Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    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.
    Parthenocarpic potential in Capsicum annuum L. is enhanced by carpelloid structures and controlled by a single recessive gene
    Tiwari, A. ; Vivian-Smith, A. ; Voorrips, R.E. ; Habets, M.E.J. ; Xue, L.B. ; Offringa, R. ; Heuvelink, E. - \ 2011
    BMC Plant Biology 11 (2011). - ISSN 1471-2229 - 15 p.
    mads-box genes - ovule development - fruit-development - sweet-pepper - arabidopsis - tomato - pollen - growth - flower - mutant
    Background Parthenocarpy is a desirable trait in Capsicum annuum production because it improves fruit quality and results in a more regular fruit set. Previously, we identified several C. annuum genotypes that already show a certain level of parthenocarpy, and the seedless fruits obtained from these genotypes often contain carpel-like structures. In the Arabidopsis bel1 mutant ovule integuments are transformed into carpels, and we therefore carefully studied ovule development in C. annuum and correlated aberrant ovule development and carpelloid transformation with parthenocarpic fruit set. Results We identified several additional C. annuum genotypes with a certain level of parthenocarpy, and confirmed a positive correlation between parthenocarpic potential and the development of carpelloid structures. Investigations into the source of these carpel-like structures showed that while the majority of the ovules in C. annuum gynoecia are unitegmic and anatropous, several abnormal ovules were observed, abundant at the top and base of the placenta, with altered integument growth. Abnormal ovule primordia arose from the placenta and most likely transformed into carpelloid structures in analogy to the Arabidopsis bel1 mutant. When pollination was present fruit weight was positively correlated with seed number, but in the absence of seeds, fruit weight proportionally increased with the carpelloid mass and number. Capsicum genotypes with high parthenocarpic potential always showed stronger carpelloid development. The parthenocarpic potential appeared to be controlled by a single recessive gene, but no variation in coding sequence was observed in a candidate gene CaARF8. Conclusions Our results suggest that in the absence of fertilization most C. annuum genotypes, have parthenocarpic potential and carpelloid growth, which can substitute developing seeds in promoting fruit development.
    A hybrid BAC physical map of potato: a framework for sequencing a heterozygous genome
    Boer, J.M. de; Borm, T.J.A. ; Jesse, T. ; Brugmans, B.W. ; Tang, X. ; Bryan, G.J. ; Bakker, J. ; Eck, H.J. van; Visser, R.G.F. - \ 2011
    BMC Genomics 12 (2011). - ISSN 1471-2164 - 60 p.
    quantitative trait loci - candidate genes - disease resistance - linkage map - tomato - aflp - solanum - markers - dna - construction
    Background Potato is the world's third most important food crop, yet cultivar improvement and genomic research in general remain difficult because of the heterozygous and tetraploid nature of its genome. The development of physical map resources that can facilitate genomic analyses in potato has so far been very limited. Here we present the methods of construction and the general statistics of the first two genome-wide BAC physical maps of potato, which were made from the heterozygous diploid clone RH89-039-16 (RH). Results First, a gel electrophoresis-based physical map was made by AFLP fingerprinting of 64478 BAC clones, which were aligned into 4150 contigs with an estimated total length of 1361 Mb. Screening of BAC pools, followed by the KeyMaps in silico anchoring procedure, identified 1725 AFLP markers in the physical map, and 1252 BAC contigs were anchored the ultradense potato genetic map. A second, sequence-tag-based physical map was constructed from 65919 whole genome profiling (WGP) BAC fingerprints and these were aligned into 3601 BAC contigs spanning 1396 Mb. The 39733 BAC clones that overlap between both physical maps provided anchors to 1127 contigs in the WGP physical map, and reduced the number of contigs to around 2800 in each map separately. Both physical maps were 1.64 times longer than the 850 Mb potato genome. Genome heterozygosity and incomplete merging of BAC contigs are two factors that can explain this map inflation. The contig information of both physical maps was united in a single table that describes hybrid potato physical map. Conclusions The AFLP physical map has already been used by the Potato Genome Sequencing Consortium for sequencing 10% of the heterozygous genome of clone RH on a BAC-by-BAC basis. By layering a new WGP physical map on top of the AFLP physical map, a genetically anchored genome-wide framework of 322434 sequence tags has been created. This reference framework can be used for anchoring and ordering of genomic sequences of clone RH (and other potato genotypes), and opens the possibility to finish sequencing of the RH genome in a more efficient way via high throughput next generation approaches.
    Regulatory control of high levels of carotenoid accumulation in potato tubers
    Zhou, X. ; McQuinn, R. ; Fei, Z. ; Wolters, A.M.A. ; Eck, J. van; Brown, C. ; Giovannoni, J.J. ; Li, L. - \ 2011
    Plant, Cell & Environment 34 (2011)6. - ISSN 0140-7791 - p. 1020 - 1030.
    lycopene epsilon-cyclase - false discovery rate - beta-carotene - transcription factor - phytoene synthase - genetic-variation - hydroxylase gene - microarray data - tomato - fruit
    Potato (Solanum tuberosum L.) tubers contain a wide range of carotenoid contents. To decipher the key factors controlling carotenoid levels in tubers, four potato lines (Atlantic, Désirée, 91E22 and POR03) were examined by a combination of biochemical, molecular and genomics approaches. These lines contained incremental levels of carotenoids, which were found to be associated with enhanced capacity of carotenoid biosynthesis as evident from norflurazon treatment. Microarray analysis of high and low carotenoid lines (POR03 versus Atlantic) revealed 381 genes that showed significantly differential expression. The carotenoid metabolic pathway genes ß-carotene hydroxylase 2 (BCH2) and ß-carotene hydroxylase 1 (BCH1), along with zeaxanthin epoxidase (ZEP), and carotenoid cleavage dioxygenase 1A (CCD1A) were among the most highly differentially expressed genes. The transcript levels of BCH2 and BCH1 were lowest in Atlantic and highest in POR03, whereas those of ZEP and CCD1A were high in low carotenoid lines and low in high carotenoid lines. The high expression of BCH2 in POR03 line was associated with enhanced response to sugars. Our results indicate that high levels of carotenoid accumulation in potato tubers were due to an increased metabolic flux into carotenoid biosynthetic pathway, as well as the differential expression of carotenoid metabolic genes.
    Mapping of the S. demissum late blight resistance gene R8 to a new locus on chromosome IX
    Jo, K.R. ; Arens, M.J.B. ; Kim, T.Y. ; Jongsma, M.A. ; Visser, R.G.F. ; Jacobsen, E. ; Vossen, J.H. - \ 2011
    Theoretical and Applied Genetics 123 (2011)8. - ISSN 0040-5752 - p. 1331 - 1340.
    potato late blight - phytophthora-infestans mont - broad-spectrum resistance - race-specific resistance - solanum-bulbocastanum - confers resistance - nucleotide-binding - field-resistance - r1 gene - tomato
    The use of resistant varieties is an important tool in the management of late blight, which threatens potato production worldwide. Clone MaR8 from the Mastenbroek differential set has strong resistance to Phytophthora infestans, the causal agent of late blight. The F1 progeny of a cross between the susceptible cultivar Concurrent and MaR8 were assessed for late blight resistance in field trials inoculated with an incompatible P. infestans isolate. A 1:1 segregation of resistance and susceptibility was observed, indicating that the resistance gene referred to as R8, is present in simplex in the tetraploid MaR8 clone. NBS profiling and successive marker sequence comparison to the potato and tomato genome draft sequences, suggested that the R8 gene is located on the long arm of chromosome IX and not on the short arm of chromosome XI as was suggested previously. Analysis of SSR, CAPS and SCAR markers confirmed that R8 was on the distal end of the long arm of chromosome IX. R gene cluster directed profiling markers CDPSw54 and CDPSw55 flanked the R8 gene at the distal end (1 cM). CDPTm21-1, CDPTm21-2 and CDPTm22 flanked the R8 gene on the proximal side (2 cM). An additional co-segregating marker (CDPHero3) was found, which will be useful for marker assisted breeding and map based cloning of R8.
    Data integration and network reconstruction with ~omics data using Random Forest regression in potato
    Acharjee, A. ; Kloosterman, B.A. ; Vos, R.C.H. de; Werij, J.S. ; Bachem, C.W.B. ; Visser, R.G.F. ; Maliepaard, C.A. - \ 2011
    Analytica Chimica Acta 705 (2011)1-2. - ISSN 0003-2670 - p. 56 - 63.
    mass-spectrometry - systems biology - microarray data - classification - metabolomics - proteomics - tomato - qtl - biomarkers - phenotypes
    In the post-genomic era, high-throughput technologies have led to data collection in fields like transcriptomics, metabolomics and proteomics and, as a result, large amounts of data have become available. However, the integration of these ~omics data sets in relation to phenotypic traits is still problematic in order to advance crop breeding. We have obtained population-wide gene expression and metabolite (LC–MS) data from tubers of a diploid potato population and present a novel approach to study the various ~omics datasets to allow the construction of networks integrating gene expression, metabolites and phenotypic traits. We used Random Forest regression to select subsets of the metabolites and transcripts which show association with potato tuber flesh color and enzymatic discoloration. Network reconstruction has led to the integration of known and uncharacterized metabolites with genes associated with the carotenoid biosynthesis pathway. We show that this approach enables the construction of meaningful networks with regard to known and unknown components and metabolite pathways.
    How filamentous pathogens co-opt plants: the ins and outs of fungal effectors
    Jonge, R. de; Bolton, M.D. ; Thomma, B.P.H.J. - \ 2011
    Current Opinion in Plant Biology 14 (2011)4. - ISSN 1369-5266 - p. 400 - 406.
    resistance gene - defense - virulence - protein - cells - host - expression - receptor - tomato - rice
    Research on effectors secreted by pathogens during host attack has dominated the field of molecular plant–microbe interactions over recent years. Functional analysis of type III secreted effectors injected by pathogenic bacteria into host cells has significantly advanced the field and demonstrated that many function to suppress host defense. Fungal and oomycete effectors are delivered outside the host plasma membrane, and although research has lagged behind on bacterial effectors, we are gradually learning more and more about the functions of these effectors. While some function outside the host cell to disarm defense, others exploit host cellular uptake mechanisms to suppress defense or liberate nutrients intracellularly. Comparative genomics suggests that the organization of effector genes drives effector evolution in many pathogen genomes.
