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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Seeds as biosocial commons : an analysis of various practices in India
Patnaik, Archana - \ 2016
University. Promotor(en): Guido Ruivenkamp; Han Wiskerke, co-promotor(en): Joost Jongerden. - Wageningen : Wageningen University - ISBN 9789462578302 - 166
rice - seeds - plant genetic resources - plant genetics - seed production - seed storage - community development - gender - social environment - india - rural development - rijst - zaden - genetische bronnen van plantensoorten - plantengenetica - zaadproductie - opslag van zaden - gemeenschapsontwikkeling - geslacht (gender) - sociaal milieu - plattelandsontwikkeling

This research investigates and describes the conservation and use of Plant Genetic Resources (PGRs), especially seeds through processes of commonisation. Seeds form an important element for sustaining human life (through food production) and social relations (by maintaining agricultural socialities). Therefore, conservation and management of PGRs in the form of seeds are essential for plant breeding, agricultural production and to meet the growing food demand of the increasing population. However, the changed use of PGRs through enclosures and appropriation of the Intellectual Property Rights creates underutilisation of these resources, risking their important societal role. Thus, this research aimed at analysing how the processes of commonisation of PGRs, especially seeds as biosocial commons emerge in the Indian context.

The research applied an in-depth qualitative research approach using case study method. It focused on four distinct issues of disconnection, collective resistance, strategies of repossession and ability of stakeholders to provide insights broadly into the processes of commonisation of PGRs. Describing the different cases it also establishes whether and how opportunities for commonisation of PGRs as biosocial commons emerge within these contexts. The research analysed four cases where one case reflected on the intellectual commons produced through institutionalisation of PGRs and the other three cases reflected on the bottom-up perspective of commons produced through Non-Governmental Organisations (NGOs).

The research through its first case, the Central Rice Research Institute (CRRI), a public ex situ genebank, describes the disconnection of PGRs, while through the second case reflects on the collective activity of resistance through management of community seed banks (CSBs) by the Deccan Development Society (DDS). The third and fourth cases involved small, local initiatives; Loka Samabaya Pratisthan (LSP) and Sambhav that fostered collective action for repossession through in situ seed banks. The research used various techniques, such as interviews with respondents, focus group discussions (FGDs) and participant observation for primary sources of data, with published and unpublished documents, reports and official websites as secondary sources.

The second chapter of the thesis looks at the issue of disconnection and argues that storing seeds at genebanks disconnects the resources from their biosocial environment. Further, the evaluation of genetic traits within the stored seeds through the scientific intervention at the genebank creates the divide between the resources (seeds) and their informational content. Thus, this chapter concludes that disconnection of seeds from their biosocial environment leads to the creation of exclusive but positive intellectual commons.

The third chapter of the thesis looks at the issue of collective resistance and argues that disconnection of the community from their local food system can generate resistance and collective activity among the community. This chapter finds that the resistance and collective activity further brought in the interaction between the resource and the stakeholders through informal social relations and seed networks.

The fourth chapter of the thesis looks at the issue of strategies of repossession and argues that socio-political and ecological context play an important role in determining the strategy for repossession and commonisation of PGRs which further inhibits or facilitates the production of seeds as biosocial commons.

The fifth chapter of the thesis analyses the ability of stakeholders and finds that apart from institutional rights other factors like the social relations, ideology, negotiations and social identity of a stakeholder determines their ability in accessing the conserved resources.

The overall finding of the research suggests that the informal seed networks in the cases analysed stimulated in establishing the biosocial relations between the stakeholders and the resources. The biosocial relation further led seeds to function as biosocial commons. The research thus proposes that strengthening of these biosocial relations through informal seed networks can lead to the commonisation of the PGRs, especially seeds as biosocial commons in the Indian context.

Resistentieveredeling - Overerving van resistentie : Kennisclip Bogo-project e-learning
Hop, M.E.C.M. - \ 2016
Groen Kennisnet
resistance breeding - disease resistance - genetic resistance - partial resistance - plant genetics - plant protection - teaching materials - resistentieveredeling - ziekteresistentie - genetisch bepaalde resistentie - partiële resistentie - plantengenetica - gewasbescherming - lesmaterialen
Deze kennisclip maakt onderdeel uit van de lesmodule Resistentie Veredeling van het CIV T&U.
Future for cytogenetics in plant genomics and breeding
Jong, J.H.S.G.M. de - \ 2015
Wageningen : Wageningen UR - ISBN 9789462573727 - 20 p.
cytogenetics - plant breeding - genomics - plant genetics - cytogenetica - plantenveredeling - genomica - plantengenetica
Farewell address upon retiring as Professor of Plant Cytogenetics at Wageningen University on 1 October 2015
'Met genetische variatie kun je heel veel doen'
Dwarswaard, A. ; Tuyl, J.M. van - \ 2015
BloembollenVisie (2015)315. - ISSN 1571-5558 - p. 24 - 25.
bloembollen - lilium - lelies - rassen (planten) - plantengenetica - plantenveredeling - landbouwkundig onderzoek - resistentie van variëteiten - ornamental bulbs - lilies - varieties - plant genetics - plant breeding - agricultural research - varietal resistance
Na ruim 42 jaar zet onderzoeker Jaap van Tuyl van PRI in Wageningen een punt achter zijn loopbaan. Menig bolgewas kreeg zijn aandacht en altijd ging het om de genetische kant ervan. Van hyacinth tot lelie, van Zantedeschia tot tulp, telkens waren het de genen die inzicht gaven. Een portret van een man die de hele wereld afreisde om vooral over lelies te vertellen.
Using natural variation to unravel the dynamic regulation of plant performance in diverse environments
Molenaar, J.A. - \ 2015
University. Promotor(en): Harro Bouwmeester; Joost Keurentjes, co-promotor(en): Dick Vreugdenhil. - Wageningen : Wageningen University - ISBN 9789462573444 - 186
planten - genomen - loci voor kwantitatief kenmerk - warmtestress - genetische kartering - groei - droogte - plantengenetica - plantenfysiologie - plants - genomes - quantitative trait loci - heat stress - genetic mapping - growth - drought - plant genetics - plant physiology


