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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Bin mapping of tomato diversity array (DArT) markers to genomic regions of Solanum lycopersicum × Solanum pennellii introgression lines
Schalkwyk, A. ; Wenzl, P. ; Smit, S. ; Lopez-Cobollo, R. ; Kilian, A. ; Bishop, G. ; Hefer, C. ; Berger, D.K. - \ 2012
Theoretical and Applied Genetics 124 (2012)5. - ISSN 0040-5752 - p. 947 - 956.
technology dart - genetic diversity - wild relatives - arabidopsis - health - barley - fruit - ssr - map
Marker-trait association studies in tomato have progressed rapidly due to the availability of several populations developed between wild species and domesticated tomato. However, in the absence of whole genome sequences for each wild species, molecular marker methods for whole genome comparisons and fine mapping are required. We describe the development and validation of a diversity arrays technology (DArT) platform for tomato using an introgression line (IL) population consisting of wild Solanum pennellii introgressed into Solanum lycopersicum (cv. M82). A tomato diversity array consisting of 6,912 clones from domesticated tomato and twelve wild tomato/Solanaceous species was constructed. We successfully bin-mapped 990 polymorphic DArT markers together with 108 RFLP markers across the IL population, increasing the number of markers available for each S. pennellii introgression by tenfold on average. A subset of DArT markers from ILs previously associated with increased levels of lycopene and carotene were sequenced, and 44% matched protein coding genes. The bin-map position and order of sequenced DArT markers correlated well with their physical position on scaffolds of the draft tomato genome sequence (SL2.40). The utility of sequenced DArT markers was illustrated by converting several markers in both the S. pennellii and S. lycopersicum phases to cleaved amplified polymorphic sequence (CAPS) markers. Genotype scores from the CAPS markers confirmed the genotype scores from the DArT hybridizations used to construct the bin map. The tomato diversity array provides additional “sequence-characterized” markers for fine mapping of QTLs in S. pennellii ILs and wild tomato species.
Genetic diversity and genetic similarities between Iranian rose species
Samiei, L. ; Naderi, R. ; Khalighi, A. ; Shahnejat-Bushehri, A.A. ; Mozaffarian, V. ; Esselink, G.D. ; Kazempour Osaloo, S. ; Smulders, M.J.M. - \ 2010
Journal of Horticultural Science and Biotechnology 85 (2010)3. - ISSN 1462-0316 - p. 231 - 237.
damascena mill. accessions - microsatellite analysis - phylogenetic-relationships - genus rosa - markers - aflp - ssr - identification - differentiation - varieties
Wild rose species were collected from different regions of Iran for a rose breeding programme. They included accessions from Rosa persica, R. foetida, R. pimpinellifolia, R. hemisphaerica, R. canina, R. iberica, R. damascena, R. beggeriana, and R. orientalis. Ten microsatellite (simple sequence repeat; SSR) markers were used to analyse the genetic variation among these rose species. The SSR markers amplified alleles in all species, even if they were from different sections within the genus. An unweighted pair group method cluster analysis (UPGMA) based on similarity values revealed five main Groups. The data showed no support for any distinction between R. canina and R. iberica, as all the accessions were placed in one Group, and accessions of these two species were more closely-related to each other within a Province than to accessions of the same species in other Provinces. Accessions of sect. Pimpinellifoliae were combined with plants from sect. Rosa and Cinnamomeae in two different Groups. Genetically, R. persica clustered distinctly from all others, with few alleles shared with the other taxa. We discuss the use of SSR markers for phylogenetic analysis when these markers are amplified in all species of a genus
Nucleotide-binding site (NBS) profiling of genetic diversity in durum wheat
Mantovani, P. ; Linden, C.G. van der; Maccaferri, M. ; Sanguineti, M.C. ; Tuberosa, R. - \ 2006
Genome 49 (2006)11. - ISSN 0831-2796 - p. 1473 - 1480.
