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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    Comparing Apples and Pears: the Hidden Diversity of Central African Bush Mangoes (Irvingiaceae)
    Gallois, Sandrine ; Andel, Tinde van; Heger, Thomas ; Sonké, Bonaventure ; Henry, Amanda G. - \ 2020
    Economic Botany (2020). - ISSN 0013-0001 - 17 p.
    Baka - Cameroon - Desbordesia - Irvingia - Klainedoxa - Mangues sauvages - NTFP - Wild edible plants

    Comparing Apples and Pears: The Hidden Diversity of Central African Bush Mangoes (Irvingiaceae). The fruits of Irvingiaceae trees, commonly known as “bush mangoes” or “mangues sauvages,” are crucial foods for Central African human populations, as well as local wildlife. Irvingiaceae oil-rich kernels play an important role in local diet, well-being, and livelihood. When collected for sale, they enter the international market of non-timber forest products (NTFPs), which represents a considerable source of income for central African countries. Despite the importance of bush mangoes, there is a general lack of precision in the literature on the exact species of Irvingiaceae present in local diets and NTFP markets. Few botanical studies include local names and uses of the different Irvingiaceae species, while ethnographical and social studies rarely corroborate their identifications by collecting vouchers. In this study, we combined ethnographic research and botanical collection to verify which Irvingiaceae species were consumed and collected for trade by the Baka, a group of forager-horticulturalists in southeastern Cameroon. We provide evidence of the floristic diversity hidden behind the term “bush mangoes”, as well as the knowledge and uses of Irvingiaceae fruits by the Baka. We discuss the importance of eight Irvingiaceae species for Baka livelihood as well as the potential threats regarding the future of these valuable trees.

    The case for improving crop carbon sink strength or plasticity for a CO2-rich future
    Dingkuhn, Michael ; Luquet, Delphine ; Fabre, Denis ; Muller, Bertrand ; Yin, Xinyou ; Paul, Matthew J. - \ 2020
    Current Opinion in Plant Biology (2020). - ISSN 1369-5266

    Atmospheric CO2 concentration [CO2] has increased from 260 to 280 μmol mol−1 (level during crop domestication up to the industrial revolution) to currently 400 and will reach 550 μmol mol−1 by 2050. C3 crops are expected to benefit from elevated [CO2] (e-CO2) thanks to photosynthesis responsiveness to [CO2] but this may require greater sink capacity. We review recent literature on crop e-CO2 responses, related source-sink interactions, how abiotic stresses potentially interact, and prospects to improve e-CO2 response via breeding or genetic engineering. Several lines of evidence suggest that e-CO2 responsiveness is related either to sink intrinsic capacity or adaptive plasticity, for example, involving enhanced branching. Wild relatives and old cultivars mostly showed lower photosynthetic rates, less downward acclimation of photosynthesis to e-CO2 and responded strongly to e-CO2 due to greater phenotypic plasticity. While reverting to such archaic traits would be an inappropriate strategy for breeding, we argue that substantial enhancement of vegetative sink vigor, inflorescence size and/or number and root sinks will be necessary to fully benefit from e-CO2. Potential ideotype features based on enhanced sinks are discussed. The generic ‘feast-famine’ sugar signaling pathway may be suited to engineer sink strength tissue-specifically and stage-specifically and help validate ideotype concepts. Finally, we argue that models better accounting for acclimation to e-CO2 are needed to predict which trait combinations should be targeted by breeders for a CO2-rich world.

    Measuring mate preferences : Absolute and comparative evaluation of potential partners
    Zandberg, Lies ; Hinde, Camilla A. ; Oers, Kees van - \ 2020
    Animal Behaviour 167 (2020). - ISSN 0003-3472 - p. 65 - 76.
    choice tests - comparative evaluation - great tit - mate choice - mate preferences - mate sampling

    Quantifying the direction and strength of mate preference is essential to improve our understanding of sexual selection. Experimental designs, however, often do not consider how individuals evaluate and compare the available options, which may affect the results significantly. Preferences are often assumed to be absolute, with individuals assigning a fixed, absolute value to a cue or potential partner they encounter. However, individuals may instead also compare the available options, in which case the social context plays an essential role in the preference for each potential partner. Here we investigated the importance of considering the choosers’ evaluation process in mate preference tests. Using a mate preference study on wild great tit, Parus major, heterozygosity, breast stripe size and yellowness as a case study, we tested whether individuals use absolute or comparative mate preferences. We analysed how the perceived average attractiveness and the variation in attractiveness of the group of potential mates affected the measured preference functions. We found that the average attractiveness of the stimulus groups affected the total time individuals spent visiting all stimulus birds, and that the variation in attractiveness within groups affected the measured preference slopes. This indicates that the social context will affect the measured responses to stimulus groups, and that great tits may use both absolute and comparative evaluation. Considering how a study species encounters and evaluates potential mates and how the social environment may affect preferences is essential when choosing an appropriate experimental design to obtain reliable measurements of mate preferences. We therefore strongly advise future studies to consider not only the absolute stimulus trait values, but also the context in which they are presented. The ability to quantify preferences accurately will increase our understanding of mate preferences, mate choice and ultimately sexual selection.

