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.

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    Aphid resistance in Capsicum maps to a locus containing LRR-RLK gene analogues
    Sun, Mengjing ; Voorrips, Roeland E. ; van’t Westende, Wendy ; Kaauwen, Martijn van; Visser, Richard G.F. ; Vosman, Ben - \ 2020
    Theoretical and Applied Genetics 133 (2020)1. - ISSN 0040-5752 - p. 227 - 237.

    Key message: A QTL for aphid resistance on pepper chromosome 2 was identified and validated. This QTL affects aphid survival and reproduction, and was fine mapped to a locus containing LRR-RLK analogues. Abstract: Myzus persicae is one of the most threatening insect pests that adversely affects pepper (Capsicum) cultivation. Resistance to aphids was previously identified in Capsicum baccatum. This study aimed at elucidating the genetics of aphid resistance in C. baccatum. A QTL analysis was carried out for M. persicae resistance in an F2 population derived from an intraspecific cross between a highly resistant plant and a susceptible plant. Survival and reproduction were used as resistance parameters. Interval mapping detected two QTLs affecting aphid survival (Rmpas-1) and reproduction (Rmprp-1), respectively, both localized in the same area and sharing the same top marker on chromosome 2. Use of this marker as co-factor in multiple-QTL mapping analysis revealed a second, minor QTL (Rmprp-2) only affecting aphid reproduction, on chromosome 4. Fine mapping confirmed the effects of Rmpas-1 and Rmprp-1 and narrowed the major QTL Rmprp-1 down to a genomic region of 96 kb which is predicted to encode four analogues of resistance genes of the receptor-like kinase family containing a leucine-rich repeat domain (LRR-RLKs). This work provides not only initial information for breeding aphid-resistant pepper varieties, but also forms the basis for future molecular analysis of gene(s) involved in aphid resistance.

    QTL mapping of insect resistance components of Solanum galapagense
    Vosman, Ben ; Kashaninia, Atiyeh ; van’t Westende, Wendy ; Meijer-Dekens, Fien ; Eekelen, Henriëtte van; Visser, Richard G.F. ; Vos, Ric C.H. de; Voorrips, Roeland E. - \ 2019
    Theoretical and Applied Genetics 132 (2019)2. - ISSN 0040-5752 - p. 531 - 541.

    Key message: QTLs for insect resistance parameters, trichome type IV development, and more than 200 non-volatile metabolites, including 76 acyl sugars, all co-locate at the end of Chromosome 2 of Solanum galapagense. Abstract: Host plant resistance is gaining importance as more and more insecticides are being banned due to environmental concerns. In tomato, resistance towards insects is found in wild relatives and has been attributed to the presence of glandular trichomes and their specific phytochemical composition. In this paper, we describe the results from a large-scale QTL mapping of data from whitefly resistance tests, trichome phenotyping and a comprehensive metabolomics analysis in a recombinant inbred line population derived from a cross between the cultivated Solanum lycopersicum and the wild relative S. galapagense, which is resistant to a range of pest insects. One major QTL (Wf-1) was found to govern the resistance against two different whitefly species. This QTL co-localizes with QTLs for the presence of trichomes type IV and V, as well as all 76 acyl sugars detected and about 150 other non-volatile phytochemicals, including methyl esters of the flavonols myricetin and quercetin. Based on these results, we hypothesize that Wf-1 is regulating the formation of glandular trichome type IV on the leaf epidermis, enabling the production and accumulation of bioactive metabolites in this type of trichomes.

