicon-pimpinellifolium - tomato - infection - genes - metabolomics - inheritance - population
Background A RIL population between Solanum lycopersicum cv. Moneymaker and S. pimpinellifolium G1.1554 was genotyped with a custom made SNP array. Additionally, a subset of the lines was genotyped by sequencing (GBS). Results A total of 1974 polymorphic SNPs were selected to develop a linkage map of 715 unique genetic loci. We generated plots for visualizing the recombination patterns of the population relating physical and genetic positions along the genome. This linkage map was used to identify two QTLs for TYLCV resistance which contained favourable alleles derived from S. pimpinellifolium. Further GBS was used to saturate regions of interest, and the mapping resolution of the two QTLs was improved. The analysis showed highest significance on Chromosome 11 close to the region of 51.3 Mb (qTy-p11) and another on Chromosome 3 near 46.5 Mb (qTy-p3). Furthermore, we explored the population using untargeted metabolic profiling, and the most significant differences between susceptible and resistant plants were mainly associated with sucrose and flavonoid glycosides. Conclusions The SNP information obtained from an array allowed a first QTL screening of our RIL population. With additional SNP data of a RILs subset, obtained through GBS, we were able to perform an in silico mapping improvement to further confirm regions associated with our trait of interest. With the combination of different¿~¿omics platforms we provide valuable insight into the genetics of S. pimpinellifolium-derived TYLCV resistance.
Response of the zoophytophagous predators Macrolophus pygmaeus and Nesidiocoris tenuis to volatiles of uninfested plants and to plants infested by prey or conspecifics
Lins, J.C. ; Loon, J.J.A. van; Bueno, V.H.P. ; Lucas-Barbosa, D. ; Dicke, M. ; Lenteren, J.C. van - \ 2014
BioControl 59 (2014)6. - ISSN 1386-6141 - p. 707 - 718.
borer tuta-absoluta - carnivorous arthropods - heteroptera miridae - biological-control - infochemical use - spider-mites - tomato - herbivores - bug - caliginosus
Knowledge about the orientation mechanisms used by two important predaceous mirids (Macrolophus pygmaeus Rambour and Nesidiocoris tenuis (Reuter)) in finding their prey (whitefly Bemisia tabaci (Gennadius) and the tomato borer Tuta absoluta (Meyrick)) is limited. In a Y-tube olfactometer, we tested the behavioral responses of naïve and experienced predators to uninfested plants, herbivore-induced plant volatiles (HIPVs) from plants infested with T. absoluta and/or B. tabaci, the sex pheromone of T. absoluta, and volatiles produced by plants injured by the predators. Nesidiocoris tenuis responds to volatiles produced by uninfested plants only after experience with the plant, whereas naïve and experienced M. pygmaeus show positive chemotaxis. Both predators are attracted to volatiles from prey-infested plants, and we provide the first evidence that experience affects this response in M. pygmaeus. Infestation of the same plant by both prey species elicited similar responses by the two predators as plants infested by either herbivore singly. Neither predator responded to sex pheromones of T. absoluta. Macrolophus pygmaeus avoided plants injured by conspecifics, while N. tenuis females were attracted by such plants. The implications of these results for augmentative biological control are discussed.
Responses of two Anthurium cultivars to high daily integrals of diffuse light
Li, T. ; Heuvelink, E. ; Noort, F. van; Kromdijk, J. ; Marcelis, L.F.M. - \ 2014
Scientia Horticulturae 179 (2014). - ISSN 0304-4238 - p. 306 - 313.
radiation-use efficiency - structural plant-model - yield components - growth analysis - photosynthesis - tomato - interception - architecture - quality - biology
Heavy shading is commonly applied during production of pot-plants in order to avoid damage caused by high light intensities; usually the daily light integral (DLI) is limited to 5–8 mol m-2 d-1 photosynthetically active radiation (PAR). However, shading carries a production penalty as light is the driving force for photosynthesis. Diffuse glass has been developed to scatter the incident light in greenhouses. This study aims at investigating the effect of diffuse glass cover and high DLI under diffuse glass cover on the growth of pot-plants; furthermore, to systematically identify and quantify the yield components which are influenced by these treatments. Experiments were carried out with two Anthurium andreanum cultivars (Royal Champion and Pink Champion) in a conventional modern glasshouse compartment covered by clear glass with DLI limited to 7.5 mol m-2 d-1 (average realized DLI was 7.2 mol m-2 d-1), and another two glasshouse compartments covered by diffuse glass with DLI limited to 7.5 (average realized DLI was 7.5 mol m-2 d-1) and 10 mol m-2 d-1 (average realized DLI was 8.9 mol m-2 d-1). Diffuse glass cover resulted in less variation of temporal photosynthetic photon flux density (PPFD) distribution compared with the clear glass cover. Under similar DLI conditions (DLI limited to 7.5 mol m-2 d-1), diffuse glass cover stimulated dry mass production per unit intercepted PPFD (RUE) in ‘Royal Champion’ by 8%; whilst this stimulating effect did not occur in ‘Pink Champion’. Under diffuse glass cover, biomass production was proportional to DLI in both cultivars (within the range 7.5–9 mol m-2 d-1). Consequently higher DLI led to more flowers, leaves and stems. Furthermore, high DLI resulted in more compact plants without light damage in leaves or flowers in both cultivars. ‘Pink Champion’ produced more biomass than ‘Royal Champion’ in all treatments because of higher RUE which resulted from a more advantageous canopy architecture for light capture and more advantageous leaf photosynthetic properties. We conclude that less shading under diffuse glass cover not only stimulates plant growth but also improves plant ornamental quality (i.e. compactness).
Filamentous pathogen effector functions: of pathogens, hosts and microbiomes
Rövenich, H. ; Boshoven, J.C. ; Thomma, B. - \ 2014
Current Opinion in Plant Biology 20 (2014). - ISSN 1369-5266 - p. 96 - 103.
chitin-triggered immunity - secreted fungal effector - potato famine pathogen - cladosporium-fulvum - protease inhibitor - magnaporthe-oryzae - plant-pathogens - genome evolution - tomato - virulence
Microorganisms play essential roles in almost every environment on earth. For instance, microbes decompose organic material, or establish symbiotic relationships that range from pathogenic to mutualistic. Symbiotic relationships have been particularly well studied for microbial plant pathogens and have emphasized the role of effectors; secreted molecules that support host colonization. Most effectors characterized thus far play roles in deregulation of host immunity. Arguably, however, pathogens not only deal with immune responses during host colonization, but also encounter other microbes including competitors, (myco)parasites and even potential co-operators. Thus, part of the effector catalog may target microbiome co-inhabitants rather than host physiology.
