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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    Genetic modification – applications
    Wiel, C.C.M. van de; Schaart, J.G. ; Lotz, L.A.P. - \ 2017
    Wageningen : Wageningen University & Research - 31
    cultivation - breeding - breeding methods - arable farming - horticulture - greenhouse horticulture - crosses - plant protection
    Genetische modificatie – toepassingen
    Wiel, C.C.M. van de; Schaart, J.G. ; Lotz, L.A.P. - \ 2017
    Wageningen : Wageningen University & Research - 29
    horticulture - greenhouse horticulture - arable farming - cultivation - genetic engineering - plant protection - crosses
    Production of interspecific Campanula hybrids by ovule culture: exploring the effecto of ovule isolation time
    Röper, A.C. ; Lütken, H. ; Christensen, B. ; Boutilier, K.A. ; Petersen, K.K. ; Müller, R. - \ 2015
    Euphytica 203 (2015). - ISSN 0014-2336 - p. 643 - 657.
    embryo rescue - inbreeding depression - breeding system - hybridization - incompatibility - trifolium - inheritance - phylogeny - endosperm - crosses
    The Campanula genus comprises several economically important ornamental plants species.Wide hybridisation is a method to increase phenotypic variability, but is limited due to interspecies hybridisation barriers.In this study we investigated whether ovule culture could be used to increase the success rate of interspecific hybridisation between C. portenschlagiana 9 C. poscharskyana and C. medium 9 C. formanekiana. The effect of different ovule isolation times on ovule germination in vitro was examined. In general, the number of collectible ovules and ovule germination was low. Interspecific hybrids between C. medium and C. formanekiana exhibited an increased number of viable ovules with later isolation time, but with different ovule germination rates. A parent-of-origin effect on both the number of collectible ovules and ovule germination was observed for C. medium 9 C. formanekiana. Histological analysis of embryo and endosperm development in collectible ovules isolated at different time points from interspecific crosses showed that the vast majority of ovules did not contain an embryo. When present, embryo development only progressed with ovule collection time in the C. medium and C. formanekiana crosses. The occurrence of miscoloured seedlings in interspecific crosses indicated incompatibilities between the parental lines that could not be prevented by reciprocal crossing. The low number of collectible ovules and germination rates might be inhibited due to fertilisation barriers.With this study, a protocol for ovule culture was established and the usefulness of ovule culture to obtain interspecific hybrids of selected Campanula species was demonstrated
    Naar een beter substraatgebruik in de champignonteelt via rassen : een genetische analyse
    Baars, J.J.P. ; Sonnenberg, A.S.M. - \ 2015
    Wageningen : Plant Research International (Rapport / Plant Research International 2015-2) - 20
    eetbare paddestoelen - agaricus bisporus - veredelen - kruisingen - stammen (biologisch) - genetische bronnen - segregatie - materialen uit biologische grondstoffen - substraten - edible fungi - agaricus bisporus - breeding - crosses - strains - genetic resources - segregation - biobased materials - substrates
    In 2014 is een nieuwe stap gezet in het project om tot een efficienter substraatgebruik te komen in de champignonteelt. Deze stap heeft twee doelen: • Het bepalen van de breeding value (hoe gedragen de stammen zich in kruisingen en welke waarde hebben ze dus in de veredeling) • Welke lijnen zijn geschikt om segregerende populaties te maken. Deze populaties zullen gebruikt worden om genomische gebieden/genen te vinden die de verschillen in efficientie in substraat gebruik kunnen verklaren. De kennis kan gebruikt worden voor zowel veredelen op substraatgebruik als het vinden van alternatieve grondstoffen voor het maken van substraat.
    Biologische efficiëntie substraatverbruik bij champignon : een genetische analyse
    Baars, J.J.P. ; Sonnenberg, A.S.M. - \ 2014
    Wageningen : Plant Research International, Business Unit Plant Breeding (Rapport / Plant Research International 2014-2) - 22
    agaricus - eetbare paddestoelen - substraten - cultuurmethoden - veredelingsmethoden - kruisingen - efficiëntie - agaricus - edible fungi - substrates - cultural methods - breeding methods - crosses - efficiency
    In 2013 is de tweede stap gezet in het project om tot een efficienter substraatgebruik te komen in de champignonteelt. Deze stap heeft twee doelen: Het bepalen van de breeding value (hoe gedragen de stammen zich in kruisingen en welke waarde hebben ze dus in de veredeling) Welke lijnen zijn geschikt om segregerende populaties te maken. Deze populaties zullen gebruikt worden om genomische gebieden/genen te vinden die de verschillen in efficientie in substraat gebruik kunnen verklaren. De kennis kan gebruikt worden voor zowel veredelen op substraatgebruik als het vinden van alternatieve grondstoffen voor het maken van substraat. Er is in 2013 een selectie gemaakt van negen wild-isolaten en één commerciëel ras van de champignon. Deze stammen dekken de hele variatie van de collectie van Plant Breeding in de efficiëntie van het substraatgebruik (uitgedrukt als g droge stof aan champignons per kg verbruikte organische stof) ook wel biologische effcientie genoemd (BE).
    Cytogenetic studies on meiotic chromosome behaviors in sterile Oriental x Trumpet lily
    Luo, J.R. ; Tuyl, J.M. van; Arens, P. ; Niu, L.X. - \ 2013
    Genetics and Molecular Research 12 (2013)4. - ISSN 1676-5680 - p. 6673 - 6684.
    immature hybrid embryos - u-type exchange - crosses - lilies - meiosis - culture - inversions - spindle - hybridization - aberrations
    In order to determine the reasons for pollen sterility in lily hybrids, four diploid sterile Oriental x Trumpet (OT) lily cultivars ('Nymph', 'Gluhwein', 'Yelloween', and 'Shocking') were used to investigate the meiotic chromosome behaviors in pollen mother cells (PMCs), using genomic in situ hybridization and conventional cytological methods. At metaphase I, chromosome associations were quite variable, not only among different genotypes but also in different PMCs of the same genotype. In addition to bivalents, a certain amount of univalent, trivalents, and quadrivalents were observed in all of the investigated genotypes. In addition, ring octavalents and ring hexavalents were observed in 'Nymph'. Even dodecavalents were observed in 'Nymph'. These abnormal chromosome associations at metaphase I implied the occurrence of chromosome interchanges (translocation) in these intersectional hybrids. At anaphase-telophase, a large number of laggard chromosomes and different kinds of chromosome bridge configurations were observed. At the tetrad stage, micronuclei and polyads were also found in many PMCs. All of these abnormal chromosome behaviors in PMCs were responsible for the pollen sterility in lily hybrids.