    Evolution of drug-resistant and virulent small colonies in phenotypically diverse populations of the human fungal pathogen Candida glabrata
    Duxbury, Sarah J.N. ; Bates, Steven ; Beardmore, Robert E. ; Gudelj, Ivana - \ 2020
    Proceedings of the Royal Society. B: Biological Sciences 287 (2020)1931. - ISSN 0962-8452 - 9 p.
    drug resistance - fungal populations - growth rate - virulence

    Antimicrobial resistance frequently carries a fitness cost to a pathogen, measured as a reduction in growth rate compared to the sensitive wild-type, in the absence of antibiotics. Existing empirical evidence points to the following relationship between cost of resistance and virulence. If a resistant pathogen suffers a fitness cost in terms of reduced growth rate it commonly has lower virulence compared to the sensitive wild-type. If this cost is absent so is the reduction in virulence. Here we show, using experimental evolution of drug resistance in the fungal human pathogen Candida glabrata, that reduced growth rate of resistant strains need not result in reduced virulence. Phenotypically heterogeneous populations were evolved in parallel containing highly resistant sub-population small colony variants (SCVs) alongside sensitive sub-populations. Despite their low growth rate in the absence of an antifungal drug, the SCVs did not suffer a marked alteration in virulence compared with the wild-type ancestral strain, or their co-isolated sensitive strains. This contrasts with classical theory that assumes growth rate to positively correlate with virulence. Our work thus highlights the complexity of the relationship between resistance, basic life-history traits and virulence.

    Insights in the Global Genetics and Gut Microbiome of Black Soldier Fly, Hermetia illucens: Implications for Animal Feed Safety Control
    Khamis, Fathiya M. ; Ombura, Fidelis L.O. ; Akutse, Komivi S. ; Subramanian, Sevgan ; Mohamed, Samira A. ; Fiaboe, Komi K.M. ; Saijuntha, Weerachai ; Loon, Joop J.A. Van; Dicke, Marcel ; Dubois, Thomas ; Ekesi, Sunday ; Tanga, Chrysantus M. - \ 2020
    Frontiers in Microbiology 11 (2020). - ISSN 1664-302X
    16S-metagenomics - genetic diversity - gut microbiome - Hermetia illucens - mitochondrial COI gene

    The utilization of the black soldier fly (BSF) Hermetia illucens L. for recycling organic waste into high-quality protein and fat biomass for animal feeds has gained momentum worldwide. However, information on the genetic diversity and environmental implications on safety of the larvae is limited. This study delineates genetic variability and unravels gut microbiome complex of wild-collected and domesticated BSF populations from six continents using mitochondrial COI gene and 16S metagenomics. All sequences generated from the study linked to H. illucens accessions KM967419.1, FJ794355.1, FJ794361.1, FJ794367.1, KC192965.1, and KY817115.1 from GenBank. Phylogenetic analyses of the sequences generated from the study and rooted by GenBank accessions of Hermetia albitarsis Fabricius and Hermetia sexmaculata Macquart separated all samples into three branches, with H. illucens and H. sexmaculata being closely related. Genetic distances between H. illucens samples from the study and GenBank accessions of H. illucens ranged between 0.0091 and 0.0407 while H. sexmaculata and H. albitarsis samples clearly separated from all H. illucens by distances of 0.1745 and 0.1903, respectively. Genetic distance matrix was used to generate a principal coordinate plot that further confirmed the phylogenetic clustering. Haplotype network map demonstrated that Australia, United States 1 (Rhode Island), United States 2 (Colorado), Kenya, and China shared a haplotype, while Uganda shared a haplotype with GenBank accession KC192965 BSF from United States. All other samples analyzed had individual haplotypes. Out of 481,695 reads analyzed from 16S metagenomics, four bacterial families (Enterobactereaceae, Dysgonomonadaceae, Wohlfahrtiimonadaceae, and Enterococcaceae) were most abundant in the BSF samples. Alpha-diversity, as assessed by Shannon index, showed that the Kenyan and Thailand populations had the highest and lowest microbe diversity, respectively; while microbial diversity assessed through Bray Curtis distance showed United States 3 (Maysville) and Netherlands populations to be the most dissimilar. Our findings on genetic diversity revealed slight phylogeographic variation between BSF populations across the globe. The 16S data depicted larval gut bacterial families with economically important genera that might pose health risks to both animals and humans. This study recommends pre-treatment of feedstocks and postharvest measures of the harvested BSF larvae to minimize risk of pathogen contamination along the insect-based feed value chain.

