Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    The Genomics of Cannabis and Its Close Relatives
    Kovalchuk, I. ; Pellino, M. ; Rigault, P. ; Velzen, R. Van; Ebersbach, J. ; Ashnest, J.R. ; Mau, M. ; Schranz, M.E. ; Alcorn, J. ; Laprairie, R.B. ; McKay, J.K. ; Burbridge, C. ; Schneider, D. ; Vergara, D. ; Kane, N.C. ; Sharbel, T.F. - \ 2020
    Annual Review of Plant Biology 71 (2020). - ISSN 1543-5008 - p. 713 - 739.
    biosynthesis pathway evolution - Cannabaceae - Cannabis sativa L. - genomics - hemp - hops - Humulus lupulus - proteomics - Y chromosome

    Cannabis sativa L. is an important yet controversial plant with a long history of recreational, medicinal, industrial, and agricultural use, and together with its sister genus Humulus, it represents a group of plants with a myriad of academic, agricultural, pharmaceutical, industrial, and social interests. We have performed a meta-analysis of pooled published genomics data, andwe present a comprehensive literature review on the evolutionary history of Cannabis and Humulus, including medicinal and industrial applications. We demonstrate that current Cannabis genome assemblies are incomplete, with sim10% missing, 10-25% unmapped, and 45S and 5S ribosomal DNA clusters as well as centromeres/satellite sequences not represented. These assemblies are also ordered at a low resolution, and their consensus quality clouds the accurate annotation of complete, partial, and pseudogenized gene copies. Considering the importance of genomics in the development of any crop, this analysis underlines the need for a coordinated effort to quantify the genetic and biochemical diversity of this species.

    Genomics of Rapid Evolution in Field Crickets
    Pascoal, Sonia ; Risse, Judith ; Zhang, Xiao ; Blaxter, Mark ; Cezard, Timothee ; Challis, Richard J. ; Gharbi, Karim ; Hunt, John ; Kumar, Sujai ; Langan, Emma ; Liu, Xuan ; Rayner, Jack G. ; Ritchie, Michael G. ; Snoek, Basten ; Trivedi, Urmi ; Bailey, Nathan W. - \ 2020
    University of Edinburgh
    PRJEB24786 - ERP106639 - Teleogryllus oceanicus - cricket - genomics
    This study reveals the genomic architecture of a rapidly evolving mutation which segregates as a single-locus, X-linked trait -- flatwing -- in wild Hawaiian field crickets (Teleogryllus oceanicus). Flatwingsilences males by eliminating sound-producing structures on their forewings. Silence protects them from an acoustically-orienting parasitoid fly (Ormia ochracea), but interferes with their ability to attract and court females for mating. Silent crickets spread rapidly on several Hawaiian islands under pressure from the flies, representing one of the fastest rates of evoutionary change documented in the wild. Here we present an annotated genome sequence of T. oceanicus along with a linkage map and QTL analysis of the trait derived from RAD-sequencing of a backcrossed mapping population. RNA-seq was used to probe the functional pathways affected by the mutation during early development, and pleiotropic effects on another signaling trait, cuticular hydrocarbons, were assessed and genetically mapped.
    Convergent Evolution of Hydrogenosomes from Mitochondria by Gene Transfer and Loss
    Lewis, William H. ; Lind, Anders E. ; Sendra, Kacper M. ; Onsbring, Henning ; Williams, Tom A. ; Esteban, Genoveva F. ; Hirt, Robert P. ; Ettema, Thijs J.G. ; Embley, T.M. - \ 2020
    Molecular Biology and Evolution 37 (2020)2. - ISSN 0737-4038 - p. 524 - 539.
    anaerobic metabolism - evolution - genomics - hydrogenosomes - microbial eukaryotes - mitochondria

