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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Fluorescent in situ hybridization shows DIPLOSPOROUS located on one of the NOR chromosomes in apomictic dandelions (Taraxacum) in the absence of a large hemizygous chromosomal region
Vasut, R.J. ; Vijverberg, K. ; Dijk, P.J. van; Jong, J.H.S.G.M. de - \ 2014
Genome 57 (2014)11-12. - ISSN 0831-2796 - p. 609 - 620.
genomic region - pennisetum-squamulatum - cenchrus-ciliaris - transposable elements - bdelloid rotifers - sequence-analysis - paspalum-simplex - gamete formation - mapping reveals - apomixis
Apomixis in dandelions (Taraxacum: Asteraceae) is encoded by two unlinked dominant loci and a third yet undefined genetic factor: diplosporous omission of meiosis (DIPLOSPOROUS, DIP), parthenogenetic embryo development (PARTHENOGENESIS, PAR), and autonomous endosperm formation, respectively. In this study, we determined the chromosomal position of the DIP locus in Taraxacum by using fluorescent in situ hybridization (FISH) with bacterial artificial chromosomes (BACs) that genetically map within 1.2-0.2 cM of DIP. The BACs showed dispersed fluorescent signals, except for S4-BAC 83 that displayed strong unique signals as well. Under stringent blocking of repeats by C(0)t-DNA fragments, only a few fluorescent foci restricted to defined chromosome regions remained, including one on the nucleolus organizer region (NOR) chromosomes that contains the 45S rDNAs. FISH with S4-BAC 83 alone and optimal blocking showed discrete foci in the middle of the long arm of one of the NOR chromosomes only in triploid and tetraploid diplosporous dandelions, while signals in sexual diploids were lacking. This agrees with the genetic model of a single dose, dominant DIP allele, absent in sexuals. The length of the DIP region is estimated to cover a region of 1-10 Mb. FISH in various accessions of Taraxacum and the apomictic sister species Chondrilla juncea, confirmed the chromosomal position of DIP within Taraxacum but not outside the genus. Our results endorse that, compared to other model apomictic species, expressing either diplospory or apospory, the genome of Taraxacum shows a more similar and less diverged chromosome structure at the DIP locus. The different levels of allele sequence divergence at apomeiosis loci may reflect different terms of asexual reproduction. The association of apomeiosis loci with repetitiveness, dispersed repeats, and retrotransposons commonly observed in apomictic species may imply a functional role of these shared features in apomictic reproduction, as is discussed.
Birth, death, and diversification of mobile promoters in prokaryotes
Passel, M.W.J. van; Nijveen, H. ; Wahl, L.M. - \ 2014
Genetics 197 (2014)1. - ISSN 0016-6731 - p. 291 - 299.
branching-process model - transposable elements - population-genetics - sequence evolution - escherichia-coli - dna - genomes - innovation - conversion - selection
A previous study of prokaryotic genomes identified large reservoirs of putative mobile promoters (PMPs), that is, homologous promoter sequences associated with nonhomologous coding sequences. Here we extend this data set to identify the full complement of mobile promoters in sequenced prokaryotic genomes. The expanded search identifies nearly 40,000 PMP sequences, 90% of which occur in noncoding regions of the genome. To gain further insight from this data set, we develop a birth–death–diversification model for mobile genetic elements subject to sequence diversification; applying the model to PMPs we are able to quantify the relative importance of duplication, loss, horizontal gene transfer (HGT), and diversification to the maintenance of the PMP reservoir. The model predicts low rates of HGT relative to the duplication and loss of PMP copies, rapid dynamics of PMP families, and a pool of PMPs that exist as a single copy in a genome at any given time, despite their mobility. We report evidence of these “singletons” at high frequencies in prokaryotic genomes. We also demonstrate that including selection, either for or against PMPs, was not necessary to describe the observed data.