    Elucidation of intergenomic recombination and chromosome translocation: meiotic evidence from interspecific hybrids of Lilium through GISH analysis
    Xie, S.L. ; Ramanna, M.S. ; Visser, R.G.F. ; Arens, P. ; Tuyl, J.M. van - \ 2013
    Euphytica 194 (2013)3. - ISSN 0014-2336 - p. 361 - 370.
    resynthesized brassica-napus - homeologous recombination - lily hybrids - rearrangements - progenies - meiosis - crosses - plants - maps
    Intergenomic exchange has been found to be a normal phenomenon in sexual polyploids. In order to distinguish whether such exchanges are derived from intergenomic recombination or translocation, 13 genotypes of an interspecific hybrid, which were previously used as parents to generate sexual polyploids, were selected for a detailed meiosis analysis. In all genotypes under study, variable numbers of bivalents (0–12) resulting from homoeologous pairing were observed. But in two genotypes (006001-6 and 006001-13), a multivalent which was either a quadri- or a trivalent, as well as a bivalent involving two Asiatic chromosomes, was observed. Two Asiatic chromosomes in 006001-6 which were non-homologous were always found to be associated together, and formed trivalent or quadrivalent with chromosomes from homoeologous genome. This indicated that there was a duplication between these two Asiatic chromosomes. Such a duplication might have resulted from the segregation of a chromosomal translocation between two non-homologous chromosomes in the Asiatic parent ‘Connecticut King’ which was transmitted to the progeny (006001-6). With the exception of two genotypes, in 11 genotypes that formed variable frequencies of bivalents, the homoeologous chromosome pairing and chiasma formation were similar to that between homologous chromosomes. After from the analysis of anaphase I stages it was evident that the expected types of chiasma formation involving non-sister chromatids gave rise to two strand single, two strand double, three strand double, four strand double and multiple exchanges. Whereas these events resulted from locus specific homoeologous exchanges, the translocations resulted from an aberrant form of non-homologous chromosomal exchange of segments. Elucidation of such differences is only possible through the analysis of meiosis using GISH.
    Grote oogst aan nieuwe Buddleja
    Hop, M.E.C.M. - \ 2013
    De Boomkwekerij 25 (2013)4. - ISSN 0923-2443 - p. 23 - 23.
    buddleja davidii - houtachtige planten als sierplanten - rassen (planten) - cultivars - nieuwe soorten - plantenveredeling - kwaliteitscontroles - kruisingen - hybride rassen - buddleja davidii - ornamental woody plants - varieties - cultivars - new species - plant breeding - quality controls - crosses - hybrid varieties
    De sortimentsvernieuwing in Buddleja zit in een stroomversnelling. PPO testte het sortiment B. davidii en licht een tipje van de sluier op over de nieuwste rassen.
    Screening for new sources of resistance to Clavibacter michiganensis subsp. michiganensis (Cmm) in tomato
    Sen, Y. ; Zhu, F. ; Vandenbroucke, H. ; Wolf, J.M. van der; Visser, R.G.F. ; Heusden, A.W. van - \ 2013
    Euphytica 190 (2013)2. - ISSN 0014-2336 - p. 309 - 317.
    bacterial canker - corynebacterium-michiganense - lycopersicon-esculentum - ssp michiganensis - seeds - pcr - quantification - crosses
    Bacterial canker of tomato, caused by Clavibacter michiganensis subsp. michiganensis (Cmm), is considered the most serious bacterial threat, resulting in high damages in production areas. Worldwide, Cmm is subjected to quarantine regulations.There is no cultivar in market containing Cmm resistance genes. This project aimed to screen tomatoes or wild relatives of tomato for resistance to Cmm, to be used for starting breeding programs. We have screened 24 different wild accessions of tomato and found several new tolerant sources: Solanum pimpinellifolium GI.1554, S. parviflorum LA735 and S. parviflorum LA2072. We also confirmed the tolerance which was reported previously in S. peruvianum LA2157, S. peruvianum PI127829, S. peruvianum LA385, S. habrochaites LA407 and S. lycopersicum cv. IRAT L3. No immunity was found. Also accessions showing a low disease score still contained high titers of bacteria as determined by a dilution plating method, using tow selective media. These results were confirmed with a TaqMan real time PCR assay, which was developed to determine and quantify Cmm in planta
    Veredelingsonderzoek naar de ontwikkeling van virusresistente broei tulpen = Application of GISH-techniques in breeding research of virus resistant forcing tulips
    Tuyl, J.M. van - \ 2012
    Wageningen : Plant Research International - 27
    tulpen - plantenvirussen - chromosoomanalyse - genetische analyse - compatibiliteit - resistentie van variëteiten - plantenveredeling - kruisingen - forceren van planten - diagnostische technieken - tulips - plant viruses - chromosome analysis - genetic analysis - compatibility - varietal resistance - plant breeding - crosses - forcing - diagnostic techniques
    Door toepassing van Genomische in situ hybridisatie (GISH), een chromosoomkleuringstechniek bij de veredeling van virusresistente broeitulpen hebben aangetoond dat er een belangrijke doorbraak is bereikt. Het is bekend dat Tulipa fosteriana TBV resistentie bezit en doorgeeft aan de Darwin (GF) hybriden (T. gesneriana x T. fosteriana). Tot nu toe waren deze Darwin hybriden steriel en was introgressie van virus resistentie in het broeisortiment onmogelijk. In een project gericht op gestapelde resistenties bij tulp zijn echter GF hybriden gevonden met fertiliteit. Hieruit zijn diverse terugkruisingspopulaties (GGF) verkregen. Met behulp van GISH is van 99 GF-hybriden de genoomsamenstelling vastgesteld. 92 bleken inderdaad echte GF-hybriden te zijn. In GGF hybriden is aanzienlijke intergenomische recombinatie aangetoond. Dit toont aan dat door introgressie van T. fosteriana chromosoomsegmenten in het T. gesneriana genoom introgressie van virusresistentie mogelijk is. In een tweede terugkruisingsgeneratie van ‘Purissima’, een GF-hybride werd voortgaande introgressie aangetoond. In deze hybriden (G x GGF) bleek nog slechts 10% van het genoom afkomstig te zijn van T. fosteriana. In dit materiaal wordt in voortgaand TTI-onderzoek met behulp van moleculaire merkers de virus resistentie aangetoond.
    Characterization of tomato genes for resistance to Oidium neolycopersici
    Seifi Abdolabad, A.R. - \ 2011
    Wageningen University. Promotor(en): Richard Visser, co-promotor(en): Yuling Bai. - S.l. : s.n. - ISBN 9789085858799 - 140
    solanum lycopersicum - plantenziekteverwekkende schimmels - oidium - meeldauw - wilde verwanten - ziekteresistentie - plaagresistentie - verdedigingsmechanismen - genen - genexpressie - genetische kartering - kruisingen - solanum lycopersicum - plant pathogenic fungi - oidium - mildews - wild relatives - disease resistance - pest resistance - defence mechanisms - genes - gene expression - genetic mapping - crosses

