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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    Factoren die het eiwitgehalte van sojabonen beïnvloeden
    Timmer, R.D. ; Visser, C.L.M. de - \ 2020
    Wageningen : Stichting Wageningen Research, Wageningen Plant Research, Business unit Open Teelten (Rapport / Stichting Wageningen Research, Wageningen Plant Research, Business unit Open Teelten WPR-833) - 26
    Enabling reusability of plant phenomic datasets with MIAPPE 1.1
    Papoutsoglou, Evangelia A. ; Faria, Daniel ; Arend, Daniel ; Arnaud, Elizabeth ; Athanasiadis, Ioannis N. ; Chaves, Inês ; Coppens, Frederik ; Cornut, Guillaume ; Costa, Bruno V. ; Ćwiek-Kupczyńska, Hanna ; Droesbeke, Bert ; Finkers, Richard ; Gruden, Kristina ; Junker, Astrid ; King, Graham J. ; Krajewski, Paweł ; Lange, Matthias ; Laporte, Marie Angélique ; Michotey, Célia ; Oppermann, Markus ; Ostler, Richard ; Poorter, Hendrik ; Ramı́rez-Gonzalez, Ricardo ; Ramšak, Živa ; Reif, Jochen C. ; Rocca-Serra, Philippe ; Sansone, Susanna Assunta ; Scholz, Uwe ; Tardieu, François ; Uauy, Cristobal ; Usadel, Björn ; Visser, Richard G.F. ; Weise, Stephan ; Kersey, Paul J. ; Miguel, Célia M. ; Adam-Blondon, Anne Françoise ; Pommier, Cyril - \ 2020
    New Phytologist (2020). - ISSN 0028-646X
    findability - interoperability - metadata - phenomics - plant phenotyping - reusability - standards

    Enabling data reuse and knowledge discovery is increasingly critical in modern science, and requires an effort towards standardising data publication practices. This is particularly challenging in the plant phenotyping domain, due to its complexity and heterogeneity. We have produced the MIAPPE 1.1 release, which enhances the existing MIAPPE standard in coverage, to support perennial plants, in structure, through an explicit data model, and in clarity, through definitions and examples. We evaluated MIAPPE 1.1 by using it to express several heterogeneous phenotyping experiments in a range of different formats, to demonstrate its applicability and the interoperability between the various implementations. Furthermore, the extended coverage is demonstrated by the fact that one of the datasets could not have been described under MIAPPE 1.0. MIAPPE 1.1 marks a major step towards enabling plant phenotyping data reusability, thanks to its extended coverage, and especially the formalisation of its data model, which facilitates its implementation in different formats. Community feedback has been critical to this development, and will be a key part of ensuring adoption of the standard.

