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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    Development of a leafy Brassica rapa fixed line collection for genetic diversity and population structure analysis
    Pang, W. ; Li, X. ; Choi, S.R. ; Dhandapani, V. ; Im, S. ; Park, M.Y. ; Jang, C.S. ; Yang, M.S. ; Ham, I.K. ; Lee, E.M. ; Kim, W. ; Lee, S.S. ; Bonnema, A.B. ; Park, S. ; Piao, Z. ; Lim, Y.P. - \ 2015
    Molecular Breeding 35 (2015)1. - ISSN 1380-3743
    genome sequencing project - microspore culture - linkage map - napus l. - microsatellite markers - repeat markers - construction - crop - association - centers
    Brassica rapa is an economically important crop with a wide range of morphologies. Developing a set of fixed lines and understanding their diversity has been challenging, but facilitates resource conservation. We investigated the genetic diversity and population structure of 238 fixed lines of leafy B. rapa with 45 new simple sequence repeat markers and 109 new NGS (next-generation sequencing)-generated single nucleotide polymorphism markers evenly distributed throughout the B. rapa genome. Phylogenetic analysis classified the vegetable fixed lines into four subgroups, with the three oil types forming a separate and relatively distant cluster. A model-based population structure analysis identified four subpopulations corresponding to geographical origins and morphological traits, and revealed extensive allelic admixture. In particular, the Chinese cabbage cluster was subdivided into three groups and showed considerable correlation with leaf- and heading-related traits (leaf and heading shape). The vegetable B. rapa fixed lines successfully developed in our study could be valuable materials for establishing a multinational Brassica rapa diversity resource. Understanding the genetic diversity and population structure could be useful for utilization of the representative genetic variation and further genomic analysis.
    QTLs for barley yield adaptation to Mediterranean environments in the ‘Nure’ × ‘Tremois’ biparental population
    Tondelli, A. ; Francia, E. ; Visioni, A. ; Comadran, J. ; Mastrangelo, A.M. ; Akar, T. ; Al-Yassina, A. ; Ceccarelli, S. ; Grando, S. ; Eeuwijk, F.A. van; Thomas, W.T.B. ; Stanca, A.M. ; Romagosa, I. ; Pecchioni, N. - \ 2014
    Euphytica 197 (2014)1. - ISSN 0014-2336 - p. 73 - 86.
    quantitative trait loci - hordeum-vulgare - drought tolerance - agronomic traits - flowering time - abiotic stress - grain-yield - major genes - linkage map - wheat
    Multi-environment trials represent a highly valuable tool for the identification of the genetic bases of crop yield potential and stress adaptation. A Diversity Array Technology®-based barley map has been developed in the ‘Nure’ × ‘Tremois’ biparental Doubled Haploid population, harbouring the genomic position of a gene set with a putative role in the regulation of flowering time and abiotic stress response in barley. The population has been evaluated in eighteen location-by-year combinations across the Mediterranean basin. QTL mapping identified several genomic regions responsible for barley adaptation to Mediterranean conditions in terms of phenology, grain yield and yield component traits. The most frequently detected yield QTL had the early flowering HvCEN_EPS2 locus (chromosome 2H) as peak marker, showing a positive effect from the early winter parent ‘Nure’ in eight field trials, and explaining up to 45.8 % of the observed variance for grain yield. The HvBM5A_VRN-H1 locus on chromosome 5H and the genomic region possibly corresponding to PPD-H2 on chromosome 1H were significantly associated to grain yield in five and three locations, respectively. Environment-specific QTLs for grain yield, and clusters of yield component QTLs not related to phenology and or developmental genes (e.g. on chromosome 4H, BIN_09) were observed as well. The results of this work provide a valuable source of knowledge and tools for both explaining the genetic bases of barley yield adaptation across the Mediterranean basin, and using QTL-associated markers for MAS pre-breeding and breeding programmes.
