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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    Effects of land-use change and rainfall in Sudano-Sahelian West Africa on the diet and nestling growth rates of an avian predator
    Buij, R. ; Folkertsma, I. ; Kortekaas, K. ; longh, H.H. De; Komdeur, J. - \ 2013
    Ibis 155 (2013)1. - ISSN 0019-1019 - p. 89 - 101.
    field energetics - breeding success - protected areas - hatching order - climate-change - foraging mode - national-park - raptors - habitat - savanna
    Raptor populations in Sudano-Sahelian West Africa are being severely affected by widespread habitat alteration which depletes prey populations, potentially aggravated by changing rainfall patterns. We studied Grasshopper Buzzards Butastur rufipennis at nests in natural and transformed habitats in the Sudano-Sahelian region of northern Cameroon to assess the effects of habbitat transformation and rainfall on nestling diet and growth.
    'Intraspecific pathogen variation' Verslag KNPV/Plantum/EPS-eendagsconferentie : Wageningen, 22 januari 2013
    Folkertsma, R.T. ; Goverse, A. ; Posthuma, E. ; Gilijamse, T. - \ 2013
    Gewasbescherming 44 (2013)2. - ISSN 0166-6495 - p. 32 - 34.
    plantenziekteverwekkers - genetische variatie - genotypische variatie - dna-sequencing - moleculaire technieken - moleculaire genetica - plantenziekten - conferenties - plant pathogens - genetic variation - genetic variance - dna sequencing - molecular techniques - molecular genetics - plant diseases - conferences
    Dinsdag 22 januari 2013 werd in Wageningen een eendagsconferentie gehouden getiteld ‘Intraspecific pathogen variation - implications and opportunities’. Deze conferentie werd georganiseerd naar aanleiding van discussies over het werken met intraspecifieke variatie voor diagnostiek en veredeling binnen de Nematodenwerkgroep van de KNPV en de Isolaten-beheerwerkgroep van Plantum. Het doel van de bijeenkomst was a.) onderzoekers uit de private en de publieke sector samenbrengen om recente ontwikkelingen te bespreken in fundamentele en toegepaste aspecten van het werken met intraspecifieke variatie, en b.) het stimuleren van uitwisselen van ideeën binnen en tussen beide groepen, voor mogelijke vervolginitiatieven.
    De nematodenwerkgroep in actie
    Molendijk, L.P.G. ; Folkertsma, R.T. - \ 2013
    Gewasbescherming 44 (2013)2. - ISSN 0166-6495 - p. 48 - 48.
    plantenparasitaire nematoden - werkgroepen - nematodenbestrijding - nematologie - plant parasitic nematodes - working groups - nematode control - nematology
    Kort jaarverslag over 2012.
    Breeding biology and nestling development of the Grasshopper Buzzard
    Buij, R. ; Kortekaas, K. ; Folkertsma, I. ; Velde, M. van der; Komdeur, J. ; Iongh, H.H. de - \ 2012
    Ostrich 83 (2012)3. - ISSN 0030-6525 - p. 137 - 146.
    prey-size hypothesis - kite milvus-migrans - sex-ratio - american kestrels - sibling aggression - brood reduction - parental investment - seasonal-variation - west-africa - growth
    Research into the effect of environmental variables on reproductive success of tropical raptors is often constrained by the lack of information on breeding biology. We provide the first detailed information of the breeding biology and nestling development of the Grasshopper Buzzard Butastur rufipennis, an Afrotropical migratory raptor threatenend by extensive land transformation in its breeding range.
    De nematodenwerkgroep in actie
    Molendijk, L.P.G. ; Folkertsma, R.T. - \ 2012
    Gewasbescherming 43 (2012)1. - ISSN 0166-6495 - p. 23 - 23.
    KNPV-werkgroep Nematoden : de nematodenwerkgroep in actie
    Molendijk, L.P.G. ; Folkertsma, R.T. - \ 2011
    Gewasbescherming 42 (2011)3. - ISSN 0166-6495 - p. 141 - 141.
    A family-based approach reveals the function of residues in the nuclear receptor ligand-binding domain
    Folkertsma, S. ; Noort, P. ; Durme, J. van; Joosten, H.J. ; Bettler, E. ; Fleuren, W. ; Oliveira, L. ; Horn, F. ; Vlieg, J. de; Vriend, G. - \ 2004
    Journal of Molecular Biology 341 (2004)2. - ISSN 0022-2836 - p. 321 - 335.
    retinoid-x-receptor - dependent transcriptional activation - pancreatic trypsin-inhibitor - protein-coupled receptors - crystal-structure - structural basis - estrogen-receptor - androgen receptor - hormone-receptors - triphosphate conformation
