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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Pea powdery mildew er1 resistance is associated to loss-of-function mutations at a MLO homologous locus
Pavan, S.N.C. ; Schiavulli, A. ; Appiano, M. ; Visser, R.G.F. ; Bai, Y. - \ 2011
Theoretical and Applied Genetics 123 (2011)8. - ISSN 0040-5752 - p. 1425 - 1431.
pisum-sativum l. - gene - markers - er-1 - ol-2 - rapd
The powdery mildew disease affects several crop species and is also one of the major threats for pea (Pisum sativum L.) cultivation all over the world. The recessive gene er1, first described over 60 years ago, is well known in pea breeding, as it still maintains its efficiency as a powdery mildew resistance source. Genetic and phytopathological features of er1 resistance are similar to those of barley, Arabidopsis, and tomato mlo powdery mildew resistance, which is caused by the loss of function of specific members of the MLO gene family. Here, we describe the obtainment of a novel er1 resistant line by experimental mutagenesis with the alkylating agent diethyl sulfate. This line was found to carry a single nucleotide polymorphism in the PsMLO1 gene sequence, predicted to result in premature termination of translation and a non-functional protein. A cleaved amplified polymorphic sequence (CAPS) marker was developed on the mutation site and shown to be fully co-segregating with resistance in F2 individuals. Sequencing of PsMLO1 from three powdery mildew resistant cultivars also revealed the presence of loss-of-function mutations. Taken together, results reported in this study strongly indicate the identity between er1 and mlo resistances and are expected to be of great breeding importance for the development of resistant cultivars via marker-assisted selection.
Shoot organogenesis in leaf explants of Hydrangea macrophylla ‘Hyd1’ and assessing genetic stability of regenerants using ISSR markers
Liu, F. ; Huang, L.L. ; Reinhoud, P. ; Jongsma, M.A. ; Wang, C. - \ 2011
Plant Cell, Tissue and Organ Culture: an international journal on in vitro culture of higher plants 104 (2011)1. - ISSN 0167-6857 - p. 111 - 117.
in-vitro regeneration - plantlets - cultures - rapd - thidiazuron - propagation - fidelity - growth - assay
For the first time, an in vitro regeneration protocol of Hydrangea macrophylla 'Hyd1' was developed. Effects of different plant growth regulators (PGRs) on shoot regeneration were investigated jointly with selecting optimal basal media and cefotaxime concentrations. The highest frequency of shoot organogenesis (100%) and mean number of shoots per explant (2.7) were found on Gamborg B5 basal medium supplemented with 2.25 mg/l 6-benzyladenine (BA), 0.1 mg/l Indole-3-butyric acid (IBA), 100 mg/l cefotaxime and 30 g/l sucrose solidified by 7 g/l agar. Regenerated shoots were rooted by culturing on perlite plus half strength liquid B5 basal medium with 0.5 mg/l NAA. Rooted plantlets were transplanted to the greenhouse with 100% survival rate. Genetic stability of 32 plantlets (one mother plant and 31 regenerants) was assessed by 44 ISSR markers. Out of 44 ISSR markers, ten markers produced clear, reproducible bands with a mean of 5.9 bands per marker. The in vitro regeneration protocol is potentially useful for the genetic transformation of Hydrangea macrophylla 'Hyd1'.
Genetic diversity and population structure of common bean (Phaseolus vulgaris L.) landraces from the East African highlands
Asfaw, A. ; Blair, M.W. ; Almekinders, C.J.M. - \ 2009
Theoretical and Applied Genetics 120 (2009)1. - ISSN 0040-5752 - p. 1 - 12.