Chromosomal organizations of major repeat families on potato (Solanum tuberosum) and further exploring in its sequenced genome
Tang, X. ; Datema, E. ; Olortegui Guzman, M.C. ; Boer, J.M. de; Eck, H.J. van; Bachem, C.W.B. ; Visser, R.G.F. ; Jong, H. de - \ 2014
Molecular Genetics and Genomics 289 (2014)6. - ISSN 1617-4615 - p. 1307 - 1319.
ty1-copia group retrotransposons - species-specific sequences - repeated dna-sequences - in-situ hybridization - somatic hybrids - lycopersicon-esculentum - satellite repeat - repetitive dna - transposable elements - metaphase chromosomes
One of the most powerful technologies in unraveling the organization of a eukaryotic plant genome is high-resolution Fluorescent in situ hybridization of repeats and single copy DNA sequences on pachytene chromosomes. This technology allows the integration of physical mapping information with chromosomal positions, including centromeres, telomeres, nucleolar-organizing region, and euchromatin and heterochromatin. In this report, we established chromosomal positions of different repeat fractions of the potato genomic DNA (Cot100, Cot500 and Cot1000) on the chromosomes. We also analysed various repeat elements that are unique to potato including the moderately repetitive P5 and REP2 elements, where the REP2 is part of a larger Gypsy-type LTR retrotransposon and cover most chromosome regions, with some brighter fluorescing spots in the heterochromatin. The most abundant tandem repeat is the potato genomic repeat 1 that covers subtelomeric regions of most chromosome arms. Extensive multiple alignments of these repetitive sequences in the assembled RH89-039-16 potato BACs and the draft assembly of the DM1-3 516 R44 genome shed light on the conservation of these repeats within the potato genome. The consensus sequences thus obtained revealed the native complete transposable elements from which they were derived
Sex or no sex: Evolutionary adaptation occurs regardless
Seidl, M.F. ; Thomma, B.P.H.J. - \ 2014
Bioessays 36 (2014)4. - ISSN 0265-9247 - p. 335 - 345.
horizontal gene-transfer - double-strand breaks - yeast candida-glabrata - genome evolution - transposable elements - saccharomyces-cerevisiae - mitotic recombination - avirulence gene - homologous recombination - cryptococcus-neoformans
All species continuously evolve to adapt to changing environments. The genetic variation that fosters such adaptation is caused by a plethora of mechanisms, including meiotic recombination that generates novel allelic combinations in the progeny of two parental lineages. However, a considerable number of eukaryotic species, including many fungi, do not have an apparent sexual cycle and are consequently thought to be limited in their evolutionary potential. As such organisms are expected to have reduced capability to eliminate deleterious mutations, they are often considered as evolutionary dead ends. However, inspired by recent reports we argue that such organisms can be as persistent as organisms with conventional sexual cycles through the use of other mechanisms, such as genomic rearrangements, to foster adaptation.
Epigenetic variation in asexually reproducing organisms
Verhoeven, K.J.F. ; Preite, V. - \ 2014
Evolution 68 (2014)3. - ISSN 0014-3820 - p. 644 - 655.
dna methylation - arabidopsis-thaliana - japanese knotweed - transgenerational plasticity - phenotypic plasticity - transposable elements - natural-populations - fallopia-japonica - mutation-rates - clonal plants
The role that epigenetic inheritance can play in adaptation may differ between sexuals and asexuals because (1) the dynamics of adaptation differ under sexual and asexual reproduction and the opportunities offered by epigenetic inheritance may affect these dynamics differently; and (2) in asexual reproduction epigenetic reprogramming mechanisms that are associated with meiosis can be bypassed, which could promote the buildup of epigenetic variation in asexuals. Here, we evaluate current evidence for an epigenetic contribution to adaptation in asexuals. We argue that two aspects of epigenetic variation should have particular relevance for asexuals, namely epigenetics-mediated phenotypic plasticity within and between generations, and heritable variation via stochastic epimutations. An evaluation of epigenetic reprogramming mechanisms suggests that some, but not all, forms of asexual reproduction enhance the likelihood of stable transmission of epigenetic marks across generations compared to sexual reproduction. However, direct tests of these predicted sexual–asexual differences are virtually lacking. Stable transmission of DNA methylation, transcriptomes, and phenotypes from parent to clonal offspring are demonstrated in various asexual species, and clonal genotypes from natural populations show habitat-specific DNA methylation. We discuss how these initial observations can be extended to demonstrate an epigenetic contribution to adaptation.
