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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Estimating genetic diversity across the neutral genome with the use of dense marker maps
Engelsma, K.A. ; Calus, M.P.L. ; Bijma, P. ; Windig, J.J. - \ 2010
Genetics, Selection, Evolution 42 (2010). - ISSN 0999-193X - 10
populatiegenetica - computersimulatie - genetische diversiteit - merkergenen - population genetics - computer simulation - genetic diversity - marker genes - linkage disequilibrium - prediction - selection - conservation - populations - haplotypes
Background With the advent of high throughput DNA typing, dense marker maps have become available to investigate genetic diversity on specific regions of the genome. The aim of this paper was to compare two marker based estimates of the genetic diversity in specific genomic regions lying in between markers: IBD-based genetic diversity and heterozygosity. Methods A computer simulated population was set up with individuals containing a single 1-Morgan chromosome and 1665 SNP markers and from this one, an additional population was produced with a lower marker density i.e. 166 SNP markers. For each marker interval based on adjacent markers, the genetic diversity was estimated either by IBD probabilities or heterozygosity. Estimates were compared to each other and to the true genetic diversity. The latter was calculated for a marker in the middle of each marker interval that was not used to estimate genetic diversity. Results The simulated population had an average minor allele frequency of 0.28 and an LD (r2) of 0.26, comparable to those of real livestock populations. Genetic diversities estimated by IBD probabilities and by heterozygosity were positively correlated, and correlations with the true genetic diversity were quite similar for the simulated population with a high marker density, both for specific regions (r = 0.19-0.20) and large regions (r = 0.61-0.64) over the genome. For the population with a lower marker density, the correlation with the true genetic diversity turned out to be higher for the IBD-based genetic diversity. Conclusions Genetic diversities of ungenotyped regions of the genome (i.e. between markers) estimated by IBD-based methods and heterozygosity give similar results for the simulated population with a high marker density. However, for a population with a lower marker density, the IBD-based method gives a better prediction, since variation and recombination between markers are missed with heterozygosity.
Persistentie van KVP-virus in gevaccineerde dieren: een risico? = Persistence of classical swine fever virus in vaccinated animals: a risk?
Loeffen, W.L.A. - \ 2008
Tijdschrift voor Diergeneeskunde 133 (2008)11. - ISSN 0040-7453 - p. 482 - 484.
landbouwbeleid - classical swine fever virus - varkenspest - varkenshouderij - ziektedistributie - verplichte vaccinatie - merkergenen - merkers - klassieke varkenspest - maatregelen - dierziektepreventie - agricultural policy - swine fever - pig farming - disease distribution - mandatory vaccination - marker genes - markers - classical swine fever - measures - animal disease prevention
Het is dit jaar geleden dat in Nederland het geval van klassieke varkenspest werd gedetecteerd. Het was het laatste geval in een epidemie die ruim een jaar had geduurd. Op dat moment waren we 429 besmette bedrijven verder, waren 12 miljoen varkens vernietigd en was de schade opgelopen tot meer dan 2 miljard euro. Om nog maar te zwijgen over de emotionele en psychotische schade bij vele betrokkenen. Sindsdien zit de angst voor een nieuwe uitbraak er goed in en zijn er veel maatregelen genomen om een herhaling te voorkomen. Een van die maatregelen is het aanpassen van het beleidsdraaiboek en het daarin opnemen van de optie om tijdens een volgende uitbraak eventueel te gaan vaccineren met een markergen. Het CV1 heeft veel onderzoek gedaan naar effectiviteit en veiligheid van een vaccinatiestrategie met markervaccins. Onder andere werd onderzocht wat de kans is dat gevaccineerde dieren na infectie een chronische infectie ontwikkelen en vervolgens langdurig infectieus zijn
Molecular markers for disease resistance in various crops obtained by NBS profiling
Scholten, O.E. ; Linden, C.G. van der; Vosman, B. - \ 2008
biologische landbouw - selectiemethoden - genetische merkers - merkergenen - ziekteresistentie - resistentieveredeling - organic farming - selection methods - genetic markers - marker genes - disease resistance - resistance breeding
Breeding for resistance is one of the major efforts in many breeding programmes. As in organic farming the use of pesticides is prohibited, resistant cultivars are of high importance. To select for resistant plants, screening assays are needed that often are laborious and require extensive knowledge on plant-pathogen interactions. To facilitate the introgression of resistance genes into adapted breeding material, molecular markers are a powerful tool.
A bioinformatics approach to marker development
Tang, J. - \ 2008
Wageningen University. Promotor(en): Jack Leunissen, co-promotor(en): Ben Vosman. - [S.l.] : S.n. - ISBN 9789085048114 - 150
bio-informatica - genetische merkers - merkergenen - nucleotidenvolgordes - moleculaire genetica - algoritmen - loci voor kwantitatief kenmerk - microsatellieten - single nucleotide polymorphism - bioinformatics - genetic markers - marker genes - nucleotide sequences - molecular genetics - algorithms - quantitative trait loci - microsatellites
The thesis focuses on two bioinformatics research topics: the development of tools for an efficient and reliable identification of single nucleotides polymorphisms (SNPs) and polymorphic simple sequence repeats (SSRs) from expressed sequence tags (ESTs) (Chapter 2, 3 and 4), and the subsequent implementation of these tools in a pipeline for narrowing down QTL intervals to facilitate the identification of candidate genes for the QTL (Chapter 5).