    Use of new generation single nucleotide polymorphism genotyping for rapid development of near-isogenic lines in rice
    Boualaphanh, C. ; Daygon, V.D. ; Calingacion, M.N. ; Sanitchon, J. ; Jothityangkoon, D. ; Mumm, R. ; Hall, R.D. ; Fitgerald, M.A. - \ 2011
    Crop Science 51 (2011)5. - ISSN 0011-183X - p. 2067 - 2073.
    oryza-sativa l. - fragrance - metabolomics - populations - phenotypes - varieties - tomato - marker - grain - gene
    Studies aimed at determining gene function or identity are greatly facilitated by introgression lines and phenotyping tools. However, developing introgression lines can take six to eight generations to reach the desired level of background purity and homozygosity. The objective of this study was to use new generation genome-wide single nucleotide polymorphism (SNP) genotyping, along with a molecular marker for the allele of interest, and a relevant phenotyping tool, to develop research populations with just four generations of backcrossing. Two populations were created for future research on aroma in rice (Oryza sativa L.): one derived from two indica parents and the other from one indica and one tropical japonica parent. The same recurrent parent was used for both populations. Single nucleotide polymorphism genotyping of BC4F2 progeny selected previously on the basis of either a marker for fragrance or the presence of the fragrant compound and on the basis of morphological similarity to the recurrent parent showed that donor introgression ranged from
    Volatile compound fingerprinting of mixed cultutre fermentations
    Bok, F.A.M. de; Janssen, P.W.M. ; Bayjanov, J.R. ; Sieuwerts, S. ; Lommen, A. ; Hylckama, J. van; Molenaar, D. - \ 2011
    Applied and Environmental Microbiology 77 (2011)17. - ISSN 0099-2240 - p. 6233 - 6239.
    chromatography-mass spectrometry - solid-phase microextraction - starter cultures - flavor - metabolomics - yogurt - identification - genomics - strains - tomato
    With the advent of the -omics era, classical technology platforms, such as hyphenated mass spectrometry, are currently undergoing a transformation toward high-throughput application. These novel platforms yield highly detailed metabolite profiles in large numbers of samples. Such profiles can be used as fingerprints for the accurate identification and classification of samples as well as for the study of effects of experimental conditions on the concentrations of specific metabolites. Challenges for the application of these methods lie in the acquisition of high-quality data, data normalization, and data mining. Here, a high-throughput fingerprinting approach based on analysis of headspace volatiles using ultrafast gas chromatography coupled to time of flight mass spectrometry (ultrafast GC/TOF-MS) was developed and evaluated for classification and screening purposes in food fermentation. GC-MS mass spectra of headspace samples of milk fermented by different mixed cultures of lactic acid bacteria (LAB) were collected and preprocessed in MetAlign, a dedicated software package for the preprocessing and comparison of liquid chromatography (LC)-MS and GC-MS data. The Random Forest algorithm was used to detect mass peaks that discriminated combinations of species or strains used in fermentations. Many of these mass peaks originated from key flavor compounds, indicating that the presence or absence of individual strains or combinations of strains significantly influenced the concentrations of these components. We demonstrate that the approach can be used for purposes like the selection of strains from collections based on flavor characteristics and the screening of (mixed) cultures for the presence or absence of strains. In addition, we show that strain-specific flavor characteristics can be traced back to genetic markers when comparative genome hybridization (CGH) data are available.
    SolRgene: an online database to explore disease resistance genes in tuber-bearing Solanum species
    Vleeshouwers, V.G.A.A. ; Finkers, H.J. ; Budding, D.J. ; Vissers, M. ; Jacobs, M.M.J. ; Berloo, R. van; Pel, M. ; Champouret, N. ; Bakker, E.H. ; Krenek, P. ; Rietman, H. ; Huigen, D.J. ; Hoekstra, R. ; Goverse, A. ; Vosman, B. ; Jacobsen, E. ; Visser, R.G.F. - \ 2011
    BMC Plant Biology 11 (2011). - ISSN 1471-2229 - 24 p.
    late blight resistance - phytophthora-infestans resistance - genome sequence - potato genome - r-gene - bulbocastanum - venturii - homolog - tomato - plant
    Background The cultivated potato (Solanum tuberosum L.) is an important food crop, but highly susceptible to many pathogens. The major threat to potato production is the Irish famine pathogen Phytophthora infestans, which causes the devastating late blight disease. Potato breeding makes use of germplasm from wild relatives (wild germplasm) to introduce resistances into cultivated potato. The Solanum section Petota comprises tuber-bearing species that are potential donors of new disease resistance genes. The aim of this study was to explore Solanum section Petota for resistance genes and generate a widely accessible resource that is useful for studying and implementing disease resistance in potato. Description The SolRgene database contains data on resistance to P. infestans and presence of R genes and R gene homologues in Solanum section Petota. We have explored Solanum section Petota for resistance to late blight in high throughput disease tests under various laboratory conditions and in field trials. From resistant wild germplasm, segregating populations were generated and assessed for the presence of resistance genes. All these data have been entered into the SolRgene database. To facilitate genetic and resistance gene evolution studies, phylogenetic data of the entire SolRgene collection are included, as well as a tool for generating phylogenetic trees of selected groups of germplasm. Data from resistance gene allele-mining studies are incorporated, which enables detection of R gene homologs in related germplasm. Using these resources, various resistance genes have been detected and some of these have been cloned, whereas others are in the cloning pipeline. All this information is stored in the online SolRgene database, which allows users to query resistance data, sequences, passport data of the accessions, and phylogenic classifications. Conclusion Solanum section Petota forms the basis of the SolRgene database, which contains a collection of resistance data of an unprecedented size and precision. Complemented with R gene sequence data and phylogenetic tools, SolRgene can be considered the primary resource for information on R genes from potato and wild tuber-bearing relatives.
    Analysis of Two in Planta Expressed LysM Effector Homologs from the Fungus Mycosphaerella graminicola Reveals Novel Functional Properties and Varying Contributions to Virulence on Wheat
    Marshall, R. ; Kombrink, A. ; Motteram, J. ; Loza-Reyes, E. ; Lucas, J. ; Hammond-Kosack, K.E. ; Thomma, B.P.H.J. ; Rudd, J.J. - \ 2011
    Plant Physiology 156 (2011)2. - ISSN 0032-0889 - p. 756 - 769.
    cladosporium-fulvum - septoria-tritici - maximum-likelihood - blotch pathogen - innate immunity - protein - resistance - host - tomato - recognition
    Secreted effector proteins enable plant pathogenic fungi to manipulate host defenses for successful infection. Mycosphaerella graminicola causes Septoria tritici blotch disease of wheat (Triticum aestivum) leaves. Leaf infection involves a long (approximately 7 d) period of symptomless intercellular colonization prior to the appearance of necrotic disease lesions. Therefore, M. graminicola is considered as a hemibiotrophic (or necrotrophic) pathogen. Here, we describe the molecular and functional characterization of M. graminicola homologs of Ecp6 (for extracellular protein 6), the Lysin (LysM) domain-containing effector from the biotrophic tomato (Solanum lycopersicum) leaf mold fungus Cladosporium fulvum, which interferes with chitin-triggered immunity in plants. Three LysM effector homologs are present in the M. graminicola genome, referred to as Mg3LysM, Mg1LysM, and MgxLysM. Mg3LysM and Mg1LysM genes were strongly transcriptionally up-regulated specifically during symptomless leaf infection. Both proteins bind chitin; however, only Mg3LysM blocked the elicitation of chitin-induced plant defenses. In contrast to C. fulvum Ecp6, both Mg1LysM and Mg3LysM also protected fungal hyphae against plant-derived hydrolytic enzymes, and both genes show significantly more nucleotide polymorphism giving rise to nonsynonymous amino acid changes. While Mg1LysM deletion mutant strains of M. graminicola were fully pathogenic toward wheat leaves, Mg3LysM mutant strains were severely impaired in leaf colonization, did not trigger lesion formation, and were unable to undergo asexual sporulation. This virulence defect correlated with more rapid and pronounced expression of wheat defense genes during the symptomless phase of leaf colonization. These data highlight different functions for MgLysM effector homologs during plant infection, including novel activities that distinguish these proteins from C. fulvum Ecp6.
    Identification and mapping of quantitative resistance to late blight (Phytophthora infestans) in Solanum habrochaites LA1777
    Junming Li, J. ; Liu, L. ; Bai, Y. ; Finkers, H.J. ; Visser, R.G.F. ; Heusden, A.W. van - \ 2011
    Euphytica 179 (2011)3. - ISSN 0014-2336 - p. 427 - 438.
    lycopersicon-pennellii - genetic backgrounds - introgression lines - qtl analysis - trait loci - tomato - esculentum - durability - library - quality
    Late blight (Phytophthora infestans) can have devastating effects on tomato production over the whole world. Most of the commercial cultivars of tomato, Solanum lycopersicum, are susceptible. Qualitative and quantitative resistance has been described in wild relatives of tomato. In general qualitative resistance can more easily be overcome by newly evolved isolates. Screening of three S. habrochaites accessions (LA1033, LA2099 and LA1777) through a whole plant assay showed that accession LA1777 had a good level of resistance to several isolates of P. infestans. To explore the potential in this wild species, an introgression line (IL) population of S. habrochaites LA1777 was used to screen individual chromosome regions of the wild species by a detached leaf assay. Two major isolates (T1,2 and T1,2,4) were used and two parameters were measured: lesion size (LS), and disease incidence (DI). Substantial variation was observed between the individual lines. QTLs were identified for LS but not for DI. The presence of five QTLs derived from LA1777 (Rlbq4a, Rlbq4b, Rlbq7, Rlbq8 and Rlbq12) results in unambiguous higher levels of resistance. All QTLs co-localized with previously described QTLs from S. habrochaites LA2099 except QTL Rlbq4b, which is therefore a novel QTL
    Exploring the spatial distribution of light interception and photosynthesis of canopies by means of a functional-structural plant model
    Sarlikioti, V. ; Visser, P.H.B. de; Marcelis, L.F.M. - \ 2011
    Annals of Botany 107 (2011)5. - ISSN 0305-7364 - p. 875 - 883.
    simulation-model - architectural model - row orientation - virtual plants - growth - tomato - crop - competition - components - vegetation
    Background and Aims - At present most process-based models and the majority of three-dimensional models include simplifications of plant architecture that can compromise the accuracy of light interception simulations and, accordingly, canopy photosynthesis. The aim of this paper is to analyse canopy heterogeneity of an explicitly described tomato canopy in relation to temporal dynamics of horizontal and vertical light distribution and photosynthesis under direct- and diffuse-light conditions. Methods - Detailed measurements of canopy architecture, light interception and leaf photosynthesis were carried out on a tomato crop. These data were used for the development and calibration of a functional–structural tomato model. The model consisted of an architectural static virtual plant coupled with a nested radiosity model for light calculations and a leaf photosynthesis module. Different scenarios of horizontal and vertical distribution of light interception, incident light and photosynthesis were investigated under diffuse and direct light conditions. Key Results - Simulated light interception showed a good correspondence to the measured values. Explicitly described leaf angles resulted in higher light interception in the middle of the plant canopy compared with fixed and ellipsoidal leaf-angle distribution models, although the total light interception remained the same. The fraction of light intercepted at a north–south orientation of rows differed from east–west orientation by 10 % on winter and 23 % on summer days. The horizontal distribution of photosynthesis differed significantly between the top, middle and lower canopy layer. Taking into account the vertical variation of leaf photosynthetic parameters in the canopy, led to approx. 8 % increase on simulated canopy photosynthesis. Conclusions - Leaf angles of heterogeneous canopies should be explicitly described as they have a big impact both on light distribution and photosynthesis. Especially, the vertical variation of photosynthesis in canopy is such that the experimental approach of photosynthesis measurements for model parameterization should be revised.
