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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The ROSEA1 and DELILA transcription factors control anthocyanin biosynthesis in Nicotiana benthamiana and Lilium flowers
Fatihah, Hasan N.N. ; Moñino López, Daniel ; Arkel, Gert van; Schaart, Jan G. ; Visser, Richard G.F. ; Krens, Frans A. - \ 2019
Scientia Horticulturae 243 (2019). - ISSN 0304-4238 - p. 327 - 337.
Anthocyanin - Flower specific promoter - Lilium spp. - N. benthamiana - Transcription factors

The activity of anthocyanin biosynthesis genes is regulated at the transcriptional level, thus manipulation of transcription factors (TFs) is an ideal strategy to alter the expression of multiple target genes. In this study, we investigated the effect of introducing ROSEA1 (ROS1, a MYB-type) and DELILA (DEL, a bHLH-type) TFs from snapdragon under control of a flower specific promoter, Floral Binding Protein 1 (FBP1) from petunia into Nicotiana benthamiana flowers and Lilium tepals. The usefulness of the FBP1 promoter was demonstrated by the generation of purplish flowers in otherwise normal-growing plants of N. benthamiana, while the expression by the 35S promoter led to the development of stunted plants with anthocyanins in all parts. N. benthamiana was successfully transformed by ROS1 alone and by a combination of ROS1 + DEL. The observed accumulation of delphinidin corresponded to the expression of NbCHS, NbF3H, NbDFR and NbANS. The effect of ROS1 + DEL on Lilium flower colour was investigated using agroinfiltration. A higher cyanidin accumulation was observed in tepals of the Oriental hybrid lily cv. ‘Perth’ resulting in deeper pink colouration at the infiltrated area. Nevertheless, the introduction of ROS1 + DEL did not produce any phenotypic changes to the white-flowered L. longiflorum cv. ‘Lincoln’ and the white Oriental hybrid lily cv. ‘Rialto’ due to other deficiencies in their anthocyanin biosynthetic pathway. Co-expression of ROS1 + DEL under control of the FBP1 promoter together with active structural anthocyanin biosynthetic genes can result in modification of Lilium flower colour.

Different approaches of combating bacterial canker in tomato: in pursuit of resistance
Muniroh binti Mohd Nadzir, Mas - \ 2018
Wageningen University. Promotor(en): Richard Visser, co-promotor(en): Sjaak van Heusden; Jan van der Wolf. - Wageningen : Wageningen University - ISBN 9789463435109 - 145
QTL mapping of insect resistance components of Solanum galapagense
Vosman, Ben ; Kashaninia, Atiyeh ; van’t Westende, Wendy ; Meijer-Dekens, Fien ; Eekelen, Henriëtte van; Visser, Richard G.F. ; Vos, Ric C.H. de; Voorrips, Roeland E. - \ 2018
Theoretical and Applied Genetics (2018). - ISSN 0040-5752 - 11 p.

Key message: QTLs for insect resistance parameters, trichome type IV development, and more than 200 non-volatile metabolites, including 76 acyl sugars, all co-locate at the end of Chromosome 2 of Solanum galapagense. Abstract: Host plant resistance is gaining importance as more and more insecticides are being banned due to environmental concerns. In tomato, resistance towards insects is found in wild relatives and has been attributed to the presence of glandular trichomes and their specific phytochemical composition. In this paper, we describe the results from a large-scale QTL mapping of data from whitefly resistance tests, trichome phenotyping and a comprehensive metabolomics analysis in a recombinant inbred line population derived from a cross between the cultivated Solanum lycopersicum and the wild relative S. galapagense, which is resistant to a range of pest insects. One major QTL (Wf-1) was found to govern the resistance against two different whitefly species. This QTL co-localizes with QTLs for the presence of trichomes type IV and V, as well as all 76 acyl sugars detected and about 150 other non-volatile phytochemicals, including methyl esters of the flavonols myricetin and quercetin. Based on these results, we hypothesize that Wf-1 is regulating the formation of glandular trichome type IV on the leaf epidermis, enabling the production and accumulation of bioactive metabolites in this type of trichomes.

