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Staff Publications

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Disentangling hexaploid genetics : towards DNA-informed breeding for postharvest performance in chrysanthemum
Geest, Geert van - \ 2017
Wageningen University. Promotor(en): R.G.F. Visser, co-promotor(en): U. van Meeteren; P.F.P. Arens. - Wageningen : Wageningen University - ISBN 9789463436427 - 142
chrysanthemum - plant breeding - postharvest quality - hexaploidy - polyploidy - quantitative trait loci - phenotypes - linkage mapping - metabolomics - polymorphism - dna - chrysanthemum - plantenveredeling - kwaliteit na de oogst - hexaploïdie - polyploïdie - loci voor kwantitatief kenmerk - fenotypen - koppelingskartering - metabolomica - polymorfisme - dna

DNA-informed selection can strongly improve the process of plant breeding. It requires the detection of DNA polymorphisms, calculation of genetic linkage, access to reliable phenotypes and methods to detect genetic loci associated with phenotypic traits of interest. Cultivated chrysanthemum is an outcrossing hexaploid with an unknown mode of inheritance. This complicates the development of resources and methods that enable the detection of trait loci. Postharvest performance is an essential trait in chrysanthemum, but is difficult to measure. This makes it an interesting but challenging trait to phenotype and detect associated genetic loci. In this thesis I describe the development of resources and methods to enable phenotyping for postharvest performance, genetic linkage map construction and detection of quantitative trait loci in hexaploid chrysanthemum.

Postharvest performance is a complicated trait because it is related to many different disorders that reduce quality. One of these disorders in chrysanthemum is disk floret degreening, which occurs after long storage. In chapter 2, we show that degreening can be prevented by feeding the flower heads with sucrose, suggesting carbohydrate starvation plays a role in the degreening process. To investigate the response to carbohydrate starvation of genotypes with different sensitivity to disk floret degreening, we investigated the metabolome of sugar-fed and carbohydrate-starved disk florets by 1H-NMR and HPAEC. We show that the metabolome is severely altered at carbohydrate starvation. In general, starvation results in an upregulation of amino acid and secondary metabolism. Underlying causes of genotypic differences explaining variation in disk floret degreening in the three investigated genotypes remained to be elucidated, but roles of regulation of respiration rate and camphor metabolism were posed as possible candidates.

In chapter 3, disk floret degreening was found to be the most important postharvest disorder after 3 weeks of storage among 44 white chrysanthemum cultivars. To investigate the inheritance of disk floret degreening, we crossed two genotypes with opposite phenotypic values of both disk floret degreening and carbohydrate content to obtain a population segregating for disk floret degreening. To phenotype the cultivar panel and the bi-parental population precisely and in a high throughput manner, we developed a method that quantified colour of detached capitula over time. This method was validated with visual observations of disk floret degreening during vase life tests. In a subset of the bi-parental population we measured carbohydrate content of the disk florets at harvest. The amount of total carbohydrates co-segregated with sensitivity to degreening, which shows that the difference in disk floret degreening sensitivity between the parents could be explained by their difference in carbohydrate content. However, the correlation was rather weak, indicating carbohydrate content is not the only factor playing a role.

In order to develop resources for DNA-informed breeding, one needs to be able to characterize DNA polymorphisms. In chapter 4, we describe the development of a genotyping array containing 183,000 single nucleotide polymorphisms (SNPs). These SNPs were acquired by sequencing the transcriptome of 13 chrysanthemum cultivars. By comparing the genomic dosage based on the SNP assay and the dosage as estimated by the read depth from the transcriptome sequencing data, we show that alleles are expressed conform the genomic dosage, which contradicts to what is often found in disomic polyploids. In line with this finding, we conclusively show that cultivated chrysanthemum exhibits genome-wide hexasomic inheritance, based on the segregation ratios of large numbers of different types of markers in two different populations.

Tools for genetic analysis in diploids are widely available, but these have limited use for polyploids. In chapter 5, we present a modular software package that enables genetic linkage map construction in tetraploids and hexaploids. Because of the modularity, functionality for other ploidy levels can be easily added. The software is written in the programming language R and we named it polymapR. It can generate genetic linkage maps from marker dosage scores in an F1 population, while taking the following steps: data inspection and filtering, linkage analysis, linkage group assignment and marker ordering. It is the first software package that can handle polysomic hexaploid and partial polysomic tetraploid data, and has advantages over other polyploid mapping software because of its scalability and cross-platform applicability.

With the marker dosage scores of the bi-parental F1 population from the genotyping array and the developed methods to perform linkage analysis we constructed an integrated genetic linkage map for the hexaploid bi-parental population described in chapter 3 and 4. We describe this process in chapter 6. With this integrated linkage map, we reconstructed the inheritance of parental haplotypes for each individual, and expressed this as identity-by-descent (IBD) probabilities. The phenotypic data on disk floret degreening sensitivity that was acquired as described in chapter 3, was used in addition to three other traits to detect quantitative trait loci (QTL). These QTL were detected based on the IBD probabilities of 1 centiMorgan intervals of each parental homologue. This enabled us to study genetic architecture by estimating the effects of each separate allele within a QTL on the trait. We showed that for many QTL the trait was affected by more than two alleles.

In chapter 7, the findings in this thesis are discussed in the context of breeding for heterogeneous traits, the implications of the mode of inheritance for breeding and the advantages and disadvantages of polyploidy in crop breeding. In conclusion, this thesis provides in general a significant step for DNA-informed breeding in polysomic hexaploids, and for postharvest performance in chrysanthemum in particular.

