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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    Mapping markers linked to porcine salmonellosis susceptibility
    Galina-Pantoja, L. ; Siggens, K. ; Schriek, M.G.M. van; Heuven, H.C.M. - \ 2009
    Animal Genetics 40 (2009)6. - ISSN 0268-9146 - p. 795 - 803.
    quantitative trait loci - differential gene-expression - population-structure - natural-resistance - linkage map - aflp - choleraesuis - infection - pig - polymorphisms
    The goal of this study was to identify pig chromosomal regions associated with susceptibility to salmonellosis. Genomic DNA from pig reference populations with differences in susceptibility to Salmonella enterica serovar Choleraesuis as quantified by spleen and liver bacterial colonization at day 7 post-infection (dpi; Van Diemen et al. 2002) was used. These samples belonged to the offspring of a sire thought to be heterozygous for genes involved in susceptibility to salmonellosis. Amplified fragment length polymorphism (AFLP) markers were created and used to determine associations with spleen or bacterial counts at 7 dpi. To position linked markers, two mapping populations, the Roslin and Uppsala PiGMaP pedigrees were used to create an integrated map which included the AFLP markers associated with salmonellosis. Twenty-six AFLP markers located in 14 different chromosomal regions in the porcine genome were found to be significantly associated with susceptibility (Chi-square P <0.05). More than one linked marker was found on chromosomes 1, 7, 13, 14 and 18. It is likely that these regions contain genes involved in Salmonella susceptibility. Regions on chromosomes 1, 7 and 14 were significantly associated with Salmonella counts in the liver and regions on chromosomes 11, 13 and 18 with counts in spleen. The identification of these chromosomal regions highlights specific areas to search for candidate genes that may be involved in innate or adaptive immunity. Further investigation into these chromosomal regions would be useful to improve our understanding of host responses to infection with this widespread pathogen.
    PHYTOCHROME B and HISTONE DEACETYLASE 6 Control Light-Induced Chromatin Compaction in Arabidopsis thaliana
    Tessadori, F. ; Zanten, M. van; Pavlova, P. ; Clifton, R. ; Pontvianne, F. ; Snoek, L.B. ; Millenaar, F.F. ; Schulkes, R.K. ; Driel, R. van; Voesenek, L.A.C.J. ; Spillane, C. ; Pikaard, C.S. ; Fransz, P.F. ; Peeters, A.J.M. - \ 2009
    Plos Genetics 5 (2009)9. - ISSN 1553-7404 - 13 p.
    natural allelic variation - inbred line population - dna methylation - flowering time - genome regulation - genetic-variation - circadian clock - linkage map - h3 lysine-9 - heterochromatin
    Natural genetic variation in Arabidopsis thaliana exists for many traits and often reflects acclimation to local environments. Studying natural variation has proven valuable in the characterization of phenotypic traits and, in particular, in identifying genetic factors controlling these traits. It has been previously shown that chromatin compaction changes during development and biotic stress. To gain more insight into the genetic control of chromatin compaction, we investigated the nuclear phenotype of 21 selected Arabidopsis accessions from different geographic origins and habitats. We show natural variation in chromatin compaction and demonstrate a positive correlation with latitude of geographic origin. The level of compaction appeared to be dependent on light intensity. A novel approach, combining Quantitative Trait Locus (QTL) mapping and microscopic examination, pointed at PHYTOCHROME-B (PHYB) and HISTONE DEACETYLASE-6 (HDA6) as positive regulators of light-controlled chromatin compaction. Indeed, mutant analyses demonstrate that both factors affect global chromatin organization. HDA6, in addition, strongly promotes the light-mediated compaction of the Nucleolar Organizing Regions (NORs). The accession Cape Verde Islands-0 (Cvi-0), which shows sequence polymorphism in the PHYB gene and in the HDA6 promotor, resembles the hda6 mutant in having reduced chromatin compaction and decreased methylation levels of DNA and histone H3K9 at the NORs. We provide evidence that chromatin organization is controlled by light intensity. We propose that chromatin plasticity is associated with acclimation of Arabidopsis to its environment. The polymorphic alleles such as PHYB and HDA6 control this process
    Genetic mapping and annotation of genomic microsatellites isolated from globe artichoke
    Acquadro, A. ; Lanteri, S. ; Scaglione, D. ; Arens, P.F.P. ; Vosman, B. ; Portis, E. - \ 2009
    Theoretical and Applied Genetics 118 (2009)8. - ISSN 0040-5752 - p. 1573 - 1587.