    Boerderij van de Toekomst kijkt anders naar teelten
    Visser, Chris de; Veldhuisen, Bram ; Tolhoek, Jan ; Klompe, Koen - \ 2020
    Beheersen Mcf: niks doen, is geen optie
    Molendijk, Leendert ; Visser, Johnny - \ 2020
    Resistente biet als nieuw 'wapen' in de strijd tegen wortelknobbelaaltjes
    Visser, Johnny ; Molendijk, Leendert - \ 2020
    Biet als wapen tegen Meloidogyne chitwoodi
    Visser, Johnny ; Molendijk, Leendert - \ 2020
    The invasive Asian bush mosquito Aedes japonicus found in the Netherlands can experimentally transmit Zika virus and Usutu virus
    Abbo, Sandra R. ; Visser, Tessa M. ; Wang, Haidong ; Göertz, Giel P. ; Fros, Jelke J. ; Abma-henkens, Marleen H.C. ; Geertsema, Corinne ; Vogels, Chantal B.F. ; Koopmans, Marion P.G. ; Reusken, Chantal B.E.M. ; Hall-Mendelin, Sonja ; Hall, Roy A. ; Oers, Monique M. Van; Koenraadt, C.J.M. ; Pijlman, Gorben P. - \ 2020
    PLoS Neglected Tropical Diseases 14 (2020)4. - ISSN 1935-2727 - 22 p.
    Background - The Asian bush mosquito Aedes japonicus is invading Europe and was first discovered in Lelystad, the Netherlands in 2013, where it has established a permanent population. In this study, we investigated the vector competence of Ae. japonicus from the Netherlands for the emerging Zika virus (ZIKV) and zoonotic Usutu virus (USUV). ZIKV causes severe congenital microcephaly and Guillain-Barré syndrome in humans. USUV is closely related to West Nile virus, has recently spread throughout Europe and is causing mass mortality of birds. USUV infection in humans can result in clinical manifestations ranging from mild disease to severe neurological impairments.
    Methodology/Principal findings - In our study, field-collected Ae. japonicus females received an infectious blood meal with ZIKV or USUV by droplet feeding. After 14 days at 28°C, 3% of the ZIKV-blood fed mosquitoes and 13% of the USUV-blood fed mosquitoes showed virus-positive saliva, indicating that Ae. japonicus can transmit both viruses. To investigate the effect of the mosquito midgut barrier on virus transmission, female mosquitoes were intrathoracically injected with ZIKV or USUV. Of the injected mosquitoes, 96% (ZIKV) and 88% (USUV) showed virus-positive saliva after 14 days at 28°C. This indicates that ZIKV and USUV can efficiently replicate in Ae. japonicus but that a strong midgut barrier is normally restricting virus dissemination. Small RNA deep sequencing of orally infected mosquitoes confirmed active replication of ZIKV and USUV, as demonstrated by potent small interfering RNA responses against both viruses. Additionally, de novo small RNA assembly revealed the presence of a novel narnavirus in Ae. japonicus.
    Conclusions/Significance - Given that Ae. japonicus can experimentally transmit arthropod-borne viruses (arboviruses) like ZIKV and USUV and is currently expanding its territories, we should consider this mosquito as a potential vector for arboviral diseases in Europe
    Tagetes geeft meerjarig positief opbrengsteffect
    Visser, Johnny ; Specken, Johan ; Hoekzema, Gerard - \ 2020
    CRISPR/Cas9 Gene Editing of Gluten in Wheat to Reduce Gluten Content and Exposure—Reviewing Methods to Screen for Coeliac Safety
    Jouanin, A.A. ; Gilissen, L.J.W.J. ; Schaart, J.G. ; Leigh, Fiona J. ; Cockram, James ; Wallington, Emma J. ; Boyd, Lesley A. ; Broeck, H.C. van den; Meer, I.M. van der; America, A.H.P. ; Visser, R.G.F. ; Smulders, M.J.M. - \ 2020
    Frontiers in Nutrition 7 (2020). - ISSN 2296-861X
    Ingestion of gluten proteins (gliadins and glutenins) from wheat, barley and rye can cause coeliac disease (CD) in genetically predisposed individuals. The only remedy is a strict and lifelong gluten-free diet. There is a growing desire for coeliac-safe, whole-grain wheat-based products, as consumption of whole-grain foods reduces the risk of chronic diseases. However, due to the large number of gluten genes and the complexity of the wheat genome, wheat that is coeliac-safe but retains baking quality cannot be produced by conventional breeding alone. CD is triggered by immunogenic epitopes, notably those present in α-, γ-, and ω-gliadins. RNA interference (RNAi) silencing has been used to down-regulate gliadin families. Recently, targeted gene editing using CRISPR/Cas9 has been applied to gliadins. These methods produce offspring with silenced, deleted, and/or edited gliadins, that overall may reduce the exposure of patients to CD epitopes. Here we review methods to efficiently screen and select the lines from gliadin gene editing programs for CD epitopes at the DNA and protein level, for baking quality, and ultimately in clinical trials. The application of gene editing for the production of coeliac-safe wheat is further considered within the context of food production and in view of current national and international regulatory frameworks.
    Automated Step Detection in Inertial Measurement Unit Data From Turkeys
    Bouwman, Aniek ; Savchuk, Anatolii ; Abbaspourghomi, Abouzar ; Visser, Bram - \ 2020
    Frontiers in Genetics Livestock Genomics 11 (2020). - ISSN 1664-8021
    accelerometer - gait analysis - inertial measurement unit - segmentation - step detection