    Replicated high-density genetic maps of two great tit populations reveal fine-scale genomic departures from sex-equal recombination rates
    Oers, K. van; Santure, A.W. ; Cauwer, I. de; Bers, N.E.M. van; Crooijmans, R.P.M.A. ; Sheldon, B.C. ; Visser, M.E. ; Slate, J. ; Groenen, M.A.M. - \ 2014
    Heredity 112 (2014)3. - ISSN 0018-067X - p. 307 - 316.
    wild bird population - linkage map - zebra finch - parus-major - synteny conservation - ficedula-albicollis - personality-traits - turkey genome - evolution - chicken
    Linking variation in quantitative traits to variation in the genome is an important, but challenging task in the study of life-history evolution. Linkage maps provide a valuable tool for the unravelling of such trait-gene associations. Moreover, they give insight into recombination landscapes and between-species karyotype evolution. Here we used genotype data, generated from a 10k single-nucleotide polymorphism (SNP) chip, of over 2000 individuals to produce high-density linkage maps of the great tit (Parus major), a passerine bird that serves as a model species for ecological and evolutionary questions. We created independent maps from two distinct populations: a captive F2-cross from The Netherlands (NL) and a wild population from the United Kingdom (UK). The two maps contained 6554 SNPs in 32 linkage groups, spanning 2010¿cM and 1917¿cM for the NL and UK populations, respectively, and were similar in size and marker order. Subtle levels of heterochiasmy within and between chromosomes were remarkably consistent between the populations, suggesting that the local departures from sex-equal recombination rates have evolved. This key and surprising result would have been impossible to detect if only one population was mapped. A comparison with zebra finch Taeniopygia guttata, chicken Gallus gallus and the green anole lizard Anolis carolinensis genomes provided further insight into the evolution of avian karyotypes.
    Development and validation of a 20K Single Nucleotide Polymorphism (SNP) whole genome genotyping array for apple (Malus × domestica Borkh)
    Bianco, L. ; Cestaro, A. ; Sargent, D.J. ; Guardo, M. Di; Jansen, J. ; Weg, W.E. van de - \ 2014
    PLoS ONE 9 (2014)10. - ISSN 1932-6203 - 9 p.
    linkage map - construction - cultivars - alignment - accurate - barley
    High-density SNP arrays for genome-wide assessment of allelic variation have made high resolution genetic characterization of crop germplasm feasible. A medium density array for apple, the IRSC 8 K SNP array, has been successfully developed and used for screens of bi-parental populations. However, the number of robust and well-distributed markers contained on this array was not sufficient to perform genome-wide association analyses in wider germplasm sets, or Pedigree-Based Analysis at high precision, because of rapid decay of linkage disequilibrium. We describe the development of an Illumina Infinium array targeting 20 K SNPs. The SNPs were predicted from re-sequencing data derived from the genomes of 13 Malus × domestica apple cultivars and one accession belonging to a crab apple species (M. micromalus). A pipeline for SNP selection was devised that avoided the pitfalls associated with the inclusion of paralogous sequence variants, supported the construction of robust multi-allelic SNP haploblocks and selected up to 11 entries within narrow genomic regions of ±5 kb, termed focal points (FPs). Broad genome coverage was attained by placing FPs at 1 cM intervals on a consensus genetic map, complementing them with FPs to enrich the ends of each of the chromosomes, and by bridging physical intervals greater than 400 Kbps. The selection also included ~3.7 K validated SNPs from the IRSC 8 K array. The array has already been used in other studies where ~15.8 K SNP markers were mapped with an average of ~6.8 K SNPs per full-sib family. The newly developed array with its high density of polymorphic validated SNPs is expected to be of great utility for Pedigree-Based Analysis and Genomic Selection. It will also be a valuable tool to help dissect the genetic mechanisms controlling important fruit quality traits, and to aid the identification of marker-trait associations suitable for the application of Marker Assisted Selection in apple breeding programs.
    ‘Schmidt's Antonovka’ is identical to ‘Common Antonovka’, an apple cultivar widely used in Russia in breeding for biotic and abiotic stresses
    Pikunova, A. ; Madduri, M. ; Sedov, E. ; Noordijk, Y. ; Peil, A. ; Troggio, M. ; Bus, V.G.M. ; Visser, R.G.F. ; Weg, W.E. van de - \ 2014
    Tree Genetics and Genomes 10 (2014)2. - ISSN 1614-2942 - p. 261 - 271.
    x-domestica borkh. - resistance gene - linkage map - scab - genome
    Progenies of ‘Schmidt's Antonovka’ (SA) have been widely used in Western breeding programs as a source of scab resistance. The identity of SA has remained obscure, especially due to the existence of a series of ‘Antonovka’ cultivars with different origins. In this paper we show Schmidt's Antonovka to be identical to ¿¿¿¿´¿¿¿¿¿ ¿¿¿¿¿¿¿¿¿¿¿¿ or ‘Common Antonovka’ (CA), an old Russian cultivar of unknown origin, by comparing simple sequence repeat (SSR) and SNP genotyping data from several first-generation descendants of SA from two European collections and a CA accession from the germplasm collection held at VNIISPK (The All-Russian Research Institute of Horticultural Breeding, Orel, Russia). The use of CA in Russian breeding programs is also briefly reviewed.