All plants are able to respond to changes in their environment by adjusting their morphology and metabolism, but large differences are observed in the effectiveness of these responses in the light of plant fitness. Between and within species large differences are observed in plant responses to drought, heat and other abiotic stresses. This natural variation is partly due to variation in the genetic composition of individuals. Within-species variation can be used to identify and study genes involved in the genetic regulation of plant performance.

Growth of the world population will, in the coming years, lead to an increased demand for food, feed and other natural products. In addition, extreme weather conditions with, amongst others, more and prolonged periods of drought and heat are expected to occur due to climate change. Therefore breeders are challenged to produce stress tolerant cultivars with improved yield under sub-optimal conditions. Knowledge about the mechanisms and genes that underlie tolerance to drought, heat and other abiotic stresses will ease this challenge.

The aim of this thesis was to identify and study the role of genes that are underlying natural variation in plant performance under drought, salt and heat stress. To reach this goal a genome wide association (GWA) mapping approach was taken in the model species Arabidopsis thaliana. A population of 350 natural accessions of Arabidopsis, genotyped with 215k SNPs, was grown under control and several stress conditions and plant performance was evaluated by phenotyping one or several plant traits per environment. Genes located in the genomic regions that were significantly associated with plant performance, were studied in more detail.

Plant performance was first evaluated upon osmotic stress (Chapter 2). This treatment resulted not only in a reduced plant size, but also caused the colour of the rosette leaves to change from green to purple-red due to anthocyanin accumulation. The latter was visually quantified and subsequent GWA mapping revealed that a large part of the variation in anthocyanin accumulation could be explained by a small genomic region on chromosome 1. The analysis of re-sequence data allowed us to associate the second most frequent allele of MYB90 with higher anthocyanin accumulation and to identify the causal SNP. Interestingly MYB75, a close relative of MYB90, was not identified by GWA mapping, although causal sequence variation of this gene for anthocyanin accumulation was identified in the Cvi x Ler and Ler x Eri-1 RIL populations. Re-sequence data revealed that one allele of MYB75 was dominating the population and that the MYB75 alleles of Cvi and Ler were both rare, explaining the lack of association at this locus in GWA mapping. For MYB90, two alleles were present in a substantial part of the population, suggesting balancing selection between them.

Next, the natural population was exposed to short-term heat stress during flowering (Chapter 3). This short-term stress has a large impact on seed set, while it hardly affects the vegetative tissues. Natural variation for tolerance against the effect of heat on seed set was evaluated by measuring the length of all siliques along the inflorescence in both heat-treated and control plants. Because the flower that opened during the treatment was tagged, we could analyse the heat response for several developmental stages separately. GWA mapping revealed that the heat response before and after anthesis involved different genes. For the heat response before anthesis strong evidence was gained that FLC, a flowering time regulator and QUL2, a gene suggested to play a role in vascular tissue development, were causal for two strong associations.

Furthermore, the impact of moderate drought on plant performance was evaluated in the plant phenotyping platform PHENOPSIS. Homogeneous drought was assured by tight regulation of climate cell conditions and the robotic weighing and watering of the pots twice a day. Because plant growth is a dynamic trait it was monitored over time by top-view imaging under both moderate drought and control conditions (Chapter 4 and 5). To characterise growth it was modelled with an exponential function. GWA mapping of temporal growth data resulted in the detection of time-dependent QTLs whereas mapping of model parameters resulted in another set of QTLs related to the entire growth period. Most of these QTLs would not have been identified if plant size had only been determined on a single day. For the QTLs detected under control conditions eight candidate genes with a growth-related mutant or overexpression phenotype were identified (Chapter 4). Genes in the support window of the drought-QTLs were prioritized based on previously reported gene expression data (Chapter 5). Additional validation experiments are needed to confirm causality of the candidate genes.