    Locomotion is an important welfare and health trait in turkey production. Current breeding values for locomotion are often based on subjective scoring. Sensor technologies could be applied to obtain objective evaluation of turkey gait. Inertial measurement units (IMUs) measure acceleration and rotational velocity, which makes them attractive devices for gait analysis. The aim of this study was to compare three different methods for step detection from IMU data from turkeys. This is an essential step for future feature extraction for the evaluation of turkey locomotion. Data from turkeys walking through a corridor with IMUs attached to each upper leg were annotated manually. We evaluated change point detection, local extrema approach, and gradient boosting machine in terms of step detection and precision of start and end point of the steps. All three methods were successful in step detection, but local extrema approach showed more false detections. In terms of precision of start and end point of steps, change point detection performed poorly due to significant irregular delay, while gradient boosting machine was most precise. For the allowed distance to the annotated steps of 0.2 s, the precision of gradient boosting machine was 0.81 and the recall was 0.84, which is much better in comparison to the other two methods (<0.61). At an allowed distance of 1 s, performance of the three models was similar. Gradient boosting machine was identified as the most accurate for signal segmentation with a final goal to extract information about turkey gait; however, it requires an annotated training dataset.

    Inundatie ter bestrijding van het maiswortelknobbelaaltje Meloidogyne chitwoodi
    Visser, J.H.M. ; Molendijk, L.P.G. - \ 2020
    Gewasbescherming 51 (2020)2. - ISSN 0166-6495 - p. 64 - 65.
    Aardappel als vanggewas voor aardappelmoeheid laat in het seizoen
    Molendijk, L.P.G. ; Visser, J.H.M. - \ 2020
    Gewasbescherming 51 (2020)2. - ISSN 0166-6495 - p. 65 - 66.
    Options to Reform the European Union Legislation on GMOs : Post-authorization and Beyond
    Eriksson, Dennis ; Custers, René ; Edvardsson Björnberg, Karin ; Hansson, Sven Ove ; Purnhagen, Kai ; Qaim, Matin ; Romeis, Jörg ; Schiemann, Joachim ; Schleissing, Stephan ; Tosun, Jale ; Visser, Richard G.F. - \ 2020
    Trends in Biotechnology 38 (2020)5. - ISSN 0167-7799 - p. 465 - 467.
    coexistence - EU - GMO - labeling - legislative reform

    We discuss options to reform the EU genetically modified organism (GMO) regulatory framework, make risk assessment and decision-making more consistent with scientific principles, and lay the groundwork for international coherence. In this third of three articles, we focus on labeling and coexistence as well as discuss the political reality and potential ways forward.