    cynara-cardunculus l. - fragment length polymorphisms - transcription factor-binding - cultured rat hepatocytes - linkage map - scolymus l. - mediterranean environment - medicago-truncatula - potential source - dna-sequences
    Cynara cardunculus includes three taxa, the globe artichoke (subsp. scolymus L. Hegi), the cultivated cardoon (var. altilis) and their progenitor, the wild cardoon (var. sylvestris). Globe artichoke is an important component of the Mediterranean rural economy, but its improvement through breeding has been rather limited and its genome organization remains largely unexplored. Here, we report the isolation of 61 new microsatellite loci which amplified a total of 208 alleles in a panel of 22 C. cardunculus genotypes. Of these, 51 were informative for linkage analysis and 39 were used to increase marker density in the available globe artichoke genetic maps. Sequence analysis of the 22 loci associated with genes showed that 9 are located within coding sequence, with the repetitive domain probably being involved in DNA binding or in protein¿protein interactions. The expression of the genes associated with 9 of the 22 microsatellite loci was demonstrated by RT-PCR.
    Large-scale Gene Ontology analysis of plant transcriptome-derived sequences retrieved by AFLP technology
    Botton, A. ; Galla, G. ; Conesa, A. ; Bachem, C.W.B. ; Ramina, A. ; Barcaccia, G. - \ 2008
    BMC Genomics 9 (2008). - ISSN 1471-2164 - 19 p.
    genome-wide expression - pseudo-testcross strategy - poa-pratensis l - cdna-aflp - candidate genes - seed-germination - cell-division - linkage map - identification - markers
    Background: After 10-year-use of AFLP (Amplified Fragment Length Polymorphism) technology for DNA fingerprinting and mRNA profiling, large repertories of genome- and transcriptome-derived sequences are available in public databases for model, crop and tree species. AFLP marker systems have been and are being extensively exploited for genome scanning and gene mapping, as well as cDNA-AFLP for transcriptome profiling and differentially expressed gene cloning. The evaluation, annotation and classification of genomic markers and expressed transcripts would be of great utility for both functional genomics and systems biology research in plants. This may be achieved by means of the Gene Ontology (GO), consisting in three structured vocabularies (i.e. ontologies) describing genes, transcripts and proteins of any organism in terms of their associated cellular component, biological process and molecular function in a species-independent manner. In this paper, the functional annotation of about 8,000 AFLP-derived ESTs retrieved in the NCBI databases was carried out by using GO terminology. Results: Descriptive statistics on the type, size and nature of gene sequences obtained by means of AFLP technology were calculated. The gene products associated with mRNA transcripts were then classified according to the three main GO vocabularies. A comparison of the functional content of cDNA-AFLP records was also performed by splitting the sequence dataset into monocots and dicots and by comparing them to all annotated ESTs of Arabidopsis and rice, respectively. On the whole, the statistical parameters adopted for the in silico AFLP-derived transcriptome-anchored sequence analysis proved to be critical for obtaining reliable GO results. Such an exhaustive annotation may offer a suitable platform for functional genomics, particularly useful in non-model species. Conclusion: Reliable GO annotations of AFLP-derived sequences can be gathered through the optimization of the experimental steps and the statistical parameters adopted. The Blast2GO software was shown to represent a comprehensive bioinformatics solution for an annotation-based functional analysis. According to the whole set of GO annotations, the AFLP technology generates thorough information for angiosperm gene products and shares common features across angiosperm species and families. The utility of this technology for structural and functional genomics in plants can be implemented by serial annotation analyses of genome- anchored fragments and organ/tissue-specific repertories of transcriptome-derived fragments.
