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Exploitation of natural plant biodiversity for the pesticide-free production of food The BIOEXPLOIT Integrated Project is a research project supported by the European Commission’s sixth framework program. It aims to reduce the application of pesticides in the production of food in Europe. Most of the pesticides used today protect food crops from fungal diseases. BIOEXPLOIT wants to achieve a reduction in pesticides usage by exploiting the natural resistance in plants to these fungal diseases. The centres of origin of crop plants harbour most of the global diversity in natural disease resistance. The currently grown cultivars of major European food crops represent only a small fraction of this global diversity in natural resistance. BIOEXPLOIT’s overall objective is to investigate wild relatives of food crop plants for novel natural resistances to fungal diseases. It also aims to develop technologies to efficiently breed these novel resistances into current cultivated food crops. BIOEXPLOIT focuses on two major European food crops for which fungicides are indispensible at the moment: Potato Wheat Contract number: FOOD-CT-2005-513959

News and events

Final BioExploit project meeting 15-16 February, 2011, congress centre "de Reehorst", Ede, the Netherlands The plan is to organize a final BIOEXPOIT ‘showcase’ meeting to disseminate significant achievements from the project to members of the European breeding community and other stakeholders. Organizing such a meeting in the autumn just before the current end date of the project (September 30th, 2010) would exclude many breeders from participation, as it is for them the busiest time of the year. Following up on a suggestion by our scientific officer at the CEC, we have permission to extent the contract duration with 6 months. This will allow us to have a final BIOEXPLOIT meeting on February 15th and 16th, 2011, which is far more convenient. Project staff office Presentation Subproject 1 Presentation Subproject 2 Presentation Subproject 3 Presentation Subproject 4 Presentation Subproject 5 Presentation Subproject 6 Presentation Subproject 7 and 8 Programme final meeting

EAPR-EUCARPIA congress "Potato Breeding after completion of the DNA Sequence of the Potato Genome" 27-30 June, 2010, Wageningen, the Netherlands Joint section meeting of the EAPR section 'Breeding and varietal assessment' and the EUCARPIA section 'potatoes', bringing together a unique mixture of breeders and biologists. Book of abstracts

Euphytica paper on the SWOT analysis on MAS in organic breeding programs Lammerts van Bueren, E.T., G. Backes, H. de Vriend, H. Østergård, 2010. The role of molecular markers and marker assisted selection in breeding for organic agriculture. Euphytica DOI 10.1007/s10681-010-0169-0.

The XIVth EUCARPIA Meeting on Genetics and Breeding of Capsicum and Eggplant, which will take place in Valencia ( Spain) from 30 August to 1 September 2010. More information on the meeting is available in the web page http://www.comav.upv.es/capsicumeggplant/ 1st announcement EUCARPIA Cereal Section Meeting Cambridge, United Kingdom 6 - 8 April 2010 Preliminary announcement We are pleased to invite you to participate at the EUCARPIA Cereal Section Meeting. The Conference will be held in Cambridge, United Kingdom between 6 and 8 April 2010. The previous successful conference of the Cereal Section in Leida, Spain proved that the Cereal Section is one of the most popular sections of EUCARPIA for plant scientists and breeders interested in the genetics and improvement of cereals. The conference is being hosted in Cambridge by the National Institute of Agricultural Botany. The main topics of the conference are: MOLECULAR AND FUNCTIONAL DIVERSITY OF DIPLOID AND POLYPLOID CEREAL GENOMES: ‘HOW CAN WE EFFECTIVELY DETECT AND EXPLOIT THIS VARIATION IN BREEDING PROGRAMMES?’ A SPECIAL SESSION ON ‘IMPROVEMENT OF BIOACTIVE COMPOUNDS IN GRAIN AND A BIOTECHNOLOGY TOOLKIT FOR PLANT BREEDERS’ will be organized by the HEALTHGRAIN FP6 project, Module 2 leader Professor Peter Shewry Deadline of application for oral and poster presentations is 1 December 2009. Registration and accommodation details will be available on the 1st circular website of the meeting (www.niab.com) and EUCARPIA homepages (http://www.eucarpia.org/). EUCARPIA offers a one year free membership for non Eucarpia member participants. We hope this will be a very successful and interesting conference for all of us. We look forward to seeing you in Cambridge! Dr Tina Barsby Prof Wayne Powell Chairman of the Organizing Committee Head of the Cereal Section Rye Working Group of EUCARPIA International Symposium on Rye Breeding & Genetics Zhodino, Belarus 29 June - 02 July 2010 e-mail: spcaf@mail.ru