Milk fat triacyglycerols : their variabiblity, relations with fatty acids, DGAT1, B polymorphs and melting fractions
Tzompa Sosa, D.A. - \ 2016
Wageningen University. Promotor(en): Toon van Hooijdonk, co-promotor(en): Hein van Valenberg; G.A. van Aken. - Wageningen : Wageningen University - ISBN 9789462577503 - 122
milk fat - triacylglycerols - fatty acids - composition - polymorphism - dairy cows - cows - crystallization - fat crystallization - melting - calorimetry - maldi-tof - thin layer chromatography - melkvet - triacylglycerolen - vetzuren - samenstelling - polymorfisme - melkkoeien - koeien - kristallisatie - vetkristallisatie - smelten - calorimetrie - maldi-tof - dunnelaagchromatografie

Milk fat (MF) triacylglycerol composition varies within a population of dairy cows. The variability of MF triacylglycerols and their structure was partially explained by the fatty acid (FA) composition of the MF, and by DGAT1 K232A polymorphism. The FA C16:0 and C18:1cis-9 play a major role in understanding the changes seen in triacylglycerol profile and structure because they are the most abundant FAs in MF and are negatively correlated. MFs with low ratio C16:0/C18:1cis-9 were decreased in triacylglycerols with 34 and 36 carbons and were increased in triacylglycerols with 52 and 54 carbons. These changes in MF composition greatly affected the crystallization behavior of MF by changing the types of polymorphs formed during its crystallization. MF with low ratio C16:0/C18:1cis-9 formed stable and metastable polymorphs (β and β’, respectively), whereas MF with high ratio C16:0/C18:1cis-9 formed exclusively metastable polymorphs (β’) when the fat was crystallized at 20°C. The changes in MF composition also affected the melting behavior of MF by changing the melting point of the MF fractions.