    Hydrogenosomes are H2-producing mitochondrial homologs found in some anaerobic microbial eukaryotes that provide a rare intracellular niche for H2-utilizing endosymbiotic archaea. Among ciliates, anaerobic and aerobic lineages are interspersed, demonstrating that the switch to an anaerobic lifestyle with hydrogenosomes has occurred repeatedly and independently. To investigate the molecular details of this transition, we generated genomic and transcriptomic data sets from anaerobic ciliates representing three distinct lineages. Our data demonstrate that hydrogenosomes have evolved from ancestral mitochondria in each case and reveal different degrees of independent mitochondrial genome and proteome reductive evolution, including the first example of complete mitochondrial genome loss in ciliates. Intriguingly, the FeFe-hydrogenase used for generating H2 has a unique domain structure among eukaryotes and appears to have been present, potentially through a single lateral gene transfer from an unknown donor, in the common aerobic ancestor of all three lineages. The early acquisition and retention of FeFe-hydrogenase helps to explain the facility whereby mitochondrial function can be so radically modified within this diverse and ecologically important group of microbial eukaryotes.

    Invasion biology, ecology, and management of western flower thrips
    Reitz, Stuart R. ; Gao, Yulin ; Kirk, William D.J. ; Hoddle, Mark S. ; Leiss, Kirsten A. ; Funderburk, Joe E. - \ 2020
    Annual Review of Entomology 65 (2020). - ISSN 0066-4170 - p. 17 - 37.
    cryptic species - genomics - integrated pest management (IPM) - invasive alien species - Orthotospovirus - Thysanoptera

    Western flower thrips, Frankliniella occidentalis, first arose as an important invasive pest of many crops during the 1970s-1980s. The tremendous growth in international agricultural trade that developed then fostered the invasiveness of western flower thrips. We examine current knowledge regarding the biology of western flower thrips, with an emphasis on characteristics that contribute to its invasiveness and pest status. Efforts to control this pest and the tospoviruses that it vectors with intensive insecticide applications have been unsuccessful and have created significant problems because of the development of resistance to numerous insecticides and associated outbreaks of secondary pests. We synthesize information on effective integrated management approaches for western flower thrips that have developed through research on its biology, behavior, and ecology. We further highlight emerging topics regarding the species status of western flower thrips, as well as its genetics, biology, and ecology that facilitate its use as a model study organism and will guide development of appropriate management practices.