Next, to search for genes that determine plant size across many environments, biomass accumulation in the natural population was determined in 25 different environments (Chapter 6). Joint analysis of these data by multi-environment GWA mapping resulted in the detection of 106 strongly associated SNPs with significant effects in 7 to 16 environments. Several genes involved in starch metabolism, leaf size control and flowering time determination were located in close proximity of the associated SNPs. Two genes, RPM1 and ACD6, were located in close proximity of SNPs with significant GxE effects. For both genes, alleles have been identified that increase resistance to bacterial infection, but that reduce biomass accumulation. The sign of the allelic effect is therefore dependent on the environmental conditions. Whole genome predictions revealed that most of the GxE interactions observed at the phenotypic level were not the consequence of strong associations with strong QxE effects, but of moderate and weak associations with weak QxE effects.

Finally, in Chapter 7 I discuss the usefulness of GWA mapping in the identification of genes underlying natural variation in plant performance under drought, heat stress and a number of other environments. Strong associations were observed for both environment-specific as well as common plant performance regulators. Some choices in phenotyping and experimental design were crucial for our success, like evaluation of plant performance over time and simplification of the quantification of the phenotype. It is suggested that follow-up work should focus on the functional characterization of the causal genes, because such analyses would be helpful to identify pathways in which the causal genes are involved and to understand why sequence variation results in changes at the phenotype level. Although translation of the findings to applications in crops is challenging, this thesis contributes to the understanding of the genetic regulation of stress response and therefore will likely contribute to the development of stress tolerant and stable yielding crops.

A systems genetics study of seed quality and seedling vigour in Brassica rapa
Basnet, R.K. - \ 2015
University. Promotor(en): Richard Visser, co-promotor(en): Guusje Bonnema; Chris Maliepaard. - Wageningen : Wageningen University - ISBN 9789462574250 - 177
brassica campestris - zaadkwaliteit - groeikracht - zaden - zaadontwikkeling - zaadkieming - zaailingen - plantengenetica - genomica - seed quality - vigour - seeds - seed development - seed germination - seedlings - plant genetics - genomics


Seed is the basic and most critical input for seed propagated agricultural crops: seed quality and seedling vigour determine plant establishment, growth and development in both natural and agricultural ecosystems. Seed quality and seedling vigour are mainly determined by the interactions of the following three components: genetic background, physiological quality and the environmental conditions during seed set, seed ripening, storage, seed germination and early seedling development. In the past, many efforts have been made to improve seed germination and seedling vigour by optimizing physiological and environmental factors (non-genetic factors); however, the paradigm has shifted to investigate genetic factors and to use these to improve crop performance by plant breeding. The aim of this thesis is to unravel the genetics of seed germination and seedling vigour under different conditions in Brassica rapa, using a systems genetics approach. Studies in many crop species have reported that seed germination and seedling vigour traits are governed by many genes and are strongly affected by environmental conditions. As salinity stress is becoming one of the most important abiotic stresses affecting crop growth and yield, we studied the genetics of seed germination and seedling vigour under neutral and salt stress conditions. For a number of crops, it has been established that larger seed size and higher seed weight indicate more reserve food and contribute positively to seedling establishment. Therefore, our hypothesis for this thesis is that transcriptional regulation of genes during seed development determines the composition and content of seed reserves, and that these seed reserves play a major role in seed germination and seedling growth, especially at the heterotrophic stage under optimal and sub-optimal conditions.

B. rapa is an extremely diverse Brassica species which includes, besides many diverse leafy vegetable types and turnips, also oilseed crops. Brassica seeds are of high economic importance for several reasons. They are the starting point of the life cycle of the crop, but also they are directly used as sources of vegetable oil or condiments. At present, B. napus is the most important source of vegetable oil worldwide, but B. rapa is often used for introgression breeding to broaden its narrow genetic base resulting in genetic improvements. Therefore, the acquired knowledge is also useful for the scientific community and plant breeders working in B. napus and other Brassica species.

In Chapter 2 we evaluated the genetic diversity of a B. rapa core collection of 168 accessions representing different crop types and geographic origins. Using the Bayesian cluster analysis software STRUCTURE, we identified four subpopulations: subpopulation 1 with accessions of Indian origin, spring oil, yellow sarson and rapid cycling; subpopulation 2 consisting of several types from Asian origins: pak choi, winter oil, mizuna, mibuna, komasuna, turnip green, oil rape and Asian turnip; subpopulation 3, which included mainly accessions of Chinese cabbage and subpopulation 4 with mostly vegetable turnip, fodder turnip and brocoletto accessions from European origin. The geographical distribution of the accessions was very much congruent with genetic, metabolic and morphological diversity. This initial study was followed by association studies for secondary metabolites from the tocopherol and carotenoids pathways, using the population structure of these four subpopulations as a correction term to control for spurious marker-trait associations (Chapter 2). Additionally, we used a machine learning approach, Random Forest (RF) regression, to find marker-trait associations. We chose the RF approach as it can handle large numbers of variables (markers, metabolites, transcript abundance) in combination with relatively small sample sets of accessions, to show its perspectives for application to the increasing amounts of data available through the different ~omics technologies. In our analysis, the markers showing significant association with metabolites identified by the RF approach overlapped with markers obtained from association mapping. Those markers could potentially be used for marker-assisted selection (MAS) in breeding for these secondary metabolites in different morphotypes or sub-populations. Knowledge of genetic distance as evaluated in this chapter allowed the choice of parents to create a segregating population for QTL analyses by maximizing genetic variation between the parents.