EAPR-EUCARPIA congress "Potato Breeding after completion of the DNA Sequence of the Potato Genome" 27-30 June, 2010, Wageningen, the Netherlands Joint section meeting of the EAPR section ‘Breeding and varietal assessment’ and the EUCARPIA section ‘potatoes’, bringing together a unique mixture of breeders and biologists. Book of abstracts

Other events

New publications

Partners The BIOEXPLOIT consortium is build from 43 organisations (i.e. academia, research institutes, plant breeding SME-s, and industry) located in 15 different countries. In total 68 principle investigators from these organisations participate in the project making it a unique assembly of diverse scientific specilisations, including plant pathology, epidemiology, population genetics, structural biology, molecular biology, molecular and classical plant breeding (see list below). The 68 research groups combined provide a work force of more than 300 individuals directly or indirectly involved in the project. Organisation Principle Investigators involved BIOEXPLOIT Special Roles Contact WWW Wageningen University (WU) Jaap Bakker Coordinator WU, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands WU-PSG Pierre de Wit Geert Smant Subproject leader Dissemination and Exploitation/ Workpackage leader Recognition complexes Aska Goverse Workpackage leader Genetic engineering Erin Bakker Arjen Schots Rients Niks Herman van Eck Matthieu Joosten Work package leader Disease resistance signalling Francine Goverse Work package leader Fungal effectors Institut National de Recherche Agronomique (INRA) Veronique Lefebvre Work package leader Training Unité de Génétique et Amélioration des Fruits et Légumes, Domaine Saint Maurice, B.P. 94, 84143 MONTFAVET cedex, France INRA Didier Andrivon Boulos Chalhoub Work package leader R gene clustering and QTls Jean-Eric Chauvin Joseph Jahier Franck Panabières Claude Pope Scottish Crop Research Institute (SCRI) Robbie Waugh Subproject leader Mappin and Cloning R genes and QTLs Scottish Crop Research Institute, Invergowrie Dundee, DD2 5DA, United Kingdom SCRI David Marshall Glenn Bryan Paul Birch John Innes Centre (JIC) James Brown Subproject leader Fungal effectors John Innes Cente, Department of Disease and Stress Biology, Norwich Research Park Colney, Norwich NR4 7UH, United Kingdom JIC Chris Ridout Lesley Boyd Sainsbury Laboratory (SL) Jonathan Jones The Sainsbury Laboratory, John Innes Centre, Colney Lane, Norwich, NR4 7UH, United Kingdom SL University of Dundee (UNIVDUN) Andrew Flavell Work package leader Marker assisted breeding University of Dundee, Plant Research Unit Division of Applied and Environmental Biology, School of Life Sciences, University of Dundee at SCRI, Invergowrie, DUNDEE DD2 5DA, United Kingdom UNIVDUN-AF Rothamsted Research (RRes) Kim Hammond Kosack Rothamsted Research, West Common, Harpenden, Herts, AL5 2JQ, United Kingdom RRes-PPI Huw Jones Institute of Plant Genetics and Crop Plant Research (IPK) Patrick Schweizer Subproject leader Exploring and Exploiting Plant Biodiversity in Genebanks IPK, Corrensstrasse 3, D-06466 Gatersleben, Germany IPK Jochen Kumlehn Centre for genetic resources, the Netherlands (CGN) Roel Hoekstra Work package leader Integrated database Centre for Genetic Resources, the Netherlands (CGN), P.O. Box 16, 6700AA Wageningen CGN Max Planck Institute for plant breeding research (MPIZ) Paul Schulze Lefert Max Planck Institute for Plant Breeding Research, Dept. of Plant Microbe Interactions, Carl-von-Linné Weg 10, D-50829 Cologne, Germany MPIZ Christane Gebhardt The Royal Veterinary and Agricultural University (KVL) Hans Thordal-Christensen Faculty of Life Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark UoC Danish Institute of Agricultural Sciences (DIAS) Mogens Støvring Hovmøller University of Aarhus, Flakkebjerg Research Centre, DK-4200 Slagelse, Denmark AU University of Helsinki (MTT) Alan Schulman MTT/BI Plant Genomics Laboratory, Institute of