    Tomato, Solanum lycopersicum, is a host for Oidium neolycopersici, the cause of powdery mildew (PM). Though cultivated tomatoes are susceptible to PM, resistance is reported in wild Solanum species. By screening wild tomato species, nine loci conferring resistance to PM have been identified, namely Ol-1, ol-2, Ol-3, Ol-4, Ol-5, Ol-6, Ol-qtl1, Ol-qtl2, andOl-qtl3. These genes are located on different chromosomes and mediate different levels of resistance by different mechanisms. In this thesis we mainly focused on the Ol genes located on chromosome 6 (Ol-1, Ol-4, Ol-5 and Ol-6) with the aim to fine-map and eventually clone these genes. In addition, we studied the contribution of different phytohormone pathways to the resistance mediated by Ol-1, ol-2, Ol-4 and Ol-qtls.

    We first focused on the Ol genes on the short arm of tomato chromosome 6, Ol-4 originating from S. peruvianum LA2172 and Ol-6 with unknown origin (Chapter 2). We showed that Ol-4 and Ol-6 are homologues of the Mi-1 gene.

    On the short arm of tomato chromosome 6, the Mi-1gene cluster is about 400 Kb in size and consists of several other genes besides the Mi-1 homologues. There are transport inhibitor responses-like (TIR-like) genes embedded in this cluster. Interestingly, the copy number of these TIR-like genes in the nematode-resistant tomatoes is less than that in nematode-susceptible ones (Chapter 3). Furthermore, lower expression of these TIR-like genes was observed in roots, but not in leaves, of nematode-resistant plants compared to nematode-susceptible plants. These observations prompted us to suggest and to discuss two different scenarios explaining how TIR-like genes could play a role in the plant response to root-knot nematodes.

