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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Genome-Wide SNP Detection, Validation, and Development of an 8K SNP Array for Apple
Chagné, D. ; Crowhurst, R.N. ; Troggio, M. ; Davey, M.W. ; Gilmore, B. ; Lawley, C. ; Vanderzande, S. ; Hellens, R.P. ; Kumar, S. ; Cestaro, A. ; Velasco, R. ; Main, D. ; Rees, J.D. ; Iezzoni, A.F. ; Mockler, T. ; Wilhelm, L. ; Weg, W.E. van de; Gardiner, S.E. ; Bassil, N. ; Peace, C. - \ 2012
PLoS ONE 7 (2012)2. - ISSN 1932-6203
x-domestica borkh. - single-nucleotide polymorphisms - transcription factor - malus-domestica - genus vitis - shelf-life - fruit - markers - diversity - discovery
As high-throughput genetic marker screening systems are essential for a range of genetics studies and plant breeding applications, the International RosBREED SNP Consortium (IRSC) has utilized the Illumina Infinium® II system to develop a medium- to high-throughput SNP screening tool for genome-wide evaluation of allelic variation in apple (Malus×domestica) breeding germplasm. For genome-wide SNP discovery, 27 apple cultivars were chosen to represent worldwide breeding germplasm and re-sequenced at low coverage with the Illumina Genome Analyzer II. Following alignment of these sequences to the whole genome sequence of ‘Golden Delicious’, SNPs were identified using SoapSNP. A total of 2,113,120 SNPs were detected, corresponding to one SNP to every 288 bp of the genome. The Illumina GoldenGate® assay was then used to validate a subset of 144 SNPs with a range of characteristics, using a set of 160 apple accessions. This validation assay enabled fine-tuning of the final subset of SNPs for the Illumina Infinium® II system. The set of stringent filtering criteria developed allowed choice of a set of SNPs that not only exhibited an even distribution across the apple genome and a range of minor allele frequencies to ensure utility across germplasm, but also were located in putative exonic regions to maximize genotyping success rate. A total of 7867 apple SNPs was established for the IRSC apple 8K SNP array v1, of which 5554 were polymorphic after evaluation in segregating families and a germplasm collection. This publicly available genomics resource will provide an unprecedented resolution of SNP haplotypes, which will enable marker-locus-trait association discovery, description of the genetic architecture of quantitative traits, investigation of genetic variation (neutral and functional), and genomic selection in apple
Development of hypo-allergenic apples: silencing of the major allergen Mal d 1 gene in 'Elstar' apple and the effect of grafting
Krath, B.N. ; Eriksen, F.D. ; Pedersen, B.H. ; Gilissen, L.J.W.J. ; Weg, W.E. van de; Dragsted, L.O. - \ 2009
Journal of Horticultural Science and Biotechnology 84 (2009)6 Isafruit Suppl. - ISSN 1462-0316 - p. 52 - 57.
controlled food challenge - birch pollen allergen - malus-domestica - double-blind - expression - protein - cloning - bet-v-1 - fruit
Many people who are allergic to birch pollen are also allergic to apple fruit, due to cross- allergenicity. Since apples are the most extensively consumed fruit in Europe, it is highly relevant to develop a hypo-allergenic apple. Apples with significantly reduced levels of the allergen, Mal d 1, may allow many apple allergics to eat them without an allergic reaction. We are currently collaborating to develop a hypo-allergenic apple within the European Integrated Research Project, ISAFRUIT (www.isafruit.org). Hypo-allergenic apple plants (Malus × domestica Borkh., ‘Elstar’) with decreased levels of Mal d 1 mRNA were produced by RNA interference (RNAi) technology. Ten genetically modified (GM) apple lines were selected. In vitro plantlets were first transferred to a greenhouse, then grafted onto wild-type M.9 rootstock to promote the development of fruit-producing trees. Levels of Mal d 1 gene silencing were measured repeatedly by quantitative real-time PCR. Compared to leaf samples from wild-type ‘Elstar’, two GM lines showed modest levels of gene silencing (up to 250-fold), whereas the other eight GM lines were significantly silenced (up to10,000-fold) in Mal d 1 gene expression. These levels of silencing were unaffected by grafting, and have been stable over more than 3 years, and throughout all developmental stages.