    Literature studies, 3D structure data, and a series of sequence analysis techniques were combined to reveal important residues in the structure and function of the ligand-binding domain of nuclear hormone receptors. A structure-based multiple sequence alignment allowed for the seamless combination of data from many different studies on different receptors into one single functional model. It was recently shown that a combined analysis of sequence entropy and variability can divide residues in five classes; (1) the main function or active site, (2) support for the main function, (3) signal transduction, (4) modulator or ligand binding and (5) the rest. Mutation data extracted from the literature and intermolecular contacts observed in nuclear receptor structures were analyzed in view of this classification and showed that the main function or active site residues of the nuclear receptor ligand-binding domain are involved in cofactor recruitment. Furthermore, the sequence entropy–variability analysis identified the presence of signal transduction residues that are located between the ligand, cofactor and dimer sites, suggesting communication between these regulatory binding sites. Experimental and computational results agreed well for most residues for which mutation data and intermolecular contact data were available. This allows us to predict the role of the residues for which no functional data is available yet. This study illustrates the power of family-based approaches towards the analysis of protein function, and it points out the problems and possibilities presented by the massive amounts of data that are becoming available in the “omics era”. The results shed light on the nuclear receptor family that is involved in processes ranging from cancer to infertility, and that is one of the more important targets in the pharmaceutical industry.
    The tomato gene Sw5 is a member of the coiled coil, nucleotide binding, leucine-rich repeat class of plant resistance genes and confers resistance to TSWV in tobacco
    Spassova, M.I. ; Prins, T.W. ; Folkertsma, R.T. ; Klein-Lankhorst, R.M. ; Hille, J. ; Goldbach, R.W. ; Prins, M. - \ 2001
    Molecular Breeding 7 (2001). - ISSN 1380-3743 - p. 151 - 161.
    Tomato spotted wilt virus is an important threat to tomato production worldwide. A single dominant resistance gene locus, Sw5, originating from Lycopersicon peruvianum, has been identified and introgressed in cultivated tomato plants. Here we present the genomic organization of a 35 250 bp fragment of a BAC clone overlapping the Sw5 locus. Two highly homologous (95€resistance gene candidates were identified within 40 kb of the CT220 marker. The genes, tentatively named Sw5-a and Sw5-b, encode proteins of 1245 and 1246 amino acids, respectively, and are members of the coiled-coil, nucleotide-binding-ARC, leucine-rich repeat group of resistance gene candidates. Promoter and terminator regions of the genes are also highly homologous. Both genes significantly resemble the tomato nematode and aphid resistance gene Mi and, to a lesser extent, Pseudomonas syringae resistance gene Prf. Transformation of Nicotiana tabacum cv. SR1 plants revealed that the Sw5-b gene, but not the Sw5-a gene, is necessary and sufficient for conferring resistance against tomato spotted wilt virus.
    The effects of founding events and agricultural practices on the genetic structure of three metapopulations of Globodera pallida
    Folkertsma, R.T. ; Koert, P. van; Rouppe van der Voort, J.N.A.M. ; Groot, K.E. de; Kammenga, J.E. ; Helder, J. ; Bakker, J. - \ 2001
    Phytopathology 91 (2001)8. - ISSN 0031-949X - p. 753 - 758.
    Construction of a bacterial artificial chromosome (BAC) library of Lycopersicon esculentum cv. Stevens and its application to physically map the Sw-5 locus
    Folkertsma, R.F. ; Spassova, M.I. ; Prins, M. ; Stevens, M.R. ; Hille, J. ; Goldbach, R.W. - \ 1999
    Molecular Breeding 5 (1999)2. - ISSN 1380-3743 - p. 197 - 207.
    Genetic variation among parthenogenetic Meloidogyne species revealed by AFLPs and 2D-protein electrophoresis contrased to morphology
    Beek, J.G. van der; Folkertsma, R. ; Zijlstra, C. ; Koert, P.H.G. van; Poley, L.M. ; Bakker, J. - \ 1998
    Fundamental and applied nematology 21 (1998)4. - ISSN 1164-5571 - p. 401 - 411.
    Physical mapping of the SW-5 resistance locus in Lycopersicon Esculentum.
    Folkertsma, R. ; Spassova, M. ; Prins, M. ; Hille, J. ; Goldbach, R. - \ 1998
    In: 4th International Symposium on Tospoviruses and Thrips in Floral and Vegetable Crops, Wageningen, The Netherlands - p. 23 - 24.
    Map-based cloning of the tomato region spanning the Sw-5 tospovirus resistance gene in tomato.
    Folkertsma, R. ; Spassova, M. ; Prins, M. ; Hille, J. ; Goldbach, R. - \ 1998
    In: Joint Meeting of the Arbeitskreis Virologie and the Nederlandse Kring voor Plantevirologie, Wageningen, The Netherlands - p. 4 - 4.
    Physical mapping of the Sw-5 resistannce locus in Lycopersicon Peruvianum.
    Folkertsma, R. ; Spassova, M. ; Prins, M. ; Hille, J. ; Goldbach, R. - \ 1998