    Reduced phloem uptake of Myzus persicae on an aphid resistant pepper accession
    Sun, Mengjing ; Voorrips, R.E. ; Steenhuis-Broers, M.M. ; Westende, W.P.C. van 't; Vosman, B. - \ 2018
    aphid resistance screening - Capsicum baccatum - EPG - callose - real-time PCR
    Background The green peach aphid (GPA), Myzus persicae, is economically one of the most threatening pests in pepper cultivation, which not only causes direct damage but also transmits many viruses. Breeding aphid resistant pepper varieties is a promising and environmentally friendly method to control aphid populations in the field and in the greenhouse. Until now, no strong sources of resistance against the GPA have been identified. Therefore the main aims of this study were to identify pepper materials with a good level of resistance to GPA and to elucidate possible resistance mechanisms. Results We screened 74 pepper accessions from different geographical areas for resistance to M. persicae. After four rounds of evaluation we identified one Capsicum baccatum accession (PB2013071) as highly resistant to M. persicae, while the accessions PB2013062 and PB2012022 showed intermediate resistance. The resistance of PB2013071 resulted in a severely reduced uptake of phloem compared to the susceptible accession, as determined by Electrical Penetration Graph (EPG) studies. Feeding of M. persicae induced the expression of callose synthase genes and resulted in callose deposition in the sieve elements in resistant, but not in susceptible plants. Conclusions Three aphid resistant pepper accessions were identified, which will be important for breeding aphid resistant pepper varieties in the future. The most resistant accession PB2013071 showed phloem-based resistance against aphid infestation.
    Resistentie tegen bladluizen in paprika
    Vosman, B. ; Sun, Mengjing ; Westende, W.P.C. van 't; Voorrips, R.E. - \ 2018
    Reduced phloem uptake of Myzus persicae on an aphid resistant pepper accession
    Sun, Mengjing ; Voorrips, Roeland E. ; Steenhuis-Broers, Greet ; van't Westende, Wendy ; Vosman, Ben - \ 2018
    BMC Plant Biology 18 (2018)1. - ISSN 1471-2229
    Aphid resistance screening - Callose - Capsicum baccatum - EPG - Real-time PCR

    Background: The green peach aphid (GPA), Myzus persicae, is economically one of the most threatening pests in pepper cultivation, which not only causes direct damage but also transmits many viruses. Breeding aphid resistant pepper varieties is a promising and environmentally friendly method to control aphid populations in the field and in the greenhouse. Until now, no strong sources of resistance against the GPA have been identified. Therefore the main aims of this study were to identify pepper materials with a good level of resistance to GPA and to elucidate possible resistance mechanisms. Results: We screened 74 pepper accessions from different geographical areas for resistance to M. persicae. After four rounds of evaluation we identified one Capsicum baccatum accession (PB2013071) as highly resistant to M. persicae, while the accessions PB2013062 and PB2012022 showed intermediate resistance. The resistance of PB2013071 resulted in a severely reduced uptake of phloem compared to the susceptible accession, as determined by Electrical Penetration Graph (EPG) studies. Feeding of M. persicae induced the expression of callose synthase genes and resulted in callose deposition in the sieve elements in resistant, but not in susceptible plants. Conclusions: Three aphid resistant pepper accessions were identified, which will be important for breeding aphid resistant pepper varieties in the future. The most resistant accession PB2013071 showed phloem-based resistance against aphid infestation.

    Broad spectrum insect resistance and metabolites in close relatives of the cultivated tomato
    Vosman, Ben ; van’t Westende, Wendy P.C. ; Henken, Betty ; Eekelen, Henriëtte D.L.M. van; Vos, Ric C.H. de; Voorrips, Roeland E. - \ 2018
    Euphytica 214 (2018)3. - ISSN 0014-2336
    Acyl sugars - Aphid - Caterpillar - Flavonoids - Lycopersicon group - Metabolomics - Thrips - Whitefly
    Wild relatives of tomato possess effective means to deal with several pests, among which are a variety of insects. Here we studied the presence of resistance components against Trialeurodes vaporariorum, Myzus persicae, Frankliniella occidentalis, and Spodoptera exigua in the Lycopersicon group of Solanum section Lycopersicon by means of bioassays and comprehensive metabolite profiling. Broad spectrum resistance was found in Solanum galapagense and a few accessions of S. pimpinellifolium. Resistance to the sap sucking insects may be based on the same mechanism, but different from the caterpillar resistance. Large and highly significant differences in the leaf metabolomes were found between S. galapagense, containing type IV trichomes, and its closest relative S. cheesmaniae, which lacks type IV trichomes. The most evident differences were the relatively high levels of different methylated forms of the flavonoid myricetin and many acyl sucrose structures in S. galapagense. Possible candidate genes regulating the production of these compounds were identified in the Wf-1 QTL region of S. galapagense, which was previously shown to confer resistance to the whitefly B. tabaci. The broad spectrum insect resistance identified in S. galapagense will be very useful to increase resistance in cultivated tomato.
    Reduced phloem uptake of Myzus persicae on an aphid resistant pepper accession
    Sun, Mengjing ; Voorrips, R.E. ; Westende, W.P.C. van 't; Vosman, B. - \ 2017
    Resistentie tegen bladluizen in paprika
    Vosman, B. ; Sun, Mengjing ; Westende, W.P.C. van 't; Voorrips, R.E. - \ 2017
    Bladluisresistentie in Paprika : Groene Veredeling Paprika
    Sun, Mengjing ; Voorrips, R.E. ; Westende, W.P.C. van 't; Vosman, B. - \ 2017
    Wageningen : Wageningen University & Research - 2 p.
    Partial preferential chromosome pairing is genotype dependent in tetraploid rose
    Bourke, Peter M. ; Arens, Paul ; Voorrips, Roeland E. ; Esselink, Danny ; Koning-Boucoiran, Carole F.S. ; Westende, Wendy van 't; Santos Leonardo, Tiago ; Wissink, Patrick ; Zheng, Chaozhi ; Geest, Geert van; Visser, Richard G.F. ; Krens, Frans A. ; Smulders, Rene ; Maliepaard, Chris - \ 2017
    The Plant Journal 90 (2017)2. - ISSN 0960-7412 - p. 330 - 343.
    high-density integrated map - meiotic chromosomal pairing behaviour - polyploid genetic linkage map - Rosa hybrida - segmental allopolyploid

