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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    Data synthesis for crop variety evaluation. A review
    Brown, David ; Bergh, Inge Van Den; Bruin, Sytze de; Machida, Lewis ; Etten, Jacob van - \ 2020
    Agronomy for Sustainable Development 40 (2020)4. - ISSN 1774-0746
    Crop varieties should fulfill multiple requirements, including agronomic performance and product quality. Variety evaluations depend on data generated from field trials and sensory analyses, performed with different levels of participation from farmers and consumers. Such multi-faceted variety evaluation is expensive and time-consuming; hence, any use of these data should be optimized. Data synthesis can help to take advantage of existing and new data, combining data from different sources and combining it with expert knowledge to produce new information and understanding that supports decision-making. Data synthesis for crop variety evaluation can partly build on extant experiences and methods, but it also requires methodological innovation. We review the elements required to achieve data synthesis for crop variety evaluation, including (1) data types required for crop variety evaluation, (2) main challenges in data management and integration, (3) main global initiatives aiming to solve those challenges, (4) current statistical approaches to combine data for crop variety evaluation and (5) existing data synthesis methods used in evaluation of varieties to combine different datasets from multiple data sources. We conclude that currently available methods have the potential to overcome existing barriers to data synthesis and could set in motion a virtuous cycle that will encourage researchers to share data and collaborate on data-driven research.
    Dierenwelzijn in de kringlooplandbouw startdocument
    Boer, I.J.M. de; Backus, G.B.C. ; Bergh, W.T.A.A.G.M. van den; Erisman, Jan Willem ; Huijbers, J.A.M. ; Kemp, B. - \ 2020
    Den Haag : RDA - 8 p.
    Dierenwelzijn in de kringlooplandbouw samenvatting
    Boer, I.J.M. de; Backus, G.B.C. ; Bergh, W.T.A.A.G.M. van den; Erisman, Jan Willem ; Huijbers, J.A.M. ; Kemp, B. - \ 2020
    Den Haag : RDA - 16 p.
    Dierenwelzijn in de kringlooplandbouw
    Boer, I.J.M. de; Backus, G.B.C. ; Bergh, W.T.A.A.G.M. van den; Erisman, Jan Willem ; Huijbers, J.A.M. ; Kemp, B. - \ 2020
    Den Haag : RDA - 39 p.
    Regulation of endoplasmic reticulum-mitochondria contacts and mitochondrial dynamics by Sel1L-Hrd1 ERAD during thermogenesis
    Zhou, Zhangsen ; Torres, Mauricio ; Sha, Haibo ; Halbrook, Christopher J. ; Bergh, Françoise van den; Reinert, Rachel B. ; Yamada, Tatsuya ; Wang, Siwen ; Luo, Yingying ; Hunter, Allen H. ; Wang, Chunqing ; Sanderson, Thomas H. ; Liu, Meilian ; Taylor, Aaron ; Sesaki, Hiromi ; Lyssiotis, Costas A. ; Wu, Jun ; Kersten, Sander ; Beard, Daniel A. ; Qi, Ling - \ 2020
    Wageningen University
    GSE145895 - PRJNA608688 - Mus musculus
    Organelles such as endoplasmic reticulum (ER) and mitochondria interact with each other at specialized domains on the ER known as mitochondria-associated membranes (MAMs). Here, using three-dimensional high-resolution imaging techniques, we show that the Sel1LHrd1 protein complex, the most conserved branch of ER-associated protein degradation (ERAD), exerts a profound impact on ER-mitochondria contacts and mitochondrial dynamics, at least in part, by regulating the turnover and hence the abundance of the MAM protein sigma receptor 1 (SigmaR1). Sel1L or Hrd1 deficiency in brown adipocytes impairs dynamic interaction between ER and mitochondria, leading to the formation of pleomorphic “megamitochondria” and, in some cases with penetrating ER tubule(s), in response to acute cold challenge. Mice with ERAD deficiency are cold sensitive and exhibit mitochondrial dysfunction in brown adipocytes. Mechanistically, endogenous SigmaR1 is targeted for proteasomal degradation by Sel1L-Hrd1 ERAD, whose accumulation in ERAD-deficient cells leads to mitofusin 2 (Mfn2) oligomerization, thereby linking ERAD to mitochondrial dynamics. Our study identifies Sel1L-Hrd1 ERAD as a critical determinant of ER-mitochondria contacts, thereby regulating mitochondrial dynamics and thermogenesis.
    Endoplasmic reticulum-associated degradation regulates mitochondrial dynamics in brown adipocytes
    Zhou, Zhangsen ; Torres, Mauricio ; Sha, Haibo ; Halbrook, Christopher J. ; Bergh, Françoise van den; Reinert, Rachel B. ; Yamada, Tatsuya ; Wang, Siwen ; Luo, Yingying ; Hunter, Allen H. ; Wang, Chunqing ; Sanderson, Thomas H. ; Liu, Meilian ; Taylor, Aaron ; Sesaki, Hiromi ; Lyssiotis, Costas A. ; Wu, Jun ; Kersten, Sander ; Beard, Daniel A. ; Qi, Ling - \ 2020
    Science 368 (2020)6486. - ISSN 0036-8075 - p. 54 - 60.

