FruitBreedomics KOM stakeholders meeting 31 03-2011 1 introduction

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FruitBreedomics KOM stakeholders meeting 31 03-2011 1 introduction

  1. 1. Laurens F. , Aranzana M.J. , Arus P. , Bonany J. , Corelli L. Patocchi A. , Peil, A. , Quilot B., Stella A., Troillard V., Velasco R., van de Weg E, … An integrated approach for increasing breeding efficiency in apple and peach 1 March 2011- 31 August 2015 FP7 large collaborative
  2. 2. <ul><li>Fruit Breeding programmes </li></ul><ul><ul><li>Numerous </li></ul></ul><ul><ul><li>Similar objectives </li></ul></ul><ul><ul><li>Low genetic variability within genitor pool </li></ul></ul><ul><ul><li>Empirical approaches </li></ul></ul>Context/ breeding
  3. 3. <ul><ul><li>Mapping of major genes and QTLs : </li></ul></ul><ul><ul><ul><li>Resistance </li></ul></ul></ul><ul><ul><ul><li>Fruit quality </li></ul></ul></ul><ul><ul><ul><li>Tree architecture </li></ul></ul></ul><ul><ul><ul><li>… </li></ul></ul></ul><ul><ul><li>Functional genomics </li></ul></ul><ul><ul><ul><li>Candidate genes (ACO, ACS, Exp7, …) </li></ul></ul></ul><ul><ul><ul><li>cDNA chips </li></ul></ul></ul><ul><ul><li>Gene cloning (Vf/apple; Ma peach, …) </li></ul></ul><ul><ul><li>… . Whole genome sequences available for apple, peach, and … strawberry </li></ul></ul>Context /Genetic studies
  4. 4. <ul><ul><li>Many researches, results, QTLs ….BUT </li></ul></ul><ul><ul><li>No (few) use in selection </li></ul></ul><ul><ul><li>Main reasons: </li></ul></ul><ul><ul><li>Low marker density (SSR) </li></ul></ul><ul><ul><ul><li>gaps </li></ul></ul></ul><ul><ul><ul><li>weak precision on the QTL mapping </li></ul></ul></ul><ul><ul><li>Lack of information on the allelic diversity </li></ul></ul><ul><ul><li>Lack of information on background and environmental effects </li></ul></ul><ul><ul><li>So far, lack of cheap and high throughput genotyping tools </li></ul></ul>Limits of the use of markers in selection
  5. 5. <ul><li>To fill in the gap between Genetics/Genomics and breeding </li></ul><ul><li>- Development + use of molecular tools (SNP , Full transcript chips) /international collaboration </li></ul><ul><li>- Better knowledge / genetics + genomics of major agronomic traits + allelic diversity  Material + tools + methodologies /breeders </li></ul><ul><li>(within and outside the consortium) </li></ul>FruitBreedomics’ aims
  6. 6. <ul><li>To fill in the gap between Genetics/Genomics and breeding </li></ul><ul><li>- Development + use of molecular tools (SNP , Full transcript chips) /international collaboration </li></ul><ul><li>- Better knowledge / genetics + genomics of major agronomic traits + allelic diversity  Material + tools + methodologies /breeders </li></ul><ul><li>(within and outside the consortium) </li></ul>FruitBreedomics’ aims
  7. 7. WP1 Breeding 1. Breeding strategies 2. Fine mapping 3. Pilot studies 4. Pipeline 5. DB interface WP2 Pre-Breeding 1. Material evaluation 2. Conventional pre breeding 3. Fast prebreeding European Breeding Platform
  8. 8. WP1 Breeding 1. Breeding strategies 2. Fine mapping 3. Pilot studies 4. Pipeline 5. DB interface WP2 Pre-Breeding 1. Material evaluation 2. Conventional pre breeding 3. Fast prebreeding European Breeding Platform Breeding stakeholders Germplasm curators
  9. 9. European Breeding Platform WP1 Breeding 1. Breeding strategies 2. Fine mapping 3. Pilot studies 4. Pipeline 5. DB interface WP2 Pre-Breeding 1. Material evaluation 2. Conventional pre breeding 3. Fast prebreeding Diversity and QTL mapping WP3 PBA 3. QTL Fine mapping 2. QTL new traits 5. Wider QTL mining 4. Genet. div . in EU Breeding 6. QTL validation 1. Adaptation Flex WP4 LD/GA 1. Phen & genet variability 2. Core collection 3. QTL mapping by GWA