microsatellite markers - disease resistance - bread wheat - germplasm - aflp - traits - ssr - map
Molecular markers are effective tools to investigate genetic diversity for resistance to pathogens. NBS (nucleotide-binding site) profiling is a OCR (polymerase chain reaction)-based approach to studying genetic variability that specifically targets chromosome regions containing R-genes and R-gene analogues. We used NBS profiling to measure genetic diversity among 58 accessions of durum wheat. Mean polymorphism rates detected using MseI and AluI as restriction enzymes were 34% and 22%, respectively. Mean number of polymorphisms per enzyme-primer combination was equal to 23.8 +/- 5.9, ranging from 13 to 31 polymorphic bands. In total, 96 markers over 190 indicated a good capacity to discriminate between accessions (the polymorphic index content ranging from 0.30 to 0.50). The results obtained with NBS profiling were compared with simple sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) data of the same set of accessions. The genetic distances computed with 190 NBS profiling markers were in close agreement with those obtained with AFLP and SSR markers (r = 0.73 and 0.76, respectively). Our results indicate that NBS profiling provides an effective means to investigate genetic diversity in durum wheat.
Assignment of allelic configuration in polyploids using the MAC-PR (microsatellite DNA allele counting peak ratios) method
Esselink, G.D. ; Nybom, H. ; Vosman, B.J. - \ 2004
Theoretical and Applied Genetics 109 (2004)2. - ISSN 0040-5752 - p. 402 - 408.
potato solanum-tuberosum - markers - l. - identification - inheritance - population - rosaceae - rapd - aflp - ssr
Polysomic inheritance frequently results in the simultaneous occurrence of several microsatellite DNA alleles on a single locus. The MAC-PR (microsatellite DNA allele counting¿peak ratios) method was recently developed for the analysis of polyploid plants and makes use of the quantitative values for microsatellite allele peak areas. To date, this approach has only been used in plants with known genetic relationships. We report here the application of MAC-PR for the first time to random samples of unknown pedigrees. We analysed six microsatellite loci using a set of tetraploid ornamental rose (Rosa x hybrida L.) varieties. For each locus, all alleles were analysed in pairwise combinations in order to determine their copy number in the individual samples. This was accomplished by calculating the ratios between the peak areas for two alleles in all of the samples where these two alleles occurred together. The allele peak ratios observed were plotted in a histogram, and those histograms that produced at least two well-separated groups were selected for further analysis. Mean allelic peak ratio values for these groups were compared to the relationships expected between alleles in hypothetical configurations of the locus investigated. Using this approach, we were able to assign precise allelic configurations (the actual genotype) to almost all of the varieties analysed for five of the six loci investigated. MAC-PR also appears to be a very effective tool for detecting null alleles in polyploid species
Analysis of the wild potato germplasm of the series Acaulia with AFLPs: implications for ex situ conservation
McGregor, C.E. ; Treuren, R. van; Hoekstra, R. ; Hintum, T.J.L. van - \ 2002
Theoretical and Applied Genetics 104 (2002)1. - ISSN 0040-5752 - p. 146 - 156.
duplicate accessions - l. germplasm - dna analysis - rapd - identification - collection - rflp - ssr
The wild potato germplasm of the series Acaulia maintained at the Centre for Genetic Resources, The Netherlands, currently consists of 314 accessions. This collection comprises seed samples of the species Solanum acaule (ssp. acaule, ssp. aemulans, ssp. palmirense and ssp. punae) and Solanum albicans collected from South America. In order to validate taxonomic classification, to investigate the extent of redundancy and to study the distribution of genetic diversity across the collection area, the entire collection was analysed with two AFLP primer pairs on two plants per accession. Within the entire sample a total number of 130 polymorphic bands were scored for the two primer pairs. An UPGMA cluster analysis grouped the majority of plants according to the species and subspecies. A total number of 16 misclassifications were identified, including four cases that did not seem to belong to the series Acaulia. Two accessions were found to consist of plants of different AFLP clusters. AFLP data also allowed the taxonomic classification of the subspecies of 97 accessions that previously were described as S. acaule only. For 126 accessions the two individuals studied displayed identical AFLP profiles. Forty six of these 126 accessions shared their profiles with both or single plants of other accessions. These were all tested for identical profiles for a third primer pair, resulting in 15 duplication groups consisting of a total number of 22 accessions and 14 single plants. Analyses of molecular variance (AMOVA) were performed to examine the distribution of genetic variation. Comparison of geographic distances between the collection site of plants and the number of AFLP polymorphisms revealed no consistent relationship between geographic distance and genetic diversity. AFLP analysis appeared to be an efficient method to verify taxonomic classification and to identify redundancies in the wild germplasm of the series Acaulia. Implications of the results for the ex situ conservation of wild potato germplasm are discussed.
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