    It has long been recognised that polyploid species do not always neatly fall into the categories of auto- or allopolyploid, leading to the term ‘segmental allopolyploid’ to describe everything in between. The meiotic behaviour of such intermediate species is not fully understood, nor is there consensus as to how to model their inheritance patterns. In this study we used a tetraploid cut rose (Rosa hybrida) population, genotyped using the 68K WagRhSNP array, to construct an ultra-high-density linkage map of all homologous chromosomes using methods previously developed for autotetraploids. Using the predicted bivalent configurations in this population we quantified differences in pairing behaviour among and along homologous chromosomes, leading us to correct our estimates of recombination frequency to account for this behaviour. This resulted in the re-mapping of 25 695 SNP markers across all homologues of the seven rose chromosomes, tailored to the pairing behaviour of each chromosome in each parent. We confirmed the inferred differences in pairing behaviour among chromosomes by examining repulsion-phase linkage estimates, which also carry information about preferential pairing and recombination. Currently, the closest sequenced relative to rose is Fragaria vesca. Aligning the integrated ultra-dense rose map with the strawberry genome sequence provided a detailed picture of the synteny, confirming overall co-linearity but also revealing new genomic rearrangements. Our results suggest that pairing affinities may vary along chromosome arms, which broadens our current understanding of segmental allopolyploidy.

    Aphid resistance in a Capsicum collection
    Voorrips, R.E. ; Steenhuis-Broers, M.M. ; Westende, W.P.C. van 't; Vosman, B. - \ 2016
    In: 2016 Proceedings of the XVIth EUCARPIA Capsicum and Eggplant Working Group Meeting. - Budapest, Hungary : Eucarpia - ISBN 9786155270277
    Aphids are a problem in pepper cultivation, causing direct damage as well as acting as vectors for viruses. Resistance to aphids is therefore a desired trait in pepper varieties, but resistant varieties are not available yet. Our research is focused on finding sources of aphid resistance and elucidation of the genetics and mechanism of resistance. In our poster we present some of our results: an efficient bioassay with Myzus persicae and a comparison of the performance of a collection of Capsicum accessions in this biotest.
    High-density SNP-based genetic maps for the parents of an outcrossed and a selfed tetraploid garden rose cross, inferred from admixed progeny using the 68k rose SNP array
    Vukosavljev, Mirjana ; Arens, Paul ; Voorrips, Roeland E. ; Westende, Wendy P.C. Van 't; Esselink, G.D. ; Bourke, Peter M. ; Cox, Peter ; De Weg, W.E. Van; Visser, Richard G.F. ; Maliepaard, Chris ; Smulders, Marinus J.M. - \ 2016
    Horticulture Research 3 (2016). - ISSN 2052-7276

    Dense genetic maps create a base for QTL analysis of important traits and future implementation of marker-assisted breeding. In tetraploid rose, the existing linkage maps include