    The endoplasmic reticulum (ER) engages mitochondria at specialized ER domains known as mitochondria-associated membranes (MAMs). Here, we used three-dimensional high-resolution imaging to investigate the formation of pleomorphic “megamitochondria” with altered MAMs in brown adipocytes lacking the Sel1L-Hrd1 protein complex of ER-associated protein degradation (ERAD). Mice with ERAD deficiency in brown adipocytes were cold sensitive and exhibited mitochondrial dysfunction. ERAD deficiency affected ER-mitochondria contacts and mitochondrial dynamics, at least in part, by regulating the turnover of the MAM protein, sigma receptor 1 (SigmaR1). Thus, our study provides molecular insights into ER-mitochondrial cross-talk and expands our understanding of the physiological importance of Sel1L-Hrd1 ERAD.

    Social dimensions of fertility behavior and consumption patterns in the Anthropocene
    Barrett, Scott ; Dasgupta, Aisha ; Dasgupta, Partha ; Neil Adger, W. ; Anderies, John ; Bergh, Jeroen van den; Bledsoe, Caroline ; Bongaarts, John ; Carpenter, Stephen ; Stuart Chapin, F. ; Crépin, Anne Sophie ; Daily, Gretchen ; Ehrlich, Paul ; Folke, Carl ; Kautsky, Nils ; Lambin, Eric F. ; Levin, Simon A. ; Mäler, Karl Göran ; Naylor, Rosamond ; Nyborg, Karine ; Polasky, Stephen ; Scheffer, Marten ; Shogren, Jason ; Jørgensen, Peter Søgaard ; Walker, Brian ; Wilen, James - \ 2020
    Proceedings of the National Academy of Sciences of the United States of America 117 (2020)12. - ISSN 0027-8424 - p. 6300 - 6307.
    Consumption - Fertility - Socially embedded preferences

    We consider two aspects of the human enterprise that profoundly affect the global environment: population and consumption. We show that fertility and consumption behavior harbor a class of externalities that have not been much noted in the literature. Both are driven in part by attitudes and preferences that are not egoistic but socially embedded; that is, each household's decisions are influenced by the decisions made by others. In a famous paper, Garrett Hardin [G. Hardin, Science 162, 1243-1248 (1968)] drew attention to overpopulation and concluded that the solution lay in people “abandoning the freedom to breed.” That human attitudes and practices are socially embedded suggests that it is possible for people to reduce their fertility rates and consumption demands without experiencing a loss in wellbeing. We focus on fertility in sub-Saharan Africa and consumption in the rich world and argue that bottom-up social mechanisms rather than top-down government interventions are better placed to bring about those ecologically desirable changes.