    Data from: Combinations of Spok genes create multiple meiotic drivers in Podospora
    Vogan, Aaron A. ; Ament-Velásquez, S.L. ; Granger-Farbos, Alexandra ; Svedberg, Jesper ; Bastiaans, Eric ; Debets, Fons ; Coustou, Virginie ; Yvanne, Hélène ; Clavé, Corinne ; Saupe, Sven J. ; Johannesson, Hanna - \ 2019
    Dryad
    podospora anserina - meiotic drive - genomics - gene drive - Podospora pauciseta - Spore-killing - Spok - genomic conflict
    Meiotic drive is the preferential transmission of a particular allele during sexual reproduction. The phenomenon is observed as spore killing in multiple fungi. In natural populations of Podospora anserina, seven spore killer types (Psks) have been identified through classical genetic analyses. Here we show that the Spok gene-family underlies the Psks. The combination of Spok genes at different chromosomal locations defines the spore killer types and creates a killing hierarchy within the same population. We identify two novel Spok homologs located within a large (74-167 kbp) region (the Spok block) that resides in different chromosomal locations in given strains. We confirm that the SPOK protein performs both killing and resistance functions and show that these activities are dependent on distinct domains, a predicted nuclease and kinase domain. Genomic and phylogenetic analyses across ascomycetes suggest that the Spok genes disperse via cross-species transfer, and evolve by duplication and diversification within lineages.
    The Nesidiocoris tenuis genome manuscript supporting data
    Pannebakker, Bart ; Ferguson, Kimberley - \ 2019
    Wageningen University & Research
    genome - biocontrol - biological control - insect - mirid - Nesidiocoris tenuis - genomics - genome assembly
    In presenting the first mirid genome, Nesidiocoris tenuis, several supporting information is made available. Following the main supplemetary material document (link), the contents are in this database: S1.2. Flow cytometry data for N. tenuis S1.3. Decontamination and potential LGT indentification S1.4. Gene list (UniProtKB list) and DAVID Reports S1.5. Full protein set S1.7. Poolseq results in full
    Distinct genomic signals of lifespan and life history evolution in response to postponed reproduction and larval diet in Drosophila
    Hoedjes, Katja M. ; Heuvel, Joost Van Den; Kapun, Martin ; Flatt, Thomas ; Zwaan, Bas - \ 2019
    University of Lausanne
    Evolution of ageing - Life History Evolution - genomics - Experimental evolution
    Reproduction and diet are two major factors controlling the physiology of aging and life history, but how they interact to affect the evolution of longevity is unknown. Moreover, while studies of large-effect mutants suggest an important role of nutrient sensing pathways in regulating aging, the genetic basis of evolutionary changes in lifespan remains poorly understood. To address these questions, we analyzed the genomes of experimentally evolved Drosophila melanogaster populations subjected to a factorial combination of two selection regimes: reproductive age (early versus postponed), and diet during the larval stage (‘low’, ‘control’, ‘high’), resulting in six treatment combinations with four replicate populations each. Selection on reproductive age consistently affected lifespan, with flies from the postponed reproduction regime having evolved a longer lifespan. In contrast, larval diet affected lifespan only in early-reproducing populations: flies adapted to the ‘low’ diet lived longer than those adapted to control diet. Here we find genomic evidence for strong independent evolutionary responses to either selection regime, as well as loci that diverged in response to both regimes, thus representing genomic interactions between the two. Overall, we find that the genomic basis of longevity is largely independent of dietary adaptation. Differentiated loci were not enriched for ‘canonical’ longevity genes, suggesting that naturally occurring genic targets of selection for longevity differ qualitatively from variants found in mutant screens. Comparing our candidate loci to those from other ‘evolve-and-resequence’ studies of longevity demonstrated significant overlap among independent experiments. This suggests that the evolution of longevity, despite its presumed complex and polygenic nature, might be to some extent convergent and predictable.
    Identification of Loci Associated with Enhanced Virulence in Spodoptera litura Nucleopolyhedrovirus Isolates Using Deep Sequencing
    Zwart, Mark P. ; Ali, Ghulam ; Strien, Elisabeth A. van; Schijlen, Elio G.W.M. ; Wang, Manli ; Werf, Wopke van der; Vlak, Just M. - \ 2019
    Viruses 11 (2019)9. - ISSN 1999-4915
    deep sequencing - genomics - Illumina - SpltNPV - Spodoptera litura nucleopolyhedrovirus - virulence

    Spodoptera litura is an emerging pest insect in cotton and arable crops in Central Asia. To explore the possibility of using baculoviruses as biological control agents instead of chemical pesticides, in a previous study we characterized a number of S. litura nucleopolyhedrovirus (SpltNPV) isolates from Pakistan. We found significant differences in speed of kill, an important property of a biological control agent. Here we set out to understand the genetic basis of these differences in speed of kill, by comparing the genome of the fast-killing SpltNPV-Pak-TAX1 isolate with that of the slow-killing SpltNPV-Pak-BNG isolate. These two isolates and the SpltNPV-G2 reference strain from China were deep sequenced with Illumina. As expected, the two Pakistani isolates were closely related with >99% sequence identity, whereas the Chinese isolate was more distantly related. We identified two loci that may be associated with the fast action of the SpltNPV-Pak-TAX1 isolate. First, an analysis of rates of synonymous and non-synonymous mutations identified neutral to positive selection on open reading frame (ORF) 122, encoding a viral fibroblast growth factor (vFGF) that is known to affect virulence in other baculoviruses. Second, the homologous repeat region hr17, a putative enhancer of transcription and origin of replication, is absent in SpltNPV-Pak-TAX1 suggesting it may also affect virulence. Additionally, we found there is little genetic variation within both Pakistani isolates, and we identified four genes under positive selection in both isolates that may have played a role in adaptation of SpltNPV to conditions in Central Asia. Our results contribute to the understanding of the enhanced activity of SpltNPV-Pak-TAX1, and may help to select better SpltNPV isolates for the control of S. litura in Pakistan and elsewhere.

