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Featured researches published by Paul Arens.


Theoretical and Applied Genetics | 1997

Use of short microsatellites from database sequences to generate polymorphisms among Lycopersicon esculentum cultivars and accessions of other Lycopersicon species

M.J.M. Smulders; G. M. M. Bredemeijer; W. Rus-Kortekaas; Paul Arens; Ben Vosman

Abstract A search of nearly 2000 sequences from Solanaceae species in the EMBL and Genbank databases yielded 220 microsatellites. Among these were 80 microsatellites from 675 Lycopersicon entries. Dinucleotide repeats, as well as (CAA)n and (TAA)n repeats, were over-represented in non-coding DNA. The other trinucleotide repeats were predominantly found in exonic DNA. PCR analysis of 44 of the microsatellite-containing Lycopersicon loci identified 36 primer pairs that yielded well-scorable fragments, or groups of fragments, in L. esculentum cultivars and accessions of Lycopersicon species. Twenty-nine of these amplified bands that were polymorphic among the four Lycopersicon species. Ten primer pairs generated polymorphic bands among seven tomato cultivars. Upon examining the number of microsatellites and the degree of polymorphisms in relation to the repeat type and motif, the type of DNA the microsatellite resided in, the length of the microsatellite, and the presence of imperfections in the microsatellite, only two significant correlations were found. (i) Imperfect repeats were less polymorphic among species than perfect repeats. (ii) The percentage of loci polymorphic among cultivars increased from 6% for the shortest loci (with eight or less repeat units) to 60% for the group with the longest repeats (12 repeat units or longer). Among the species, however, all length classes contained about 83% polymorphic loci. In general, 2–4 alleles were found for each locus among the samples of the test set. In a few cases, up to eight alleles were found. A combination of these microsatellite loci can therefore be useful in distinguishing cultivars of tomato, which are genetically very closely related to each other.


Molecular Ecology | 1998

Molecular genetic analysis of black poplar (Populus nigra L.) along Dutch rivers

Paul Arens; H. Coops; J. Jansen; B. Vosman

The genetic structure of remaining black poplar (Populus nigra) trees on the banks of the Dutch Rhine branches was investigated using the AFLP technique. In total, 143 trees, including one P. deltoides and some P. x euramericana, were analysed using six AFLP primer combinations which generated 319 polymorphic bands. The AFLP patterns showed that some of the trees sampled as P. nigra were clearly different. These deviating patterns were also observed for the P. deltoides tree and all trees already identified as hybrid P. x euramericana. Hybrids between the two species are morphologically sometimes difficult to distinguish from the species itself. Two important possible source populations for recolonization of the riverbanks of the river Rhine, consisting of mature flowering P. nigra trees, appeared to consist of only a few genotypes each. In contrast, young black poplar trees growing alone or in small groups downstream of the possible source populations appeared to be predominantly generatively derived because no clones of mature trees were found among them. Therefore vegetative propagation seems a very local strategy whereas colonization of new areas appears to occur through generative propagation. Whether the genetic diversity within these black poplars is sufficient for recolonization of river banks and survival of the metapopulation is a question for further research.


Theoretical and Applied Genetics | 1995

A genetic map of potato (Solanum tuberosum) integrating molecular markers, including transposons, and classical markers.

Jeanne M. E. Jacobs; H.J. van Eck; Paul Arens; B. Verkerk-Bakker; B. te Lintel Hekkert; H.J.M. Bastiaanssen; A. El-Kharbotly; Andy Pereira; E. Jacobsen; Willem J. Stiekema

A genetic map of potato (Solanum tuberosum L.) integrating molecular markers with morphological and isozyme markers was constructed using a backcross population of 67 diploid potato plants. A general method for map construction is described that differs from previous methods employed in potato and other outbreeding plants. First, separate maps for the female and male parents were constructed. The female map contained 132 markers, whereas the male map contained 138 markers. Second, on the basis of the markers in common the two integrated parental maps were combined into one with the computer programme JoinMap. This combined map consisted of 175 molecular markers, 10 morphological markers and 8 isozyme markers. Ninety-two of the molecular markers were derived from DNA sequences flanking either T-DNA inserts in potato or reintegrated maize transposable elements originating from these T-DNA constructs. Clusters of distorted segregation were found on chromosomes 1,2,8 and 11 for the male parent and chromosome 5 for both parents. The total length of the combined map is 1120 cM.