    Then, we studied the Ol-1 and Ol-5, which are located on the long arm of chromosome 6, and originated from different S. habrochaites accessions. Ol-1 is closely linked to Ol-5. With fine-mapping, we narrowed down this locus to a 73 Kb interval which contains at least 10 putative genes. Interestingly we observed an interaction between chromosome regions harboring Ol-1 and Ol-5, indicating that the interaction between Ol-1 and Ol-5 is needed to confer PM resistance. Both Ol-1 and Ol-5 trigger delayed cell death that is distinguishable from hypersensitive response (HR), the hallmark of R gene response to biotrophic pathogens. The delayed cell death associated with Ol-1 and Ol-5 resembles the autophagic PCD. We observed that Ol-1 and Ol-5 were both required for on-time and effective cell death to stop PM. If one of these two genes was not present, cell deathcould not happen or not be effective enough to stop pathogen growth.

    Finally, we investigated the involvement of phytohormone pathways in PM resistance conferred by the Olgenes, including Ol-1, ol-2, Ol-4 and Ol-qtls (Chapter 5). There is overwhelming evidence implicating plant hormones in plant responses to pathogens. In this experiment we, in addition to Ol-1 and Ol-4, included other resistance loci for PM resistance in tomato. The first one is ol-2, a homologue of the barley mlo gene and derived from S. lycopersicum var cerasiforme LA1230. This gene confers resistance to PM by triggering callose deposition and, thereby, cell wall fortification. The other is Ol-qtls, a combination of three QTLs for PM resistance associated with both delayed cell deathand callose deposition. NILs carrying Ol-1, ol-2, Ol-4 and Ol-qtls, plus the background of these NILs (S. lycopersicum cv Moneymaker, MM), provided us the possibility to compare the involvement of hormonal pathways in different kinds of tomato responses. These responses include basal defense, cell wall fortification, delayed cell death,and HR. We quantified the expression of marker genes for the pathways of salicylic acid (SA), jasmonic acid (JA), abscisic acid (ABA), and ethylene (ET) over a time-course after inoculation with PM. As a complementary approach, we crossed our NILs with tomato mutants for JA, ET and ABA. Our results suggested that Ol-4-mediated resistance probably relies on the SA pathway. Ol-1 and Ol-qtls require ET to promote the delayed cell deathfor PM resistance. JA deficiency can compromise resistance mediated by ol-2. Our results also suggested that ABA is required for those interactions demanding callose deposition, resistance associated with ol-2 and Ol-qtls. These results present a nice example of the involvement of different phytohormones in different phases of resistance against PM in tomato. Altogether, this thesis describes different tomato resistance mechanisms triggered by different resistance genes in the same pathosystem, underscoring the plant ability to adopt diverse molecular mechanisms to defense itself against intruders.