Molecular determination and genetic modification of flower colour in Lilium spp
Fatihah Hasan Nudin, Nur - \ 2018
Wageningen University. Promotor(en): Richard Visser, co-promotor(en): Frans Krens. - Wageningen : Wageningen University - ISBN 9789463435208 - 170
Systematic review and meta-analysis of non-pharmacological interventions to treat malnutrition in older people. The SENATOR project (ONTOP series) and MaNuEL Knowledge Hub projecta
Correa-Perez, Andrea ; Abraha, Iosef ; Groot, C.P.G.M. de; Schueren, Marian A.E. de van der; Visser, Marjolein ; Volkert, Dorothee - \ 2018
Do apes smell like humans? The role of skin bacteria and volatiles of primates in mosquito host selection
Verhulst, Niels O. ; Umanets, Alexander ; Weldegergis, Berhane T. ; Maas, Jeroen P.A. ; Visser, Tessa M. ; Dicke, Marcel ; Smidt, Hauke ; Takken, Willem - \ 2018
Journal of Experimental Biology 221 (2018). - ISSN 0022-0949
Apes - Host preference - Mosquitoes - Primates - Vector diseases - Zoophilic

Anthropophilic mosquitoes are effective vectors of human disease because of their biting preferences. To find their host, these mosquitoes are guided by human odours, primarily produced by human skin bacteria. By analysing the skin bacterial and skin volatile profiles of humans, bonobos, chimpanzees, gorillas, lemurs and cows, we investigated whether primates that are more closely related to humans have a skin bacterial community and odour profile that is similar to that of humans. We then investigated whether this affected discrimination between humans and closely related primates by anthropophilic and zoophilic mosquitoes that search for hosts. Humans had a lower skin bacterial diversity than the other animals and their skin bacterial composition was more similar to that in other primates than it was to the skin bacteria of cows. Like the skin bacterial profiles, the volatile profiles of the animal groups were clearly different from each other. The volatile profiles of cows and lemurs were more closely related to the human profiles than expected. Human volatiles were indeed preferred above cow volatiles by anthropophilic mosquitoes and no preference was observed when tested against non-human primate odour, except for bonobo volatiles, which were preferred over human volatiles. Unravelling the differences between mosquito hosts and their effect on host selection is important for a better understanding of cross-species transmission of vector-borne diseases.

The identification of allelic variation in potato
Willemsen, Johan - \ 2018
Wageningen University. Promotor(en): Richard Visser, co-promotor(en): Herman van Eck. - Wageningen : Wageningen University - ISBN 9789463435130 - 206
Morphological and genetic characterization of the leafy head of Chinese cabbage (Brassica rapa)
Sun, Xiao Xue - \ 2018
Wageningen University. Promotor(en): Guusje Bonnema; Richard Visser. - Wageningen : Wageningen University - ISBN 9789463435024 - 133
Exploring natural genetic variation in tomato sucrose synthases on the basis of increased kinetic properties
Dinh, Quy Dung ; Finkers, Richard ; Westphal, Adrie H. ; Dongen, Walter M.A.M. van; Visser, Richard G.F. ; Trindade, Luisa M. - \ 2018
PLoS One 13 (2018)10. - ISSN 1932-6203 - p. e0206636 - e0206636.