    Yield and water use of eggplants (Solanum melongena L.) under full and deficit irrigation irrigation regimes
    Karam, F. ; Saliba, R. ; Skaf, F. ; Breidy, J. ; Rouphael, Y. ; Balendonck, J. - \ 2011
    Agricultural Water Management 98 (2011)8. - ISSN 0378-3774 - p. 1307 - 1316.
    use efficiency - drip irrigation - drought - tomato - growth - agriculture - management - responses - quality - pepper
    Field experiments were conducted in 2008 and 2009 to determine the effects of deficit irrigation on yield and water use of field grown eggplants. A total of 8 irrigation treatments (four each year), which received different amounts of irrigation water, were evaluated. In 2008, deficit irrigation was applied at full vegetative growth (WS-V), pre-flowering (WS-F) and fruit ripening (WS-R), while in 2009 deficit irrigation was applied during the whole growing season at 80 (WS-80), 60 (WS-60) and 40% (WS-40) of field capacity. Deficit-irrigated treatments were in both years compared to a well irrigated control. Regular readings of soil water content (SWC) in 2008 and 2009 showed that average soil water deficit (SWD) in the control was around 30% of total available water (TAW) while in deficit-irrigated treatments it varied between 50 and 75% of TAW. In 2008, deficit irrigation reduced fruit fresh yield by 35, 25 and 33% in WS-V, WS-F and WS-R treatments, respectively, when compared to the control (33.0 t ha-1). However, the reduction in fresh yield in response to deficit irrigation was compensated by an increase in fruit mean weight. Results obtained in 2009 showed that fruit fresh yield in the control was 33.7 t ha-1, while it was 12, 39 and 60% less in WS-80, WS-60 and WS-40 treatments, respectively. On the other hand, fruit dry matter content and water productivity were found to increase significantly in both years in deficit-irrigated treatments. Applying deficit irrigation for 2 weeks prior to flowering (WS-F) resulted in water saving of the same magnitude of the WS-80 treatment, with the least yield reduction, making more water available to irrigate other crops, and thereby considered optimal strategies for drip-irrigated eggplants in the semi-arid climate of the central Bekaa Valley of Lebanon.
    Extensive metabolic cross-talk in melon fruit revealed by spatial and developmental combinatorial metabolomics
    Moing, A. ; Aharoni, A. ; Biais, B. ; Rogachev, I. ; Meir, S. ; Brodsky, L. ; Allwood, J.W. ; Erban, A. ; Dunn, W.B. ; Kay, S. ; Koning, S. ; Vos, C.H. de; Jonker, H.H. ; Mumm, R. ; Deborde, C. ; Maucourt, M. ; Bernillon, S. ; Gibon, Y. ; Hansen, T.H. ; Husted, S. ; Goodacre, R. ; Kopka, J. ; Schjoerring, J.K. ; Rolin, D. ; Hall, R.D. - \ 2011
    New Phytologist 190 (2011)3. - ISSN 0028-646X - p. 683 - 696.
    mass-spectrometry data - cucumis-melo - gas-chromatography - network analysis - aroma volatiles - gene-expression - tomato - plants - l. - identification
    Celiac disease (CD) is a chronic inflammatory disease affecting the small intestinal mucosa. The causative agents have been identified as gluten proteins from wheat, barley and rye, and the only available treatment for CD patients is a lifelong gluten-free diet. Non-gluten containing cereals would be a valuable contribution to the gluten-free diet. In this respect, oats are a good choice. However, commercial lots of oat flakes and flour frequently are contaminated with wheat, barley and rye, and two studies have reported that some peptides derived from the gluten-like avenin storage proteins of oat can trigger an immune response in some CD patients. In the present study we have initiated the investigation whether all oat varieties contain similar amounts of potentially harmful sequences by biochemical and immunological methods. We confirm that commercial oat preparations are contaminated with other cereals that contain gluten or gluten-like proteins. Moreover, our results demonstrate that contamination-free oat varieties differ in their capacity to stimulate an avenin-sensitive gamma-gliadin specific T cell line derived from a patient with CD, indicative for differences in the two known avenin epitopes among oat varieties, implying that selection and breeding of completely safe oat varieties for all CD patients may be a realistic possibility.
    Potato virus X and Tobacco mosaic virus-based vectors compatible with the Gateway-TM cloning system
    Lacorte, C.C. ; Ribeiro, S.G. ; Lohuis, H. ; Goldbach, R.W. ; Prins, M.W. - \ 2010
    Journal of Virological Methods 164 (2010)1-2. - ISSN 0166-0934 - p. 7 - 13.
    transient expression - gene-expression - viral vectors - plants - tomato - rna - proteins - recombination - resistance
    Virus-based expression vectors are important tools for high-level production of foreign proteins and for gene function analysis through virus induced gene silencing. To exploit further their advantages as fast, high yield replicons, a set of vectors was produced by converting and adapting Potato virus X (PVX) and Tobacco mosaic virus (TMV)-based vectors to allow easy cloning of foreign sequences by the Gateway™ cloning system. Target genes were cloned efficiently by recombination and successfully expressed in Nicotiana benthamiana following inoculation by Agrobacterium (agroinfection). Using green fluorescent protein (GFP) as marker, high-level expression with both PVX-GW and TMV-GW vectors was confirmed. A Gateway inserted phytoene desaturase gene (pds) fragment in PVX-GW and TMV-GW vectors (PVX-GW-PDS and TMC-GW-PDS), induced gene silencing of the endogenous pds gene in N. benthamiana as evidenced by chlorotic leaves. The PVX-GW vector was adapted further by cloning the GFP gene upstream of the Gateway sequences, allowing the easy production of GFP fusions after recombination of a target gene. Subcellular localization of resulting GFP fusion was validated by recombining and expressing the coat protein gene from Tomato chlorotic mottle virus, revealing its nuclear localization. A PVX-GW transient expression assay of a nucleocapsid protein gene fragment of Tomato spotted wilt virus and of a single chain antibody against this protein was shown to confer effective resistance to TSWV infection.
    A distinct tospovirus causing necrotic straek on alstroemeria sp. in Colombia
    Mehraban, A. ; Botermans, M. ; Verhoeven, J.Th.J. ; Meekes, E. ; Saaijer, J. ; Peters, D. ; Goldbach, R.W. ; Kormelink, R.J.M. - \ 2010
    Archives of Virology 155 (2010)3. - ISSN 0304-8608 - p. 423 - 428.
    spotted wilt virus - rna segment - tomato - identification - chrysanthemum - sequence - protein - isolate - brazil
    A tospovirus causing necrotic streaks on leaves was isolated from Alstroemeria sp. in Colombia. Infected samples reacted positively with tomato spotted wilt virus (TSWV) antiserum during preliminary serological tests. Further analysis revealed a close serological relationship to tomato chlorotic spot virus (TCSV) and groundnut ringspot virus (GRSV). A major part of the S-RNA segment, encompassing the nucleocapsid (N) protein gene, the 5' untranslated region and a part of the intergenic region 3' of the N gene, was cloned and sequenced. The deduced N protein sequence showed highest amino acid identity (82%) to that of TCSV, indicating that the virus represents a new tospovirus species, for which the name Alstroemeria necrotic streak virus (ANSV) is coined. Phylogenetic analysis based on the N protein sequence revealed that this Alstroemeria-infecting tospovirus clustered with tospoviruses from the American continent. Frankliniella occidentalis was identified as potential vector species for ANSV.
    Systemic colonization of potato plants by a soil-borne, GFP-tagged strain of Dickeya sp. Biovar 3
    Czajkowski, R.L. ; Boer, W. de; Velvis, H. ; Wolf, J.M. van der - \ 2010
    Phytopathology 100 (2010)2. - ISSN 0031-949X - p. 134 - 142.
    carotovora subsp atroseptica - erwinia-chrysanthemi - ralstonia-solanacearum - seed potatoes - host-range - pectobacterium - infection - tomato - genes - lenticels
    Colonization of potato plants by soilborne, green fluorescent protein (GFP)-tagged Dickeya sp. IPO2254 was investigated by selective plating, epifluorescence stereo microscopy (ESM), and confocal laser scanning microscopy (CLSM). Replicated experiments were carried out in a greenhouse using plants with an intact root system and plants from which ca. 30% of the lateral roots was removed. One day after soil inoculation, adherence of the pathogen on the roots and the internal colonization of the plants were detected using ESM and CLSM of plant parts embedded in an agar medium. Fifteen days post-soil inoculation, Dickeya sp. was found on average inside 42% of the roots, 13% of the stems, and 13% of the stolons in plants with undamaged roots. At the same time-point, in plants with damaged roots, Dickeya sp. was found inside 50% of the roots, 25% of the stems, and 25% of the stolons. Thirty days postinoculation, some plants showed true blackleg symptoms. In roots, Dickeya sp. was detected in parenchyma cells of the cortex, both inter- and intracellularly. In stems, bacteria were found in xylem vessels and in protoxylem cells. Microscopical observations were confirmed by dilution spread-plating the plant extracts onto agar medium directly after harvest. The implications of infection from soilborne inoculum are discussed.
    A photothermal model of leaf area index for greenhouse crops
    Xu, R. ; Dai, J. ; Luo, W. ; Yin, X. ; Li, Y. ; Tai, X. ; Han, L. ; Chen, Y. ; Lin, L. ; Li, G. ; Zou, C. ; Du, W. ; Diao, M. - \ 2010
    Agricultural and Forest Meteorology 150 (2010)4. - ISSN 0168-1923 - p. 541 - 552.
    millet pennisetum-typhoides - simulation-model - growth-model - plant-growth - temperature - tomato - stand
    Leaf area index (LAI) is an important variable for modelling canopy photosynthesis and crop water use. In many crop simulation models, prediction of LAI is very sensitive to errors in the value of parameter “specific leaf area” (SLA), which often relies on destructive measurements to determine. In this study, we present a model for predicting LAI of greenhouse crops based on the quantification of easily measured morphological traits as affected by temperature and radiation. Our model predicts LAI based on canopy light interception as a function of node development rate along with specific leaf size and elongation rates characteristics defined on a leaf number basis. Growth studies with five greenhouse crops (cucumber, sweet pepper, chrysanthemum, tulip and lilium) were conducted in different greenhouses and different sites during 2003 to 2009. The model was evaluated, in comparison with two commonly used methods for predicting LAI – the growing degree days (GDD) based model and SLA based model, using independent data from other experiments. The coefficient of determination (r2) and the root mean squared error (RMSE) between the predicted and measured values using our photothermal method are 0.99 and 0.95 (r2, RMSE) for leaf number, 0.98 and 0.01 m for specific leaf length, and 0.98 and 0.13 m2 m-2 for canopy LAI. For the GDD-based model, the r2 and RMSE are 0.93 and 4.23, 0.82 and 0.04 m, 0.87 and 0.48 m2 m-2 for the three traits, respectively. For the SLA-based model, the r2 and RMSE for canopy LAI is 0.81 and 1.24 m2 m-2 when using the estimated SLA data as input or 0.94 and 0.25 m2 m-2 when using the measured SLA data as input. So, our model better predicts LAI for greenhouse crops at different latitudes and a range of planting densities and pruning systems. Although calibrations for specific light regime, pruning practices and cultivars are needed, the fact that production conditions in commercial greenhouse production are often well controlled and production practices are often rather standardized implies a general applicability of our model.