Major histocompatibility (MH) polymorphism of common carp : link with disease resistance
Rakus, K.L. - \ 2008
Wageningen University. Promotor(en): Huub Savelkoul; A. Pilarczyk, co-promotor(en): Geert Wiegertjes; I. Irnazarow. - [S.l.] : S.n. - ISBN 9789085852445 - 169
karper - major histocompatibility complex - polymorfisme - ziekteresistentie - genen - immuniteitsreactie - immunologie - visteelt - aquacultuur - carp - major histocompatibility complex - polymorphism - disease resistance - genes - immune response - immunology - fish culture - aquaculture
The impact of diseases caused by a wide range of pathogens (viruses, bacteria
and parasites) is the most important problem in aquaculture of common carp (Cyprinus
carpio L.). Genetic selection aimed at obtaining population of more resistant common
carp is potential and sustainable approach to disease control in semi-intensive carp pond
farming. Genes of the major histocompatibility complex (MHC) are candidate marker
genes for studies on association with disease resistance. The MHC contains some of the
most polymorphic genes known to date and are considered crucial to adaptive
immunity. MHC molecules bind both self and foreign peptides and present them to T
lymphocytes (T cells). MHC class I molecules present endogenously derived peptides to
CD8+ T cells, while MHC class II molecules present exogenously derived peptides to
CD4+ T cells. Each MHC molecule has the ability to bind and present different groups
of peptides in more or less successful ways. This can influence the immune response of
an organism since the peptides derived from a certain pathogen may either not be
presented by specific MHC molecules, which can result in higher susceptibility or, may
be bound with a high affinity by specific MHC molecules which could lead to increased
resistance to the pathogenic organism.
In teleosts, unlike to humans, tetrapods and cartilaginous fish, class I and class II
genes are not linked and segregate independently, which allows for association studies
of only class I or only class II MH genes with disease resistance. MHC class II
molecules generally have a broader spectrum of action in the immune system than the
MHC class I genes. There are also observations that suggest a more intense selection
pressure and a more rapid evolution of MH class II than class I alleles in fish. Although
the expression of both MH class II chains is equivalent, the beta chain generally has a
higher degree of polymorphism than the alpha chain. This thesis addressed possible
implementations of MH class II B genes for selection aimed at improving of a common
carp resistance in semi-intensive pond farming.
In common carp there are two paralogous groups of MH class II B genes, Cyca-
DAB1-like and Cyca-DAB3-like genes. In a preliminary study, we examined the
polymorphism for the Cyca-DAB1-like and Cyca-DAB3-like genes in different
European common carp lines (chapter 2). These carp lines were of various
geographical origins and part of carp live gene bank, which is maintained at the Institute
of Ichthyobiology and Aquaculture in Gołysz. Previous observations over a period of at least 15 years revealed significant differences between lines in survival rate and parasite
load under natural conditions. Also, differences in resistance to atypical Aeromonas
salmonicida in laboratory based challenge tests was observed, suggesting genetic
differences in resistance between the carp lines. Analysis of polymorphism of MH class
II B genes in selected carp lines revealed a ubiquitous presence and high polymorphism
of Cyca-DAB1-like but not Cyca-DAB3-like genes. The observed allelic polymorphism
for Cyca-DAB1-like genes rather than Cyca-DAB3-like genes stimulated further studies
into the association of Cyca-DAB1-like allelic polymorphism and disease resistance of
common carp.
In order to study association between Cyca-DAB1-like gene polymorphism and
resistance of common carp we optimized a technique designated polymerase chain
reaction -restriction fragments- single strand conformation polymorphism (PCR-RFSSCP)
to be able to screen and type large numbers of individual carp (chapter 3). The
advantages of this technique are simplicity, high sensitivity and low costs. PCR-RFSSCP
analysis of n = 79 carp individuals from 8 lines challenged with Aeromonas
hydrophila revealed the presence of different genotypes consisting of unique
combinations of Cyca-DAB1 and Cyca-DAB2 sequences. We found four alleles for the
Cyca-DAB1 (*02-*05) gene but only one allele for Cyca-DAB2 (*02). We noted that the
Cyca-DAB2 gene was either homozygous or absent. The degree of heterozygosity of the
Cyca-DAB1 and Cyca-DAB2 genes clearly correlated with the number of SSCP bands.
Thus, we proved that PCR-RF-SSCP is a reliable technique that can be used for
screening large number of individuals for investigating the Cyca-DAB1 and Cyca-DAB2
genes polymorphism in common carp.
Previously, we performed a long-term divergent selection of common carp for
antibody production, which successfully resulted in carp lines with a different immune
response. We studied the segregation of Cyca-DAB genes with the DNP-specific
antibody response and we showed that the presence of Cyca-DAB1-like, but not Cyca-
DAB3-like genes, preferentially leads to a high DNP-specific antibody response in carp
(chapter 4). Background genes other than Cyca-DAB genes also influenced the level of
antibody response. We also studied the transcription of both Cyca-DAB1-like and Cyca-
DAB3-like genes in different organs of carp. The constitutive transcription for both
Cyca-DAB1-like and Cyca-DAB3-like genes was high, although Cyca-DAB1-like genes consistently showed slightly higher mRNA transcription than Cyca-DAB3-like genes in
some immunological relevant organs. Sequence information, constitutive transcription
levels and co-segregation data indicated that both paralogous Cyca-DAB1-like and
Cyca-DAB3-like groups represent functional MH class II B genes.
We then proceeded to study association of Cyca-DAB1-like genotypes with
resistance to four different pathogens; the bacterium Aeromonas hydrophila, the
ectoparasite Argulus japonicus, and the blood parasite Trypanoplasma borreli (chapter
5) and the viral pathogen Cyprinid herpesvirus-3 (CyHV-3) (chapter 6). We used a
large number of individuals of different carp lines and revealed, using PCR-RF-SSCP,
the presence of n = 9 unique Cyca-DAB1-like genotypes, of which three genotypes (B,
D, and E) were most common (chapter 5). In general, Cyca-DAB2 was often
homozygous or absent while allelic polymorphism was detected in Cyca-DAB1 gene.
We could detect significant associations between genotype E and abundance of
A. japonicus and between genotype D and higher level of parasitaemia after T. borreli
infection. We also observed a significant association between Cyca-DAB1
heterozygosity and lower level of parasitaemia after T. borreli infection. In chapter 6,
we showed a strong association between Cyca-DAB1-like genotypes and resistance or
susceptibility to CyHV-3. One genotype (E) performed significantly better, resulting in
carp more resistant to CyHV-3, while three other genotypes (B, H and J) could be
linked to higher susceptibility to the virus. Subsequent analysis of the alleles that
compose the Cyca-DAB1-like genotypes linked one particular allele (Cyca-DAB1*05)
to significantly increased, and two alleles (Cyca-DAB1*02 and Cyca-DAB1*06) to
significantly decreased resistance to CyHV-3. The resistant genotype E did not
comprise the Cyca-DAB2 gene and consisted of a homozygous Cyca-DAB1*05 allele.
Phylogenetic analysis of all Cyca-DAB1 alleles showed that the Cyca-DAB1*05 allele
represents the oldest allele in our study (chapter 7). We discussed the possibility for
using Cyca-DAB1 allelic polymorphism as a potential genetic marker in future breeding
programs of common carp (chapter 7). We expect that selection of carp for particular
MH class II B genotypes or alleles could allow for an increased survival upon challenge
with selected pathogens and possibly, increased survival rate under pond conditions.
Transferrin polymorphism of common carp: link with disease resistance
Jurecka, P.M. - \ 2008
Wageningen University. Promotor(en): Huub Savelkoul; A. Pilarczyk, co-promotor(en): Geert Wiegertjes; I. Irnazarow. - [S.l.] : S.n. - ISBN 9789085852438 - 178
karper - transferrine - polymorfisme - ziekteresistentie - genetisch bepaalde resistentie - trypanoplasma borreli - experimentele infectie - genexpressie - stikstofoxide - macrofagen - immunologie - carp - transferrin - polymorphism - disease resistance - genetic resistance - trypanoplasma borreli - experimental infection - gene expression - nitric oxide - macrophages - immunology
Iron is fundamental to the biology of eukaryotic cells since it plays a key role in many
metabolic functions. Iron concentrations are tightly regulated, for example by ferritin,
because excessive iron leads to tissue damage. Iron cannot cross cellular membranes
directly and most cells acquire iron from the iron transporting protein transferrin (Tf),
via transferrin receptors. During nutritional immunity the body reacts with a metabolic
adjustment in order to render important nutrients unavailable to invading
microorganisms. However, pathogens also have evolved a range of mechanisms to
acquire iron from the host (chapter 1).
In the study described in this thesis, we used a natural host-parasite model of common
carp (Cyprinus carpio L.) infected with Trypanoplasma borreli, a protozoan
kinetoplastid, extracellular blood parasite of carp to get more insight in the competition
for iron between host and parasite. Transferrin of common carp is highly polymorphic
with several alleles identified according to differences in electrophoretic mobility. We
studied the implications of Tf polymorphisms for iron binding and modulation of
immune function.
We performed a series of challenge experiments infecting five genetically different,
commercially exploited carp lines with T. borreli. Our results indicated that Tf genotype
may influence the susceptibility to pathogens. We observed a significant association of
the DD genotype of Tf with low parasitaemia in two resistant carp lines (Polish ‘R2’
and ‘K’), but a reverse association in the most susceptible carp line ‘D’ (chapter 2). We
also showed that variation in resistance to T. borreli could be controlled by sex-related
genetic factors. Examination of parasite growth in vitro, in culture media supplemented
with 3% serum taken from fish with different Tf genotypes, showed a faster decrease in
number of parasites in media supplemented with serum from DD-typed animals
(chapter 2).
In general, pathogens also have mechanisms to acquire iron from the host. We
developed a method for Tf depletion of carp serum using specific antibodies to carp Tf,
and compared T. borreli multiplication and survival in the presence or absence of Tf in
vitro. Parasites were dying in medium containing Tf-depleted serum, which clearly
showed that Tf is essential for parasite growth and multiplication (chapter 3). We
isolated two allelic forms of carp Tf (alleles D and G) to purity using rivanol
precipitation and ion-exchange chromatography (chapter 5). We showed that parasite
growth in vitro could be reconstituted by the addition of purified Tf to Tf-depleted serum (chapter 3). We observed differences in T. borreli multiplication and survival in
culture media containing different sera typed differently for Tf genotypes (chapter 3).
We identified four complete coding sequences for common carp Tf alleles C, D, F and
G, and confirmed the overall similarity of the carp Tf three-dimensional structure to Tfs
of other species. We could show that carp Tf differs significantly in critical iron-binding
sites in the N-lobe of the molecule, as compared to other non-cyprinid fish species
(chapter 4). The substitution of a majority of the iron-coordinating residues in the Nlobe
indeed seems to affect the ability to bind iron, which may be compensated for by
higher serum concentrations of Tf (chapter 7). Comparison of constitutive gene
expression of two Tf alleles D and G showed a comparably high gene expression level
in liver and small but consistent differences in gene expression for allele D over allele G
in other immunologically important organs (chapter 4). Our data suggest that the allelic
polymorphism is not related to differences in iron binding and/or binding to the host Tf
receptor but could be linked with other factors, such as competition for iron with
pathogens (chapter 4).
Transferrin itself may also exert effects that are not directly linked with maintaining
iron levels and Tf cleavage products have been shown to stimulate macrophages to
produce large amounts of nitric oxide (NO). To study the induction of NO in carp head
kidney-derived macrophages, we isolated two allelic forms of carp Tf (alleles D and G)
to purity and showed that the level of activation of macrophages by Tf was different for
the D and G allele (chapter 5). Differences in NO levels induced could be related to
different cleavage forms of the two alleles D and G, as shown by Western blot,
confirming that full-length Tf cannot induce NO. The D-type Tf cleavage products
induced significantly higher nitric oxide (NO) production than cleavage products of Gtype
Tf. (chapter 5).
Transferrin uptake by trypanosome parasites involves Tf binding to a receptor. The
TfR-Tf complex then is internalised and transported to lysosomes, where Tf is
proteolytically degraded. We described the cloning and sequencing of a cathepsin L-like
cysteine proteinase from T. borreli and production of a recombinant and biologically
active enzyme (chapter 6). We demonstrated that the T. borreli cysteine proteinase is
able to digest host transferrin. Likely, Tf cleavage fragments are released from the
trypanosomes while iron would remain parasite-associated, possibly contributing to thepathogenicity of the parasite by inducing high amounts of NO in carp macrophages
(chapter 7).
Our study dealt with different aspects of Tf polymorphism, discussing the role of Tf in
immunity of common carp and the influence of allelic polymorphism on competition for
iron between host and pathogen (chapter 7). Further investigations should shed more
light on the selective advantage of particular alleles to provide a basis for incorporating
Tf as a genetic marker in marker-assisted selection programmes for increased resistance
to diseases. This could contribute to improved survival of carp kept under semiintensive
farming systems in ponds.
Genetics, chemistry and ecology of a qualitative glucosinolate polymorphism in Barbarea vulgaris
Leur, H. van - \ 2008
Wageningen University. Promotor(en): Wim van der Putten; Louise Vet, co-promotor(en): N.M. van Dam. - [S.l.] : S.n. - ISBN 9789085049005 - 168
barbarea vulgaris - polymorfisme - glucosinolaten - verdedigingsmechanismen - herbivoren - insectenplagen - heritability - co-evolutie - barbarea vulgaris - polymorphism - glucosinolates - defence mechanisms - herbivores - insect pests - heritability - coevolution
Like many other plants, chemical defence compounds are involved in the defense of Barbarea vulgaris against natural enemies. Barbarea vulgaris produces glucosinolates, which are present in most crucifers such as cabbage, mustard, and the scientific model species Arabidopsis thaliana. Glucosinolates form, together with an enzyme (myrosinase), a two-component system: the enzyme and glucosinolates are stored in spatially separated compartments. Upon cell disruption they come into contact, and the glucosinolates are catabolised by the enzyme. For generalist herbivores the glucosinolates, and especially their breakdown products, are often toxic and protect the plants against herbivory. However, specialist herbivores often use these same compounds to recognize suitable host plants. The breakdown products are also responsible for the specific taste to many cabbage and mustard species
There are over 100 different glucosinolates, each with a different chemical structure. The structure determines, amongst other factors, which breakdown product will be formed upon damage. Every plant species has its own typical composition of glucosinolates. I studied how these glucosinolate profiles may affect plant resistance against herbivores.
In a screening of several Dutch populations it was found that Barbarea vulgaris plants differed in glucosinolate profile. The majority of the plants contained mainly glucobarbarin, a glucosinolate typical for this species and named after the genus Barbarea. Also populations sampled in Germany, Belgium, France, and Switserland, consisted completely of plants with mainly glucobarbarin. In half of the Dutch populations I found that a minority of the plants (2-22%) produced another glucosinolate, named gluconasturtiin. The difference in the chemical structure between these two glucosinolates is very small; glucobarbarin has only one hydroxyl group more than gluconasturtiin. However, this small structural difference may be of large biological relevance. When gluconasturtiin reacts with myrosinase a toxic and unpalatable isothiocyanate is formed, whereas glucobarbarin, due to the position of the hydroxyl group, produces oxazolidinethions. It is unknown whether these oxazolidinethiones are toxic, but in mammals they can inhibit the iodine intake, thereby causing thyroid problems. The Barbarea vulgaris glucosinolate polymorphism thus has two chemotypes. I characterized these chemotypes and used them to study the effects of different glucosinolates on herbivores.
The difference in glucosinolate profile is consistently present in all plant organs of B. vulgaris, but it is larger in the aboveground organs than in the roots. The glucosinolate profile does not change upon induction by insects nor upon artificial induction by addition of jasmonic acid. I crossed plants, analysed the chemotype of the offspring and showed that the ability to produce glucobarbarin is heritable and regulated by a dominant gene. Based on the assumption that there is a specific enzyme that converts gluconasturtiin to glucobarbarin by a single hydroxylation step, I identified some candidate genes. Further research is needed to determine whether one of these candidate genes is indeed responsible the difference between the chemotypes.
Subsequently, I studied the effect of chemotype on leaf and root herbivores. Plants with mainly glucobarbarin turned out to be very resistant to the generalist leaf-eating larvae of the Mamestra brassicae moth. Almost none of the larvae survived on plants with mainly glucobarbarin. If the larvae were given the choice, they strongly preferred to feed on plants with mainly gluconasturtiin. However, female moths deposited approximately the same number of eggs on each chemotype. Larvae of the specialist small cabbage white grew equally well on each chemotype and did not distinguish between the chemotypes in choice experiments. Larvae of the specialist cabbage root fly, however, performed worse on roots of the gluconasturtiin type than on roots of the glucobarbarin type. Plants responded to the root fly infection by a reduction of the root and shoot biomass with 50%, and decreased levels of nutrients such as sugars and amino acids.
In order to translate the results obtained in the greenhouse to the natural situation, I planted plants of both chemotypes in an experimental garden. Over a period of two years, the numbers of several herbivores were counted on each chemotype every week during the growth season. This revealed that some aboveground insects had a preference for a certain chemotype, and others did not. Butterflies of the small cabbage white preferred to oviposit on plants with gluconasturtiin, but flea beetles and gall midges were more abundant on plants with glucobarbarin. The cabbage aphid and the green peach aphid did not show any preference and were equally abundant on both chemotypes. Three to four times a year, I dug up a subset of the plants to analyse the root herbivores and the soil nematode community. The numbers and community structure of these belowground organisms did not differ between the chemotypes.
Additionally, I investigated whether there are other chemical differences between the chemotypes, apart from glucosinolate profile, that could explain the preference of the above insect species. Therefore, I performed extensive metabolomics analyses, using LC-TOF-MS. Multivariate analyses showed that the major chemical differences between the chemotypes was due to differences in glucosinolates. These differences were larger in shoots than in roots. Apart from glucosinolates only eight unidentified compounds differed between the chemotypes. Known defense compounds such as flavonoids and saponins were identified but did not differ between the chemotypes. Therefore, it is very likely that the differences in herbivore performance and preference are predominantly caused by the differences in glucosinolate profile.
Based on my results, I conclude that the structure of glucosinolates can cause significant differences in resistance against several herbivores. However, in the case of B. vulgaris there is no supreme chemotype that is more resistant in all cases. Which of the two chemotypes accrues the largest benefit in a natural environment thus will depend on the herbivore community in their population. In this way the B. vulgaris glucosinolate polymorphism can be maintained in natural populations.