    Genetic diversity and population structure of locally adapted South African chicken lines: Implications for conservation.
    Marle-Koster, E. van; Hefer, C.A. ; Nel, L.H. ; Groenen, M.A.M. - \ 2008
    South African Journal of Animal Science = Suid-Afrikaanse Tydskrif Vir Veekun 38 (2008)4. - ISSN 0375-1589 - p. 271 - 281.
    kippen - inheems vee - rassen (dieren) - differentiatie - genetische variatie - genetische diversiteit - microsatellieten - merkers - bevolkingsstructuur - conservering - zuid-afrika - fowls - native livestock - breeds - differentiation - genetic variation - genetic diversity - microsatellites - markers - population structure - conservation - south africa - domestic-animal diversity - microsatellite markers - linkage map - naked neck - polymorphisms - biodiversity - genome
    In this study microsatellite markers were applied to investigate the genetic diversity and population structure of the six local chicken lines kept in the “Fowls for Africa” program, for better clarification of parameters for breed differentiation and genetic conservation of this valuable resource. The lines included the Black Australorp, Potchefstroom Koekoek, New Hampshire, Ovambo, Lebova- Venda and a Naked Neck line. Unbiased estimates for heterozygosity ranged from 50% in the Potchefstroom Koekoek to as high as 65% in the Naked Neck chickens. FIS values varied from as low as 0.16 for the Black Australorp line to as high as 0.35 for the Ovambo chickens. The FST values indicated moderate to high genetic differentiation between the Naked Neck and New Hampshire (0.11); Ovambo and Naked Neck lines (0.12), and Naked Neck and Lebowa- Venda (0.14). A total of 13% of the total genetic variation observed was between the chicken lines and 87% within the lines, supporting moderate genetic differentiation. Population structure was assessed using STRUCTURE where the Black Australorp was genetically best defined. Although six clusters for the different populations could be distinguished, the other lines were not as clearly defined, with individual birds tending to share more than one cluster. Results support a broad classification of these lines and further investigation of unique alleles is recommended for conservation of the lines within the program.
    Genetic variability of cultivated cowpea in Benin assessed by random amplified polymorphic DNA
    Zannou, A. ; Kossou, D.K. ; Ahanchédé, A. ; Zoundjihékpon, J. ; Agbicodo, E. ; Struik, P.C. ; Sanni, A. - \ 2008
    African journal of biotechnology 7 (2008)24. - ISSN 1684-5315 - p. 4407 - 4414.
    linkage map - diversity - aflp - markers - populations - model - wild
    Characterization of genetic diversity among cultivated cowpea [Vigna unguiculata (L.) Walp.] varieties is important to optimize the use of available genetic resources by farmers, local communities, researchers and breeders. Random amplified polymorphic DNA (RAPD) markers were used to evaluate the genetic diversity in 70 cowpea accessions collected throughout Benin. Nine random primers were screened on 24 accessions to assess their ability to reveal polymorphisms in cowpea and four of them were selected for use in characterizing the total sample. A total of 32 amplified bands were generated by the four primers. The number of loci detected varied from 5 to 11. RAPD profiles were analysed and amplified polymorphic DNA fragments were used to construct a dendrogram, clustering the accessions into nine groups at a similarity index of 71% based on the Unweighted Pair-Group Method using Arithmetic Averages. The genetic diversity among the cowpea cultivars investigated was large and the RAPD proved to be a useful technique to characterise it. Based on the molecular variance, the fixation index suggests a large differentiation of cowpea cultivars in Benin.