Evolution of uni- and bifactorial sexual compatibility systems in fungi
Nieuwenhuis, B.P.S. ; Billiard, S. ; Vuilleumier, S. ; Petit, E. ; Hood, M.E. ; Giraud, T. - \ 2013
Heredity 111 (2013)6. - ISSN 0018-067X - p. 445 - 455.
mating-type locus - schizophyllum-commune - microbotryum-violaceum - wood-decay - cryptococcus-neoformans - transposable elements - self-incompatibility - tilletia-indica - ustilago-maydis - gene
Mating systems, that is, whether organisms give rise to progeny by selfing, inbreeding or outcrossing, strongly affect important ecological and evolutionary processes. Large variations in mating systems exist in fungi, allowing the study of their origin and consequences. In fungi, sexual incompatibility is determined by molecular recognition mechanisms, controlled by a single mating-type locus in most unifactorial fungi. In Basidiomycete fungi, however, which include rusts, smuts and mushrooms, a system has evolved in which incompatibility is controlled by two unlinked loci. This bifactorial system probably evolved from a unifactorial system. Multiple independent transitions back to a unifactorial system occurred. It is still unclear what force drove evolution and maintenance of these contrasting inheritance patterns that determine mating compatibility. Here, we give an overview of the evolutionary factors that might have driven the evolution of bifactoriality from a unifactorial system and the transitions back to unifactoriality. Bifactoriality most likely evolved for selfing avoidance. Subsequently, multiallelism at mating-type loci evolved through negative frequency-dependent selection by increasing the chance to find a compatible mate. Unifactoriality then evolved back in some species, possibly because either selfing was favoured or for increasing the chance to find a compatible mate in species with few alleles. Owing to the existence of closely related unifactorial and bifactorial species and the increasing knowledge of the genetic systems of the different mechanisms, Basidiomycetes provide an excellent model for studying the different forces that shape breeding systems.
Genome-wide survey of repetitive DNA elements in the button mushroom Agaricus bisporus
Foulongne-Oriol, M. ; Murat, C. ; Castanera, R. ; Ramírez, L. ; Sonnenberg, A.S.M. - \ 2013
Fungal Genetics and Biology 55 (2013). - ISSN 1087-1845 - p. 6 - 21.
simple sequence repeats - rice blast fungus - magnaporthe-oryzae - neurospora-crassa - chromosome ends - transposable elements - molecular markers - variable-number - evolution - microsatellites
Repetitive DNA elements are ubiquitous constituents of eukaryotic genomes. The biological roles of these repetitive elements, supposed to impact genome organization and evolution, are not completely elucidated yet. The availability of whole genome sequence offers the opportunity to draw a picture of the genome- wide distribution of these elements and provide insights into potential mechanisms of genome plasticity. The present study uses in silico approaches to describe tandem repeats and transposable elements distribution in the genome of the button mushroom, Agaricus bisporus. Transposable elements comprised 12.43% of the assembled genome, and 66% of them were found clustered in the centromeric or telomeric regions. Methylation of retrotransposon has been demonstrated. A total of 1996 mini-, 4062 micro-, and 37 satellites motifs were identified. The microsatellites appeared widely and evenly spread over the whole genome sequence, whereas the minisatellites were not randomly distributed. Indeed, minisatellites were found to be associated with transposable elements clusters. Telomeres exhibited a specific sequence with a TnAGn signature. A comparison between the two available genome sequences of A. bisporus was also performed and sheds light on the genetic divergence between the two varieties. Beyond their role in genome structure, repeats provide a virtually endless source of molecular markers useful for genetic studies in this cultivated species.
Effector diversification within compartments of the Leptosphaeria maculans genome affected by repeat induced point mutations
Rouxel, T. ; Grandaubert, J. ; Hane, J.K. ; Hoede, C. ; Wouw, A. ; Couloux, A. ; Dominguez, V. ; Anthouard, V. ; Bally, P. ; Bourras, S. ; Cozijnsen, A.J. ; Ciuffetti, L.M. ; Degrave, A. ; Dilmaghani, A. ; Duret, L. ; Fudal, L. ; Goodwin, S.B. ; Gout, L. ; Glaser, N. ; Linglin, J. ; Kema, G.H.J. ; Lapalu, N. ; Lawrence, C.B. ; May, K. ; Meyer, M. ; Ollivier, B. ; Poulain, J. ; Schoch, C.L. ; Simon, A. ; Spatafora, J.W. ; Stachowiak, A. ; Turgeon, B.G. ; Tyler, B.M. ; Vincent, D. ; Weissenbach, J. ; Amselem, J. ; Quesneville, H. ; Oliver, R.P. ; Wincker, P. ; Balesdent, M.H. ; Howlett, B.J. - \ 2011
Nature Communications 2 (2011). - ISSN 2041-1723 - p. 202 - 202.