    High-resolution mapping of the barley Ryd3 locus controlling tolerance to BYDV
    Lüpken, T. ; Stein, N. ; Perovic, D. ; Habekuss, A. ; Serfling, A. ; Krämer, I. ; Hähnel, U. ; Steuernagel, B. ; Scholz, U. ; Ariyadasa, R. ; Martis, M. ; Mayer, K. ; Niks, R.E. ; Collins, N.C. ; Friedt, W. ; Ordon, F. - \ 2014
    Molecular Breeding 33 (2014)2. - ISSN 1380-3743 - p. 477 - 488.
    yellow-dwarf-virus - hordeum-vulgare l. - recessive bymovirus resistance - leaf rust resistance - comparative genomics - consensus map - winter barley - linkage map - yd2 gene - sequence
    Barley yellow dwarf disease (BYD) is transmitted by aphids and is caused by different strains of Barley yellow dwarf virus (BYDV) and Cereal yellow dwarf virus (CYDV). Economically it is one of the most important diseases of cereals worldwide. Besides chemical control of the vector, growing of tolerant/resistant cultivars is an effective way of protecting crops against BYD. The Ryd3 gene in barley (Hordeum vulgare L.) confers tolerance to BYDV-PAV and BYDV-MAV and the locus was previously mapped on the short arm of barley chromosome 6H near the centromere. We applied a strategy for high-resolution mapping and marker saturation at the Ryd3 locus by exploiting recent genomic tools available in barley. In a population of 3,210 F2 plants, 14 tightly linked markers were identified, including 10 that co-segregated with Ryd3. The centromeric region where Ryd3 is located suffers suppressed recombination or reduced recombination rate, suggesting potential problems in achieving (1) map-based cloning of Ryd3 and (2) marker selection of the resistance in breeding programmes without the introduction of undesirable traits via linkage drag.
    Integrated linkage map of haliotis midae linnaeus based on microsatellite and SNP markers
    Vervalle, Jessica ; Hepple, Juli Ann ; Jansen, Suzaan ; Plessis, Jana Du ; Wang, Peizheng ; Rhode, Clint ; Roodt-Wilding, Rouvay - \ 2013
    Journal of Shellfish Research 32 (2013)1. - ISSN 0730-8000 - p. 89 - 103.
    abalone - Haliotis midae - linkage map - microsatellites - single nucleotide polymorphisms

    The South African abalone Haliotis midae Linnaeus is the most important aquaculture species in South Africa. Marker-assisted selection is envisioned to play an integral part of the genetic improvement program of abalone, and therefore the generation of linkage maps for quantitative trait loci analyses are necessary. This study reports on a first-generation linkage map for H. midae based on microsatellite and single nucleotide polymorphism (SNP) markers. Ten full-sib families were screened with a total of 508 molecular markers derived from genomic and expressed sequence tag sequences. Linkage maps were constructed for each of the families and combined to create an integrated linkage map. The integrated linkage map consists of 186 markers that included 116 microsatellites and 70 SNPs. These markers mapped to 18 linkage groups, which corresponds to the haploid chromosome number of H. midae. The average genome length was estimated at 1,312 cM, displaying an average marker interval of 6.88 cM with 80% genome coverage. The female map is 1.16-fold longer than the male map, indicating differences in recombination rate between the sexes. The association of markers with known genes as well as with transposon elements was also investigated. This study resulted in the first linkage map constructed for any haliotid in which both microsatellite and SNP markers were used, and the results provide a framework for future applications in quantitative trait loci identification.