    Quantitative trait loci analysis of phytate and phosphate concentrations in seeds and leaves of Brassica rapa
    Jianjun Zhao, Jianjun ; Jamar, D.C.L. ; Lou, P. ; Wang, Y. ; Wu, J. ; Wang, X. ; Bonnema, A.B. ; Koornneef, M. ; Vreugdenhil, D. - \ 2008
    Plant, Cell & Environment 31 (2008)7. - ISSN 0140-7791 - p. 887 - 900.
    phytic-acid - arabidopsis-thaliana - natural variation - comparative genomics - flowering time - linkage map - phosphorus - sequence - accumulation - resistance
    Phytate, being the major storage form of phosphorus in plants, is considered to be an anti-nutritional substance for human, because of its ability to complex essential micronutrients. In the present study, we describe the genetic analysis of phytate and phosphate concentrations in Brassica rapa using five segregating populations, involving eight parental accessions representing different cultivar groups. A total of 25 quantitative trait loci (QTL) affecting phytate and phosphate concentrations in seeds and leaves were detected, most of them located in linkage groups R01, R03, R06 and R07. Two QTL affecting seed phytate (SPHY), two QTL affecting seed phosphate (SPHO), one QTL affecting leaf phosphate and one major QTL affecting leaf phytate (LPHY) were detected in at least two populations. Co-localization of QTL suggested single or linked loci to be involved in the accumulation of phytate or phosphate in seeds or leaves. Some co-localizing QTL for SPHY and SPHO had parental alleles with effects in the same direction suggesting that they control the total phosphorus concentration. For other QTL, the allelic effect was opposite for phosphate and phytate, suggesting that these QTL are specific for the phytate pathway
    Evolution of the polymorphism at molecular markers in QTL and non-QTL regions in selected chicken lines
    Loywyck, V. ; Bed'hom, B. ; Pinard-van der Laan, M.H. ; Pitel, F. ; Verrier, E. ; Bijma, P. - \ 2008
    Genetics, Selection, Evolution 40 (2008). - ISSN 0999-193X - p. 639 - 661.
    effective population-size - quantitative trait loci - laying hens - antibody-responses - immune-response - allele frequency - genetic drift - linkage map - signatures - chromosome
    We investigated the joint evolution of neutral and selected genomic regions in three chicken lines selected for immune response and in one control line. We compared the evolution of polymorphism of 21 supposedly neutral microsatellite markers versus 30 microsatellite markers located in seven quantitative trait loci (QTL) regions. Divergence of lines was observed by factor analysis. Five supposedly neutral markers and 12 markers in theQTL regions showed values greater than 0.15. However, the non-significant difference (P > 0.05) between matrices of genetic distances based on genotypes at supposedly neutral markers on the one hand, and at markers in QTL regions, on the other hand, showed that none of the markers in the QTL regions were influenced by selection. A supposedly neutral marker and a marker located in the QTL region on chromosome 14 showed temporal variations in allele frequencies that could not be explained by drift only. Finally, to confirm thatmarkers located inQTL regions on chromosomes 1, 7 and 14 were under the influence of selection, simulations were performed using haplotype dropping along the existing pedigree. In the zone located on chromosome 14, the simulation results confirmed that selection had an effect on the evolution of polymorphism of markers within the zone
    Comparison of information content for microsatellites and SNPs in poultry and cattle
    Schopen, G.C.B. ; Bovenhuis, H. ; Visker, M.H.P.W. ; Arendonk, J.A.M. van - \ 2008
    Animal Genetics 39 (2008)4. - ISSN 0268-9146 - p. 451 - 453.
    quantitative trait loci - linkage map - genetic-map - markers - genome - population - chicken
    Data were available for 12 poultry microsatellites and 29 poultry single nucleotide polymorphisms (SNPs), and for 34 cattle microsatellites and 36 cattle SNPs. Stochastic permutation was used to determine the number of SNPs needed to obtain the same average information content as a given number of microsatellites. For poultry, the information content averaged 0.71 for the 12 microsatellites compared to 0.72 for the 29 SNPs. For cattle, the information content averaged 0.92 for the 34 microsatellites compared with 0.79 for the 36 SNPs. This study shows that, for each microsatellite, three SNPs are needed to obtain the same average information content.
