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 FAIR Funder pilot programme to make it easy for funders to require and for grantees to produce FAIR Data
Wittenburg, Peter ; Sustkova, Hana Pergl ; Montesanti, Annalisa ; Bloemers, Margreet ; Waard, S.H. de; Musen, Mark A. ; Graybeal, John ; Hettne, Kristina M. ; Jacobsen, Annika ; Pergl, Robert ; Hooft, Rob W.W. ; Staiger, Christine ; Gelder, Celia W.G. van; Knijnenburg, Sebastiaan L. ; Arkel, A.C. van; Meerman, Bert ; Wilkinson, Mark D. ; Sansone, S.A. ; Rocca-Serra, Philippe ; McQuilton, Peter ; Gonzalez-Beltran, Alejandra N. ; Aben, G.J.C. ; Henning, P. ; Menezes Alencar, Maria Simone de; Ribeiro, C. ; Silva, C.R.L. ; Sayao, Luis ; Sales, Luana ; Veiga, Viviane ; Lima, Jefferson ; Dib, Simone ; Xavier dos Santos, Paula dos; Murtinho, R. ; Tendel, Jakob ; Schaap, B.F. ; Brouwer, P.M. ; Gavai, A.K. ; Bouzembrak, Yamine ; Marvin, Hans J.P. ; Mons, Albert ; Kuhn, Tobias ; Gambardella, A.A. ; Miranda Azevedo, Ricardo de; Muhonen, Vesa ; Naald, Mira van der; Smit, N.W. ; Buys, M.J. ; Bruin, Taco F. de; Schoots, Fieke ; Goodson, H.J.E. ; Rzepa, Henry S. ; Jeffery, Keith G. ; Shanahan, Hugh P. ; Axton, M. ; Tkachenko, Veniamin ; Deslattes Maya, Anne ; Meyers, Natalie ; Conlon, Michael ; Haak, Laurel L. ; Schultes, Erik - \ 2019
arXiv - 13 p.
There is a growing acknowledgement in the scientific community of the importance of making experimental data machine findable, accessible, interoperable, and reusable (FAIR). Recognizing that high quality metadata are essential to make datasets FAIR, members of the GO FAIR Initiative and the Research Data Alliance (RDA) have initiated a series of workshops to encourage the creation of Metadata for Machines (M4M), enabling any self-identified stakeholder to define and promote the reuse of standardized, comprehensive machine-actionable metadata. The funders of scientific research recognize that they have an important role to play in ensuring that experimental results are FAIR, and that high quality metadata and careful planning for FAIR data stewardship are central to these goals. We describe the outcome of a recent M4M workshop that has led to a pilot programme involving two national science funders, the Health Research Board of Ireland (HRB) and the Netherlands Organisation for Health Research and Development (ZonMW). These funding organizations will explore new technologies to define at the time that a request for proposals is issued the minimal set of machine-actionable metadata that they would like investigators to use to annotate their datasets, to enable investigators to create such metadata to help make their data FAIR, and to develop data-stewardship plans that ensure that experimental data will be managed appropriately abiding by the FAIR principles. The FAIR Funders design envisions a data-management workflow having seven essential stages, where solution providers are openly invited to participate. The initial pilot programme will launch using existing computer-based tools of those who attended the M4M Workshop.
Costs of regulating ammonia emissions from livestock farms near Natura 2000 areas - analyses of case farms from Germany, Netherlands and Denmark
Jacobsen, Brian H. ; Latacz-Lohmann, Uwe ; Luesink, Harry ; Michels, Rolf ; Ståhl, Lisa - \ 2019
Journal of Environmental Management 246 (2019). - ISSN 0301-4797 - p. 897 - 908.
Abatement costs - Ammonia emissions - Livestock regulation - Natura 2000 - Nitrogen deposition

