Publications (4)7.13 Total impact

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    ABSTRACT: The first hurdle in developing microsatellite markers, cloning, has been overcome by next generation sequencing. The second hurdle is testing to differentiate polymorphic from non-polymorphic loci. The third hurdle, somewhat hidden, is that only polymorphic markers with a large effective number of alleles are sufficiently informative to be deployed in multiple studies. Both steps are laborious and still done manually. We have developed a strategy in which we first screen reads from multiple genotypes for repeats that show the most length variants, and only these are subsequently developed into markers. We validated our strategy in tetraploid garden rose using Illumina paired-end transcriptome sequences of 11 roses. Out of 48 tested two markers failed to amplify but all others were polymorphic. Ten loci amplified more than one locus, indicating duplicated genes or gene families. Completely avoiding duplicated loci will be difficult because the range of numbers of predicted alleles of highly polymorphic single- and multi-locus markers largely overlapped. Of the remainder, half were replicate markers (i.e., multiple primer pairs for one locus), indicating the difficulty of correctly filtering short reads containing repeat sequences. We subsequently refined the approach to eliminate multiple primer sets to the same loci. The remaining 18 markers were all highly polymorphic, amplifying on average 11.7 alleles per marker (range = 6 to 20) in 11 tetraploid roses, exceeding the 8.2 alleles per marker of the 24 most polymorphic markers genotyped previously. This strategy, therefore, represents a major step forward in the development of highly polymorphic microsatellite markers. This article is protected by copyright. All rights reserved.
    Molecular Ecology Resources 06/2014; DOI:10.1111/1755-0998.12289
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    ABSTRACT: For the first time genetic diversity among modern garden rose cultivars has been evaluated using a set of 24 microsatellite markers covering most chromosomes. A total of 518 different alleles were obtained in the set of 138 rose cultivars and this led to the conclusion that in terms of genetic diversity cut roses can be considered as a subgroup of the garden roses. Genetic differentiation among types of garden roses (Fst = 0.022) was four times that among cut roses, and similar in magnitude to the differentiation among breeders, due to the fact that horticultural groups and breeders overlap largely in classification. Winter hardy Svejda's cultivars (Canadian Explorer roses) showed the least similarities to European roses, and introgression from wild species for winter hardiness was clearly visible. Roses of Harkness and Olesen shared a similar genepool. Comparison of the differentiation among linkage groups indicated that linkage group 5 is potentially a region containing important QTLs for winter hardiness. Linkage group 6 contains the largest amount of genetic diversity, while linkage group 2 is the most differentiated among types of garden roses.
    Scientia Horticulturae 10/2013; 162:320-332. DOI:10.1016/j.scienta.2013.08.015
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    ABSTRACT: Under the adagio “Conservation by utilisation is the best way forward for a long-term sustainable protection of the remaining resources” the GENEROSE-project focuses on 3 major objectives: 1) sustainable conservation of wild resources by attributing them an extra value in landscaping or for disease resistance breeding; 2) development of efficient screening techniques for fungal disease resistance and 3) strategies to overcome crossing barriers between wild species and cultivated roses. The project integrates biotechnology (DNA markers for biodiversity evaluation and resistance mapping, flow cytometry for pollen sorting) with original breeding work (use of wild species) and direct potential end-use evaluation by rose breeders and growers. Apart from the ornamental value of possible new wild features, disease resistant cultivars will promote rose production with a lower environmental impact.