    Cuscuta reflexa invasion induces Ca2+ release in its host
    Albert, M. ; Krol, A.R. van der; Kaldenhoff, R. - \ 2010
    Plant Biology 12 (2010)3. - ISSN 1435-8603 - p. 554 - 557.
    lupinus-albus l - parasite cuscuta - calcium - cells - defense - tomato - plants - roxb - arabidopsis - activation
    Cuscuta reflexa induces a variety of reaction in its hosts. Some of these are visual reactions, and it is clear that these morphological changes are preceded by events at the molecular level, where signal transduction is one of the early processes. Calcium (Ca(2+)) release is the major second messenger during signal transduction, and we therefore studied Ca(2+) spiking in tomato during infection with C. reflexa. Bioluminescence in aequorin-expressing tomato was monitored for 48 h after the onset of Cuscuta infestation. Signals at the attachment sites were observed from 30 to 48 h. Treatment of aequorin-expressing tomato leaf disks with Cuscuta plant extracts suggested that the substance that induced Ca(2+) release from the host was closely linked to parasite haustoria
    Evidence for RNA recombination between distinct isolates of Pepino mosaic virus.
    Hasiów-Jaroszewska, B. ; Kuzniar, A. ; Peters, S.A. ; Leunissen, J.A.M. ; Pospieszny, H. - \ 2010
    Acta Biochimica Polonica 57 (2010)3. - ISSN 0001-527X - p. 385 - 388.
    plant-virus - tomato - evolution
    Genetic recombination plays an important role in the evolution of virus genomes. In this study we analyzed publicly available genomic sequences of Pepino mosaic virus (PepMV) for recombination events using several bioinformatics tools. The genome-wide analyses not only confirm the presence of previously found recombination events in PepMV but also provide the first evidence for double recombinant origin of the US2 isolate.
    Use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening
    Costa, F. ; Alba, R. ; Schouten, H.J. ; Soglio, V. ; Gianfranceschi, L. ; Serra, S. ; Musacchi, S. ; Sansavini, S. ; Costa, G. ; Fei, Z. ; Giovannoni, J. - \ 2010
    BMC Plant Biology 10 (2010). - ISSN 1471-2229 - 36 p.
    cdna microarrays - ethylene biosynthesis - climacteric fruit - sequence tags - melon fruit - tomato - genomics - identification - morphogenesis - biochemistry
    Background - Fruit development, maturation and ripening consists of a complex series of biochemical and physiological changes that in climacteric fruits, including apple and tomato, are coordinated by the gaseous hormone ethylene. These changes lead to final fruit quality and understanding of the functional machinery underlying these processes is of both biological and practical importance. To date many reports have been made on the analysis of gene expression in apple. In this study we focused our investigation on the role of ethylene during apple maturation, specifically comparing transcriptomics of normal ripening with changes resulting from application of the hormone receptor competitor 1-Methylcyclopropene. Results - To gain insight into the molecular process regulating ripening in apple, and to compare to tomato (model species for ripening studies), we utilized both homologous and heterologous (tomato) microarray to profile transcriptome dynamics of genes involved in fruit development and ripening, emphasizing those which are ethylene regulated. The use of both types of microarrays facilitated transcriptome comparison between apple and tomato (for the later using data previously published and available at the TED: tomato expression database) and highlighted genes conserved during ripening of both species, which in turn represent a foundation for further comparative genomic studies. The cross-species analysis had the secondary aim of examining the efficiency of heterologous (specifically tomato) microarray hybridization for candidate gene identification as related to the ripening process. The resulting transcriptomics data revealed coordinated gene expression during fruit ripening of a subset of ripening-related and ethylene responsive genes, further facilitating the analysis of ethylene response during fruit maturation and ripening. Conclusion - Our combined strategy based on microarray hybridization enabled transcriptome characterization during normal climacteric apple ripening, as well as definition of ethylene-dependent transcriptome changes. Comparison with tomato fruit maturation and ethylene responsive transcriptome activity facilitated identification of putative conserved orthologous ripening-related genes, which serve as an initial set of candidates for assessing conservation of gene activity across genomes of fruit bearing plant species
    Conserved fungal LysM effector Ecp6 prevents chitin-triggered immunity in plants
    Jonge, R. de; Esse, H.P. van; Kombrink, A. ; Shinya, T. ; Desaki, Y. ; Bours, R.M.E.H. ; Krol, A.R. van der; Shibuya, N. ; Joosten, M.H.A.J. ; Thomma, B.P.H.J. - \ 2010
    Science 329 (2010). - ISSN 0036-8075 - p. 953 - 955.
    receptor-like kinase - cladosporium-fulvum - virulence factor - binding - defense - tomato - cells - avr4 - recognition - arabidopsis
    Multicellular organisms activate immunity upon recognition of pathogen-associated molecular patterns (PAMPs). Chitin is the major component of fungal cell walls, and chitin oligosaccharides act as PAMPs in plant and mammalian cells. Microbial pathogens deliver effector proteins to suppress PAMP-triggered host immunity and to establish infection. Here, we show that the LysM domain–containing effector protein Ecp6 of the fungal plant pathogen Cladosporium fulvum mediates virulence through perturbation of chitin-triggered host immunity. During infection, Ecp6 sequesters chitin oligosaccharides that are released from the cell walls of invading hyphae to prevent elicitation of host immunity. This may represent a common strategy of host immune suppression by fungal pathogens, because LysM effectors are widely conserved in the fungal kingdom
    Diversity, distribution, and evolution of Solanum bulbocastanum late blight resistance genes
    Lokossou, A.A. ; Rietman, H. ; Wang, M. ; Krenek, P. ; Schoot, J. van der; Henken, G. ; Hoekstra, R. ; Vleeshouwers, V.G.A.A. ; Vossen, E.A.G. van der; Visser, R.G.F. ; Jacobsen, E. ; Vosman, B. - \ 2010
    Molecular Plant-Microbe Interactions 23 (2010)9. - ISSN 0894-0282 - p. 1206 - 1216.
    phytophthora-infestans resistance - broad-spectrum resistance - potato late blight - nbs-lrr genes - disease resistance - r-gene - arabidopsis-thaliana - avirulence genes - cultivated potato - tomato
    Knowledge on the evolution and distribution of late blight resistance genes is important for a better understanding of the dynamics of these genes in nature. We analyzed the presence and allelic diversity of the late blight resistance genes Rpi-blb1, Rpi-blb2, and Rpi-blb3, originating from Solanum bulbocastanum, in a set of tuber-bearing Solanum species comprising 196 different taxa. The three genes were only present in some Mexican diploid as well as polyploid species closely related to S. bulbocastanum. Sequence analysis of the fragments obtained from the Rpi-blb1 and Rpi-blb3 genes suggests an evolution through recombinations and point mutations. For Rpi-blb2, only sequences identical to the cloned gene were found in S. bulbocastanum accessions, suggesting that it has emerged recently. The three resistance genes occurred in different combinations and frequencies in S. bulbocastanum accessions and their spread is confined to Central America. A selected set of genotypes was tested for their response to the avirulence effectors IPIO-2, Avr-blb2, and Pi-Avr2, which interact with Rpi-blb1, Rpi-blb2, and Rpi-blb3, respectively, as well as by disease assays with a diverse set of isolates. Using this approach, some accessions could be identified that contain novel, as yet unknown, late blight resistance factors in addition to the Rpi-blb1, Rpi-blb2, and Rpi-blb3 genes.
    The use of attenuated isolates of Pepino mosaic virus for cross-protection
    Schenk, M.F. ; Hamelink, R. ; Vlugt, R.A.A. van der; Vermunt, A.M.W. ; Kaarsemaker, R.C. ; Stijger, C.C.M.M. - \ 2010
    European Journal of Plant Pathology 127 (2010)2. - ISSN 0929-1873 - p. 249 - 261.
    genomic rna - tomato - sequence - population - resistance - potyvirus - disease - strain - range - spain
    Pepino mosaic virus (PepMV) has recently emerged as a highly infectious viral pathogen in tomato crops. Greenhouse trials were conducted under conditions similar to commercial tomato production. These trials examined whether tomato plants can be protected against PepMV by a preceding infection with an attenuated isolate of this virus. Two potential attenuated isolates that displayed mild leaf symptoms were selected from field isolates. Two PepMV isolates that displayed severe leaf symptoms were also selected from field isolates to challenge the attenuated isolates. The isolates with aggressive symptoms were found to reduce bulk yields by 8 and 24% in single infections, respectively. Yield losses were reduced to a 0–3% loss in plants that were treated with either one of the attenuated isolates, while no effects were observed on the quality of the fruits. After the challenge infection, virus accumulation levels and symptom severity of the isolates with aggressive symptoms were also reduced by cross-protection. Infection with the attenuated isolates alone did neither affect bulk yield, nor quality of the harvested tomato fruits.
    Identification of a resistance gene Rpi-dlc1 to Phytophthora infestans in European accessions of Solanum dulcamara
    Golas, T.M. ; Sikkema, A. ; Gros, J. ; Feron, R.M.C. ; Berg, R.G. van den; Weerden, G.M. van der; Mariani, C. ; Allefs, J.J.H.M. - \ 2010
    Theoretical and Applied Genetics 120 (2010)4. - ISSN 0040-5752 - p. 797 - 808.
    late-blight resistance - broad-spectrum resistance - race-specific resistance - potato late blight - r-gene - disease-resistance - chromosome-ix - bulbocastanum - tomato - locus
    Initial screening of 14 Solanum dulcamara accessions enabled the identification of individuals resistant and susceptible to Phytophthora infestans. Crosses between contrasting genotypes resulted in three F2–BC1 populations segregating for resistance to late blight in a laboratory assay and under field conditions. Genetic profiling of one of these populations using 128 AFLP primers generated three markers linked to the resistant phenotype. Blast analysis of the sequenced markers resulted in a plausible gene position on the distal end of the long arm of chromosome 9 that could be confirmed by CAPS markers. Thus, we describe a first resistant gene, named Rpi-dlc1, from S. dulcamara, a Solanum species native to Europe. In addition, one population was tested for broadness of resistance responses using a set of seven additional P. infestans isolates, varying in virulence. This indicated the possible presence of additional Rpi genes.
    Volatile organic compounds as a diagnostic marker of late blight infected potato plants: A pilot study
    Laothawornkitkul, J. ; Jansen, R.M.C. ; Smid, H.M. ; Bouwmeester, H.J. ; Muller, J. ; Bruggen, A.H.C. van - \ 2010
    Crop Protection 29 (2010)8. - ISSN 0261-2194 - p. 872 - 878.
    phytophthora-infestans - botrytis-cinerea - damaged plants - in-vitro - tomato - leaves - lipoxygenase - emissions - variability - biosensor
    Volatiles from potato plants infected with Phytophthora infestans (Mont.) de Bary were monitored by in situ headspace sampling. The sampling was done in four periods i.e. 28–42, 52–66, 76–90, and 100–114 h after inoculation (HAI). The headspace samples were analyzed by a gas chromatography–flame ionization detector (GC–FID) to assess the differences in volatile fingerprints between the infected-plant group and control groups, i.e. non-inoculated-plant and empty-vessel groups. The samples were subsequently analyzed by gas chromatography–mass spectrometry to identify specific peaks observed by GC–FID. Spore germination, infection, symptom development and sporulation were also monitored to ascertain the disease developmental stage when marker volatiles were first generated. The first symptoms of infection were visible after two days. Three marker volatiles i.e. (E)-2-hexenal, 5-ethyl-2(5H)-furanone and benzene-ethanol were found in the third and fourth trapping periods (3–4 days after inoculation) when sporangiophores were already formed. The volatile metabolites from blighted plants could be applied for sensor development to detect the occurrence of the disease in the field as well as for investigation of volatile production in relation to plant responses to infection.