Biotechnology, P.O. Box 56, Viikinkaari 4, Viikki Biocenter, FIN-00014 Helsinki, Finland MTT Plant Research International (PRI) Gert Kema PRI, PO Box 16, 6700 AA Wageningen, The Netherlands PRI Ben Vosman Plant Breeding and Acclimatization Institute (IHAR) Jerzy Czembor IHAR Radzików, 05-870 Blonie, Poland IHAR Ewa Zimnoch- Guzowska Pawel Czembor The Volcani Center (ARO) Uri Kushnir A.R.O. Volcani Center, POB 6, Bet Dagan 50250, Israel VOLCANI University of Haifa (UH) Eviatar Nevo Institute of Evolution, University of Haifa, Mt. Carmel, Haifa 31905, Israel UH University of Bologna (UNIBO) Roberto Tuberosa UNIBO, Dept. of Agro-environmental Science and Technology (DiSTA), Viale G. Fanin 44 40127 Bologna, ITALY UNIBO Instituto Vasco de Investigación y Desarrollo Agrario (NEIKER) Enrique Ritter NEIKER Granja Modelo, Apartado 48, E-01080 Vitoria, Spain NEIKER Romenian Academy Institute for Biochemistry (IBAR) Andrei Petrescu Workpackage leader Protein Structure Modelling IBAR, Splaiul Independentei 296, 060031 Bucharest 17, Romania IBAR Petrescu University of Amsterdam (UvA) Ben Cornelissen Workpackage leader Resistance Mechanisms UvA, Swammerdam Institute for Life Sciences, Kruislaan 318, 1098 SM Amsterdam, The Netherlands UVA Frank Takken Subproject leader Resistance Mechanisms Instituto Nacional de Investigaciones Forestales Agricolas y Pecuarias (INIFAP) Oswaldo Rubio-Covarrubias Programa de papa INIFAP, Conjunto SEDAGRO s/n, Metepec, Estado de México CP 52140, México INIFAP Swiss Federal Institute of Technology Zurich (ETHZ) Bruce McDonald Work package leader Fungal Effector Molecules ETHZ, Institute of Plant Sciences, Phytopathology, Universitaetstr. 2, 8092 Zuerich, Switzerland ETHZ University of Zürich (UNIZH ) Beat Keller Workpackage leader Allelic Mining UNIZ, Zollikerstrasse 107, 8008 Zürich, Switzerland UNIZ Tina Jordan Agricultural Research Institute Hungarian Academy of Sciences (MV), Zoltan Bedo MV, Brunszvik u. 2., H-2462 Martonvásár, Hungary MV Risø National Laboratory (RNL) Hanne Østergård Risø National Laboratory, Department of Plant Research, P.O. Box 49, DK-4000 Roskilde, Denmark RISOE OEST European Association for Research on Plant Breeding (EUCARPIA) Zoltan Bedo Workpackage leader Dissemination MV, Brunszvik u. 2., H-2462 Martonvásár, Hungary EUCARPIA European Association for Potato Research (EAPR) Paul Struik EAPR, Haarweg 33, 6700 AK Wageningen, The Netherlands EAPR Keygene N.V. Anker Sørensen Subproject leader Marker Assisted Breeding Keygene NV, PO Box 216, 6700 AE Wageningen, The Netherlands KEYGENE NIAB NIAB NIAB Jane Thomas NIAB, Huntingdon Road, Cambridge CB3 OLE, UK NIAB Rosemary Bayles Società Produttori Sementi Bologna Andrea Massi Research Division, Via Macero, 1, 40050 Argelato (BO), Italy PSB Stichting Stimulering Aardappelonderzoek (SSA), vacancy SSA, Vossenburghkade 68, 2800AL Gouda, The Netherlands Federation Nationale des Producteurs de Plants de Pomme de Terre (FNPPPT) Thierry Gokelaere FNPPPT, 9, rue d'Athènes, 75009 PARIS, France FNPPPT Bioplante (BIOP) Philippe Lonnet FLORIMOND DESPREZ, BP41 59242 Cappelle en Pévèle, France BIOPLANTE Agrovegetal S.A. (AGROV), Ignacio Solis Martel Agrovegetal S.A., Demetrio de los Ríos 15 41003 SEVILLA, SPAIN AGROVEGETAL Zamarte Potato Breeding (HZZ) Andrzej Pawlak Zamarte Breeding Company Ltd., 89-430 Kamien Kraj., Poland DANKO Hodowla Roślin Sp.z o.o. Zofia Banaszak Choryń 27 64-000 Kościan, Poland APPACALE Felisa Ortega APPACALE, C/ Valle de Mena, 13, P. I. Villalonquejar, 09001 Burgos, Spain APPACALE Saaten Union Resistenzlabor GmbH (SURL) Jens Weyen Subproject leader Genetic Engineering SURL, Hovedisser Strasse 92, 33818 Leopoldshoehe, Germany SURL Solana Research GmbH Jens Luebeck Zuchtstation Windeby, D-24340 Windeby, Germany Solana ARC Seibersdorf research GmbH Bodo Trognitz Biotechnology Dept., A-2444 Seibersdorf, Austria ARC KWS Lochow GmbH Viktor Korzun KWS Lochow GmbH, Bollersener Weg 5,D-29303 Bergen, Germany KWS