    Combinations of Spok genes create multiple meiotic drivers in Podospora
    Vogan, Aaron A. ; Ament-Velásquez, S.L. ; Granger-Farbos, Alexandra ; Svedberg, Jesper ; Bastiaans, Eric ; Debets, Alfons J.M. ; Coustou, Virginie ; Yvanne, Hélène ; Clavé, Corinne ; Saupe, Sven J. ; Johannesson, Hanna - \ 2019
    eLife 8 (2019). - ISSN 2050-084X
    evolutionary biology - fungi - gene drive - genetics - genomic conflict - genomics - Podospora - selfish genetic element - spore killer

    Meiotic drive is the preferential transmission of a particular allele during sexual reproduction. The phenomenon is observed as spore killing in multiple fungi. In natural populations of Podospora anserina, seven spore killer types (Psks) have been identified through classical genetic analyses. Here we show that the Spok gene family underlies the Psks. The combination of Spok genes at different chromosomal locations defines the spore killer types and creates a killing hierarchy within a population. We identify two novel Spok homologs located within a large (74-167 kbp) region (the Spok block) that resides in different chromosomal locations in different strains. We confirm that the SPOK protein performs both killing and resistance functions and show that these activities are dependent on distinct domains, a predicted nuclease and kinase domain. Genomic and phylogenetic analyses across ascomycetes suggest that the Spok genes disperse through cross-species transfer, and evolve by duplication and diversification within lineages.

    Accelerating Climate Resilient Plant Breeding by Applying Next-Generation Artificial Intelligence
    Harfouche, Antoine L. ; Jacobson, Daniel A. ; Kainer, David ; Romero, Jonathon C. ; Harfouche, Antoine H. ; Scarascia Mugnozza, Giuseppe ; Moshelion, Menachem ; Tuskan, Gerald A. ; Keurentjes, Joost J.B. ; Altman, Arie - \ 2019
    Trends in Biotechnology 37 (2019)11. - ISSN 0167-7799 - p. 1217 - 1235.
    augmented breeding - explainable AI - field phenomics - genomics - next-generation artificial intelligence - smart farming

    Breeding crops for high yield and superior adaptability to new and variable climates is imperative to ensure continued food security, biomass production, and ecosystem services. Advances in genomics and phenomics are delivering insights into the complex biological mechanisms that underlie plant functions in response to environmental perturbations. However, linking genotype to phenotype remains a huge challenge and is hampering the optimal application of high-throughput genomics and phenomics to advanced breeding. Critical to success is the need to assimilate large amounts of data into biologically meaningful interpretations. Here, we present the current state of genomics and field phenomics, explore emerging approaches and challenges for multiomics big data integration by means of next-generation (Next-Gen) artificial intelligence (AI), and propose a workable path to improvement.

    In silico prediction and characterisation of secondary metabolite clusters in the plant pathogenic fungus Verticillium dahliae
    Shi-Kunne, Xiaoqian ; Pedro Jové, Roger de; Depotter, Jasper R.L. ; Ebert, Malaika K. ; Seidl, Michael F. ; Thomma, Bart P.H.J. - \ 2019
    FEMS Microbiology Letters 366 (2019)7. - ISSN 0378-1097
    fungi - genomics - natural product - pathogen - Verticillium

    Fungi are renowned producers of natural compounds, also known as secondary metabolites (SMs) that display a wide array of biological activities. Typically, the genes that are involved in the biosynthesis of SMs are located in close proximity to each other in so-called secondary metabolite clusters. Many plant-pathogenic fungi secrete SMs during infection in order to promote disease establishment, for instance as cytocoxic compounds. Verticillium dahliae is a notorious plant pathogen that can infect over 200 host plants worldwide. However, the SM repertoire of this vascular pathogen remains mostly uncharted. To unravel the potential of V. dahliae to produce SMs, we performed in silico predictions and in-depth analyses of its secondary metabolite clusters. Using distinctive traits of gene clusters and the conserved signatures of core genes 25 potential SM gene clusters were identified. Subsequently, phylogenetic and comparative genomics analyses were performed, revealing that two putative siderophores, ferricrocin and TAFC, DHN-melanin and fujikurin may belong to the SM repertoire of V. dahliae.

