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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    Dataset for the annotations of the transcriptome of the hemp cultivar C. sativa ‘Finola’ (finola1) and the marihuana cultivar C. sativa ‘Purple Kush’
    Petit Pedro, Jordi ; Salentijn, Elma ; Loo, Robert van; Caldas Paulo, Joao ; Denneboom, Christel ; Trindade, Luisa - \ 2020
    Wageningen University & Research
    GWAS - Cannabis sativa - hemp - fibre quality - cell wall composition - RAD-sequencing - QTL - sex determination - flowering time - plant breeding
    This dataset contains the annotations of the two transcriptomes of the hemp cultivar C. sativa ‘Finola’ (finola1) and the marihuana cultivar C. sativa ‘Purple Kush’, aligned to the C. sativa ‘Purple Kush’ (canSat3 version GAC 000230575.1) assembly from the C. sativa Genome Browser Gateway (van Bakel et al., 2011). The annotations were performed using Local Blast and the data is provided in gff files. Gff means General Feature Format and it's a simple tab-delimited text file for describing genomic features. The files are ready to be uploaded in a genomic viewer.
    Dataset of the RADseq data and genotyping from a panel of 123 hemp accessions
    Petit Pedro, Jordi ; Salentijn, Elma ; Loo, Robert van; Caldas Paulo, Joao ; Denneboom, Christel ; Trindade, Luisa - \ 2020
    Wageningen University and Research
    GWAS - Cannabis sativa - hemp - fibre quality - cell wall composition - RAD-sequencing - QTL - sex determination - flowering time - plant breeding
    This dataset contains the raw RADseq data and genotyping data from a panel of 123 hemp (Cannabis sativa L.) accessions. For extra information about the RAD sequencing data analysis and the SNP marker selection, read the materials and methods of the paper 'Elucidating the genetic architecture of fibre quality in hemp (Cannabis sativa L.) using the Genome-Wide Association Study'.
    Genetic Variability of Morphological, Flowering, and Biomass Quality Traits in Hemp (Cannabis sativa L.)
    Petit, Jordi ; Salentijn, Elma M.J. ; Paulo, Maria João ; Thouminot, Claire ; Dinter, Bert Jan van; Magagnini, Gianmaria ; Gusovius, Hans Jörg ; Tang, Kailei ; Amaducci, Stefano ; Wang, Shaoliang ; Uhrlaub, Birgit ; Müssig, Jörg ; Trindade, Luisa M. - \ 2020
    Frontiers in Plant Science 11 (2020). - ISSN 1664-462X
    Cannabis sativa - cell wall composition - fiber quality - flowering time - genetic variability - genotype-by-environment (G×E) interactions - hemp - sex determination

    Hemp (Cannabis sativa L.) is a bast-fiber crop well-known for the great potential to produce sustainable fibers. Nevertheless, hemp fiber quality is a complex trait, and little is known about the phenotypic variability and heritability of fiber quality traits in hemp. The aim of this study is to gain insights into the variability in fiber quality within the hemp germplasm and to estimate the genetic components, environmental components, and genotype-by-environment (G×E) interactions on fiber quality traits in hemp. To investigate these parameters, a panel of 123 hemp accessions was phenotyped for 28 traits relevant to fiber quality at three locations in Europe, corresponding to climates of northern, central, and southern Europe. In general, hemp cultivated in northern latitudes showed a larger plant vigor while earlier flowering was characteristic of plants cultivated in southern latitudes. Extensive variability between accessions was observed for all traits. Most cell wall components (contents of monosaccharides derived from cellulose and hemicellulose; and lignin content), bast fiber content, and flowering traits revealed large genetic components with low G×E interactions and high broad-sense heritability values, making these traits suitable to maximize the genetic gains of fiber quality. In contrast, contents of pectin-related monosaccharides, most agronomic traits, and several fiber traits (fineness and decortication efficiency) showed low genetic components with large G×E interactions affecting the rankings across locations. These results suggest that pectin, agronomic traits, and fiber traits are unsuitable targets in breeding programs of hemp, as their large G×E interactions might lead to unexpected phenotypes in untested locations. Furthermore, all environmental effects on the 28 traits were statistically significant, suggesting a strong adaptive behavior of fiber quality in hemp to specific environments. The high variability in fiber quality observed in the hemp panel, the broad range in heritability, and adaptability among all traits prescribe positive prospects for the development of new hemp cultivars of excellent fiber quality.