    Replicated high-density genetic maps of two great tit populations reveal fine-scale genomic departures from sex-equal recombination rates
    Oers, K. van; Santure, A.W. ; Cauwer, I. de; Bers, N.E.M. van; Crooijmans, R.P.M.A. ; Sheldon, B.C. ; Visser, M.E. ; Slate, J. ; Groenen, M. - \ 2013
    Wageningen UR
    linkage map - heterochiasmy - chromosomal rearrangements - population comparison
    Linking variation in quantitative traits to variation in the genome is an important, but challenging task in the study of life-history evolution. Linkage maps provide a valuable tool for the unravelling of such trait-gene associations. Moreover, they give insight into recombination landscapes and between- species karyotype evolution. Here we used genotype data, generated from a 10k SNP-chip, of over 2000 individuals to produce high-density linkage maps of the great tit (Parus major), a passerine bird, which serves as a model species for ecological and evolutionary questions. We created independent maps from two distinct populations: a captive F2-cross from The Netherlands (NL) and a wild population from the United Kingdom (UK). The two maps contained 6554 SNPs in 32 linkage groups, spanning 2010 cM and 1917 cM for the NL and UK populations respectively, and were similar in size and marker order. Subtle levels of heterochiasmy within and between chromosomes were remarkably consistent between the populations, suggesting that local departures from sex-equal recombination rates have evolved. This key and surprising result would have been impossible to detect if only one population was mapped. A comparison with zebra finch Taeniopygia guttata, chicken Gallus gallus and the green anole lizard Anolis carolinensis genomes provided further insight into the evolution of avian karyotypes.
    Chromosome evolution in Solanum traced by cross-species BAC-FISH
    Szinay, D. ; Wijnker, E. ; Berg, R.G. van den; Visser, R.G.F. ; Jong, J.H.S.G.M. de; Bai, Y. - \ 2012
    New Phytologist 195 (2012)3. - ISSN 0028-646X - p. 688 - 698.
    l. section lycopersicon - resistance gene - mill. wettst. - linkage map - tomato - solanaceae - potato - reveals - rearrangements - recombination
    Chromosomal rearrangements are relatively rare evolutionary events and can be used as markers to study karyotype evolution. This research aims to use such rearrangements to study chromosome evolution in Solanum. Chromosomal rearrangements between Solanum crops and several related wild species were investigated using tomato and potato bacterial artificial chromosomes (BACs) in a multicolour fluorescent in situ hybridization (FISH). The BACs selected are evenly distributed over seven chromosomal arms containing inversions described in previous studies. The presence / absence of these inversions among the studied Solanum species were determined and the order of the BAC-FISH signals was used to construct phylogenetic trees. Compared with earlier studies, data from this study provide support for the current grouping of species into different sections within Solanum; however, there are a few notable exceptions, such as the tree positions of S. etuberosum (closer to the tomato group than to the potato group) and S. lycopersicoides (sister to S. pennellii). These apparent contradictions might be explained by interspecific hybridization events and / or incomplete lineage sorting. This cross-species BAC painting technique provides unique information on genome organization, evolution and phylogenetic relationships in a wide variety of species. Such information is very helpful for introgressive breeding.
    A century of poultry genetics
    Tixier-Boichard, M. ; Leenstra, F.R. ; Flock, D. ; Hocking, A.D. ; Weigend, S. - \ 2012
    Worlds Poultry Science Journal 68 (2012)2. - ISSN 0043-9339 - p. 307 - 321.
    major histocompatibility complex - chicken genome - nucleolar organizer - molecular-cloning - linked factors - linkage map - egg-white - rfp-y - diversity - selection
    The 20th Century saw an astonishing advance in our understanding of genetics and the scientific basis of the genetic improvement of farm animals. The application of genetic principles to chickens in the 1950s and 1960s led to a rapid change in the productivity and efficiency of laying hens and broiler chickens, turkeys and ducks. Subsequently, the application of increasingly powerful computers and sophisticated mathematical algorithms has increased the range of traits that could be successfully incorporated into breeding programs. Random sample tests of the performance of laying hens enjoyed a period of popularity and more recently the few remaining tests included husbandry systems in addition to strain evaluation. Characterisation of avian blood groups has led to the identification of the B21 haplotype that confers resistance to Marek's disease and to selection for this locus in commercial lines. The decade following the millennium saw the publication of the genome sequence of the chicken and the identification of millions of single nucleotide polymorphisms that, coupled with technological advances, made the application of whole genome selection practical in poultry. In parallel, the molecular basis for some Mendelian traits described a century ago is now being deciphered. Similar technologies have been applied to study genetic diversity in chickens and have provided insights into the evolution and domestication of chicken breeds. Finally, in this review, the recent development of the European Poultry Genetics Symposia coordinated by Working Group 3 ‘Genetics and Breeding’ that was based on combining the British Poultry Breeders Round Table and AVIAGEN from West and Eastern Europe, is discussed