In Chapter 4, a doubled haploid (DH) population from a cross of genetically diverse morphotypes of B. rapa, an oil-type yellow sarson (YS143) and a vegetable pak choi (PC175) (Chapter 2), was used to evaluate the genetic basis of seed germination and seedling vigour traits under both non-stress and salt stress conditions. The yellow sarson parent had larger seed size and higher thousand-seed weight than the pak choi parent, and displayed earlier onset, higher uniformity in germination, faster germination and maximum germination, and higher root- and shoot- lengths and biomass under both non-stress and salt stress conditions. Positive correlations of thousand-seed weight with earliness, speed and uniformity of germination and maximum germination percentage, supports that larger seeds germinate earlier, faster, more uniformly and to a higher maximum germination percentage than smaller seeds. Thus, we conclude that yellow sarson had higher seed quality and seedling vigour than pak choi. However yellow sarson also contributed negative alleles to seed germination, as illustrated by its allele of the QTL at A05 which decreases the uniformity of seed germination. In addition we also observed that yellow sarson seedling growth was more affected by salt stress than pak choi. All traits were scored over the DH population, and this clearly showed transgressive variation for most traits. Eight QTL hotspots were identified for seed weight, seed germination, and root and shoot lengths. A QTL hotspot for seed germination on A02 co-located with a homologue of the FLOWERING LOCUS C (BrFLC2) genes and its cis-acting expression QTL (cis-eQTL). FLC2 (BrFLC2 in B. rapa) is an important repressor of flowering time in both A. thaliana and B. rapa and recently, FLC2 was reported for its pleiotropic effect on seed germination in A. thaliana. A QTL hotspot on A05 with salt stress specific QTL co-located with the FATTY ACID DESATURASE 2 (BrFAD2) gene and its cis-eQTL. Besides the role of FAD2 in fatty acid desaturation, the up-regulation of this gene was associated with enhanced seed germination and hypocotyl elongation under salinity in B. napus (BnFAD2) and A. thaliana (FAD2). We observed epistatic interactions between the QTL hotspots at the BrFLC2 and BrFAD2 loci, and between other QTL hotspots.

Seed development is regulated by many dynamic metabolic processes controlled by complex networks of spatially and temporally expressed genes. Therefore, morphological characteristics and the transcriptional signatures of developing seeds from yellow- and brown/black-seeded genotypes were studied to get to know the timing of key metabolic processes, to explore the major transcriptional differences and to identify the optimum stage for a genetical genomics study for B. rapa seed traits (Chapter 3). This is the first study of genome-wide profiling of transcript abundance during seed development in B. rapa. Most transcriptional changes occurred between 25 and 35 days after pollination (between the bent-cotyledon stage and the stage when the embryo fully fills the seed), which is later than in the related species B. napus. A weighted gene co-expression network analysis (WGCNA) identified 47 gene modules with different co-expression patterns, of which 17 showed a genotype effect, 4 modules a time effect during seed development and 6 modules both genotype and time effects. Based on the number of genes in gene modules, the predominant variation in gene expression was according to developmental stages rather than morphotype differences. We identified 17 putative cis-regulatory elements (motifs) for four co-regulated gene clusters of genes related to lipid metabolism. The identification of key physiological events, major expression patterns, and putative cis-regulatory elements provides useful information to construct gene regulatory networks in B. rapa developing seeds and provides a starting point for a genetical genomics study of fatty acid composition and additional seed traits in Chapter 5.