Project

Project summary Strategic objectives addressed To understand the molecular components involved in durable disease resistance To explore and exploit the natural biodiversity in disease resistance To accelerate the introduction of marker-assisted breeding and genetic engineering in the EU plant breeding industry To coordinate and integrate resistance breeding research, to provide training in new technologies, to disseminate the results, and to transfer knowledge and technologies to industry Although disease resistance is an important trait in plant breeding, many diseases are still hard to control without the use of pesticides. Considering the risks for human health and the environment, many pesticides should have been banned already many years ago, but are still tolerated because no suitable alternatives are available. Although world-wide huge investments have been made to create transgenic plants with various types of resistances, the European plant breeding industry has been confronted with continuous doubts about the commercial future of genetically modified (GM) crops. Due to the public debate on Genetically Modified Organisms (GMOs), most European companies have been reluctant to invest in plant biotechnology. This situation has lead to an undesirable status quo, in which no alternatives for harmful pesticides are developed, and promising new DNA technologies remain unexplored. The aim of this project is to force a break-through by developing efficient and rational breeding strategies using genomics and post-genomics tools to exploit natural host plant resistance. Two strategies will be followed to design new resistant varieties: i) marker-assisted breeding and ii) genetic engineering. In the shade of the discussions on GMOs, marker-assisted breeding has gone through a silent revolution and has become a realistic option for developing new varieties with multiple resistances. The development of high trough-put technologies for selecting plants at the seedling stage will shorten the time between the first cross involving wild species and introduction on the market considerably, for some crops even with 50%. Genetic variation in wild accessions of crop species and in their wild relatives is still largely unexplored. It has been estimated that less than 0.1 % of the biodiversity in resistance is being used in commercial varieties. A major goal of this project is to exploit these genetic resources for designing resistant varieties, either made with or without genetic engineering. The relative importance of genetic engineering for the SMEs to develop new varieties for the regular market in this project is still difficult to predict and will depend on the attitude of the consumer. The fact that these GM approaches will only use natural plant genes, which have been used for more than 50 years in traditional plant breeding, may have a positive effect on the attitude of the European consumers. Regardless the public opinion towards GM crops, marker-assisted breeding will have a high priority in this project, because it is according to various opinion leaders compatible with organic farming. In addition, in view of the continuous advances in developing new high through-put technologies, it is expected that in many situations marker-assisted breeding will become more efficient than genetic engineering, even without considering the time consuming and costly procedures to introduce GM varieties on the market. This Integrated Project will focus on wheat and potato - the two most important staple crops for all consumers in the EU - for which pesticides, mainly fungicides, are indispensable at the moment. Despite their importance as food crops for Europe, investments in genomics and post-genomics research on wheat and potato have been severely lagging behind when compared with rice or even tomato. In addition, wheat and potato have not been the favourite plant species of the scientific community to unravel disease resistance, and, as a consequence, basic knowledge and tools to design new resistances are often poorly developed. The coming years a critical mass on genomics research in wheat and potato will be essential to strengthen the competitiveness of European SMEs. Despite the expansion activities of multinational companies in Europe, SMEs play still an important role in plant breeding. However, the opening of the European market for GM food and the increasing possibilities to grow GM varieties in Europe leads to a new situation where innovating activities are of utmost importance to survive in a highly competitive market. Considering the commercial activities of the European plant breeding industry, the results of BIOEXPLOIT will also have a major impact on various other crop species.

