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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Reverse breeding in Arabidopsis thaliana generates homozygous parental lines from a heterozygous plant
Wijnker, T.G. ; Dun, K.P.M. van; Snoo, C.B. ; Lelivelt, C.L.C. ; Keurentjes, J.J.B. ; Naharudin, N.S. ; Ravi, M. ; Chan, S.W.L. ; Jong, J.H.S.G.M. de; Dirks, R. - \ 2012
Nature Genetics 44 (2012). - ISSN 1061-4036 - p. 467 - 470.
genome - dna - construction - meiosis - genes - rflp - map
Traditionally, hybrid seeds are produced by crossing selected inbred lines. Here we provide a proof of concept for reverse breeding, a new approach that simplifies meiosis such that homozygous parental lines can be generated from a vigorous hybrid individual. We silenced DMC1, which encodes the meiotic recombination protein DISRUPTED MEIOTIC cDNA1, in hybrids of A. thaliana, so that non-recombined parental chromosomes segregate during meiosis. We then converted the resulting gametes into adult haploid plants, and subsequently into homozygous diploids, so that each contained half the genome of the original hybrid. From 36 homozygous lines, we selected 3 (out of 6) complementing parental pairs that allowed us to recreate the original hybrid by intercrossing. In addition, this approach resulted in a complete set of chromosome-substitution lines. Our method allows the selection of a single choice offspring from a segregating population and preservation of its heterozygous genotype by generating homozygous founder lines
High resolution mapping of a novel late blight resistance gene Rpi-avll, from the wild Bolivian species Solanum avilesii
Verzaux, E.C. ; Budding, D.J. ; Vetten, N. de; Niks, R.E. ; Vleeshouwers, V.G.A.A. ; Vossen, E.A.G. van der; Jacobsen, E. ; Visser, R.G.F. - \ 2011
American Journal of Potato Research 88 (2011)6. - ISSN 1099-209X - p. 511 - 519.
marker-assisted selection - potato-virus-y - phytophthora-infestans - disease-resistance - quantitative resistance - cultivated potato - bulbocastanum - rflp - qtl - microsatellites
Both Mexico and South America are rich in Solanum species that might be valuable sources of resistance (R) genes to late blight (Phytophthora infestans). Here, we focus on an R gene present in the diploid Bolivian species S. avilesii. The genotype carrying the R gene was resistant to eight out of 10 Phytophthora isolates of various provenances. The identification of a resistant phenotype and the generation of a segregating population allowed the mapping of a single dominant R gene, Rpi-avl1, which is located in an R gene cluster on chromosome 11. This R gene cluster is considered as an R gene “hot spot”, containing R genes to at least five different pathogens. High resolution mapping of the Rpi-avl1 gene revealed a marker co-segregating in 3890 F1 individuals, which may be used for marker assisted selection in breeding programs and for further cloning of Rpi-avl1
Microsatellite Markers in and around Rice Genes: Applications in Variety Identification and DUS Testing
Bonow, S. ; Pinho, E.V.R. Von; Vieira, M.G.C. ; Vosman, B. - \ 2009
Crop Science 49 (2009)3. - ISSN 0011-183X - p. 880 - 886.
oryza-sativa l. - diversity - cultivars - bread - sequence - plants - rflp - dna
In Brazil, rice (Oryza sativa L.) varieties adapted to different ecological regions are available on the market. However, these varieties exhibit highly similar morphologies, which makes their identification difficult. In this study we identified microsatellites in and around genes that are useful for the identification of the main rice varieties cultivated in Brazil. Thirteen microsatellites were selected from the region upstream of MADS-box genes and 37 were derived from expressed sequence tags (ESTs). Of the 50 microsatellites selected, 19 were polymorphic, and a small set of five primer pairs was sufficient to discriminate among the 37 rice varieties studied. The polymorphic information content (PIC) value of the 19 microsatellite markers varied between 0.05 and 0.94. Unweighted pair group method with arithmetic mean (UPGMA) analysis showed that these markers group the 37 varieties according to their subspecies, indica or japonica. These results indicate that it is possible to identify informative microsatellites in and around rice genes, and that these markers are capable of discriminating between closely related varieties of rice. Moreover, our findings suggest that microsatellite markers can play an important role as a source of additional information to supplement the morphological descriptors recommended by International Union for the Protection of New Varieties of Plants (UPOV).
A high-density, integrated genetic linkage map of lettuce (Lactuca spp.)