    Characterisation of sugar beet (Beta vulgaris L. ssp. vulgaris) varieties using microsatellite markers
    Smulders, M.J.M. ; Esselink, G. ; Everaert, I. ; Riek, J. de; Vosman, B. - \ 2010
    BMC Genetics 11 (2010). - ISSN 1471-2156 - 11 p.
    genetic diversity - linkage map - wild relatives - flow - crop - identification - populations - database - complex - tomato
    Background - Sugar beet is an obligate outcrossing species. Varieties consist of mixtures of plants from various parental combinations. As the number of informative morphological characteristics is limited, this leads to some problems in variety registration research. Results - We have developed 25 new microsatellite markers for sugar beet. A selection of 12 markers with high quality patterns was used to characterise 40 diploid and triploid varieties. For each variety 30 individual plants were genotyped. The markers amplified 3-21 different alleles. Varieties had up to 7 different alleles at one marker locus. All varieties could be distinguished. For the diploid varieties, the expected heterozygosity ranged from 0.458 to 0.744. The average inbreeding coefficient Fis was 0.282 +/- 0.124, but it varied widely among marker loci, from Fis = +0.876 (heterozygote deficiency) to Fis = -0.350 (excess of heterozygotes). The genetic differentiation among diploid varieties was relatively constant among markers (Fst = 0.232 +/- 0.027). Among triploid varieties the genetic differentiation was much lower (Fst = 0.100 +/- 0.010). The overall genetic differentiation between diploid and triploid varieties was Fst = 0.133 across all loci. Part of this differentiation may coincide with the differentiation among breeders' gene pools, which was Fst = 0.063. Conclusions - Based on a combination of scores for individual plants all varieties can be distinguished using the 12 markers developed here. The markers may also be used for mapping and in molecular breeding. In addition, they may be employed in studying gene flow from crop to wild populations.
    Interfamily transfer of a plant pattern-recognition receptor confers broad-spectrum bacterial resistance
    Lacombe, S. ; Rougon-Cardoso, A. ; Sherwood, E. ; Peeters, N. ; Dahlbeck, D. ; Esse, H.P. van; Smoker, M. ; Rallapalli, G. ; Thomma, B.P.H.J. ; Staskawicz, B. ; Jones, J.D.G. ; Zipfel, C. - \ 2010
    Nature Biotechnology 28 (2010)4. - ISSN 1087-0156 - p. 365 - 369.
    pseudomonas-syringae - innate immunity - disease resistance - transgenic plants - arabidopsis - perception - tomato - gene - effectors - defense
    Plant diseases cause massive losses in agriculture. Increasing the natural defenses of plants may reduce the impact of phytopathogens on agricultural productivity. Pattern-recognition receptors (PRRs) detect microbes by recognizing conserved pathogen-associated molecular patterns (PAMPs)1, 2, 3. Although the overall importance of PAMP-triggered immunity for plant defense is established2, 3, it has not been used to confer disease resistance in crops. We report that activity of a PRR is retained after its transfer between two plant families. Expression of EFR (ref. 4), a PRR from the cruciferous plant Arabidopsis thaliana, confers responsiveness to bacterial elongation factor Tu in the solanaceous plants Nicotiana benthamiana and tomato (Solanum lycopersicum), making them more resistant to a range of phytopathogenic bacteria from different genera. Our results in controlled laboratory conditions suggest that heterologous expression of PAMP recognition systems could be used to engineer broad-spectrum disease resistance to important bacterial pathogens, potentially enabling more durable and sustainable resistance in the field
    Microsatellite genotyping of apple (Malus × domestica Borkh.) genetic resources in the Netherlands: application in collection management and variety identification
    Treuren, R. van; Kemp, H. ; Ernsting, G. ; Jongejans, B. ; Houtman, H. ; Visser, L. - \ 2010
    Genetic Resources and Crop Evolution 57 (2010)6. - ISSN 0925-9864 - p. 853 - 865.
    appels - genenbanken - genotypen - genetische merkers - microsatellieten - genetische diversiteit - fenotypen - apples - gene banks - genotypes - genetic markers - microsatellites - genetic diversity - phenotypes - molecular characterization - ssr markers - construction - polymorphism - database - tomato - plants - dna
    A highly informative set of 16 microsatellite markers was used to fingerprint 695 apple accessions from eight Dutch collections. Among the total sample, 475 different genotypes were distinguished based on multi-locus microsatellite variation, revealing a potential redundancy within the total sample of 32%. The majority of redundancies were found between collections, rather than within collections. No single collection covered the total observed diversity well, as each collection consisted of about 50% of unique accessions. These findings reflected the fact that most collection holders focus on common Dutch varieties, as well as on region-specific diversity. Based on the diversity patterns observed, maintenance of genetic resources by a network of co-operating collection holders, rather than by collecting the total diversity in a single collection appears to be an efficient approach. Comparison of microsatellite and passport data showed that for many accessions the marker data did not provide support for the registered variety names. Verification of accessions showed that discrepancies between passport and molecular data were largely due to documentation and phenotypic determination errors. With the help of the marker data the varietal names of 45 accessions could be corrected. Microsatellite genotyping of apple appears to be an efficient tool in the management of collections and in variety identification. The development of a marker database was considered relevant as a reference instrument in variety identification and as a source of information about thus far unexplored diversity that could be of interest in the development of new apple varieties
    A novel approach to locate Phytophthora infestans resistance genes on the potato genetic map
    Jacobs, M.M.J. ; Vosman, B. ; Vleeshouwers, V.G.A.A. ; Visser, R.G.F. ; Henken, G. ; Berg, R.G. van den - \ 2010
    Theoretical and Applied Genetics 120 (2010)4. - ISSN 0040-5752 - p. 785 - 796.
    late-blight resistance - broad-spectrum resistance - disease-resistance - solanum-bulbocastanum - r-gene - chromosome-ix - tomato - plant - homologs - genome
    Mapping resistance genes is usually accomplished by phenotyping a segregating population for the resistance trait and genotyping it using a large number of markers. Most resistance genes are of the NBS-LRR type, of which an increasing number is sequenced. These genes and their analogs (RGAs) are often organized in clusters. Clusters tend to be rather homogenous, viz. containing genes that show high sequence similarity with each other. From many of these clusters the map position is known. In this study we present and test a novel method to quickly identify to which cluster a new resistance gene belongs and to produce markers that can be used for introgression breeding. We used NBS profiling to identify markers in bulked DNA samples prepared from resistant and susceptible genotypes of small segregating populations. Markers co-segregating with resistance can be tested on individual plants and directly used for breeding. To identify the resistance gene cluster a gene belongs to, the fragments were sequenced and the sequences analyzed using bioinformatics tools. Putative map positions arising from this analysis were validated using markers mapped in the segregating population. The versatility of the approach is demonstrated with a number of populations derived from wild Solanum species segregating for P. infestans resistance. Newly identified P. infestans resistance genes originating from S. verrucosum, S. schenckii, and S. capsicibaccatum could be mapped to potato chromosomes 6, 4, and 11, respectively.
    Fruit size QTL analysis of an F1 population derived from a cross between a domesticated sweet cherry cultivar and a wild forest sweet cherry
    Zhang, G. ; Sebolt, A.M. ; Sooriyapathirana, S.S. ; Wang, D. ; Bink, M.C.A.M. ; Olmstead, J.W. ; Iezzoni, A.F. - \ 2010
    Tree Genetics and Genomes 6 (2010)1. - ISSN 1614-2942 - p. 25 - 36.
    prunus-persica l. - genetic-linkage map - mesocarp cells - avium l. - microsatellite markers - quality traits - peach - tomato - batsch - weight
    Maximizing fruit size is critical for profitable sweet cherry (Prunus avium L.) production. Yet, despite its importance, little is known about the genetic control of fruit size. The objective of this study was to identify quantitative trait loci (QTLs) for fruit size and two essential components of fruit size, mesocarp cell number and size. This study utilized a double pseudo-testcross population derived from reciprocal crosses between a sweet cherry cultivar with ~8 g fruit, ¿Emperor Francis¿ (EF), and a wild forest sweet cherry selection with ~2 g fruit, ¿New York 54¿ (NY). A total of 190 F1 progeny previously utilized for the construction of the linkage maps were evaluated in 2006 and 2007 for fruit weight, length, and diameter; mesocarp cell number and length; and pit length and diameter. In 2008, a subset of this population was again evaluated for fruit weight. Correlation analysis revealed that the three fruit size traits were highly correlated with each other, and mesocarp cell number, not cell length, was correlated with fruit size. Three QTLs were identified for each fruit size trait, and one QTL was identified for mesocarp cell number. Fruit size QTLs were found on linkage group 2 on the EF map (EF 2) and linkage groups 2 and 6 on the NY map (NY 2 and NY 6). On EF 2, the cell number QTL clustered with the fruit size QTL, suggesting that the underlying basis of the fruit size increase associated with this QTL was an increase in mesocarp cell number. On NY 6, pit length and diameter QTLs clustered with those for fruit size, suggesting that the underlying morphological basis of this fruit size QTL is the difference in pit size
    Using SNP markers to dissect linkage disequilibrium at a major quantitative trait locus for resistance to the potato cyst nematode Globodera pallida on potato chromosome V
    Achenbach, U. ; Caldas Paulo, M.J. ; Ilarionova, E. ; Lübeck, J. ; Strahwald, J. ; Tacke, E. ; Hofferbert, H.R. - \ 2009
    Theoretical and Applied Genetics 118 (2009)3. - ISSN 0040-5752 - p. 619 - 629.
    high-resolution map - pathogen resistance - solanum-spegazzinii - disease resistance - dna variation - late blight - genome - rostochiensis - tomato - segments
    The damage caused by the parasitic root cyst nematode Globodera pallida is a major yield-limiting factor in potato cultivation . Breeding for resistance is facilitated by the PCR-based marker 'HC', which is diagnostic for an allele conferring high resistance against G. pallida pathotype Pa2/3 that has been introgressed from the wild potato species Solanum vernei into the Solanum tuberosum tetraploid breeding pool. The major quantitative trait locus (QTL) controlling this nematode resistance maps on potato chromosome V in a hot spot for resistance to various pathogens including nematodes and the oomycete Phytophthora infestans. An unstructured sample of 79 tetraploid, highly heterozygous varieties and breeding clones was selected based on presence (41 genotypes) or absence (38 genotypes) of the HC marker. Testing the clones for resistance to G. pallida confirmed the diagnostic power of the HC marker. The 79 individuals were genotyped for 100 single nucleotide polymorphisms (SNPs) at 10 loci distributed over 38 cM on chromosome V. Forty-five SNPs at six loci spanning 2 cM in the interval between markers GP21-GP179 were associated with resistance to G. pallida. Based on linkage disequilibrium (LD) between SNP markers, six LD groups comprising between 2 and 18 SNPs were identified. The LD groups indicated the existence of multiple alleles at a single resistance locus or at several, physically linked resistance loci. LD group C comprising 18 SNPs corresponded to the 'HC' marker. LD group E included 16 SNPs and showed an association peak, which positioned one nematode resistance locus physically close to the R1 gene family
    Nitrogen Uptake Efficiency and Growth of Bell Pepper in Relation to Time of Exposure to Fertilizer Solution
    Scholberg, J.M.S. ; Zotarelli, L. ; Tubbs, R.S. ; Dukes, M.D. ; Munoz-Carpena, R. - \ 2009
    Communications in Soil Science and Plant Analysis 40 (2009)13-14. - ISSN 0010-3624 - p. 2111 - 2131.