Natura 2000 areas are designated according to the EU's Birds and Habitats Directives in order to protect particular habitats and species. A variety of these habitats and species are particularly sensitive to deposition of nitrogen caused by ammonia emissions. Livestock farming is the primary source of this pollution. The purpose of this paper is to compare the costs of reaching the ammonia emission targets for different livestock farms near Natura 2000 sites in the Netherlands, Germany (Schleswig-Holstein), and Denmark. These countries have some of the highest NH3 deposition rates in Europe, and Germany in particular will have to implement new measures to reach the NEC requirements for 2030. This will also benefit nature sites in Denmark as a large share of the ammonia emissions is dispersed over long distances. The general regulation includes implementation of BAT technologies and emission ceilings. The analysis looks at regulatory aspects, the emission requirements and the cost of implementing the technologies to reduce emissions further. The selected case farms are a finisher farm and a dairy farm, and the distance to a Natura 2000 site is 400 and 2000 m. In all three countries, relatively few livestock farms are situated near or inside Natura 2000 areas. The regulatory approach is very different in the three countries and key issues are: additional deposition from projects, neighbouring livestock farms (cumulation), the inclusion of background deposition and the use of the critical loads concept. The Dutch PAS system is interesting as projected reductions in emissions are distributed as additional “room for development” today. The costs for the case farm with finishers in Schleswig-Holstein are the highest as the Filter Decree requires the use of air scrubbers. The findings suggest that farms 400 m from a Natura 2000 site in the Netherlands face lower and less costly constraints than in the other countries, whereas the opposite is the case for farms 2000 m from Natura 2000 sites. The requirements near Natura 2000, where strict requirements apply, are so high that farms will expand at a different site instead.

Balanced harvest: concept, policies, evidence, and management implications
Zhou, Shijie ; Kolding, Jeppe ; Garcia, Serge M. ; Plank, Michael J. ; Bundy, Alida ; Charles, Anthony ; Hansen, Cecilie ; Heino, Mikko ; Howell, Daniel ; Jacobsen, Nis S. ; Reid, David G. ; Rice, Jake C. ; Zwieten, Paul A.M. van - \ 2019
Reviews in Fish Biology and Fisheries 29 (2019)3. - ISSN 0960-3166 - p. 711 - 733.
Ecological effect - Ecosystem approach to fishery - Ecosystem structure - Fishing intensity - Production - Selectivity - Sustainability

Balanced harvest has been proposed to reduce fishing impact on ecosystems while simultaneously maintaining or even increasing fishery yield. The concept has attracted broad interest, but also received criticisms. In this paper, we examine the theory, modelling studies, empirical evidence, the legal and policy frameworks, and management implications of balanced harvest. The examination reveals unresolved issues and challenges from both scientific and management perspectives. We summarize current knowledge and address common questions relevant to the idea. Major conclusions include: balanced harvest can be expressed in several ways and implemented on multiple levels, and with different approaches e.g. métier based management; it explicitly bridges fisheries and conservation goals in accordance with international legal and policy frameworks; modelling studies and limited empirical evidence reveal that balanced harvest can reduce fishing impact on ecosystem structure and increase the aggregate yield; the extent of balanced harvest is not purely a scientific question, but also a legal and social choice; a transition to balanced harvest may incur short-term economic costs, while in the long-term, economic results will vary across individual fisheries and for society overall; for its application, balanced harvest can be adopted at both strategic and tactical levels and need not be a full implementation, but could aim for a “partially-balanced” harvest. Further objective discussions and research on this subject are needed to move balanced harvest toward supporting a practical ecosystem approach to fisheries.

Future water quality monitoring : improving the balance between exposure and toxicity assessments of real-world pollutant mixtures
Altenburger, Rolf ; Brack, Werner ; Burgess, Robert M. ; Busch, Wibke ; Escher, Beate I. ; Focks, Andreas ; Mark Hewitt, L. ; Jacobsen, Bo N. ; Alda, Miren López de; Ait-Aissa, Selim ; Backhaus, Thomas ; Ginebreda, Antoni ; Hilscherová, Klára ; Hollender, Juliane ; Hollert, Henner ; Neale, Peta A. ; Schulze, Tobias ; Schymanski, Emma L. ; Teodorovic, Ivana ; Tindall, Andrew J. ; Aragão Umbuzeiro, Gisela de; Vrana, Branislav ; Zonja, Bozo ; Krauss, Martin - \ 2019
Environmental Sciences Europe 31 (2019)1. - ISSN 2190-4707
Bioanalysis - Chemical and ecological status - Ecological assessment - Mixture toxicity - Water framework directive - Water monitoring