    A high-resolution map of the Nile tilapia genome: a resource for studying cichlids and other percomorphs
    Guyon, R. ; Rakotomanga, M. ; Azzouzi, N. ; Coutanceau, J.P. ; Bonillo, C. ; Cotta, H. D'; Pepey, E. ; Soler, L. ; Rodier-Goud, M. ; Hont, A. D'; Conte, M.A. ; Bers, N.E.M. van; Penman, D.J. ; Hitte, C. ; Crooijmans, R.P.M.A. ; Kocher, T.D. ; Ozouf-Costaz, C. ; Baroiller, J.F. ; Galibert, F. - \ 2012
    BMC Genomics 13 (2012). - ISSN 1471-2164
    radiation hybrid map - genetic-linkage map - oreochromis-niloticus - sex determination - tetraodon-nigroviridis - zebrafish genome - fish - sequence - construction - evolution
    Background: The Nile tilapia (Oreochromis niloticus) is the second most farmed fish species worldwide. It is also an important model for studies of fish physiology, particularly because of its broad tolerance to an array of environments. It is a good model to study evolutionary mechanisms in vertebrates, because of its close relationship to haplochromine cichlids, which have undergone rapid speciation in East Africa. The existing genomic resources for Nile tilapia include a genetic map, BAC end sequences and ESTs, but comparative genome analysis and maps of quantitative trait loci (QTL) are still limited. Results: We have constructed a high-resolution radiation hybrid (RH) panel for the Nile tilapia and genotyped 1358 markers consisting of 850 genes, 82 markers corresponding to BAC end sequences, 154 microsatellites and 272 single nucleotide polymorphisms (SNPs). From these, 1296 markers could be associated in 81 RH groups, while 62 were not linked. The total size of the RH map is 34,084 cR(3500) and 937,310 kb. It covers 88% of the entire genome with an estimated inter-marker distance of 742 Kb. Mapping of microsatellites enabled integration to the genetic map. We have merged LG8 and LG24 into a single linkage group, and confirmed that LG16-LG21 are also merged. The orientation and association of RH groups to each chromosome and LG was confirmed by chromosomal in situ hybridizations (FISH) of 55 BACs. Fifty RH groups were localized on the 22 chromosomes while 31 remained small orphan groups. Synteny relationships were determined between Nile tilapia, stickleback, medaka and pufferfish. Conclusion: The RH map and associated FISH map provide a valuable gene-ordered resource for gene mapping and QTL studies. All genetic linkage groups with their corresponding RH groups now have a corresponding chromosome which can be identified in the karyotype. Placement of conserved segments indicated that multiple inter-chromosomal rearrangements have occurred between Nile tilapia and the other model fishes. These maps represent a valuable resource for organizing the forthcoming genome sequence of Nile tilapia, and provide a foundation for evolutionary studies of East African cichlid fishes.
    Growth of Daphnia magna males and females fed with the cyanobacterium Microcystis aeruginosa and the green alga Scenedesmus obliquus in different proportions
    Lürling, M.F.L.L.W. ; Beekman, W. - \ 2006
    Acta Hydrochimica et Hydrobiologica 34 (2006)4. - ISSN 0323-4320 - p. 375 - 382.
