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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Model-based evaluation of maturity type of potato using a diverse set of standard cultivars and a segregating diploid population
Khan, M.S. ; Eck, H.J. van; Struik, P.C. - \ 2013
Potato Research 56 (2013)2. - ISSN 0014-3065 - p. 127 - 146.
solanum-tuberosum - competitive ability - light interception - path coefficient - leaf appearance - rapd markers - late blight - crop - growth - l.
The objective of this paper is to evaluate the performance of the conventional system of classifying maturity type in potato and to provide a concept of maturity type based on crop physiology. We present an approach in which physiological traits are used to quantify and assess maturity type unambiguously for a set of varieties covering a wide range of maturity classes and a diploid F1 population separating for maturity and well-adapted to Dutch growing conditions, both grown in six environments. We defined physiological maturity based on four traits: the duration of maximum green canopy, the area under the green canopy cover progress curve, and the rate and duration of tuber bulking. The results indicated that physiological maturity type criteria tended to define maturity classes less ambiguously than the conventional criterion. Moreover, the conventional criterion was subject to more random noise and lacked stability and/or repeatability compared with the physiological traits. The physiological maturity criteria also illustrated the physiological trade-offs that existed between the selected traits and underlined the subtle complexities in classifying maturity type. This study highlighted the capabilities of different maturity type criteria in discriminating between different maturity classes among the large set of genotypes. Our new approach involving key physiological traits could be beneficial in offering physiology-based criteria to re-define maturity type. An improved criterion based on important physiological traits would allow relating the maturity to crop phenology and physiology. These new criteria may be amenable to further genetic analysis and could help in designing strategies for potato ideotype breeding for genotypes with specific maturity types
The role of Schmidt 'Antonovka' in apple scab resistance breeding
Bus, V.G.M. ; Weg, W.E. van de; Peil, A. ; Dunemann, F. ; Zini, E. ; Laurens, F.N.D. ; Blazek, J. ; Hanke, V. ; Forsline, P.L. - \ 2012
Tree Genetics and Genomes 8 (2012)4. - ISSN 1614-2942 - p. 627 - 642.
venturia-inaequalis - dresden-pillnitz - molecular characterization - candidate genes - broad-spectrum - rapd markers - race 6 - malus - cultivars - pathogen
'Antonovka' has long been recognised as a major source of scab (Venturia inaequalis) resistance useful for apple breeding worldwide. Both major gene resistances in the form of the Rvi10 and Rvi17 and quantitative resistance, collectively identified as VA, have been identified in different accessions of 'Antonovka'. Most of the 'Antonovka' scab resistance used in apple-breeding programmes around the world can be traced back to Schmidt 'Antonovka' and predominantly its B VIII progenies 33,25 (PI 172623), 34,6 (PI 172633), 33,8 (PI 172612) and 34,5 (PI 172632). Using genetic profile reconstruction, we have identified "common 'Antonovka' " as the progenitor of the B VIII family, which is consistent with it having been a commercial cultivar in Poland and the single source of scab resistance used by Dr. Martin Schmidt. The major 'Antonovka' scab resistance genes mapped to date are located either very close to Rvi6, or about 20-25 cM above it, but their identities need further elucidation. The presence of the 139 bp allele of the CH-Vf1 microsatellite marker known to be associated with Rvi17 (Va1) in most of the 'Antonovka' germplasm used in breeding suggests that it plays a central role in the resistance. The nature and the genetic relationships of the scab resistance in these accessions as well as a number of apple cultivars derived from 'Antonovka', such as, 'Freedom', 'Burgundy' and 'Angold', are discussed. The parentage of 'Reglindis' is unclear, but the cultivar commercialised as 'Reglindis' was confirmed to be an Rvi6 cultivar.
Development of a locus-specific, co-dominant SCAR marker for assisted-selection of the Sw-5 (Tospovirus resistance) gene cluster in a wide range of tomato accessions
Dianese, E.C. ; Fonseca, M.E.N. ; Goldbach, R.W. ; Kormelink, R.J.M. ; Inoue-Nagata, A.K. ; Resende, R.O. de; Boiteux, L.S. - \ 2010
Molecular Breeding 25 (2010)1. - ISSN 1380-3743 - p. 133 - 142.