    In: NWO-SON Working Society Nucleic Acids Research, Lunteren, The Netherlands (1998)
    A QTL for broad spectrum resistance to cyst nematode species (Globodera spp.) maps to a resistance gene cluster in potato.
    Rouppe van der Voort, J.N.A.M. ; Lindeman, W. ; Folkertsma, R. ; Hutten, R.C.B. ; Overmars, H. ; Vossen, E. van der; Jacobsen, E. ; Bakker, J. - \ 1998
    Theoretical and Applied Genetics 96 (1998). - ISSN 0040-5752 - p. 654 - 661.
    Broad-spectrum resistance in potato to the potato cyst nematode (PCN) species Globodera rostochiensis and G. pallida is commonly regarded as a polygenically inherited trait. Yet, by use of QTL analysis and a selected set of PCN populations, resistance to both PCN species could be ascribed to the action of locus Grp1. Grp1 confers major resistance to G. rostochiensis line Ro5-22 and G. pallida population Pa2-D383 and partial resistance to G. pallida population Pa3-Rookmaker. Grp1 was mapped on chromosome 5 using previously characterized AFLP markers. Cleaved amplified polymorphic sequence (CAPS) markers available for RFLP loci GP21 and GP179 revealed that Grp1 maps on a genomic region harboring other resistance factors to viral, fungal and nematodal pathogens. The present data indicate that Grp1 is a compound locus which contains multiple genes involved in PCN resistance.
    Mapping of the cyst nematode resistance locus Gpa2 in potato using a strategy based on comigrating AFLP markers.
    Rouppe van der Voort, J.N.A.M. ; Eck, H. van; Wolters, P. ; Hutten, R. ; Zandvoort, P. van; Folkertsma, R. ; Jacobsen, E. ; Helder, H. ; Bakker, J. - \ 1998
    In: ALW-NWO dagen, Lunteren, The Netherlands (1998)
    Genetic variation among parthenogenetic Meloidogyne species revealed by AFLPs and 2D protein electrophoresis contrasted to morphology
    Beek, J.G. van der; Folkertsma, R. ; Zijlstra, C. ; Koert, P.H.G. van; Poleij, L.M. ; Bakker, J. - \ 1997
    Fundamental and applied nematology (1997). - ISSN 1164-5571
    Molecular evidence that Meloidogyne hapla, M. Chitwoodi and M. Fallax are distinct biological entities
    Beek, J.G. van der; Folkertsma, R. ; Poley, L.M. ; Koert, P.H.G. van; Bakker, J. - \ 1997
    Fundamental and applied nematology 20 (1997)5. - ISSN 1164-5571 - p. 513 - 520.
    Six isolates of Meloidogyne hapla, including four race A and two race B isolates, eight isolates of M. chitwoodi, and five isolates of M. fallax were submitted to two-dimensional gel electrophoresis (2-DGE) to study the similarity between the various isolates of the three species based upon total soluble proteins. For each isolate, two independent samples of 50 young egg-producing females were extracted from roots. Each sample was used to produce one mini 2-D gel. Mini 2-DGE showed an average of 400 protein spots per gel. Within each species, every gel was compared to all the others to identify two types of polymorphic spots: isoelectric point (IP) variants and present-absent (PA) variants. Thirteen PA and nine IP variants were observed among M. hapla isolates, eight PA and no IP variants among M. chitwoodi isolates, and two PA and no IP variants among M. fallax isolates, which represents 5.0, 2.2, and 0.6 % polymorphisms among isolates of the three respective species. These percentages imply small intraspecific variation within each of these species. They also confirm these species to be clearly delineated biological groups, as similarity between these species is significantly lower than similarity between isolates within each species (Van der Beek et al., unpubl.). Using UPGMA, the nine IP variants of M. hapla resulted in a similarity dendrogram, which clearly separated the race A isolates from the race B isolates.
    Storage of potato cyst nematodes at -80°C.
    Folkertsma, R.T. ; Helder, J. ; Gommers, F.J. ; Bakker, J. - \ 1997
    Fundamental and applied nematology 20 (1997)3. - ISSN 1164-5571 - p. 209 - 302.
    Genetic diversity of the potato cyst nematode in the Netherlands
    Folkertsma, R.T. - \ 1997
    Agricultural University. Promotor(en): R.W. Goldbach; F.J. Gommers; J. Bakker. - S.l. : Folkertsma - ISBN 9789054857488 - 88
    plantenplagen - pratylenchus - heteroderidae - tylenchidae - solanum tuberosum - aardappelen - genetische variatie - overerving - rassen (dieren) - rassen (taxonomisch) - moleculaire genetica - plantenveredeling - ziekteresistentie - plaagresistentie - globodera pallida - globodera rostochiensis - plant pests - pratylenchus - heteroderidae - tylenchidae - solanum tuberosum - potatoes - genetic variation - inheritance - breeds - races - molecular genetics - plant breeding - disease resistance - pest resistance - globodera pallida - globodera rostochiensis