Journal of Vegetation Science | 2008

Plant functional group composition and large-scale species richness in European agricultural landscapes

Jaan Liira; Torsten Schmidt; Tsipe Aavik; Paul Arens; Isabel Augenstein; Debra Bailey; Regula Billeter; R. Bukácek; Françoise Burel; Geert De Blust; Raphaël De Cock; J. Dirksen; Peter J. Edwards; Roman Hamerský; Felix Herzog; Stefan Klotz; Ingolf Kühn; Didier Le Coeur; Pavlina Miklová; Martina Roubalova; Oliver Schweiger; M.J.M. Smulders; Walter van Wingerden; Rob Bugter; Martin Zobel

Abstract Question: Which are the plant functional groups respondcing most clearly to agricultural disturbances? Which are the relative roles of habitat availability, landscape configuration and agricultural land use intensity in affecting the functional composition and diversity of vascular plants in agricultural landscapes? Location: 25 agricultural landscape areas in seven European countries. Methods: We examined the plant species richness and abundance in 4 km × 4 km landscape study sites. The plant functional group classification was derived from the BIOLFLOR database. Factorial decomposition of functional groups was applied. Results: Natural habitat availability and low land use intensity supported the abundance and richness of perennials, sedges, pteridophytes and high nature quality indicator species. The abundance of clonal species, C and S strategists was also correlated with habitat area. An increasing density of field edges explained a decrease in richness of high nature quality species and an increase in richness of annual graminoids. Intensive agriculture enhanced the richness of annuals and low nature quality species. Conclusions: Habitat patch availability and habitat quality are the main drivers of functional group composition and plant species richness in European agricultural landscapes. Linear elements do not compensate for the loss of habitats, as they mostly support disturbance tolerant generalist species. In order to conserve vascular plant species diversity in agricultural landscapes, the protection and enlargement of existing patches of (semi-) natural habitats appears to be more effective than relying on the rescue effect of linear elements. This should be done in combination with appropriate agricultural management techniques to limit the effect of agrochemicals to the fields. Nomenclature: Tutin et al. (2001).


Landscape Ecology | 2007

Genetic population differentiation and connectivity among fragmented Moor frog (Rana arvalis) populations in The Netherlands

Paul Arens; Theo van der Sluis; Wendy van’t Westende; Ben Vosman; C.C. Vos; M.J.M. Smulders

We studied the effects of landscape structure, habitat loss and fragmentation on genetic differentiation of Moor frog populations in two landscapes in The Netherlands (Drenthe and Noord-Brabant). Microsatellite data of eight loci showed small to moderate genetic differentiation among populations in both landscapes (FST values 0.022 and 0.060, respectively). Both heterozygosity and population differentiation indicate a lower level of gene flow among populations in Noord-Brabant, where populations were further apart and have experienced a higher degree of fragmentation for a longer period of time as compared to populations in Drenthe. A significant isolation-by-distance pattern was found in Drenthe, indicating a limitation in dispersal among populations due to geographic distance. In Noord-Brabant a similar positive correlation was obtained only after the exclusion of a single long-time isolated population. After randomised exclusion of populations a significant additional negative effect of roads was found but not of other landscape elements. These results are discussed in view of improving methodology of assessing the effects of landscape elements on connectivity.