    State transitions in cyanobacteria studied with picosecond fluorescence at room temperature
    Bhatti, Ahmad Farhan ; Choubeh, Reza Ranjbar ; Kirilovsky, Diana ; Wientjes, Emilie ; Amerongen, Herbert van - \ 2020
    Biochimica et Biophysica Acta. B, Bioenergetics 1861 (2020)10. - ISSN 0005-2728
    Cyanobacteria - Excited-state quenching - State transition - Time-resolved spectroscopy

    Cyanobacteria can rapidly regulate the relative activity of their photosynthetic complexes photosystem I and II (PSI and PSII) in response to changes in the illumination conditions. This process is known as state transitions. If PSI is preferentially excited, they go to state I whereas state II is induced either after preferential excitation of PSII or after dark adaptation. Different underlying mechanisms have been proposed in literature, in particular i) reversible shuttling of the external antenna complexes, the phycobilisomes, between PSI and PSII, ii) reversible spillover of excitation energy from PSII to PSI, iii) a combination of both and, iv) increased excited-state quenching of the PSII core in state II. Here we investigated wild-type and mutant strains of Synechococcus sp. PCC 7942 and Synechocystis sp. PCC 6803 using time-resolved fluorescence spectroscopy at room temperature. Our observations support model iv, meaning that increased excited-state quenching of the PSII core occurs in state II thereby balancing the photochemistry of photosystems I and II.

    A History of Pigs in China: From Curious Omnivores to Industrial Pork
    Lander, Brian ; Schneider, Mindi ; Brunson, Katherine - \ 2020
    The Journal of Asian Studies (2020). - ISSN 0021-9118 - p. 1 - 25.
    Pigs have played a central role in the subsistence and culture of China for millennia. The close relationship between pigs and people began when humans gradually domesticated wild pigs over 8,000 years ago. While pigs initially foraged around settlements, population growth led people to pen their pigs, which made them household trash processors and fertilizer producers. Household pigs were in daily contact with people, who bred them to fatten quickly and produce larger litters. Early modern Europeans found Chinese pigs far superior to their own and bred the two to create the breeds now employed in industrial pork production around the world, including China. In recent decades, industrial farms that scientifically control every aspect of pigs’ lives have spread rapidly. Until recently, most Chinese people ate pork only on special occasions; their ability in recent decades to eat it regularly exemplifies China's increasing prosperity. Meanwhile, vast areas of North and South American farmland are now devoted to growing soybeans to feed hundreds of millions of pigs in China, and the methane, manure, and antibiotic resistance they produce creates environmental and health problems on a global scale.
    Behoud en duurzaam gebruik van aquatische genetische bronnen : Verkenning van prioriteiten voor de WOT Genetische Bronnen
    Abbink, Wout ; Hiemstra, Sipke-Joost - \ 2020
    Wageningen : Centre for Genetic Resources, the Netherlands (CGN), Wageningen University & Research (CGN rapport 48) - 18
    The Centre for Genetic Resources, The Netherlands, (CGN) of Wageningen University and Research (WUR), carries out Statutory Research Tasks (WOT) for the Dutch Ministry of Agriculture, Nature and Food Quality (LNV) to support the conservation and sustainable use of genetic resources for food and agriculture (www.wur.nl/cgn). With respect to recent developments in the FAO Commission on Genetic Resources for Food and Agriculture on Aquatic genetic resources, LNV asked CGN to explore the need to also include WOT on Aquatic genetic resources in the next 5-year WOT program that runs from 2021 to 2025. The FAO defines aquatic genetic resources as 'farmed aquatic species and their wild relatives'. In the Netherlands these include several relevant species of shellfish, fish and seaweeds. Priorities have been determined based on interviews with experts and representatives from the aquaculture sector, and by using literature sources. Monitoring of genetic diversity in relevant species of shellfish, fish and seaweed, both wild and cultured populations, is a general priority area for aquatic genetic resources in the Netherlands. Next, based on the monitoring data, advise will be formulated for in situ and/or ex situ conservation measures for the most relevant aquatic genetic resources. CGN manages genebank facilities for long term cryoconservation of genetic diversity in livestock species, that can also be used for the purpose of cryoconservation of priority species of shellfish, fish and seaweeds.
    Zooming in on mechanistic predator–prey ecology : Integrating camera traps with experimental methods to reveal the drivers of ecological interactions
    Smith, Justine A. ; Suraci, Justin P. ; Hunter, Jennifer S. ; Gaynor, Kaitlyn M. ; Keller, Carson B. ; Palmer, Meredith S. ; Atkins, Justine L. ; Castañeda, Irene ; Cherry, Michael J. ; Garvey, Patrick M. ; Huebner, Sarah E. ; Morin, Dana J. ; Teckentrup, Lisa ; Weterings, Martijn J.A. ; Beaudrot, Lydia - \ 2020
    Journal of Animal Ecology (2020). - ISSN 0021-8790
    antipredator behaviour - camera trap - detection - experiments - landscape of fear - predator recognition - prey selection