    The potato cyst nematodes Globodera rostochiensis (Woll.) Skarbilovich and G. pallida (Stone) originate from the Andes region in South America and have been introduced into Western Europe since 1850. Both species are successful colonizers. Once primary founders have established vital populations, an area is rapidly colonized by secondary founding events. The mode of spread results in patchy distribution patterns. Analyses of the processes that influence the spatial variations in virulence are of major importance for the control by means of host plant resistance. The ability to unravel the mosaic distribution patterns of the two species and their pathotypes enables breeders and growers to anticipate on the dynamics of virulent populations. The aim of this thesis was to analyse the intra- and interspecific variation of G. rostochiensis and G. pallida in the Netherlands and to obtain insight in the processes that determine the spatial variations in protein, DNA and (a)virulence polymorphisms.

    interspecific variation

    The molecular variation between the sibling species G.rostochiensis and G.pallida is remarkably large. The RAPD technique revealed a total of 250 DNA fragments, of which only nine DNA fragments were common to both species (Chapter 3). Similar results were obtained with the AFLP assay. A total of 1000 AFLP fragments was amplified, of which only 64 fragments could be identified in both species (Chapter 4). These results agreed with previous investigations using 2-DGE and show that morphologically nearly indistinguishable organisms can be quite distinct the molecular level.

    The extensive genetic differentiation of G.rostochiensis and G . pallida offers perspectives for the development of a diagnostic assay. In addition the PCR technique enables the amplification of species specific fragments from small numbers of cysts extracted from soil samples. For example, G. rostochiensis specific DNA fragments can be amplified from single juveniles (Chapter 1).

    intraspecific variation

    The intraspecific variation of G.rostochiensis as revealed by RAPDs and AFLPs is relatively low (Chapter 3 and 4). The proportion of polymorphic DNA fragments among nine G. rostochiensis populations was 19% and 15.8%, respectively. Three clusters of populations were identified and each cluster could be described by one or more specific DNA fragments.