Functional analysis of the conserved transcriptional regulator CfWor1 in Cladosporium fulvum reveals diverse roles in the virulence of plant pathogenic fungi
Ökmen, B. ; Collemare, J. ; Griffiths, S.A. ; Burgt, A. van der; Cox, R. ; Wit, P.J.G.M. de - \ 2014
Molecular Microbiology 92 (2014)1. - ISSN 0950-382X - p. 10 - 27.
avirulence gene avr9 - dna-binding domains - candida-albicans - alternaria-brassicicola - magnaporthe-grisea - master regulator - expression - tomato - family - penetration
Fungal Wor1-like proteins are conserved transcriptional regulators that are reported to regulate the virulence of several plant pathogenic fungi by affecting the expression of virulence genes. Here, we report the functional analysis of CfWor1, the homologue of Wor1 in Cladosporium fulvum. ¿cfwor1 mutants produce sclerotium-like structures and rough hyphae, which are covered with a black extracellular matrix. These mutants do not sporulate and are no longer virulent on tomato. A CE.CfWor1 transformant that constitutively expresses CfWor1 produces fewer spores with altered morphology and is also reduced in virulence. RNA-seq and RT-qrtPCR analyses suggest that reduced virulence of ¿cfwor1 mutants is due to global downregulation of transcription, translation and mitochondrial respiratory chain. The reduced virulence of the CE.CfWor1 transformant is likely due to downregulation of effector genes. Complementation of a non-virulent ¿fosge1 (Wor1-homologue) mutant of Fusarium oxysporum f. sp. lycopersici with CfWor1 restored expression of the SIX effector genes in this fungus, but not its virulence. Chimeric proteins of CfWor1/FoSge1 also only partially restored defects of the ¿fosge1 mutant, suggesting that these transcriptional regulators have functionally diverged. Altogether, our results suggest that CfWor1 primarily regulates development of C.¿fulvum, which indirectly affects the expression of a subset of virulence genes.
Increased difficulties to control late blight in Tunisia are caused by a genetically diverse Phytophthora infestans population next to the clonal lineage NA-01
Harbaoui, K. ; Hamada, W. ; Li, Y. ; Vleeshouwers, V.G.A.A. ; Lee, T.A.J. van der - \ 2014
Plant Disease 98 (2014)7. - ISSN 0191-2917 - p. 898 - 908.
genotypic diversity - durable resistance - potato - tomato - plant - netherlands - virulence
In Tunisia, late blight caused by Phytophthora infestans is a serious threat to potato and tomato. The Mediterranean weather conditions can be conducive to infection in all seasons and the host crops, tomato and potato, are grown year round. Potato is planted and harvested in two to four overlapping intervals from August to June and tomato is grown both in open fields and in greenhouses. The consequences of these agricultural practices and the massive import of seed potato on the genetic variation of P. infestans are largely unknown. We conducted a survey in which 165 P. infestans isolates, collected from five subregions in Tunisia between 2006 and 2008, on which we studied genotypic diversity through nuclear (simple-sequence repeat [SSR]) markers and combined this with a previous study on their mitochondrial haplotypes (mtDNA). The phylogenetic analysis revealed the presence of a major clonal lineage (NA-01, A1 mating type, mitochondrial haplotype Ia). Isolates belonging to this clonal lineage were found in all regions and showed a relatively simple virulence pattern on a potato differential set carrying different Solanum demissum resistance genes. Apart from isolates belonging to this NA-01 clonal lineage, a group of isolates was found that showed a high genetic diversity, comprising both mating types and a more complex race structure that was found in the regions where late blight on potato was more difficult to control. The population on potato and tomato seems to be under different selection pressures. Isolates collected from tomato showed a low genetic diversity even though potato isolates collected simultaneously from the same location showed a high genetic diversity. Based on the SSR profile comparison, we could demonstrate that the four major clonal lineages found in the Netherlands and also in other European countries could not be found in Tunisia. Despite the massive import of potato seed from Europe, the P. infestans population in Tunisia was found to be clearly distinct
OsJAR1 is required for JA-regulated floret opening and anther dehiscence in rice
Xiao, Y. ; Charnikhova, T. ; Mulder, P.P.J. ; Heijmans, J. ; Hoogenboom, A. ; Agalou, A. ; Michel, C. ; Morel, J.B. ; Dreni, L. ; Kater, M.M. ; Bouwmeester, H.J. ; Wang, B. ; Zhu, Z. ; Ouwerkerk, P.B.F. - \ 2014
Plant Molecular Biology 86 (2014)1-2. - ISSN 0167-4412 - p. 19 - 33.
jasmonic acid biosynthesis - male-sterile mutant - l-isoleucine - methyl jasmonate - gene encodes - arabidopsis - enzyme - proteins - tomato - (+)-7-iso-jasmonoyl-l-isoleucine
Jasmonates are important phytohormones regulating reproductive development. We used two recessive rice Tos17 alleles of OsJAR1, osjar1-2 and osjar1-3, to study the biological function of jasmonates in rice anthesis. The florets of both osjar1 alleles stayed open during anthesis because the lodicules, which control flower opening in rice, were not withering on time. Furthermore, dehiscence of the anthers filled with viable pollen, was impaired, resulting in lower fertility. In situ hybridization and promoter GUS transgenic analysis confirmed OsJAR1 expression in these floral tissues. Flower opening induced by exogenous applied methyl jasmonate was impaired in osjar1 plants and was restored in a complementation experiment with transgenics expressing a wild type copy of OsJAR1 controlled by a rice actin promoter. Biochemical analysis showed that OsJAR1 encoded an enzyme conjugating jasmonic acid (JA) to at least Ile, Leu, Met, Phe, Trp and Val and both osjar1 alleles had substantial reduction in content of JA-Ile, JA-Leu and JA-Val in florets. We conclude that OsJAR1 is a JA-amino acid synthetase that is required for optimal flower opening and closing and anther dehiscence in rice
Torradoviruses are transmitted in a semi-persistent and stylet-borne manner by three whitefly vectors
Verbeek, M. ; Bekkum, P.J. van; Dullemans, A.M. ; Vlugt, R.A.A. van der - \ 2014
Virus Research 186 (2014). - ISSN 0168-1702 - p. 55 - 60.
plant-virus transmission - picorna-like virus - bemisia-tabaci - tomato - aleyrodidae - efficiency - diseases
Members of the genus Torradovirus (family Secoviridae, type species Tomato torrado virus, ToTV) are spherical plant viruses transmitted by the whitefly species Trialeurodes vaporariorum and Bemisia tabaci. Knowledge on the mode of vector transmission is lacking for torradoviruses. Here, the mode of transmission was determined for Tomato marchitez virus (ToMarV). A minimal acquisition access period (AAP) and inoculation access period (IAP) of approximately 2h each was required for its transmission by T. vaporariorum, while optimal transmission required an AAP and IAP of at least 16h and 8h, respectively. Whiteflies could retain the virus under non-feeding conditions for at least 8h without loss of transmission efficiency, but upon feeding on a non-host plant in between the AAP and IAP they retained the virus for no more than 8h. Similar conditions supported transmission of isolates of ToTV and Tomato chocolàte virus (ToChV) by T. vaporariorum and B. tabaci. Additionally, similar experiments revealed the banded-winged whitefly (Trialeurodes abutilonea) as a vector for all three virus species. The results are congruent with acquisition and retention periods for semi-persistent virus transmission. RT-PCR detection analysis of ToTV and ToMarV in the vector's body revealed their presence in the stylet, but not in the head where the pharynx of the foregut is located. The results altogether indicate a semi-persistent stylet-borne mode of vector transmission for torradoviruses. Additionally, this is the first group of spherical viruses transmitted by at least three different species of whiteflies
Development of late blight resistant potatoes by cisgenic stacking
Jo, K.R. ; Kim, C.J. ; Kim, S.J. ; Kim, T.J. ; Bergervoet-van Deelen, J.E.M. ; Jongsma, M.A. ; Visser, R.G.F. ; Jacobsen, E. ; Vossen, J.H. - \ 2014
BMC Biotechnology 14 (2014). - ISSN 1472-6750
broad-spectrum resistance - cultivar sarpo mira - phytophthora-infestans - solanum-bulbocastanum - r-gene - plants - transformation - genomics - tomato - biotechnology
Background Phytophthora infestans, causing late blight in potato, remains one of the most devastating pathogens in potato production and late blight resistance is a top priority in potato breeding. The introduction of multiple resistance (R) genes with different spectra from crossable species into potato varieties is required. Cisgenesis is a promising approach that introduces native genes from the crops own gene pool using GM technology, thereby retaining favourable characteristics of established varieties. Results We pursued a cisgenesis approach to introduce two broad spectrum potato late blight R genes, Rpi-sto1 and Rpi-vnt1.1 from the crossable species Solanum stoloniferum and Solanum venturii, respectively, into three different potato varieties. First, single R gene-containing transgenic plants were produced for all varieties to be used as references for the resistance levels and spectra to be expected in the respective genetic backgrounds. Next, a construct containing both cisgenic late blight R genes (Rpi-vnt1.1 and Rpi-sto1), but lacking the bacterial kanamycin resistance selection marker (NPTII) was transformed to the three selected potato varieties using Agrobacterium-mediated transformation. Gene transfer events were selected by PCR among regenerated shoots. Through further analyses involving morphological evaluations in the greenhouse, responsiveness to Avr genes and late blight resistance in detached leaf assays, the selection was narrowed down to eight independent events. These cisgenic events were selected because they showed broad spectrum late blight resistance due to the activity of both introduced R genes. The marker-free transformation was compared to kanamycin resistance assisted transformation in terms of T-DNA and vector backbone integration frequency. Also, differences in regeneration time and genotype dependency were evaluated. Conclusions We developed a marker-free transformation pipeline to select potato plants functionally expressing a stack of late blight R genes. Marker-free transformation is less genotype dependent and less prone to vector backbone integration as compared to marker-assisted transformation. Thereby, this study provides an important tool for the successful deployment of R genes in agriculture and contributes to the production of potentially durable late blight resistant potatoes.