    Genome Improvement and Genetic Map Construction for Aethionema arabicum, the First Divergent Branch in the Brassicaceae Family.
    Nguyen, T.P. ; Mülich, Cornelia ; Mohammadin, Setareh ; Bergh, E. van den; Platts, A.E. ; Haas, Fabian B. ; Rensing, Stefan A. ; Schranz, M.E. - \ 2019
    Genes, Genomes and Genomics 9 (2019)11. - ISSN 1749-0383 - p. 3521 - 3530.
    The genus Aethionema is a sister-group to the core-group of the Brassicaceae family that includes Arabidopsis thaliana and the Brassica crops. Thus, Aethionema is phylogenetically well-placed for the investigation and understanding of genome and trait evolution across the family. We aimed to improve the quality of the reference genome draft version of the annual species Aethionema arabicum. Second, we constructed the first Ae. arabicum genetic map. The improved reference genome and genetic map enabled the development of each other. We started with the initially published genome (version 2.5). PacBio and MinION sequencing together with genetic map v2.5 were incorporated to produce the new reference genome v3.0. The improved genome contains 203 MB of sequence, with approximately 94% of the assembly made up of called (non-gap) bases, assembled into 2,883 scaffolds (with only 6% of the genome made up of non-called bases (Ns)). The N50 (10.3 MB) represents an 80-fold increase over the initial genome release. We generated a Recombinant Inbred Line (RIL) population that was derived from two ecotypes: Cyprus and Turkey (the reference genotype. Using a Genotyping by Sequencing (GBS) approach, we generated a high-density genetic map with 749 (v2.5) and then 632 SNPs (v3.0) was generated. The genetic map and reference genome were integrated, thus greatly improving the scaffolding of the reference genome into 11 linkage groups. We show that long-read sequencing data and genetics are complementary, resulting in an improved genome assembly in Ae. arabicum. They will facilitate comparative genetic mapping work for the Brassicaceae family and are also valuable resources to investigate wide range of life history traits in Aethionema.
    Decline in AmpC β-lactamase-producing escherichia coli in a Dutch teaching hospital (2013-2016)
    Drijver, Evert den; Verweij, Jaco J. ; Verhulst, Carlo ; Oome, Stijn ; Soer, Joke ; Willemsen, Ina ; Schrauwen, Eefje J.A. ; Kluytmans-van den Bergh, Marjolein F.Q. ; Kluytmans, Jan A.J.W. - \ 2018
    PLoS ONE 13 (2018)10. - ISSN 1932-6203

    Objective The objective of this study is to determine the prevalence of rectal carriage of plasmid- and chromosome-encoded AmpC β-lactamase-producing Escherichia coli and Klebsiella spp. in patients in a Dutch teaching hospital between 2013 and 2016. Methods Between 2013 and 2016, hospital-wide yearly prevalence surveys were performed to determine the prevalence of AmpC β-lactamase-producing E. coli and Klebsiella spp. rectal carriage. Rectal swabs were taken and cultured using an enrichment broth and selective agar plates. All E. coli and Klebsiella spp. isolates were screened for production of AmpC β-lactamase using phenotypic confirmation tests and for the presence of plasmid-encoded AmpC (pAmpC) genes. E. coli isolates were screened for chromosome-encoded AmpC (cAmpC) promoter/attenuator alterations. Results Fifty (2.4%) of 2,126 evaluable patients were identified as rectal carrier of AmpC β-lactamase- producing E. coli. No carriage of AmpC β-lactamase producing Klebsiella spp. was found. Nineteen (0.9%) patients harboured isolates with pAmpC genes and 30 (1,4%) patients harboured isolates with cAmpC promoter/attenuator alterations associated with AmpC β-lactamase overproduction. For one isolate, no pAmpC genes or cAmpC promotor/ attenuator alterations could be identified. During the study period, a statistically significant decline in the prevalence of rectal carriage with E. coli with cAmpC promotor/attenuator alterations was found (p = 0.012). The prevalence of pAmpC remained stable over the years. Conclusions The prevalence of rectal carriage of AmpC-producing E. coli and Klebsiella spp. in patients in Dutch hospitals is low and a declining trend was observed for E. coli with cAmpC promotor/ attenuator alterations.