    Development of a high-throughput microsatellite typing approach for forensic and population genetic analysis of wild and domestic African Bovini
    Greyling, B.J. ; Kryger, P. ; Plessis, S. du; Hooft, W.F. van; Helden, P. van; Getz, W.M. ; Bastos, A.D.S. - \ 2008
    African journal of biotechnology 7 (2008)5. - ISSN 1684-5315 - p. 655 - 660.
    syncerus caffer - polymorphic bovine - southern africa - linkage map - buffalo - markers - identification - cattle
    Conservation management and forensic traceability of African buffalo and cattle rely on the timely provision of unbiased and accurate genetic information. An approach in which 17 cattle microsatellite markers are co-electrophoresed, following amplification in three core multiplex reactions was established for this purpose. Mean allelic richness per locus was 8.24 and 6.47, for buffalo and Bonsmara cattle, respectively, whilst an unbiased match probability of 6.5x×10-17 and 1.03 × 10-16 was obtained for each. These results confirm the usefulness of this rapid, cost-effective typing approach for forensic, paternity and fine-scale genetic analyses of wild and domestic African Bovini tribe members
    Expressed sequence tag-derived microsatellite markers of perennial ryegrass (Lolium perenne L.).
    Studer, B. ; Asp, T. ; Frei, U. ; Hentrup, S. ; Meally, H. ; Guillard, A. ; Barth, S. ; Muylle, H. ; Roldan-Ruiz, I. ; Barre, P. ; Boucoiran, C.F.S. ; Stunnenberg, G. ; Dolstra, O. ; Skot, L. ; Skot, K.P. ; Turner, B. ; Humphreys, M. ; Kolliker, R. ; Roulund, N. ; Nielsen, K.K. ; Lubberstedt, T. - \ 2008
    Molecular Breeding 21 (2008)4. - ISSN 1380-3743 - p. 533 - 548.
    repeat ssr markers - multiflorum lam. - linkage map - plants - transferability - construction - reveals - qtl
    An expressed sequence tag (EST) library of the key grassland species perennial ryegrass (Lolium perenne L.) has been exploited as a resource for microsatellite marker development. Out of 955 simple sequence repeat (SSR) containing ESTs, 744 were used for primer design. Primer amplification was tested in eight genotypes of L. perenne and L. multiflorum representing (grand-) parents of four mapping populations and resulted in 464 successfully amplified EST-SSRs. Three hundred and six primer pairs successfully amplified products in the mapping population VrnA derived from two of the eight genotypes included in the original screening and revealed SSR polymorphisms for 143 ESTs. Here, we report on 464 EST-derived SSR primer sequences of perennial ryegrass established in laboratory assays, providing a dedicated tool for marker assisted breeding and comparative mapping within and among forage and turf grasses. Electronic supplementary material The online version of this article (doi:10.1007/s11032-007-9148-0) contains supplementary material, which is available to authorized users.
    High diversity of genes for nonhost resistance of barley to heterologous rust fungi
    Jafary, H. ; Albertazzi, G. ; Marcel, T.C. ; Niks, R.E. - \ 2008
    Genetics 178 (2008)4. - ISSN 0016-6731 - p. 2327 - 2339.