    Camera trap technology has galvanized the study of predator–prey ecology in wild animal communities by expanding the scale and diversity of predator–prey interactions that can be analysed. While observational data from systematic camera arrays have informed inferences on the spatiotemporal outcomes of predator–prey interactions, the capacity for observational studies to identify mechanistic drivers of species interactions is limited. Experimental study designs that utilize camera traps uniquely allow for testing hypothesized mechanisms that drive predator and prey behaviour, incorporating environmental realism not possible in the laboratory while benefiting from the distinct capacity of camera traps to generate large datasets from multiple species with minimal observer interference. However, such pairings of camera traps with experimental methods remain underutilized. We review recent advances in the experimental application of camera traps to investigate fundamental mechanisms underlying predator–prey ecology and present a conceptual guide for designing experimental camera trap studies. Only 9% of camera trap studies on predator–prey ecology in our review use experimental methods, but the application of experimental approaches is increasing. To illustrate the utility of camera trap-based experiments using a case study, we propose a study design that integrates observational and experimental techniques to test a perennial question in predator–prey ecology: how prey balance foraging and safety, as formalized by the risk allocation hypothesis. We discuss applications of camera trap-based experiments to evaluate the diversity of anthropogenic influences on wildlife communities globally. Finally, we review challenges to conducting experimental camera trap studies. Experimental camera trap studies have already begun to play an important role in understanding the predator–prey ecology of free-living animals, and such methods will become increasingly critical to quantifying drivers of community interactions in a rapidly changing world. We recommend increased application of experimental methods in the study of predator and prey responses to humans, synanthropic and invasive species, and other anthropogenic disturbances.

    A Living Collection of Rare Trees (KennisOnline in beeld 2020)
    Buiteveld, J. - \ 2020
    Wageningen : Wageningen University & Research
    The Flevopolder houses a living gene bank with wild examples of indigenous trees and shrubs, such as the wild apple. WUR researcher Joukje Buiteveld explains why the gene bank is important and how it contributes to long-term sustainable forest and nature management.
    Forced zika virus infection of culex pipiens leads to limited virus accumulation in mosquito saliva
    Abbo, Sandra R. ; Vogels, Chantal B.F. ; Visser, Tessa M. ; Geertsema, Corinne ; Oers, Monique M. Van; Koenraadt, Constantianus J.M. ; Pijlman, Gorben P. - \ 2020
    Viruses 12 (2020)6. - ISSN 1999-4915
    Arbovirus - Culex pipiens - Flavivirus - Midgut barrier - The Netherlands - Vector competence - Zika virus

    Zika virus (ZIKV) is a mosquito-borne pathogen that caused a large outbreak in the Americas in 2015 and 2016. The virus is currently present in tropical areas around the globe and can cause severe disease in humans, including Guillain-Barré syndrome and congenital microcephaly. The tropical yellow fever mosquito, Aedes aegypti, is the main vector in the urban transmission cycles of ZIKV. The discovery of ZIKV in wild-caught Culex mosquitoes and the ability of Culex quinquefasciatus mosquitoes to transmit ZIKV in the laboratory raised the question of whether the common house mosquito Culex pipiens, which is abundantly present in temperate regions in North America, Asia and Europe, could also be involved in ZIKV transmission. In this study, we investigated the vector competence of Cx. pipiens (biotypes molestus and pipiens) from the Netherlands for ZIKV, using Usutu virus as a control. After an infectious blood meal containing ZIKV, none of the tested mosquitoes accumulated ZIKV in the saliva, although 2% of the Cx. pipiens pipiens mosquitoes showed ZIKV-positive bodies. To test the barrier function of the mosquito midgut on virus transmission, ZIKV was forced into Cx. pipiens mosquitoes by intrathoracic injection, resulting in 74% (molestus) and 78% (pipiens) ZIKV-positive bodies. Strikingly, 14% (molestus) and 7% (pipiens) of the tested mosquitoes accumulated ZIKV in the saliva after injection. This is the first demonstration of ZIKV accumulation in the saliva of Cx. pipiens upon forced infection. Nevertheless, a strong midgut barrier restricted virus dissemination in the mosquito after oral exposure and we, therefore, consider Cx. pipiens as a highly inefficient vector for ZIKV.