    Microsatellite allele dose and configuration establishment (MADCE): an integrated approach for genetic studies in allopolyploids
    Dijk, T. van; Noordijk, Y. ; Dubos, T. ; Bink, M.C.A.M. ; Visser, R.G.F. ; Weg, W.E. van de - \ 2012
    BMC Plant Biology 12 (2012). - ISSN 1471-2229
    polysomic inheritance - octoploid strawberry - diploid fragaria - dosage analysis - linkage map - dna - evolution - potato - genome - plants
    BACKGROUND: Genetic studies in allopolyploid plants are challenging because of the presence of similar sub-genomes, which leads to multiple alleles and complex segregation ratios. In this study, we describe a novel method for establishing the exact dose and configuration of microsatellite alleles for any accession of an allopolyploid plant species. The method, named Microsatellite Allele Dose and Configuration Establishment (MADCE), can be applied to mapping populations and pedigreed (breeding) germplasm in allopolyploids. RESULTS: Two case studies are presented to demonstrate the power and robustness of the MADCE method. In the mapping case, five microsatellites were analysed. These microsatellites amplified 35 different alleles based on size. Using MADCE, we uncovered 30 highly informative segregating alleles. A conventional approach would have yielded only 19 fully informative and six partially informative alleles. Of the ten alleles that were present in all progeny (and thereby ignored or considered homozygous when using conventional approaches), six were found to segregate by dosage when analysed with MADCE. Moreover, the full allelic configuration of the mapping parents could be established, including null alleles, homozygous loci, and alleles that were present on multiple homoeologues. In the second case, 21 pedigreed cultivars were analysed using MADCE, resulting in the establishment of the full allelic configuration for all 21 cultivars and a tracing of allele flow over multiple generations. CONCLUSIONS: The procedure described in this study (MADCE) enhances the efficiency and information content of mapping studies in allopolyploids. More importantly, it is the first technique to allow the determination of the full allelic configuration in pedigreed breeding germplasm from allopolyploid plants. This enables pedigree-based marker-trait association studies the use of algorithms developed for diploid crops, and it may increase the effectiveness of LD-based association studies. The MADCE method therefore enables researchers to tackle many of the genotyping problems that arise when performing mapping, pedigree, and association studies in allopolyploids. We discuss the merits of MADCE in comparison to other marker systems in polyploids, including SNPs, and how MADCE could aid in the development of SNP markers in allopolyploids.
    A hybrid BAC physical map of potato: a framework for sequencing a heterozygous genome
    Boer, J.M. de; Borm, T.J.A. ; Jesse, T. ; Brugmans, B.W. ; Tang, X. ; Bryan, G.J. ; Bakker, J. ; Eck, H.J. van; Visser, R.G.F. - \ 2011
    BMC Genomics 12 (2011). - ISSN 1471-2164 - 60 p.
    quantitative trait loci - candidate genes - disease resistance - linkage map - tomato - aflp - solanum - markers - dna - construction
    Background Potato is the world's third most important food crop, yet cultivar improvement and genomic research in general remain difficult because of the heterozygous and tetraploid nature of its genome. The development of physical map resources that can facilitate genomic analyses in potato has so far been very limited. Here we present the methods of construction and the general statistics of the first two genome-wide BAC physical maps of potato, which were made from the heterozygous diploid clone RH89-039-16 (RH). Results First, a gel electrophoresis-based physical map was made by AFLP fingerprinting of 64478 BAC clones, which were aligned into 4150 contigs with an estimated total length of 1361 Mb. Screening of BAC pools, followed by the KeyMaps in silico anchoring procedure, identified 1725 AFLP markers in the physical map, and 1252 BAC contigs were anchored the ultradense potato genetic map. A second, sequence-tag-based physical map was constructed from 65919 whole genome profiling (WGP) BAC fingerprints and these were aligned into 3601 BAC contigs spanning 1396 Mb. The 39733 BAC clones that overlap between both physical maps provided anchors to 1127 contigs in the WGP physical map, and reduced the number of contigs to around 2800 in each map separately. Both physical maps were 1.64 times longer than the 850 Mb potato genome. Genome heterozygosity and incomplete merging of BAC contigs are two factors that can explain this map inflation. The contig information of both physical maps was united in a single table that describes hybrid potato physical map. Conclusions The AFLP physical map has already been used by the Potato Genome Sequencing Consortium for sequencing 10% of the heterozygous genome of clone RH on a BAC-by-BAC basis. By layering a new WGP physical map on top of the AFLP physical map, a genetically anchored genome-wide framework of 322434 sequence tags has been created. This reference framework can be used for anchoring and ordering of genomic sequences of clone RH (and other potato genotypes), and opens the possibility to finish sequencing of the RH genome in a more efficient way via high throughput next generation approaches.