Environmental water quality monitoring aims to provide the data required for safeguarding the environment against adverse biological effects from multiple chemical contamination arising from anthropogenic diffuse emissions and point sources. Here, we integrate the experience of the international EU-funded project SOLUTIONS to shift the focus of water monitoring from a few legacy chemicals to complex chemical mixtures, and to identify relevant drivers of toxic effects. Monitoring serves a range of purposes, from control of chemical and ecological status compliance to safeguarding specific water uses, such as drinking water abstraction. Various water sampling techniques, chemical target, suspect and non-target analyses as well as an array of in vitro, in vivo and in situ bioanalytical methods were advanced to improve monitoring of water contamination. Major improvements for broader applicability include tailored sampling techniques, screening and identification techniques for a broader and more diverse set of chemicals, higher detection sensitivity, standardized protocols for chemical, toxicological, and ecological assessments combined with systematic evidence evaluation techniques. No single method or combination of methods is able to meet all divergent monitoring purposes. Current monitoring approaches tend to emphasize either targeted exposure or effect detection. Here, we argue that, irrespective of the specific purpose, assessment of monitoring results would benefit substantially from obtaining and linking information on the occurrence of both chemicals and potentially adverse biological effects. In this paper, we specify the information required to: (1) identify relevant contaminants, (2) assess the impact of contamination in aquatic ecosystems, or (3) quantify cause–effect relationships between contaminants and adverse effects. Specific strategies to link chemical and bioanalytical information are outlined for each of these distinct goals. These strategies have been developed and explored using case studies in the Danube and Rhine river basins as well as for rivers of the Iberian Peninsula. Current water quality assessment suffers from biases resulting from differences in approaches and associated uncertainty analyses. While exposure approaches tend to ignore data gaps (i.e., missing contaminants), effect-based approaches penalize data gaps with increased uncertainty factors. This integrated work suggests systematic ways to deal with mixture exposures and combined effects in a more balanced way, and thus provides guidance for future tailored environmental monitoring.

‘Droogstand afwegen per individuele koe’: Korte droogstand kost melk, minder ziekten
Hoeij, Renny van; Kok, Akke ; Knegsel, Ariette van - \ 2019

Kan de droogstand korter dan de traditionele zes tot acht weken? Wageningen
UR toont aan dat rigoureus kiezen voor korter of niet droogzetten te veel
productie kost, maar wel positief uitpakt voor de gezondheid. De onderzoekers
stellen dat de optimale droogstandsstrategie verschilt per individuele koe. Om
dit te bepalen, ontwikkelden ze een beslismodel.

Why interventions in the seed systems of roots, tubers and bananas crops do not reach their full potential
Almekinders, Conny J.M. ; Walsh, Steve ; Jacobsen, Kim S. ; Andrade-Piedra, Jorge L. ; McEwan, Margaret A. ; Haan, Stef de; Kumar, Lava ; Staver, Charles - \ 2019
Food Security 11 (2019)1. - ISSN 1876-4517 - p. 23 - 42.
Decentralized multipliers - Farmer demand - Seed quality - Vegetative multiplication

Seed systems for roots, tuber, and banana (RTB) crops receive relatively little attention from development-oriented research and commercial seed sector actors, despite their importance for food security, nutrition and rural livelihoods. We review RTB seed systems—with particular reference to potato, sweetpotato, cassava, yam and banana —to reflect on current seed system development approaches and the unique nature of these systems. We refer to our own experiences, literature and 13 case studies of RTB seed system interventions to identify gaps in our knowledge on farmer practices in sourcing and multiplying seed, and processes affecting seed quality. Currently, most approaches to developing RTB seed systems favour decentralised multiplication models to make quality seed available to smallholder farmers. Nevertheless, arguments and experiences show that in many situations, the economic sustainability of these models cannot be guaranteed, among others because the effective demand of farmers for seed from vegetatively propagated crops is unclear. Despite the understudied nature of farmers’ agronomic and social practices in relation to seed production and sourcing in RTB crops, there is sufficient evidence to show that local RTB seed systems are adaptive and dynamic. Our analysis suggests the paramount importance of understanding farmers’ effective demand for seed and how this affects the sustainable supply of quality seed from specialized producer-entrepreneurs, regardless of the seed system paradigm. From the case studies we learnt that few interventions are designed with a rigorous understanding of these issues; in particular, what types of interventions work for which actors, where, and why, although this is a necessary condition for prioritizing investments to increase the use of improved seed by smallholder farmers.