iberian peninsula - markers - variability - origin - fabaceae - allozyme - centers - races - pool - rapd
The East African highlands are a region of important common bean production and high varietal diversity for the crop. The objective of this study was to uncover the diversity and population structure of 192 landraces from Ethiopia and Kenya together with four genepool control genotypes using morphological phenotyping and microsatellite marker genotyping. The germplasm represented different common bean production ecologies and seed types common in these countries. The landraces showed considerable diversity that corresponded well to the two recognized genepools (Andean and Mesoamerican) with little introgression between these groups. Mesoamerican genotypes were predominant in Ethiopia while Andean genotypes were predominant in Kenya. Within each country, landraces from different collection sites were clustered together indicating potential gene flow between regions within Kenya or within Ethiopia. Across countries, landraces from the same country of origin tended to cluster together indicating distinct germplasm at the national level and limited gene flow between the two countries highlighting divided social networks within the regions and a weak trans-national bean seed exchange especially for landrace varieties. One exception to this may be the case of small red-seeded beans where informal cross-border grain trade occurs. We also observed that genetic divergence was slightly higher for the Ethiopian landraces compared to Kenyan landraces and that Mesoamerican genotypes were more diverse than the Andean genotypes. Common beans in eastern Africa are often cultivated in marginal, risk-prone farming systems and the observed landrace diversity should provide valuable alleles for adaptation to stressful environments in future breeding programs in the region
Genetic variability in yam cultivars from Guinea-Sudan of Benin assessed by random amplified polymorphic DNA
Zannou, A. ; Agbicodo, E. ; Zoundjihékpon, J. ; Struik, P.C. ; Ahanchédé, A. ; Kossou, D.K. ; Sanni, A. - \ 2009
African journal of biotechnology 8 (2009)1. - ISSN 1684-5315 - p. 26 - 36.
cayenensis/dioscorea-rotundata complex - diversity - markers - rapd - populations - allozyme - model - aflp
Yam (Dioscorea spp.) is an important food and cash crop in the Guinea-Sudan zone of Benin. The genetic diversity of about 70 cultivars of Dioscorea cayenensis/Dioscorea rotundata (Guinea yam) and about 20 cultivars of Dioscorea alata (water yam) was analysed using random amplified polymorphic DNA (RAPD). The amplified bands revealed high polymorphism. These polymorphic DNA fragments were used to construct dendrograms, clustering all accessions into 18 groups: 12 for D. cayenensis/D. rotundata and six for D. alata. The analysis of molecular variance revealed highly significant variation among species, among groups within species, and among cultivars within groups. The study showed that the genetic diversity changed along a spatial gradient. In general, there was a tendency that most of the varieties from the north-east and north-west of the zone investigated appeared to be distinctive from the ones of the centre. However, few varieties were distributed randomly and did not reflect any specific relation to their zone of collection. The current study suggests that the Guinea-Sudan zone of Benin has a large gene pool of yam varieties. Yam farmers may have played a significant role in the enrichment and the maintenance of the genetic diversity of yam.
Natural hybridization between Populus nigra L. and P. x canadensis Moench. Hybrid offspring competes for niches along the Rhine river in the Netherlands
Smulders, M.J.M. ; Beringen, R. ; Volosyanchuk, R. ; Vanden Broeck, A. ; Schoot, J. van der; Arens, P.F.P. ; Vosman, B. - \ 2008
Tree Genetics and Genomes 4 (2008)4. - ISSN 1614-2942 - p. 663 - 675.
poplar populus - black poplar - microsatellite markers - cultivated poplars - genetic diversity - populations - deltoides - aflp - rapd - dna
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.
Marker-assisted optimization of an expert-based strategy for the acquisition of modern lettuce varieties to improve a genebank collection
Treuren, R. van; Hintum, T.J.L. van; Wiel, C.C.M. van de - \ 2008
Genetic Resources and Crop Evolution 55 (2008)2. - ISSN 0925-9864 - p. 319 - 330.
genetic-variation - bremia-lactucae - accessions - construction - resistance - database - tomato - aflps - rapd
To regularly improve the composition of the lettuce collection of the Centre for Genetic Resources, the Netherlands (CGN) with modern varieties, feedback from crop experts is used to select approximately 10% of the new material for incorporation in the collection. In the present study, assessments of six experts were compared to microsatellite data of 414 new varieties and 1408 existing accessions. Based on the microsatellite data, the extent to which the genetic diversity of the collection would be enriched (added value) was calculated for specific sets of new varieties. When individual assessments of experts were evaluated, the total added value of expert-based selections was not significantly higher compared to randomly chosen groups, except for a single expert. Unfamiliarity with new varieties was shown to be a crucial factor in the assessment of crop experts. According to the current acquisition protocol that seeks for consensus among experts, varieties are selected based on recommendations from at least three experts. This protocol also did not perform better than randomly chosen groups of new varieties. However, significantly better results were obtained with alternative protocols. It was concluded that breeding value was a more decisive criterion in the current acquisition protocol than maximal extension of the genetic diversity within the collection. A modified protocol addressing both commercial and diversity aspects was suggested in order to meet the demands of plant breeders as well as conservationists
A Natural infrageneric classification for Cicer (Leguminoseae, Cicereae)
Davies, A.M.R. ; Maxted, N. ; Maesen, L.J.G. van der - \ 2007
Blumea 52 (2007)2. - ISSN 0006-5196 - p. 379 - 400.