Truco, M.J. ; Antonise, R. ; Lavelle, D. ; Ochoa, O. ; Kozik, A. ; Witsenboer, H. ; Fort, S.B. ; Jeuken, M.J.W. ; Kesseli, R.V. ; Lindhout, P. ; Michelmore, R. ; Peleman, J. - \ 2007
Theoretical and Applied Genetics 115 (2007)6. - ISSN 0040-5752 - p. 735 - 746.
brassica-napus - aflp markers - recombination - sativa - populations - construction - genome - rflp - identification - exploitation
An integrated map for lettuce comprising of 2,744 markers was developed from seven intra- and inter-specific mapping populations. A total of 560 markers that segregated in two or more populations were used to align the individual maps. 2,073 AFLP, 152 RFLP, 130 SSR, and 360 RAPD as well as 29 other markers were assigned to nine chromosomal linkage groups that spanned a total of 1,505 cM and ranged from 136 to 238 cM. The maximum interval between markers in the integrated map is 43 cM and the mean interval is 0.7 cM. The majority of markers segregated close to Mendelian expectations in the intra-specific crosses. In the two L. saligna × L. sativa inter-specific crosses, a total of 155 and 116 markers in 13 regions exhibited significant segregation distortion. Data visualization tools were developed to curate, display and query the data. The integrated map provides a framework for mapping ESTs in one core mapping population relative to phenotypes that segregate in other populations. It also provides large numbers of markers for marker assisted selection, candidate gene identification, and studies of genome evolution in the Compositae
A high density barley microsatellite consensus map with 775 SSR loci
Varshney, R.K. ; Marcel, T.C. ; Ramsay, L. ; Russell, J. ; Roder, M.S. ; Stein, N. ; Waugh, R. ; Langridge, P. ; Niks, R.E. ; Graner, A. - \ 2007
Theoretical and Applied Genetics 114 (2007)6. - ISSN 0040-5752 - p. 1091 - 1103.
simple sequence repeats - genetic-linkage maps - hordeum-vulgare l. - abiotic stress - aflp markers - bread wheat - genome - diversity - plants - rflp
A microsatellite or simple sequence repeat (SSR) consensus map of barley was constructed by joining six independent genetic maps based on the mapping populations 'Igri x Franka', 'Steptoe x Morex', 'OWBRec x OWBDom', 'Lina x Canada Park', 'L94 x Vada' and 'SusPtrit x Vada'. Segregation data for microsatellite markers from different research groups including SCRI (Bmac, Bmag, EBmac, EBmag, HVGeneName, scsssr), IPK (GBM, GBMS), WUR (GBM), Virginia Polytechnic Institute (HVM), and MPI for Plant Breeding (HVGeneName), generated in above mapping populations, were used in the computer program RECORD to order the markers of the individual linkage data sets. Subsequently, a framework map was constructed for each chromosome by integrating the 496 "bridge markers" common to two or more individual maps with the help of the computer programme JoinMapA (R) 3.0. The final map was calculated by following a "neighbours" map approach. The integrated map contained 775 unique microsatellite loci, from 688 primer pairs, ranging from 93 (6H) to 132 (2H) and with an average of 111 markers per linkage group. The genomic DNA-derived SSR marker loci had a higher polymorphism information content value (average 0.61) as compared to the EST/gene-derived SSR loci (average 0.48). The consensus map spans 1,068 cM providing an average density of one SSR marker every 1.38 cM. Such a high-density consensus SSR map provides barley molecular breeding programmes with a better choice regarding the quality of markers and a higher probability of polymorphic markers in an important chromosomal interval. This map also offers the possibilities of thorough alignment for the (future) physical map and implementation in haplotype diversity studies of barley.
QTL analysis of variation for vigour in rose
Yan, Z. ; Visser, P.B. ; Hendriks, T. ; Prins, T.W. ; Stam, P. ; Dolstra, O. - \ 2007
Euphytica 154 (2007)1-2. - ISSN 0014-2336 - p. 53 - 62.
genetic-linkage maps - quantitative trait loci - aflp markers - construction - rflp - rapd
The improvement of energy efficiency in the greenhouse production of cut rose and pot rose can be achieved through the use of rose cultivars having vigorous growth. A better understanding of the inheritance of vigour and its related traits will assist the breeding activities. Quantitative trait locus (QTL) analyses were performed with the help of an integrated linkage map of a diploid rose population originating from a cross between Rosa multiflora-derived genotypes. The underlying datasets for ten vigour-related traits were collected in an evaluation study of this population in two greenhouse experiments with suboptimal temperatures for growth. We identified ten chromosomal regions, scattered over the seven linkage groups, containing QTLs for these traits. Considering each trait separately, we detected a total of 42 QTLs. Among these QTLs, 24 were found in both of the experiments, eight and ten were specific to either of the two experiments. The number of QTLs for individual traits varied from three to five with a respective contribution to the phenotypic variation from 12 to 35%. QTLs for highly correlated traits frequently co-localized, indicating a common genetic basis. Clustering of QTLs for different traits was noted in some chromosome regions, for instance, one on chromosome 2 included major QTLs for eight of ten traits under study, suggesting co-localization of several separate genes or/and the occurrence of various genes having pleiotropic effects. The discovery of markers associated to QTL regions is in roses the first step towards marker-assisted selection for vigour improvement enabling the transfer of useful QTL-alleles of R. multiflora to pot and cut roses
Vigour evaluation for genetics and breeding in rose
Yan, Z. ; Dolstra, O. ; Hendriks, T. ; Prins, T.W. ; Stam, P. ; Visser, P.B. - \ 2005
Euphytica 145 (2005)3. - ISSN 0014-2336 - p. 339 - 347.