transposable elements - molecular evolution - pathogen effectors - brassica-napus - gene-transfer - oilseed rape - stem canker - avirulence - plant - fungal
Fungi are of primary ecological, biotechnological and economic importance. Many fundamental biological processes that are shared by animals and fungi are studied in fungi due to their experimental tractability. Many fungi are pathogens or mutualists and are model systems to analyse effector genes and their mechanisms of diversification. In this study, we report the genome sequence of the phytopathogenic ascomycete Leptosphaeria maculans and characterize its repertoire of protein effectors. The L. maculans genome has an unusual bipartite structure with alternating distinct guanine and cytosine-equilibrated and adenine and thymine (AT)-rich blocks of homogenous nucleotide composition. The AT-rich blocks comprise one-third of the genome and contain effector genes and families of transposable elements, both of which are affected by repeat-induced point mutation, a fungal-specific genome defence mechanism. This genomic environment for effectors promotes rapid sequence diversification and underpins the evolutionary potential of the fungus to adapt rapidly to novel host-derived constraints
Comparative sequence analysis of the potato cyst nematode resistance locus H1 reveals a major lack of co-linearity between three haplotypes in potato (Solanum tuberosum ssp.)
Finkers-Tomczak, A.M. ; Bakker, E.H. ; Boer, J.M. de; Vossen, E.A.G. van der; Achenbach, U. ; Golas, T.M. ; Suryaningrat, S. ; Smant, G. ; Bakker, J. ; Goverse, A. - \ 2011
Theoretical and Applied Genetics 122 (2011)3. - ISSN 0040-5752 - p. 595 - 608.
gene conferring resistance - quantitatively-inherited resistance - plant-parasitic nematodes - broad-spectrum resistance - late blight resistance - high-resolution map - globodera-rostochiensis - disease resistance - transposable elements - soybean roots
The H1 locus confers resistance to the potato cyst nematode Globodera rostochiensis pathotypes 1 and 4. It is positioned at the distal end of chromosome V of the diploid Solanum tuberosum genotype SH83-92-488 (SH) on an introgression segment derived from S. tuberosum ssp. andigena. Markers from a high-resolution genetic map of the H1 locus (Bakker et al. in Theor Appl Genet 109:146–152, 2004) were used to screen a BAC library to construct a physical map covering a 341-kb region of the resistant haplotype coming from SH. For comparison, physical maps were also generated of the two haplotypes from the diploid susceptible genotype RH89-039-16 (S. tuberosum ssp. tuberosum/S. phureja), spanning syntenic regions of 700 and 319 kb. Gene predictions on the genomic segments resulted in the identification of a large cluster consisting of variable numbers of the CC-NB-LRR type of R genes for each haplotype. Furthermore, the regions were interspersed with numerous transposable elements and genes coding for an extensin-like protein and an amino acid transporter. Comparative analysis revealed a major lack of gene order conservation in the sequences of the three closely related haplotypes. Our data provide insight in the evolutionary mechanisms shaping the H1 locus and will facilitate the map-based cloning of the H1 resistance gene.
Stress-induced DNA methylation changes and their heritability in asexual dandelions
Verhoeven, K.J.F. ; Jansen, J.J. ; Dijk, P.J. ; Biere, A. - \ 2010
New Phytologist 185 (2010)4. - ISSN 0028-646X - p. 1108 - 1118.
transposable elements - arabidopsis-thaliana - epigenetic inheritance - phenotypic plasticity - disease resistance - plant evolution - gene-expression - tobacco plants - genome - hypomethylation
DNA methylation can cause heritable phenotypic modifications in the absence of changes in DNA sequence. Environmental stresses can trigger methylation changes and this may have evolutionary consequences, even in the absence of sequence variation. However, it remains largely unknown to what extent environmentally induced methylation changes are transmitted to offspring, and whether observed methylation variation is truly independent or a downstream consequence of genetic variation between individuals.•Genetically identical apomictic dandelion (Taraxacum officinale) plants were exposed to different ecological stresses, and apomictic offspring were raised in a common unstressed environment. We used methylation-sensitive amplified fragment length polymorphism markers to screen genome-wide methylation alterations triggered by stress treatments and to assess the heritability of induced changes.•Various stresses, most notably chemical induction of herbivore and pathogen defenses, triggered considerable methylation variation throughout the genome. Many modifications were faithfully transmitted to offspring. Stresses caused some epigenetic divergence between treatment and controls, but also increased epigenetic variation among plants within treatments.•These results show the following. First, stress-induced methylation changes are common and are mostly heritable. Second, sequence-independent, autonomous methylation variation is readily generated. This highlights the potential of epigenetic inheritance to play an independent role in evolutionary processes, which is superimposed on the system of genetic inheritance.