    capsicum-annuum-l - vegetable crops - root-growth - drip irrigation - nutrient-uptake - nitrate uptake - soil - accumulation - nutrition - tomato
    Irrigation of high-value vegetable crops on sandy soils with poor waterretention capacities may result in fertilizer nitrogen (N) displacement below the effective root zone prior to complete crop uptake. As a result, fertilizer N-uptake efficiency (FUE) of vegetable crops is often relatively low, thereby increasing the potential risk of groundwater contamination. The objective of this study was to determine how time of exposure of the root zone to the N fertilizer (which is referred to as "fertilizer residence time'' or t(R)), as related to irrigation management, affects N uptake, FUE, growth, and yield of bell pepper (Capsicum annuum L.). Plants were grown in PVC columns with 45 kg of soil equipped with a drainage valve in the bottom of the column. Weekly irrigation with dissolved fertilizers (potassium nitrate; KNO3) was applied 1, 3, or 7 d before weekly removal of residual soil N by leaching. Weekly N uptake rates were calculated by comparing total N recovery between unplanted (reference) and planted columns. At 77d after planting, increasing the t(R) from 1 to 3 or 7 d increased the weekly N uptake from 1.4 to 10.8 and/or 13.3 kg N ha(-1), respectively. Total calculated plant N accumulations were 19, 72, and 106 kg N ha(-1) for the 1-, 3-, and 7d t(R) treatments, with overall FUE values being 8, 31, and 45%, respectively. It is concluded that during initial growth crop, uptake capacity is limiting, and more frequent (daily) fertilizer injection into the irrigation water may be required to enhance FUE. It is proposed also that via sound or innovative irrigation management practices, fertilizer retention in the root zone can be enhanced, thereby improving crop growth, yield, and FUE while reducing production cost and potential environmental impacts.
    Endophytic Colonization of Potato (Solanum tuberosum L.) by a Novel Competent Bacterial Endophyte, Pseudomonas putida Strain P9, and Its Effect on Associated Bacterial Communities
    Andreote, F.D. ; Araujo, W.L. ; Azevedo, J.L. ; Elsas, J.D. van; Rocha, U.N. da; Overbeek, L.S. van - \ 2009
    Applied and Environmental Microbiology 75 (2009)11. - ISSN 0099-2240 - p. 3396 - 3406.
    gradient gel-electrophoresis - 16s ribosomal-rna - soil microbial community - ralstonia-solanacearum - rhizosphere bacteria - systemic resistance - fluorescens strain - sequence data - plant-growth - tomato
    Pseudomonas putida strain P9 is a novel competent endophyte from potato. P9 causes cultivar-dependent suppression of Phytophthora infestans. Colonization of the rhizoplane and endosphere of potato plants by P9 and its rifampin-resistant derivative P9R was studied. The purposes of this work were to follow the fate of P9 inside growing potato plants and to establish its effect on associated microbial communities. The effects of P9 and P9R inoculation were studied in two separate experiments. The roots of transplants of three different cultivars of potato were dipped in suspensions of P9 or P9R cells, and the plants were planted in soil. The fate of both strains was followed by examining colony growth and by performing PCR-denaturing gradient gel electrophoresis (PCR-DGGE). Colonies of both strains were recovered from rhizoplane and endosphere samples of all three cultivars at two growth stages. A conspicuous band, representing P9 and P9R, was found in all Pseudomonas PCR-DGGE fingerprints for treated plants. The numbers of P9R CFU and the P9R-specific band intensities for the different replicate samples were positively correlated, as determined by linear regression analysis. The effects of plant growth stage, genotype, and the presence of P9R on associated microbial communities were examined by multivariate and unweighted-pair group method with arithmetic mean cluster analyses of PCR-DGGE fingerprints. The presence of strain P9R had an effect on bacterial groups identified as Pseudomonas azotoformans, Pseudomonas veronii, and Pseudomonas syringae. In conclusion, strain P9 is an avid colonizer of potato plants, competing with microbial populations indigenous to the potato phytosphere. Bacterization with a biocontrol agent has an important and previously unexplored effect on plant-associated communities.
    Life history parameters of Trialeurodes vaporariorum (Westwood) (Hemiptera: Aleyrodidae) at different environmental conditions on two bean cultivars
    Manzano, M.R. ; Lenteren, J.C. van - \ 2009
    Neotropical Entomology 38 (2009)4. - ISSN 1519-566X - p. 452 - 458.
    amitus-fuscipennis macgown - greenhouse - platygasteridae - homoptera - gennadius - dynamics - tomato - hym.
    Life-history parameters of the greenhouse whitefly Trialeurodes vaporariorum (Westwood), an important pest of bean crops in Colombia, were determined in environmental control chambers on two dry bean (Phaseolus vulgaris) cultivars (cv.). Trialeurodes vaporariorum longevity on cv. Chocho decreased as temperature increased from 22.6 d at 19ºC to 5.9 d at 26ºC. Fecundity was significantly lower at 19ºC (8.6 eggs/female), as compared to 22ºC (32.6 eggs/female) and 26ºC (33.3 eggs/female) on cv. Chocho. Fecundity on cv. ICA-Pijao was much higher (127.2 eggs/female) than on cv. Chocho (32.6 eggs/female) at 19ºC. The intrinsic rate of population increase (rm) was highest at 22ºC (0.061), intermediate at 19ºC (0.044) and lowest at 26ºC (0.035) on cv. Chocho, and was 0.072 on cv. ICA-Pijao at 19ºC. Life history parameters of T. vaporariorum are compared to those of one of its natural enemies, the parasitoid Amitus fuscipennis MacGown & Nebeker. Finally, data are presented on the distribution of the parasitoid related to the altitude for the Valle del Cauca, Colombia
    Implementation of two high through-put techniques in a novel application: detecting point mutations in large EMS mutated plant populations
    Gady, A.L.F. ; Hermans, F.W.K. ; Wal, M.H.B.J. van de; Loo, E.N. van; Visser, R.G.F. ; Bachem, C.W.B. - \ 2009
    Plant Methods 5 (2009). - ISSN 1746-4811 - 14 p.
    sensitive capillary-electrophoresis - chemically-induced mutations - resolution melting analysis - arabidopsis-thaliana - gene mutation - in-silico - discovery - tomato - zebrafish - disease
    Background - The establishment of mutant populations together with the strategies for targeted mutation detection has been applied successfully to a large number of organisms including many species in the plant kingdom. Considerable efforts have been invested into research on tomato as a model for berry-fruit plants. With the progress of the tomato sequencing project, reverse genetics becomes an obvious and achievable goal. Results - Here we describe the treatment of Solanum lycopersicum seeds with 1% EMS and the development of a new mutated tomato population. To increase targeted mutant detection throughput an automated seed DNA extraction has been combined with novel mutation detection platforms for TILLING in plants. We have adapted two techniques used in human genetic diagnostics: Conformation Sensitive Capillary Electrophoresis (CSCE) and High Resolution DNA Melting Analysis (HRM) to mutation screening in DNA pools. Classical TILLING involves critical and time consuming steps such as endonuclease digestion reactions and gel electrophoresis runs. Using CSCE or HRM, the only step required is a simple PCR before either capillary electrophoresis or DNA melting curve analysis. Here we describe the development of a mutant tomato population, the setting up of two polymorphism detection platforms for plants and the results of the first screens as mutation density in the populations and estimation of the false-positives rate when using HRM to screen DNA pools. Conclusion - These results demonstrate that CSCE and HRM are fast, affordable and sensitive techniques for mutation detection in DNA pools and therefore allow the rapid identification of new allelic variants in a mutant population. Results from the first screens indicate that the mutagen treatment has been effective with an average mutation detection rate per diploid genome of 1.36 mutation/kb/1000 lines
    The status of biological control of plant diseases in soilless cultivation
    Postma, J. - \ 2009
    In: Recent Developments in Management of Plant Diseases Dordrecht : Springer Netherlands (Plant Pathology in the 21st Century 1) - ISBN 9781402088032 - p. 133 - 146.
    pythium-aphanidermatum - fusarium-oxysporum - growing systems - greenhouse horticulture - indigenous microflora - microbial-populations - crown rot - tomato - cucumber - root
    Avoidance of plant diseases has been a major driver for the development of soilless cultivation systems. Nevertheless, diseases still occur in these systems and the need for additional control measures exist. Traditionally, control has relied on the use of chemical fungicides but environmental pressure to reduce chemical usage in the environment, and fewer active ingredients registered for use, has stimulated the development of biological methods of disease control. One approach has been to utilise microbial inoculants as straight replacements for chemical pesticides and some commercial products are now available. Sufficient root colonization and activity are key issues for effective biocontrol. Another approach has been to create growing systems with improved suppressiveness towards plant diseases. The challenge is to combine the available strategies into environmentally and economically sound soilless plant production systems with low risks for pathogen outbreaks. Soilless systems have the potential of creating a balance between a pathogen-free start and a suppressive microflora. Keywords Biological control - Disease-suppressive substrate - Hydroponics - Recirculated nutrient solution - Microbial populations - Rhizosphere - Root pathogens
    Sequencing the potato genome: outline and first results to come from the elucidation of the sequence of the world's third most important food crop
    Visser, R.G.F. ; Bachem, C.W.B. ; Boer, J.M. de; Bryan, G.J. ; Chakrabati, S.K. ; Feingold, S. ; Gromadka, R. ; Ham, R.C.H.J. van; Huang, S. ; Jacobs, J.M.E. ; Kuznetsov, Boris ; Melo, P. de; Milbourne, D. ; Orjeda, G. ; Sagredo, Boris ; Tang, X. - \ 2009
    American Journal of Potato Research 86 (2009)6. - ISSN 1099-209X - p. 417 - 429.