Seed degeneration of banana planting materials: strategies for improved farmer access to healthy seed
Jacobsen, K. ; Omondi, B.A. ; Almekinders, C. ; Alvarez, E. ; Blomme, G. ; Dita, M. ; Iskra-Caruana, M.I. ; Ocimati, W. ; Tinzaara, W. ; Kumar, P.L. ; Staver, C. - \ 2019
Plant Pathology 68 (2019)2. - ISSN 0032-0862 - p. 207 - 228.
Vegetatively propagated crops suffer from yield loss and reduced stand density and longevity caused by the build‐up of certain pests and pathogens between successive plantings via infected planting material. Here, six seedborne phytosanitary problems of banana are reviewed to evaluate whether a seed degeneration framework is a useful tool to identify approaches to achieve healthier planting materials. Phytoparasitic nematodes and weevils generate gradual declines in yields and in sucker health. Fusarium wilt and banana bunchy top virus cause progressive mat collapse across the field. Symptomless suckers from any mat in infested fields represent a risk of transmitting the disease to a new field. Xanthomonas and ralstonia wilts, due to incomplete systemicity, are intermediate in their threat to yield loss and frequency of transmission in suckers. Losses to banana streak virus are triggered by abiotic stress, although sucker transmission of episomal banana streak virus also contributes. A qualitative equation described here for seed degeneration covers a cycle beginning with the quality and risk factors of the planting material used to plant a new field and ends with the quality and risk factors of the suckers extracted from the field to plant a new field. This review of five planting material multiplication methods commonly used in banana contrasts their differing usefulness to address seed degeneration in the small farm context. It is proposed that initiatives to offset banana seed degeneration should integrate the role of off‐farm actors into decentralized initiatives rather than attempt to duplicate national seed certification frameworks from other true seed or vegetatively propagated crops.
Understanding root, tuber, and banana seed systems and coordination breakdown : a multi-stakeholder framework
Bentley, Jeffery W. ; Andrade-Piedra, Jorge ; Demo, Paul ; Dzomeku, Beloved ; Jacobsen, Kim ; Kikulwe, Enoch ; Kromann, Peter ; Kumar, P.L. ; McEwan, Margaret ; Mudege, Netsayi ; Ogero, Kwame ; Okechukwu, Richardson ; Orrego, Ricardo ; Ospina, Bernardo ; Sperling, Louise ; Walsh, Stephen ; Thiele, Graham - \ 2018
Journal of Crop Improvement 32 (2018)5. - ISSN 1542-7528 - p. 599 - 621.
Bananas and plantains - root crops - seed security - seed systems - tuber crops - vegetatively propagated crops (VPC)

Vegetatively propagated crop (VPC) seed tends to remain true to varietal type but is bulky, often carries disease, and is slow to produce. So VPC seed needs to be handled differently than that of other crops, e.g., it tends to be sourced locally, often must be fresh, and it is less often sold on the market. Hence, a framework was adapted to describe and support interventions in such seed systems. The framework was used with 13 case studies to understand VPC seed systems for roots, tubers, and bananas, including differing roles and sometimes conflicting goals of stakeholders, and to identify potential coordination breakdowns when actors fail to develop a shared understanding and vision. In this article, we review those case studies. The framework is a critical tool to (a) document VPC seed systems and build evidence; (b) diagnose and treat coordination breakdown and (c) guide decision-makers and donors on the design of more sustainable seed system interventions for VPCs. The framework can be used to analyze past interventions and will be useful for planning future VPC seed programs.