    puccinia-hordei - leaf rust - linkage map - iii effector - defense - plants - pathogens - qtls - identification - accumulation
    Inheritance studies on the nonhost resistance of plants would normally require interspecific crosses that suffer from sterility and abnormal segregation. Therefore, we developed the barley¿Puccinia rust model system to study, using forward genetics, the specificity, number, and diversity of genes involved in nonhost resistance. We developed two mapping populations by crossing the line SusPtrit, with exceptional susceptibility to heterologous rust species, with the immune barley cultivars Vada and Cebada Capa. These two mapping populations along with the Oregon Wolfe Barley population, which showed unexpected segregation for resistance to heterologous rusts, were phenotyped with four heterologous rust fungal species. Positions of QTL conferring nonhost resistance in the three mapping populations were compared using an integrated consensus map. The results confirmed that nonhost resistance in barley to heterologous rust species is controlled by QTL with different and overlapping specificities and by an occasional contribution of an R-gene for hypersensitivity. In each population, different sets of loci were implicated in resistance. Few genes were common between the populations, suggesting a high diversity of genes conferring nonhost resistance to heterologous pathogens. These loci were significantly associated with QTL for partial resistance to the pathogen Puccinia hordei and with defense-related genes
    Identification and genetic mapping of highly polymorphic microsatellite loci from an EST database of the septoria tritici blotch pathogen Mycosphaerella graminicola
    Goodwin, S.B. ; Lee, T.A.J. van der; Cavaletto, J.R. ; Lintel Hekkert, B. te; Crane, C.F. ; Kema, G.H.J. - \ 2007
    Fungal Genetics and Biology 44 (2007)5. - ISSN 1087-1845 - p. 398 - 414.
    simple sequence repeats - magnaporthe-grisea - lobaria-pulmonaria - ascochyta-rabiei - fungal genomes - ribosomal dna - linkage map - markers - wheat - population
    A database of 30,137 EST sequences from Mycosphaerella graminicola, the septoria tritici blotch fungus of wheat, was scanned with a custom software pipeline for di- and trinucleotide units repeated tandemly six or more times. The bioinformatics analysis identified 109 putative SSR loci, and for 99 of them, flanking primers were developed successfully and tested for amplification and polymorphism by PCR on five field isolates of diverse origin, including the parents of the standard M. graminicola mapping population. Seventy-seven of the 99 primer pairs generated an easily scored banding pattern and 51 were polymorphic, with up to four alleles per locus, among the isolates tested. Among these 51 loci, 23 were polymorphic between the parents of the mapping population. Twenty-one of these as well as two previously published microsatellite loci were positioned on the existing genetic linkage map of M. graminicola on 13 of the 24 linkage groups. Most (66%) of the primer pairs also amplified bands in the closely related barley pathogen Septoria passerinii, but only six were polymorphic among four isolates tested. A subset of the primer pairs also revealed polymorphisms when tested with DNA from the related banana black leaf streak (Black Sigatoka) pathogen, M. fijiensis. The EST database provided an excellent source of new, highly polymorphic microsatellite markers that can be multiplexed for high-throughput genetic analyses of M. graminicola and related species
    In silico identification and mapping of microsatellite markers on Sus scrofa chromosome 4
    Wijk, H.J. van; Liefers, S.C. ; Buschbell, H. ; Dibbits, B.W. ; Harlizius, B. ; Groenen, M.A.M. - \ 2007
    Animal Biotechnology 18 (2007)4. - ISSN 1049-5398 - p. 251 - 261.
    carcass composition - porcine genome - linkage map
    Apolipoprotein B (APOB) serves an essential role in the assembly and secretion of triglyceride-rich lipoproteins and lipids transport. This study was designed to clone the full-length cDNA of the chicken APOB gene, to characterize the expression profile, and investigate the differential expression between layer and broiler of the chicken APOB gene. The full-length cDNA sequence (14,150-bp) that contained a 13,896-bp ORF encoding 4,631 amino acids was obtained by RT-PCR, RACE, and bioinformatics analysis. qReal-Time PCR analysis showed that the chicken APOB gene was highly expressed in kidney, liver, and intestine. The results of differential expression showed that the APOB gene was more highly expressed in intestine and kidney in Bai'er layer than in broiler, but there was no significant difference in liver between the two breeds. The results of this study provided basic molecular information for studying the role of APOB in the energy transportation in avian species.