Theoretical and Applied Genetics | 1992

Identification of highly polymorphic DNA regions in tomato

Ben Vosman; Paul Arens; W. Rus-Kortekaas; M.J.M. Smulders

SummaryThis paper describes the use of oligonucleotide probes to reveal highly polymorphic DNA regions in pomato. With a (GATA)4 probe the level of polymorphism detected is high enough to identify all 15 tomato cultivars used in this study. Individual plants of one cultivar all showed the same cultivar-specific DNA-finger-print. In an F2-population of self-fertilized cv. Sonatine, GATA-containing loci segregated in a Mendelian (3∶1) fashion. Experiments with in-vitro propagated plant material showed that the DNA-fingerprints are not affected by tissue-culture procedures. This indicates that changes in the genetic integrity, which often accompany in-vitro propagation (somaclonal variation), are not extended to the DNA detected with the (GATA)4 probe. The relative high stability and the Mendelian segregation of (GATA)4-derived DNA-fingerprints make them ideally suited for identification of tomato cultivars.


Theoretical and Applied Genetics | 1998

The use of semi-automated fluorescent microsatellite analysis for tomato cultivar identification

G. M. M. Bredemeijer; Paul Arens; D. Wouters; D. Visser; Ben Vosman

Abstract The objectives of this study were to evaluate the usefulness of a fluorescent-analysis method for genotyping PCR-based tomato microsatellite markers (or STMSs) and to establish the value of these markers to generate unique DNA profiles of tomato cultivars. The analyses were performed using forward primers labelled with a fluorochrom and using an ALF express DNA sequencer. In general, analysis of the tomato STMSs revealed distinct allelic peaks. PCR artefacts like stuttering and differential amplification were observed for several tomato STMS markers, but in most cases these artefacts did not seriously hamper allele designation. Comparison of fluorescent and silver-stained allelic profiles revealed a similar distribution of alleles among the test cultivars. Sixteen tomato cultivars were DNA-typed for 20 selected STMS markers using the fluorescent approach. Length polymorphism among the PCR products was detected with 18 of these markers, yielding gene diversity values from 0.06 to 0.74. The number of alleles per microsatellite locus ranged from 2 to 8. As few as four STMSs were sufficient to differentiate between all 16 cultivars, indicating that these markers are especially suitable for a species like tomato which has low levels of variation as detected by other types of markers.


Molecular Breeding | 1996

Mapping of resistance to the potato cyst nematode Globodera rostochiensis from the wild potato species Solanum vernei.

Jeanne M. E. Jacobs; Herman J. van Eck; Karin Horsman; Paul Arens; Brigitte Verkerk-Bakker; E. Jacobsen; Andy Pereira; Willem J. Stiekema

A population of diploid potato (Solanum tuberosum) was used for the genetic analysis and mapping of a locus for resistance to the potato cyst nematode Globodera rostochiensis, introgressed from the wild potato species Solanum vernei. Resistance tests of 108 genotypes of a F1 population revealed the presence of a single locus with a dominant allele for resistance to G. rostochiensis pathotype Ro1. This locus, designated GroV1, was located on chromosome 5 with RFLP markers. Fine-mapping was performed with RAPD and SCAR markers. The GroV1 locus was found in the same region of the potato genome as the S. tuberosum ssp. andigena H1 nematode resistance locus. Both resistance loci could not excluded to be allelic. The identification of markers flanking the GroV1 locus offers a valuable strategy for marker-assisted selection for introgression of this nematode resistance.