    Genetic mapping in Lilium: mapping of major genes and quantitative trait loci for several ornamental traits and disease resistances
    Shahin, A. ; Arens, P.F.P. ; Heusden, S. van; Linden, C.G. van der; Kaauwen, M.P.W. van; Nadeem Khan, M. ; Schouten, H.J. ; Weg, W.E. van de; Visser, R.G.F. ; Tuyl, J.M. van - \ 2011
    Plant Breeding 130 (2011)3. - ISSN 0179-9541 - p. 372 - 382.
    diversity arrays technology - linkage map - zea-mays - segregation distortion - wild relatives - durum-wheat - markers - dart - construction - pollination
    Construction of genetic linkage maps for lily was achieved using two populations, LA and AA that share one parent ‘Connecticut King’. Three different molecular marker systems (AFLP™, DArT and NBS profiling) were used in generating linkage maps for ‘Connecticut King’. The LA and the AA populations consist of 20 and 21 linkage groups (LGs), respectively. Average density between markers was 3.9 cM for the LA and 5 cM for the AA population. Several horticultural traits were mapped for the first time in Lilium and showed to be single gene based. We propose to name these genes as LFCc for flower colour, lfs for flower spots, LSC for stem colour, lal for antherless phenotype and lfd for flower direction whereby upper and lower case names refer to dominant and recessive genes, respectively. Additionally, resistance to Lily mottle virus (LMoV) was mapped as a locus on LG AA10. For Fusarium resistance, the Kruskal–Wallis test identified six putative quantitative trait loci (QTL) in the AA population of which one QTL (explaining 25% of the variation in resistance) could be confirmed by interval mapping
    A major SNP resource for dissection of phenotypic and genetic variation in Pacific white shrimp (Litopenaeus vannamei)
    Ciobanu, D.C. ; Bastiaansen, J.W.M. ; Magrin, J. ; Rocha, J.L. ; Jiang, D.H. ; Yu, N. ; Geiger, B. ; Deeb, N. ; Rocha, D. ; Gong, H. ; Kinghorn, B.P. ; Plastow, G.S. ; Steen, H.A.M. van der; Mileham, A.J. - \ 2010
    Animal Genetics 41 (2010)1. - ISSN 0268-9146 - p. 39 - 47.
    taura-syndrome virus - pig skeletal-muscle - linkage map - glycogen-content - penaeus - markers - mutation - resistance - discovery - growth
    Bioinformatics and re-sequencing approaches were used for the discovery of sequence polymorphisms in Litopenaeus vannamei. A total of 1221 putative single nucleotide polymorphisms (SNPs) were identified in a pool of individuals from various commercial populations. A set of 211 SNPs were selected for further molecular validation and 88% showed variation in 637 samples representing three commercial breeding lines. An association analysis was performed between these markers and several traits of economic importance for shrimp producers including resistance to three major viral diseases. A small number of SNPs showed associations with test weekly gain, grow-out survival and resistance to Taura Syndrome Virus. Very low levels of linkage disequilibrium were revealed between most SNP pairs, with only 11% of SNPs showing an r2-value above 0.10 with at least one other SNP. Comparison of allele frequencies showed small changes over three generations of the breeding programme in one of the commercial breeding populations. This unique SNP resource has the potential to catalyse future studies of genetic dissection of complex traits, tracing relationships in breeding programmes, and monitoring genetic diversity in commercial and wild populations of L. vannamei
    Genome-wide SNP detection in the great tit Parus major using high throughput sequencing
    Bers, N.E.M. van; Oers, K. van; Dibbits, B.W. ; Groenen, M.A.M. ; Crooijmans, R.P.M.A. - \ 2010
    Molecular Ecology 19 (2010)Suppl. s1. - ISSN 0962-1083 - p. 89 - 99.