    The elephant in the room: How a technology’s name affects its interpretation
    Boersma, Reginald ; Poortvliet, P.M. ; Gremmen, Bart - \ 2019
    Public Understanding of Science 28 (2019)2. - ISSN 0963-6625 - p. 218 - 233.
    attitudes - genomics - learning - nanotechnology - public education

    In this work, using experiments, we investigate the role of the name of a technology on the informed evaluation of that technology. We argue that a name can influence interpretations by activating cognitive structures. Using genomics-accelerated breeding as a case, we show that the name ‘genomics’ makes people evaluate related information as similar to genetic modification. Replacing the name ‘genomics’ with ‘natural crossing’ causes evaluations similar to those for traditional breeding. The results show that a name can have a strong influence on public attitudes, and we call for more consideration in choosing a name for a technology.

    Converging phenomics and genomics to study natural variation in plant photosynthetic efficiency
    Bezouw, Roel F.H.M. van; Keurentjes, Joost J.B. ; Harbinson, Jeremy ; Aarts, Mark G.M. - \ 2018
    The Plant Journal 97 (2018)1. - ISSN 0960-7412 - p. 112 - 133.
    genome-wide association study - genomics - high-throughput phenotyping - phenomics - photosynthesis - trait discovery

    In recent years developments in plant phenomic approaches and facilities have gradually caught up with genomic approaches. An opportunity lies ahead to dissect complex, quantitative traits when both genotype and phenotype can be assessed at a high level of detail. This is especially true for the study of natural variation in photosynthetic efficiency, for which forward genetics studies have yielded only a little progress in our understanding of the genetic layout of the trait. High-throughput phenotyping, primarily from chlorophyll fluorescence imaging, should help to dissect the genetics of photosynthesis at the different levels of both plant physiology and development. Specific emphasis should be directed towards understanding the acclimation of the photosynthetic machinery in fluctuating environments, which may be crucial for the identification of genetic variation for relevant traits in food crops. Facilities should preferably be designed to accommodate phenotyping of photosynthesis-related traits in such environments. The use of forward genetics to study the genetic architecture of photosynthesis is likely to lead to the discovery of novel traits and/or genes that may be targeted in breeding or bio-engineering approaches to improve crop photosynthetic efficiency. In the near future, big data approaches will play a pivotal role in data processing and streamlining the phenotype-to-gene identification pipeline.

    Meiotic drive of female-inherited supernumerary chromosomes in a pathogenic fungus
    Habig, Michael ; Kema, Gert Hj ; Holtgrewe Stukenbrock, Eva - \ 2018
    eLife 7 (2018). - ISSN 2050-084X - 20 p.
    accessory chromosome - B chromosome - chromosomes - gene expression - genetics - genomics - meiotic drive - selfish genetic elements - tetrad analysis - Zymoseptoria tritici

    Meiosis is a key cellular process of sexual reproduction that includes pairing of homologous sequences. In many species however, meiosis can also involve the segregation of supernumerary chromosomes, which can lack a homolog. How these unpaired chromosomes undergo meiosis is largely unknown. In this study we investigated chromosome segregation during meiosis in the haploid fungus Zymoseptoria tritici that possesses a large complement of supernumerary chromosomes. We used isogenic whole chromosome deletion strains to compare meiotic transmission of chromosomes when paired and unpaired. Unpaired chromosomes inherited from the male parent as well as paired supernumerary chromosomes in general showed Mendelian inheritance. In contrast, unpaired chromosomes inherited from the female parent showed non-Mendelian inheritance but were amplified and transmitted to all meiotic products. We concluded that the supernumerary chromosomes of Z. tritici show a meiotic drive and propose an additional feedback mechanism during meiosis, which initiates amplification of unpaired female-inherited chromosomes.