genetic-relationships - genus cicer - phylogenetic-relationships - isozyme polymorphism - sequences - turkey - rapd - dna - morphology - diversity
A comprehensive morphological survey and analysis of all taxonomically recognised wild species of Cicer L. (Leguminosae, Cicereae) is presented. The data (104 characters from 152 herbarium specimens representing 34 of the 44 recognised taxa in the genus Cicer with supplementary data for the remaining taxa taken from the literature) were analysed using multivariate statistics (cluster analysis, factor analysis and ordination techniques). The results are discussed in the context of extant classifications and the re-organisation of a novel infrageneric classification also incorporating information from published genetic data. A revised classification with 3 subgenera, 5 sections and 2 series is proposed.
Assignment tests for variety identification compared to genetic similarity-based methods using experimental datasets from different marker systems in sugar beet
Riek, J. de; Everaert, I. ; Esselink, D. ; Calsyn, E. ; Smulders, M.J.M. ; Vosman, B. - \ 2007
Crop Science 47 (2007)5. - ISSN 0011-183X - p. 1964 - 1974.
beta-vulgaris l - linkage map - aflp - construction - regression - database - rapd - l.
High genetic variation within sugar beet (Beta vulgaris L.) varieties hampers reliable classification procedures independent of the type of marker technique applied. Datasets on amplified fragment length polymorphisms, sequence tagged microsatellite sites, and cleaved amplified polymorphic sites markers in eight sugar beet varieties were subjected to supervised classifiers, methods in which individual assignments are made to predefined classes, and unsupervised classifiers, defined afterward on the similarity in marker composition from sampled individuals. Major issues addressed are (i) which classification method gives the most consistent results when three marker techniques are compared, and (ii) given different classification techniques available, for which marker technique is the output generated least constrained by the way data analysis is performed. Assignment tests showed a higher consistency across classifications independent from the marker technique. A good allocation to the proper variety was obtained, together with a reliable allocation pattern among the other varieties. Both aspects deal with the variation within a variety and the distance to other varieties. Assignment data were transformed into an average similarity measure, similarity by assignment (Sax,y), which is a new genetic distance measure with interesting properties
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
Microsatellite analysis of Rosa damascena Mill. accessions reveals genetic similarity between genotypes used for rose oil production and old Damask rose varieties
Rusanov, K. ; Kovacheva, N. ; Vosman, B.J. ; Zhang, L. ; Rajapakse, S. ; Atanassov, A. ; Atanassov, I. - \ 2005
Theoretical and Applied Genetics 111 (2005)4. - ISSN 0040-5752 - p. 804 - 809.
black poplar - markers - aflp - diversity - identification - cultivars - hybrida - turkey - tree - rapd
Damask roses are grown in several European and Asiatic countries for rose oil production. Twenty-six oil-bearing Rosa damascena Mill. accessions and 13 garden Damask roses were assayed by molecular markers. Microsatellite genotyping demonstrated that R. damascena Mill. accessions from Bulgaria, Iran, and India and old European Damask rose varieties possess identical microsatellite profiles, suggesting a common origin. At the same time, the data indicated that modern industrial oil rose cultivation is based on a very narrow genepool and that oil rose collections contain many genetically identical accessions. The study of long-term vegetative propagation of the Damask roses also reveals high somatic stability for the microsatellite loci analyzed
The establishment of 'essential derivation' among rose varieties, using AFLP
Vosman, B.J. ; Visser, D.L. ; Voort, J.R. van der; Smulders, M.J.M. ; Eeuwijk, F.A. van - \ 2004
Theoretical and Applied Genetics 109 (2004)8. - ISSN 0040-5752 - p. 1718 - 1725.