Sucrose synthase (SuSy) is one key enzyme directly hydrolyzing sucrose to supply substrates for plant metabolism, and is considered to be a biomarker for plant sink strength. Improvement in plant sink strength could lead to enhanced plant growth and yield. Cultivated tomatoes are known to have a narrow genetic diversity, which hampers further breeding for novel and improved traits in new cultivars. In this study, we observed limited genetic variation in SuSy1, SuSy3 and SuSy4 in 53 accessions of cultivated tomato and landraces, but identified a wealth of genetic diversity in 32 accessions of related wild species. The variation in the deduced amino acid sequences was grouped into 23, 22, and 17 distinct haplotypes for SuSy1/3/4, respectively. Strikingly, all known substrate binding sites were highly conserved, as well as most of the phosphorylation sites except in SuSy1. Two SuSy1 and three SuSy3 protein variants were heterologously expressed to study the effect of the amino acid changes on enzyme kinetic properties, i.e. maximal sucrose hydrolyzing capacity (Vmax), affinity for sucrose (Km), and catalytic efficiency (Vmax/Km) at 25°C and 16°C. SuSy1-haplotype#3 containing phosphorylation site Ser-16 did not have an improvement in the kinetic properties compared to the reference SuSy1-haplotype#1 containing Arg-16. Meanwhile SuSy3-haplotype#9 from a wild accession, containing four amino acid changes S53A, S106I, E727D and K741E, showed an increase in Vmax/Km at 16°C compared to the reference SuSy3-haplotype#1. This study demonstrates that SuSy kinetic properties can be enhanced by exploiting natural variation, and the potential of this enzyme to improve sucrose metabolism and eventually sink strength in planta.