    Ontwerp Boerderij van de Toekomst
    Visser, Chris de; Sukkel, Wijnand ; Kempenaar, Corné ; Wal, Tamme van der; Wolf, Pieter de; Visser, Andries ; Smit, Bert ; Schoorlemmer, Herman ; Schoutsen, Maureen ; Klompe, Koen ; Veldhuisen, Bram ; Selin-Noren, Isabella ; Dijk, Chris van; Hol, Stefan ; Voort, Marcel van der; Janssens, Bas - \ 2020
    Wageningen : Stichting Wageningen Research, Wageningen Plant Research, Business unit Open Teelten (Rapport / Stichting Wageningen Research, Wageningen Plant Research, Business unit Open Teelten WPR-823) - 45
    Risico insleep ziektes via voerresten in mest
    Evenhuis, Bert ; Molendijk, Leendert ; Visser, Johnny - \ 2020
    Bodemmaatregelen op dalgrond in de Veenkoloniën: effecten op bodemkwaliteit, opbrengst en financiële meerwaarde : Analyse van de resultaten van de systeemproef Bodemkwaliteit Veenkoloniën 2014-2017
    Haan, Janjo de; Asperen, Paulien van; Visser, Johnny ; Burgt, Geert Jan van der; Smit, Elsbeth ; Dawson, Andrew ; Klompe, Koen - \ 2020
    Wageningen : Stichting Wageningen Research, Wageningen Plant Research, Businessunit WUR Open Teelten (Rapport / Stichting Wageningen Research, Wageningen Plant Research, Businessunit WUR Open Teelten WPR-831) - 69
    In een langjarig experiment op proefbedrijf Valthermond wordt op dalgrond met gemiddeld 11% organische stof een vijftal maatregelen in een vierjarige akkerbouwvruchtwisseling vergeleken met de standaard werkwijze, in vier herhalingen. De maatregelen Tagetes, Compost, sturen Ca/Mg-verhouding, Steenmeel zijn elk op hun eigen wijze gericht op verbetering van de bodemkwaliteit. Ook een combinatie van alle maatregelen is onderzocht. Over de maatregelen heen liggen varianten van grondbewerking (NKG en Spitten) in duplo. Na vier jaar blijkt de maatregel Tagetes (de teelt van zomergerst vervangen door een hoofdteelt Tagetes) zowel meer opbrengst op te leveren in de aardappelteelt als economisch rendabel te zijn, ondanks de opbrengstderving door het wegvallen van de verkoop van gerst. De andere strategieën hebben weinig of geen effect op de opbrengst en de kosten zijn hoger dan de eventuele extra inkomsten door opbrengstverhoging. NKG lijkt een positief effect te hebben op de opbrengst maar dat is nog niet statistisch significant. Wel leidt NKG tot kostenbesparing ten opzichte van Spitten door lagere machinekosten en lager brandstofverbruik. Veranderingen in bodemkwaliteit zijn nog nauwelijks waargenomen. Dat komt naar verwachting mede doordat die effecten meer tijd nodig hebben om zich te tonen. De nitraatnorm voor grondwater wordt meestal overschreden, onafhankelijk van de maatregel. Waar de norm wel gehaald wordt ligt het aan bodem en grondwater, niet aan de bemestingsstrategie. Het onderzoek wordt voortgezet.
    Hoe past de zee in de circulaire bio-economie?
    Visser, S.M. ; Bult, T.P. ; Kruiderink, Simkje - \ 2020
    Wageningen Environmental Research
    Warts wars : The resistant potatoes strike back
    Prodhomme, Charlotte - \ 2020
    Wageningen University. Promotor(en): R.G.F. Visser, co-promotor(en): J.H. Vossen; H.J. van Eck. - Wageningen : Wageningen University - ISBN 9789463952934 - 278

    Potato wart disease, caused by the obligate biotrophic Chytrid fungus Synchytrium endobioticum, is one of the most important quarantine diseases of potato. This disease was named after the symptoms caused by the pathogen, which are the proliferation of meristematic tissues leading to the formation of warts, mainly on the below-ground sprouts of potato plants. The quarantine status of S. endobioticum is due to the production of spores that can remain viable in the soil for more than 40 years, the lack of chemical control and the severe yield losses. In Europe, more than 40 different pathotypes of S. endobioticum have been recorded and only resistance to pathotype 1 is commonly deployed in the breeding germplasm. The breeding and cultivation of potato varieties resistant to a wider spectrum of pathotypes is crucial for quarantine practice to reduce the propagation of the pathogen. Therefore, the identification of genes bringing resistance to the most frequent pathotypes of the pathogen and the development of diagnostic markers for marker assisted selection (MAS) is urgently needed.

    In this thesis, genes involved in resistance to pathotypes 1, 2, 6 and 18 of S. endobioticum were identified to make an inventory of the different resistance sources at hand for potato breeders. In Chapter 2, we investigated the distribution of the pathotype 1 resistance in a variety panel representative of the potato breeding material. Breeding programs of the 20th century were very successful in producing varieties resistant to pathotype 1 as 77% of the panel varieties were found to be resistant. To identify markers linked with pathotype 1 resistance, we used previously produced genotypic and phenotypic data to perform a Genome-Wide Association Study (GWAS). The GWAS resulted in the identification of markers associated with pathotype 1 resistance on the north arm of chromosome 11. In this region, the major effect gene Sen1 was previously identified. Sen1 is the main source of pathotype 1 resistance in the variety panel and no common ancestral donor could be identified due to the inability to define identity-by-descent (IBD).