Implementation of SNPs in pig genetics: LD and QTL analysis
Jungerius, B.J. - \ 2004
Wageningen University. Promotor(en): Martien Groenen; B.A. van Oost, co-promotor(en): Marinus te Pas. - Wageningen : S.n. - ISBN 908504071X - 128
varkens - genetische merkers - obesitas - kwantitatieve kenmerken - dna-sequencing - nucleotiden - polymorfisme - genetische analyse - genetica - dierveredeling - pigs - genetic markers - obesity - quantitative traits - dna sequencing - nucleotides - polymorphism - genetic analysis - genetics - animal breeding
Chicken fatness: from QTL to candidate gene
Jennen, D.G.J. - \ 2004
Wageningen University. Promotor(en): Martien Groenen, co-promotor(en): Richard Crooijmans. - [S.l.] : S.n. - ISBN 9085040698 - 167
vleeskuikens - pluimvee - pluimveevet - lichaamsvet - kwantitatieve kenmerken - genkartering - genlokalisatie - genoomanalyse - genen - polymorfisme - genetica - broilers - poultry - poultry fat - body fat - quantitative traits - gene mapping - gene location - genome analysis - genes - polymorphism - genetics
Molecular genetic analysis of the pathogenicity of the potato cyst nematode Globodera rostochiensis
Qin, L. - \ 2001
Wageningen University. Promotor(en): J. Bakker; J. Helder, co-promotor(en): G. Smant. - S.l. : S.n. - ISBN 9789058084521
plantenparasitaire nematoden - globodera rostochiensis - complementair dna - polymorfisme - genexpressie - pathogeniteit - moleculaire genetica - bio-informatica - plant parasitic nematodes - globodera rostochiensis - pathogenicity - complementary dna - polymorphism - gene expression - molecular genetics - bioinformatics