Since Brassica seeds are sources of vegetable oil, genetic studies of the gene regulatory mechanisms underlying lipid metabolism is of high importance, not only in relation to seed and seedling vigour, but also for Brassica oilseed breeding. In Chapter 5, an integrative approach of QTL mapping for fatty acids composition and for transcript abundance (eQTL) of genes related to lipid metabolism, together with gene co-expression networks was used to unravel the genetic regulation of seed fatty acid composition in the DH population of B. rapa. In this study, a confounding effect of flowering time variation was observed on fatty acid QTLs (metabolite level) at linkage group A02 and of seed colour variation on eQTLs (transcript level) at linkage group A09. At A02, fatty acid QTLs from 2009 seeds co-locate with the genetic position of a gene-targeted marker for BrFLC2, its cis-QTL, and a major flowering time QTL. Flowering time variation is very obvious in this DH population and the BrFLC2 gene at A02 (16.7 cM) is the major regulator of flowering time, with a non-functional allele in the yellow sarson parent. When QTL analysis was performed on seeds from 2011, from DH lines that flowered synchronously due to staggered sowing, this fatty acid QTL hotspot disappeared. The 2011 seed lot was used for further analysis combining fatty acid QTLs with eQTLs in this study. On A09, a large trans-eQTL hotspot was co-localized with a major seed colour QTL, in the region where the causal gene, the bHLH transcription factor BrTT8, was cloned. The role of this gene in seed colour development was functionally proven in B. rapa. As the yellow sarson and pak choi parents of this population have contrasting seed coat colour (Chapter 3) the DH lines segregated for seed colour. When seed colour variation was used as a co-variate in our statistical model, we could exclude its confounding effect on eQTL mapping. We compared the fatty acid QTL and eQTL results from the analyses before and after seed colour correction and later discuss the results from the analysis after correction. The distribution of major QTLs for fatty acids showed a relationship with the types of fatty acids: linkage group A03 contained major QTLs for monounsaturated fatty acids (MUFAs), A04 for saturated fatty acids (SFAs) and A05 for polyunsaturated fatty acids (PUFAs). Using a genetical genomics approach, eQTL hotspots were found at major fatty acid QTLs on A03, A04 and A05 and on A09. Finally, an eQTL-guided gene co-expression network of lipid metabolism related genes showed major hubs at the genes BrPLA2-ALPHA, BrWD-40, a number of seed storage protein genes and a transcription factor BrMD-2, suggesting essential roles of these genes in lipid metabolism. Several genes, such as BrFAE1, BrTAG1, BrFAD2, BrFAD5, BrFAD7, which were reported as important genes for fatty acid composition in seeds in other studies of related species, had relatively lower degrees of connection in the networks. However their cis-eQTLs co-localized with specific fatty acid QTLs, making them candidate genes for the observed variation. We hypothesize that these play a role in modifying fatty acid content or composition across genotypes, rather than playing essential roles in the pathway itself. These results suggest the need of a global study of lipid metabolism rather than a strict focus on the fatty acid biosynthesis pathway per se. This study gives a starting point for understanding the genetic regulation of lipid metabolism, by identification of a number of key regulatory genes, identified as major hub genes, and candidate genes for fatty acid QTLs.

In the final chapter (Chapter 6) we summarize and critically discuss the relationships among phenotypic traits, metabolites and expression variation as well as the co-localization of QTLs from these different levels. In this thesis, we developed methodology to integrate transcriptomics and metabolomics data sets and to construct gene regulatory networks related to major fatty acids, and found a set of (possible) candidate genes involved in lipid metabolism. In the future, we recommend to integrate the genome-wide transcriptome data set with all major seed metabolites and phenotypic data on seed and seedling vigour to directly link all three components: transcriptome, metabolome and phenotypic traits, and ultimately expand the knowledge on the genetic regulation of seed metabolites, seed quality and seedling vigour in B. rapa to other Brassica species.

Richard Immink": 'Van tulp en lelie weten we nog steeds heel weinig'
Dwarswaard, A. - \ 2014
BloembollenVisie (2014)299. - ISSN 1571-5558 - p. 22 - 22.
bloembollen - tulpen - lelies - landbouwkundig onderzoek - plantengenetica - dna - ornamental bulbs - tulips - lilies - agricultural research - plant genetics
Bijna twee jaar geleden werd prof. dr. ir. Richard Immink voor een dag in de week benoemd tot “bollenprof”. Samen met twee assistenten-in-opleiding voert hij fundamenteel onderzoek uit aan tulp en lelie. Tijd voor een tussenbalans in drie afleveringen. In deze eerste aflevering legt Richard Immink uit waar het in dit project om draait: genetische geheimen ontrafelen van tulp en lelie.
Genetics and bioenergy potential of forage maize: deconstructing the cell wall
Torres, A.F. - \ 2014
University. Promotor(en): Richard Visser, co-promotor(en): Luisa Trindade; Oene Dolstra. - Wageningen : Wageningen University - ISBN 9789462570375 - 202
zea mays - maïs - voedergewassen - plantengenetica - bio-energie - celwanden - bioethanol - bioconversie - industriële grondstoffen - brandstofgewassen - maize - fodder crops - plant genetics - bioenergy - cell walls - bioconversion - feedstocks - fuel crops

Despite gaining prominence in scientific spheres and political agendas worldwide, the production of biofuels from plant biomass is yet to achieve an economic stronghold in the renewable-energy sector. Plant lignocellulose has evolved to resist chemical and enzymatic deconstruction, and its conversion into liquid fuels requires energetically stringent processes that currently render the industry economically and environmentally unviable.

To address this challenge, experts have envisioned the development of advanced bioenergy crops which require lower energetic and chemical inputs for their effective fractionation. At its core, this approach requires an in-depth understanding of the composition, synthesis and breeding amenability of the plant cell wall; the principal constituent of total plant dry biomass and the most recalcitrant fraction of the crop at physiological maturity to deconstruction. To this end, the primary aim of this thesis was to dissect and elucidate the biochemical and genetic factors controlling cell wall characteristics relevant to the development of bioenergy grasses with improved processing quality for cellulosic based fuel production. A focus on maize was warranted as it currently represents the de facto model system for bioenergy crop research; offering an unrivalled platform to underpin the complex genetic architecture of cell wall biosynthesis, develop advanced bioenergy-crop breeding strategies and translate cell wall research into innovations and commercial products.

