Janny Peters | Radboud University Nijmegen (original) (raw)

Papers by Janny Peters

Theoretical and Applied Genetics, 2004

To efficiently determine the chromosomal location of phenotypic mutants, we designed a genome-wid... more To efficiently determine the chromosomal location of phenotypic mutants, we designed a genome-wide mapping strategy that can be used in any crop for which a dense AFLP (Amplified Fragment Length Polymorphism) map is available or can be made. The AFLP technique is particularly suitable to initiate map-based cloning projects because it detects many markers per reaction. First a standard set of AFLP primer combinations that results in a framework of AFLP markers well dispersed over the genome is selected. These primer combinations are applied to a limited number of mutant individuals from a segregating population to register linkage and non-linkage of the AFLP markers to the gene-of-interest. Further delineation of the area of interest is accomplished by analyzing the remaining recombinants and additional mutant individuals with AFLP markers that lie within the identified region. We illustrate the usefulness of the method by mapping three rotunda (ron) leaf-form mutant loci of Arabidopsis thaliana and show that in the initial phase of map-based cloning projects a 400–600 kb interval can be identified for the average mutant locus within a few weeks. Once such an area is identified and before initiating the more time-consuming fine-mapping procedure, it is essential to examine publicly available databases for candidate genes and known mutants in the identified region. The 390-kb interval on chromosome 4 that harbors the ron2 mutation, also carries a known flower mutant, leunig (lug); upon crossing, the two mutants appeared to be allelic. When no such candidates are found, the mapping procedure should be continued. We present a strategy to efficiently select recombinants that can be used for fine mapping.

Theoretical and Applied Genetics, 2002

AFLP mapping in Petunia hybrida was undertaken with the intention of building a high-density gene... more AFLP mapping in Petunia hybrida was undertaken with the intention of building a high-density genetic map suitable for applications such as map-based gene cloning. In total five maps were constructed from two mapping populations, with placement of more than 800 markers. Despite the large number of markers the resulting map is roughly ten-fold smaller than those of other plant species, including the closely related tomato. Low levels of recombination are reflected in clusters of tightly linked markers, both AFLPs and RFLPs, in all the maps. Clustering patterns vary between mapping populations, however, such that loci tightly linked in one population may be separable in another. Combined with earlier reports of aberrant meiotic pairing and recombination, our results suggest that, for species like petunia, map-based cloning may be more complex than in model species such as arabidopsis and tomato.

Diamine oxidase and peroxidase, associated with the wall in pinto bean (Phaseolus vulgaris L. var... more Diamine oxidase and peroxidase, associated with the wall in pinto bean (Phaseolus vulgaris L. var Pinto) leaves, can be washed out by vacuum infiltration and assayed without grinding the leaf. The diamine oxidase activity is inhibited in vivo by exposure of the plants to ozone (dose of 0.6 microliters per liter x hour), whereas the peroxidase activity associated with the wall space is stimulated. This dose does not cause obvious necrosis or chlorosis of the leaf. These alterations are greater when the dose of ozone exposure is given as a triangular pulse (a slow rise to a peak of 0.24 microliters per liter followed by a slow fall) compared to that given as a constant square wave pulse of 0.15 microliters per liter for the same 4 hour period. Exposure of the plants to sulfur dioxide (at a concentration of 0.4 microliters per liter for 4 hours) does not result in any change in the diamine oxidase or peroxidase activities, yet the total sulfhydryl content of the leaf is increased, demonstrating the entry of sulfur dioxide. These two pollutants, with different chemical reactivities, affect the activities of the extracellular enzymes in different manners.

For nearly a century Petunia has served as a model species for genetic and cytological studies. T... more For nearly a century Petunia has served as a model species for genetic and cytological studies. The list of mapped loci has grown from one for each of the seven chromosomes to more than 150, to which can be added several hundred, mostly AFLP-based, molecular markers. Mapping efforts provided early evidence for a number of phenomena which now appear to apply to a great number of plant and animal species, including a tendency toward tightly clustered gene family members, suppression of recombination in wide crosses, frequent chromosomal rearrangements, and active transposable element systems.