Chapter 1 provides an introduction to molecular markers, SNP and SSR markers, illustrated by a number of applications of molecular markers, as well as existing programs for their detection.
After analysis of existing problems and programs for the detection SNPs, a new algorithm is described to reliably identify SNPs and indels in EST data from diploid and polyploid species (Chapter 2). The algorithm is implemented in a program called QualitySNP. This program uses three filters to identify reliable SNPs: filter one screens for potential SNPs by requiring at least two sequences per represented allele; filter two uses a haplotype-based strategy to filter out clusters with paralogs and false SNPs caused by sequence errors; finally, filter three calculates a confidence score for every putative SNP according to the number of occurrences of each allele in high and low quality regions.
For the detection of non-synonymous SNPs (nsSNP), synonymous SNPs and SNPs in UTRs, a program was developed as well. Furthermore, these programs were implemented in a pipeline that includes the identification of SNPs and nsSNPs, as well as a storage and retrieval system. Using this pipeline, large numbers of SNPs could be identified in potato ESTs. QualitySNP is available for running on LINUX and UNIX systems; the program, user manual and examples are available at http://www.bioinformatics.nl/tools/snpweb/ .
Chapter 3 describes a web-based implementation of the QualitySNP algorithm, called HaploSNPer, which is a tool for the detection of alleles and SNPs in user-specified input sequences from both diploid and polyploid species. HaploSNPer tries to find homologous sequences in user-specified sequence databases using a user-supplied seed sequence, or in a collection of input sequences. All alleles and associated SNPs are identified on clusters of these homologous sequences using QualitySNP. HaploSNPer provides a user-friendly interface for visualization of SNPs and alleles, which allows the selection of informative SNPs and allele specific makers. Currently HaploSNPer is available for nine animal and thirteen plant species, and is available from http://www.bioinformatics.nl/tools/haplosnper/ .
Chapter 4 presents a new tool, called PolySSR, to identify polymorphic SSRs rather than just SSRs based on public EST sequence data derived from heterozygotes and/or different genotypes. Based on PolySSR a pipeline was developed to automatically develop primers for putatively polymorphic SSR markers, taking into account SNPs in the SSR flanking regions, thus improving the success rate of the potential markers. Furthermore, SSR positions in coding or UTR regions of genes are identified by the pipeline. The pipeline also includes a searchable database for these SSRs.
The value of PolySSR was demonstrated by the fact that nearly all tested SSRs predicted to be polymorphic were indeed validated as polymorphic, and also most designed primers produced clear amplicons. Large numbers of polymorphic SSRs were identified from publicly available ESTs in potato, tomato, rice, Arabidopsis, brassica and chicken using the pipeline. They are stored into a database, which is available at http://www.bioinformatics.nl/tools/polyssr/ . PolySSR not only decreases the cost of designing and testing primers, it also brings a new approach to use the redundancy and heterozygosity of ESTs for developing SSRs that was ignored before. Analysis of the data obtained with polySSR showed that a larger percentage of short SSRs identified in the species used in the study were polymorphic than that of long SSRs. From this it is clear that in the past we have ‘forgotten’ a whole class of putatively informative markers.
QualitySNP and PolySSR have been implemented into a pipeline called GeneTagger to find candidate genes underlying a QTL using the strategy of narrowing the QTL interval (Chapter 5). The pipeline first detects the syntenic region of a QTL interval in the species under study in a model species based on marker sequences linked to the QTL. Next, within the syntenic regions identified in the model species genes are identified that might have a function related to the QTL or genes within the regions that are not part of a large gene family. Based on their map position in the model species a number of genes are selected for marker development. To facilitate marker development, ESTs derived from the target species are analyzed using QualitySNP, PolySSR and other tools. Based on identified genetic variations in the selected genes, molecular markers can be developed for accurate fine-mapping of the QTL and ultimately identification of the gene underlying the QTL effect. The pipeline has been used to narrow the clubroot resistance QTL. The tool is available from the website http://www.bioinformatics.nl/tools/genetagger/ .
Finally, merits and shortcomings of the tools that have been developed as well as related bioinformatics questions that arose during these studies are discussed in Chapter 6.