spotted-wilt-virus - lycopersicon-esculentum - thrips transmission - tswv resistance - rapd markers - peruvianum - sw5
The best levels of broad-spectrum Tospovirus resistance reported in tomatoes thus far are conferred by the Sw-5 locus. This locus contains at least five paralogues (denoted Sw-5a through Sw-5e), of which Sw-5b represents the actual resistance gene. Here we evaluated a panel of seven PCR primer pairs matching different sequences within a genomic region spanning the Sw-5a and Sw-5b gene cluster. Primer efficiency evaluation was done employing tomato isolines with and without the Sw-5 locus. One primer pair produced a single and co-dominant polymorphism between susceptible and resistant isolines. Sequence analysis of these amplicons indicated that they were specific for the Sw-5 locus and their differences were due to insertions/deletions. The polymorphic SCAR amplicon encompass a conserved sequence of the promoter region of the functional Sw-5b gene, being located in the position -31 from its open reading frame. This primer pair was also evaluated in field assays and with a collection of accessions known to be either susceptible or resistant to tospoviruses. An almost complete correlation was found between resistance under greenhouse/field conditions and the presence of the marker. Therefore, this primer pair is a very useful tool in marker-assisted selection systems in a large range of tomato accessions.
Development of microsatellite markers for identifying Brazilian coffee arabica varieties
Vieira, E.S.N. ; Pinho, E.V.R. Von; Carvalho, M.G.G. ; Esselink, G. ; Vosman, B. - \ 2010
Genetics and Molecular Biology 33 (2010)3. - ISSN 1415-4757 - p. 507 - 514.
sequence repeat markers - genetic diversity - molecular characterization - chloroplast dna - rapd markers - identification - cultivars - aflp - introgression - canephora
Microsatellite markers, also known as SSRs (Simple Sequence Repeats), have proved to be excellent tools for identifying variety and determining genetic relationships. A set of 127 SSR markers was used to analyze genetic similarity in twenty five Coffea arabica varieties. These were composed of nineteen commercially important Brazilians and six interspecific hybrids of Coffea arabica, Coffea canephora and Coffea liberica. The set used comprised 52 newly developed SSR markers derived from microsatellite enriched libraries, 56 designed on the basis of coffee SSR sequences available from public databases, 6 already published, and 13 universal chloroplast microsatellite markers. Only 22 were polymorphic, these detecting 2-7 alleles per marker, an average of 2.5. Based on the banding patterns generated by polymorphic SSR loci, the set of twenty-five coffee varieties were clustered into two main groups, one composed of only Brazilian varieties, and the other of interspecific hybrids, with a few Brazilians. Color mutants could not be separated. Clustering was in accordance with material genealogy thereby revealing high similarity
Mapping quantitative trait loci (QTLs) for fatty acid composition in an interspecific cross of oil palm
Singh, R. ; Tan, S.G. ; Panandam, L.M. ; Rahman, R.A. ; Ooi, L.C.L. ; Low, E.T.L. ; Sharma, M. ; Jansen, J. ; Cheah, S.C. - \ 2009
BMC Plant Biology 9 (2009). - ISSN 1471-2229
elaeis-guineensis jacq. - genetic-linkage map - marker-assisted selection - brassica-napus - rapd markers - eucalyptus-grandis - pseudo-testcross - seed oil - microsatellite - identification
Marker Assisted Selection (MAS) is well suited to a perennial crop like oil palm, in which the economic products are not produced until several years after planting. The use of DNA markers for selection in such crops can greatly reduce the number of breeding cycles needed. With the use of DNA markers, informed decisions can be made at the nursery stage, regarding which individuals should be retained as breeding stock, which are satisfactory for agricultural production, and which should be culled. The trait associated with oil quality, measured in terms of its fatty acid composition, is an important agronomic trait that can eventually be tracked using molecular markers. This will speed up the production of new and improved oil palm planting materials. Result: A map was constructed using AFLP, RFLP and SSR markers for an interspecific cross involving a Colombian Elaeis oleifera (UP1026) and a Nigerian E. guinneensis (T128). A framework map was generated for the male parent, T128, using Joinmap ver. 4.0. In the paternal (E.guineensis) map, 252 markers (199 AFLP, 38 RFLP and 15 SSR) could be ordered in 21 linkage groups (1815cM). Interval mapping and multiple-QTL model (MQM) mapping (also known as composite interval mapping, CIM) were used to detect quantitative trait loci (QTLs) controlling oil quality (measured in terms of iodine value and fatty acid composition). At a 5% genome-wide significance threshold level, QTLs associated with iodine value (IV), myristic acid (C14:0), palmitic acid (C16:0), palmitoleic acid (C16:1), stearic acid (C18:0), oleic acid (C18:1) and linoleic acid (C18:2) content were detected. One genomic region on Group 1 appears to be influencing IV, C14:0, C16:0, C18:0 and C18:1 content. Significant QTL for C14:0, C16:1, C18:0 and C18:1 content was detected around the same locus on Group 15, thus revealing another major locus influencing fatty acid composition in oil palm. Additional QTL for C18:0 was detected on Group 3. A minor QTL for C18:2 was detected on Group 2. CONCLUSION: This study describes the first successful detection of QTLs for fatty acid composition in oil palm. These QTLs constitute useful tools for application in breeding programmes
Construction of an integrated consensus map of the Apple genome based on four mapping populations
N'Diaye, A. ; Weg, W.E. van de; Kodde, L.P. ; Koller, B. ; Dunemann, F. ; Thiermann, M. ; Tartarini, S. ; Gennari, F. ; Durel, C.E. - \ 2008
Tree Genetics and Genomes 4 (2008)4. - ISSN 1614-2942 - p. 727 - 743.