Relocation of genes generates non-conserved chromosomal segments in Fusarium graminearum that show distinct and co-regulated gene expression patterns
Zhao, C. ; Waalwijk, C. ; Wit, P.J.G.M. de; Tang, D. ; Lee, T.A.J. van der - \ 2014
BMC Genomics 15 (2014). - ISSN 1471-2164 - 17 p.
polyketide synthase genes - gibberella-zeae - rna-seq - oxysporum - evolution - reveals - resistance - virulence - tomato - yeast
BACKGROUND: Genome comparisons between closely related species often show non-conserved regions across chromosomes. Some of them are located in specific regions of chromosomes and some are even confined to one or more entire chromosomes. The origin and biological relevance of these non-conserved regions are still largely unknown. Here we used the genome of Fusarium graminearum to elucidate the significance of non-conserved regions. RESULTS: The genome of F. graminearum harbours thirteen non-conserved regions dispersed over all of the four chromosomes. Using RNA-Seq data from the mycelium of F. graminearum, we found weakly expressed regions on all of the four chromosomes that exactly matched with non-conserved regions. Comparison of gene expression between two different developmental stages (conidia and mycelium) showed that the expression of genes in conserved regions is stable, while gene expression in non-conserved regions is much more influenced by developmental stage. In addition, genes involved in the production of secondary metabolites and secreted proteins are enriched in non-conserved regions, suggesting that these regions could also be important for adaptations to new environments, including adaptation to new hosts. Finally, we found evidence that non-conserved regions are generated by sequestration of genes from multiple locations. Gene relocations may lead to clustering of genes with similar expression patterns or similar biological functions, which was clearly exemplified by the PKS2 gene cluster. CONCLUSIONS: Our results showed that chromosomes can be functionally divided into conserved and non-conserved regions, and both could have specific and distinct roles in genome evolution and regulation of gene expression
Lettuce necrotic leaf curl virus, a new plant virus infecting lettuce and a proposed member of the genus Torradovirus
Verbeek, M. ; Dullemans, A.M. ; Raaij, H.M.G. van; Verhoeven, J.Th.J. ; Vlugt, R.A.A. van der - \ 2014
Archives of Virology 159 (2014)4. - ISSN 0304-8608 - p. 801 - 805.
stranded rna viruses - picorna-like virus - tomato - family
A new virus was isolated from a lettuce plant grown in an open field in the Netherlands in 2011. This plant was showing conspicuous symptoms that consisted of necrosis and moderate leaf curling. The virus was mechanically transferred to indicator plants, and a total RNA extract of one of these indicator plants was used for next-generation sequencing. Analysis of the sequences that were obtained and further biological studies showed that the virus was related to, but clearly distinct from, viruses belonging to the genus Torradovirus. The name “lettuce necrotic leaf curl virus” (LNLCV) is proposed for this new torrad
Positive selection and intragenic recombination contribute to high allelic diversity in effector genes of Mycosphaerella fijiensis, causal agent of the black leaf streak disease of banana
Stergiopoulos, I. ; Cordovez da Cunha, V. ; Okmen, B. ; Beenen, H.G. ; Kema, G.H.J. ; Wit, P.J.G.M. de - \ 2014
Molecular Plant Pathology 15 (2014)5. - ISSN 1464-6722 - p. 447 - 460.
pathogen cladosporium-fulvum - phylogenetic analysis - musa-acuminata - cf-4-mediated resistance - population-genetics - maximum-likelihood - evolution - proteins - fungal - tomato
Previously, we have determined the nonhost-mediated recognition of the MfAvr4 and MfEcp2 effector proteins from the banana pathogen Mycosphaerella fijiensis in tomato, by the cognate Cf-4 and Cf-Ecp2 resistance proteins, respectively. These two resistance proteins could thus mediate resistance against M.¿fijiensis if genetically transformed into banana (Musa spp.). However, disease resistance controlled by single dominant genes can be overcome by mutated effector alleles, whose products are not recognized by the cognate resistance proteins. Here, we surveyed the allelic variation within the MfAvr4, MfEcp2, MfEcp2-2 and MfEcp2-3 effector genes of M.¿fijiensis in a global population of the pathogen, and assayed its impact on recognition by the tomato Cf-4 and Cf-Ecp2 resistance proteins, respectively. We identified a large number of polymorphisms that could reflect a co-evolutionary arms race between host and pathogen. The analysis of nucleotide substitution patterns suggests that both positive selection and intragenic recombination have shaped the evolution of M.¿fijiensis effectors. Clear differences in allelic diversity were observed between strains originating from South-East Asia relative to strains from other banana-producing continents, consistent with the hypothesis that M.¿fijiensis originated in the Asian-Pacific region. Furthermore, transient co-expression of the MfAvr4 effector alleles and the tomato Cf-4 resistance gene, as well as of MfEcp2, MfEcp2-2 and MfEcp2-3 and the putative Cf-Ecp2 resistance gene, indicated that effector alleles able to overcome these resistance genes are already present in natural populations of the pathogen, thus questioning the durability of resistance that can be provided by these genes in the field.