Improving and assessing viral vectors for recombinant protein production in plants
Lacorte, C.C. - \ 2006
Wageningen University. Promotor(en): R.W. Goldbach, co-promotor(en): M.W. Prins. - [S.l.] : S.n. - ISBN 9085045398 - 119
planten - recombinant eiwitten - genetische vectoren - genexpressie - aardappelvirus x - tabaksmozaïekvirus - merkergenen - recombinant vaccins - plants - recombinant proteins - genetic vectors - gene expression - potato virus x - Tobacco mosaic virus - marker genes - recombinant vaccines
Epigenetics of the locomotory system in zebrafish
Meulen, T. van der - \ 2005
Wageningen University. Promotor(en): Johan van Leeuwen, co-promotor(en): Sander Kranenbarg; Henk Franssen. - Wageningen : - ISBN 9085043220 - 191
danio rerio - skeletspierstelsel - epigenetica - biologische ontwikkeling - ontogenie - merkergenen - lichaamsbeweging - biofysica - diermodellen - dierproeven - mechanische invloeden - musculoskeletal system - epigenetics - biological development - ontogeny - marker genes - exercise - biophysics - animal models - animal experiments - mechanical influences
Development of tools and strategies towards marker assisted selection and gene cloning
Brugmans, B.W. - \ 2005
Wageningen University. Promotor(en): Richard Visser, co-promotor(en): Herman van Eck. - [S.l.] : S.n. - ISBN 9085042275 - 120
plantenveredelingsmethoden - selectiemethoden - merkergenen - Solanum tuberosum - aardappelen - genetische merkers - plant breeding methods - selection methods - marker genes - potatoes - genetic markers
Molecular Characterisation of a Lettuce Germplasm Collection
Hintum, T.J.L. van - \ 2003
In: Proceedings of the Eucarpia Leafy Vegetables 2003, Proceedings of the Eucarpia Meeting on Leafy Vegetables Genetics and Breeding, Noordwijkerhout, the Netherlands, 19-21 March, 2003. - Wageningen : Centre for Genetic Resources - p. 99 - 104.
lactuca - germplasm - genenbanken - merkergenen - genetische bronnen - gene banks - marker genes - genetic resources
Marker-assisted introgression: speed at any cost
Stam, P. - \ 2003
In: Eucarpia Leafy Vegetables / Th.J.L. van Hintum, A. Lebeda, D. Pink, J.W. Schut [S.l.] : S.n. - p. 117 - 124.
genetische merkers - merkergenen - plantenveredeling - introgressie - genetic markers - marker genes - plant breeding - introgression
Conservation of genetic diversity : assessing genetic variation using marker estimated kinships
Eding, H. - \ 2002
Wageningen University. Promotor(en): E.W. Brascamp; T.H.E. Meuwissen. - S.l. : S.n. - ISBN 9789058085566 - 119
genetische diversiteit - genetische bronnen van diersoorten - genetische variatie - conservering - verwantschap - merkergenen - microsatellieten - rassen (dieren) - kwantitatieve genetica - genetic diversity - animal genetic resources - genetic variation - conservation - kinship - marker genes - microsatellites - breeds - quantitative genetics
<p>This dissertation focuses on assessing genetic diversity in a quantitative way through the use of Malecots coefficients of kinship. Kinships between and within populations and individuals can be estimated using microsatellite marker genes that are assumed to be selectively neutral.</p><p>Genetic diversity is estimated from such Marker Estimated Kinships (MEK) by (1 - average (MEK)), where genetic diversity of a set of breeds is defined as the maximum genetic variation in a population that can be bred from this set of breeds. The concept of core sets is applied to livestock genetic diversity and a new measure of genetic diversity present in a set of breeds, based on the mean kinship within a core set, is developed. Log-linear (mixed) models can be used to simultaneously estimate kinships and the probability for alleles alike in state (AIS). Error variance of the kinship estimates may lead to populations that have incorrectly received a null-contribution. An analysis of a data set concerning African cattle populations, using the developed methods is described. Effects of conservation by breed type or regional versus continental conservation are examined, in terms of efficiency of conservation and changes of priorities of breeds.</p>
Nutrigenomics, nieuwe mogelijkheden voor de voedingswetenschap
Kok, F.J. ; Schouten, E.G. - \ 2001
Voeding Nu 2 (2001). - ISSN 1389-7608 - p. 16 - 17.
merkergenen - genetische merkers - voedselwetenschappen - voedingsmiddelen - voedselanalyse - moleculaire biologie - interacties - genotype-voeding interactie - metabolisme - voedingsonderzoek bij de mens - voedselveiligheid - ziektepreventie - marker genes - genetic markers - food sciences - foods - food analysis - molecular biology - interactions - genotype nutrition interaction - metabolism - human nutrition research - food safety - disease prevention
Men verwacht dat het genomics-onderzoek ons inzicht in de werkingsmechanismen van voeding zal verbeteren. Het 'Centre for Human NutriGenomics' is een breed samenwerkingsverband tussen Wageningen Universiteit, Rikilt, Plant Research International, TNO Voeding, Universiteit Maastricht en het RIVM (http:www.nutrigenomics.nl)
Molecular aspects of growth and fruiting of the edible mushroom Agaricus bisporus
Groot, P.W.J. de - \ 1999
Radboud Universiteit Nijmegen. Promotor(en): L.J.L.D. van Griensven, co-promotor(en): J. Visser; P.J. Schaap. - Nijmegen : P.W.J. de Groot - ISBN 9789090123493 - 191
agaricus bisporus - paddestoelen - schimmelmorfologie - plantenontwikkeling - merkergenen - genkartering - mushrooms - fungal morphology - plant development - marker genes - gene mapping
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