    toxic cyanobacteria - sex determination - microviridin-j - inhibition - survival - pulicaria - food - lr - reproduction - responses
    Laboratory experiments were used to study the sensitivity of both male and female Daphnia magna to a toxic cyanobacterium, Microcystis aeruginosa. Male and female D. magna were fed with M. aeruginosa and a green alga (Scenedesmus obliquus) in different mixtures that included 0%, 25%, 50%, 75% and 100% Microcystis. Growth of both males and females declined with increasing proportion of Microcystis in the diet. Males were slightly less sensitive to Microcystis than females with EC50 for growth inhibition at 72% and 63% Microcystis in the diet, respectively. On monospecific Microcystis diet, mortality rates for males (0.16 d-1) and females (0.17 d-1) were similar. The reproductive rate of females was the most sensitive endpoint with an EC50 of 42% Microcystis in the diet, whereas population growth rates were the least sensitive (EC50 of 74% Microcystis). Microcystis in the diet severely depressed growth and reproduction in Daphnia and poses a severe threat to its survival in which only a switch in reproductive strategy might provide Daphnia a refuge to a Microcystis environment that gradually becomes uninhabitable.
    Mode of action, origin and structure of the Paternal Sex Ratio chromosome in the parasitoid wasp Trichogramma kaykai
    Vugt, J.J.F.A. van - \ 2005
    Wageningen University. Promotor(en): Joop van Lenteren; Rolf Hoekstra, co-promotor(en): Hans de Jong; R. Stouthamer. - - 120
    trichogramma - chromosomen - geslachtsverhouding - geslachtsbepaling - parasitoïden - diploïdie - chromatine - transposons - trichogramma - parasitoids - chromosomes - sex ratio - sex determination - diploidy - chromatin - transposable elements
    Selfish genetic elements are defined as genetic elements that have a replication advantage relative to the rest of the genome. They are ubiquitous in nature and were extensively reported for almost all species studied so far. A special type of selfish genetic element, the sex ratio distorter, is most frequent in arthropods and changes the offspring sex ratio of its host. An example of an extremely selfish male biasing sex ratio distorter is the paternal sex ratio (PSR) chromosome in the parasitoid wasps Trichogramma kaykai and Nasonia vitripennis . These wasps have an arrhenotokous sex determination in which fertilized diploid eggs develop into females and males develop from unfertilized haploid eggs. Only part of the male wasps contains this additional B chromosome, which upon fertilizationeliminates the paternal genome, while keeping itself and the maternal chromosomes intact. The resulting haploid embryo develops into a B chromosome-carrying male. This extremely selfish B chromosome was first discovered in N. vitripennis . The recent discovery of a second PSR chromosome in the unrelated wasp T. kaykai provided an opportunity for a comparative study on PSR chromosomes. In this study I determined the mechanism, the origin and structure of the PSR chromosome in T. kaykai and compared my results with previous studies on the PSR chromosome in N. vitripennis .