    Ethics and the Welfare of Fish
    Bovenkerk, B. ; Meijboom, Franck - \ 2020
    In: The welfare of fish / Kristiansen, T.S., Fernö, A., Pavlidis, M.A., van de Vis, H., Cham : Springer (Animal Welfare ) - ISBN 9783030416744 - p. 19 - 42.
    To what extent fish can experience suffering and enjoyment is not just an empirical question, but one that also calls for ethical reflection. This is firstly, because animal welfare research is value laden and secondly, because the empirical evidence requires a normative framework in order to become action guiding in practices involving fish, such as aquaculture. In this chapter, we describe the role of ethics and different ethical theories that have been applied in animal ethics and that are relevant for discussions on fish welfare. We particularly focus on utilitarian, rights based, relational, and virtue ethical animal ethics theories. We furthermore argue that fish welfare is a term that combines moral norms and biological concepts. After all, when we implement fish welfare measures we have already made certain normative choices. We illustrate the integration between ethics and science in seven steps, from implementing fish welfare at the farm level, to weighing welfare against other values, defining and measuring welfare, to the questions of why welfare is morally relevant and what this means for the moral status of fish. We then consider the question of whether fish should be attributed to moral status and hence whether their welfare should be taken into account in our moral deliberations. However, not all moral concerns regarding our treatment of fish can be addressed by focussing on welfare. We discuss a number of concerns beyond welfare that need to be taken into consideration in a moral discussion on how to relate to fish: does the killing of fish constitute a moral harm? and how should we morally evaluate the process of domesticating fish in aquaculture? The chapter concludes by pointing out a number of moral issues in four practices involving fish: aquaculture, wild fisheries, experimentation, and recreation.
    Genetic Variation in Complex Traits in Transgenic α-Synuclein Strains of Caenorhabditis elegans
    Wang, Yiru ; Sluijs, L. van; Nie, Yu ; Sterken, M.G. ; Harvey, Simon C. ; Kammenga, J.E. - \ 2020
    Genes 11 (2020)7. - ISSN 2073-4425
    Different genetic backgrounds can modify the effect of mutated genes. Human α-synuclein (SNCA) gene encodes α-synuclein, and its oligomeric complexes accumulate with age and mediate the disruption of cellular homeostasis, resulting in the neuronal death that is characteristic of Parkinson’s Disease. Polymorphic variants modulate this complex pathologic mechanism. Previously, we constructed five transgenic introgression lines of a Caenorhabditis elegans model of α-synuclein using genetic backgrounds that are genetically diverse from the canonical wild-type Bristol N2. A gene expression analysis revealed that the α-synuclein transgene differentially affects genome-wide transcription due to background modifiers. To further investigate how complex traits are affected in these transgenic lines, we measured the α-synuclein transgene expression, the overall accumulation of the fusion protein of α-synuclein and yellow fluorescent protein (YFP), the lysosome-related organelles, and the body size. By using quantitative PCR (qPCR), we demonstrated stable and similar expression levels of the α-synuclein transgene in different genetic backgrounds. Strikingly, we observed that the levels of the a-synuclein:YFP fusion protein vary in different genetic backgrounds by using the COPAS™ biosorter. The quantification of the Nile Red staining assay demonstrates that α-synuclein also affects lysosome-related organelles and body size. Our results show that the same α-synuclein introgression in different C. elegans backgrounds can produces differing effects on complex traits due to background modifiers. View Full-Text
    Will legal international rhino horn trade save wild rhino populations?
    Eikelboom, Jasper A.J. ; Nuijten, Rascha J.M. ; Wang, Yingying X.G. ; Schroder, Bradley ; Heitkönig, Ignas M.A. ; Mooij, Wolf M. ; Langevelde, Frank van; Prins, Herbert H.T. - \ 2020
    Global Ecology and Conservation 23 (2020). - ISSN 2351-9894
    CITES - Conservation - Socioeconomics - South Africa - Traditional Chinese medicine - Wildlife crime