Sourcing overseas biomass for EU ambitions: assessing net sustainable export potential from various sourcing countries
Mai-Moulin, Thuy ; Visser, Lotte ; Fingerman, Kevin R. ; Elbersen, Wolter ; Elbersen, Berien ; Nabuurs, Gert-Jan ; Fritsche, Uwe R. ; Campo Colmenar, Inés Del; Rutz, Dominik ; Diaz-Chavez, Rocio A. ; Roozen, Axel ; Weck, Mathijs ; Iriarte, Leire ; Pelkmans, Luc ; Sanchez Gonzalez, David ; Janssen, Rainer ; Junginger, Martin - \ 2018
Biofuels Bioproducts and Biorefining (2018). - ISSN 1932-104X - 32 p.
Low‐cost sustainable biomass availability in the European Union may not be able to meet increasing demand; exploring the option of importing biomass is therefore imperative for the years to come. This article assesses sustainable biomass export potential from Brazil, Colombia, Indonesia, Kenya, Ukraine, and the United States by applying a number of sustainability criteria. Only biomass types with the highest potential are selected, to take advantage of economies of scale, e.g. pulpwood, wood waste, and residues in the United States, and agricultural residues in Ukraine. This study found that, except for the United States, pellet markets in the sourcing regions are largely undeveloped. The export potential depends strongly on pellet mill capacity and assumed growth rates in the pellet industry. Results show that the United States, Ukraine, Indonesia, and Brazil offer the highest biomass export potential. In the Business As Usual 2030 scenario, up to 204 PJ could potentially be mobilized; in the High Export scenario this could increase to 1423 PJ, with 89% of the potential being available for costs ranging from 6.4 to 15 €/GJ. These potentials meet the European Commission requirements for a 70% reduction in greenhouse gas emissions set in the Renewable Energy Directive. The total export potentials do not reflect the net possible import potentials to the European Union, as biomass could be imported to other countries where there is a demand for it, where less strict sustainability requirements are applied, and which are proximate to the sourcing regions, notably South Korea, Japan, and China.
Data from: A high-density SNP chip for genotyping great tit (Parus major) populations and its application to studying the genetic architecture of exploration behaviour
Kim, J.M. ; Santure, Anna W. ; Barton, H.J. ; Quinn, John L. ; Cole, Ella F. ; Visser, M.E. ; Sheldon, B.C. ; Groenen, M. ; Oers, K. van; Slate, J. - \ 2018
adaptation - ecological genetics - genomics/proteomics - natural selection and contemporary evolution - population genetics - empirical - quantitative genetics
High density SNP microarrays (‘SNP chips’) are a rapid, accurate and efficient method for genotyping several hundred thousand polymorphisms in large numbers of individuals. While SNP chips are routinely used in human genetics and in animal and plant breeding, they are less widely used in evolutionary and ecological research. In this paper we describe the development and application of a high density Affymetrix Axiom chip with around 500 000 SNPs, designed to perform genomics studies of great tit (Parus major) populations. We demonstrate that the per-SNP genotype error rate is well below 1% and that the chip can also be used to identify structural or copy number variation (CNVs). The chip is used to explore the genetic architecture of exploration behaviour (EB), a personality trait that has been widely studied in great tits and other species. No SNPs reached genome-wide significance, including at DRD4, a candidate gene. However, EB is heritable and appears to have a polygenic architecture. Researchers developing similar SNP chips may note: (i) SNPs previously typed on alternative platforms are more likely to be converted to working assays, (ii) detecting SNPs by more than one pipeline, and in independent datasets, ensures a high proportion of working assays, (iii) allele frequency ascertainment bias is minimised by performing SNP discovery in individuals from multiple populations and (iv) samples with the lowest call rates tend to also have the greatest genotyping error rates.
Designing plant varieties with information technology
Visser, R.G.F. ; Finkers, H.J. - \ 2018
Prophyta - Focus on Europe (2018). - p. 28 - 30.
A field which could potentially lead to a further boost in plant breeding is the information technology. By a clever use of computers, a wide variety of (partially) curated (linked) data, and smart software and bioinformatics techniques, we can start to much better predict, design and select potential future improved varieties.
A European Multi Lake Survey dataset of environmental variables, phytoplankton pigments and cyanotoxins
Mantzouki, E. ; Campbell, J. ; Loon, E. van; Visser, P. ; Konstantinou, I. ; Antoniou, M. ; Giuliani, G. ; Machado-Vieira, D. ; Gurjão de Oliveira, A. ; Maronić, D.Š. ; Stević, F. ; Pfeiffer, T.Ž. ; Vucelić, I.B. ; Žutinić, P. ; Udovič, M.G. ; Plenković-Moraj, A. ; Tsiarta, N. ; Bláha, L. ; Geriš, R. ; Fránková, M. ; Christoffersen, K.S. ; Warming, T.P. ; Feldmann, T. ; Laas, A. ; Panksep, K. ; Tuvikene, L. ; Kangro, K. ; Häggqvist, K. ; Salmi, P. ; Arvola, L. ; Fastner, J. ; Straile, D. ; Rothhaupt, K.O. ; Fonvielle, J. ; Grossart, H.P. ; Avagianos, C. ; Kaloudis, T. ; Triantis, T. ; Zervou, S.K. ; Hiskia, A. ; Gkelis, S. ; Panou, M. ; McCarthy, V. ; Senerpont Domis, L.N. de; Seelen, L. ; Verstijnen, Y. ; Lürling, M. ; Maliaka, V. ; Faassen, E.J. - \ 2018
Scientific Data 5 (2018). - ISSN 2052-4463 - 13 p.
Under ongoing climate change and increasing anthropogenic activity, which continuously challenge ecosystem resilience, an in-depth understanding of ecological processes is urgently needed. Lakes, as providers of numerous ecosystem services, face multiple stressors that threaten their functioning. Harmful cyanobacterial blooms are a persistent problem resulting from nutrient pollution and climate-change induced stressors, like poor transparency, increased water temperature and enhanced stratification. Consistency in data collection and analysis methods is necessary to achieve fully comparable datasets and for statistical validity, avoiding issues linked to disparate data sources. The European Multi Lake Survey (EMLS) in summer 2015 was an initiative among scientists from 27 countries to collect and analyse lake physical, chemical and biological variables in a fully standardized manner. This database includes in-situ lake variables along with nutrient, pigment and cyanotoxin data of 369 lakes in Europe, which were centrally analysed in dedicated laboratories. Publishing the EMLS methods and dataset might inspire similar initiatives to study across large geographic areas that will contribute to better understanding lake responses in a changing environment.
Effects of experimental light at night on extra-pair paternity in a songbird
Jong, Maaike de; Lamers, Koosje P. ; Eugster, Mark ; Ouyang, Jenny Q. ; Silva, Arnaud Da; Mateman, A.C. ; Grunsven, Roy H.A. van; Visser, Marcel E. ; Spoelstra, Kamiel - \ 2018
Journal of Experimental Zoology Part A: Ecological and Integrative Physiology 329 (2018)8-9. - ISSN 2471-5638 - p. 441 - 448.
artificial light at night - extra-pair paternity - great tit - light color - light pollution - Parus major