This thesis exposed that the biomass-to-fuel conversion of crops is a highly complex trait dependent on both, the balance and synergy between multiple cell wall components, and the inherent effectiveness of the conversion technology. Concerning the production of cellulosic ethanol via the combined operations of dilute-acid pretreatment and enzymatic saccharification, our results revealed that the chemical mechanisms affecting biomass conversion efficiency depend on pretreatment severity. Whereas at harsh pretreatments biomass conversion efficiency was primarily influenced by the inherent efficacy of thermochemical cell wall deconstruction, at milder pretreatments, maximum fermentable glucose release was observed for maize genotypes exhibiting systematic cell wall changes leading to higher ruminal cell wall digestibility. These results confirmed that the selection and use of cellulosic feedstocks that best match the processing conditions used in the industry can aid in reaching industrial goals aimed at improving the commercial and environmental performance of cellulosic fuels.

In turn, the exhaustive characterization of a forage maize doubled haploid (DH) population demonstrated the vast degree of genetic diversity in maize cell wall composition and bioconversion potential amenable to breeding. Principally, these findings suggest that natural diversity in the biochemical composition of the maize cell wall and its physical properties is primarily ascribed to variation in the balance, monomeric make-up, and extent of cross-linking of non-cellulosic cell wall polymers (i.e. lignin and hemicellulose). Indeed, correlation analyses confirmed that the extent of enzymatic depolymerization of maize biomass was strongly and negatively associated to the concentration of cell wall phenolics, but positively impacted by the degree of glucuronoarabinoxylan (GAX) glycosylation and extent of hemicellulose-to-hemicellulose cross-linking. Our results also showed that natural variation in cell wall content and composition is quantitatively inherited and putatively ascribed to the segregation of multiple genetic loci with minor additive effects. In our population, genotypic diversity for cell wall composition and quality was found to be controlled by 52 quantitative trait loci (QTLs). From eight QTLs regulating bioconversion properties, five were previously unidentified and warrant further investigation.

Despite the apparent complexity of cell wall genetics, however, the high heritability and environmentally stability of cell wall compositional and degradability properties guarantee high selection efficacy during the development of superior DH/inbred material, and predispose that multi-environment testing will only be necessary at advanced stages of bioenergy-maize breeding programs. Moreover, because genetic variation for complex cell wall characteristics appears to be predominantly additive, preliminary selection at the inbred level will expectedly lead to successful hybrid selection; thereby minimizing the need for recurrent test-crossing procedures and evaluations. In this regard, maize cell wall bioconversion efficiency constitutes an excellent selection criterion for immediate application in modern maize breeding programs.

Ultimately, the convergence of classical selection schemes with inexpensive genotyping, advanced biometric models, high-throughput cell wall phenotyping and doubled haploid (DH) production technologies can accelerate development and commercial release of maize cultivars for bioenergy applications. To play a determinant role in the development and realization of sustainable and cost-effective cellulosic fuel processing technologies, however, novel dual-purpose maize cultivars (i.e. delivering both, grain for feed or food and fiber materials for bioconversion) will have to surpass the performance in lignocellulose processing quality and biomass yields of the best elite germplasm. These prospects seem realistic as the parallel advance of grain yield and stover productivity and quality characteristics is a feasible undertaking. Conceptually, the advance of superior bioenergy cultivars (surpassing the performance of modern elite material) would allow us to make the currently available biomass-to-fuel conversion systems more cost-effective and sustainable, and may also have favorable consequences for the ideal size and geographical distribution of biofuel refineries.

Molecular and genetic basis of freezing tolerance in crucifer species
Heo, J. - \ 2014
University. Promotor(en): Eric Schranz, co-promotor(en): P.H. van Tienderen; C.S. Testerink. - Wageningen : Wageningen University - ISBN 9789461738691 - 129
brassicaceae - invriezen - koudetolerantie - moleculaire biologie - plantengenetica - loci voor kwantitatief kenmerk - genen - kouderesistentie - freezing - cold tolerance - molecular biology - plant genetics - quantitative trait loci - genes - cold resistance

Understanding genetic variation for freezing tolerance is important for unraveling an adaptative strategy of species and for finding out an effective way to improve crop productivity to unfavorable winter environments. The aim of this thesis was to examine natural variation for components of freezing tolerance beyond what has been done using the model organism Arabidopsis thaliana. Experiments using B. stricta were carried out to identify potentially novel and beneficial traits, and loci related to cold acclimation, or using a number of related Brassicaceae species were performed to understand mechanism for cold deacclimation. Our results strongly indicate differential regulatory mechanisms are involved in cold acclimation as well as cold deacclimation.Although we are still far from understanding those mechanisms, we have shown that exploiting natural variation using wild species provides new perspectives on ecologically important adaptation to cold, and may contribute to improve tolerance in crucifer species.