seedling-vigor - linkage map - traits - growth - potato - rflp - aflp - construction - resistance - markers
Breeding of cut and pot rose cultivars for efficient production under low-energy conditions in greenhouses will be facilitated by understanding the inheritance of vigour. To get insight into the genetic variation of vigour-related traits, a diploid rose population was employed for an evaluation study in greenhouses in The Netherlands and Denmark. For all the traits investigated the population showed a continuous quantitative variation as well as a considerable transgression. For most of the traits, the genetic variation found among the tested entries was highly significant and tended to be large in comparison to the effects of genotype by environment interaction. The heritability based on means of the traits was high and ranged from 68 to 92%. Strong simple correlations (r = 0.65 to 0.95) were found among the traits shoot length, leaf area, leaf dry weight, stem dry weight, total dry weight and growth rate. The total dry weight and leaf area are suggested to be good parameters for early selection of rose genotypes with vigorous growth under suboptimal growth conditions.
Genetic and economic aspects of marker-assisted reduction of redundancy from a wild potato germplasm collection
Treuren, R. van; Magda, A. ; Hoekstra, R. ; Hintum, T.J.L. van - \ 2004
Genetic Resources and Crop Evolution 51 (2004)3. - ISSN 0925-9864 - p. 277 - 290.
rapd analysis - aflp markers - dna - accessions - conservation - identification - management - diversity - resources - rflp
The wild potato germplasm collection of the series Acaulia, maintained at the Centre for Genetic Resources, The Netherlands, consists of 314 accessions. In previous investigations, 15 potential duplication groups with a total of 36 accessions were identified based on AFLP analysis of a limited sample per accession. In the present study, the potential redundancies, plus one additional accession, were studied with increased sample sizes to examine intra- and inter-accession variation more accurately, with the aim to reduce the size of the collection. No variation was observed within two potential duplication groups, whereas only limited differentiation among accessions was detected within seven groups, resulting in a total of 15 redundant accessions (nearly 5% of the collection). A cluster analysis of all the accessions of the collection showed that these nine groups each had a distinct identity. It was decided to maintain the accessions of the remaining six groups as separate entries based on the large differentiation observed among accessions and the absence of a clear identity. An analysis of molecular variance in the set of 37 accessions showed that 91% of the observed variation could be found among accessions. This variance component appeared unaffected when the set was analysed without the 15 redundant accessions. The invested costs to identify redundancies in the series Acaulia by AFLP analysis are estimated at k 57.3, whereas the savings achieved by reduction of the collection are estimated at k 21.0 per generation. However, a cost-benefit analysis should not only focus on the short-term return of investments, but should also consider the value of newly obtained data and information. These include taxonomic information about accessions, optimised sampling strategies, optimised regeneration procedures, additional data for core collection formation and more efficient utilisation of germplasm.
Application of ISSR markers in the genus Lycopersicon
Tikunov, Y.M. ; Khrustaleva, L.I. ; Karlov, G.I. - \ 2003
Euphytica 131 (2003)1. - ISSN 0014-2336 - p. 71 - 81.
sequence repeat issr - molecular linkage maps - microsatellite markers - tomato genome - phylogenetic-relationships - genetic diversity - chloroplast dna - rflp - rapd - polymorphism
The level of polymorphism in tomato was studied using ISSR-PCR. Five tomato species: Lycopersicon esculentum, Lycopersicon pennellii, Lycopersicon cheesmanii, Lycopersicon humboldtii, Lycopersicon hirsutum and two Lycopersicon esculentum substitution lines IL 6-3 and WSL 6 were analyzed. ISSR-PCR was performed with fourteen primers. Nine of these fourteen primers were individually able to distinguish all tomato species. The data were used to create a phylogenetic tree of the five tomato species. The tree showed complete correspondence to previous phylogenetic investigations. ISSR-PCR on two Lycopersicon esculentum substitution lines IL 6-3 and WSL 6 enabled us to place thirteen ISSR markers on the classical map of Lycopersicon esculentum chromosome 6. Some of the markers were not located in the pericentromeric region. Using one ISSR and one RGA (Resistance-gene analogs) primer resulted in fingerprints having some new bands compared with ISSR fingerprints.
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.