Planta, 1998

A single pulse of red light (R) given to 4-d-old etiolated high-pigment-1 (hp-1) mutant tomato (S... more A single pulse of red light (R) given to 4-d-old etiolated high-pigment-1 (hp-1) mutant tomato (Solanum lycopersicum L.) seedlings followed by a 3-d dark period is demonstrated to result in a block of greening in subsequent white light. Wild-type seedlings green normally under this regime. The block of greening in the hp-1 mutant depends on the length of the dark period before and after the R pulse and operates via the low-fluence-response mode of phytochrome action. This block of greening takes place in hp-1 double mutants lacking either phytochrome A or phytochrome B1, but is absent in the hp-1 triple mutant lacking both phytochromes A and B1. These observations enable a screen to be devised for new phytochrome B1 mutants either within the photoreceptor or mutants defective in phytochrome B1-signalling steps which result in loss of capacity to green, by mutagenising the phytochrome A-deficient hp-1, fri double mutant.

Biological Letters, 2005

The declining Western European population of the Red-backed Shrike (Lanius collurio) is hypothesi... more The declining Western European population of the Red-backed Shrike (Lanius collurio) is hypothesised to be a part of the same metapopulation as the Dutch population, at the edge of the contracting western range. Due to habitat fragmentation the Dutch population is mainly situated in the Bargerveen reserve (4060 pairs) with a few local populations of 15 pairs present in other parts of The Netherlands. Previous studies showed that all locations are complemented by a high number of immigrants. The origin of the immigrants and the level of genetic variation in this population, which acts as a sink, can be investigated by molecular markers. In this pilot study we investigated the possibility of using 4 microsatellite markers to study the genetic structure of the Red-backed Shrike populations in Bargerveen and in the north of Denmark, on the basis of 10 individuals per population. All loci were variable, and both populations were comparable in mean number of alleles and distinct private alleles. In both populations, the observed heterozygosity was relatively low, and the inbreeding coefficient high. In the future, this project should be continued at a larger scale to obtain data for the genetic structure of the Western European Red-backed Shrike across a larger part of its range. The analysis needs to be enlarged with more loci and more independent individuals per population.

Journal of Ecology, 2009

1. An increasing body of evidence suggests that within-species diversity plays an important role ... more 1. An increasing body of evidence suggests that within-species diversity plays an important role for community and ecosystem functioning, alters complex trophic interactions and affects patterns of species diversity and coexistence. Nonetheless, we lack a good understanding of how genotypic trait variation translates into shifts in the relative abundance of genotypes within populations.2. In this study, we show that genotypic selection strongly alters dominance relationships among genotypes over a period of 5 years. This resulted in remarkably consistent changes in the proportional representation of genotypes, and in a concomitant decline of diversity and evenness in our experimental populations.3. High growth rates and the production of large offspring were positively associated with genotypic performance. Vegetative abundances of genotypes translated monotonically into flowering frequencies.4. Synthesis. We conclude that genotypic selection markedly affects patterns of diversity and consistently alters genotypic abundance and mean trait distributions in plant populations over a relatively short period of time.