    Basal resistance of barley to adapted and non-adapted forms of Blumeria graminis
    Aghnoum, R. - \ 2009
    Wageningen University. Promotor(en): Richard Visser, co-promotor(en): Rients Niks. - [S.l. : S.n. - ISBN 9789085854197 - 132
    hordeum vulgare - gerst - blumeria - blumeria graminis - ziekteresistentie - verdedigingsmechanismen - genetische analyse - loci voor kwantitatief kenmerk - puccinia hordei - kruisingen - plantenveredeling - resistentieveredeling - hordeum vulgare - barley - blumeria - blumeria graminis - disease resistance - defence mechanisms - genetic analysis - quantitative trait loci - puccinia hordei - crosses - plant breeding - resistance breeding
    In the barley-Blumeria interaction, resistance at penetration stage in association with papilla formation is a commonly occurring mechanism. This mechanism of defense reduces the infection severity by adapted powdery mildew pathogen (basal resistance to Blumeria graminis f.sp. hordei, Bgh) and fully protects the plant against non-adapted powdery mildew pathogens (non-host resistance to non-adapted forms of B. graminis). In this thesis we followed an integrated approach based on QTL mapping and candidate gene analysis. It was our objective to determine which of the known candidate genes have a map position that coincides with one of the QTLs detected in our mapping study. Such candidate genes might determine the natural variation of basal resistance against powdery mildew in barley. We also investigated whether the genotypic variation in level of resistance of barley to the non-adapted wheat powdery mildew, B. graminis f.sp. tritici (Bgt) could be used to develop an experimental line to determine the inheritance of non-host resistance of barley to this pathogen. Finally we aimed to determine whether the basal resistance of barley to powdery mildew is being suppressed by prior attack by a different pathogenic haustorium forming fungus, Puccinia hordei.
    Chapter 1 presents an introduction about basal resistance of barley to powdery mildew and briefly lists evidence on molecular associations between basal, mlo-mediated and non-host resistance. In Chapter 2, we performed QTL analysis for powdery mildew resistance at seedling and at adult plant stage in six mapping populations of barley. In that analysis quantitative resistance of barley to powdery mildew was found to be based on a large number of genes, with only few detected in more than one mapping population. These QTLs for powdery mildew resistance in barley are mainly plant growth stage dependent. From gene-expression, gene silencing and transient transformation assays 39 genes emerged that increased or decreased basal resistance of barley to the powdery mildew fungus. They are considered candidate genes that might be responsible for natural variation in level of basal resistance. By looking for polymorphism in those genes, we could determine the map position of 23 of these candidate genes. Mapping positions of three more genes, mlo, Ror1 and Ror2, were already available, and these were also considered as candidate genes in our study.To compare the map position of QTLs in different mapping populations with the map positions of the 26 candidate genes, we constructed an improved high-density integrated linkage map of barley. This improved map was based on the marker data of seven mapping populations of barley. More than 43% of the markers on our improved integrated map target ESTs or gene sequences (gene-targeted markers, GTM) and can be used for candidate gene identification. Six out of the 26 candidate genes co-localized with QTLs for basal powdery mildew resistance. They are interesting targets for further studies, since their allelic forms may be responsible for part of the differences in basal resistance between the parents in our mapping study. Chapter 3 reports the development of two experimental barley lines with extremely high and low level of basal resistance to barley powdery mildew. These lines were obtained by convergent crossing between the most resistant and the most susceptible lines, respectively, from four mapping populations of barley studied in Chapter 2. We consider the extremely susceptible and resistant lines developed here as valuable material to be used in further experiments to characterize the molecular basis of basal resistance to powdery mildew. The results suggest that phenotypic selection is sufficiently efficient to achieve high levels of basal resistance. We report some difficulties in the application of marker assisted selection that might make that approach unnecessary and less efficient to achieve a similar high level of basal resistance. In Chapter 4 the development of two more experimental lines is described. These lines have, at the seedling stage an unprecedented level of susceptibility to the non-adapted wheat powdery mildew. A large collection of barley germplasm was screened and some rare barley accessions were identified with rudimentary susceptibility to the wheat powdery mildew, Bgt. Those accessions were intercrossed in two cycles, and resulted in the two exceptional research lines, called SusBgt SC and SusBgt DC. The quantitative variation among barley accessions and in the progenies after convergent crossing suggest a polygenic basis of this non-host resistance. Component analysis of the infection process suggested that non-host resistance factors are Blumeria-form specific. The developed lines will serve to elucidate the genetic basis of non-host resistance in barley to wheat powdery mildew, and are useful tools in gene expression and complementation studies on non-host resistance. In Chapter 5 we reported that a compatible interaction of barley-Puccinia hordei induces increased papilla based resistance to a challenge infection by a compatible powdery mildew isolate. These pathogens differ in strategies to suppress plant cell defense. We showed that the level of rust-induced mildew resistance varies among barley accessions and is not determined by the virulent/avirulent spectra of the challenger isolate. Macroarray gene expression analysis showed that several genes involved in metabolism and photosynthesis were highly down-regulated and a few genes involved in plant defense including a pathogenesis related protein (PR-1) and cysteine synthase were highly up-regulated in the double inoculated treatment. Our histological and gene expression analyses are compatible with the hypothesis that the rust “primes” the basal mildew resistance genes prior to the challenge mildew infection. In Chapter 6, the results obtained in the previous Chapters are being discussed. The perspectives of the experimental barley lines that were developed in this study for the identification of genes that determine basal resistance of barley to adapted and non-adapted Blumeria graminis forms are highlighted.