    broad-spectrum resistance - quantitative trait loci - late blight resistance - phytophthora-infestans - solanum-bulbocastanum - disease resistance - bacterial wilt - gene-cluster - tomato - system
    Potato is a member of the Solanaceae, a plant family that includes several other economically important species, such as tomato, eggplant, petunia, tobacco and pepper. The Potato Genome Sequencing Consortium (PGSC) aims to elucidate the complete genome sequence of potato, the third most important food crop in the world. The PGSC is a collaboration between 13 research groups from China, India, Poland, Russia, the Netherlands, Ireland, Argentina, Brazil, Chile, Peru, USA, New Zealand and the UK. The potato genome consists of 12 chromosomes and has a (haploid) length of approximately 840 million base pairs, making it a medium-sized plant genome. The sequencing project builds on a diploid potato genomic bacterial artificial chromosome (BAC) clone library of 78000 clones, which has been fingerprinted and aligned into ~7000 physical map contigs. In addition, the BAC-ends have been sequenced and are publicly available. Approximately 30000 BACs are anchored to the Ultra High Density genetic map of potato, composed of 10000 unique AFLPTM markers. From this integrated genetic-physical map, between 50 to 150 seed BACs have currently been identified for every chromosome. Fluorescent in situ hybridization experiments on selected BAC clones confirm these anchor points. The seed clones provide the starting point for a BAC-by-BAC sequencing strategy. This strategy is being complemented by whole genome shotgun sequencing approaches using both 454 GS FLX and Illumina GA2 instruments. Assembly and annotation of the sequence data will be performed using publicly available and tailor-made tools. The availability of the annotated data will help to characterize germplasm collections based on allelic variance and to assist potato breeders to more fully exploit the genetic potential of potato
    GpaXIltar originating from Solanum tarijense is a major resistance locus to Globodera pallida and is localised on chromosome 11 of potato
    Tan, M.Y.A. ; Park, T.H. ; Alles, R. ; Hutten, R.C.B. ; Visser, R.G.F. ; Eck, H.J. van - \ 2009
    Theoretical and Applied Genetics 119 (2009)8. - ISSN 0040-5752 - p. 1477 - 1487.
    broad-spectrum resistance - comigrating aflp markers - cyst-nematode - confers resistance - gene-cluster - tuberosum - linkage - tomato - virus - dna
    Resistance to Globodera pallida Rookmaker (Pa3), originating from wild species Solanum tarijense was identified by QTL analysis and can be largely ascribed to one major QTL. GpaXI tar l explained 81.3% of the phenotypic variance in the disease test. GpaXI tar l is mapped to the long arm of chromosome 11. Another minor QTL explained 5.3% of the phenotypic variance and mapped to the long arm of chromosome 9. Clones containing both QTL showed no lower cyst counts than clones with only GpaXI tar l . After Mendelising the phenotypic data, GpaXI tar l could be more precisely mapped near markers GP163 and FEN427, thus anchoring GpaXI tar l to a region with a known R-gene cluster containing virus and nematode resistance genes
    Genetic differences in fruit-set patterns are determined by differences in fruit sink strength and a source : sink threshold for fruit set
    Wubs, A.M. ; Ma, Y.T. ; Heuvelink, E. ; Marcelis, L.F.M. - \ 2009
    Annals of Botany 104 (2009)5. - ISSN 0305-7364 - p. 957 - 964.
    pepper capsicum-annuum - flower abscission - cultivars - cucumber - growth - competition - position - tomato - susceptibility - temperature
    Background and Aims: Fruit set in indeterminate plant species largely depends on the balance between source and sink strength. Plants of these species show fluctuations in fruit set during the growing season. It was tested whether differences in fruit sink strength among the cultivars explained the differences in fruit-set patterns. Methods: Capsicum was chosen as a model plant. Six cultivars with differences in fruit set, fruit size and plant growth were evaluated in a greenhouse experiment. Fruit-set patterns, generative and vegetative sink strength, source strength and the source : sink ratio at fruit set were determined. Sink strength was quantified as potential growth rate. Fruit set was related to total fruit sink strength and the source : sink ratio. The effect of differences observed in above-mentioned parameters on fruit-set patterns was examined using a simple simulation model. Key Results: Sink strengths of individual fruits differed greatly among cultivars. Week-to-week fruit set in large-fruited cultivars fluctuated due to large fluctuations in total fruit sink strength, but in small-fruited cultivars, total fruit sink strength and fruit set were relatively constant. Large variations in week-to-week fruit set were correlated with a low fruit-set percentage. The source : sink threshold for fruit set was higher in large-fruited cultivars. Simulations showed that within the range of parameter values found in the experiment, fruit sink strength and source : sink threshold for fruit set had the largest impact on fruit set: an increase in these parameters decreased the average percentage fruit set and increased variation in weekly fruit set. Both were needed to explain the fruit-set patterns observed. The differences observed in the other parameters (e.g. source strength) had a lower effect on fruit set. Conclusions: Both individual fruit sink strength and the source : sink threshold for fruit set were needed to explain the differences observed between fruit-set patterns of the six cultivars
    Transcription analysis of apple fruit development using cDNA microarrays
    Soglio, V. ; Costa, F. ; Molthoff, J.W. ; Weemen-Hendriks, M. ; Schouten, H.J. ; Gianfranceschi, L. - \ 2009
    Tree Genetics and Genomes 5 (2009)4. - ISSN 1614-2942 - p. 685 - 698.
    expressed-sequence-tags - beta-cyanoalanine synthase - malus-pumila mill. - gene-expression - ethylene biosynthesis - domestica borkh. - tomato - model - identification - maturation
    The knowledge of the molecular mechanisms underlying fruit quality traits is fundamental to devise efficient marker-assisted selection strategies and to improve apple breeding. In this study, cDNA microarray technology was used to identify genes whose expression changes during fruit development and maturation thus potentially involved in fruit quality traits. The expression profile of 1,536 transcripts was analysed by microarray hybridisation. A total of 177 genes resulted to be differentially expressed in at least one of the developmental stages considered. Gene ontology annotation was employed to univocally describe gene function, while cluster analysis allowed grouping genes according to their expression profile. An overview of the transcriptional changes and of the metabolic pathways involved in fruit development was obtained. As expected, August and September are the two months where the largest number of differentially expressed genes was observed. In particular, 85 genes resulted to be up-regulated in September. Even though most of the differentially expressed genes are involved in primary metabolism, several other interesting functions were detected and will be presented.
    A high-resolution map of the Grp1 locus on chromosome V of potato harbouring broad-spectrum resistance to the cyst nematode species Globodera pallida and Globodera rostochiensis
    Finkers-Tomczak, A.M. ; Danan, S. ; Dijk, T. van; Beyene, A. ; Bouwman-Smits, L. ; Overmars, H.A. ; Eck, H.J. van; Goverse, A. ; Bakker, J. ; Bakker, E.H. - \ 2009
    Theoretical and Applied Genetics 119 (2009)1. - ISSN 0040-5752 - p. 165 - 173.
    gene conferring resistance - phytophthora-infestans - disease resistance - solanum-spegazzinii - mapping qtls - r1 gene - cluster - tomato - arabidopsis - virus
    The Grp1 locus confers broad-spectrum resistance to the potato cyst nematode species Globodera pallida and Globodera rostochiensis and is located in the GP21-GP179 interval on the short arm of chromosome V of potato. A high-resolution map has been developed using the diploid mapping population RHAM026, comprising 1,536 genotypes. The flanking markers GP21 and GP179 have been used to screen the 1,536 genotypes for recombination events. Interval mapping of the resistances to G. pallida Pa2 and G. rostochiensis Ro5 resulted in two nearly identical LOD graphs with the highest LOD score just north of marker TG432. Detailed analysis of the 44 recombinant genotypes showed that G. pallida and G. rostochiensis resistance could not be separated and map to the same location between marker SPUD838 and TG432. It is suggested that the quantitative resistance to both nematode species at the Grp1 locus is mediated by one or more tightly linked R genes that might belong to the NBS-LRR class
    Health monitoring of plants by their emitted volatiles: trichome damage and cell membrane damage are detectable at greenhouse scale
    Jansen, R.M.C. ; Hofstee, J.W. ; Wildt, J. ; Verstappen, F.W.A. ; Bouwmeester, H.J. ; Posthumus, M.A. ; Henten, E.J. van - \ 2009
    Annals of Applied Biology 154 (2009)3. - ISSN 0003-4746 - p. 441 - 452.
    gewasbescherming - monitoring - vluchtige verbindingen - gaschromatografie - massaspectrometrie - solanum lycopersicum - tomaten - gewasmonitoring - glastuinbouw - plant protection - monitoring - volatile compounds - gas chromatography - mass spectrometry - solanum lycopersicum - tomatoes - crop monitoring - greenhouse horticulture - reaction mass-spectrometry - organic-compounds - gas-chromatography - methyl salicylate - leaf volatiles - cotton plants - voc emissions - jasmonic acid - tomato - herbivory
    Pathogen attack and herbivore infestation have a major impact on plant health. In a model study, these two plant health issues were simulated to study whether plant health can be monitored at greenhouse scale through the analysis of volatile organic compounds (VOCs) in greenhouse atmosphere. To simulate pathogen attack and herbivore infestation, we repeatedly stroked the stems of tomato plants (Lycopersicon esculentum) and repeatedly removed their side shoots. In addition, we studied the effect of fruit picking on the concentration of plant-emitted VOCs in greenhouse atmosphere. Analysis of air samples obtained before these treatments revealed up to 17 VOCs that are known to be released from tomato plants, of which the most dominant one was the monoterpene ß-phellandrene. When plants were 7 weeks old, the concentration of this VOC was approximately 0.06 ppbv before treatment. When plants were 12 weeks old, this concentration was raised to approximately 0.14 ppbv. Stroking of the stems, removing the side shoots and fruit picking resulted in an increase in the concentrations of all mono- and most sesquiterpenes up to 60-fold, which was expected because these VOCs are well-known constituents of trichomes. The treatments did not result in substantially increased concentrations of the stress-related compounds ¿-copaene, methyl salicylate and (E,E)-4,8,12-trimethyl-1,3,7,11-tridecatetraene. In contrast to stroking and fruit picking, shoot removal resulted in the emission of the lipoxygenase-derived product (Z)-3-hexenol in greenhouse atmosphere expressing cell membrane degradation. The findings presented in this paper focus on the feasibility of monitoring plant health through the analysis of VOCs in greenhouse air, but findings might also be relevant for atmospheric chemistry.
    Quantification of temperature, CO2, and light effects on crop photosynthesis as a basis for model-based greenhouse climate control
    Körner, O. ; Heuvelink, E. ; Niu, Q. - \ 2009
    Journal of Horticultural Science and Biotechnology 84 (2009)2. - ISSN 1462-0316 - p. 233 - 239.
    glasshouse crops - canopy - balance - tomato - design - system
    Detailed measurements of crop photosynthesis at supra-optimal temperatures and high CO2 levels, to validate models for use in model-based greenhouse climate control, are still lacking. We performed CO2 gas exchange measurements to estimate gross crop photosynthesis (Pgc) from measured net crop gas exchange in the daytime, and at night, with temperature and CO2 conditions higher than the normal temperature range, and with two crops of different architecture: tomato, and cut chrysanthemum. From these measurements, Pgc was predicted at photosynthetic photon flux densities (IPPFD) of 300, 600, 900 and 1,200 ¿mol m-2 s-1 for different temperatures (from 20°C to 33°C) and CO2 concentrations (400, 700, and 1,000 ¿mol mol-1). From these predictions, the optimum temperature that maximised Pgc was determined. CO2 concentration had a strong and similar effect on Pgc in both crops, and this effect decreased with increasing CO2 level. For example, at 32°C, there was a 55% or 49% increase in Pgc between 400 and 1,000 ¿mol mol-1 CO2 in chrysanthemum and tomato, respectively. A clear shift to higher optimum temperatures at elevated CO2 levels was observed, and was different for the two crops. Chrysanthemum had a lower temperature optimum than tomato for a maximum Pgc (e.g., at 1,000 ¿mol mol-1 CO2 and 600 ¿mol m-2 s-1 IPPFD, the difference was 3.1°C). Compared to leaf photosynthesis, crop photosynthesis had a lower temperature optimum (the difference could be several °C), and the shift in optimum temperature from a low to a high CO2 level was lower for a canopy compared to a leaf. Therefore, optimising the leaf photosynthetic rate in model-based greenhouse climate control would not result in optimum crop photosynthesis
    Characterization of Rhamnosidases from Lactobacillus plantarum and Lactobacillus acidophilus.