A new strategy to identify pathogenicity factors from the potato cyst nematode Globodera rostochiensis is developed. cDNA-AFLP technology and in situ hybridization allowed us to efficiently select putative pathogenicity factors among thousands of expressed genes. As a result, an unprecedented number of putative pathogenicity factors from this obligatory plant parasite were cloned.

A powerful bioinformatics tool named GenEST to link expression data generated from cDNA-AFLP directly to cDNA sequence data was developed. This computer program would be very useful for functional genomics studies in other systems as well.

A RanBPM (Ran-Binding Protein in Microtubule organization)-like gene family was identified. The proteins encoded by these genes are probably secreted by the nematode into plant cells and might manipulate the host cell development by changing the dynamic instability of microtubules.

A promoter region from the potato cyst nematode was shown to be functional in a distantly related nematode species Caenorhabditis elegans . This promoter could be a valuable tool to drive gene expression in transgenic plant-parasitic nematode species to assess the relative importance of putative pathogenicity factors.

A paper based from one chapter of this thesis will be submitted to Science. In view of their press embargo policy, I will not discussed the detail of this particular finding here.

Flying for life : wing dimorphism in closely related species of the genus Calathus (Coleoptera: Carabidae)
Aukema, B. - \ 1995
Agricultural University. Promotor(en): J.C. van Lenteren; P.J. den Boer. - S.l. : Aukema - ISBN 9789054854074 - 168
carabidae - ongewervelde dieren - vleugels - polymorfisme - carabidae - invertebrates - wings - polymorphism

Factors governing wing dimorphism in ground beetles (Coleoptera: Carabidae) of the Calathus melanocephalus complex have been studied in relation to dispersal by flight. In Western Europe this complex consists of three well-defined species, as was shown by cross-breeding experiments and morphological studies: Calathus cinctus Motschulsky (= C. erythroderus Gemminger & Harold), Calathus melanocephalus (Linnaeus) and Calathus mollis (Marsham). The synonymy of Calathus erythroderus with C.cinctus was established. To stabilize the nomenclature of the species involved lectotypes were designated for Carabus melanocephalus Linnaeus and Carabus mollis Marsham. Action undertaken to conserve the specific name of Carabus mollis Marsham was approved by the International Commission on Zoological Nomenclature. Data on morphology, life history and distribution of the three species involved were listed and an identification key is included.

Calathus cinctus and C. melanocephalus are wing-dimorphic with either strongly reduced wings (short winged or brachypterous) or fully developed wings (long winged or macropterous), whereas C . mollis is always macropterous. Long winged beetles are considered potential flyers, representing the dispersal morph of these species. Populations of C. cinctus and C. melanocephalus showed different proportions of long winged beetles.

Wing dimorphism in Calathus cinctus and C . melanocephalus was found to be genetically determined and to be inherited in a simple Mendelian fashion with brachyptery dominant to macroptery. In C.cinctus the long winged genotype is always expressed, whereas in C . melanocephalus the expression of the long winged genotype is under environmental control. It was shown that at least temperature and food-supply affected the expression of the long winged genotype in C.melanocephalus: more favourable temperatures (i.e. relatively high temperatures) and a higher food-supply resulted in a higher number of long winged beetles compared with less favourable temperatures (i.e. both low and extremely high temperatures) and a lower food-supply.

Wing-morph frequencies in populations of wing-dimorphic species may also be affected by differences in fitness between short and long winged beetles. Fecundity (egg production and oviposition period), development time, and growth were studied in this respect.