    The mode of action of the Trichogramma PSR chromosome was revealed by examining microscopic preparations of freshly fertilized eggs. This chromosome modifies the paternal genome into a dense chromatin mass at the beginning of the first mitotic division, while the PSR chromosome itself escapes its own destructive effect and continues embryo development with the maternal chromosomes. Comparing the modes of action of the Trichogramma and Nasonia PSR chromosomes suggests that both systems are identical, except for the diameter of the paternal chromatin mass (PCM) and the occurrence of PCM-associated nuclei. However, their molecular mechanism remains unknown. Furthermore, both PSR chromosomes share the main structural characteristics of B chromosomes: They are much smaller than the normal chromosomes and contain high amounts of transposable elements and tandem repetitive DNA. B chromosomes are thought to accumulate transposable elements because they do not recombine meiotically with the normal chromosomes. Repeats have proven to be an important factor for the transmission efficiency of the Nasonia PSR chromosomes and are also thought to correlate with the B chromosome size in general. However, none of the DNA sequences found on the Trichogramma PSR chromosome were found on the Nasonia PSR chromosome or visa versa. About two thirds of the Trichogramma PSR chromosome comprises tandem arrays of 45S ribosomal DNA (rDNA), while on the Nasonia PSR chromosome three B chromosome specific repeat families are located and one repeat family that is also present on the Nasonia genome. 45S rDNA consists of three conserved genes essential for protein processing separated by three spacer sequences that are hypervariable between species but conserved within species. These spacer sequences are therefore often used for taxonomic purposes. One of the spacer sequences of the 45S rDNA on the Trichogramma PSR chromosome, i.e. ITS2, contains at least five different sequences that resemble either the ITS2 of T. kaykai or the related T. oleae . We therefore concluded that this B chromosome originated from T. oleae or a T. oleae -like species. Retrotransposon analysis revealed that the Nasonia PSR chromosome most likely originated from the Nasonia related wasp genus Trichomalopsis . Though both PSR chromosomes have a similar mode of action, the absence of any sequence homology between both chromosomes implies different PSR chromosome ancestors. This again makes it less likely that the molecular mechanism of paternal genome loss is identical. Future studies should focus on comparing the molecular mode of action and DNA sequence homology of both PSR chromosomes and revealing the incidence of more PSR chromosomes in other haplo-diploid organisms. This will not only provide more knowledge on the mechanism of early embryogenesis and in particular on the paternal chromosome processing following fertilization, but also on the origin and evolution of PSR chromosomes. Extending our knowledge on PSR chromosomes is expected most useful for the control of pest insects with haplo-diploid sex determination systems like the Argentine ant. Without females such insect populations will quickly perish.
    Na het seksen mesten? : onderzoek met haantjes van legrassen
    Middelkoop, J.H. van; Harn, J. van; Wiers, W.J. - \ 2003
    De Pluimveehouderij 33 (2003)6. - ISSN 0166-8250 - p. 10 - 11.
    kuikenproductie - geslachtsbepaling - hanen - afmesten - voedering - marketing - mestresultaten - voederconversie - vleesopbrengst - productiekosten - chick production - sex determination - cocks - finishing - feeding - marketing - fattening performance - feed conversion - meat yield - production costs
    Bij het mesten van haantjes van legrassen is er niet alleen het probleem van het vinden van een afzetmarkt die dit economisch haalbaar maakt, maar er is ook het probleem van de pikkerij.
    Translocations and sex ratio distortion in the onion fly, Hylemya antiqua (Meigen), and their relevance to genetic control
    Vosselman, L. - \ 1980
    Landbouwhogeschool Wageningen. Promotor(en): J. Sybenga. - Wageningen : Vosselman - 117
    agromyzidae - anthomyiidae - calliphoridae - chromosoomtranslocatie - drosophilidae - genetische gewasbescherming - genetica - glossinidae - insecten - muscidae - geslacht (sex) - geslachtsbepaling - steriele insecten techniek - sterilisatie - tachinidae - tephritidae - stofverplaatsing - schizophora - agromyzidae - anthomyiidae - calliphoridae - chromosome translocation - drosophilidae - genetic control - genetics - glossinidae - insects - muscidae - sex - sex determination - sterile insect release - sterilization - tachinidae - tephritidae - translocation - schizophora
    Experiments on sex determination of the onion fly, Hylemya antiqua (Meigen), are reported in the first two chapters. The main purpose was to establish if the sex ratio distortion observed in certain crosses, was based on a mechanism which could be used for genetic purposes. Two types of males, XY 1 and XXY 2 , were found and the aberrant sex ratios appeared only to occur in progenies of XXY 2 (and some XXY 2 Y 2 ) males. A numerical variation for Y 2 was frequently observed in embryos, larval ganglion cells and especially in testes, which is caused by numerical non-disjunction in somatic cells. The sex ratio distortion is attributed to such a numerical variation of Y 2 between primordial germ cells. Some progenies with a highly distorted sex ratio in male direction descended probably from XXY 2 Y 2 males. Since an effective selection of XXY 2 Y 2 males is not possible, this type of sex ratio distortion is not suited for application in a genetic control method. Other subjects treated in chapters 1 and 2 are gynandromorphism, a polymorphism with respect to the length of the X-chromosome and X-polysomy. In the progeny of one cross a chromosome morphologically identical to Y 2 but lacking its holandric inheritance was found. From its inheritance in various crosses it could be concluded that it was nothing more than a (mutated) non-functional Y 2 chromosome.