Silencing of DND1 in potato and tomato impedes conidial germination, attachment and hyphal growth of Botrytis cinerea
Sun, K. ; Tuinen, A. van; Kan, J.A.L. van; Wolters, A.M.A. ; Jacobsen, E. ; Visser, R.G.F. ; Bai, Y. - \ 2017
BMC Plant Biology 17 (2017). - ISSN 1471-2229
Botrytis cinerea, a necrotrophic pathogenic fungus, attacks many crops including potato and tomato. Major genes for complete resistance to B. cinerea are not known in plants, but a few quantitative trait loci have been described in tomato. Loss of function of particular susceptibility (S) genes appears to provide a new source of resistance to B. cinerea in Arabidopsis.
In this study, orthologs of Arabidopsis S genes (DND1, DMR6, DMR1 and PMR4) were silenced by RNAi in potato and tomato (only for DND1). DND1 well-silenced potato and tomato plants showed significantly reduced diameters of B. cinerea lesions as compared to control plants, at all-time points analysed. Reduced lesion diameter was also observed on leaves of DMR6 silenced potato plants but only at 3 days post inoculation (dpi). The DMR1 and PMR4 silenced potato transformants were as susceptible as the control cv Desiree. Microscopic analysis was performed to observe B. cinerea infection progress in DND1 well-silenced potato and tomato leaves. A significantly lower number of B. cinerea conidia remained attached to the leaf surface of DND1 well-silenced potato and tomato plants and the hyphal growth of germlings was hampered.
This is the first report of a cytological investigation of Botrytis development on DND1-silenced crop plants. Silencing of DND1 led to reduced susceptibility to Botrytis, which was associated with impediment of conidial germination and attachment as well as hyphal growth. Our results provide new insights regarding the use of S genes in resistance breeding.
Sustainable Nitrogen Management in Denmark
Dalgaard, Tommy ; Brock, S. ; Graversgaard, Morten ; Hansen, Brigitte ; Hashemi, F. ; Häsler, B. ; Hertel, O. ; Hutchings, N.J. ; Jacobsen, B.H. ; Stoumann Jensen, L. ; Kjeldsen, Chris ; Olesen, J.E. ; Schjorring, J.K. ; Sigsgaard, T. ; Stubkjaer Andersen, P. ; Termansen, Mette ; Vejre, H. ; Vestergaard Odgaard, M. ; Vries, W. de; Wiborg, I.A. - \ 2017
In: Innovative solutions for sustainable management of nitrogen. - Aarhus University and the Research Alliance - ISBN 9788793398825 - p. 13 - 16.
Innovative solutions for sustainable management of nitrogen : Conference proceedings
Dalgaard, Tommy ; Olesen, J.E. ; Schjorring, J.K. ; Jensen, J.S. ; Vejre, H. ; Andersen, P.S. ; Gundersen, P. ; Jacobsen, B.H. ; Jensen, J. ; Häsler, B. ; Termansen, Mette ; Hertel, O. ; Brock, S. ; Kronvang, B. ; Svenning, Jens Christian ; Sigsgaard, T. ; Hansen, B. ; Thorling, L. ; Højberg, A.L. ; Wiborg, I.A. ; Piil, K. ; Kjeldsen, Chris ; Graversgaard, Morten ; Hutchings, N. ; Vries, W. de; Christensen, J. ; Mukendi, T. - \ 2017
- 142 p.
A framework for modeling adaptive forest management and decision making under climate change
Yousefpour, Rasoul ; Temperli, Christian ; Jacobsen, Jette Bredahl ; Thorsen, Bo Jellesmark ; Meilby, Henrik ; Lexer, Manfred J. ; Lindner, Marcus ; Bugmann, Harald ; Borges, Jose G. ; Palma, João H.N. ; Ray, Duncan ; Zimmermann, Niklaus E. ; Delzon, Sylvain ; Kremer, Antoine ; Kramer, Koen ; Reyer, Christopher P.O. ; Lasch-Born, Petra ; Garcia-Gonzalo, Jordi ; Hanewinkel, Marc - \ 2017
Ecology and Society 22 (2017)4. - ISSN 1708-3087
Behavioral adaptation - Europe - Forest management - Knowledge management - Mathematical programming - Process-based models - Spatial planning
Adapting the management of forest resources to climate change involves addressing several crucial aspects to provide a valid basis for decision making. These include the knowledge and belief of decision makers, the mapping of management options for the current as well as anticipated future bioclimatic and socioeconomic conditions, and the ways decisions are evaluated and made. We investigate the adaptive management process and develop a framework including these three aspects, thus providing a structured way to analyze the challenges and opportunities of managing forests in the face of climate change. We apply the framework for a range of case studies that differ in the way climate and its impacts are projected to change, the available management options, and how decision makers develop, update, and use their beliefs about climate change scenarios to select among adaptation options, each being optimal for a certain climate change scenario. We describe four stylized types of decision-making processes that differ in how they (1) take into account uncertainty and new information on the state and development of the climate and (2) evaluate alternative management decisions: the “no-change,” the “reactive,” the “trend-adaptive,” and the “forward-looking adaptive” decision-making types. Accordingly, we evaluate the experiences with alternative management strategies and recent publications on using Bayesian optimization methods that account for different simulated learning schemes based on varying knowledge, belief, and information. Finally, our proposed framework for identifying adaptation strategies provides solutions for enhancing forest structure and diversity, biomass and timber production, and reducing climate change-induced damages. They are spatially heterogeneous, reflecting the diversity in growing conditions and socioeconomic settings within Europe.
Susceptibility genes : an additional source for improved resistance
Sun, Kaile - \ 2017
Wageningen University. Promotor(en): R.G.F. Visser, co-promotor(en): E. Jacobsen; Y. Bai. - Wageningen : Wageningen University - ISBN 9789463431415 - 174
solanum tuberosum - potatoes - solanum lycopersicum - tomatoes - genes - susceptibility - plant pathogenic fungi - phytophthora infestans - disease resistance - plant breeding - solanum tuberosum - aardappelen - solanum lycopersicum - tomaten - genen - vatbaarheid - plantenziekteverwekkende schimmels - phytophthora infestans - ziekteresistentie - plantenveredeling