In both Calathus cinctus and C.melanocephalus long winged females showed a significantly higher egg production than short winged females, and they also tended to produce eggs during a longer period. Considerable differences in fecundity were observed between the species: the highest egg production was found in Calathus cinctus, a species with a late start and a long oviposition period, and the lowest egg production was found in C . mollis, a species with an early start and a comparably long oviposition period. Calathus melanocephalus showed an egg production intermediate between those of C . cinctus and C.mollis, with an early start and a relatively short oviposition period.

In all three species development times were generally shorter at higher temperatures and longer at lower temperatures, but in both Calathus cinctus and C . melanocephalus a general relationship between temperature and development time was found neither for wing-morph nor for sex. Development time and growth of long winged genotypes of Calathus melanocephalus were strongly influenced by food- supply: with a higher food-supply shorter development times and higher hatching weights were found. Long winged beetles of both sexes developed faster and were heavier than short winged ones reared under similar conditions, and females weighed more than males.

Under laboratory conditions both long winged males and females of the three species studied built up functional flight muscles and were capable of flight. Flight activity in the field, however, was only observed in Calathus cinctus. Building up flight muscles, flight, and subsequent resorption of flight muscles only occurred in the pre- oviposition period, but mating and even ovarian development may occur during the flight period too.

The dispersal abilities of the three species studied are supposed to be different because there are large differences in flight potential between the species. In Calathus cinctus and C.melanocephalus only part of the individuals is long winged and has flight potential, whereas in Calathus mollis all individuals have this ability. Moreover, in Calathus cinctus the long winged genotype, and so the potential for flight, is always expressed, whereas in C . melanocephalus the expression of the long winged genotype depends on environmental conditions, such as temperature and food- supply, and therefore the flight potential for flight is partly expressed only.

Differences in flight potential were clearly associated with differences in life histories and habitat selection. Calathus cinctus occupies temporary habitats, showing a high potential for flight and a high turnover of populations, whereas C . melanocephalus occurs in less temporary habitats, showing a much lower potential for flight and a relatively low turnover of populations. Calathus mollis inhabits coastal dunes and blowing sands, showing a maximum potential for flight, obviously to keep pace with changes in this extreme environment.

The higher fecundity of long winged females, closely linked with larger body size and higher weight, is considered to benefit the colonization abilities of the species.

The wing-morph determination found in Calathus cinctus and C . melanocephalus fitted the current model, but a trade-off between flightlessness and fecundity was not found. Both flight capability and high fecundity are considered to represent closely linked characters of species adapted to unstable, temporary habitats.

Wing dimorphism is supposed to be maintained by a 'balance' between the loss of long winged genotypes by flight activities and the frequency of successful (re)colonizations. In Calathus cinctus both the loss of long winged genotypes and the colonization success is supposed to be high (a short term, opportunistic 'strategy'), whereas in C . melanocephalus both the loss of long winged genotypes and the colonization success is supposed to be low. However, in the latter species the maintenance of wing dimorphism is favoured by the environmental control of the expression of long winged genotypes (a long term, more ensuring 'strategy').

Rearing conditions and behaviour in pigs
Schouten, W.G.P. - \ 1985
Landbouwhogeschool Wageningen. Promotor(en): P.R. Wiepkema, co-promotor(en): G. van Putten. - s.l. : S.n. - 151
biggen - dierenwelzijn - huisvesting, dieren - polymorfisme - piglets - animal welfare - animal housing - polymorphism

During the last three decades the housing conditions of our livestock have been changed drastically (chapter 1). Amongst others, reduced floor space per animal and the monotony of the environment are the most striking changes.

As in other animals, the actual situation strongly influences the behaviour of pigs. However, the effects of early experience on later behaviour in pigs are still not well documented. The aim of this exploratory study was to investigate these effects.

In chapter 2 the design, the general material and methods of the entire series of investigations are described. To be able to distinguish the effects of early experiences (in casu rearing environment) on later behaviour, as clearly as possible, rearing conditions were chosen that differ greatly. Four litters of eight piglets each were reared in either a farrowing crate (the impoverished environment) or in a large straw pen (the enriched environment). The behavioural development during the first eight weeks of life and the differences therein for the two rearing conditions are described in chapter 3. The behaviour of the piglets was assessed by the focal animal observation method of individual piglets. Observations were made at fixed hours during day time.

It was found that vital behaviours like ingestion (feeding, drinking and sucking) and resting were not strongly influenced by rearing condition. The same holds for nosing littermates, a behaviour that presumably plays an important role in mutual recognition. On the other hand, great differences between rearing conditions were discovered in exploratory and redirected exploratory behaviour (massaging or nibbling at littermates or sow). Piglets in the enriched environment showed more exploration than those in the impoverished condition. However, the development of exploration over the first eight weeks of life of the piglets was similar in both housing conditions; exploration increased with age. This might mean that the development of exploration is under endogenous control, while the level of exploration depends on the relative enrichment of the environment. Piglets in the impoverished environment performed much more massaging of or nibbling at littermates or sow than the piglets in the enriched condition. These behaviours are generally considered as redirected exploratory behaviours. The high amount of massaging of or nibbling at littermates and the restricted lying area presumably are the main causes of the high level of restlessness (standing and sitting) of the piglets in the impoverished environment.

After eight weeks of rearing, six piglets per litter went to a commercial fattening farm and two gilts per litter were kept for breeding. The fattening pens had a full slatted concrete floor. For the pigs reared in the farrowing crate these pens embodied a relatively enrichment; the floor space was larger and a plank at the bottom of a welded mesh gate proved to be an excellent object for biting, nibbling or chewing. For the straw reared pigs the fattening pens were a relative impoverishment of the environment. During fattening the behaviour of the pigs was assessed by means of 24 hour time-lapse video recordings (chapter 4), which were also made during rearing. From an age of two weeks onwards a diurnal activity rhythm was found independent of rearing conditions. The similarities and differences in behaviour in the two rearing conditions obtained by means of the focal animal observation, described in chapter 3, were found also by means of these video recordings. The relative enrichment of the fattening pens increased exploration in the crate reared pigs. In straw reared pigs the opposite was found. It was argued that because of the experience with a simpler environment the crate reared pigs needed more time than the straw reared pigs to assimilate the new environment. In spite of the low level of redirected explorative behaviour during rearing, the straw reared pigs showed as much of this behaviour during the fattening period as did the crate reared piglets. Thus, massaging of or nibbling at littermates appeares to be almost completely determined by the actual situation. The high level of restlessness found in crate piglets persisted over the entire fattening period (till the age of 24 weeks). Although restlessness increased in straw reared pigs during fattening, these animals' score was always lower than that of the crate reared ones.