    Wild vertebrate populations all over the globe are in decline, with poaching being the second-most-important cause. The high poaching rate of rhinoceros may drive these species into extinction within the coming decades. Some stakeholders argue to lift the ban on international rhino horn trade to potentially benefit rhino conservation, as current interventions appear to be insufficient. We reviewed scientific and grey literature to scrutinize the validity of reasoning behind the potential benefit of legal horn trade for wild rhino populations. We identified four mechanisms through which legal trade would impact wild rhino populations, of which only the increased revenue for rhino farmers could potentially benefit rhino conservation. Conversely, the global demand for rhino horn is likely to increase to a level that cannot be met solely by legal supply. Moreover, corruption is omnipresent in countries along the trade routes, which has the potential to negatively affect rhino conservation. Finally, programmes aimed at reducing rhino horn demand will be counteracted through trade legalization by removing the stigma on consuming rhino horn. Combining these insights and comparing them with criteria for sustainable wildlife farming, we conclude that legalizing rhino horn trade will likely negatively impact the remaining wild rhino populations. To preserve rhino species, we suggest to prioritize reducing corruption within rhino horn trade, increasing the rhino population within well-protected ’safe havens’ and implementing educational programmes and law enforcement targeted at rhino horn consumers.

    Divergent evolution of pcf/scr74 effectors in oomycetes is associated with distinct recognition patterns in solanaceous plants
    Lin, Xiao ; Wang, Shumei ; Rond, Laura de; Bertolin, Nicoletta ; Wouters, Roland H.M. ; Wouters, Doret ; Domazakis, Emmanouil ; Bitew, Mulusew Kassa ; Win, Joe ; Dong, Suomeng ; Visser, Richard G.F. ; Birch, Paul ; Kamoun, Sophien ; Vleeshouwers, Vivianne G.A.A. - \ 2020
    mBio 11 (2020)3. - ISSN 2161-2129 - p. 1 - 12.
    Apoplastic effector - MAMP - Phytophthora infestans - Potato late blight - Surface immune receptor

    Plants deploy cell surface receptors known as pattern-recognition re ceptors (PRRs) that recognize non-self molecules from pathogens and microbes to defend against invaders. PRRs typically recognize microbe-associated molecular patterns (MAMPs) that are usually widely conserved, some even across kingdoms. Here, we report an oomycete-specific family of small secreted cysteine-rich (SCR) proteins that displays divergent patterns of sequence variation in the Irish potato famine pathogen Phytophthora infestans. A subclass that includes the conserved effector PcF from Phytophthora cactorum activates immunity in a wide range of plant species. In contrast, the more diverse SCR74 subclass is specific to P. infestans and tends to trigger immune responses only in a limited number of wild potato genotypes. The SCR74 response was recently mapped to a G-type lectin receptor kinase (GLecRK) locus in the wild potato Solanum microdontum subsp. gigantophyllum. The G-LecRK locus displays a high diversity in Solanum host species compared to other solanaceous plants. We propose that the diversification of the SCR74 proteins in P. infestans is driven by a fast coevolutionary arms race with cell surface immune receptors in wild potato, which contrasts the presumed slower dynamics between conserved apoplastic effectors and PRRs. Understanding the molecular determinants of plant immune responses to these divergent molecular patterns in oomycetes is expected to contribute to deploying multiple layers of disease resistance in crop plants. IMPORTANCE Immune receptors at the plant cell surface can recognize invading microbes. The perceived microbial molecules are typically widely conserved and therefore the matching surface receptors can detect a broad spectrum of pathogens. Here we describe a family of Phytophthora small extracellular proteins that consists of conserved subfamilies that are widely recognized by solanaceous plants. Remarkably, one subclass of SCR74 proteins is highly diverse, restricted to the late blight pathogen Phytophthora infestans and is specifically detected in wild potato plants. The diversification of this subfamily exhibits signatures of a coevolutionary arms race with surface receptors in potato. Insights into the molecular interaction between these potato-specific receptors and the recognized Phytophthora proteins are expected to contribute to disease resistance breeding in potato.