quantitative trait loci - genetic-linkage map - x-domestica borkh. - malus-pumila mill. - zea-mays l - scab resistance - venturia-inaequalis - rapd markers - qtl analysis - microsatellite markers
An integrated consensus genetic map for apple was constructed on the basis of segregation data from four genetically connected crosses (C1¿=¿Discovery × TN10-8, C2¿=¿Fiesta × Discovery, C3¿=¿Discovery × Prima, C4¿=¿Durello di Forli × Fiesta) with a total of 676 individuals using CarthaGene® software. First, integrated female¿male maps were built for each population using common female¿male simple sequence repeat markers (SSRs). Then, common SSRs over populations were used for the consensus map integration. The integrated consensus map consists of 1,046 markers, of which 159 are SSR markers, distributed over 17 linkage groups reflecting the basic chromosome number of apple. The total length of the integrated consensus map was 1,032 cM with a mean distance between adjacent loci of 1.1 cM. Markers were proportionally distributed over the 17 linkage groups (¿ 2¿=¿16.53, df¿=¿16, p¿=¿0.41). A non-uniform marker distribution was observed within all of the linkage groups (LGs). Clustering of markers at the same position (within a 1-cM window) was observed throughout LGs and consisted predominantly of only two to three linked markers. The four integrated female¿male maps showed a very good colinearity in marker order for their common markers, except for only two (CH01h01, CH05g03) and three (CH05a02z, NZ02b01, Lap-1) markers on LG17 and LG15, respectively. This integrated consensus map provides a framework for performing quantitative trait locus (QTL) detection in a multi-population design and evaluating the genetic background effect on QTL expression.
Diversity and linkage disequilibrium analysis wihtin a selected set of cultivated tomatoes
Berloo, R. van; Zhu, A. ; Ursem, R.A. ; Verbakel, H. ; Gort, G. ; Eeuwijk, F.A. van - \ 2008
Theoretical and Applied Genetics 117 (2008). - ISSN 0040-5752 - p. 89 - 101.
fragment-length-polymorphism - lycopersicon-esculentum - genetic diversity - rapd markers - aflp markers - software - accessions - stability - inference - map
Within the Dutch genomics initiative the ¿Centre for Biosystems Genomics¿ (CBSG) a major research effort is directed at the identification and unraveling of processes and mechanisms affecting fruit quality in tomato. The basis of this fruit quality program was a diverse set of 94 cultivated tomato cultivars, representing a wide spectrum of phenotypes for quality related traits. This paper describes a diversity study performed on these cultivars, using information of 882 AFLP markers, of which 304 markers had a known map position. The AFLP markers were scored as much as possible in a co-dominant fashion. We investigated genome distribution and coverage for the mapped markers and conclude that it proved difficult to arrive at a dense and uniformly distributed coverage of the genome with markers. Mapped markers and unmapped markers were used to investigate population structure. A clear substructure was observed which seemed to coincide with a grouping based on fruit size. Finally, we studied amount and decay of linkage disequilibrium (LD) along the chromosomes. LD was observed over considerable (genetic) distances. We discuss the feasibility of marker-trait association studies and conclude that the amount of genetic variation in our set of cultivars is limited, but that there exists scope for association studies
QTL methodology for response curves on the basis of non-linear mixed models, with an illustration to senescence in potato
Malosetti, M. ; Visser, R.G.F. ; Celis Gamboa, B.C. ; Eeuwijk, F.A. van - \ 2006
Theoretical and Applied Genetics 113 (2006)2. - ISSN 0040-5752 - p. 288 - 300.
quantitative trait loci - growth trajectories - molecular markers - flanking markers - mixture model - water-deficit - rapd markers - inbred lines - linkage maps - leaf growth
The improvement of quantitative traits in plant breeding will in general benefit from a better understanding of the genetic basis underlying their development. In this paper, a QTL mapping strategy is presented for modelling the development of phenotypic traits over time. Traditionally, crop growth models are used to study development. We propose an integration of crop growth models and QTL models within the framework of non-linear mixed models. We illustrate our approach with a QTL model for leaf senescence in a diploid potato cross. Assuming a logistic progression of senescence in time, two curve parameters are modelled, slope and inflection point, as a function of QTLs. The final QTL model for our example data contained four QTLs, of which two affected the position of the inflection point, one the senescence progression-rate, and a final one both inflection point and rate.