In chapter 4, a measure for the synchrony of activity is defined; if n is the number of animals in a pen, than n states or classes of
activity are possible namely 1, 2, 3 n animals being active simultaneously. The measure of synchrony of activity was defined as the ratio of the occurrence of class n (all animals active) divided by the sum of occurrence of all classes (1+2+3+.....+n).

During the first eight weeks of life straw piglets showed a higher synchrony of activity than the crate piglets. Thereafter this difference was not as clear. A strong negative correlation was found between massaging of or nibbling at littermates (SN-pig) and the synchrony of activity. After ruling out the age effect, this correlation was still high; in the first eight weeks r=-0,87 and in the fattening period r=-0,81. Thus, a high synchrony of activity reduces the probability of SN-pig and hence of restlessness.

After having been reared for eight weeks in the two different housing systems, two crate reared gilts and two straw reared ones were housed in a large straw pen and inseminated in their second oestrus. Fourteen days before the expected farrowing date the gilts were housed individually in a straw pen. The behaviour of these gilts during day time was observed from five days before till 13 days after farrowing (chapter 5).

With respect to nursing (that is, the animal is lying on the side with fully exposed udder and more than half of the total number of piglets is active at the udder) on the first day after farrowing more nursing in straw reared gilts than in the crate reared ones was found. No further differences in behaviour were found between crate or straw reared gilts before and after farrowing.

During farrowing crate reared gilts showed more restlessness than the straw reared gilts. This difference was already visible on the first day before farrowing. Obviously, the acquired restlessness persisted even after having been housed in an enriched environment for ten months.

Data from six hours continuous observation during farrowing were submitted to a sequential and cluster analysis. Straw reared gilts showed two clear clusters of behaviour:

1) Behaviours directly involved in the farrowing process: sliding into, lying, nursing, delivery and expelling of the placenta.

2) Behaviours directed towards the physical environment: nestbuilding, standing and sitting, and exploration.

In crate reared gilts one great cluster was found in which sliding into, lying, nursing, delivery of the piglets and expelling of the placenta were taken together; this cluster also contained nestbuilding, comfort behaviour and biting and snapping.

Another cluster was formed by standing and sitting, and exploration. From the sequential analysis it was clear that crate reared gilts more easily switched from behaviours involved in the farrowing process itself to behaviours that interfere with the farrowing process.

During the first eight weeks of life standing and sitting appeared to be good strategies to avoid or to escape from being massaged or nibbled at; the animals also learned that unpleasant or stressfull situations can be avoided this way. However, this standing and sitting behaviour which also occurred during farrowing as reaction to a novel stressfull situation, is not very adaptive in terms of survival value for the offspring. Because the duration of farrowing did not differ between crate and straw reared gilts, both groups of gilts were probably equally stressed. If this is so, the differences in behaviour found during farrowing can not be attributed to differences in amount of stress experienced by crate and straw reared gilts respectively.

From the results of the study presented in chapter 3 (differential rearing) it appeared that two major factors - bedding and floor space - influenced the behaviour of the piglets.

In chapter 6 the effect of bedding (straw) on the behaviour of piglets is described. Four litters of eight piglets each were housed in farrowing pens; the sows were tethered. During the first two weeks of life two litters were provided with a straw bedding while two other litters were not. From the third week on the substrate was exchanged every week from straw to bare floor and vice versa. It appeared that active behaviour of the piglets strongly depended on the presence or absence of straw. When straw was not available, the piglets immediately directed their exploratory behaviour towards littermates and sow. The piglets also became more restless (more standing and sitting) and started agonistic behaviour more easily. Furthermore, it became clear that the total amount of exploratory and redirected exploratory behaviour performed on a bare floor did not reach the level of exploratory behaviour of piglets of the same age on straw. This suggests that exploratory behaviour in a barren environment cannot be satisfied fully by alternatives or redirected behaviours as used by the piglets. In chapter 7 the effect of pen size on the development of agonistic behaviour in piglets is described. Three different pen sizes were used: 1) 28 m 2with a loose sow; 2) 6.7 m 2and 3) 3.5 m 2; in the latter two the sow was tethered. All pens contained straw bedding.

By using a fine grained ethogram of agonistic behaviour and applying sequential analysis, several differences between the pen sizes were found in the development of agonistic behaviour.

As already shown in chapter 3, pen size did not influence the development of individual recognition (nosing littermates). However, there were significant differences in the development of agonistic behaviour. Piglets housed in pens of 3.5 m 2did not develop threat behaviour (standing in front), did not learn to inhibit biting and to place headknocks exclusively on the head or shoulders of other piglets. Typical sequences of agonistic behaviour were also different for the three sizes. After week 4, in the largest pen 37.8% of all headknocks were preceded by threatening, in the 6.7 m 2pen it was 29.5% and in the 3.5 m 2only 3.9%. In the 3.5 m 2pen more than 40% of headknocks were preceded by exploration or other unspecified behaviour. Because threat behaviour lacked almost entirely in the piglets in the smallest pens, the start of an agonistic interaction was highly unpredictable for this group of animals. This unpredictability of the behaviour of littermates further contributed to the restlessness in these cages. Unlike the piglets in the 6.7 m 2and 28 m 2pens, the piglets in the smallest pen did not change the pattern of their agonistic behaviour anymore after week 3. Therefore, the agonistic of the latter piglets may be classified as infantile; presumably, this will not improve later in life. Therefore, these piglets must be considered to be not very well equiped for social grouping as adults.

In the general discussion (chapter 8), two main points are selected for a more detailed discussion: first, the immediate effects of rearing in different environments on the behaviour of piglets and secondly, the effects of this differential rearing on later behaviour around farrowing.