Subproject 1. Identifying targets for durable resistance by analysing fungal effector molecules. Plants have developed an advanced and highly specific surveillance system to detect invading pathogens. Pathogens betray their presence by passively or actively releasing effector molecules at the interface with the host. These effector molecules collectively facilitate growth and reproduction of the fungus on a host plant. Co-evolution between pathogens and plants has resulted in numerous resistance genes capable of recognising a wide range of effector molecules (avirulence genes). Only a small number of these resistance genes is known and currently used for pest control in agriculture. Some of these resistance genes have a prolonged life span in agro-ecosystems, because they recognise fungal effector molecules that are essential for the fitness of the pathogen. In Subproject 1 we will undertake a large-scale search to identify and to characterise pathogen effector molecules from Phytophthora infestans, Septoria tritici, Blumeria spp., and Puccinia spp. The output of Subproject 1 will be a range of pathogen genes encoding effector molecules of which some are recognised by cognate R proteins studied in Subproject 2. Laboratory and field experiments will be undertaken to study the cost of losing avirulence effector activity for the pathogen as predictor of durable resistance. The evolution of avirulence genes in response to selection in agriculture will be studied, to predict resistance deployment strategies that maximise the durability of resistance. The fungal effector molecules will be used in Subproject 2 to determine the recognition specificity of resistance genes. Subproject 3 will use Avr - R gene pairs to reveal the mechanisms underlying recognition specificity and activation of disease resistance signalling in resistance responses. For Subproject 4 the fungal effector molecules will be captured in expression libraries to facilitate a high throughput screening of the allelic variance in customised core collections on resistance loci using agroinfiltration assays. In Subproject 5 specific avirulence genes will be used as a molecular marker for marker-assisted breeding.

Subproject 2. Mapping, isolating and characterising genes responsible for qualitative and quantitative disease resistance in potato and wheat. In Subproject 2 we will identify, clone, and characterise the genomic organisation and molecular structure of novel disease resistance loci (R genes and QTLs) to the major fungal pathogens of wheat and potato i.e. Septoria tritici, Blumeria spp., Puccinia spp., Fusarium spp., and Phytophthora infestans. To facilitate genetic and physical mapping existing segregating populations will be used from external studies and current breeding programmes of the SMEs. In addition, germplasm with novel disease resistances identified in genebanks in Subproject 4 will serve as major input for Subproject 2. This resistant germplasm will be converted into immortalised segregating mapping populations. Using marker technologies developed in Subproject 5 molecular markers will be used that are closely linked and polymorphic to the resistance traits for genetic mapping of these populations. Physical maps and BAC libraries will subsequently be generated to clone the resistance gene or the QTL, and to study the genomic organisation of R gene clusters and major QTLs. This knowledge will provide insight in the evolution of R genes and QTLs, their genomic diversity, and the degree of synteny in chromosomal segments carrying these R genes and QTLs. The protein sequences of orthologous and paralogous resistance loci will be used to model surface topology of the protein structure and to identify amino acids involved in pathogen recognition specificity. The data of matching avirulence gene (SP1) and R gene (SP2) pair will collectively feed into Subproject 5 for marker-assisted breeding and Subproject 6 for genetic engineering these resistance traits. A principle deliverable of Subproject 2 are the R gene loci and QTLs that will be used for allele mining of the plant biodiversity in wild germplasm of related plant species in genebanks (SP4). This cyclic interaction between the Subprojects 2 and 4 plays an important role in this integrated project. Subproject 2 will also feed into Subproject 3 to unravel the mechanism underlying innate resistance.