Tissue location of resistance in apple to the rosy apple aphid established by electrical penetration graphs
Marchetti, E. ; Civolani, S. ; Leis, M. ; Chicca, M. ; Tjallingii, W.F. ; Pasqualini, E. ; Baroni, P. - \ 2009
Bulletin of Insectology 62 (2009)2. - ISSN 1721-8861 - p. 203 - 208.
dysaphis-plantaginea - stylet penetration - malus-domestica - myzus-persicae - inoculation - salivation - cultivars - homoptera - viruses
A study of the constitutive resistance of the apple cultivar Florina, Malus domestica Borkh. (Rosaceae), to the rosy apple aphid, Dysaphis plantaginea (Passerini) (Homoptera Aphididae), was performed for the first time by the electrical penetration graph (DC-EPG) system, using the susceptible apple cultivar Smoothe as control. All experiments were conducted with apterous adult virginoparae. The results showed a constitutive resistance in Florina due to a much longer period before the first probe reflecting surface factors. Some weak indications were found for pre-phloem resistance and initiating phloem access was not affected as inferred from equal time to show phloem salivation. However, the complete absence of phloem ingestion indicates a major resistance factor in the phloem sieve elements, most likely in the sieve element sap. Surface factors could have affected tissue related variables and this should be studied further. Anyhow, the strong constitutive resistance in Florina, either on the surface alone or in the phloem as well, effectively prevented reliable experiments on induced resistance, previously detected by molecular methods.
Genomic characterization of putative allergen genes in peach/almond and their synteny with apple
Chen, L. ; Zhang, S. ; Illa, E. ; Song, L. ; Wu, S. ; Howad, W. ; Arus, P. ; Weg, W.E. van de; Chen, K. ; Gao, Z.S. - \ 2008
BMC Genomics 9 (2008). - ISSN 1471-2164 - 15 p.
lipid transfer protein - peach prunus-persica - major allergen - malus-domestica - allelic diversity - food allergens - linkage maps - l. batsch - expression - cloning
Background - Fruits from several species of the Rosaceae family are reported to cause allergic reactions in certain populations. The allergens identified belong to mainly four protein families: pathogenesis related 10 proteins, thaumatin-like proteins, lipid transfer proteins and profilins. These families of putative allergen genes in apple (Mal d 1 to 4) have been mapped on linkage maps and subsequent genetic study on allelic diversity and hypoallergenic traits has been carried out recently. In peach (Prunus persica), these allergen gene families are denoted as Pru p 1 to 4 and for almond (Prunus dulcis)Pru du 1 to 4. Genetic analysis using current molecular tools may be helpful to establish the cause of allergenicity differences observed among different peach cultivars. This study was to characterize putative peach allergen genes for their genomic sequences and linkage map positions, and to compare them with previously characterized homologous genes in apple (Malus domestica). Results - Eight Pru p/du 1 genes were identified, four of which were new. All the Pru p/du 1 genes were mapped in a single bin on the top of linkage group 1 (G1). Five Pru p/du 2 genes were mapped on four different linkage groups, two very similar Pru p/du 2.01 genes (A and B) were on G3, Pru p/du 2.02 on G7,Pru p/du 2.03 on G8 and Pru p/du 2.04 on G1. There were differences in the intron and exon structure in these Pru p/du 2 genes and in their amino acid composition. Three Pru p/du 3 genes (3.01¿3.03) containing an intron and a mini exon of 10 nt were mapped in a cluster on G6. Two Pru p/du 4 genes (Pru p/du 4.01 and 4.02) were located on G1 and G7, respectively. The Pru p/du 1 cluster on G1 aligned to the Mal d 1 clusters on LG16; Pru p/du 2.01A and B on G3 to Mal d 2.01A and B on LG9; the Pru p/du 3 cluster on G6 to Mal d 3.01 on LG12; Pru p/du 4.01 on G1 to Mal d 4.03 on LG2; and Pru p/du 4.02 on G7 to Mal d 4.02 on LG2. Conclusion - A total of 18 putative peach/almond allergen genes have been mapped on five linkage groups. Their positions confirm the high macro-synteny between peach/almond and apple. The insight gained will help to identify key genes causing differences in allergenicity among different cultivars of peach and other Prunus species.
Measurement of lipid transfer protein in 88 apple cultivars
Sancho, A.I. ; Ree, R. van; Leeuwen, A. van; Meulenbroek, E.J. ; Weg, W.E. van de; Gilissen, L.J.W.J. ; Puehringer, H. ; Laimer, M. ; Martinelli, A. ; Zaccharini, M. ; Vazquez-Cortes, S. ; Fernandez-Rivas, M. ; Hoffmann-Sommergruber, K. ; Clare Mills, E.N. ; Zuidmeer, L. - \ 2008
International Archives of Allergy and Immunology 146 (2008)1. - ISSN 1018-2438 - p. 19 - 26.