Comparing genetic diversity in agroforestry systems with natural forest: a case study of the important timber tree Vitex fischeri in central Kenya
Lengkeek, A.G. ; Muchugi Mwangi, A. ; Agufa, C.A.C. ; Ahenda, J.O. ; Dawson, I.K. - \ 2006
Agroforestry Systems 67 (2006)3. - ISSN 0167-4366 - p. 293 - 300.
rapd markers - arbitrary primers - differentiation - conservation - africa - populations - leguminosae - pcr
It is possible that current tree domestication practices undertaken by farmers reduce the genetic base of tree resources on farms, raising concerns regarding the productivity, sustainability and conservation value of agroforestry ecosystems. Here, we assessed possible changes in genetic variation during domestication in the important and heavily utilised timber species, Vitex fischeri Gu¿rke (syn. Vitex keniensis), by comparing geographically proximate forest and farm material in central Kenya. Employing RAPD analysis, a total of 104 polymorphic markers revealed by five arbitrary primers were scored in a total of 65 individuals, 32 from forest and 33 from farmland. Despite concerns of possible genetic erosion, forest and farm stands did not differ significantly in levels of genetic variation, with H values of 0.278 and 0.269, respectively. However, Mantel tests did reveal greater geographically related associative genetic structure among individuals in farm rather than forest material, with r M values of 0.217 and 0.114, respectively. A more detailed analysis of structure suggested this could be due to local variation in origin of some on-farm trees. Implications of data for the genetic management of V. fischeri stands during farmer-led tree domestication activities are discussed. At present, there appears little reason to reject on-farm V. fischeri as a source of germplasm for future on-farm planting or for conservation purposes, although this situation may change and will require monitoring
AFLP genetic polymorphism in wild barley (Hordeum spontaneum) populations in Israel
Turpeinen, T. ; Vanhala, T. ; Nevo, E. ; Nissila, E. - \ 2003
Theoretical and Applied Genetics 106 (2003)7. - ISSN 0040-5752 - p. 1333 - 1339.
allozyme polymorphisms - natural-selection - ecological stress - rapd markers - diversity - differentiation - evolution - koch
The genetic diversity produced by the amplified fragment length polymorphism (AFLP) method was studied in 94 genotypes of wild barley, Hordeum spontaneum (C. Koch) Thell., originating from ten ecologically and geographically different locations in Israel. Eight primer pairs produced 204 discernible loci of which 189 (93%) were polymorphic. Each genotype had a unique banding profile and the genetic similarity coefficient varied between 0.74 and 0.98. The phenogram generated from these similarities by the UPGMA method did not group genotypes strictly according to their geographical origin, which pattern was also seen in the principal coordinate (PCO) plot. Genetic diversity was larger within (69%) than among (31%) populations. Associations between ecogeographical variables and the mean gene diversity were found at one primer pair. The results are discussed and compared with data obtained by the simple sequence repeat (SSR) method
Identification of QTLs associated with yield and its components in Miscanthus sinensis
Atienza, S.G. ; Satovic, Z. ; Petersen, K.K. ; Dolstra, O. ; Martin, A. - \ 2003
Euphytica 132 (2003)3. - ISSN 0014-2336 - p. 353 - 361.
quantitative trait loci - pinus-taeda l. - wood property traits - loblolly-pine - rapd markers - x-giganteus - biomass - quality - growth - dna
Yield and its components (stem-, leaf- and top-yield) were analyzed in a population derived from the cross between F1.1 andF1.7 entries of Miscanthus sinensisAnders. Both lines are offspring of the cross between MS-90-2 and MS-88-110. The aim of this work was to identify QTLs for yield and its components suitable to develop a Marker Aided Selection (MAS) program in M. sinensis.QTL analyses were performed using a previous linkage map based on RAPD markers which was constructed using a new mapping strategy named `offspring cross¿ that is useful for mapping in forest and fruit trees. The MapQTL 4.0 package was used to perform QTL analyses. Twenty potential QTLs were detected over two years of analyses. Out of these, 6 were associated with yield,8 with stem-yield, 2 with leaf-yield and 4with top-yield. These results constitute an initial step to develop a MAS program for biomass production
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