Subproject 3. Unravelling the molecular mechanisms underlying innate resistance to plant pathogens. The principle objective of Subproject 3 is to study the mechanism underlying recognition specificity and subsequent activation of the defence response in plants to avirulent plant pathogens. The activities in this Subproject will collectively establish a molecular inventory of the components in recognition complexes and disease resistance signalling pathways. The molecular inventory of innate disease resistance will be built by using proteomics (e.g. mass spectrometry of complex components) and (post)genomics tools (e.g. RNA profiling of activated defence responses and virus induced gene silencing). We also aim to clarify the biophysical and biochemical principles in the R protein activation and disease resistance signal transduction components identified in the previous two workpackages. It will also provide an in planta validation of intra- and intermolecular protein-protein interactions identified earlier in the Subproject. Defence responses activated by different classes of R proteins recognising a variety of plant pathogens have shown to involve molecular interactors that are conserved throughout the plant kingdom. The idea is that Avr-induced recognition complexes in plants activate disease resistance signalling pathways that converge into a relatively small number of conserved interconnected molecular networks. The input of Subproject 3 will, therefore, initially come from external studies involving Avr-R gene pairs from other plant microbe interactions to serve as model for the pathogens under scrutiny of BIOEXPLOIT. At a later stage of the project the focus of this Subproject will shift to Avr-R gene pairs identified in Subprojects 1 and 2. The data generated in the Subproject 2 and 3 collectively will facilitate the engineering of novel recognition specificities in R proteins. The genetic loci of disease signalling components will be further studied in subproject 4 to reveal potential allelic variation.

Subproject 4. Exploring natural biodiversity on genetic loci associated with disease resistance in wheat and potato accessions in genebanks. The genetic variation in wild accessions of wheat and potato is still largely unexplored. Only a small fraction of the natural biodiversity in disease resistance is currently included in the genetic bases of commercial varieties. A major goal of this Subproject is to explore the genetic resources stored in genebanks for designing new varieties. To this purpose we will establish in Subproject 4 customised core collections containing the allelic variance at genetic loci associated with major R genes and QTLs for resistance. The genetic variation at disease resistance loci identified in Subproject 2 will be mined by extensive genotyping and subsequent phenotyping of wild germplasm. Existing breeding programmes from the SMEs will be integrated at this level to assess the allelic variation in breeding materials used in these programmes. Efficient molecular methods for targeted genotypic and phenotypic evaluation of wheat and potato genebanks will be developed to facilitate a high throughput-screening format. The outputs of Subproject 4 will feedback into Subproject 2 to initiate the cloning of the novel disease resistance alleles, and will feed forward into Subproject 5 to initiate marker-assisted breeding of the exotic resistance allele into an elite background. Phenotyping the allelic variance in the customised core collections will include the biodiversity in the centres of origin of the fungal and oomycete pathogens. Subproject 1 will feed into the phenotypic evaluations of allelic variation by providing pathogen-derived effector expression libraries for use as molecular markers. Furthermore, Subproject 4 will facilitate the phenotypic screening of all intermediate breeding phases from germplasm to the elite variety.

Subproject 5. Increasing disease resistance in potato and wheat through marker-assisted breeding (MAB). The principle of marker-assisted breeding is a realistic option for developing new varieties with multiple disease resistances. The development of high through-put technologies for selecting plants at the seedling stage may shorten the time between the first cross involving wild species and introduction on the market considerably, for some crops even up to 50%. SMEs play a prominent role in the plant breeding industry in wheat and potato, but often lack the investment capital to develop and validate marker-assisted breeding in their commercial breeding programmes. It is expected that the application of marker-assisted breeding will probably increase exponentially when a high throughput format is combined with low cost molecular markers. The overall objective of Subproject 5 is to develop and to validate high throughput molecular marker technologies for implementation in commercial breeding programmes. Subproject 2 and existing breeding programmes will feed polymorphic molecular markers linked to disease resistance loci into subproject 5. These markers will be converted to reliable, robust and cheap PCR based markers. HTP protocols for these markers will be developed and validated in existing breeding programmes of participating SMEs. Two recent developments in multiplex HTP marker technologies, the AFLP and/or SNPWave and Tagged Microarray Marker technology, will be investigated for their potential in commercial breeding programmes. The technological innovations in this Subproject will be directly applied to the introgression breeding of R genes and QTLs identified in Subproject 2 and in existing commercial breeding programmes. A novelty in these disease resistance breeding programmes will be the application of Avr genes as molecular markers in phenotypic resistance screening. The activities comprise stacking or pyramiding of novel identified or known resistance sources, validation of the effectiveness of sources or marker-assisted backcross of sources into elite germplasm. The outputs of Subproject 5 are validated breeding lines, molecular markers, and HTP protocols that will either feedback into the commercial breeding programme of the participating SME, or will be made available to the plant breeding industry in general through the Technology Transfer Platform.