The amount of floor space mainly influenced the development of agonistic behaviour. The complexity of the environment and especially the presence of bedding proved to be an important factor in preventing the occurrence of redirected explorative behaviour and restlessness. From the findings described in chapter 3 and 7, it is argued that the socialization period of piglets falls in the second and third week of life. The effect of reduced floor space, increased unpredictability of the behaviour of conspecifics, and strongly resembles the effect of social isolation as found in other species. In both situations the animals do not learn to control their social environment.

Impoverishment of the environment causes redirected exploratory behaviour. The piglets learn to deal with this behaviour of their peers conspecifics by avoidance or escape reactions, mainly consisting of standing and sitting. In later life the same animals showed regression of this behaviour, in that they performed the same response in reaction to a novel and stressfull situation like farrowing. This type of response is maladaptive in this situation because of possible detrimental effects for the piglets.

Environments inducing redirected exploratory behaviour and preventing the development of social skills do not contribute in a positive way to the welfare of the animals. For practical pig breeding the rearing situation might be very important because of its effects upon the behaviour in later life of the animals.

Regulation of caste differentiation in the honey bee (Apis mellifera L.)
Goewie, E.A. - \ 1978
Landbouwhogeschool Wageningen. Promotor(en): J. de Wilde. - Wageningen : Veenman - 76
apidae - polymorfisme - apidae - polymorphism

The nutritional environment of honey-bee larvae affects the juvenile hormone (JH) titre of larval haemolymph and tissues. In this investigation the mechanism for the regulation of caste differentiation has been studied.

Chemo- and mechanoreceptors are found on larval mouthparts. Chemoreceptors on maxillae and labium are innervated by 5 bipolar neurons, making contact with the larval environment through one pore. Labral chemoreceptors are innervated by 4 bipolar neurons, probably also making contact with the environment through one pore.

All chemoreceptors studied are sensitive to sugars and salts. No sensitivity to other separately tested food components is found. This result is confirmed when considering receptor responses generated by diluted worker jelly (WJ) and royal jelly (RJ). Thus larval food components other than sugars and salts may not affect directly caste differentiation. Sugars possibly function as phagostimulants, regulating the amount of food consumed. The rate of food intake is considered to be the releasing factor for corpus allatum (CA) activity. Possibly neural stimuli arising from stretch receptors on the oesophageal or abdominal wall or indirectly from the brain may be involved.

Salts possibly function as inhibitors of the food intake. However, when adding salts to the food of queen larvae in the colony, the larvae leave the food deposited on the bottom of the cell. Food consumption is not restricted to the present food, but larvae receive also directly offered food from nurse bees. Therefore inhibition of food consumption by addition of salt in colony experiments resulted in a small number of intermediates only. Inhibition of food intake by starvation did not improve results to a large extent. A high rate of mortality and a small number of intermediates were obtained. Though not conclusive, some indication exists that limitation of food intake during the first three days of larval life, inhibits queen induction.

The neuroendocrine system of the larva corresponds in its main features with the classical pattern. In the pars intercerebralis 12 MNSC on both parts of the brain are found. Their axons innervate for one part the corpora cardiaca (CC) and for the other the CA, transporting neurosecretory granules, synthesized in the MNSC. Neurosecretory granules are accumulated in axon endings in the CC and in the neurosecretory fibres within the CA. Release phenomena are observed in the axon endings in the CC. CA are also innervated by two other axons. These axons never contained neurosecretory material throughout larval development.

Ultrastructural studies of CA in younger larvae reveal cycles of synthetic activities. MNSC however show little differentiation at that time. MNSC become active in larvae from about 60 hours of age. At the end of larval development CA innervating axons from the MNSC (nervus corporis allati or NCA) contain considerable amounts of neurosecretory material. Therefore MNSC can not be considered to trigger CA activity. Studies of synthesis, transport and secretion of elementary granules correlated with synthetic activities of the CA rather suggest that the neurosecretory substance inhibits CA activity.

These results are investigated further in detailed studies on MNSC and CA after changing the food of worker larvae into RJ and after application of JH to worker larvae. The activities of MNSC and CA are studied with quantitative electron- microscopical techniques. The effect of the change of food on the activity of MNSC and CA was determined after different periods. The change of larval nutrition appears not to affect the activity of the MNSC, but to stimulate CA activity. Prior to the increase of the CA activity pinocytosis at the periphery of the CA is observed. This process seems to be responsible for the increase in volume of the CA after intake of RJ by the larva. However pinocytosis is not considered as the trigger for the CA activity. Other processes not observed with the electron microscope might precede this phenomenon.

In JH treated worker larvae MNSC become activated at first. Increased amounts of neurosecretory material can be observed in the NCA, which coincides with the inhibition of CA activity. The decrease in CA activity after JH application can be explained by a feed back mechanism via the MNSC.

Results and conclusions are interpreted and discussed, resulting in a possible scheme of the mechanism of the caste differentiation in the honey bee.

Nutritional aspects of development and wing dimorphism in the aphid Myzus persicae
Harrewijn, P. - \ 1977
Wageningen : Ponsen en Looijen - 98
diervoeding - aphididae - chemie - embryologie - voer - ontogenie - fysiologie - polymorfisme - zoölogie - animal nutrition - chemistry - embryology - feeds - ontogeny - physiology - polymorphism - zoology
Studies on the physiology of phase induction in Locusta migratoria migratorioides R. & F.
Staal, G.B. - \ 1961
Wageningen University. Promotor(en): J. de Wilde. - Wageningen : Veenman - 126
acrididae - sprinkhanen - insecten - plantenplagen - hormonen - endocrinologie - polymorfisme - acrididae - locusts - insects - plant pests - hormones - endocrinology - polymorphism - cum laude
External conditions such as lack of food and the consequent population density control the swarming of the migratory locust. The transformation is of metabolism and larval development as well as of behaviour. The proportions of body parts and the pigmentation change. As insect development is regulated by juvenile hormone and moulting hormone, there was also the possibility that they were involved in phase polymorphism.

The possibility of endocrine control was studied in some types of migratory locust by removing or implanting glands, by cutting nerves and by rearing under different conditions. For the surgical studies a technique was developed for routine operations on large numbers of second-instar larvae and for rapidly measuring the volume of endocrine glands. The green pigmentation of the solitary and the yellow of the gregarious imago was controlled by the juvenile hormone. Body proportions were also thus controlled independent of metamorphic regulation. Moulting hormone had a spectacular effect on development, moulting and body proportions. The studies may be of use in locust control with insect hormones.

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