molecular markers - identification - construction - database - rapd
In the International Union for the Protection of New Varieties of Plants Act of 1991, mutation is mentioned as one of the mechanisms to obtain an `essentially derived' variety (EDV). For the implementation of the EDV concept in the case of mutation, it is important that the level of genetic relatedness between an initial variety and derived mutant varieties can clearly be distinguished from the level of relatedness between arbitrary pairs of varieties without a derivation relation. Conditions to be fulfilled for such a distinction include enough genetic differentiation in the germplasm pool of interest, sufficiently low levels of genomic sampling error and technical laboratory error and high reproducibility within and between laboratories. In rose, mutants or `sports' are frequently observed during multiplication, making it a suitable crop for studying the possibilities for introduction of the EDV concept in ornamentals. We studied genetic similarities among 83 rose varieties, including 13 mutant groups. Twelve AFLP primer combinations generated 284 polymorphic markers and 114 monomorphic (fixed) bands. Pair-wise Jaccard similarities between original varieties and derived mutants were close to 1.0 (>0.96), whereas all similarities between original varieties were below 0.80, with 75% of the non-mutant similarities even being below 0.50. Values less than 1.0 for similarity among original varieties and their mutants were to a major extent due to scoring errors. Error rates in automated scoring proved to be lower than those in manually scored and transferred data. Experimental errors, even between laboratories, turned out to be very small. On the basis of a consistent and large difference between similarities, relations between an original variety and its mutants can easily be identified and distinguished from relations between original varieties. These results open the way for implementing the essential derivation concept in rose.
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
Microsatellite DNA marker inheritance indicates preferential pairing between two highly homologous genomes in polyploid and hemisexual dogroses, Rosa L. sect. Caninae DC
Nybom, H. ; Esselink, D. ; Werlemarkt, G. ; Vosman, B.J. - \ 2004
Heredity 92 (2004)3. - ISSN 0018-067X - p. 139 - 150.
cultivar identification - skewed distribution - ssr markers - plants - drawings - rapd - hybridization - dogroses - apomixis - crosses
According to previous cytological evidence, the hemisexual dog-rose species, Rosa sect. Caninae, transmit only seven chromosomes (derived from seven bivalents) through their pollen grains, whereas egg cells contain 21, 28 or 35 chromosomes (derived from seven bivalents and 14, 21 or 28 univalents) depending on ploidy level. Two sets of reciprocal pairwise interspecific crosses involving the pentaploid species pair R. dumalis and R. rubiginosa, and the pentaploid/tetraploid species pair R. sherardii and R. villosa, were analysed for 13 and 12 microsatellite DNA loci, respectively. Single loci were represented by a maximum of three simultaneously occurring alleles in R. villosa, and four alleles in the other three parental plants. In the experimentally derived offspring, the theoretical maximum of five alleles was found for only one locus in the pentaploid progenies. Microsatellite DNA allele composition was identical with that of the maternal parent in 10 offspring plants, which were probably derived through apomixis. Almost all microsatellite DNA alleles were shared with the maternal parent also in the remaining offspring, but 1-4 alleles shared only with the paternal parent, indicating sexual seed formation. Analysis of quantitative peak differences allowed a tentative estimation of allelic configuration in the individual plants, and suggested that bivalent formation preferentially takes place between chromosomes that consistently share the same microsatellite alleles and therefore appear to be highly homologous. Moreover, alleles that were shared between the species in each cross combination comparatively often appear to reside on the bivalent-forming chromosomes, whereas species-specific alleles instead occur comparatively often on the univalent-forming chromosomes and are therefore inherited through the maternal parent only. Recombination then takes place between very similar genomes also in interspecific crosses, resulting in a reproduction system that is essentially a mixture between apomixis and selfing.
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.
Genetic variation in the endangered Wild apple (Malus sylvestris (L.) Mill.) in Belgium as revealed by AFLP and microsatellite markers. Consequences for conservation
Coart, E. ; Vekemans, X. ; Smulders, M.J.M. ; Wagner, I. ; Huylenbroeck, J. van; Bockstaele, E. van; Rold¿¡n-Ruiz, I. - \ 2003
Molecular Ecology 12 (2003). - ISSN 0962-1083 - p. 845 - 857.