    The meiotic segregation of a Y 1 -linked translocation T61 is reported in the third chapter. The high percentage of alternate segregation observed in T61-heterozygous males (22 YXY 2) was in good accordance with the high fertility of this translocation (95%). Because of an early separation (or asynapsis) of the centromeric regions of the acrocentric X and Y 2, chain quadrivalents with X and Y 2in terminal position predominated in diakinesis/ prometaphase I stages. In these chain quadrivalents adjacent l is supposed to be unstable since neither X nor Y 2have a neighbouring centromere in trans-position. The very low frequency of adjacent 2 is attributed to a preferential coorientation of homologous centromeres. The suitability of T61 for genetic sexing (preferential killing of females) is discussed.

    Double-translocation heterozygous T14/T61 males (2 62 Y6 26XY 2) were produced by intercrossing T14-homozygous females (2 62 66 26 2XX) and T61-heterozygous males (22 Y66XY 2) These double heterozygotes showed several segregation types but for predominated. The total frequency of duplication/deficiency gametes was 60-65%. Application possibilities for these heterozygotes in genetic control of the onion fly are discussed.

    The meiotic segregation of five different autosomal reciprocal translocations are given in chapter 5. For translocation T14, which has very short interstitial segments, significant differences in segregation between the sexes were found. In males the ratio of alt.: adj.1:adj.2 was about 7:3:0 and in females 8:1:3. It is assumed that the very intimate meiotic pairing in males (without chiasmata) results in relatively very short "Coorientation Determining Distances" (CDD's) between the homologous centromeres. Due to these short CDD's a preferential coorientation between homologous centromeres is expected favouring alternate and adjacent l segregation. On the contrary, in females chiasmata act very probably as reference points for coorientation. Due to variable positions of the centromeres, in T14-heterozygous females less pronounced differences in CDD's between homologous and non-homologous are expected as in males. This is suggested to be the reason that in females a coorientation between non-homologous centromeres can occur resulting in a certain frequency of adjacent 2. The very low frequencies or absence of adjacent 2 in the other four translocations is attributed to their longer interstitial segments.

    For translocation T14 a pure breeding stock of homozygotes could be obtained using egg-hatch percentages and cytology for the recognition of the karyotypes (chapter 6). In cage experiments under laboratory conditions the competitiveness of the translocation homozygotes was tested. Starting from an initial population consisting of equal numbers of translocation homozygotes (TT) and wild type flies (++), the karyotype frequencies were determined for three successive, non-overlapping generations. The results obtained did not suggest substantial differences in fitness between TT and ++. In field cage experiments (chapter 7) a high diapause sensitivity was found for the translocation homozygotes as well as for the laboratory strain of wild type flies (++) used. As a consequence of this high diapause sensitivity the fitness of the homozygotes could not be determined under field conditions.

    In the "General Discussion" different application possibilities of translocations for genetic control of the onion fly are discussed. A summary of unpublished data concerning the egg-hatch and pupal survival of eight threechromosome double-translocation heterozygotes and three more complex translocation heterozygotes is also presented there. The aim of these experiments was to determine if perhaps a double translocation could be isolated meeting the conditions for a stable equilibrium. However, neither of these translocations met these conditions. Firstly, the frequencies of duplication/deficiency gametes were not high enough; secondly, insufficient complementation occurred and, thirdly, the recombination percentages in the differential segments were too high (resulting in undesirable karyotypes). Two of three double translocations tested, appeared to be viable as homozygotes in the adult stage.

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