Inzetten van plantversterkers vraagt om meer kennis : 'Gemakkelijke' oplossing met chemie is voorbij (interview met André van der Wurff en Filip van Noort)
Arkesteijn, M. ; Wurff, A.W.G. van der; Noort, F.R. van - \ 2014
Onder Glas 11 (2014)5. - p. 66 - 67.
glastuinbouw - sierplanten - potplanten - plantgezondheid - verdedigingsmechanismen - ziekteresistentie - plantengenetica - landbouwkundig onderzoek - proeven - greenhouse horticulture - ornamental plants - pot plants - plant health - defence mechanisms - disease resistance - plant genetics - agricultural research - trials
Dat planten ziek kunnen worden door stress is bekend. Bij een verminderde weerbaarheid, zoals in de stekfase, de overgang van vegetatief naar generatief of gewoon door de klimaatomstandigheden, krijgen schimmels en bacteriën eerder de kans met uitval of beschadiging als gevolg. Door ‘plantversterkers’ toe te voegen, kunnen planten zich beter weren tegen aanvallen van buitenaf. Maar welke middelen werken nu echt en hoe?
Arabidopsis in Wageningen
Koornneef, M. - \ 2013
Wageningen : Wageningen University, Wageningen UR - ISBN 9789461736130 - 13
arabidopsis thaliana - plantengenetica - onderzoek - onderzoeksprojecten - plantenfysiologie - plant genetics - research - research projects - plant physiology
Arabidopsis thaliana is the plant species that in the past 25 years has developed into the major model species in plant biology research. This was due to its properties such as short generation time, its small genome and its easiness to be transformed. Wageningen University has played an important role in the development of this model, based on interdisciplinary collaborations using genetics as a major tool to investigate aspects of physiology, development, plant-microbe interactions and evolution.
De tomatenkaart is klaar, wat nu?
Finkers, H.J. ; Visser, R.G.F. - \ 2013
Kennis Online 10 (2013)mei. - p. 3 - 5.
moleculaire genetica - plantengenetica - dna-sequencing - tomaten - rassen (planten) - plantenveredeling - genetische bronnen van plantensoorten - genomen - molecular genetics - plant genetics - dna sequencing - tomatoes - varieties - plant breeding - plant genetic resources - genomes
In 2012 publiceerde Nature de genomische sequentie van de tomaat. Maar daarmee is het werk niet af, zegt Richard Finkers. Hij bepaalde de basenvolgorde van nog eens 150 verwanten van de modeltomaat, om plantenveredelaars in staat te stellen op zoek te gaan naar nieuwe genen in oude rassen.
Weerbaarheid, ook tegen plantenvirussen
Kock, M.J.D. de; Stijger, I. - \ 2013
Vakblad voor de Bloemisterij 68 (2013)10. - ISSN 0042-2223 - p. 30 - 31.
plantenvirussen - plantenziekten - teeltsystemen - diagnostische technieken - bodembacteriën - bodemschimmels - plantengenetica - landbouwkundig onderzoek - vermeerderingsmateriaal - plant viruses - plant diseases - cropping systems - diagnostic techniques - soil bacteria - soil fungi - plant genetics - agricultural research - propagation materials
Virus afbreken, symptomen onderdrukken en infectie voorkomen. Dit zijn de drie strategieën die de weerbaarheid van de plant en het teeltsysteem tegen virussen kunnen verhogen. Soms is het al direct toepasbaar.
Next Generation Plant Breeding
Goud, J.C. - \ 2012
Gewasbescherming 43 (2012)6. - ISSN 0166-6495 - p. 188 - 190.
plantenveredeling - plantenveredelingsmethoden - innovaties - plantengenetica - moleculaire genetica - conferenties - selectiemethoden - resistentieveredeling - plant breeding - plant breeding methods - innovations - plant genetics - molecular genetics - conferences - selection methods - resistance breeding
Van 11-14 november 2012 vond in de Reehorst de conferentie ‘Next Generation Plant Breeding’ plaats. Tijdens deze bijeenkomst kwamen de grote uitdagingen van de toekomstige plantenveredeling aan de orde: de opkomst van nieuwe sequencing-technieken, de bijbehorende enorme hoeveelheid gegevens die geproduceerd wordt, inzicht in de genetica van de plant, de bijbehorende statistische methoden, geautomatiseerde waarneming van planten, en veel meer. Een impressie.
Soil Ecology and Ecosystem Services
Wall, D.H. ; Bardgett, R.D. ; Behan-Pelletier, V. ; Herrick, J.E. ; Jones, T.H. ; Ritz, K. ; Six, J. ; Strong, D.R. ; Putten, W.H. van der - \ 2012
Oxford : Oxford University Press - ISBN 9780199575923 - 406
bodemecologie - bodembiologie - ecosysteemdiensten - agro-ecosystemen - biologische bodemactiviteit - bodemflora - bodembiodiversiteit - plantengenetica - soil ecology - soil biology - ecosystem services - agroecosystems - biological activity in soil - soil flora - soil biodiversity - plant genetics
This book synthesizes contributions from leading soil scientists and ecologists, describing cutting-edge research that provides a basis for the maintenance of soil health and sustainability. It covers these advances from a unique perspective of examining the ecosystem services produced by soil biota across different scales - from biotic interactions at microscales to communities functioning at regional and global scales. The book leads the user towards an understanding of how the sustainability of soils, biodiversity, and ecosystem services can be maintained and how humans, other animals, and ecosystems are dependent on living soils and ecosystem services.
Tomatenveredeling gaat in het vervolg een stuk sneller : alle 35.000 genen in kaart gebracht