x-domestica borkh. - populus-nigra l. - aflp markers - population-structure - introgression - diversity - conservation - distances - rapd
The genetic variation within and between wild apple samples (Malus sylvestris) and cultivated apple trees was investigated with amplified fragment length polymorphisms (AFLP) and microsatellite markers to develop a conservation genetics programme for the endangered wild apple in Belgium. In total, 76 putative wild apples (originating from Belgium and Germany), six presumed hybrids and 39 cultivars were typed at 12 simple sequence repeats (SSR) and 139 amplified fragment length polymorphism (AFLP) loci. Principal co-ordinate analysis and a model-based clustering method classified the apples into three major gene pools: wild Malus sylvestris genotypes, edible cultivars and ornamental cultivars. All presumed hybrids and two individuals (one Belgian, one German) sampled as M. sylvestris were assigned completely to the edible cultivar gene pool, revealing that cultivated genotypes are present in the wild. However, gene flow between wild and cultivated gene pools is shown to be almost absent, with only three genotypes that showed evidence of admixture between the wild and edible cultivar gene pools. Wild apples sampled in Belgium and Germany constitute gene pools that are clearly differentiated from cultivars and although some geographical pattern of genetic differentiation among wild apple populations exists, most variation is concentrated within samples. Concordant conclusions were obtained from AFLP and SSR markers, which showed highly significant correlations in both among-genotypes and among-samples genetic distances
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.
Development and characterisation of 140 new microsatellites in apple (Malus x domestica Borkh.)
Liebhard, R. ; Gianfranceschi, L. ; Koller, B. ; Ryder, C.D. ; Tarchini, R. ; Weg, W.E. van de; Gessler, C. - \ 2002
Molecular Breeding 10 (2002)4. - ISSN 1380-3743 - p. 217 - 241.
scab resistance - linkage map - genetic diversity - aflp markers - ssr markers - rapd - vf - identification - polymorphism - construction
The availability of suitable genetic markers is essential to efficiently select and breed apple varieties of high quality and with multiple disease resistances. Microsatellites (simple sequence repeats, SSR) are very useful in this respect since they are codominant, highly polymorphic, abundant and reliably reproducible. Over 140 new SSR markers have been developed in apple and tested on a panel of 7 cultivars and 1 breeding selection. Their high level of polymorphism is expressed with an average of 6.1 alleles per locus and an average heterozygosity (H) of 0.74. Of all SSR markers, 115 have been positioned on a genetic linkage map of the cross Fiesta × Discovery. As a result, all 17 linkage groups, corresponding to the 17 chromosomes of apple, were identified. Each chromosome carries at least two SSR markers, allowing the alignment of any apple molecular marker map both with regard to identification as well as to orientation of the linkage groups. To test the degree of conservation of the SSR flanking regions and the transferability of the SSR markers to other Rosaceae species, 15 primer pairs were tested on a series of Maloideae and Amygdaloideae species. The usefulness of the newly developed microsatellites in genetic mapping is demonstrated by means of the genetic linkage map. The possibility of constructing a global apple linkage map and the impact of such a number of microsatellite markers on gene and QTL mapping is discussed
A comparative study of molecular and morphological methods of describing relationships between perennial ryegrass (Lolium perenne L.) varieties
Roldán-Ruiz, I. ; Eeuwijk, F.A. van; Gilliland, T.J. ; Dubreuil, P. ; Dillmann, C. ; Lallemand, J. ; Loose, M. De; Baril, C.P. - \ 2001
Theoretical and Applied Genetics 103 (2001)8. - ISSN 0040-5752 - p. 1138 - 1150.
european barley germplasm - genetic diversity - species relationships - aflp markers - dna - cultivars - rapd - rflps - pedigree - plant
A sample set of registered perennial ryegrass varieties was used to compare how morphological characterisation and AFLP® (AFLP® is a registered trademark of Keygene N.V.) and STS molecular markers described variety relationships. All the varieties were confirmed as morphologically distinct, and both the STS and AFLP markers exposed sufficient genetic diversity to differentiate these registered ryegrass varieties. Distances obtained by each of the approaches were compared, with special attention given to the coincidences and divergences between the methods. When correlations between morphological, AFLP and STS distances were calculated and the corresponding scatter-plots constructed, the variety relationships appeared to be rather inconsistent across the methods, especially between morphology and the molecular markers. However, some consistencies were found for closely related material. An implication could be that these molecular-marker techniques, while not yet suited to certain operations in the traditional registration of new varieties, could be suitable methods for investigating disputable distinctness situations or possible EDV (EDV= essentially derived variety. An EDV is a variety being clearly distinct from, but conforming in the expression of the essential characteristics of, an ¿initial variety' (IV) from which it is found to have been predominantly derived) relationships, subject to establishing standardised protocols and statistical techniques. Some suggestions for such a protocol, including a statistical test for distinctness, are given
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