Subproject 6. Increasing disease resistance in potato and wheat through genetic engineering. Genetic engineering allows the rapid introduction of new genetic variation derived from unrelated species into crop species and it enables designing disease resistance by modifying natural resistance genes. Our goal is to obtain durable broad-spectrum resistance by introducing synthetic expression cassettes combining R genes and/or genes involved in disease signalling and to create novel recognition specificities by the manipulation of R genes using site-directed mutagenesis and domain swaps. A second objective is to mediate broad resistance in wheat by expressing mutated host transcription factors (defence response [DR] genes ) regulating disease resistance or susceptibility mechanisms. Subproject 2 and Subproject 4 will feed majorR genes and genes controlling QTLs for resistance into subproject 6. Subproject 3 will feed defence response genes into subproject 6. The aim is to build resistance cassettes of natural and modified genes in a standard elite background. The resistance cassettes may include components of the R protein containing recognition complexes identified in subproject 3. The output of Subproject 6 will be GM wheat and potato harbouring one or more natural or modified R genes, DR genes, or QTLs in an elite European background or in the background of an elite variety from a breeding programme of participating SMEs.

Subproject 7. Coordinating and integrating research and providing training.

Subproject 8. Disseminating project results and transferring technology to the industry. Because the impact of genomic research on classical breeding is relatively new, there are no traditional strong links between breeders and genomics-orientated researchers. BIOEXPLOIT will provide a new platform for communication among researchers from different disciplines. Within this project we will also establish a Technology Transfer Platform to exploit the knowledge generated within this project. To increase the awareness among consumers with regard to marker-assisted breeding and GM techniques, we will organise workshops and symposia for a broad audience. The attitude of the consumers now and in future will be of utmost importance for private companies to decide which route should be taken to develop varieties with durable resistance.

Training

Overview BIOEXPLOIT has developed a training program with four instruments. People in and outside the BIOEXPLOIT consortium can participate in the trainingprogram. The four training instruments include: Workshops PhD summerschools Distance learning courses Fellowships

Workshops These activities are aimed at young researchers within the project and, whenever possible these courses, will be merged with ongoing courses at Universities and Graduate Schools. Workshops will take one to two weeks and will be focussed on developing practical skills in marker-assisted breeding, genetic mapping, QTL analyses, chromosome haplotyping, developing markers for routine purposes, etc. Workshop on the role of Marker assisted Selection in breeding varieties for organic agriculture; 25-27 February 2009, Wageningen, the Netherlands The aim of the workshop is to facilitate a broad discussion with invited speakers on the state of the art and progress in relation to whether, when and how breeding programs for organic agriculture can benefit from Marker Assisted Selection (MAS). summarise this into a policy paper edited by the organisers. This paper will identify and clarify key issues based on the presentations and a participant-driven SWOT analysis of role of MAS in breeding for organic agriculture. Background The workshop is a follow-up of the discussion on MAS in plant breeding programs for organic agriculture, organised by COST SUSVAR and ECO-PB in January 2005 in Driebergen, the Netherlands. Now it is time for an update and further deepening of the issues involved since, in the meantime, science has made progress, practical breeders have gained more experience with MAS, and questions for breeding for organic agriculture may be more articulated. This progress has been supported by the EU project BioExploit (Exploitation of natural plant biodiversity for the pesticide-free production of food, http://www.bioexploit.net/) developing efficient and rational breeding strategies using e.g. MAS, and members of the EUCARPIA Section Organic and Low-input Agriculture (www.eucarpia.org). The workshop will discuss basic selection principles as well as contrast breeding strategies according to organic principles and MAS in a few cases combining major crops and important traits. Participants Breeders and researchers involved and/or interested in plant breeding for organic agriculture with or without detailed knowledge on molecular techniques. Policy makers and opinion leaders among the stakeholders. Proceedings workshop Presentations workshop

PhD summerschools These activities are aimed at young researchers within the project and, whenever possible these courses, will be merged with ongoing courses at Universities and Graduate Schools. Summer Schools and Winter Schools will take three to four days and leading scientists will be invited to present overviews on specialised subjects. This will involve both basic knowledge as well as presenting the most recent knowledge, enabling researchers to upgrade their knowledge in a very short period. PhD Summer School: 'On the evolution of Plant Pathogen Interactions: from Principles to Practice'; 18-20 June 2008, Wageningen, the Netherlands Content The course comprises 14 lectures by experts from various fields, both in- and outside the plant biology community. Lecturers will present an overview of their scientific discipline, not just covering their own research. Fundamental or molecular oriented topics will be alternated by applied or ecology oriented topics. PhD Students will act as chairmen during the discussions. There will be ample time for questions and discussions with the audience. The meeting is especially attractive for Ph.D. students, but the program will also be of interest for post-docs and other scientist as well. All lectures and poster abstracts will be published in an abstract book. Proceedings Summerschool