Klein Lankhorst, R.M. ; Heuvelink, E. ; Kierkels, T. - \ 2012
Onder Glas 9 (2012)10. - p. 26 - 27.
tomaten - genen - plantengenetica - verworven kenmerken - rassen (planten) - solanum lycopersicum - plantenveredeling - glastuinbouw - groenten - tomatoes - genes - plant genetics - acquired characters - varieties - plant breeding - greenhouse horticulture - vegetables
Tomaat hoort sinds deze zomer tot de top-drie van meest inzichtelijke gewassen. Alle 35.000 genen zijn in kaart gebracht en van 60% is nu bekend welke functie ze hebben. En het inzicht groeit nog dagelijks. Deze kennis is een gouden schat voor veredelaars. Hun werk wordt er gemakkelijker en sneller door.
The genetic and molecular basis of natural variation for plant growth and related traits in Arabidopsis thaliana
Pieper, B. - \ 2009
University. Promotor(en): Maarten Koornneef, co-promotor(en): M. Reymond. - [S.l.] : S.n. - ISBN 9789085854685 - 131
arabidopsis thaliana - moleculaire genetica - groei - loci voor kwantitatief kenmerk - bloei - genetische variatie - genkartering - plantengenetica - molecular genetics - growth - quantitative trait loci - flowering - genetic variation - gene mapping - plant genetics
Plant growth is a complex quantitative trait of which the (eco)physiological aspects have been researched in great detail. In contrast, little is known about the genetic basis and molecular basis of plant growth. Most of what is known today has been discovered by using reverse genetic approaches that target single genes. Forward genetics using naturally occurring variation provides the possibility to investigate genetic effects within the context of the genetic background. This thesis describes the results of a study that aimed at elucidating the genetic basis and the underlying molecular basis of natural genetic variation for plant growth and related traits in Arabidopsis thaliana. A set of over 30 growth related traits has been quantified in two Arabidopsis RIL populations, derived from crosses between the accessions Landsberg erecta (Ler) x Kashmir-2 and Landsberg erecta x Shakdara (Sha) respectively. The projected rosette area (PRA) and Feret diameter of each plant was measured repeatedly during its growth using digital image analysis and. A logistic model and a linear model were fitted to the PRA data for quantification of plant growth rate. The dimensions of the largest rosette leaves, plant hight and chlorophyll content index were measured. Furthermore, flowering time and leaf numbers were recorded. A selection of 15 traits was used to perform a multi-trait QTL analysis using mixed-model methodology. A total 19 QTL were detected of which some art similar locations in both populations. QTL important for flowering time were also found to explain nearly half of the genetic variance for plant growth rate. These QTL mainly mapped to similar locations in both populations indicating a common genetic basis for the affected traits in the studied accessions. However, population specific QTL with no effect on flowering time accounted for the remaining genetic variance explained for plant growth. These QTL were chosen for follow-up studies in order to elucidate the underlying molecular basis. The detected QTL effects were validated in a selected set of near isogenic lines (NILs). These NILs will provide the opportunity to fine-map the QTL in order to identify the genes, and in particular the DNA polymorphisms responsible for these effects. For a single QTL fine-mapping could be advanced efficiently, currently down to 151 genes, due to particularly penetrant effects on plant morphology. QTL that also affected flowering time were not the main interest of these studies because they mapped to positions of genes that were already described for their role in the regulation of this trait. However, although the relation between flowering time and plant growth of such QTL had been described in literature, no distinction between pleiotropy and closely linked QTL could be made so far. A QTL that effected flowering time and plant growth rate, among other traits, located on the bottom end of chromosome 5 has been fine-mapped and cloned using NILs with introgressions of Sha in the genetic background of Ler. Fine-mapping achieved a resolution at which it could be proven that the cluster of MAF2-MAF5 (MADS affecting flowering) genes was underlying the detected QTL effects on flowering time. The effects on plant growth were fine-mapped to a slightly larger region this included an additional 3 genes. Although it was known that these genes affect flowering time, their role in natural variation for this trait had not been directly shown before. Sequence analysis of the cluster showed that Sha carried a fusion consisting of the 5’ portion of MAF2 and the 3’ portion of MAF3. An intact MAF3 gene was not found in this accession. Recently it was shown that such MAF2/MAF3 fusions are relatively common among Arabidopsis accessions but the loss of MAF3 makes Sha unique. Genomic complementation indicated that neither MAF2, MAF3 nor MAF4 can explain the QTL effects by itself. The current hypothesis is therefore that both MAF2 and MAF3 are required in the regulation of flowering time to reconstitute the phenotypical value of Ler in a NIL.
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