    "Duurzame resistentie komt binnen handbereik"
    Graaf, J. de; Schouten, H.J. - \ 2009
    Milieu : opinieblad van de Vereniging van Milieuprofessionals 15 (2009)1. - ISSN 1873-5436 - p. 6 - 7.
    plaagresistentie - appels - aardappelen - verbetering - natuurlijke immuniteit - kruisingen - pest resistance - apples - potatoes - improvement - natural immunity - crosses
    Volgens Dr. Henk Schouten, verbonden aan Wageningen Universiteit en Research Centre, zijn resistente appels en aardappels binnen handbereik door natuurlijke genen in te brengen. Hij verwacht dat over zes jaar de eerste onbespoten aardappels op tafel staan. De belangrijkste hinderpaal is de achterlopende regelgeving. "Als daar een oplossing voor komt, ligt verduurzaming van allerlei teelten binnen handbereik", aldus Henk Schouten
    QTL mapping designs for aquaculture.
    Massault, C. ; Bovenhuis, H. ; Haley, C.S. ; Koning, D.J. de - \ 2008
    Aquaculture 285 (2008)1-4. - ISSN 0044-8486 - p. 23 - 29.
    quantitative-trait loci - outbred populations - complex traits - linkage maps - marker loci - power - sib - crosses - l.
    Rapid development of genomics technology is providing new opportunities for genetic studies, including QTL mapping, in many aquaculture species. This paper investigates the strengths and limitations of QTL mapping designs for fish and shellfish under three different controlled breeding schemes. For each controlled breeding scheme, the potential and limitations are described for typical species and are illustrated by three different designs using interval mapping. The results show that, regardless of the species, the family structure is extremely important in experimental designs. The heritability of the QTL (controlled by its allele frequency and effect on the trait) also has an important impact on the power to detect QTL, while the overall polygenic heritability of the trait is less important. Marker density does not greatly affect the power when the distance between markers is less than 10 cM; but ideally spacing should not exceed 20 cM. For each of the systems studied, it is possible to design an experiment that would have an 80% power to detect a QTL of moderate effect (explaining between 1.5 and 5% of the trait variation) by genotyping 1000 or fewer individuals.
    Toetsing van afspraken over coëxistentie van genetisch gemodificeerde (GG) en niet-GG maïsproductie in Nederland : resultaten van metingen aan de mate van vermenging door uitkruising onder praktijkomstandigheden in 2006 en 2007
    Wiel, C.C.M. van de; Dolstra, O. ; Groeneveld, R.M.W. ; Kok, E.J. ; Scholtens-Toma, I.M.J. ; Thissen, J.T.N.M. ; Lotz, L.A.P. ; Smulders, M.J.M. - \ 2008
    Wageningen : Plant Research International (Rapport / Plant Research International 184) - 24
    zea mays - maïs - rassen (planten) - kruisingen - monitoring - registreren - genetische modificatie - transgene planten - proeven - onderzoek - zea mays - maize - varieties - crosses - monitoring - recording - genetic engineering - transgenic plants - trials - research
    Resultaten van metingen aan de mate van vermenging door uitkruising in een praktijktoets in de jaren 2006 en 2007 tussen transgene en conventionele maïsteelten op isolatieafstand van 25 m
    Intergenomic recombination and introgression breeding in Longiflorum x Asiatic lilies
    Shujun Zhou, - \ 2007
    Wageningen University. Promotor(en): Richard Visser, co-promotor(en): Jaap van Tuyl. - [S.l.] : S.n. - ISBN 9789085046370 - 110
    lilium - introgressie - plantenveredeling - recombinatie - sporogenie - soortkruising - genomen - kruisen - kruisingen - lilium - introgression - plant breeding - recombination - sporogony - interspecific hybridization - genomes - crossing - crosses
    Lily, one of the economically most important ornamental crops, belongs to the genus Lilium of the family Liliaceae. There are about 80 species in Lilium which are categorized into seven sections, i.e., Lilium, Martagon, Pseudolirium, Archelirion, Sinomartagon, Leucolirion and Oxypetala. Usually, it is not so difficult to cross between the species within each section and the hybrids are fertile. However, it is very difficult to cross the species belonging to different sections. With cut style pollination followed by embryo rescue techniques, such distant interspecific crosses can be possible, but the hybrids are highly sterile. All modern lily cultivars have originated from hybridization among wild lily species. The three main lily cultivar groups, viz., Longiflorum, Asiatic and Oriental, originated from hybridization within one section, i.e., Leucolirion, Sinomartagon and Archelirion respectively. Up to now, about 150 Longiflorum, 4000 Asiatic cultivars, and 2000 Oriental cultivars have been registered. The genomes of Longiflorum (Leucolirion), Asiatic (Sinomartagon) and Oriental (Archelirion) are represented as L (Longiflorum), A (Asiatic) and O (Oriental) genome respectively. They possess quite different valuable traits, and one of the main goals of modern lily breedingareto combine the three distinctive groups in new cultivars. 

    In this thesis, crosses among diploid Asiatic and Longiflorum cultivars, diploid F1 LA hybrids, triploid BC1 cultivars, allotetraploidand allopentaploid lilies were made. 11 diploid F1 LA hybrids and 19 triploids BC1 cultivars which were supplied by the Dutch lily breeding companies, and 23 new BC1, five BC2 and seven BC3 progenies were analyzed with conventional cytological methods, flow cytometry and genomic in situ hybridization.

    The configurations of metaphase I during meioses of the F1 LA hybrids are quantitatively variable, ranging from no bivalent to 12 bivalents in different pollen mother cells. This implies that LA hybrids have abnormal meiosis and normal meiosis, and indicates that LA hybrids have possibilities to produce aneuploid gametes, 2n gametes and n gametes (Chapter 2). Because the bivalents disjoin and the univalents divide simultaneously at anaphase I of the observed pollen mother cells, it is concluded that F1 LA hybrids have more potential to produce IMR 2n gametes than FDR 2n gametes I (Chapter 2). However, most of the BC1 progenies result from FDR 2n gametes and less from IMR 2n gametes. Probably, FDR 2n gametes have better viability than IMR 2n gametes because of chromosome and gene imbalance in the latter (Chapters 3 & 4).

    Besides the mode of 2n gamete formation, some crossover events, e.g., single, threestranddouble, four strand double, four strand triple crossover, etc, are clearly elucidated based on the GISH results from anaphase I of F1 LA hybrids (Chapter 2). The intergenomic recombinant chromosomes of triploid BC1 progenies mainly originate from single crossover (Chapters 3 & 4). The intergenomic recombinant chromosomes caused by other crossover events are confirmed in diploid BC1 progenies (Chapter 4).

    Based on GISH analysis of 19 BC1 cultivars from the Dutch lily breeding companies, 17 of the BC1 cultivars are eutriploid and two hypertriploid (Chapter 3). Nevertheless, among 45 new BC1 progenies, 10 of them are diploid, while the others are triploid (Chapter 4). This is the first reported finding that LA hybrid can produce functional haploid gametes. This finding might be valuable for lily introgression breeding.

    Only limited BC2 progenies, which originated from crosses between triploid BC1 cultivars and diploid Asiatic cultivars, were analyzed with GISH. They were predominantly diploid and they contained very few Longiflorum chromosomes or segments (Chapter 5).