Biological Invasions, 2009

The zebra mussel, Dreissena polymorpha is an aquatic nuisance invasive species originally native ... more The zebra mussel, Dreissena polymorpha is an aquatic nuisance invasive species originally native to the Ponto-Caspian region where it is found in lakes and delta areas of large rivers draining into the Black and Caspian seas. The dispersal of D. polymorpha began at the end of the 18th century, at a time when shipping trade become increasingly important and many canals were built for linking different navigable river systems in Europe. Over the past 200 years, zebra mussels spread to most of the lakes, rivers and waterways in Europe by a combination of natural and anthropogenic dispersal mechanisms. D. polymorpha invaded Spain around 2001, being found for the first time in the Riba-roja reservoir at the lower part of the Ebro River, North-East Spain. The relatively late invasion of Spain was most likely caused by the presence of the Pyrenees, which isolated the Iberian Peninsula from the rest of the European continent, and acted as a barrier to the dispersal of D. polymorpha. In recent studies, molecular genetic methods have successfully been used to determine phylo-geographic relationships, which may reflect invasion corridors and can help retrace source populations. Zebra mussels from populations in Great Britain, The Netherlands, Belgium, France, Germany, Spain, Italy, Romania and North America were analyzed using PCR based amplified fragment length polymorphism (AFLP)-fingerprinting to determine the source population of D. polymorpha in Spain. The phylogenetic analyses and pair-wise genetic distances revealed that the recent invasion of zebra mussels in Spain is most likely from France.

Chromosome Research, 2006

We analyzed changes in gene expression during male meiosis in Petunia by combining the meiotic st... more We analyzed changes in gene expression during male meiosis in Petunia by combining the meiotic staging of pollen mother cells from a single anther with cDNA-AFLP transcript profiling of mRNA from the synchronously developing sister anthers. The transcript profiling experiments focused on the identification of genes with a modulated expression profile during meiosis, while premeiotic archesporial cells and postmeiotic microspores served as a reference. About 8000 transcript tags, estimated at 30% of the total transcriptome, were generated, of which around 6% exhibited a modulated gene expression pattern at meiosis. Cluster analysis revealed a transcriptional cascade that coincides with the initiation and progression through all stages of the two meiotic divisions. Fragments that exhibited high expression specifically during meiosis I were characterized further by sequencing; 90 out of the 293 sequenced fragments showed homology with known genes, belonging to a wide range of gene classes, including previously characterized meiotic genes. In-situ hybridization experiments were performed to determine the spatial expression pattern for five selected transcript tags. Its concurrence with cDNA-AFLP transcript profiles indicates that this is an excellent approach to study genes involved in specialized processes such as meiosis. Our data set provides the potential to unravel unique meiotic genes that are as yet elusive to reverse genetics approaches.

Plant Molecular Biology, 2006

Based upon the phenotype of young, dark-grown seedlings, a cytokinin-resistant mutant, cnr1, has ... more Based upon the phenotype of young, dark-grown seedlings, a cytokinin-resistant mutant, cnr1, has been isolated, which displays altered cytokinin- and auxin-induced responses. The mutant seedlings possess short hypocotyls and open apical hooks (in dark), and display agravitropism, hyponastic cotyledons, reduced shoot growth, compact rosettes and short roots with increased adventitious branching and reduced number of root hairs. A number of these features invariably depend upon auxin/cytokinin ratio but the cnr1 mutant retains normal sensitivity towards auxin as well as auxin polar transport inhibitor, TIBA, although upregulation of primary auxin-responsive Aux/IAA genes is reduced. The mutant shows resistance towards cytokinin in hypocotyl/root growth inhibition assays, displays reduced regeneration in tissue cultures (cytokinin response) and decreased sensitivity to cytokinin for anthocyanin accumulation. It is thus conceivable that due to reduced sensitivity to cytokinin, the cnr1 mutant also shows altered auxin response. Surprisingly, the mutant retains normal sensitivity to cytokinin for induction of primary response genes, the type-A Arabidopsis response regulators, although the basal level of their expression was considerably reduced as compared to the wild-type. The zeatin and zeatin riboside levels, as estimated by HPLC, and the cytokinin oxidase activity were comparable in the cnr1 mutant and the wild-type. The hypersensitivity to red light (in hypocotyl growth inhibition assay), partial photomorphogenesis in dark, and hypersensitivity to sugars, are some other features displayed by the cnr1 mutant. The lesion in the cnr1 mutant has been mapped to the top of chromosome 1 where no other previously known cytokinin-resistant mutant has been mapped, indicating that the cnr1 mutant defines a novel locus involved in hormone, light and sugar signalling.