    CRISPR/Cas9-targeted mutagenesis of the tomato susceptibility gene PMR4 for resistance against powdery mildew
    Santillán Martínez, Miguel I. ; Bracuto, Valentina ; Koseoglou, Eleni ; Appiano, Michela ; Jacobsen, Evert ; Visser, Richard G.F. ; Wolters, Anne-Marie A. ; Bai, Yuling - \ 2020
    BMC Plant Biology 20 (2020)1. - ISSN 1471-2229
    CRISPR/Cas9 - PMR4 - Powdery mildew - Susceptibility gene - Targeted mutagenesis

    Background: The development of CRISPR/Cas9 technology has facilitated targeted mutagenesis in an efficient and precise way. Previously, RNAi silencing of the susceptibility (S) gene P owdery M ildew R esistance 4 (PMR4) in tomato has been shown to enhance resistance against the powdery mildew pathogen Oidium neolycopersici (On). Results: To study whether full knock-out of the tomato PMR4 gene would result in a higher level of resistance than in the RNAi-silenced transgenic plants we generated tomato PMR4 CRISPR mutants. We used a CRISPR/Cas9 construct containing four single-guide RNAs (sgRNAs) targeting the tomato PMR4 gene to increase the possibility of large deletions in the mutants. After PCR-based selection and sequencing of transformants, we identified five different mutation events, including deletions from 4 to 900-bp, a 1-bp insertion and a 892-bp inversion. These mutants all showed reduced susceptibility to On based on visual scoring of disease symptoms and quantification of relative fungal biomass. Histological observations revealed a significantly higher occurrence of hypersensitive response-like cell death at sites of fungal infection in the pmr4 mutants compared to wild-type plants. Both haustorial formation and hyphal growth were diminished but not completely inhibited in the mutants. Conclusion: CRISPR/Cas-9 targeted mutagenesis of the tomato PMR4 gene resulted in mutants with reduced but not complete loss of susceptibility to the PM pathogen On. Our study demonstrates the efficiency and versatility of the CRISPR/Cas9 system as a powerful tool to study and characterize S-genes by generating different types of mutations.

    Effecten van hoefdieren op Natura 2000-boshabitattypen op de Veluwe
    Ouden, Jan den; Lammertsma, Denise ; Jansman, Hugh - \ 2020
    Wageningen : Wageningen Environmental Research (Wageningen Environmental Research rapport 3013) - 89
    De provincie Gelderland heeft gevraagd om nader inzicht te krijgen in de relatie tussen de populatiegroottes van hoefdieren en de kwaliteit van de belangrijkste Natura 2000-boshabitattypen op de Veluwe: de Beuken-eikenbossen met hulst (H9120) en de Oude eikenbossen (H9190). Kernvragen richtten zich op de maximale aantallen van verschillende hoefdiersoorten waarbij bosverjonging mogelijk blijft en welk wildbeheer gewenst is om Natura 2000-doelen in stand te houden. Het rapport bespreekt, op basis van een literatuurstudie, de invloed van hoefdieren op bosverjonging en het voorkomen van populaties (bijzondere) kwaliteitssoorten in de habitats. De nadruk ligt hierbij vooral op het edelhert, ree en wild zwijn. Het wildbeheer wordt uitgewerkt aan de hand van een aantal scenario’s, waarna aanbevelingen worden gedaan om de heersende wilddruk op de boshabitats te verlagen. Een belangrijke aanbeveling daarbij is om bij het vaststellen van de benodigde mate van ingrijpen in de populatiegroottes van hoefdieren, en bij het beoordelen van de effectiviteit van uitgevoerde maatregelen, zich niet alleen te baseren op aantalsschattingen, maar vooral te evalueren op basis van monitoring van ecologische effecten.
    The origin and widespread occurrence of Sli-based self-compatibility in potato
    Clot, Corentin R. ; Polzer, Clara ; Prodhomme, Charlotte ; Schuit, Cees ; Engelen, Christel J.M. ; Hutten, Ronald C.B. ; Eck, Herman J. van - \ 2020
    Theoretical and Applied Genetics (2020). - ISSN 0040-5752

    Self-compatible (SC) diploid potatoes allow innovative potato breeding. Therefore, the Sli gene, originally described in S. chacoense, has received much attention. In elite S. tuberosum diploids, spontaneous berry set is occasionally observed. We aimed to map SC from S. tuberosum origin. Two full-sib mapping populations from non-inbred diploids were used. Bulks were composed based on both pollen tube growth and berry set upon selfing. After DNA sequencing of the parents and bulks, we generated k-mer tables. Set algebra and depth filtering were used to identify bulk-specific k-mers. Coupling and repulsion phase k-mers, transmitted from the SC parent, mapped in both populations to the distal end of chromosome 12. Intersection between the k-mers from both populations, in coupling phase with SC, exposed a shared haplotype of approximately 1.5 Mb. Subsequently, we screened read archives of potatoes and wild relatives for k-mers specific to this haplotype. The well-known SC clones US-W4 and RH89-039-16, but surprisingly, also S. chacoense clone M6 were positives. Hence, the S. tuberosum source of SC seems identical to Sli. Furthermore, the candidate region drastically reduced to 333 kb. Haplotype-specific KASP markers were designed and validated on a panel of diploid clones including another renown SC dihaploid G254. Interestingly, k-mers specific to the SC haplotype were common in tetraploid varieties. Pedigree information suggests that the SC haplotype was introduced into tetraploid varieties via the founder “Rough Purple Chili”. We show that Sli is surprisingly widespread and indigenous to the cultivated gene pool of potato.