Recent developments in the molecular discrimination of formae speciales of Fusarium oxysporum
Lievens, B. ; Rep, M. ; Thomma, B.P.H.J. - \ 2008
Pest Management Science 64 (2008)11. - ISSN 1526-498X - p. 781 - 788.
vegetative compatibility groups - polymerase-chain-reaction - f-sp basilici - sp radicis-cucumerinum - transposable elements - genetic diversity - plant-pathogens - sp ciceris - i-3-mediated resistance - nectria-haematococca
Rapid and reliable detection and identification of potential plant pathogens is required for taking appropriate and timely disease management measures. For many microbial species of which all strains generally are plant pathogens on a known host range, this has become quite straightforward. However, for some fungal species this is quite a challenge. One of these is Fusarium oxysporum Schlechtend:Fr., which, as a species, has a very broad host range, while individual strains are usually highly host-specific. Moreover, many strains of this fungus are non-pathogenic soil inhabitants. Thus, with regard to effective disease management, identification below the species level is highly desirable. So far, the genetic basis of host specificity in F. oxysporum is poorly understood. Furthermore, strains that infect a particular plant species are not necessarily more closely related to each other than to strains that infect other hosts. Despite these difficulties, recently an increasing number of studies have reported the successful development of molecular markers to discriminate F. oxysporum strains below the species level.
AFLP analysis of genetic diversity in populations of Botrytis elliptica and Botrytis tulipae from the Netherlands
Staats, M. ; Baarlen, P. van; Kan, J.A.L. van - \ 2007
European Journal of Plant Pathology 117 (2007)3. - ISSN 0929-1873 - p. 219 - 235.
chestnut blight fungus - botryotinia-fuckeliana - cryphonectria-parasitica - transposable elements - cinerea - recombination - polymorphism - specificity - lineages - marker
The objective of this study was to assess the genetic diversity and to infer the mode of reproduction of Botrytis elliptica and B. tulipae in the Netherlands. First, three molecular typing methods were compared for their ability to differentiate isolates of B. tulipae, B. elliptica, and B. cinerea. The methods compared were multilocus sequencing, restriction analysis of the ribosomal intergenic spacer (IGS) region, and amplified fragment length polymorphism (AFLP) analysis. AFLP fingerprinting provided the most efficient method to differentiate isolates within each Botrytis species and therefore this method was used for population analyses of B. elliptica and B. tulipae. Isolates of both species were sampled during successive growing seasons in experimental field plots in Lisse and other locations in the Netherlands. Among 174 B. elliptica isolates, 105 genotypes could be discriminated and 87 genotypes were found only once, reflecting high genotypic variation. Clonal genotypes were found only within growing seasons and in one location. Linkage disequilibrium analyses indicated that between 9.4% and 19.3% of the loci in clone-corrected samples were linked. The multilocus association index provided no evidence for random mating. We conclude that sexual recombination occurs in the B. elliptica population. Among the 170 B. tulipae isolates, 25 genotypes could be discriminated and four genotypes were found only once, reflecting a low genotypic variation. Clonal genotypes were frequently found in different growing seasons and different locations. Linkage disequilibrium analyses indicated that between 25.2% and 48.6% of the loci in clone-corrected samples were linked. We conclude that the B. tulipae population is mainly clonal with some recombination.
Nonneutral GC3 and retroelement codon mimicry in Phytophthora
Jiang, R.H.Y. ; Govers, F. - \ 2006
Journal of Molecular Evolution 63 (2006)4. - ISSN 0022-2844 - p. 458 - 472.
dna-base composition - transposable elements - genome evolution - unicellular organisms - expressed sequences - usage biases - g+c content - gene - infestans - fungi
Phytophthora is a genus entirely comprised of destructive plant pathogens. It belongs to the Stramenopila, a unique branch of eukaryotes, phylogenetically distinct from plants, animals, or fungi. Phytophthora genes show a strong preference for usage of codons ending with G or C (high GC3). The presence of high GC3 in genes can be utilized to differentiate coding regions from noncoding regions in the genome. We found that both selective pressure and mutation bias drive codon bias in Phytophthora. Indicative for selection pressure is the higher GC3 value of highly expressed genes in different Phytophthora species. Lineage specific GC increase of noncoding regions is reminiscent of whole-genome mutation bias, whereas the elevated Phytophthora GC3 is primarily a result of translation efficiency-driven selection. Heterogeneous retrotransposons exist in Phytophthora genomes and many of them vary in their GC content. Interestingly, the most widespread groups of retroelements in Phytophthora show high GC3 and a codon bias that is similar to host genes. Apparently, selection pressure has been exerted on the retroelement's codon usage, and such mimicry of host codon bias might be beneficial for the propagation of retrotransposons
Toward closing rice telomere gaps: mapping and sequence characterization of rice subtelomere regions.