Plant Journal, 2008

BLAST searchable databases containing insertion flanking sequences have revolutionized reverse ge... more BLAST searchable databases containing insertion flanking sequences have revolutionized reverse genetics in plant research. The development of such databases has so far been limited to a small number of model species and normally requires extensive labour input. Here we describe a highly efficient and widely applicable method that we adapted to identify unique transposon-flanking genomic sequences in Petunia. The procedure is based on a multi-dimensional pooling strategy for the collection of DNA samples; up to thousands of different templates are amplified from each of the DNA pools separately, and knowledge of their source is safeguarded by the use of pool-specific (sample) identification tags in one of the amplification primers. All products are combined into a single sample that is subsequently used as a template for unidirectional pyrosequencing. Computational analysis of the clustered sequence output allows automatic assignment of sequences to individual DNA sources. We have amplified and analysed transposon-flanking sequences from a Petunia transposon insertion library of 1000 individuals. Using 30 DNA isolations, 70 PCR reactions and two GS20 sequencing runs, we were able to allocate around 10 000 transposon flanking sequences to specific plants in the library. These sequences have been organized in a database that can be BLAST-searched for insertions into genes of interest. As a proof of concept, we have performed an in silico screen for insertions into members of the NAM/NAC transcription factor family. All in silico-predicted transposon insertions into members of this family could be confirmed in planta.

Plant Molecular Biology, 2004

We have isolated an Arabidopsis mutant impaired in light- and brassinosteroid (BR) induced respon... more We have isolated an Arabidopsis mutant impaired in light- and brassinosteroid (BR) induced responses, as well as in sugar signalling. The bls1 (brassinosteroid, light and sugar1) mutant displays short hypocotyl, expanded cotyledons, and de-repression of light-regulated genes in young seedlings, and leaf differentiation and silique formation on prolonged growth in dark. In light, the bls1 mutant is dwarf and develops a short root, compact rosette, with reduced trichome number, and exhibits delayed bolting. The activity of the BR inducible TCH4 and auxin inducible SAUR promoters, fused with GUS gene, is also altered in seedlings harbouring bls1 mutant background. In addition, the bls1 mutant is hypersensitive to metabolizable sugars. The short hypocotyl phenotype in dark, short root phenotype in light and sugar hypersensitivity could be rescued with BR application. Moreover, the bls1 mutant also showed higher expression of a BR biosynthetic pathway gene CPD, which is known to be feedback-regulated by BR. Using a genome-wide AFLP mapping strategy, the bls1 mutant has been mapped to a 1.4 Mb region of chromosome 5. Since no other mutant with essentially a similar phenotype has been assigned to this region, we suggest that the bls1 mutant defines a novel locus involved in regulating endogenous BR levels, with possible ramifications in integrating light, hormone and sugar signalling.

Plant Physiology, 2007

Plant Physiology Preview. ABSTRACT A fast neutron-mutagenised population of Arabidopsis thaliana ... more Plant Physiology Preview. ABSTRACT A fast neutron-mutagenised population of Arabidopsis thaliana Col-0 WT plants was screened for floral phenotypes and a novel mutant, termed hawaiian skirt (hws), was identified that failed to shed its reproductive organs. The mutation is the consequence of a 28bp deletion that introduces a premature amber termination codon into the ORF of a putative F-box protein (At3g61590). The most striking anatomical characteristic of hws plants is seen in flowers where individual sepals are fused along the lower part of their margins. Crossing of the abscission marker, Pro PGAZAT :GUS into the mutant reveals that whilst floral organs are retained it is not the consequence of a failure of abscission zone cells to differentiate. Anatomical analysis indicates that the fusion of sepal margins precludes shedding even though abscission, albeit delayed, does occur. Spatial and temporal characterisation, using Pro HWS :GUS or Pro HWS :GFP fusions, has identified HWS expression to be restricted to the stele and lateral root cap, cotyledonary margins, tip of the stigma, pollen, abscission zones, and developing seeds. Comparative phenotypic analyses performed on the hws mutant, Col-0 WT, and Pro 35S :HWS ectopically expressing lines has revealed that loss of HWS results in greater growth of both aerial and below-ground organs whilst overexpressing the gene brings about a converse effect. These observations are consistent with HWS playing an important role in regulating plant growth and development.