    Developing an infrastructure to collect methane data from multiple farms
    Bergh, E. van den; Haas, Y. de; Kamphuis, C. - \ 2018
    A flexible data architecture to automate collection of (near) real-time methane sensor data at commercial dairy farms
    Kamphuis, C. ; Haas, Y. de; Bergh, E. van den - \ 2018
    - 1 p.
    Wageningen Data Exchange Service
    Bergh, E. van den; Janssen, H. ; Ringersma, J. ; Knibbe, Willem Jan - \ 2018
    Data Management Service at Wageningen University
    Bergh, E. van den; Ringersma, J. ; Knibbe, Willem Jan - \ 2018
    - 1 p.
    Xanthomonas Wilt of Banana (BXW) in Central Africa : Opportunities, challenges, and pathways for citizen science and ICT-based control and prevention strategies
    McCampbell, Mariette ; Schut, Marc ; Bergh, Inge Van den; Schagen, Boudy van; Vanlauwe, Bernard ; Blomme, Guy ; Gaidashova, Svetlana ; Njukwe, Emmanuel ; Leeuwis, Cees - \ 2018
    NJAS Wageningen Journal of Life Sciences 86-87 (2018). - ISSN 1573-5214 - p. 89 - 100.
    Agricultural transformation - Banana wilt disease - Digital innovation - Environmental monitoring - ICT4Ag - Systems analysis
    Xanthomonas Wilt of Banana (BXW) is a complex problem in the African Great Lakes Region that is affecting the livelihoods of millions of smallholder farmers. Since the first disease reports from Uganda and the Democratic Republic of Congo in 2001, BXW has been studied widely. The majority of these studies focus on the technological or biophysical dimensions, while aspects and influence of socio-cultural, economic and institutional dimensions only recently started to gain attention. This paper provides an in-depth analysis of the broader BXW problem using a systems perspective, with the aim to add to the understanding about reasons for poor uptake of appropriate disease management practices, and limited ability to prevent rather than control BXW in the region. We comprehensively describe and analyse the various problem dimensions, and determine relations with data, information, knowledge, and connectivity. Building on this, the paper explores and discusses entry-points for the use of Information and Communication Technologies (ICT) and citizen science tools to better address BXW in banana production systems.
    Agroecological integration of shade- and drought-tolerant food/feed crops for year-round productivity in banana-based systems under rain-fed conditions in Central Africa
    Blomme, G. ; Ocimati, W. ; Groot, J.C.J. ; Ntamwira, J. ; Bahati, L. ; Kantungeko, D. ; Remans, R. ; Tittonell, P. - \ 2018
    In: 10th International Symposium on Banana. - International Society for Horticultural Science (Acta Horticulturae ) - ISBN 9789462611924 - p. 41 - 54.
    Intensification - Resilience - Small-scale farming - Year-round productivity - Yield gaps
    Yield gaps in banana-based production systems have increased in the past two decades due to declining soil fertility, drought and biotic stresses. Sustainable, environmentally sound and economically viable strategies for intensification in these systems are urgently needed. Agroecological practices, such as the integration of shade- and drought-tolerant crops, nitrogen-fixing and cover crops could potentially improve soil fertility and moisture retention, reduce the weed burden, narrow yield gaps and increase overall plot/farm productivity in these systems. In Malaysia, leguminous crops like Pueraria phaseoloides, Calopogonium caeruleum and Centrosema pubescens are often cultivated as cover crops (to suppress weeds, and reduce moisture loss and soil erosion) in young rubber and oil palm plantations with low shade levels. Even in mature oil palm plantations with less than 30% light intensity, various shade-tolerant crops are grown, e.g., elephant foot yam, turmeric and arrow root. In humid tropical Africa, Colocasia (taro) and Xanthosoma (cocoyam) are reported to tolerate shade conditions and hence often planted under perennial banana/plantain plantations. Drought tolerance is a less common feature of most annual crops grown in the humid tropics. A few root and tuber crops (e.g., cassava, taro, yam and sweetpotato) remain in the field during the dry season in Central Africa and are then harvested according to household needs. This paper also reports on crops (Mucuna, lablab and chickpea) with potential for integration into banana-based systems during the dry season, if planted during the last month of the rainy season. These crops are reported to use the residual soil moisture content for continued growth during the dry season months. The paper concludes with detailed descriptions (from a literature review) on drought- and shade-tolerance characteristics of various crops which have long been integrated in Central African banana-based cropping systems, crops with a more recent cultivation history and crops with potential for system integration.
    Managing the interactions between soil abiotic factors to alleviate the effect of Fusarium wilt in bananas
    Segura, R.A. ; Stoorvogel, J.J. ; Samuels, J.Z. ; Sandoval, J.A. - \ 2018
    In: 10th International Symposium on Banana. - International Society for Horticultural Science (Acta Horticulturae ) - ISBN 9789462611924 - p. 163 - 168.
    Biomass - Micronutrients - Panama disease - Plant disease - Soil fertility