    As we faced limitations to design markers fully diagnostic for pathotype 1 resistance using the GWAS approach, we aimed to develop new tools to identify haplotype specific SNPs. In Chapter 3, we developed a new set of workflows, called Comparative Subsequence Sets Analysis (CoSSA), for the genetic analysis of traits of interest and the identification of haplotype specific SNPs. CoSSA can be used for any crop as it is suitable for polyploids and can be used with or without a reference genome. We applied CoSSA to identify Sen3, a dominant gene conferring resistance to all tested pathotypes. Sen3 was fine-mapped to the resistance gene cluster C76 on the north arm of chromosome 11.

    Furthermore, we used CoSSA for the fine-mapping of Sen1 in Chapter 4. Sen1 was mapped to the same R gene cluster as Sen3. We performed a candidate gene analysis and showed that Sen1 encodes a nucleotide-binding domain, leucine rich containing (NLR) protein from the TNL group. The two identified candidate genes were cloned and tested in complementation assays with AvrSen1, the S. endobioticum effector protein which triggers Hypersensitive Responses (HR) in Sen1 plants. These findings will serve as novel tools to study the interactions between potato and S. endobioticum.

    In Chapter 5, we made an, as complete as possible at this moment, inventory of the dominant potato wart disease resistance (Sen) genes and QTLs present in the potato breeding germplasm. We combined the GWAS and CoSSA strategies to identify two new major genes, Sen4 and Sen5, which are involved in resistance to pathotypes 2, 6 and 18. We also identified several wart disease resistance QTLs which, in combination with the dominant genes, can contribute to improve resistance to the higher pathotypes. To avoid any confusion between the previously and newly identified QTLs, we introduced a new naming system which allows to differentiate each resistant haplotype identified. Finally, we screened a broad panel of potato varieties and wild Solanum species for the genes Sen1, Sen2, Sen3, Sen4 and Sen5.

    To put it in a nutshell, a complete picture of the major potato wart disease resistance sources present in the breeding germplasm is given in this thesis. Haplotype specific markers have been designed for all the major genes and QTLs mapped, which will facilitate the breeding of resistant varieties. Finally, the development of CoSSA will facilitate the mapping of traits of interest and the design of haplotype specific markers for any crop.

    Workshop bodempathogenen
    Postma, Joeke ; Termorshuizen, Aad ; Visser, Johnny - \ 2020
    Nutrients translocation & plant growth in tissue culture
    Li, Huayi - \ 2020
    Wageningen University. Promotor(en): R.G.F. Visser, co-promotor(en): F.A. Krens. - Wageningen : Wageningen University - ISBN 9789463953283 - 161

    In conventional plant micropropagation exogenous sucrose is generally taken up by plants from the medium. Any treatment that improves sucrose assimilation or translocation might promote plant growth and micropropagation efficiency. Transpiration is widely believed to be at a very low level in vitro and subsequently the water flow and nutrient translocation are supposed to be marginal. We investigated the relation between growth and sucrose translocation on the one hand and leaf transpiration on the other hand in vitro. It was found that both transpiration, including the transpiration roles of surface cuticle and of stomatal activity, and sucrose assimilation attributed by water transport contributed to biomass accumulation in plants as the main reason for growth. It was also examined the role of sucrose transporter genes in the process of exogenous sucrose translocation in roots. The results demonstrated the importance of SWEET11 and SWEET12 genes in exogenous sucrose assimilation and translocation in vitro. In addition we emphasized the contribution of aquaporin plasma membrane intrinsic proteins PIP1 to the growth of in vitro plants through investigating physiological characteristics in miRNA-induced-PIP1s-silenced plants. As a woody plant Malus domestica ‘Gala’ was used to test whether increased transpiration generally can lead to improved plantlet growth in shoot culture and to demonstrate the relationship between transpiration, stomatal and cuticular transpiration, and plantlet growth in vitro. A follow up of this research should focus on plantlet growth promotion by cuticle manipulation and sucrose assimilation and translocation via fresh cut section.

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