Distance learning courses E-learning Within the BioExploit education project, digital learning modules are developed, in order to bring scientific knowledge available to a public of applied plant breeders. This is being done through the development of e-learning/distance learning modules. The modules do not emphasize dissemination of the latest research data, but rather focus on bringing standard knowledge and tools into practice. http://www.flickr.com/photos/remkovandokkum/ (CC BY 2.0) Theory, practice and implementation Many procedures are everyday practice in scientific research, but they are not used by small-scale breeding companies, especially in developing countries. Our aim is to build a course through which employees at breeding companies all over the world can obtain the knowledge they need. The modules will provide step-by-step procedures, resulting in know-how to implement these subjects in the local breeding practice. Links to basic aspects will also be included. Modules The first module will focus on Marker-assisted selection. Later modules will deal with Disease resistance and Genetically modified crops.

Fellowships These are intended to promote exchange of knowledge, technology, and skills. The target group of the short-term fellowships are scientists from Non-European countries, in particular young scientists from developing countries. The calls for the training openings for scientists outside the consortium will be advertised through EAPR, EUCARPIA, and the website of the project. All training fellowships will comprise work directly related to the specific technology and expertise that is developed within the BIOEXPLOIT. The short-term fellowships will be of demonstrable benefit to the trainee, and range from one month to a maximum duration of 4 months. BioExploit Training Fellowship Application Form BioExploit On Site Visit Application Form

Dissemination

Project deliverables Exploitable knowledge and its use 2009 Link to exploitable knowledge and its use 2009 2008 Link to exploitable knowledge and its use 2008 2007 Link to exploitable knowledge and its use 2007 2006 Link to exploitable knowledge and its use 2006 Dissemination of knowledge 2009 Link to dessemination of knowledge 2009 2008 Link to dissemination of knowledge 2008 2007 Link to dissemination of knowledge 2007 2006 Link to dissemination of knowledge 2006

Publications

Scientific

The BioExploit project Aska Goverse , Geert Smant , Liesbeth Bouwman, Erin Bakker & Jaap Bakker link to abstract in Potato Research Volume 52, Number 3/ August, 2009

Unlocking wheat genetic resources for the molecular identification of ... Navreet K. Bhullara, Kenneth Streetb, Michael Mackayc, Nabila Yahiaouia,1, and Beat Kellera,2 link to publication

STANDing strong, resistance proteins instigators of plant defence Ewa Lukasik and Frank LW Takken link to article

To Nibble at Plant Resistance Proteins F. L. W. Takken, et al. link to publication

General

Meetings Scientific Meeting, 31 March and 1 April 2009, Wageningen, The Netherlands Proceedings Scientific Meeting

Presentations

Excursions and demonstrations

Vacancies Two PhD-studentships at the University of Copenhagen, Faculty of Life Sciences PhD projects in barley powdery mildew effector biology, February 2011 Powdery mildew fungi are obligate biotrophs, for which it is imperative to have a "haustorial" structure inside the living host cell for nutrient uptake. Defences are manifested at two stages: 1) during penetration of the epidermal cell wall when a protective cell wall apposition is formed, and 2) during the subsequent haustorial stage when the attacked epidermal cell can undergo a programmed cell death reaction. To counteract these defences, the fungus secretes hundreds of effector proteins that enter the host cell and interact with defence components. Advertisement Postdoc position at the University of Copenhagen, Faculty of Life Sciences Postdoc for vesicle traffic studies in plant defence, February 2011 In the Defence Genetics research group, we wish to employ a postdoc to con-duct research on vesicle trafficking processes related to plant defence against powdery mildew fungi. The Defence Genetics group is studying penetration resistance against these pathogens and has previously found evidence that syn-taxins and ARF GTPases are required for multivesicular body fusion with the plasma membrane during the manifestation of this defence. In the present pro-ject, this atypical membrane fusion event will be studied in more detail using barley and Arabidopsis. Advertisement

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