oral allergy syndrome - malus-domestica - rosaceae fruits - plant foods - in-vivo - pollen - ige - allergenicity - reactivity - mal-d-3
Background: Fruits are a major cause of food allergy in adults. Lipid transfer proteins (LTP) are implicated in severe allergic reactions to fruits, but little is known about LTP content in different cultivars. Objective: Determination of the levels of LTP in a wide range of apple cultivars. Methods: LTP was measured in apples from 53 cultivars grown in Italy and 35 grown in The Netherlands, using three different immunoassays: a competitive ELISA (cELISA), a sandwich ELISA (sELISA) and a RAST inhibition (RI). Selected cultivars were evaluated using the basophil histamine release test (BHR), skin prick test (SPT) and double-blind, placebo-controlled food challenge (DBPCFC). Results: LTP levels measured with the three immunoassays were significantly correlated, as judged by Pearson's correlation (0.61 <Rp <0.65; p <0.0001), but differed with respect to the actual quantities: 3.4-253.2 (sELISA), 2.7-120.2 (cELISA) and 0.4-47.3 µg/g tissue (RI). Between cultivars, LTP titers varied over about a two-log range. Pilot in vitro and in vivo biological testing (BHR, SPT and DBPCFC) with selected cultivars supported the observed differences in LTP levels. Conclusions: Around 100-fold differences in LTP levels exist between apple cultivars. Whether the lowest observed levels of LTP warrant designation as hypo-allergenic requires more extensive confirmation by oral challenges. Determination of cultivar variation in LTP levels provides important information for growers and consumers. Comparison to earlier reported Mal d 1 levels in the same cultivars reveals that a designation as low allergenic does not always coincide for both allergens.
Genomic characterization and linkage mapping of the apple allergen genes Mal d 2 (thaumatin-like protein) and Mal d 4 (profilin)
Gao, Z.S. ; Weg, W.E. van de; Schaart, J.G. ; Arkel, G. van; Breiteneder, H. ; Hoffmann-Sommergruber, K. ; Gilissen, L.J.W.J. - \ 2005
Theoretical and Applied Genetics 111 (2005)6. - ISSN 0040-5752 - p. 1087 - 1097.
cross-reactivity - malus-domestica - pollen profilin - heterologous expression - cloning - arabidopsis - family - ige - identification - potency
Four classes of apple allergens (Mal d 1, ¿2, ¿3 and ¿4) have been reported. By using PCR cloning and sequencing approaches, we obtained genomic sequences of Mal d 2 (thaumatin-like protein) and Mal d 4 (profilin) from the cvs Prima and Fiesta, the two parents of a European reference mapping population. Two copies of the Mal d 2 gene (Mal d 2.01A and Mal d 2.01B) were identified, which primarily differed in the length of a single intron (378 or 380 nt) and in one amino acid in the signal peptide. Both Mal d 2.01A and Mal d 2.01B were mapped at identical position on linkage group 9. Genomic characterization of four Mal d 4 genes (Mal d 4.01A and B, Mal d 4.02A and Mal d 4.03A) revealed their complete gDNA sequences which varied among genes in length from 862 to 2017 nt. They all contained three exons of conserved length: 123, 138, and 135 nt. Mal d 4.01 appeared to be duplicated in two copies and located on linkage group 9. Mal d 4.02A and Mal d 4.03A were single copy genes located on linkage group 2 and 8, respectively
Localisation and distribution of the major allergens in apple fruits
Marzban, G. ; Puehringer, H. ; Dey, R. ; Brynda, S. ; Ma, Y. ; Martinelli, A. ; Zaccarini, M. ; Weg, W.E. van de; Housley, Z. ; Kolarich, D. ; Altmann, F. ; Laimer, M. - \ 2005
Plant Science 169 (2005)2. - ISSN 0168-9452 - p. 387 - 394.
lipid transfer protein - birch pollen allergen - bet v 1 - malus-domestica - genes - food - positions - mal-d-1 - cloning - family
The importance of apple allergens, in particular Mal d 1, a Bet v 1 homologue for the pollen-fruit syndrome in Northern Europe, and Mal d 3, responsible for true fruit allergy in Southern Europe, has been repeatedly emphasized. However, little is known about the distribution pattern of major allergens in fruits and whether differences exist among different cultivars. Transcript expression of Mal d 1 isoforms and Mal d 3 was examined by RealTime-PCR and Northern analysis, respectively. An immuno-tissue-print (ITP) assay was developed to localise major allergens in apple fruit tissue and a Mal d 1 specific, patient independent ELISA was established. ITP analyses show that Mal d 1 and Mal d 2 are distributed throughout the apple pulp and peel, while Mal d 3 is restricted to the peel. Data obtained by ELISA reveal a variation of Mal d 1 content ranging from 0.84 to 33.17 ¿g/g fresh weight in 39 selected cultivars. Different apple cultivars show a markedly different expression of major allergens; this finding will influence the development of diagnostic tools as well as the dietary management of allergic individuals
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