Potato is affected by several diseases. Although, resistance can be obtained by introgression of major resistance genes from wild species, this has rarely been durable. Hence, other sources of resistance are highly needed. New research with a focus on loss of function mutations has led to the identification of disease susceptibility (S) genes in plants. The research in this thesis was aimed at the identification and characterization of potato S genes involved in the interaction with Phytophthora infestans and Botrytis cinerea. We selected 11 Arabidopsis thaliana S genes and silenced their potato orthologs by RNAi in the potato cultivar Desiree. The silencing of six genes resulted in resistance to P. infestans. Moreover, silencing of StDND1 reduced the infection of B. cinerea. Microscopic analysis showed that spore attachment and/or germination of P. infestans and B. cinerea was hampered on the leaf surface of StDND1-silenced potato plants. On StDMR1- and StDMR6-silenced potato plants, hyphal growth of P. infestans was arrested by the hypersensitive response-like cell death. Our results demonstrate that impairment of plant S genes may open a new way for breeding potatoes with resistance to pathogens like P. infestans and B. cinerea.

Silencing of six susceptibility genes results in potato late blight resistance
Sun, Kaile ; Wolters, Anne-Marie A. ; Vossen, Jack H. ; Rouwet, Maarten E. ; Loonen, Annelies E.H.M. ; Jacobsen, Evert ; Visser, Richard G.F. ; Bai, Yuling - \ 2016
Transgenic Research 25 (2016)5. - ISSN 0962-8819 - p. 731 - 742.
Late blight - Potato - Resistance - RNAi - Susceptibility gene

Phytophthora infestans, the causal agent of late blight, is a major threat to commercial potato production worldwide. Significant costs are required for crop protection to secure yield. Many dominant genes for resistance (R-genes) to potato late blight have been identified, and some of these R-genes have been applied in potato breeding. However, the P. infestans population rapidly accumulates new virulent strains that render R-genes ineffective. Here we introduce a new class of resistance which is based on the loss-of-function of a susceptibility gene (S-gene) encoding a product exploited by pathogens during infection and colonization. Impaired S-genes primarily result in recessive resistance traits in contrast to recognition-based resistance that is governed by dominant R-genes. In Arabidopsis thaliana, many S-genes have been detected in screens of mutant populations. In the present study, we selected 11 A. thalianaS-genes and silenced orthologous genes in the potato cultivar Desiree, which is highly susceptible to late blight. The silencing of five genes resulted in complete resistance to the P. infestans isolate Pic99189, and the silencing of a sixth S-gene resulted in reduced susceptibility. The application of S-genes to potato breeding for resistance to late blight is further discussed.

Towards Sustainable Potato Late Blight Resistance by Cisgenic R Gene Pyramiding
Kwang-Ryong Jo, ; Zhu, S. ; Bai, Y. ; Hutten, R.C.B. ; Kessel, G.J.T. ; Vleeshouwers, V.G.A.A. ; Jacobsen, E. ; Visser, R.G.F. ; Vossen, J.H. - \ 2016
In: Plant Pathogen Resistance Biotechnology / Collinge, David B., Hoboken, NJ : John Wiley and Sons - ISBN 9781118867761 - p. 171 - 191.
This chapter provides an overview of the possibilities of genetic modification (GM) potato breeding in general and specifically to combat the most important disease, late blight. Potato plants are vulnerable to a number of pests and diseases. An enigmatic question concerns whether individual Rpi genes can confer sufficient broad-spectrum resistance to impart durability. The presence of Rpi genes or transcripts as determined using molecular markers does not warrant their functional expression. Late blight resistance resources from crossable species can be deployed for intragenic or cisgenic breeding strategies. The chapter presents and discusses a pipeline for cisgenic late blight resistance breeding that was developed at Wageningen UR Plant Breeding. If only two Rpi genes are present, often isolates can be identified that overcome recognition mediated by one Rpi gene but not by the other. The late blight-resistant GM potato which was probably closest to commercialization was “Fortuna”.
Assumptions behind size-based ecosystem models are realistic
Andersen, Ken H. ; Blanchard, Julia L. ; Fulton, Elizabeth A. ; Gislason, Henrik ; Jacobsen, Nis Sand ; Kooten, Tobias van - \ 2016
ICES Journal of Marine Science 73 (2016)6. - ISSN 1054-3139 - p. 1651 - 1655.
Balanced harvesting - Cohort biomass - Size-spectrum model