Plant Molecular Biology, 1998

The structure of the gene encoding the apoprotein of phytochrome B1 (PHYB1) in tomato has been de... more The structure of the gene encoding the apoprotein of phytochrome B1 (PHYB1) in tomato has been determined from genomic and cDNA sequences. In contrast to PHYA, PHYB1 lacks an intron upstream of the first ATG. A single transcription start site was found by 5′ RACE at –116. Tomato PHYB1 spans 7 kb starting from the first ATG. The coding region is organized into four exons as for other angiosperm PHY. The deduced apoprotein consists of 1131 amino acids, with a molecular mass of 125.4 kDa. Tomato phytochrome B1 shares 78% and 74% identity with Arabidopsis phytochromes B and D, respectively. Along with the normally spliced full-length transcripts, sequences of reverse transcriptase-PCR clones revealed five types of alternative transcripts. Each type of alternative transcript was missing a considerable part of the coding region, including the chromophore-binding site. The four putative PHYB1 mutants in tomato, which are temporarily red-light insensitive (tri), were each confirmed to have a mutation in PHYB1. Each mutation arose from a different, single-base substitution. Allele tri1 is presumably a null because the mutation introduces a stop at codon 92. In tri3, val-238 is replaced by Phe. The importance of this valine residue is evidenced by the fact that the tri3 phenotype is as strong as that of tri1. Alleles tri2 and tri4 encode proteins truncated at their C-termini. The former lacks either 170 or 438 amino acids, depending upon which of two types of splicing occurs during transcript maturation, while the latter lacks 225.

Plant Cell, 1995

It has previously been shown that the organ-specific expression of two members of the ribulose-1,... more It has previously been shown that the organ-specific expression of two members of the ribulose-1,s-bisphosphate carboxylase/oxygenase small subunit (rbcS) gene family is post-transcriptionally regulated in Lemna gibba. While both small subunit genes encoding SSUl and SSU58 were transcribed at comparable levels in root and frond nuclei, SSUl mRNA accumulated to high levels in both roots and fronds in contrast to SSU5B mRNA, which was of very low abundance in the roots compared with the fronds. In this study, we have used two approaches to pinpoint the step(s) at which SSUl and SSU58 mRNAs are differentially accumulated in these organs. In the first approach, total nuclear steady state mRNA was isolated from roots and fronds, and the amount of each transcript was measured by RNase protection assays and compared with the transcription rates in isolated nuclei. In the second approach, cordycepin was used to inhibit mRNA synthesis in Lemna fronds or roots, and the rate of decay of each mRNA was measured by RNA gel blot analysis or RNase protection assays. Our findings indicate that the differential accumulation of SSUl and SSU5B mRNAs in the fronds versus the roots is determined primarily in the nuclear compartment. In addition, SSUl was found to have a longer half-life in total steady state mRNA than SSUBB had in both organs. This feature probably accounts for SSUl being the predominantly expressed family member.

Journal of Experimental Botany, 1987

... Trifolium pratense L., Glycine max Merr. and Phaseolus vulgaris L. FRANK M. MAAS1, LUIT J. DE... more ... Trifolium pratense L., Glycine max Merr. and Phaseolus vulgaris L. FRANK M. MAAS1, LUIT J. DE KOK, JANNY L. PETERS AND PIETER JC KUIPER ... Page 8. 1466 Maas et al.—Effects of H^S and SO-, on Plants Tnfolium pretense Glyone max Phaseolu5 vu&#x27;garis| I 2 O I I &quot; 08r ...