    Soil management offers various options to alleviate the effects of Fusarium wilt caused by Fusarium oxysporum f. sp. cubense (Foc) in bananas. Nevertheless, it receives little attention as a strategy in Fusarium wilt management. Literature provides ample evidence linking soil conditions such as soil texture and fertility to the spread and severity of plant diseases. However, the inconsistency of results between case studies limits the attention of soil management in crop disease management. The present study aimed at unravelling the role of soil abiotic factors on nutrient concentrations in plant tissue, biomass production and the incidence of Fusarium wilt (Foc race 1) in bananas (‘Gros Michel’, AAA) under field conditions. A large field trial was established in which the effects of soil pH and nutrients (N, Ca, Mg and Mn) were studied. Around 30% of the plants showed symptoms of Fusarium wilt at flowering in the first season. However, Fusarium wilt incidence did not vary between treatments. Soil pH showed significant interactions with soil N and Mn concentrations resulting in a lower bunch weight and increased micronutrient concentrations in the pseudostem. With a higher pH, bunch weight increased, although higher Mn concentrations suppressed this positive effect. Interactions between a high soil pH and Ca and Mg resulted in a higher bunch weight and lower micronutrient concentrations in the pseudostem. The results can be used to develop soil management strategies for improving banana productivity in infected plantations.
    Effects of Xanthomonas wilt and other banana diseases on ecosystem services in banana-based agroecosystems
    Ocimati, W. ; Groot, J.C.J. ; Tittonell, P. ; Taulya, G. ; Blomme, G. - \ 2018
    In: 10th International Symposium on Banana. - International Society for Horticultural Science (Acta Horticulturae ) - ISBN 9789462611924 - p. 19 - 32.
    Drought tolerance - Landscape - Multiple functions - Provisioning - Regulatory - Shade tolerance - Supporting
    Banana plantations are multifunctional agroecosystems that besides their main provisioning service also deliver a range of supporting, regulatory and cultural services that are largely unvalorized. Banana is perennial in nature with plantations as old as 50 years reported in the African Great Lakes region. Banana is cultivated in a wide range of agroecologies (from sea level to 2400 m a.s.l.) and cropping systems, where it contributes to various ecosystem services (ES). These include regulating soil erosion, water cycles and quality, and nutrient recycling. However, the outbreak of Xanthomonas wilt of banana (XW) along with some of its management practices, such as uprooting mats/entire fields, is devastating banana production and rendering landscapes bare and prone to degradation. Yet this process is also leading to diversification of agroecosystems in over 70% of farms in the African Great Lakes region with unknown but potentially positive consequences for resilience and adaptation, as well as for local diets. The sustainability of these alternative land-uses is variable. This study reviews the different services offered by banana plantations and the impacts, positive or negative, that XW-driven diversification may have on these services. It suggests the need to consider explicitly the consequences of pests and diseases for the full range of ES provided by the crop and an ES-broad framework for estimation of losses, and planning resources and strategies for disease management. The study also suggests strategies, such as incorporation of shade- and drought-tolerant cover crops, hedges and agroforestry trees, to augment the supply of key ES within XW-affected agroecosystems/landscapes.
    CorNet: Assigning function to networks of co-evolving residues by automated literature mining
    Bergh, Tom Van Den; Tamo, Giorgio ; Nobili, Alberto ; Tao, Yifeng ; Tan, Tianwei ; Bornscheuer, Uwe T. ; Kuipers, Remko K.P. ; Vroling, Bas ; Jong, René M. De; Subramanian, Kalyanasundaram ; Schaap, Peter J. ; Desmet, Tom ; Nidetzky, Bernd ; Vriend, Gert ; Joosten, Henk-Jan - \ 2017
    PLoS ONE 12 (2017)5. - ISSN 1932-6203 - p. e0176427 - e0176427.
    CorNet is a web-based tool for the analysis of co-evolving residue positions in protein super-family sequence alignments. CorNet projects external information such as mutation data extracted from literature on interactively displayed groups of co-evolving residue positions to shed light on the functions associated with these groups and the residues in them. We used CorNet to analyse six enzyme super-families and found that groups of strongly co-evolving residues tend to consist of residues involved in a same function such as activity, specificity, co-factor binding, or enantioselectivity. This finding allows to assign a function to residues for which no data is available yet in the literature. A mutant library was designed to mutate residues observed in a group of co-evolving residues predicted to be involved in enantioselectivity, but for which no literature data is available yet. The resulting set of mutations indeed showed many instances of increased enantioselectivity.
    Comparative genomics and trait evolution in Cleomaceae, a model family for ancient polyploidy
    Bergh, Erik van den - \ 2017
    Wageningen University. Promotor(en): M.E. Schranz; Y. van de Peer. - Wageningen : Wageningen University - ISBN 9789463431705 - 106
    capparaceae - genomics - polyploidy - evolution - genomes - reproductive traits - flowers - colour - glucosinolates - genetic variation - biosystematics - taxonomy - identification - capparaceae - genomica - polyploïdie - evolutie - genomen - voortplantingskenmerken - bloemen - kleur - glucosinolaten - genetische variatie - biosystematiek - taxonomie - identificatie