Cloning and functional characterization of the Rvi15 (Vr2) gene for apple scab resistance
Schouten, H.J. ; Brinkhuis, J. ; Burgh, S. van der; Schaart, J. ; Groenwold, R. ; Broggini, G.A.L. ; Gessler, C. - \ 2014
Tree Genetics and Genomes 10 (2014)2. - ISSN 1614-2942 - p. 251 - 260.
malus x domestica - venturia-inaequalis - cladosporium-fulvum - cisgenic plants - plasma-membrane - vf gene - tomato - locus - proteins - pathogen
Apple scab, caused by Venturia inaequalis, is a serious disease of apple. Previously, the scab resistance Rvi15 (Vr2) from the accession GMAL 2473 was genetically mapped, and three candidate resistance genes were identified. Here, we report the cloning and functional characterization of these three genes, named Vr2-A, Vr2-B, and Vr2-C. Each gene was cloned with its native promoter, terminator and introns, and inserted into the susceptible apple cultivar ‘Gala’. Inoculation of the plants containing Vr2-A and Vr2-B induced no resistance symptoms, but abundant sporulation. However, inoculation of the plants harboring Vr2-C showed a hypersensitive response with clear pinpoint pits, and no or very little sporulation. We conclude that Vr2-C is the Rvi15 (Vr2) gene. This gene belongs to the Toll and mammalian interleukin-1 receptor protein nucleotide-binding site leucine-rich repeat structure resistance gene family. The proteins of this gene family reside in the cytoplasm, whereas V. inaequalis develops in the apoplast, between the epidermis and cuticle, without making haustoria. The spatial separation of the recognizing resistance protein and the pathogen is discussed. This is the second cloned gene for apple scab resistance, and out of these two the only one leading to a symplastic protein.
Genetic mapping of gummy stem blight (Didymella bryoniae) resistance genes in Cucumis sativus-hystrix introgression lines
Lou, L. ; Wang, H.Y. ; Qian, C.T. ; Liu, J. ; Bai, Y. ; Chen, J.F. - \ 2013
Euphytica 192 (2013)3. - ISSN 0014-2336 - p. 359 - 369.
interspecific hybridization - north-carolina - field-tests - genome - rearrangements - cucurbitaceae - tomato - crops - leaf - dna
Gummy stem blight (GSB, Didymella bryoniae (Auersw.) Rehm) is a devastating disease occurring worldwide in cucumber (Cucumis sativus L.) production and causing considerable yield loss. No commercially available cultivars are resistant to GSB. By screening 52 introgression lines (ILs) derived from the cross of C. hystrix x C. sativus and eight cucumber cultivar/lines through a whole plant assay, three ILs (HH1-8-1-2, HH1-8-5, HH1-8-1-16) were identified as GSB resistant lines. Six common introgression regions in these three ILs were on Chromosomes 1, 4, and 6. To further map the resistance in the ILs, three mapping populations (2009F(2), 2009F(2)' and 2010F(2)) from a cross between resistant IL HH1-8-1-2 and susceptible 8419 were constructed and used for QTL mapping with SSR markers. Two quantitative trait loci (QTLs) were identified; one on Chromosome 4 and the other on Chromosome 6. The interval for Chromosome 4 QTL is 12 cM spanning 3.569 Mbp, and the interval for Chromosome 6 QTL is 11 cM covering 1.299 Mbp. The mapped QTLs provide a foundation for map-based cloning of the genes and establishing an understanding of the associated mechanisms underlying GSB resistance in cucumber.
Feeding behaviour and performance of different populations of the black currant-lettuce aphid, Nasonovia ribisnigri, on resistant and susceptible lettuce
Broeke, C.J.M. ten; Dicke, M. ; Loon, J.J.A. van - \ 2013
Entomologia Experimentalis et Applicata 148 (2013)2. - ISSN 0013-8703 - p. 130 - 141.
host-plant resistance - myzus-persicae - potato aphid - tissue localization - lactuca-sativa - gene mi - tomato - leaf - homoptera - biotypes
When crops are bred for resistance to herbivores, these herbivores are under strong selection pressure to overcome this resistance, which may result in the emergence of virulent biotypes. This is a growing problem for crop species attacked by aphids. The Nr-gene in lettuce confers near-complete resistance against the black currant-lettuce aphid, Nasonovia ribisnigri (Mosely) (Hemiptera: Aphididae). Since 2007, populations of N.ribisnigri have been reported in several locations in Europe to infest resistant lettuce varieties that possess the Nr-gene. The objective of this study was to analyse the behaviour and level of virulence of several N.ribisnigri populations observed to have colonized Nr-locus-containing lettuce lines. We analysed the stylet penetration and feeding behaviour, and the performance of these N.ribisnigri populations on resistant and susceptible lettuce lines. Large variation in the degree of virulence to the Nr-locus-containing lettuce lines was found among populations of the Nr:1 biotype. The German population was highly virulent on the Nr-containing resistant lettuce lines, and showed similar feeding behaviour and performance on both the susceptible and resistant lettuces. The French population from Paris was the second most virulent, though reproduction on the resistant lines was reduced. The French population from Perpignan and a population from Belgium, however, showed reduced performance and feeding rate on the resistant compared to the susceptible lettuces. The lettuce background in which the Nr-gene is expressed influences the level of resistance to the various Nr:1 aphid populations, because the performance and feeding behaviour differed between the aphids on the cultivars (romaine lettuce) compared to the near-isogenic lines (butterhead/iceberg lettuce). This study also shows that being able to feed on a plant not automatically implies that a population can successfully develop on that plant, because aphids showed phloem ingestion during the 8-h recording period on resistant lettuce, but were not able to survive and reproduce on the same lettuce line.
Genomic analysis of the native European Solanum species, S. dulcamara
Agostino, N.D. ; Golas, T. ; Geest, H. van; Bombarely, A. ; Dawood, T. ; Zethof, J. ; Driedonks, N. ; Wijnker, T.G. ; Bargsten, J. ; Nap, J.P. ; Mariani, C. ; Rieu, I. - \ 2013
BMC Genomics 14 (2013). - ISSN 1471-2164 - 14 p.
phytophthora-infestans - solanaceae - identification - evolution - polymorphism - sequence - tomato - potato - genes
Background - Solanum dulcamara (bittersweet, climbing nightshade) is one of the few species of the Solanaceae family native to Europe. As a common weed it is adapted to a wide range of ecological niches and it has long been recognized as one of the alternative hosts for pathogens and pests responsible for many important diseases in potato, such as Phytophthora. At the same time, it may represent an alternative source of resistance genes against these diseases. Despite its unique ecology and potential as a genetic resource, genomic research tools are lacking for S. dulcamara. We have taken advantage of next-generation sequencing to speed up research on and use of this non-model species. Results - In this work, we present the first large-scale characterization of the S. dulcamara transcriptome. Through comparison of RNAseq reads from two different accessions, we were able to predict transcript-based SNP and SSR markers. Using the SNP markers in combination with genomic AFLP and CAPS markers, the first genome-wide genetic linkage map of bittersweet was generated. Based on gene orthology, the markers were anchored to the genome of related Solanum species (tomato, potato and eggplant), revealing both conserved and novel chromosomal rearrangements. This allowed a better estimation of the evolutionary moment of rearrangements in a number of cases and showed that chromosomal breakpoints are regularly re-used. Conclusion - Knowledge and tools developed as part of this study pave the way for future genomic research and exploitation of this wild Solanum species. The transcriptome assembly represents a resource for functional analysis of genes underlying interesting biological and agronomical traits and, in the absence of the full genome, provides a reference for RNAseq gene expression profiling aimed at understanding the unique biology of S. dulcamara. Cross-species orthology-based marker selection is shown to be a powerful tool to quickly generate a comparative genetic map, which may speed up gene mapping and contribute to the understanding of genome evolution within the Solanaceae family.
Changes in sour cherry (Prunus cerasus L.) antioxidants during nectar processing and in vitro gastrointestinal digestion.