    Seasonal risk of low pathogenic avian influenza virus introductions into free-range layer farms in the Netherlands
    Gonzales, Jose L. ; Pritz-Verschuren, Sylvia ; Bouwstra, Ruth ; Wiegel, Jeanine ; Elbers, Armin R.W. ; Beerens, Nancy - \ 2020
    Transboundary and Emerging Diseases (2020). - ISSN 1865-1674
    Avian influenza - risk factors - seasonality - virus introduction

    Poultry can become infected with avian influenza viruses (AIV) via (in) direct contact with infected wild birds. Free-range chicken farms in the Netherlands were shown to have a higher risk for introduction of low pathogenic avian influenza (LPAI) virus than indoor chicken farms. Therefore, during outbreaks of highly pathogenic avian influenza (HPAI), free-range layers are confined indoors as a risk mitigation measure. In this study, we characterized the seasonal patterns of AIV introductions into free-range layer farms, to determine the high-risk period. Data from the LPAI serological surveillance programme for the period 2013–2016 were used to first estimate the time of virus introduction into affected farms and then assess seasonal patterns in the risk of introduction. Time of introduction was estimated by fitting a mathematical model to seroprevalence data collected longitudinally from infected farms. For the period 2015–2016, longitudinal follow-up included monthly collections of eggs for serological testing from a cohort of 261 farms. Information on the time of introduction was then used to estimate the monthly incidence and seasonality by fitting harmonic and Poisson regression models. A significant yearly seasonal risk of introduction that lasted around 4 months (November to February) was identified with the highest risk observed in January. The risk for introduction of LPAI viruses in this period was on average four times significantly higher than the period of low risk around the summer months. Although the data for HPAI infections were limited in the period 2014–2018, a similar risk period for introduction of HPAI viruses was observed. The results of this study can be used to optimize risk-based surveillance and inform decisions on timing and duration of indoor confinement when HPAI viruses are known to circulate in the wild bird population.

    Above- and Below-ground Cascading Effects of Wild Ungulates in Temperate Forests
    Ramirez, Ignacio ; Jansen, Patrick A. ; Ouden, Jan den; Moktan, Laxmi ; Herdoiza, Natalie ; Poorter, Lourens - \ 2020
    Ecosystems (2020). - ISSN 1432-9840
    decomposition - invertebrate - litter - mineralization - regeneration - rodent - soil quality - temperate forest - Ungulate

    Ungulates have become abundant in many temperate forests, shifting tree species composition by browsing and altering soil physical conditions by trampling. Whether these effects cascade down to other trophic levels and ecosystem processes is poorly understood. Here, we assess the paths through which ungulates have cascading effects on other trophic levels (regeneration, litter, invertebrates, rodents and organic matter decomposition). We compared ungulate effects by comparing 15 response variables related to different trophic levels between paired fenced and unfenced plots in twelve temperate forest sites across the Netherlands, and used pathway analysis model to identify the (in)direct pathways through which ungulates have influenced these variables. We found that plots with ungulates (that is, unfenced) compared to plots without (that is, fenced) had lower litter depth, sapling diversity, sapling density, rodent activity, macro-invertebrate biomass, decomposition rate of tea bags, pine and birch litter and higher soil compaction. These findings were used in a path analysis to establish potential causal relationships, which showed that ungulate presence: decreased sapling density, which indirectly decreased rodent activity; decreased litter depth, which indirectly reduced invertebrate diversity; increased soil compaction, which also decreased invertebrate diversity. Soil pH decreased invertebrate biomass, which also increased nitrogen mineralization. Yet, we did not find cascading effects of ungulates on decomposition rates. Importantly, an increase in ungulate abundance strengthens the cascading effects in this system. Our results suggest that ungulates can trigger cascading effects on lower trophic levels, yet decomposition and mineralization rates are resilient to ungulate browsing and trampling. Therefore, temperate forests conservation could benefit by limiting ungulate abundance.

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