Preliminary genetic linkage map of Miscanthus sinensis with RAPD markers
Atienza, S.G. ; Satovic, Z. ; Petersen, K.K. ; Dolstra, O. ; Martin, A. - \ 2002
Theoretical and Applied Genetics 105 (2002)6-7. - ISSN 0040-5752 - p. 946 - 952.
eucalyptus-urophylla - arbitrary primers - isozyme markers - aflp - rflp - dna - microsatellite - genomes - polymorphisms - construction
We have used an "offspring cross" mapping strategy in combination with the random amplified polymorphic DNA (RAPD) assay to construct the first genetic map of the species Miscanthus sinensis (2n = 2x = 38). This map is based on an outbred population of 89 individuals resulting from the cross between two genotypes from a previously designed cross. Consequently, both parents are fullsibs. The same proportion of bi-parental markers (heterozygotic in both parents) and pseudo-testcross markers (heterozygotic in one parent and null in the other), mono-parental markers, have been obtained. A total of 383 RAPD markers were analysed within the 89 F1 plants. Out of these markers, 257 were mapped into 28 linkage groups which spanned a total map length of around 1,074.5 cM with an average density of 4.2 cM per marker. Out of 257 mapped markers, 62 were inherited from F1.1 (P1), 63 from F1.7 (P7) and 132 were bi-parental markers. The contribution to the map was equal from both parents. This map provides a useful tool for genetic analyses of agronomically interesting characters in M. sinensis such as flowering, yield, plant height, stem diameter and mineral constitution. The offspring cross mapping strategy is proposed to obtain a higher efficiency in developing integrated maps including both parents
A novel method for the construction of genome wide transcriptome maps
Brugmans, B.W. ; Fernandez del Carmen, A. ; Bachem, C.W.B. ; Os, H. van; Eck, H.J. van; Visser, R.G.F. - \ 2002
The Plant Journal 31 (2002)2. - ISSN 0960-7412 - p. 211 - 222.
differential gene-expression - cdna-aflp - linkage maps - arabidopsis-thaliana - potato - markers - rflp - sequence - tomato - profiles
Expression profiling by cDNA-AFLP is commonly used to display the transcriptome of a specific tissue, treatment or developmental stage. In this paper, cDNA-AFLP has been used to study transcripts expressed in segregating populations from Arabidopsis thaliana and potato (Solanum tuberosum ). The genetic differences between the offspring genotypes are thus visualized as polymorphisms in the transcriptome. We show that polymorphic transcripts can be used as genetic markers and allow the construction of a linkage map. The resulting map shows that, in contrast to genomic markers, the transcriptome-derived markers did not cluster in particular areas of the chromosome, and that cDNA-AFLP markers are targeted specifically to transcriptionally active regions. The cDNA-AFLP markers used in mapping are derived from DNA polymorphisms in transcripts, rather than differences in expression regulation. The high potential of transcriptome markers as opposed to (anonymous) genomic markers for applications in genetic analyses, marker-assisted breeding and map-based cloning is discussed.
A combined amplified fragment length polymorphism and randomly amplified polymorphism DNA genetic linkage map of Mycosphaerella graminicola, the Septoria tritici leaf blotch pathogen of wheat
Kema, G.H.J. ; Goodwin, S.B. ; Hamza, S. ; Verstappen, E.C.P. ; Cavaletto, J.R. ; Lee, T.A.J. van der; Weerdt, M. de; Bonants, P.J.M. ; Waalwijk, C. - \ 2002
Genetics 161 (2002)4. - ISSN 0016-6731 - p. 1497 - 1505.
electrophoretic karyotype - aflp markers - resistance - rflp - construction - pathosystem - populations - avirulence - cultivars - virulence
An F-1 mapping population of the septoria tritici blotch pathogen of wheat, Mycosphaerella graminicola, was generated by crossing the two Dutch field isolates IPO323 and IPO94269. AFLP and RAPD marker data sets were combined to produce a high-density genetic linkage map. The final map contained 223 AFLP and 57 RAPD markers, plus the biological traits mating type and avirulence, in 23 linkage groups spanning 1216 cM. Many AFLPs and some RAPD markers were clustered. When markers were reduced to 1 per cluster, 229 unique positions were mapped, with an average distance of 5.3 cM between markers. Because M. graminicola probably has 17 or 18 chromosomes, at least 5 of the 23 linkage groups probably will need to be combined with others once additional markers are added to the map. This was confirmed by pulsed-field gel analysis; probes derived from 2 of the smallest linkage groups hybridized to two of the largest chromosome-sized bands, revealing a discrepancy between physical and genetic distance. The utility of the map was demonstrated by identifying molecular markers tightly linked to two genes of biological interest, mating type and avirulence. Bulked segregant analysis was used to identify additional molecular markers closely linked to these traits. This is the first genetic linkage map for any species in the genus Mycosphaerella or the family Mycosphaerellaceae.
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