Toydemir, G. ; Capanoglu, E. ; Kamiloglu, S. ; Boyacioglu, D. ; Vos, C.H. de; Hall, R.D. ; Beekwilder, M.J. - \ 2013
Journal of Functional Foods 5 (2013)3. - ISSN 1756-4646 - p. 1402 - 1413.
phenolic-compounds - vitamin-c - anthocyanins - extract - tomato - degradation - metabolome - capacities - cultivars - stability
Sour cherry (Prunus cerasus L.) is rich in polyphenols, and like its processed products, is especially rich in anthocyanins. We have applied HPLC, spectrophotometric and on-line antioxidant detection methods to follow the fate of cherry antioxidants during an entire multi-step industrial-scale processing strategy. This was performed for 22 sampling points, with five independent repeats from a commercial cherry nectar production process. Anthocyanins contributed to >50% of the total antioxidant capacity of the samples. An in vitro gastrointestinal (GI) digestion system was used to investigate serum availability of antioxidants. In this system anthocyanin bioavailability was much higher in the processed nectar than in the fresh fruit. Together these results indicate that processed sour cherry nectar is a rich source of stable antioxidants with high bioavailability, auguring well for the potential health-promoting capacity of sour cherry products.
Biosynthesis of Antinutritional Alkaloids in Solanaceous Crops Is Mediated by Clustered Genes
Itkin, M. ; Heinig, U. ; Tzfadia, O. ; Bhide, A.J. ; Shinde, B. ; Cardenas, P.D. ; Bocobza, S.E. ; Unger, T. ; Malitsky, S. ; Finkers, H.J. ; Tikunov, Y.M. ; Bovy, A.G. ; Chikate, Y. ; Singh, P. ; Rogachev, I. ; Beekwilder, J. ; Giri, A.P. ; Aharoni, A. - \ 2013
Science 341 (2013)6142. - ISSN 0036-8075 - p. 175 - 179.
glycoalkaloids - potato - plant - metabolites - pathways - saponins - tomato
Steroidal glycoalkaloids (SGAs) such as a-solanine found in solanaceous food plants—as, for example, potato—are antinutritional factors for humans. Comparative coexpression analysis between tomato and potato coupled with chemical profiling revealed an array of 10 genes that partake in SGA biosynthesis. We discovered that six of them exist as a cluster on chromosome 7, whereas an additional two are adjacent in a duplicated genomic region on chromosome 12. Following systematic functional analysis, we suggest a revised SGA biosynthetic pathway starting from cholesterol up to the tetrasaccharide moiety linked to the tomato SGA aglycone. Silencing GLYCOALKALOID METABOLISM 4 prevented accumulation of SGAs in potato tubers and tomato fruit. This may provide a means for removal of unsafe, antinutritional substances present in these widely used food crops.
Industrial processing effects on phenolic compounds in sour cherry (Prunus cerasus L.) fruit
Toydemir, G. ; Capanoglu, E. ; Gomez-Roldan, M.V. ; Vos, R.C.H. de; Boyacioglu, D. ; Hall, R.D. ; Beekwilder, M.J. - \ 2013
Food Research International 53 (2013)1. - ISSN 0963-9969 - p. 218 - 225.
anthocyanins - tomato - tool - polyphenolics - metabolomics
The processed juice (or nectar) of the sour cherry, Prunus cerasus L., is widely consumed in the Balkan region and Turkey. Sour cherry is known to be rich in polyphenolic compounds, such as anthocyanins and procyanidins. In this work, the effects of processing of sour cherry fruit to nectar on polyphenolic compounds was studied. From a Turkish industrial nectar production factory, five fruit batches were sampled during the processing from fruit to nectar, and for each batch 22 sampling points in the process were investigated. Untargeted LC–MS analysis revealed 193 compounds in sour cherry, of which 38 could be putatively identified. Only seven compounds were affected by the process from fruit to nectar, among which were five phenolic compounds. Waste residues such as press cake contained hardly any anthocyanins, while 87% of the major fruit anthocyanin, cyanidin-3-(2G-glucosylrutinoside), was found in the final nectar. In contrast, procyanidins showed a lower recovery (62%), and were still well represented in the discarded press cake. In comparison with other fruit juices, the recovery of anthocyanins in sour cherry nectar is remarkably high.
Phenotypic, Molecular, and Pathological Characterization of Colletotrichum acutatum Associated with Andean Lupine and Tamarillo in the Ecuadorian Andes
Falconi, C. ; Visser, R.G.F. ; Heusden, A.W. van - \ 2013
Plant Disease 97 (2013)6. - ISSN 0191-2917 - p. 819 - 827.
phytophthora-infestans - phylogenetic-relationships - olive anthracnose - ribosomal dna - sensu-lato - strawberry - identification - diversity - gloeosporioides - tomato
Anthracnose is a serious problem of both Andean lupine and tamarillo in Ecuador. Morphological features, internal transcribed spacer (ITS) sequences, and host specificity were used to characterize Colletotrichum isolates from lupine and tamarillo. Based on phenotypic and molecular characterization, the causal agent of anthracnose on both hosts was Colletotrichum acutatum. All isolates were identified in a C. acutatum-specific polymerase chain reaction assay. Colony diameter, conidia shape, and insensitivity to benomyl also placed isolates from both hosts in the C. acutatum group. However, a detailed analysis of the ITS sequences placed the lupine and tamarillo isolates from the Ecuadorian Andean zone in two clades, with both lupine and tamarillo isolates in each clade. C. acutatum isolates from Andean lupine were distinct from other C. acutatum isolates on lupine around the world. In cross-infection studies, the diameter of lesions produced by isolates from each host was compared on the main stem of two tamarillo and three lupine cultivars. Some isolates produced larger lesions on the host from which they were isolated but others showed similar aggressiveness on their alternate host. Isolates from both hosts were biotrophic on lupine stems, producing little necrosis and abundant sporulation whereas, on tamarillo stems, they produced dark lesions with few conidia. The collection of C. acutatum isolates from lupine and tamarillo provides interesting material for the study quantitative host adaptation.
The efficiency of drip irrigation unpacked
Kooij, S. van der; Zwarteveen, M.Z. ; Boesveld, H. ; Kuper, M. - \ 2013
Agricultural Water Management 123 (2013). - ISSN 0378-3774 - p. 103 - 110.
water-use efficiency - furrow irrigation - surface irrigation - root distribution - cotton yield - fruit yield - productivity - soil - l. - tomato
Drip irrigation figures prominently in water policy debates as a possible solution to water scarcity problems, based on the assertion that it will improve water use efficiencies. We use this article to carefully trace the scientific basis of this assertion. Through a systematic review of the literature, we show that the term efficiency means different things to different people, and can refer to different elements in the water balance. Most articles claim that drip irrigation is irrigation water use efficient and crop water use efficient, but different studies use different definitions of these terms. In addition, measured efficiency gains not only refer to different capacities of the technology, but are also based on very specific boundary (scale) assumptions. We conclude that efficiency gains from drip irrigation will only be achieved under narrowly defined operational conditions, and just apply to very specific spatial and temporal scales. Hence, and unlike what generalized statements in policy documents and the overall enthusiasm for drip as a water saving tool suggest, expectations of increased water efficiencies associated with drip will only be realized, and are just realizable, in very specific circumstances.