    wild bird population - natural-populations - climate-change - linkage map - phenotypic plasticity - future-directions - genotyping assay - passerine bird - dna-sequences - evolution
    Identifying genes that underlie ecological traits will open exiting possibilities to study gene–environment interactions in shaping phenotypes and in measuring natural selection on genes. Evolutionary ecology has been pursuing these objectives for decades, but they come into reach now that next generation sequencing technologies have dramatically lowered the costs to obtain the genomic sequence information that is currently lacking for most ecologically important species. Here we describe how we generated over 2 billion basepairs of novel sequence information for an ecological model species, the great tit Parus major. We used over 16 million short sequence reads for the de novo assembly of a reference sequence consisting of 550 000 contigs, covering 2.5% of the genome of the great tit. This reference sequence was used as the scaffold for mapping of the sequence reads, which allowed for the detection of over 20 000 novel single nucleotide polymorphisms. Contigs harbouring 4272 of the single nucleotide polymorphisms could be mapped to a unique location on the recently sequenced zebra finch genome. Of all the great tit contigs, significantly more were mapped to the microchromosomes than to the intermediate and the macrochromosomes of the zebra finch, indicating a higher overall level of sequence conservation on the microchromosomes than on the other types of chromosomes. The large number of great tit contigs that can be aligned to the zebra finch genome shows that this genome provides a valuable framework for large scale genetics, e.g. QTL mapping or whole genome association studies, in passerines.
    The development of Arabidopsis as a plant model
    Koornneef, M. ; Meinke, D.W. - \ 2010
    The Plant Journal 61 (2010). - ISSN 0960-7412 - p. 909 - 921.
    thaliana l heynh - agrobacterium-mediated transformation - dna insertion mutagenesis - recombinant inbred lines - embryo-lethal mutants - linkage map - natural variation - crucifer arabidopsis - reverse genetics - high-frequency
    Twenty-five years ago, Arabidopsis thaliana emerged as the model organism of choice for research in plant biology. A consensus was reached about the need to focus on a single organism to integrate the classical disciplines of plant science with the expanding fields of genetics and molecular biology. Ten years after publication of its genome sequence, Arabidopsis remains the standard reference plant for all of biology. We reflect here on the major advances and shared resources that led to the extraordinary growth of the Arabidopsis research community. We also underscore the importance of continuing to expand and refine our detailed knowledge of Arabidopsis while seeking to appreciate the remarkable diversity that characterizes the plant kingdom
    Regional differences in recombination hotspots between two chicken populations
    Elferink, M.G. ; As, P. van; Veenendaal, A. ; Crooijmans, R.P.M.A. ; Groenen, M.A.M. - \ 2010
    BMC Genetics 11 (2010). - ISSN 1471-2156
    ascites-related traits - whole genome scan - linkage map - physical map - broilers - markers
    Background Although several genetic linkage maps of the chicken genome have been published, the resolution of these maps is limited and does not allow the precise identification of recombination hotspots. The availability of more than 3.2 million SNPs in the chicken genome and the recent advances in high throughput genotyping techniques enabled us to increase marker density for the construction of a high-resolution linkage map of the chicken genome. This high-resolution linkage map allowed us to study recombination hotspots across the genome between two chicken populations: a purebred broiler line and a broiler × broiler cross. In total, 1,619 animals from the two different broiler populations were genotyped with 17,790 SNPs. Results The resulting linkage map comprises 13,340 SNPs. Although 360 polymorphic SNPs that had not been assigned to a known chromosome on chicken genome build WASHUC2 were included in this study, no new linkage groups were found. The resulting linkage map is composed of 31 linkage groups, with a total length of 3,054 cM for the sex-average map of the combined population. The sex-average linkage map of the purebred broiler line is 686 cM smaller than the linkage map of the broiler × broiler cross. Conclusions In this study, we present a linkage map of the chicken genome at a substantially higher resolution than previously published linkage maps. Regional differences in recombination hotspots between the two mapping populations were observed in several chromosomes near the telomere of the p arm; the sex-specific analysis revealed that these regional differences were mainly caused by female-specific recombination hotspots in the broiler × broiler cross.
    Distribution of genetic diversity in wild European populations of prickly lettuce (Lactuca serriola): implications for plant genetic resources management
    Wiel, C.C.M. van de; Sretenovic Rajicic, T. ; Treuren, R. van; Dehmer, K.J. ; Linden, C.G. van der; Hintum, T.J.L. van - \ 2010
    Plant genetic resources: characterization and utilization 8 (2010)2. - ISSN 1479-2621 - p. 171 - 181.
    molecular markers - linkage map - asteraceae - evolution - netherlands - acquisition - cluster - spp. - aflp - l.