    The intraspecific variation of G.pallida, as revealed with RAPDs or AFLPs, is larger in comparison with G.rostochiensis (Chapter 3 and 4). The proportion of polymorphic RAPD fragments among 17 populations was 46%. For the AFLP assay this figure was 23% polymorphic AFLP fragments among 15 populations. The majority of the populations displayed a continuous range of variations. Only a few clearly diverged clusters could be discriminated on the basis of specific DNA fragments.

    Various groups have applied the RAPD technique to study the genetic divergence among conspecific populations of plant parasitic nematodes. The validity of this technique was evaluated in chapter 4 by comparison of the clustering of 36 G.pallida populations based on RAPD and 2-DGE data. Both data sets demonstrated that the majority of the G.pallida populations were not clearly differentiated from each other. The overall correlation between the distance matrices derived from both data sets was low. Careful examination of the separate dendrograms showed similarity in clustering only for clearly diverged populations or groups of populations.

    Although the AFLP and RAPD technique are simple, fast and require only minute amounts of biological material, they are not suitable to resolve the subtle differences among potato cyst nematode populations. Quantitative variation in allele frequencies is often not resolved with those techniques, which is, among others, due to the virtual inability to recognize co-dominant alleles and the non-linear amplification of DNA fragments. In chapter 6 and 7 the genetic variation was studied by analysing pools of individuals with 2-DGE. The ratios between the protein quantities produced by the codominant alleles are appropriate measures for the allele frequencies. The correctness of this method has been confirmed by 2-DGE of single individuals (De Boer etal ., 1992)

    bottleneck effects on the secondary founders

    The intraspecific variation among potato cyst nematode populations in Europe is predominantly determined by the genetic constitution of the primary founders, directly or indirectly introduced from South America, and the effect of random genetic drift on the secondary founders. To obtain insight in these processes, 226 G.pallida populations from the Netherlands were analyzed with 2- DGE. The results strongly suggest that these populations originate from one source, or in case of multiple introductions, from a number of sources with a similar genetic makeup.

    The genetic differentiation of the 226 G.pallida populations indicate that the colonization of the Netherlands has been accompanied by extensive random genetic drift. Only a limited proportion of the populations appeared to be identical. It is also shown, that the bottleneck effects differ between regions. Significant variation in population structure was observed between the three investigated areas. The genetic variation within G.pallida populations from north Friesland and the IJsselmeerpolders is in general smaller than within populations from the northeast Netherlands. A plausible explanation for this phenomena is the low multiplication rate of potato cyst nematodes due to wider crop rotation schemes in the IJsselmeerpolders and north Friesland. These factors result in a slow expansion of newly founded populations, which enhances the effect of drift.

    gene-pool similarity concept

    The gene-pool similarity concept rests on the hypothesis that in the absence of selection pressure by host plant resistance, degrees of similarity between populations revealed by molecular techniques are also reflected at virulence loci, including those not yet resolved. To test this concept, the genetic variation revealed by 2-DGE among 102 G.pallida populations was compared with the variation in virulence towards two resistant cultivars. This analysis showed that a decrease in genetic distance among populations is accompanied with a decrease in variation in virulence. In addition it is demonstrated that the gene pool similarity concept is also applicable to loci determining the variation in fitness among populations. The variation in Pf/Pi values among the 102 populations on Désirée is in general smaller between closely related populations than between distantly related populations.

    breeding for resistance

    Breeding for resistance has been dominated by trial-and-error approaches, which has stimulated the view that control by means of host plant resistance is unavoidably a short-term approach due to the 'appearance' of virulent populations. The pervasive myth that breeding for resistance against potato cyst nematodes is a lost arms race is challenged by the results of this thesis. Until recently it was assumed that the genetic variation of G.pallida in the Netherlands was too large to produce potato cultivars with broad-spectrum resistance. In this thesis it is shown that the genetic diversity introduced from the Andes region has been limited and that the variation among the Dutch G.pallida populations is mainly the result of random genetic drift. The elaborate analysis of 226 Dutch G.pallida populations offers perspectives to obtain potato cultivars with broad and durable resistance. The gene pool similarities revealed by 2-DGE can be used as guidance in testing the effectiveness of new sources of resistance.

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