    Using RNA-Seq to assemble a rose transcriptome with more than 13,000 full-length expressed genes and to develop the WagRhSNP 68k Axiom SNP array for rose (Rosa L.)
    Koning, C.F.S. ; Esselink, G. ; Vukosavljev, M. ; Westende, W.P.C. van 't; Gitonga, V.W. ; Krens, F.A. ; Voorrips, R.E. ; Weg, W.E. van de; Schulz, D. ; Debener, T. ; Maliepaard, C.A. ; Arens, P.F.P. ; Smulders, M.J.M. - \ 2015
    Frontiers in Plant Science 6 (2015). - ISSN 1664-462X - 10 p.
    powdery mildew - markers - tool - identification - resistance - genome - diversity - sequences - platform - plant
    In order to develop a versatile and large SNP array for rose, we set out to mine ESTs from diverse sets of rose germplasm. For this RNA-Seq libraries containing about 700 million reads were generated from tetraploid cut and garden roses using Illumina paired-end sequencing, and from diploid Rosa multiflora using 454 sequencing. Separate de novo assemblies were performed in order to identify single nucleotide polymorphisms (SNPs) within and between rose varieties. SNPs among tetraploid roses were selected for constructing a genotyping array that can be employed for genetic mapping and marker-trait association discovery in breeding programs based on tetraploid germplasm, both from cut roses and from garden roses. In total 68,893 SNPs were included on the WagRhSNP Axiom array. Next, an orthology-guided assembly was performed for the construction of a non-redundant rose transcriptome database. A total of 21,740 transcripts had significant hits with orthologous genes in the strawberry (Fragaria vesca L.) genome. Of these 13,390 appeared to contain the full-length coding regions. This newly established transcriptome resource adds considerably to the currently available sequence resources for the Rosaceae family in general and the genus Rosa in particular.
    Development of the WagRhSNP AXIOM SNP Array Based on Sequences from Tetraploid Cut Roses and Garden Roses
    Smulders, M.J.M. ; Voorrips, R.E. ; Esselink, G. ; Santos Leonardo, T.M. ; Westende, W.P.C. van 't; Vukosavljev, M. ; Koning-Boucoiran, C.F.S. ; Weg, W.E. van de; Arens, P.F.P. ; Schulz, D. ; Debener, T. ; Bellon, L. ; Mittmann, M. ; Pirani, A. ; Webster, T. ; Brew, F. ; Cox, P. ; Maliepaard, C.A. - \ 2015
    In: Proceedings VIth International Symposiul on Rose Research and Cultivation. - ISHS - ISBN 9789462610552 - p. 177 - 184.
    Rose, as many other important ornamental, vegetable and field crops, is polyploid. This poses constraints in genetic analyses due to the occurrence of multiple alleles at marker and trait loci and the existence of multiple allele dosages. Developments in marker discovery (next generation sequencing), detection (SNP arrays) and analysis (software for dosage scoring) now make it feasible to develop high-density molecular marker maps for the homologous chromosomes in tetraploids separately, and thus perform QTL analysis in tetraploids. We developed a SNP array for rose to develop genetic maps in tetraploid garden roses and cut roses, which are to be used for inheritance studies and genetic mapping. Here we have indicated the general strategy followed for developing a SNP array and for scoring and using the SNP data generated, and elaborated on the activities undertaken to use the WagRhSNP Axiom array in rose. The array design is not proprietary but can be used by all researchers working in rose
    Efficient development of highly polymorphic microsatellite markers based on polymorphic repeats in transcriptome sequences of multiple individuals
    Vukosavljev, M. ; Esselink, G. ; Westende, W.P.C. van 't; Cox, P. ; Visser, R.G.F. ; Arens, P. ; Smulders, M.J.M. - \ 2015
    Molecular Ecology Resources 15 (2015)1. - ISSN 1755-098X - p. 17 - 27.
    est-ssr markers - genetic-linkage maps - in-silico - rose - l. - diversity - transferability - construction - variability - identification
    The first hurdle in developing microsatellite markers, cloning, has been overcome by next generation sequencing. The second hurdle is testing to differentiate polymorphic from non-polymorphic loci. The third hurdle, somewhat hidden, is that only polymorphic markers with a large effective number of alleles are sufficiently informative to be deployed in multiple studies. Both steps are laborious and still done manually. We have developed a strategy in which we first screen reads from multiple genotypes for repeats that show the most length variants, and only these are subsequently developed into markers. We validated our strategy in tetraploid garden rose using Illumina paired-end transcriptome sequences of 11 roses. Out of 48 tested two markers failed to amplify but all others were polymorphic. Ten loci amplified more than one locus, indicating duplicated genes or gene families. Completely avoiding duplicated loci will be difficult because the range of numbers of predicted alleles of highly polymorphic single- and multi-locus markers largely overlapped. Of the remainder, half were replicate markers (i.e., multiple primer pairs for one locus), indicating the difficulty of correctly filtering short reads containing repeat sequences. We subsequently refined the approach to eliminate multiple primer sets to the same loci. The remaining 18 markers were all highly polymorphic, amplifying on average 11.7 alleles per marker (range = 6 to 20) in 11 tetraploid roses, exceeding the 8.2 alleles per marker of the 24 most polymorphic markers genotyped previously. This strategy, therefore, represents a major step forward in the development of highly polymorphic microsatellite markers.