Yang, T.J. ; Yu, Y. ; Chang, S.B. ; Jong, J.H.S.G.M. de; Oh, C.S. ; Ahn, S.N. ; Fang, E. ; Wing, R.A. - \ 2005
Theoretical and Applied Genetics 111 (2005)3. - ISSN 0040-5752 - p. 467 - 478.
parasite trypanosoma-cruzi - genomic dna-sequences - chromosomal organization - transposable elements - repetitive sequences - in-vitro - cloning - genes - arabidopsis - repeat
Despite the collective efforts of the international community to sequence the complete rice genome, telomeric regions of most chromosome arms remain uncharacterized. In this report we present sequence data from subtelomere regions obtained by analyzing telomeric clones from two 8.8 × genome equivalent 10-kb libraries derived from partial restriction digestion with HaeIII or Sau3AI (OSJNPb HaeIII and OSJNPc Sau3AI). Seven telomere clones were identified and contain 25¿100 copies of the telomere repeat (CCCTAAA)n on one end and unique sequences on the opposite end. Polymorphic sequence-tagged site markers from five clones and one additional PCR product were genetically mapped on the ends of chromosome arms 2S, 5L, 10S, 10L, 7L, and 7S. We found distinct chromosome-specific telomere-associated tandem repeats (TATR) on chromosome 7 (TATR7) and on the short arm of chromosome 10 (TATR10s) that showed no significant homology to any International Rice Genome Sequencing Project (IRGSP) genomic sequence. The TATR7, a degenerate tandem repeat which is interrupted by transposable elements, appeared on both ends of chromosome 7. The TATR10s was found to contain an inverted array of three tandem repeats displaying an interesting secondary folding pattern that resembles a telomere loop (t-loop) and which may be involved in a protective function against chromosomal end degradation
Mode of action, origin and structure of the Paternal Sex Ratio chromosome in the parasitoid wasp Trichogramma kaykai
Vugt, J.J.F.A. van - \ 2005
Wageningen University. Promotor(en): Joop van Lenteren; Rolf Hoekstra, co-promotor(en): Hans de Jong; R. Stouthamer. - - 120
trichogramma - chromosomen - geslachtsverhouding - geslachtsbepaling - parasitoïden - diploïdie - chromatine - transposons - trichogramma - parasitoids - chromosomes - sex ratio - sex determination - diploidy - chromatin - transposable elements
Molecular analysis of plant architecture in Arabidopsis thaliana using activation tagging.
Chalfun Junior, A. - \ 2004
Wageningen University. Promotor(en): Maarten Koornneef; Gerco Angenent. - Wageningen : S.n. - ISBN 9789085040361 - 144
arabidopsis thaliana - transposons - dna - mutanten - plantenontwikkeling - plantenmorfologie - moleculaire genetica - genexpressie - arabidopsis thaliana - transposable elements - dna - mutants - plant development - plant morphology - molecular genetics - gene expression
Insertion-Sequence-Mediated Mutations Isolated During Adaptation to Growth and Starvation in Lactococcus lactis.
Visser, J.A.G.M. de; Akkermans, A.D.L. ; Hoekstra, R.F. ; Vos, W.M. de - \ 2004
Genetics 168 (2004)3. - ISSN 0016-6731 - p. 1145 - 1157.
term experimental evolution - escherichia-coli - transposable elements - beneficial mutations - adaptive evolution - stationary-phase - populations - rearrangements - generations - diversity
We studied the activity of three multicopy insertion sequence (IS) elements in 12 populations of Lactococcus lactis IL1403 that evolved in the laboratory for 1000 generations under various environmental conditions (growth or starvation and shaken or stationary). Using RFLP analysis of single-clone representatives of each population, nine IS-mediated Mutations were detected across all environmental conditions and all involving IS981. When it was assumed that these mutations were neutral, their frequency was higher tinder shaken than under stationary conditions, possibly due to oxygen stress. We characterized seven of the nine mutations at the molecular level and studied their population dynamics where possible. Two were simple insertions into new positions and the other five were recombinational deletions (of 0 kb) among existing and new copies of IS981; in all but one case these mutations disrupted gene functions. The best candidate beneficial mutations were two deletions of which similar versions were detected in two populations each. One of these two parallel deletions, affecting a gene involved in bacteriophage resistance, showed intermediate rearrangements and may also have resulted from increased local transposition rates.