Physiological and morphological changes during early and later stages of fruit growth in Capsicum annuum
Tiwari, A. ; Vivian-Smith, A. ; Ljung, K. ; Offringa, R. ; Heuvelink, E. - \ 2013
Physiologia Plantarum 147 (2013)3. - ISSN 0031-9317 - p. 396 - 406.
polar auxin transport - cell expansion - sweet-pepper - sink strength - tomato - arabidopsis - set - endoreduplication - fertilization - parthenocarpy
Fruit-set involves a series of physiological and morphological changes that are well described for tomato and Arabidopsis, but largely unknown for sweet pepper (Capsicum annuum). The aim of this paper is to investigate whether mechanisms of fruit-set observed in Arabidopsis and tomato are also applicable to C. annuum. To do this, we accurately timed the physiological and morphological changes in a post-pollinated and un-pollinated ovary. A vascular connection between ovule and replum was observed in fertilized ovaries that undergo fruit development, and this connection was absent in unfertilized ovaries that abort. This indicates that vascular connection between ovule and replum is an early indicator for successful fruit development after pollination and fertilization. Evaluation of histological changes in the carpel of a fertilized and unfertilized ovary indicated that increase in cell number and cell diameter both contribute to early fruit growth. Cell division contributes more during early fruit growth while cell expansion contributes more at later stages of fruit growth in C. annuum. The simultaneous occurrence of a peak in auxin concentration and a strong increase in cell diameter in the carpel of seeded fruits suggest that indole-3-acetic acid stimulates a major increase in cell diameter at later stages of fruit growth. The series of physiological and morphological events observed during fruit-set in C. annuum are similar to what has been reported for tomato and Arabidopsis. This indicates that tomato and Arabidopsis are suitable model plants to understand details of fruit-set mechanisms in C. annuum.
Large subclonal variation in Phytophthora infestans populations associated with Ecuadorian potato landraces
Delgado, R.A. ; Monteros-Altamiro, A.R. ; Li, Y. ; Visser, R.G.F. ; Lee, T.A.J. van der; Vosman, B. - \ 2013
Plant Pathology 62 (2013). - ISSN 0032-0862 - p. 1081 - 1088.
late blight resistance - phenotypic variation - plant-pathogen - mating-type - virulence - diversity - solanum - tomato - genes - variability
The population of Phytophthora infestans on potato landraces in three provinces (Carchi, Chimborazo and Loja) of Ecuador was analysed. All isolates (n = 66) were of the A1 mating type. Simple sequence repeats (SSR) were used to assess the genetic diversity of the isolates. The P. infestans isolates from the potato landraces grouped in a single clade together with reference isolates belonging to the clonal lineage EC-1. In the 66 SSR profiles obtained, 31 multilocus genotypes were identified. The 66 isolates constituted 49 different races according to the Solanum demissum differential set ( R1 to R11). The P. infestans population was complex and virulent on 4 to 11 R genes. Analysis showed that the subclonal variation in the Ecuadorian EC-1 clone is increasing over time and is much larger than clonal variation in lineages in the Netherlands and Nicaragua, suggesting high mutation rates and little or no selection in Ecuador
Verticillium dahliae Sge1 differentially regulates expresssion of eandidate effector genes
Santhanam, P. ; Thomma, B.P.H.J. - \ 2013
Molecular Plant-Microbe Interactions 26 (2013)2. - ISSN 0894-0282 - p. 249 - 256.
plant-pathogenic fungi - fusarium-oxysporum - transcriptional regulator - tomato - albicans - virulence - requires - protein - genome - life
The ascomycete fungus Verticillium dahliae causes vascular wilt diseases in hundreds of dicotyledonous plant species. However, thus far, only few V. dahliae effectors have been identified, and regulators of pathogenicity remain unknown. In this study, we investigated the role of the V. dahliae homolog of Sge1, a transcriptional regulator that was previously implicated in pathogenicity and effector gene expression in Fusarium oxysporum. We show that V. dahliae Sge1 (VdSge1) is required for radial growth and production of asexual conidiospores, because VdSge1 deletion strains display reduced radial growth and reduced conidia production. Furthermore, we show that VdSge1 deletion strains have lost pathogenicity on tomato. Remarkably, VdSge1 is not required for induction of Ave1, the recently identified V. dahliae effector that activates resistance mediated by the Ve1 immune receptor in tomato. Further assessment of the role of VdSge1 in the induction of the nine most highly in-planta-induced genes that encode putative effectors revealed differential activity. Although the expression of one putative effector gene in addition to Ave1 was not affected by VdSge1 deletion, VdSge1 appeared to be required for the expression of six putative effector genes, whereas two of the putative effectors genes were found to be negatively regulated by VdSge1. In conclusion, our data suggest that VdSge1 differentially regulates V. dahliae effector gene expression.
Population structure of Phytophthora infestans in China – geographic clusters and presence of the EU genotype Blue_13
Li, Y. ; Lee, T.A.J. van der; Zhu, J.H. ; Jin, G.H. ; Lan, C.Z. ; Zhu, S.X. ; Zhang, R.F. ; Liu, B.W. ; Zhao, Z.J. ; Kessel, G.J.T. ; Huang, S.W. ; Jacobsen, E. - \ 2013
Plant Pathology 62 (2013)4. - ISSN 0032-0862 - p. 932 - 942.
potato - diversity - haplotypes - virulence - markers - tomato - dna
The population structure of Phytophthora infestans in China was studied and three mitochondrial haplotypes (Ia, IIa, IIb) were observed. Genetic analysis with 10 highly informative SSR markers identified 68 different genotypes, including three dominant clonal lineages. In the Chinese P. infestans population, the genotypes were strongly clustered according to their geographic origin. One of dominant clonal lineages was genetically similar to Blue_13, a dominant clonal lineage found in Europe since 2004. This is the first report of Blue_13 outside Europe. Only one mating type (A1) was found in the northern and southeastern provinces, but in southern and northwestern China both mating types were observed. The mating type ratio and SSR allele frequencies indicate that in China the sexual cycle of P. infestans is rare. These results emphasize that the migration of asexual propagules and the generation of subclonal variation are the dominant driving factors of the population structure of P. infestans in China. They may also have implications for the role of monitoring P. infestans populations in potato late blight management strategies in China
Metabolomics and molecular marker analysis to explore pepper (Capsicum sp.) biodiversity
Wahyuni, Y. ; Ballester, A.R. ; Tikunov, Y.M. ; Vos, C.H.R. de; Pelgrom, K.T.B. ; Maharijaya, A. ; Sudarmonowati, E. ; Bino, R.J. ; Bovy, A.G. - \ 2013
Metabolomics 9 (2013)1. - ISSN 1573-3882 - p. 130 - 144.
acyclic diterpene glycosides - annuum l. - capsaicinoid content - mass-spectrometry - volatile fraction - hs-spme - fruit - tomato - chinense - constituents
An overview of the metabolic diversity in ripe fruits of a collection of 32 diverse pepper (Capsicum sp.) accessions was obtained by measuring the composition of both semi-polar and volatile metabolites in fruit pericarp, using untargeted LC–MS and headspace GC–MS platforms, respectively. Accessions represented C. annuum, C. chinense, C. frutescens and C. baccatum species, which were selected based on variation in morphological characters, pungency and geographic origin. Genotypic analysis using AFLP markers confirmed the phylogenetic clustering of accessions according to Capsicum species and separated C. baccatum from the C. annuum–C. chinense–C. frutescens complex. Species-specific clustering was also observed when accessions were grouped based on their semi-polar metabolite profiles. In total 88 semi-polar metabolites could be putatively identified. A large proportion of these metabolites represented conjugates of the main pepper flavonoids (quercetin, apigenin and luteolin) decorated with different sugar groups at different positions along the aglycone. In addition, a large group of acyclic diterpenoid glycosides, called capsianosides, was found to be highly abundant in all C. annuum genotypes. In contrast to the variation in semi-polar metabolites, the variation in volatiles corresponded well to the differences in pungency between the accessions. This was particularly true for branched fatty acid esters present in pungent accessions, which may reflect the activity through the acyl branch of the metabolic pathway leading to capsaicinoids. In addition, large genetic variation was observed for many well-established pepper aroma compounds. These profiling data can be used in breeding programs aimed at improving metabolite-based quality traits such as flavour and health-related metabolites in pepper fruits.