    Beekwilder, M.J. ; Marcozzi, D. ; Vecchi, S. ; Vos, C.H. de; Janssen, P. ; Francke, C. ; Hylckama Vlieg, J.E.T. van; Hall, R.D. - \ 2009
    Applied and Environmental Microbiology 75 (2009)11. - ISSN 0099-2240 - p. 3447 - 3454.
    alpha-l-rhamnosidase - complete genome sequence - rat small-intestine - aspergillus-aculeatus - escherichia-coli - acid - identification - transporter - expression - tomato
    Lactobacilli are known to use plant materials as a food source. Many such materials are rich in rhamnose-containing polyphenols, and thus it can be anticipated that lactobacilli will contain rhamnosidases. Therefore, genome sequences of food-grade lactobacilli were screened for putative rhamnosidases. In the genome of Lactobacillus plantarum, two putative rhamnosidase genes (ram1Lp and ram2Lp) were identified, while in Lactobacillus acidophilus, one rhamnosidase gene was found (ramALa). Gene products from all three genes were produced after introduction into Escherichia coli and were then tested for their enzymatic properties. Ram1Lp, Ram2Lp, and RamALa were able to efficiently hydrolyze rutin and other rutinosides, while RamALa was, in addition, able to cleave naringin, a neohesperidoside. Subsequently, the potential application of Lactobacillus rhamnosidases in food processing was investigated using a single matrix, tomato pulp. Recombinant Ram1Lp and RamALa enzymes were shown to remove the rhamnose from rutinosides in this material, but efficient conversion required adjustment of the tomato pulp to pH 6. The potential of Ram1Lp for fermentation of plant flavonoids was further investigated by expression in the food-grade bacterium Lactococcus lactis. This system was used for fermentation of tomato pulp, with the aim of improving the bioavailability of flavonoids in processed tomato products. While import of flavonoids into L. lactis appeared to be a limiting factor, rhamnose removal was confirmed, indicating that rhamnosidase-producing bacteria may find commercial application, depending on the technological properties of the strains and enzymes
    Metabolism of carotenoids and apocarotenoids during ripening of raspberry fruit
    Beekwilder, M.J. ; Meer, I.M. van der; Simic, A. ; Uitdewilligen, J. ; Arkel, J. van; Vos, C.H. de; Jonker, H.H. ; Verstappen, F.W.A. ; Bouwmeester, H.J. ; Sibbesen, O. ; Qvist, I. ; Mikkelsen, J.D. ; Hall, R.D. - \ 2008
    BioFactors 34 (2008)1. - ISSN 0951-6433 - p. 57 - 66.
    beta-ionone - cleavage dioxygenase - functional-characterization - mammary carcinogenesis - tomato - biosynthesis - accumulation - inhibition - expression - apoptosis
    Carotenoids are important lipophilic antioxidants in fruits. Apocarotenoids such as ¿-ionone and ß-ionone, which are breakdown products of carotenoids, are important for the flavor characteristics of raspberry fruit, and have also been suggested to have beneficial effects on human health. Raspberry is one of the few fruits where fruit ripening is accompanied by the massive production of apocarotenoids. In this paper, changes in levels of carotenoids and apocarotenoids during raspberry fruit ripening are described. In addition, the isolation and characterization of a gene encoding a carotenoid cleavage dioxygenase (CCD), which putatively mediates the degradation of carotenoids to apocarotenoids during raspberry fruit ripening, is reported. Such information helps us to better understand how these compounds are produced in plants and may also enable us to develop novel strategies for improved apocarotenoid production in fruits or indeed, alternative production systems
    Amitus fuscipennis, an alternative to the biological control of Trialeurodes vaporariorum by Encarsia formosa?
    Vis, R.M.J. de; Lenteren, J.C. van - \ 2008
    Bulletin of Insectology 61 (2008)2. - ISSN 1721-8861 - p. 313 - 325.
    parasite-host relationship - bemisia-argentifolii - foraging behavior - life-history - tomato - aleyrodidae - greenhouse - hymenoptera - homoptera - platygasteridae
    Biological control of Trialeurodes vaporariorum (Homoptera Aleyrodidae) by Amitus fuscipennis (Hymenoptera Platygastridae) with or without Encarsia formosa (Hymenoptera Aphelinidae) was tested in both a glasshouse and a plastic greenhouse during two consecutive production cycles of a beef tomato crop on the Bogotá Plateau in Colombia. The mean temperature was around 16 °C in the plastic greenhouse and around 17 °C in the glasshouse. A. fuscipennis was introduced at a rate of 5 pupae per m2 per week during the first 13 weeks of the first cycle. During the second cycle, 2.5 pupae of both E. formosa and A. fuscipennis per m2 per week were introduced during the first 13 weeks. During the first cycle, control was obtained for 5 months in the plastic greenhouse and 3 months in the glasshouse, after which the population of T. vaporariorum adults increased to a maximum of 50 adults per plant. Parasitism was initially higher than 80% but then decreased to 56% in the plastic greenhouse and to 20% in the glasshouse. During the second cycle, biological control was successful in both greenhouses. Populations of T. vaporariorum were lower than 1.2 adults per plant and parasitism, caused mainly by E. formosa, was near 90% most of the time. Therefore, E. formosa is recommended to keep populations of T. vaporariorum at low levels in unheated greenhouses on the Bogotá Plateau. When high populations of T. vaporariorum are to be expected or control of high-density spots is required, A. fuscipennis could be a beneficial addition to E. formosa.
    Transport and compartmentation of phosphite in higher plant cells - kinetic and 31P nuclear magnetic resonance studies
    Danova-Alt, R. ; Dijkema, C. ; Waard, P. de; Köck, M. - \ 2008
    Plant, Cell & Environment 31 (2008)10. - ISSN 0140-7791 - p. 1510 - 1521.
    phytophthora-palmivora - suspension cells - saccharomyces-cerevisiae - physiological-responses - fungicide phosphonate - starvation responses - arabidopsis - inhibition - tomato - deprivation
    Phosphite (Phi, H(2)PO(3)(-)), being the active part of several fungicides, has been shown to influence not only the fungal metabolism but also the development of phosphate-deficient plants. However, the mechanism of phosphite effects on plants is still widely unknown. In this paper we analysed uptake, subcellular distribution and metabolic effects of Phi in tobacco BY-2 cells using in vivo(31)P nuclear magnetic resonance ((31)P-NMR) spectroscopy. Based on the kinetic properties of the phosphate transport system of tobacco BY-2 cells, it was demonstrated that phosphite inhibited phosphate uptake in a competitive manner. To directly follow the fate of phosphate and phosphite in cytoplasmic and vacuolar pools of tobacco cells, we took advantage of the pH-sensitive chemical shift of the Phi anion. The NMR studies showed a distinct cytoplasmic accumulation of Phi in Pi-deprived cells, whereas Pi resupply resulted in a rapid efflux of Phi. Pi-preloaded cells shifted Phi directly into vacuoles. These studies allowed for the first time to follow Phi flux processes in an in vivo setting in plants. On the other hand, the external Pi nutrition status and the metabolic state of the cells had a strong influence on the intracellular compartmentalization of xenobiotic Phi.
    Genetic mapping and transcription analyses of resistance gene loci in potato using NBS profiling
    Brugmans, B.W. ; Wouters, D.C.A.E. ; Os, H. van; Hutten, R.C.B. ; Linden, C.G. van der; Visser, R.G.F. ; Eck, H.J. van; Vossen, E.A.G. van der - \ 2008
    Theoretical and Applied Genetics 117 (2008)8. - ISSN 0040-5752 - p. 1379 - 1388.
    disease-resistance - confers resistance - map - tomato - genome - construction - arabidopsis - proteins - sequence - analogs
    NBS profiling is a method for the identification of resistance gene analog (RGA) derived fragments. Here we report the use of NBS profiling for the genome wide mapping of RGA loci in potato. NBS profiling analyses on a minimal set of F1 genotypes of the diploid mapping population previously used to generate the ultra dense (UHD) genetic map of potato, allowed us to efficiently map polymorphic RGA fragments relative to 10,000 existing AFLP markers. In total, 34 RGA loci were mapped, of which only 13 contained RGA sequences homologous to RGAs genetically positioned at approximately similar positions in potato or tomato. The remaining RGA loci mapped either at approximate chromosomal regions previously shown to contain RGAs in potato or tomato without sharing homology to these RGAs, or mapped at positions not yet identified as RGA-containing regions. In addition to markers representing RGAs with unknown functions, segregating markers were detected that were closely linked to four functional R genes that segregate in the UHD mapping population. To explore the potential of NBS profiling in RGA transcription analyses, RNA isolated from different tissues was used as template for NBS profiling. Of all the fragments amplified approximately 15% showed putative intensity or absent/present differences between different tissues suggesting putative tissue specific RGA or R gene transcription. Putative absent/present differences between individuals were also found. In addition to being a powerful tool for generating candidate gene markers linked to R gene loci, NBS profiling, when applied to cDNA, can be instrumental in identifying those members of an R gene cluster that are transcribed, and thus putatively functional.
    Marker-assisted optimization of an expert-based strategy for the acquisition of modern lettuce varieties to improve a genebank collection
    Treuren, R. van; Hintum, T.J.L. van; Wiel, C.C.M. van de - \ 2008
    Genetic Resources and Crop Evolution 55 (2008)2. - ISSN 0925-9864 - p. 319 - 330.
    genetic-variation - bremia-lactucae - accessions - construction - resistance - database - tomato - aflps - rapd
    To regularly improve the composition of the lettuce collection of the Centre for Genetic Resources, the Netherlands (CGN) with modern varieties, feedback from crop experts is used to select approximately 10% of the new material for incorporation in the collection. In the present study, assessments of six experts were compared to microsatellite data of 414 new varieties and 1408 existing accessions. Based on the microsatellite data, the extent to which the genetic diversity of the collection would be enriched (added value) was calculated for specific sets of new varieties. When individual assessments of experts were evaluated, the total added value of expert-based selections was not significantly higher compared to randomly chosen groups, except for a single expert. Unfamiliarity with new varieties was shown to be a crucial factor in the assessment of crop experts. According to the current acquisition protocol that seeks for consensus among experts, varieties are selected based on recommendations from at least three experts. This protocol also did not perform better than randomly chosen groups of new varieties. However, significantly better results were obtained with alternative protocols. It was concluded that breeding value was a more decisive criterion in the current acquisition protocol than maximal extension of the genetic diversity within the collection. A modified protocol addressing both commercial and diversity aspects was suggested in order to meet the demands of plant breeders as well as conservationists
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