    Exploring the hybrid speciation continuum in birds
    Ottenburghs, Jente - \ 2018
    Ecology and Evolution 8 (2018)24. - ISSN 2045-7758 - p. 13027 - 13034.
    adaptation - admixture - genomics - introgression - mito-nuclear discordance - reproductive isolation

    Hybridization is increasingly recognized as a creative evolutionary force contributing to adaptation and speciation. Homoploid hybrid speciation—the process in which hybridization results in a stable, fertile, and reproductively isolated hybrid lineage where there is no change in ploidy—has been documented in several taxa. Hybridization can directly contribute to reproductive isolation or reinforce it at a later stage. Alternatively, hybridization might not be related to the evolution of reproductive isolation. To account for these different scenarios, I propose to discriminate between two types of hybrid speciation: type I where reproductive isolation is a direct consequence of hybridization and type II where it is the by-product of other processes. I illustrate the applicability of this classification scheme with avian examples. To my knowledge, seven hybrid bird species have been proposed: Italian sparrow, Audubon's warbler, Genovesa mockingbird, Hawaiian duck, red-breasted goose, golden-crowned manakin, and a recent lineage of Darwin's finches on the island of Daphne Major (“Big Bird”). All studies provide convincing evidence for hybridization, but do not always confidently discriminate between scenarios of hybrid speciation and recurrent introgressive hybridization. The build-up of reproductive isolation between the hybrid species and their parental taxa is mainly driven by premating isolation mechanisms and comparable to classical speciation events. One hybrid species can be classified as type I (“Big Bird”) while three species constitute type II hybrid species (Italian sparrow, Audubon's warbler, and golden-crowned manakin). The diversity in hybrid bird species across a range of divergence times also provides an excellent opportunity to study the evolution of hybrid genomes in terms of genome stabilization and adaptation.

    Data from: Recent natural selection causes adaptive evolution of an avian polygenic trait
    Bosse, M. ; Spurgin, Lewis G. ; Laine, Veronika N. ; Cole, Ella F. ; Firth, Josh A. ; Gienapp, Phillip ; Gosler, Andrew G. ; McMahon, Keith ; Poissant, Jocelyn ; Verhagen, I.C. ; Groenen, M. ; Oers, C.H.J. ; Sheldon, Ben C. ; Visser, M.E. ; Slate, Jon - \ 2017
    Wageningen University & Research
    adaptation - evolution - genomics - natural selection - bill length - birds - Parus major
    We used extensive data from a long-term study of great tits (Parus major) in the United Kingdom and Netherlands to better understand how genetic signatures of selection translate into variation in fitness and phenotypes. We found that genomic regions under differential selection contained candidate genes for bill morphology and used genetic architecture analyses to confirm that these genes, especially the collagen gene COL4A5, explained variation in bill length. COL4A5 variation was associated with reproductive success, which, combined with spatiotemporal patterns of bill length, suggested ongoing selection for longer bills in the United Kingdom. Last, bill length and COL4A5 variation were associated with usage of feeders, suggesting that longer bills may have evolved in the United Kingdom as a response to supplementary feeding.
    Prospects of whole-genome sequence data in animal and plant breeding
    Binsbergen, Rianne van - \ 2017
    Wageningen University. Promotor(en): R.F. Veerkamp; F.A. Eeuwijk, co-promotor(en): M.P.L. Calus. - Wageningen : Wageningen University - ISBN 9789463431903 - 220
    next generation sequencing - dna sequencing - quantitative trait loci - cattle - genomics - solanum lycopersicum - animal breeding - plant breeding - next generation sequencing - dna-sequencing - loci voor kwantitatief kenmerk - rundvee - genomica - solanum lycopersicum - dierveredeling - plantenveredeling