Light pollution is increasing worldwide and significantly affects animal behavior. In birds, these effects include advancement of morning activity and onset of dawn song, which may affect extra-pair paternity. Advanced dawn song of males may stimulate females to engage in extra-pair copulations, and the earlier activity onset may affect the males’ mate guarding behavior. Earlier work showed an effect of light at night on extra-pair behavior, but this was in an area with other anthropogenic disturbances. Here, we present a two-year experimental study on effects of light at night on extra-pair paternity of great tits (Parus major). Previously dark natural areas were illuminated with white, red, and green LED lamps and compared to a dark control. In 2014, the proportion of extra-pair young in broods increased with distance to the red and white lamps (i.e., at lower light intensities), but decreased with distance to the poles in the dark control. In 2013, we found no effects on the proportion of extra-pair young. The total number of offspring sired by a male was unaffected by artificial light at night in both years, suggesting that potential changes in female fidelity in pairs breeding close to white and red light did not translate into fitness benefits for the males of these pairs. Artificial light at night might disrupt the natural patterns of extra-pair paternity, possibly negates potential benefits of extra-pair copulations and thus could alter sexual selection processes in wild birds.

Apoplastic effectors, MAMPs and surface immune receptors : the battlefront of the Phytophthora infestans - potato interaction
Lin, Xiao - \ 2018
Wageningen University. Promotor(en): Richard Visser, co-promotor(en): Vivianne Vleeshouwers. - Wageningen : Wageningen University - ISBN 9789463433259 - 196
Zoeken naar de beste genen : ruim 100 jaar plantenveredeling
Linden, Gerard van der; Visser, Richard - \ 2018
Looking for the best genes : over 100 years of plant breeding
Linden, Gerard van der; Visser, Richard - \ 2018
Researchers “grow” model of ideal plant in simulated greenhouse: 3D modelling rapidly gaining ground
Visser, Pieter de; Swinkels, Gert-Jan - \ 2018
Unraveling the causes of adaptive benefits of synonymous mutations in TEM-1 β-lactamase
Zwart, Mark P. ; Schenk, Martijn F. ; Hwang, Sungmin ; Koopmanschap, Bertha ; Lange, Niek de; Pol, Lion van de; Nga, Tran T.T. ; Szendro, Ivan G. ; Krug, Joachim ; Visser, J.A.G.M. de - \ 2018
Heredity 121 (2018)5. - ISSN 0018-067X - p. 406 - 421.

While synonymous mutations were long thought to be without phenotypic consequences, there is growing evidence they can affect gene expression, protein folding, and ultimately the fitness of an organism. In only a few cases have the mechanisms by which synonymous mutations affect the phenotype been elucidated. We previously identified 48 mutations in TEM-1 β-lactamase that increased resistance of Escherichia coli to cefotaxime, 10 of which were synonymous. To better understand the molecular mechanisms underlying the beneficial effect of these synonymous mutations, we made a series of measurements for a panel containing the 10 synonymous together with 10 non-synonymous mutations as a reference. Whereas messenger levels were unaffected, we found that total and functional TEM protein levels were higher for 5 out of 10 synonymous mutations. These observations suggest that some of these mutations act on translation or a downstream process. Similar effects were observed for some small-benefit non-synonymous mutations, suggesting a similar causal mechanism. For the synonymous mutations, we found that the cost of resistance scales with TEM protein levels. A resistance landscape for four synonymous mutations revealed strong epistasis: none of the combinations of mutations exceeded the resistance of the largest-effect mutation and there were synthetically neutral combinations. By considering combined effects of these mutations, we could infer that functional TEM protein level is a multi-dimensional phenotype. These results suggest that synonymous mutations may have beneficial effects by increasing the expression of an enzyme with low substrate activity, which may be realized via multiple, yet unknown, post-transcriptional mechanisms.

Nieuw-Zeelandse visser vreest big brother aan boord
Helmond, Edwin van - \ 2018
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