    Allopentaploid lilies have relatively good male fertility as determined from their pollen germination. They were successfully crossed with Asiatic cultivars and Longiflorum cultivars. Most of the BC3 progenies were pseudoeuploids that possessed euploid chromosome numbers (2n=3x=36) but the parental genomes were aneuploid as a result of chromosome substitutions. Apart from this, one aneuploid (2n=3x+1=37) was also present. Both the pseudoeuploids and the aneuploids might contribute to genetic variation and are potentially useful for selection.   

    Based on the results of lily interploid crosses (2x-3x, 2x-4x, 2x-5x and their reciprocals), diploid, triploid, tetraploid, and pentaploid lilies could be used as male parents when they had some degree of male fertility. Most diploid and triploid lilies could be used as female parents regardless of their male fertility. On the contrary, allotetraploid and allopentaploid lilies could hardly be used as female parents even though they had good fertility as estimated from pollen germination tests. The success and failure of interploid crosses in lilies depends on the viability of the gametes and the ploidy level of the secondary nucleus. From the process of tetrasporic eight-nucleate embryo sac formation in Lilium , it is derived that diploid, triploid, tetraploid, and pentaploid lilies produce tetraploid, hexaploid, octaploid and decaploid secondary nuclei in their embryo sacs respectively. Thus, It is suggested that tetraploid secondary nucleus might be ideal for lily endosperm development; hexaploid secondary nucleus are acceptable; but octaploid or higher secondary nuclei are not ideal (Chapter 5).

    The difference between 2x-4x and 4x-2x or 2x-5x and 5x-2x is obvious, because one was successful and the other not. A clear difference was also observed between 2x-3x and 3x-2x and between AA x LA and LA x AA. The difference is possibly caused by the frequency of functional gametes, ploidy level of endosperm and the interaction between embryo development and endosperm development (Chapter 5).