Journal of Experimental Botany, 2004

Leaf development in Arabidopsis thaliana is considered to be a two-step process. In the first ste... more Leaf development in Arabidopsis thaliana is considered to be a two-step process. In the first step, a leaf primordium is formed that involves a switch from indeterminate to leaf developmental fate in the shoot apical meristem cells. The second step, known as leaf morphogenesis, consists of post-initiation developmental events such as patterned cell proliferation, cell expansion, and cell differentiation. The results are presented of the molecular and genetic analyses of the rotunda2 (ron2) mutants of Arabidopsis, which were isolated based on their wide and serrated vegetative leaf lamina. The RON2 gene was positionally cloned and was identical to LEUNIG (LUG); it encodes a transcriptional co-repressor that has been described to affect flower development. Morphological and histological analyses of expanded leaves indicated that RON2 (LUG) acts at later stages of leaf development by restricting cell expansion during leaf growth. Real-time reverse-transcription polymerase chain reaction was used to quantify the expression of KNOX, WUSCHEL, YABBY3, LEAFY, ASYMMETRIC LEAVES, and GIBBERELLIN OXIDASE genes in expanding and fully expanded rosette leaf laminas of the wild type and ron2 and lug mutants. SHOOTMERI-STEMLESS was expressed in wild-type leaves and down-regulated in the mutants. The results indicate that RON2 (LUG) has a function in later stages of leaf development.

Plant Physiology, 1998

Three light-regulated genes, chlorophyll a/b-binding protein (CAB), ribulose-1,5-bisphosphate car... more Three light-regulated genes, chlorophyll a/b-binding protein (CAB), ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit, and chalcone synthase (CHS), are demonstrated to be upregulated in the high-pigment-1 (hp-1) mutant of tomato (Lycopersicon esculentum Mill.) compared with wild type (WT). However, the pattern of up-regulation of the three genes depends on the light conditions, stage of development, and tissue studied. Compared with WT, the hp-1 mutant showed higher CAB gene expression in the dark after a single red-light pulse and in the pericarp of immature fruits. However, in vegetative tissues of light-grown seedlings and adult plants, CAB mRNA accumulation did not differ between WT and the hp-1 mutant. The ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit mRNA accumulated to a higher level in the hp-1 mutant than WT under all light conditions and tissues studied, whereas CHS gene expression was up-regulated in deetiolated vegetative hp-1-mutant tissues only. The CAB and CHS genes were shown to be phytochrome regulated and both phytochrome A and B1 play a role in CAB gene expression. These observations support the hypothesis that the HP-1 protein plays a general repressive role in phytochrome signal transduction.

Photochemistry and Photobiology, 1989

The photocontrol of anthocyanin synthesis in dark-grown seedlings of tomato (Lycopersicon esculen... more The photocontrol of anthocyanin synthesis in dark-grown seedlings of tomato (Lycopersicon esculentum Mill.) has been studied in an aurea (au) mutant which is deficient in the labile type of phytochrome, a high pigment (hp) mutant which has the wild-type level of phytochrome and the double mutant au/hp, as well as the wild type. The hp mutant demonstrates phytochrome control of anthocyanin synthesis in response to a single red light (RL) pulse, whereas there is no measurable response in the wild type and au mutant. After pretreatment with 12 h blue light (BL) the phytochrome regulation of anthocyanin synthesis is 10-fold higher in the hp mutant than in the wild type, whilst no anthocyanin is detectable in the au mutant, thus suggesting that it is the labile pool of phytochrome which regulates anthocyanin synthesis. The au/hp double mutant exhibits a small (3% of that in the hp mutant) RL/far-red light (FR)-reversible regulation of anthocyanin synthesis following a BL pretreatment. It is proposed that the hp mutant is hypersensitive to the FR-absorbing form of phytochrome (Pfr) and that this (hypersensitivity) establishes response to the low level of Pfl. (below detection limits in phytochrome assays) in the au/hp double mutant.