A recent publication about balanced harvesting (Froese et al., ICES Journal of Marine Science; 73: 1640-1650) contains several erroneous statements about size-spectrum models. We refute the statements by showing that the assumptions pertaining to size-spectrum models discussed by Froese et al. are realistic and consistent. We further show that the assumption about density-dependence being described by a stock recruitment relationship is responsible for determining whether a peak in the cohort biomass of a population occurs late or early in life. Finally, we argue that there is indeed a constructive role for a wide suite of ecosystem models to evaluate fishing strategies in an ecosystem context.

The Solanum demissumR8 late blight resistance gene is an Sw-5 homologue that has been deployed worldwide in late blight resistant varieties
Vossen, Jack H. ; Arkel, Gert van; Bergervoet-van Deelen, Marjan ; Jo, Kwang Ryong ; Jacobsen, Evert ; Visser, Richard G.F. - \ 2016
Theoretical and Applied Genetics 129 (2016)9. - ISSN 0040-5752 - p. 1785 - 1796.
Cisgenesis - Disease resistance gene - NB-LRR - Phytophthora infestans - Potato late blight

The potato late blight resistance geneR8has been cloned.R8is found in five late blight resistant varieties deployed in three different continents. R8 recognises Avr8 and is homologous to the NB-LRR protein Sw-5 from tomato.Abstract: The broad spectrum late blight resistance gene R8 from Solanum demissum was cloned based on a previously published coarse map position on the lower arm of chromosome IX. Fine mapping in a recombinant population and bacterial artificial chromosome (BAC) library screening resulted in a BAC contig spanning 170 kb of the R8 haplotype. Sequencing revealed a cluster of at least ten R gene analogues (RGAs). The seven RGAs in the genetic window were subcloned for complementation analysis. Only one RGA provided late blight resistance and caused recognition of Avr8. From these results, it was concluded that the newly cloned resistance gene was indeed R8. R8 encodes a typical intracellular immune receptor with an N-terminal coiled coil, a central nucleotide binding site and 13 C-terminal leucine rich repeats. Phylogenetic analysis of a set of representative Solanaceae R proteins shows that R8 resides in a clearly distinct clade together with the Sw-5 tospovirus R protein from tomato. It was found that the R8 gene is present in late blight resistant potato varieties from Europe (Sarpo Mira), USA (Jacqueline Lee, Missaukee) and China (PB-06, S-60). Indeed, when tested under field conditions, R8 transgenic potato plants showed broad spectrum resistance to the current late blight population in the Netherlands, similar to Sarpo Mira.

Durable Late Blight Resistance in Potato Through Dynamic Varieties Obtained by Cisgenesis : Scientific and Societal Advances in the DuRPh Project
Haverkort, A.J. ; Boonekamp, P.M. ; Hutten, R. ; Jacobsen, E. ; Lotz, L.A.P. ; Kessel, G.J.T. ; Vossen, J.H. ; Visser, R.G.F. - \ 2016
Potato Research (2016). - ISSN 0014-3065 - p. 35 - 66.
Cisgenesis - Conventional breeding - Food security - Multi-gene resistance - True-to-type

From 2006 through 2015, a research project on Durable Resistance in potato against Phytophthora (DuRPh) was carried out at Wageningen University and Research Centre. Its objective was to develop a proof of principle for durable resistance against late blight by cisgenesis. This public-funded project aimed at stimulating research on genetic modification and public debate on innovative genetic techniques. It was decided to clone and transfer late blight resistance (R) genes of crossable wild potato species (cisgenes) by Agrobacterium tumefaciens-mediated transformation without non-potato genes. A stack of multiple R genes were planned to be inserted into established varieties, thereby creating a dynamic variety in which the composition of the stacks may vary over space and time. Cisgenic plants were selected based on the expression of all inserted R genes and trueness-to-type. Within the project, 13 R genes from wild potato species were genetically mapped and three of them were cloned. Four varieties were transformed with one to three R genes. This was initially done using kanamycin resistance provided by a selectable marker gene of synthetic origin in order to quickly test the performance and stability of the introduced R genes and stacked R gene combinations. Once the functioning thereof was confirmed, marker-free transformations were conducted; thus, true cisgenic events were selected. The results about the different R genes, their chromosomal location, their specificity, the background dependence, the maximum size of a stack, its regeneration time and associated somaclonal variation frequency and its stability were studied. After selection and characterisation in the laboratory, the best cisgenic events were assessed in field trials for late blight resistance. This showed that inserted R genes were capable of turning a susceptible variety into a resistant one. Maximising longevity of the resistance was assured through resistance management research. It was shown that stacking of multiple R genes and monitoring how to deploy these stacks spatially and temporally could reduce fungicide use by over 80%. Communications through media and field demonstrations were manifold to allow public and policymakers to decide if cisgenesis is an acceptable tool to make potato farming more sustainable. Future deployment of the DuRPh strategy will depend largely on its status as a genetically modified crop or its exemption thereof. Worldwide near eradication of late blight would increase global annual potato production by close to 80 million tons, thereby contributing considerably to the needed additional global future food supply.