    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
    A high-density consensus map of barley to compare the distribution of QTLs for partial resistance to Puccinia hordei and of defence gene homologues
    Marcel, T.C. ; Varshney, R.K. ; Barbieri, M. ; Jafary, H. ; Kock, M.J.D. de; Graner, A. ; Niks, R.E. - \ 2007
    Theoretical and Applied Genetics 114 (2007)3. - ISSN 0040-5752 - p. 487 - 500.
    powdery mildew resistance - quantitative trait loci - aflp markers - microsatellite markers - disease-resistance - ssr-markers - linkage map - genome - rice - cloning
    A consensus map of barley was constructed based on three reference doubled haploid (DH) populations and three recombinant inbred line (RIL) populations. Several sets of microsatellites were used as bridge markers in the integration of those populations previously genotyped with RFLP or with AFLP markers. Another set of 61 genic microsatellites was mapped for the first time using a newly developed fluorescent labelling strategy, referred to as A/T labelling. The final map contains 3,258 markers spanning 1,081 centiMorgans (cM) with an average distance between two adjacent loci of 0.33 cM. This is the highest density of markers reported for a barley genetic map to date. The consensus map was divided into 210 BINs of about 5 cM each in which were placed 19 quantitative trait loci (QTL) contributing to the partial resistance to barley leaf rust (Puccinia hordei Otth) in five of the integrated populations. Each parental barley combination segregated for different sets of QTLs, with only few QTLs shared by any pair of cultivars. Defence gene homologues (DGH) were identified by tBlastx homology to known genes involved in the defence of plants against microbial pathogens. Sixty-three DGHs were located into the 210 BINs in order to identify candidate genes responsible for the QTL effects. Eight BINs were co-occupied by a QTL and DGH(s). The positional candidates identified are receptor-like kinase, WIR1 homologues and several defence response genes like peroxidases, superoxide dismutase and thaumatin
    Further isolation of AFLP and LMS markers for the mapping of the Ol-2 locus related to powdery mildew (Oidium neolycopersici) resistance in tomato (Solanum lycopersicum L.)
    Ricciardi, L. ; Lotti, C. ; Pavan, S.N.C. ; Bai, Y. ; Lindhout, P. ; Giovanni, C. de - \ 2007
    Plant Science 172 (2007)4. - ISSN 0168-9452 - p. 746 - 755.
    bulked segregant analysis - mediated suppression-pcr - conferring resistance - disease-resistance - molecular markers - linkage map - gene ol-1 - identification - dna - chromosome-6
    Tomato powdery mildew (Oidium neolycopersici) is a new plant disease that in recent years has frequently occurred in open field and protected environments to cause serious damage to tomato crops. Currently, the development of resistant cultivars appear to be the best eco-compatible solution to control the fungus. Several studies are in progress to increase knowledge on a recessive gene named ol-2 that confers complete resistance to powdery mildew. In this paper, we report results of research aimed at further isolation of new PCR-based markers linked to ol-2. This goal was pursued by means of bulk segregant analysis (BSA) applied to an F2 population segregating for the ol-2 gene and derived from the pair cross between a resistant line of Solanum lycopersicum L. var. cerasiforme and the susceptible cultivar Super Marmande. Eight new amplified fragment length polymorphism (AFLP) markers tightly linked to ol-2 were isolated, adding useful mapping information to the chromosome four region where Ol-2 locus is located. Results from the application of the ligation-mediated suppression PCR (LMS-PCR) technique are also reported for the first time in plant material. These results, combined with those obtained applying low ionic strength single strand conformation polymorphism (LIS-SSCP) analysis, were of value to detect polymorphism between parents characterised by high genetic similarities and also useful in avoiding "linkage drag" during marker assisted selection (MAS) programs
    Innate nonhost immunity in barley to different heterologous rust fungi is controlled by sets of resistance genes with different and overlapping specificities
    Jafary, H. ; Szabo, L.J. ; Niks, R.E. - \ 2006
    Molecular Plant-Microbe Interactions 19 (2006)11. - ISSN 0894-0282 - p. 1270 - 1279.