    Genetic variation in Lactuca serriola, the closest wild relative of cultivated lettuce, was studied across Europe from the Czech Republic to the United Kingdom, using three molecular marker systems, simple sequence repeat (SSR, microsatellites), AFLP and nucleotide-binding site (NBS) profiling. The ‘functional’ marker system NBS profiling, targeting disease resistance genes of the NBS/LRR family, did not show marked differences in genetic diversity parameters to the other systems. The autogamy of the species resulted in low observed heterozygosity and high population differentiation. Intra-population variation ranged from complete homogeneity to nearly complete heterogeneity. The highest genetic diversity was found in central Europe. The SSR results were compared to SSR variation screened earlier in the lettuce collection of the Centre for Genetic Resources, the Netherlands (CGN). In the UK, practically only a single SSR genotype was found. This genotype together with a few other common SSR genotypes comprised a large part of the plants sampled on the continent. Among the ten most frequent SSR genotypes observed, eight were already present in the CGN collection. Overall, the CGN collection appears to already have a fair representation of genetic variation from NW Europe. The results are discussed in relation to sampling strategies for improving genebank collections of crop wild relatives.
    Characterisation of sugar beet (Beta vulgaris L. ssp. vulgaris) varieties using microsatellite markers
    Smulders, M.J.M. ; Esselink, G. ; Everaert, I. ; Riek, J. de; Vosman, B. - \ 2010
    BMC Genetics 11 (2010). - ISSN 1471-2156 - 11 p.
    genetic diversity - linkage map - wild relatives - flow - crop - identification - populations - database - complex - tomato
    Background - Sugar beet is an obligate outcrossing species. Varieties consist of mixtures of plants from various parental combinations. As the number of informative morphological characteristics is limited, this leads to some problems in variety registration research. Results - We have developed 25 new microsatellite markers for sugar beet. A selection of 12 markers with high quality patterns was used to characterise 40 diploid and triploid varieties. For each variety 30 individual plants were genotyped. The markers amplified 3-21 different alleles. Varieties had up to 7 different alleles at one marker locus. All varieties could be distinguished. For the diploid varieties, the expected heterozygosity ranged from 0.458 to 0.744. The average inbreeding coefficient Fis was 0.282 +/- 0.124, but it varied widely among marker loci, from Fis = +0.876 (heterozygote deficiency) to Fis = -0.350 (excess of heterozygotes). The genetic differentiation among diploid varieties was relatively constant among markers (Fst = 0.232 +/- 0.027). Among triploid varieties the genetic differentiation was much lower (Fst = 0.100 +/- 0.010). The overall genetic differentiation between diploid and triploid varieties was Fst = 0.133 across all loci. Part of this differentiation may coincide with the differentiation among breeders' gene pools, which was Fst = 0.063. Conclusions - Based on a combination of scores for individual plants all varieties can be distinguished using the 12 markers developed here. The markers may also be used for mapping and in molecular breeding. In addition, they may be employed in studying gene flow from crop to wild populations.
    Ethylene-induced hyponastic growth in Arabidopsis thaliana is controlled by ERECTA
    Zanten, M. van; Snoek, L.B. ; Eck-Stouten, E. van; Proveniers, M.C.G. ; Torii, K.U. ; Voesenek, L.A.C.J. ; Peeters, A.J.M. ; Millenaar, F.F. - \ 2010
    The Plant Journal 61 (2010)1. - ISSN 0960-7412 - p. 83 - 95.
    natural allelic variation - receptor-like kinase - quantitative trait loci - inbred line population - shade-avoidance - genetic-variation - secretory peptide - circadian clock - abscisic-acid - linkage map
    Plants can respond quickly and profoundly to detrimental changes in their environment. For example, Arabidopsis thaliana can induce an upward leaf movement response through differential petiole growth (hyponastic growth) to outgrow complete submergence. This response is induced by accumulation of the phytohormone ethylene in the plant. Currently, only limited information is available on how this response is molecularly controlled. In this study, we utilized quantitative trait loci (QTL) analysis of natural genetic variation among Arabidopsis accessions to isolate novel factors controlling constitutive petiole angles and ethylene-induced hyponastic growth. Analysis of mutants in various backgrounds and complementation analysis of naturally occurring mutant accessions provided evidence that the leucin-rich repeat receptor-like Ser/Thr kinase gene, ERECTA, controls ethylene-induced hyponastic growth. Moreover, ERECTA controls leaf positioning in the absence of ethylene treatment. Our data demonstrate that this is not due to altered ethylene production or sensitivity
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