Development of a broodstock diet to improve developmental competence of embryos in European eel, Anguilla anguilla
Støttrup, J.G. ; Tomkiewicz, J. ; Jacobsen, C. ; Heinsbroek, L.T.N. - \ 2016
Aquaculture Nutrition 22 (2016)4. - ISSN 1353-5773 - p. 725 - 737.
Arachidonic acid - Broodstock nutrition - Egg quality - Larval production - Omega-3 fatty acids

We examined the effect of dietary arachidonic acid (ARA) and eicosapentaenoic acid (EPA) on the production of embryos and hatched larvae in the European eel, Anguilla anguilla. Two diets with high and intermediate levels of ARA and low and intermediate levels of EPA (Feed 1: ARA 1.9%, EPA 4.2%; Feed 2: ARA 1.2%, EPA 5.1% of total fatty acids) were tested against a commercial diet (DE: ARA: 0.5%, EPA: 8.2% of total fatty acids). After 24 weeks of feeding, ARA levels in the muscles and ovaries increased to 0.9% and 1.3% of total fatty acids, respectively, in Feed 1 and were significantly higher than in Feed 2 and DE. Female broodstock was not fed during hormonal treatment to induce vitellogenesis and ovulation. EPA levels in females fed the test diets decreased in the both muscle and ovary and were significantly lower in eggs from females fed Feed 1. The highest percentage of stripped females, producing viable eggs and larvae, were those females fed the highest dietary ARA levels (Feed 1). The level of lipid peroxidation products in eggs was similar among treatment, indicating that the lowest dietary levels of vitamin C and vitamin E were sufficient. In the unfertilized eggs, ARA levels were also highest (1.1% of total fatty acids) in the diet with highest ARA levels (Feed 1).

Down-regulation of Arabidopsis DND1 orthologs in potato and tomato leads to broad-spectrum resistance to late blight and powdery mildew
Sun, K. ; Wolters, A.M.A. ; Loonen, A.E.H.M. ; Huibers, R.P. ; Vlugt, R.A.A. van der; Goverse, A. ; Jacobsen, E. ; Visser, R.G.F. ; Bai, Y. - \ 2016
Transgenic Research 25 (2016). - ISSN 0962-8819 - p. 123 - 138.
Multiple susceptibility genes (S), identified in Arabidopsis, have been shown to be functionally conserved in crop plants. Mutations in these S genes result in resistance to different pathogens, opening a new way to achieve plant disease resistance. The aim of this study was to investigate the role of Defense No Death 1 (DND1) in susceptibility of tomato and potato to late blight (Phytophthora infestans). In Arabidopsis, the dnd1 mutant has broad-spectrum resistance against several fungal, bacterial, and viral pathogens. However this mutation is also associated with a dwarfed phenotype. Using an RNAi approach, we silenced AtDND1 orthologs in potato and tomato. Our results showed that silencing of the DND1 ortholog in both crops resulted in resistance to the pathogenic oomycete P. infestans and to two powdery mildew species, Oidium neolycopersici and Golovinomyces orontii. The resistance to P. infestans in potato was effective to four different isolates although the level of resistance (complete or partial) was dependent on the aggressiveness of the isolate. In tomato, DND1-silenced plants showed a severe dwarf phenotype and autonecrosis, whereas DND1-silenced potato plants were not dwarfed and showed a less pronounced autonecrosis. Our results indicate that S gene function of DND1 is conserved in tomato and potato. We discuss the possibilities of using RNAi silencing or loss-of-function mutations of DND1 orthologs, as well as additional S gene orthologs from Arabidopsis, to breed for resistance to pathogens in crop plants.
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