    2n gametes and n gametes might play different roles in lily breeding. The former is more useful for polyploid breeding; the latter may be valuable for introgression breeding. We could not over- or underestimate either of them, because the LA hybrids which could produce functional 2n gametes or n gametes are very limited. Especially, it is more difficult to find LA hybrids which produce functional n gametes. The advantages of 2n gametes over mitotic doubling in lily breeding have been well confirmed (Chapters 3 and 4). One of the further tasks is how to use the LA hybrids which produce viable n gametes in lily breeding.
    Mapping QTLs and QTL x environment interaction for CIMMYT maize drought stress program using factorial regression and partial least squares methods
    Vargas, M. ; Eeuwijk, F.A. van; Crossa, J. ; Ribaut, J.M. - \ 2006
    Theoretical and Applied Genetics 112 (2006)6. - ISSN 0040-5752 - p. 1009 - 1023.
    quantitative trait loci - marker-assisted selection - tropical maize - flanking markers - genotype - identification - interval - strategies - components - crosses
    The study of QTL x environment interaction (QEI) is important for understanding genotype x environment interaction (GEI) in many quantitative traits. For modeling GEI and QEI, factorial regression (FR) models form a powerful class of models. In FR models, covariables (contrasts) defined on the levels of the genotypic and/or environmental factor(s) are used to describe main effects and interactions. In FR models for QTL expression, considerable numbers of genotypic covariables can occur as for each putative QTL an additional covariable needs to be introduced. For large numbers of genotypic and/or environmental covariables, least square estimation breaks down and partial least squares (PLS) estimation procedures become an attractive alternative. In this paper we develop methodology for analyzing QEI by FR for estimating effects and locations of QTLs and QEI and interpreting QEI in terms of environmental variables. A randomization test for the main effects of QTLs and QEI is presented. A population of F-2 derived F-3 families was evaluated in eight environments differing in drought stress and soil nitrogen content and the traits yield and anthesis silking interval (ASI) were measured. For grain yield, chromosomes 1 and 10 showed significant QEI, whereas in chromosomes 3 and 8 only main effect QTLs were observed. For ASI, QTL main effects were observed on chromosomes 1, 2, 6, 8, and 10, whereas QEI was observed only on chromosome 8. The assessment of the QEI at chromosome 1 for grain yield showed that the QTL main effect explained 35.8% of the QTL + QEI variability, while QEI explained 64.2%. Minimum temperature during flowering time explained 77.6% of the QEI. The QEI analysis at chromosome 10 showed that the QTL main effect explained 59.8% of the QTL + QEI variability, while QEI explained 40.2%. Maximum temperature during flowering time explained 23.8% of the QEI. Results of this study show the possibilities of using FR for mapping QTL and for dissecting QEI in terms of environmental variables. PLS regression is efficient in accounting for background noise produced by other QTLs.
    Progenies of allotriploids of Oriental x Asiatic lilies (Lilium) examined by GISH analysis
    Barba Gonzalez, R. ; Silfhout, A.A. van; Visser, R.G.F. ; Ramanna, M.S. ; Tuyl, J.M. van - \ 2006
    Euphytica 151 (2006)2. - ISSN 0014-2336 - p. 243 - 250.
    nuclear-dna amounts - lily hybrids - crosses - recombination - culture - angiosperms - narcissus - liliaceae
    With the aim of utilizing allotriploid (2n = 3x = 36) lily hybrids (Lilium) in introgression breeding, different types of crosses were made. First, using diploid Asiatic lilies (2n = 2x = 24), reciprocal crosses (3x ¿ 2x and 2x ¿ 3x) were made with allotriploid hybrids (AOA) obtained by backcrosses of F1 Oriental × Asiatic hybrids (OA) to Asiatic cultivars (A). Secondly, the AOA allotriploids were crossed with allotetraploid (OAOA, 2n = 4x = 48), in 3x ¿ 4x combination. Finally, the AOA allotriploids where crossed to 2n gamete producer F1 OA hybrids (3x ¿ 2x (2n)). Two types of triploids were used as parents in the different types of crosses, derived from: (a) mitotic polyploidization and (b) sexual polyploidization. Ploidy level of the progeny was determined by estimating the DNA values through flowcytometry as well as chromosome counting. The aneuploid progeny plants from 3x ¿ 2x and reciprocal crosses had approximate diploid levels and in 3x ¿ 4x crosses and 3x ¿ 2x (2n) the progeny had approximate tetraploid levels. Balanced euploid gametes (x, 2x and 3x) were formed in the AOA genotypes. Recombinant chromosomes were found in the progenies of all crosses, except in the case of 2x ¿ 3x crosses through genomic in situ hybridization (GISH) analyses. Recombinant chromosomes occurred in the F1 OA hybrid when the triploid AOA hybrid was derived through sexual polyploidization, but not through mitotic polyploidization with two exceptions. Those recombinant chromosomes were transmitted to the progenies in variable frequencies.
    QTL analysis of cadmium and zinc accumulation in the heavy metal hyperaccumulator Thlaspi caerulescens
    Deniau, A.X. ; Pieper, B. ; Bookum, W.M. ten; Lindhout, P. ; Aarts, M.G.M. - \ 2006
    Theoretical and Applied Genetics 113 (2006)5. - ISSN 0040-5752 - p. 907 - 920.
    linkage maps - arabidopsis-thaliana - aflp markers - construction - populations - tolerance - crosses - genes - brassicaceae - transport
    Thlaspi caerulescens (Tc; 2n = 14) is a natural Zn, Cd and Ni hyperaccumulator species belonging to the Brassicaceae family. It shares 88% DNA identity in the coding regions with Arabidopsis thaliana (At) (Rigola et al. 2006). Although the physiology of heavy metal (hyper)accumulation has been intensively studied, the molecular genetics are still largely unexplored. We address this topic by constructing a genetic map based on AFLP® markers and expressed sequence tags (ESTs). To establish a genetic map, an F2 population of 129 individuals was generated from a cross between a plant from a Pb/Cd/Zn-contaminated site near La Calamine, Belgium, and a plant from a comparable site near Ganges (GA), France. These two accessions show different degrees of Zn and, particularly, Cd accumulation. We analyzed 181 AFLP markers (of which 4 co-dominant) and 13 co-dominant EST sequences-based markers and mapped them to seven linkage groups (LGs), presumably corresponding to the seven chromosomes of T. caerulescens. The total length of the genetic map is 496 cM with an average density of one marker every 2.5 cM. This map was used for Quantitative Trait Locus (QTL) mapping in the F2. For Zn as well as Cd concentration in root we mapped two QTLs. Three QTLs and one QTL were mapped for Zn and Cd concentration in shoot, respectively. These QTLs explain 23.8¿60.4% of the total variance of the traits measured. We found only one common locus (LG6) for Zn and Cd (concentration in root) and one common locus for shoot and root concentrations of Zn (LG1) and of Cd (LG3). For all QTLs, the GA allele increased the trait value except for two QTLs for Zn accumulation in shoot (LG1 and LG4) and one for Zn concentration in root (LG1).
    Unique genomic configuration revealed by microsatellite DNA in polyploid dogroses, Rosa sect.Caninae.
    Nybom, H. ; Esselink, G.D. ; Werlemarkt, G. ; Leus, I.E. ; Vosman, B.J. - \ 2006
    Journal of Evolutionary Biology 19 (2006)2. - ISSN 1010-061X - p. 635 - 648.
    skewed distribution - molecular markers - origin - evolution - l. - inheritance - apomixis - behavior - complex - crosses
    An allopolyploid complex with high genomic integrity has been studied. Dogroses transmit only seven chromosomes (from seven bivalents) through the pollen, whereas 21, 28 or 35 chromosomes (from seven bivalents and 14, 21 or 28 univalents) come from the egg cells. Seedlings derived from two interspecific crosses were analysed with flow cytometry and molecular markers to determine ploidy level, mode of reproduction and genomic constitution. Evidence was obtained for the formation of unreduced male and female gametes, which can take part in fertilization (producing seedlings with higher ploidy than the parental plants) or in apomictic reproduction. Random amplified polymorphic DNA (RAPD) and microsatellite analyses indicated that three seedlings (5%) were derived through apomixis, whereas the other 49 were hybrids. Bivalent formation appears to involve chromosomes that consistently share the same microsatellite alleles. Allele-sharing between the maternally transmitted and highly conserved univalent-forming chromosomes reflected the taxonomic distance between different genotypes. The frequently recombining bivalent-forming chromosomes were taxonomically less informative
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