A taste of sweet pepper: Volatile and non-volatile chemical composition of fresh sweet pepper (Capsicum annuum) in relation to sensory evaluation of taste
Eggink, P.M. ; Maliepaard, C.A. ; Tikunov, Y.M. ; Haanstra, J.P.W. ; Bovy, A.G. ; Visser, R.G.F. - \ 2012
Food Chemistry 132 (2012)1. - ISSN 0308-8146 - p. 301 - 310.
bell peppers - gas-chromatography - tomato - fruit - flavor - metabolomics - frutescens - diversity - quality - aroma
In this study volatile and non-volatile compounds, as well as some breeding parameters, were measured in mature fruits of elite sweet pepper (Capsicum annuum) lines and hybrids from a commercial breeding program, several cultivated genotypes and one gene bank accession. In addition, all genotypes were evaluated for taste by a trained descriptive sensory expert panel. Metabolic contrasts between genotypes were caused by clusters of volatile and non-volatile compounds, which could be related to metabolic pathways and common biochemical precursors. Clusters of phenolic derivatives, higher alkanes, sesquiterpenes and lipid derived volatiles formed the major determinants of the genotypic differences. Flavour was described with the use of 14 taste attributes, of which the texture related attributes and the sweet-sour contrast were the most discriminatory factors. The attributes juiciness, toughness, crunchiness, stickiness, sweetness, aroma, sourness and fruity/apple taste could be significantly predicted with combined volatile and non-volatile data. Fructose and (E)-2-hexen-1-ol were highly correlated with aroma, fruity/apple taste and sweetness. New relations were found for fruity/apple taste and sweetness with the compounds p-menth-1-en-9-al, (E)-beta-ocimene, (Z)-2-penten-1-ol and (E)-geranylacetone. Based on the overall biochemical and sensory results, the perspectives for flavour improvement by breeding are discussed.
On the species status of the root-knot nematode Meloidogyne mayaguensis Rammah & Hirschmann, 1988
Karssen, G. ; Liao, J. ; Kan, Z. ; Heese, E. van; Nijs, L.J.M.F. - \ 2012
ZooKeys 181 (2012). - ISSN 1313-2989 - p. 67 - 77.
n-sp meloidogynidae - populations - enterolobii - phenotypes - tomato - china
Holo- and paratypes of the root-knot nematodes Meloidogyne mayaguensis Rammah & Hirschmann, 1988 and M. enterolobii Yang & Eisenback, 1983 were morphometrically and morphologically compared. All observed female, male and second-stage juvenile morphometrical and morphological characters are identical for the two studied species. Additionally, contradictions between the original species descriptions were unravelled. The present study of holo- and paratypes confirms the taxonomical status of Meloidogyne mayaguensis as a junior synonym for M. enterolobii.
Quantitative economic impact assessment of an invasive plant disease under uncertainty - a case study for potato spindle tuber viroid (PSTVd) invasion into the European Union
Soliman, T. ; Mourits, M.C.M. ; Oude Lansink, A.G.J.M. ; Werf, W. van der - \ 2012
Crop Protection 40 (2012). - ISSN 0261-2194 - p. 28 - 35.
solanum-jasminoides - 1st report - tomato - virus - rantonnetii - netherlands - strains
International treaties require that phytosanitary measures against introduction and spread of invasive plant pests are justified by a science-based pest risk analysis, including an assessment of potential economic consequences. This study evaluates the economic justification of the currently applied phytosanitary measures against potato spindle tuber viroid (PSTVd). It assesses the impact of an unregulated EU infestation, while accounting for uncertainty due to scarcity of data. Expert opinions were elicited to describe the possible range of PSTVd spread. Stochastic simulations, based on the assessments of separate experts, indicated that the direct impacts exceed the costs of current phytosanitary measures (€5.6 M/year) with a probability of 44%, but with large differences between experts making it hard to justify the measures solely by the expected savings in direct impacts. The direct impact on potato producers was estimated with partial budgeting. This impact is 2.1 M€, based on an assumed prevalence of PSTVd of 0.73%, while the direct impact on tomato producers was estimated at 3.5 M€. The total economic impact, considering price changes and higher costs for consumers, was estimated at 4.4 M€ for potatoes and 5.7 M€ for tomatoes. Consumers bore 92% of the total costs of invasion in the case of potato and 77% in the case of tomato. If the presence of PSTVd would imply export restrictions, resulting in an annual loss of more than 1% of the total EU export value of potatoes and tomatoes, the cost of current phytosanitary measures would also be justified. The potential economic impacts of PSTVd into the European Union are therefore demonstrably of importance when considering market effects or export losses but questionable if only accounting for the direct losses. The large degree of uncertainty in the prevalence of disease contributes to the justifiability of measures based on the precautionary principle. The assessment approach can be useful for assessing the economic justification of phytosanitary measures.
Marker2sequence, mine your QTL regions for candidate genes
Chibon, P.Y.F.R.P. ; Schoof, H. ; Visser, R.G.F. ; Finkers, H.J. - \ 2012
Bioinformatics 28 (2012)14. - ISSN 1367-4803 - p. 1921 - 1922.
genome sequence - tomato - web
Marker2sequence (M2S) aims at mining quantitative trait loci (QTLs) for candidate genes. For each gene, within the QTL region, M2S uses data integration technology to integrate putative gene function with associated gene ontology terms, proteins, pathways and literature. As a typical QTL region easily contains several hundreds of genes, this gene list can then be further filtered using a keyword-based query on the aggregated annotations. M2S will help breeders to identify potential candidate genes for their traits of interest.
Chromosome evolution in Solanum traced by cross-species BAC-FISH
Szinay, D. ; Wijnker, E. ; Berg, R.G. van den; Visser, R.G.F. ; Jong, J.H.S.G.M. de; Bai, Y. - \ 2012
New Phytologist 195 (2012)3. - ISSN 0028-646X - p. 688 - 698.
l. section lycopersicon - resistance gene - mill. wettst. - linkage map - tomato - solanaceae - potato - reveals - rearrangements - recombination
Chromosomal rearrangements are relatively rare evolutionary events and can be used as markers to study karyotype evolution. This research aims to use such rearrangements to study chromosome evolution in Solanum. Chromosomal rearrangements between Solanum crops and several related wild species were investigated using tomato and potato bacterial artificial chromosomes (BACs) in a multicolour fluorescent in situ hybridization (FISH). The BACs selected are evenly distributed over seven chromosomal arms containing inversions described in previous studies. The presence / absence of these inversions among the studied Solanum species were determined and the order of the BAC-FISH signals was used to construct phylogenetic trees. Compared with earlier studies, data from this study provide support for the current grouping of species into different sections within Solanum; however, there are a few notable exceptions, such as the tree positions of S. etuberosum (closer to the tomato group than to the potato group) and S. lycopersicoides (sister to S. pennellii). These apparent contradictions might be explained by interspecific hybridization events and / or incomplete lineage sorting. This cross-species BAC painting technique provides unique information on genome organization, evolution and phylogenetic relationships in a wide variety of species. Such information is very helpful for introgressive breeding.