Functional genomics strategies with transposons in rice
Greco, R. - \ 2003
Wageningen University. Promotor(en): Maarten Koornneef, co-promotor(en): A.B. Pereira. - Wageningen : Wageningen Universiteit - ISBN 9789058089168 - 182
rijst - oryza - genexpressie - transposons - transpositie - transcriptie - mutagenese - genexpressieanalyse - rice - oryza - gene expression - transposable elements - transposition - transcription - mutagenesis - genomics
Two approaches for induction and isolation of starch mutants in potato (Solanum tuberosum L.): random versus gene targeted mutagenesis = Twee benaderingen voor de inductie en isolatie van zetmeelmutanten in aardappel (Solanum tuberosum L.): ongerichte versus gen gerichte mutagenese
Hoogkamp, T.J.H. - \ 2001
Wageningen University. Promotor(en): E. Jacobsen; R.G.F. Visser. - S.l. : S.n. - ISBN 9789058084538 - 92
aardappelen - solanum tuberosum - plantenveredeling - geïnduceerde mutaties - zetmeel - transposons - haploïdie - mutanten - transpositie - potatoes - solanum tuberosum - plant breeding - induced mutations - starch - transposable elements - haploidy - mutants - transposition

In this thesis two approaches were used to induce structural mutations in potato starch biosynthesis genes in potato. First production of new monoploid amf genotypes through parthenogenesis made it possible to initiate mutation breeding for amfae double mutants. Two amf monoploids were selected which fulfilled most of the prerequisites. By inducing a mutation in one of the branching enzymes in an amf -mutant it is possible to select a double mutant having less branched amylopectin. This mutation can easily be identified by iodine staining. Amylose-free starch will stain red and less branched amylopectin will stain blue, like amylose containing starch. Mutations were induced by X-ray irradiation of leaf explants followed by adventitious shoot regeneration and microtuber induction or followed by several rounds of multiplication of axillary buds and microtuber induction. In both cases the starch of microtubers was stained with iodine to screen for aberrant types. In 56 tuber samples blue or otherwise aberrant starch granules were found. With this kind of observations, the concept of mutation breeding for starch variants in monoploid potatoes is proven. A second way to induce structural mutations was the use of the Ac ( Activator )/ Ds ( Dissociation ) transposase system of maize in potato where the Ds transposon is activated by a transposase source. In this study the Ds element was linked to the GBSS gene, of which the phenotypic effect of deactivation is known i.e. red staining starch after iodine staining. The known amf mutation was used as a model system to gather more information about the transposition frequency of the Ds transposable elements in potato and to test the tagging of the wildtype GBSS gene. To activate the Ds element four Ds transposon containing plants were combined with the Ac transposase via cross combination or double transformation. Excision rates ranged from 14.8-48.4 %. Three phenotypic starch mutants were found after screening by iodine staining of tuber cut surfaces. These amylose-free mutants were analyzed by in vitro tests, Southern blot hybridization and sequencing. Strong indications were found that inactivation of the GBSS gene was caused by a transposable element.

Identification of potato genes involved in Phytophthora infestans resistance by transposon mutagenesis
Enckevort, L.J.G. van - \ 2000
Agricultural University. Promotor(en): E. Jacobsen; A. Pereira. - S.l. : S.n. - ISBN 9789058083432 - 144
aardappelen - solanum tuberosum - phytophthora infestans - plantenziekteverwekkende schimmels - ziekteresistentie - transposons - merken van genen - selectie - plantenveredeling - transpositie - mutagenese - potatoes - solanum tuberosum - phytophthora infestans - plant pathogenic fungi - disease resistance - transposable elements - transposition - mutagenesis - gene tagging - selection - plant breeding

The late blight disease, caused by the oomycete Phytophthora infestans (Mont.) de Bary, is a serious threat to the potato crop every growing season. This has, for example, led to the disastrous Irish famine in the middle of the 19 th century, and continued in the 20 th century to remain a serious problem for potato growers. Since the early 1980s P. infestans populations changed more rapidly and epidemics even increased in their severity. Resistance breeding stimulated the introduction of resistance genes ( R genes) from wild Solanum species into cultivated potato, Solanum tuberosum , but newly occurring virulent races of P. infestans circumvented these R gene mediated resistances and no cultivars with durable resistance were obtained. At the moment, methods using fungicides supervised by spraying control via decision support systems are the only available control measures.