    The rapid decrease in costs of DNA sequencing implies that whole-genome sequence data will be widely available in the coming few years. Whole-genome sequence data includes all base-pairs on the genome that show variation in the sequenced population. Consequently, it is assumed that the causal mutations (e.g. quantitative trait loci; QTL) are included, which allows testing a given trait directly for association with a QTL, and might lead to discovery of new QTL or higher accuracies in genomic predictions compared to currently available marker panels. The main aim of this thesis was to investigate the benefits of using whole-genome sequence data in breeding of animals and plants compared to currently available marker panels. First the potential and benefits of using whole-genome sequence data were studied in (dairy) cattle. Accuracy of genotype imputation to whole-genome sequence data was generally high, depending on the used marker panel. In contrast to the expectations, genomic prediction showed no advantage of using whole-genome sequence data compared to a high density marker panel. Thereafter, the use of whole-genome sequence data for QTL detection in tomato (S. Lycopersicum) was studied. In a recombinant inbred line (RIL) population, more QTL were found when using sequence data compared to a marker panel, while increasing marker density was not expected to provide additional power to detect QTL. Next to the RIL population, also in an association panel it was shown that, even with limited imputation accuracy, the power of a genome-wide association study can be improved by using whole-genome sequence data. For successful application of whole-genome sequence data in animals or plants, genotype imputation will remain important to obtain accurate sequence data for all individuals in a cost effective way. Sequence data will increase the power of QTL detection in RIL populations, association panels or outbred populations. Added value of whole-genome sequence data in genomic prediction will be limited, unless more information is known about the biological background of traits and functional annotations of DNA. Also statistical models that incorporate this information and that can efficiently handle large datasets have to be developed.

    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.

    Anaerobic microbial processes for energy conservation and biotransformation of pollutants
    Luz Ferreira Martins Paulo, Lara da - \ 2017
    Wageningen University. Promotor(en): A.J.M. Stams, co-promotor(en): D.Z. Sousa. - Wageningen : Wageningen University - ISBN 9789463431125 - 234
    anaerobic microbiology - anaerobes - energy conservation - biotransformation - pollutants - heavy metals - sulfates (inorganic salts) - nickel - cobalt - methanosarcina barkeri - genomics - polymerase chain reaction - anaërobe microbiologie - anaërobe micro-organismen - energiebehoud - biotransformatie - verontreinigende stoffen - zware metalen - sulfaten (anorganische zouten) - nikkel - kobalt - methanosarcina barkeri - genomica - polymerase-kettingreactie

    Anaerobic microbial processes are commonly applied in the treatment of domestic and industrial wastewaters. Anaerobic digestion (AD) of wastewater has received a great deal of attention, but many aspects related to the complex interactions between microorganism, and how that is affected by the presence of certain toxic, are not yet fully understood. A particular case of this is the effect of heavy metals or chlorinated compounds. These compounds are known to have a strong impact in methanogens, a phylogenetic diverse group responsible for the last step of the AD process. The negative effect of sulphate towards methanogenesis is mainly related to outcompetition of methanogens by sulphate-reducing bacteria (SRB), or to toxicity caused by the sulphide generated from sulphate reduction. Heavy metals are part of many enzymes and cofactors and, in low concentrations, may beneficiate microbial activity. However, high concentrations of metals may disrupt enzyme function and structure. In cases where metal concentration is high, the presence of sulphate or sulphide might be favourable because sulphide precipitate with metals and detoxify the environment. In Chapter 2 we provide a review on the current knowledge on the effects of heavy metals and sulphate on AD, with special focus on methanogenesis. From this literature study, it came out that the influence of some metals, such as Co, is not extensively studied and that the potential of biologically produced sulphide as metal detoxification method in AD is still quite unexplored. In Chapter 3 we explored different strategies to improve methane production. Low concentrations of Ni and Co were supplemented to anaerobic sludge and the impact on methane production was evaluated. Although in contrast with other studies, no beneficial effect of metal supplementation was observed. Further on, the impact of high concentrations of Ni and Co added to anaerobic sludge was evaluated, as well as the use of sulphide as a detoxification strategy. This was evaluated in terms of impact on methane production and in changes in the microbial communities. The results showed that sulphide can be used as a method for metal detoxification, but in the case of biological produced sulphide, the competition between SRB and methanogens needs to be considered.

    Chlorinated compounds are widely used and commonly found in wastewaters. Several methanogenic metal-containing cofactors are reported to be involved in reductive dechlorination. Therefore, in Chapters 4 and 5 the potential of metal supplementation to enhance the dechlorination process was studied. In Chapter 4, the enrichment of methanogenic cultures able to perform reductive dechlorination of 1,2-dichloroethene (DCE) and tetrachlorethene (TCE) using different inoculum sources and substrates is described. Differences in physiological performance and in the microbial communities were evaluated. The results showed that the microbial community can be influenced by inoculum and substrate as well as by the chlorinated compound used. The enriched cultures presenting the best dechlorination performance were selected and used for metal supplementation studies with Ni, Co, and Fe. The results showed a clear positive impact of metal addition, both on methane production and reductive dechlorination. Further research on metal supplementation to enhance dechlorination was performed in pure cultures of Methanosarcina barkeri, a methanogen known to be able to reduce DCE (Chapter 5). In this case, it was observed that metal supplementation could improve methane production and reductive dechlorination, but the effect is dependent on the metal and concentration used. It was found that methanogenesis and reductive dechlorination can be affected in a different way by the same metal.