MSClust: a tool for unsupervised mass spectra extraction of chromatography-mass spectrometry ion-wise aligned data
Tikunov, Y.M. ; Laptenok, S. ; Hall, R.D. ; Bovy, A.G. ; Vos, C.H. de - \ 2012
Metabolomics 8 (2012)4. - ISSN 1573-3882 - p. 714 - 718.
metabolomics approach - plant metabolomics - peak alignment - tomato - ms - metabolism - volatiles
Mass peak alignment (ion-wise alignment) has recently become a popular method for unsupervised data analysis in untargeted metabolic profiling. Here we present MSClust—a software tool for analysis GC–MS and LC–MS datasets derived from untargeted profiling. MSClust performs data reduction using unsupervised clustering and extraction of putative metabolite mass spectra from ion-wise chromatographic alignment data. The algorithm is based on the subtractive fuzzy clustering method that allows unsupervised determination of a number of metabolites in a data set and can deal with uncertain memberships of mass peaks in overlapping mass spectra. This approach is based purely on the actual information present in the data and does not require any prior metabolite knowledge. MSClust can be applied for both GC–MS and LC–MS alignment data sets
Characterization of the natural variation in Arabidopsis thaliana metabolome by the analysis of metabolic distance
Houshyani Hassanzadeh, B. ; Kabouw, P. ; Muth, D. ; Vos, R.C.H. de; Bino, R.J. ; Bouwmeester, H.J. - \ 2012
Metabolomics 8 (2012)suppl. 1. - ISSN 1573-3882 - p. 131 - 145.
genomic diversity - mass-spectrometry - functional genomics - mildew resistance - plants - tomato - biosynthesis - pathogens - volatiles - defense
Metabolite fingerprinting is widely used to unravel the chemical characteristics of biological samples. Multivariate data analysis and other statistical tools are subsequently used to analyze and visualize the plasticity of the metabolome and/or the relationship between those samples. However, there are limitations to these approaches for example because of the multi-dimensionality of the data that makes interpretation of the data obtained from untargeted analysis almost impossible for an average human being. These limitations make the biological information that is of prime importance in untargeted studies be partially exploited. Even in the case of full exploitation, current methods for relationship elucidation focus mainly on between groups variation and differences. Therefore, a measure that is capable of exploiting both between- and within-group biological variation would be of great value. Here, we examined the natural variation in the metabolome of nine Arabidopsis thaliana accessions grown under various environmental conditions and established a measure for the metabolic distance between accessions and across environments. This data analysis approach shows that there is just a minor correlation between genetic and metabolic diversity of the nine accessions. On the other hand, it delivers so far in Arabidopsis unexplored chemical information and is shown to be biologically relevant for resistance studies.
Construction of an integrated microsatellite and key morphological characteristic database of potato varieties on the EU common catalogue
Reid, A. ; Hof, L. ; Felix, G. ; Rucker, B. ; Tams, S. ; Milczynska, E. ; Esselink, G. ; Uenk-Stunnenberg, G.E. ; Vosman, B. ; Weitz, A. - \ 2011
Euphytica 182 (2011)2. - ISSN 0014-2336 - p. 239 - 249.
identification - markers - tomato - plants
The European Union Common Catalogue (EUCC) for potato contains over 1000 varieties. Each year member states add varieties to the list after they have undergone Distinctness, Uniformity and Stability (DUS) testing according to international guidelines. A rapid and robust method for variety identification to aid the management and maintenance of existing variety collections and for the screening of new candidate varieties would therefore be a highly useful tool for DUS testing stations. A database containing key morphological characteristics and microsatellite data was constructed for varieties on the 2006 list of the EUCC for potato. Rules for scoring SSR markers in different laboratories were established to allow a harmonized scoring of markers. Almost all varieties (99.5%) were shown to have unique molecular profiles and in pair wise comparisons 99.99% of all variety pairs could be distinguished. This clearly shows the versatility of the markers and database for identifying potato samples.
A strategy for fast structural elucidation of metabolites in small volume plant extracts using automated MS-guided LC-MS-SPE-NMR
Hooft, J.J.J. van der; Mihaleva, V.V. ; Vos, R.C.H. de; Bino, R.J. ; Vervoort, J.J.M. - \ 2011
Magnetic Resonance in Chemistry 49 (2011)Suppl. S1. - ISSN 0749-1581 - p. S55 - S60.
nuclear-magnetic-resonance - solid-phase extraction - natural-products research - liquid-chromatography - mass-spectrometry - flavonoids - tomato - identification - metabolomics - hyphenation
Fast and reliable metabolite identification based on automated MS-guided HPLC-MS-SPE-NMR metabolite extraction combined with an automated 1H NMR spectrum fitting was developed. Positional isomers as structure 1 and 2 were easily distinguished. In many metabolomics studies, metabolite identification by mass spectrometry (MS) often is hampered by the lack of good reference compounds, and hence, NMR information is essential for structural elucidation, especially for the very large group of secondary metabolites. The classical approach for compound identification is to perform time-consuming and laborious HPLC fractionations and purifications, before (re)dissolving the molecules in deuterated solvents for NMR measurements. Hence, a more direct and easy purification protocol would save time and efforts. Here, we propose an automated MS-guided HPLC-MS-solid phase extraction-NMR approach, which was used to fully characterize flavonoid structures present in crude tomato plant extracts. NMR spectra of plant metabolites, automatically trapped and purified from LC-MS traces, were successfully obtained, leading to the structural elucidation of the metabolites. The MS-based trapping enabled a direct link between the mass signals and NMR peaks derived from the selected LC-MS peaks, thereby decreasing the time needed for elucidation of the metabolite structures. In addition, automated 1H NMR spectrum fitting further speeded up the candidate rejection process. Our approach facilitates the more rapid unraveling of yet unknown metabolite structures and can therefore make untargeted metabolomics approaches more powerful
Towards F1 Hybrid Seed Potato Breeding
Lindhout, P. ; Meijer, D.A. ; Schotte, T. ; Hutten, R.C.B. ; Visser, R.G.F. ; Eck, H.J. van - \ 2011
Potato Research 54 (2011)4. - ISSN 0014-3065 - p. 301 - 312.
plantenveredeling - plantenveredelingsmethoden - hybridisatie - hybriden - diploïdie - zelfincompatibiliteit - aardappelen - plant breeding - plant breeding methods - hybridization - hybrids - diploidy - self incompatibility - potatoes - species solanum-chacoense - inhibitor sli gene - self-compatibility - quantitative trait - diploid potatoes - yield - heterosis - sequence - markers - tomato
Compared to other major food crops, progress in potato yield as the result of breeding efforts is very slow. Genetic gains cannot be fixed in potato due to obligatory out-breeding. Overcoming inbreeding depression using diploid self-compatible clones should enable to replace the current method of out-breeding and clonal propagation into an F1 hybrid system with true seeds. This idea is not new, but has long been considered unrealistic. Severe inbreeding depression and self-incompatibility in diploid germplasm have hitherto blocked the development of inbred lines. Back-crossing with a homozygous progenitor with the Sli gene which inhibits gametophytic self-incompatibility gave self-compatible offspring from elite material from our diploid breeding programme. We demonstrate that homozygous fixation of donor alleles is possible, with simultaneous improvement of tuber shape and tuber size grading of the recipient inbred line. These results provide proof of principle for F1 hybrid potato breeding. The technical and economic perspectives are unprecedented as these will enable the development of new products with combinations of useful traits for all stakeholders in the potato chain. In addition, the hybrid’s seeds are produced by crossings, rendering the production and voluminous transport of potato seed tubers redundant as it can be replaced by direct sowing or the use of healthy mini-tubers, raised in greenhouses.