    As more and more species have been sequenced, evidence has been piling up for a fascinating phenomenon that seems to occur in all plant lineages: paleopolyploidy. Polyploidy has historically been a much observed and studied trait, but until recently it was assumed that polyploids were evolutionary dead-ends due to their sterility. However, many studies since the 1990’s have challenged this notion by finding evidence for ancient genome duplications in many genomes of current species. This lead to the observation that all seed plants share at least one ancestral polyploidy event. Another polyploidy event has been proven to lie at the base of all angiosperms, further signifying the notion that ancient polyploidy is widespread and common. These findings have led to questions regarding the apparent disadvantages that can be observed in a first generation polyploid. If these disadvantages can be overcome however, duplication of a genome also presents an enormous potential for evolutionary novelty. Duplicated copies of genes are able to acquire changes that can lead to specialization of the duplicated pair into two functions (subfunctionalization) or the development of one copy towards an entirely new function (neofunctionalization).

    Currently, most research towards polyploidy has focused on the economically and scientifically important Brassicaceae family containing the model plant Arabidopsis thaliana and many crops such as cabbage, rapeseed, broccoli and turnip. In this thesis, I lay the foundations for the expansion of this scope to the Cleomaceae, a widespread cosmopolitan plant family and a sister family of Brassicaceae. The species within Cleomaceae are diverse and exhibit many scientifically interesting traits. They are also in a perfect position phylogenetically to draw comparisons with the much more studied Brassicaceae. I describe the Cleomaceae and their relevance to polyploid research in more detail in the Introduction. I then describe the important first step towards setting up the genetic framework of this family with the sequencing of Tarenaya hassleriana in Chapter 1.

    In Chapter 2, I have studied the effects of polyploidy on the development of C4 photosynthesis by comparing the transcriptome of C3 photosynthesis based species Tarenaya hassleriana with the C4 based Gynandropsis gynandra. C4 photosynthesis is an elaboration of the more common C3 form of photosynthesis that concentrates CO2 in specific cells leading to decreased photorespiration by the RuBisCO and higher photosynthetic efficieny in low CO2 environments. I find that polyploidy has not led to sub- or neofunctionalization towards the development of this trait, but instead find evidence for another important phenomenon in postpolyploid evolution: the dosage balance hypothesis. This hypothesis states that genes which are dependent on specific dosage levels of their products will be maintained in duplicate; any change in their function would lead to dosage imbalance which would have deleterious effects on their pathway. We show that most genes involved in photosynthesis have returned to single copy in G. gynandra and that the changes leading to C4 have mostly taken place at the expression level confirming current assumptions on the development of this trait.

    In Chapter 3, I have studied the effects of polyploidy on an important class of plant defence compounds: glucosinolates. These compounds, sometimes referred to as ‘mustard oils’, play an important role in the defence against herbivores and have radiated widely in Brassicaceae to form many different ‘flavors’ to deter specific herbivores. I show that in Cleomaceae many genes responsible for these compounds have benefited from the three rounds of polyploidy that T. hassleriana has undergone and that many duplicated genes have been retained. We also show that more than 75% is actively expressed in the plant, proving that the majority of these duplications has an active function in the plant.

    Finally, in Chapter 4 I investigate a simple observation made during experiments with T. hassleriana in the greenhouse regarding the variation in flower colour between different individuals: some had pink flowers and some purple. Using LC-PDA mass spectrometry we find that the two colours are caused by different levels of two anthocyanin pigments, with cyanidin dominating in the purple flowers and pelargonidin being more abundant in pink flowers. Through sequence comparison and synteny analysis between A. thaliana and T. hassleriana we find the orthologs of the genes involved in this pathway. Using a Genotyping by Sequencing method on a cross between these two flower colours, we produce a collection of SNP markers on the reference genome. With these SNPs, we find two significant binary trait loci, one of which corresponds to the location of the F3’H ortholog which performs the conversion of a pelargonidin precursor to a cyanidin precursor.

    In the General Conclusion, I combine all findings of the previous chapters and explain how they establish part of a larger species framework to study ancient polyploidy in angiosperms. I then put forth what these findings can mean for possible future research and the directions that are worth to be explored further.

    Over kavelgrenzen. Het geslaagde verzet tegen de ruilverkaveling Arkemheen
    Cruijningen, P.J. van - \ 2016
    In: Gelderland grensland / Verhoeven, Dolly, Wingens, Marc, Bergh, van den, Simon, Gubbels, Maarten, Vantilt - ISBN 9789460043000 - p. 210 - 219.
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