    puccinia-hordei - linkage map - leaf rust - plant defense - arabidopsis - identification - prehaustorial - perception - morphology - pathogens
    We developed an evolutionary relevant model system, barley-Puccini rust fungi, to study the inheritance and specificity of plant factors that determine to what extent innate nonhost immunity can be suppressed. A mapping population was developed from a cross between an experimental barley line (Suspired) with exceptional susceptibility to several heterogonous (nonhost) rust fungi and regular, immune, cv. Veda. Seedlings were inoculated with five heterogonous and two homologous (host) species of rust fungi. Resistance segregated quantitatively for each of the rust fungi. In total, 18 chromosomal regions were implicated. For each rust species, a different set of genes was effective. Of the 18 chromosomal regions, 11 were significantly effective to only one rust species and 7 were effective to more than one rust species, implying genetic linkage or pleiotropy. One resistance (R) gene for hypersensitive resistance to Puccinia hordei-secalini was mapped, suggesting occasional contribution of R genes to nonhost resistance in barley. Quantitative trait loci (QTLs) with effects to multiple rust fungi did not tend to be particularly effective to rust species that were phylogenetically related, as determined from their internal transcribed spacer sequence. We suggest that the QTLs described here play a role as specific and quantitative recognition factors that are specifically negated by the rust to successfully suppress innate immunity.
    Construction of a 10,000-marker ultradense genetic recombination map of potato: providing a framework for accelerated gene isolation and a genomewide physical map
    Os, H. van; Andrzejewski, S. ; Bakker, E.H. ; Barrena, I. ; Bryan, G.J. ; Caromel, B. ; Ghareeb, B. ; Isidore, E. ; Jong, W. de; Koert, P. van; Lefebvre, V. ; Milbourne, D. ; Ritter, E. ; Rouppe van der Voort, J.N.A.M. ; Rousselle-Bourgeois, F. ; Vliet, J.M. van; Waugh, R. ; Visser, R.G.F. ; Bakker, J. ; Eck, H.J. van - \ 2006
    Genetics 173 (2006)2. - ISSN 0016-6731 - p. 1075 - 1087.
    quantitative trait loci - sequence-tagged sites - solanum-tuberosum - linkage map - resistance-gene - aflp markers - mapping strategy - density - tomato - populations
    An ultradense genetic linkage map with >10,000 AFLP loci was constructed from a heterozygous diploid potato population. To our knowledge, this is the densest meiotic recombination map ever constructed. A fast marker-ordering algorithm was used, based on the minimization of the total number of recombination events within a given marker order in combination with genotyping error-detection software. This resulted in "skeleton bin maps," which can be viewed as the most parsimonious marker order. The unit of distance is not expressed in centimorgans but in "bins." A bin is a position on the genetic map with a unique segregation pattern that is separated from adjacent bins by a single recombination event. Putative centromeres were identified by a strong clustering of markers, probably due to cold spots for recombination. Conversely, recombination hot spots resulted in large intervals of up to 15 cM without markers. The current level of marker saturation suggests that marker density is proportional to physical distance and independent of recombination frequency. Most chromatids (92%) recombined once or never, suggesting strong chiasma interference. Absolute chiasma interference within a chromosome arm could not be demonstrated. Two examples of contig construction and map-based cloning have demonstrated that the marker spacing was in accordance with the expected physical distance: approximately one marker per BAC length. Currently, the markers are used for genetic anchoring of a physical map of potato to deliver a sequence-ready minimal tiling path of BAC contigs of specific chromosomal regions for the potato genome sequencing consortium (http://www.potatogenome.net).
    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.
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