    Genetic diversity and differentiation in roses: A gardenrose perspective
    Vukosavljev, M. ; Zhang, J. ; Esselink, G. ; Westende, W.P.C. van 't; Cox, P. ; Visser, R.G.F. ; Arens, P. ; Smulders, M.J.M. - \ 2013
    Scientia Horticulturae 162 (2013). - ISSN 0304-4238 - p. 320 - 332.
    population-structure - markers - identification - varieties - assignment
    tFor the first time genetic diversity among modern garden rose cultivars has been evaluated using a setof 24 microsatellite markers covering most chromosomes. A total of 518 different alleles were obtainedin the set of 138 rose cultivars and this led to the conclusion that in terms of genetic diversity cut rosescan be considered as a subgroup of the garden roses.Genetic differentiation among types of garden roses (Fst= 0.022) was four times that among cut roses,and similar in magnitude to the differentiation among breeders, due to the fact that horticultural groupsand breeders overlap largely in classification. Winter hardy Svejda’s cultivars (Canadian Explorer roses)showed the least similarities to European roses, and introgression from wild species for winter hardinesswas clearly visible. Roses of Harkness and Olesen shared a similar genepool. Comparison of the differen-tiation among linkage groups indicated that linkage group 5 is potentially a region containing importantQTLs for winter hardiness. Linkage group 6 contains the largest amount of genetic diversity, while linkagegroup 2 is the most differentiated among types of garden roses.
    Avenin diversity analysis of the genus Avena (oat). Relevance for people with celiac disease
    Londono, D.M. ; Westende, W.P.C. van 't; Goryunova, S.V. ; Salentijn, E.M.J. ; Broeck, H.C. van den; Meer, I.M. van der; Visser, R.G.F. ; Gilissen, L.J.W.J. ; Smulders, M.J.M. - \ 2013
    Journal of Cereal Science 58 (2013)1. - ISSN 0733-5210 - p. 170 - 177.
    gluten-free diet - t-cell epitopes - natural variation - oats - wheat - varieties - prolamins - gliadins - toxicity - proteins
    Oat is widely consumed by people with celiac disease (CD). Its safety has been disputed because two peptides from oat avenins can be recognized as T cell epitopes by some CD patients. Differential signals of gluten-specific monoclonal antibodies and in-vitro T cells to oat varieties have suggested the existence of differences in immunogenicity. We aimed to clarify the nature of such responses by cloning avenin genes from 13 Avena species. A single oat plant contained up to 10 avenin genes. Avenin proteins clustered in four groups of which two contained the two avenin CD epitopes. All Avena species examined harbored avenins of these two groups, and as a consequence all contained avenins with the two avenin-specific epitopes, which makes it very unlikely to find oat cultivars that are devoid of these sequences. The established gluten epitopes from wheat, rye and barley were not present in oat avenins; some variants with two and three amino acid substitutions occurred, but they were predicted not to resist proteolysis in the gastro-intestinal tract. Perfect recognition sites of antibodies R5 and G12 were also not present in avenins. Thus, their signals to oat should not be interpreted as differences in immunogenicity for CD patients.
    Oat avenins do not contain coeliac disease epitopes known from wheat, rye and barley
    Londono, D.M. ; Westende, W.P.C. van 't; Goryunova, S.V. ; Salentijn, E.M.J. ; Broeck, H.C. van den; Meer, I.M. van der; Visser, R.G.F. ; Gilissen, L.J.W.J. ; Smulders, M.J.M. - \ 2012
    Towards a large Axiom genotyping array for tetraploid rose
    Smulders, M.J.M. ; Koning-Boucoiran, C.F.S. ; Vukosavljev, M. ; Esselink, G. ; Westende, W.P.C. van 't; Voorrips, R.E. ; Weg, W.E. van de; Debener, T. ; Maliepaard, C.A. - \ 2012
    Development of safe foods for celiac patients- A multidisciplinary approach.
    Gilissen, L.J.W.J. ; Broeck, H.C. van den; Westende, W.P.C. van 't; Londono, D.M. ; Salentijn, E.M.J. ; Meer, I.M. van der; Smulders, M.J.M. - \ 2010
    Food for thought : food science news, technology and development from the Netherlands 3 (2010). - p. 1 - 4.
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