Tree Genetics & Genomes | 2008

Natural hybridisation between Populus nigra L. and P. x canadensis Moench. Hybrid offspring competes for niches along the Rhine river in the Netherlands

M.J.M. Smulders; R. Beringen; R. Volosyanchuk; A. Vanden Broeck; J.R. van der Schoot; Paul Arens; Ben Vosman

Black poplar (Populus nigra L.) is a major species for European riparian forests but its abundance has decreased over the decades due to human influences. For restoration of floodplain woodlands, the remaining black poplar stands may act as source population. A potential problem is that P. nigra and Populus deltoides have contributed to many interspecific hybrids, which have been planted in large numbers. As these Populus x canadensis clones have the possibility to intercross with wild P. nigra trees, their offspring could establish themselves along European rivers. In this study, we have sampled 44 poplar seedlings and young trees that occurred spontaneously along the Rhine river and its tributaries in the Netherlands. Along these rivers, only a few native P. nigra L. populations exist in combination with many planted cultivated P. x canadensis trees. By comparison to reference material from P. nigra, P. deltoides and P. x canadensis, species-specific AFLP bands and microsatellite alleles indicated that nearly half of the sampled trees were not pure P. nigra but progeny of natural hybridisation that had colonised the Rhine river banks. The posterior probability method as implemented in NewHybrids using microsatellite data was the superior method in establishing the most likely parentage. The results of this study indicate that offspring of hybrid cultivated poplars compete for the same ecological niche as native black poplars.


BMC Genomics | 2012

Generation and analysis of expressed sequence tags in the extreme large genomes Lilium and Tulipa

Arwa Shahin; Martijn van Kaauwen; Danny Esselink; Joachim W. Bargsten; Jaap M. van Tuyl; Richard G. F. Visser; Paul Arens

BackgroundBulbous flowers such as lily and tulip (Liliaceae family) are monocot perennial herbs that are economically very important ornamental plants worldwide. However, there are hardly any genetic studies performed and genomic resources are lacking. To build genomic resources and develop tools to speed up the breeding in both crops, next generation sequencing was implemented. We sequenced and assembled transcriptomes of four lily and five tulip genotypes using 454 pyro-sequencing technology.ResultsSuccessfully, we developed the first set of 81,791 contigs with an average length of 514 bp for tulip, and enriched the very limited number of 3,329 available ESTs (Expressed Sequence Tags) for lily with 52,172 contigs with an average length of 555 bp. The contigs together with singletons covered on average 37% of lily and 39% of tulip estimated transcriptome. Mining lily and tulip sequence data for SSRs (Simple Sequence Repeats) showed that di-nucleotide repeats were twice more abundant in UTRs (UnTranslated Regions) compared to coding regions, while tri-nucleotide repeats were equally spread over coding and UTR regions. Two sets of single nucleotide polymorphism (SNP) markers suitable for high throughput genotyping were developed. In the first set, no SNPs flanking the target SNP (50 bp on either side) were allowed. In the second set, one SNP in the flanking regions was allowed, which resulted in a 2 to 3 fold increase in SNP marker numbers compared with the first set. Orthologous groups between the two flower bulbs: lily and tulip (12,017 groups) and among the three monocot species: lily, tulip, and rice (6,900 groups) were determined using OrthoMCL. Orthologous groups were screened for common SNP markers and EST-SSRs to study synteny between lily and tulip, which resulted in 113 common SNP markers and 292 common EST-SSR. Lily and tulip contigs generated were annotated and described according to Gene Ontology terminology.ConclusionsTwo transcriptome sets were built that are valuable resources for marker development, comparative genomic studies and candidate gene approaches. Next generation sequencing of leaf transcriptome is very effective; however, deeper sequencing and using more tissues and stages is advisable for extended comparative studies.

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M.J.M. Smulders

Wageningen University and Research Centre

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Ben Vosman

Wageningen University and Research Centre

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Richard G. F. Visser

Wageningen University and Research Centre

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Jaap M. van Tuyl

Wageningen University and Research Centre

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Arwa Shahin

Wageningen University and Research Centre

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M.S. Ramanna

Wageningen University and Research Centre

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Roeland E. Voorrips

Wageningen University and Research Centre

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Songlin Xie

Wageningen University and Research Centre

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Chris Maliepaard

Wageningen University and Research Centre

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J.M. van Tuyl

Wageningen University and Research Centre

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