    Finally, in Chapter 6 the impact of sulphate on a methane-producing bioelectrochemical system (BES), an emerging technology that can be applied to wastewater treatment, was studied. The results showed an unexpected fast sulphate removal in the system and a limited impact caused by sulphate addition on methane production. The sulphate removal could only partially be explained by microbial activity, but the results demonstrated the ability of microbial communities to evolve and adapt to new operational conditions.

    In conclusion, the work presented in this thesis gave insights on the impact of heavy metals and sulphate in methanogenic systems. Furthermore, different approaches to maximise methane production were evaluated. In particular, it was shown that metal supplementation can be a promising strategy to improve anaerobic microbial processes, such as methanogenesis and reductive dechlorination.

    Milk progesterone measures to improve genomic selection for fertility in dairy cows
    Tenghe, Amabel Manyu Mefru - \ 2017
    Wageningen University. Promotor(en): R.F. Veerkamp; B. Berglund, co-promotor(en): D. J. de Koning; A.C. Bouwman. - Wageningen : Wageningen University - ISBN 9789463431330 - 179
    dairy cows - fertility - progesterone - milk - genomics - genetic improvement - heritability - genetic parameters - dairy performance - reproductive traits - animal genetics - animal breeding - dairy farming - melkkoeien - vruchtbaarheid - progesteron - melk - genomica - genetische verbetering - heritability - genetische parameters - melkresultaten - voortplantingskenmerken - diergenetica - dierveredeling - melkveehouderij

    Improved reproductive performance has a substantial benefit for the overall profitability of dairy cattle farming by decreasing insemination and veterinary treatment costs, shortening calving intervals, and lowering the rate of involuntary culling. Unfortunately, the low heritability of classical fertility traits derived from calving and insemination data makes genetic improvement by traditional animal breeding slow. Therefore, there is an interest in finding novel measures of fertility that have a higher heritability or using genomic information to aid genetic selection for fertility. The overall objective of this thesis was to explore the use of milk progesterone (P4) records and genomic information to improve selection for fertility in dairy cows. In a first step, the use of in-line milk progesterone records to define endocrine fertility traits was investigated, and genetic parameters estimated. Several defined endocrine fertility traits were heritable, and showed a reasonable repeatability. Also, the genetic correlation of milk production traits with endocrine fertility traits were considerably lower than the correlations of milk production with classical fertility traits. In the next step 17 quantitative trait loci (QTL) associated with endocrine fertility traits, were identified on Bos taurus autosomes (BTA) 2, 3, 8, 12, 15, 17, 23, and 25 in a genome-wide association study with single nucleotide polymorphisms. Further, fine-mapping of target regions on BTA 2 and 3, identified several associated variants and potential candidate genes underlying endocrine fertility traits. Subsequently, the optimal use of endocrine fertility traits in genomic evaluations was investigated; using empirical and theoretical predictions for single-trait models, I showed that endocrine fertility traits have more predictive ability than classical fertility traits. The accuracy of genomic prediction was also substantially improved when endocrine and classical fertility traits were combined in multi-trait genomic prediction. Finally, using deterministic predictions, the potential accuracy of multi-trait genomic selection when combining a cow training population measured for the endocrine trait commencement of luteal activity (C-LA), with a training population of bulls with daughter observations for a classical fertility trait was investigated. Results showed that for prediction of fertility, there is no benefit of investing in a cow training population when the breeding goal is based on classical fertility traits. However, when considering a more biological breeding goal for fertility like C-LA, accuracy is substantially improved when endocrine traits are available from a limited number of farms.

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