Characteristic for R gene type mediated resistance reactions is the hypersensitive response (HR) leading to local cell death causing necrotic spots at the site of attempted infection. Genetic analysis of HR mediated resistances showed that activation of HR is highly specific and induced upon recognition between a specific R gene in the plant and a corresponding avirulence gene ( Avr gene) in the pathogen. Insights in the molecular mechanisms underlying this HR resistance reaction in Solanum species might facilitate the development of potato cultivars that are more durable in maintaining a resistance phenotype.

A two component Ac-Ds transposon tagging strategy in diploidised potato was developed to identify and isolate genes involved in the R1 gene mediated resistance response to P. infestans . Transposable elements are molecular genetic tools to mutate and identify genes. The transposable elements Ac and Ds were first characterised in maize and their molecular isolation led to the identification of maize genes that were tagged by these elements. The autonomous Ac element is able to transpose by itself and also to induce transposition of the non-autonomous Ds element that is transposase defective. Introduction of these elements in heterologous species demonstrated their utility for isolating genes in self-fertilising plant species. Also in the highly heterozygous and tetraploid potato, the Ac and Ds transposable elements were shown to be functional. A cell autonomous visual marker gene for potato, the granule bound starch synthase gene ( GBSS gene), enabled a refined characterisation of Ac transposition in potato. Further molecular characterisation showed high levels of Ac-Ds transposition both somatically and germinally, so that suitable populations could be generated for tagging purposes.

The production of clones homozygous for the gene of interest that are normally required for efficient tagging strategies, turned out to be time consuming in potato due to self-incompatibility at the diploid level. Therefore, an alternative method based on somatic transposition was developed for the direct selection of transposition events instead of recovering germinally transmitted transpositions. Highly chimaeric Ac-Ds seedlings with active Ds transposition linked to the R1 resistance gene on chromosome 5 of potato were selected. Protoplasts were isolated from actively transposing seedlings and using the hygromycin excision selection marker, regenerants could be selected with new independent Ds insertions. The resulting R1 resistant transposon mutagenised population of almost 2000 hygromycin resistant regenerants formed an ideal start for the identification of an R1 tagged mutant, or other Ds insertional mutants with an altered R1 resistance response.

The somatically regenerated tagging population was analysed for the P. infestansR1 type HR resistance response, using a detached leaf assay for P.infestans inoculation. In a primary screening, 33 potential R1 resistance variants showing partial susceptibility to P. infestans race 0 were identified. These results were further quantified using stringent inoculation conditions on replicate samples leading to the identification of four putative mutants with a distinctly altered R1 resistance response. In these putative mutants less than 50% of the inoculated leaves showed the R1 type HR response and clear colonisation with sporulation of P. infestans was observed. The flanking sequences of the Ds insertion sites in these putative R1 mutants were analysed and in two cases a potential biological correlation between the insertion sequences and the phenotype was evident. One putative mutant contained a Ds insertion in a region with auxin and abscisic acid response cis-elements homologous to a specific region (TAPIR) of the tomato defence related genes TAPG2 and TAP1 .

The second P. infestansR1 resistance mutant, mutant 1000 with a striking susceptible phenotype was characterised in more detail. Two Ds insertions were identified and the insertion site flanking sequences both showed high homology to serine/threonine protein kinases. The Ds insertion sites turned out to be homologous but not identical, indicating two independent Ds insertions in homologous but not identical genes. Both sequences showed protein identity to all the conserved regions of serine/threonine protein kinases and they contained a conserved intron position. The closest homology was to the serine/threonine protein kinase domain of the Xanthomonas resistance gene Xa21 , which is involved in the induction of a HR resistance response in rice. This indicates that the isolated Solanum tuberosum protein kinase (StPK) homologs are candidate genes involved in resistance gene activity in potato. Further specific molecular analyses identified at least 11 homologs by sequence, which probably belong to a large family of serine/threonine protein kinases in potato. Both homologs in which the Ds transposons are inserted were present in susceptible parental potato clones. Therefore, it is unlikely that the isolated sequences represent the R1 gene itself. The mutated StPKs were designated rpr1 and rpr2 , r equired for P hytophthora infestansr esistance gene 1 and 2. Studying these mutants and the StPKs involved might help in understanding the pathway leading to HR resistance in potato.

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