  10. 10. European Breeding Platform WP1 Breeding 1. Breeding strategies 2. Fine mapping 3. Pilot studies 4. Pipeline 5. DB interface WP2 Pre-Breeding 1. Material evaluation 2. Conventional pre breeding 3. Fast prebreeding Diversity and QTL mapping WP3 PBA 3. QTL Fine mapping 2. QTL new traits 5. Wider QTL mining 4. Genet. div . in EU Breeding 6. QTL validation 1. Adaptation Flex WP4 LD/GA 1. Phen & genet variability 2. Core collection 3. QTL mapping by GWA Breeding stakeholders Germplasm curators
  11. 11. WP5 Trait knowledge 1. Biotic stresses : Monilia 2. Fruit quality : texture, fiber 3. Abiotic stresses: chilling reqrt, water stress WP1 Breeding 1. Breeding strategies 2. Fine mapping 3. Pilot studies 4. Pipeline 5. DB interface WP2 Pre-Breeding 1. Material evaluation 2. Conventional pre breeding 3. Fast prebreeding European Breeding Platform Diversity and QTL mapping WP3 PBA 3. QTL Fine mapping 2. QTL new traits 5. Wider QTL mining 4. Genet. div . in EU Breeding 6. QTL validation 1. Adaptation Flex WP4 LD/GA 1. Phen & genet variability 2. Core collection 3. QTL mapping by GWA
  12. 12. WP5 Trait knowledge 1. Biotic stresses : Monilia 2. Fruit quality : texture, fiber 3. Abiotic stresses: chilling reqrt, water stress WP1 Breeding 1. Breeding strategies 2. Fine mapping 3. Pilot studies 4. Pipeline 5. DB interface WP2 Pre-Breeding 1. Material evaluation 2. Conventional pre breeding 3. Fast prebreeding European Breeding Platform Diversity and QTL mapping WP3 PBA 3. QTL Fine mapping 2. QTL new traits 5. Wider QTL mining 4. Genet. div . in EU Breeding 6. QTL validation 1. Adaptation Flex WP4 LD/GA 1. Phen & genet variability 2. Core collection 3. QTL mapping by GWA Breeding stakeholders Germplasm curators
  13. 13. PFR RosBREED ARC WP5 Trait knowledge 1. Biotic stresses 2. Fruit quality 3. Abiotic stresses WP1 Breeding 1. Breeding strategies 2. Fine mapping 3. Pilot studies 4. Pipeline 5. DB interface WP2 Pre-Breeding 1. Material evaluation 2. Conventional pre breeding 3. Fast prebreeding European Breeding Platform Diversity and QTL mapping WP3 PBA 3. QTL Fine mapping 2. QTL new traits 5. Wider QTL mining 4. Genet. div . in EU Breeding 6. QTL validation 1. Adaptation Flex WP4 LD/GA 1. Phen & genet variability 2. Core collection 3. QTL mapping by GWA WP6 SNP chips Low Medium Low cost MAB High
  14. 14. WP5 Trait knowledge 1. Biotic stresses 2. Fruit quality 3. Abiotic stresses WP1 Breeding 1. Breeding strategies 2. Fine mapping 3. Pilot studies 4. Pipeline 5. DB interface WP2 Pre-Breeding 1. Material evaluation 2. Conventional pre breeding 3. Fast prebreeding European Breeding Platform Diversity and QTL mapping WP3 PBA 3. QTL Fine mapping 2. QTL new traits 5. Wider QTL mining 4. Genet. div . in EU Breeding 6. QTL validation 1. Adaptation Flex WP4 LD/GA 1. Phen & genet variability 2. Core collection 3. QTL mapping by GWA WP6 SNP chips Low Medium Low cost MAB High Breeding stakeholders
  15. 15. RosBREED (US) GDR WP5 Trait knowledge 1. Biotic stresses 2. Fruit quality 3. Abiotic stresses WP1 Breeding 1. Breeding strategies 2. Fine mapping 3. Pilot studies 4. Pipeline 5. DB interface WP2 Pre-Breeding 1. Material evaluation 2. Conventional pre breeding 3. Fast prebreeding European Breeding Platform Diversity and QTL mapping WP3 PBA 3. QTL Fine mapping 2. QTL new traits 5. Wider QTL mining 4. Genet. div . in EU Breeding 6. QTL validation 1. Adaptation Flex WP4 LD/GA 1. Phen & genet variability 2. Core collection 3. QTL mapping by GWA WP7 bioinfo FruitBreed DB
  16. 16. WP5 Trait knowledge 1. Biotic stresses 2. Fruit quality 3. Abiotic stresses WP1 Breeding 1. Breeding strategies 2. Fine mapping 3. Pilot studies 4. Pipeline 5. DB interface WP2 Pre-Breeding 1. Material evaluation 2. Conventional pre breeding 3. Fast prebreeding European Breeding Platform Diversity and QTL mapping WP3 PBA 3. QTL Fine mapping 2. QTL new traits 5. Wider QTL mining 4. Genet. div . in EU Breeding 6. QTL validation 1. Adaptation Flex WP4 LD/GA 1. Phen & genet variability 2. Core collection 3. QTL mapping by GWA WP7 bioinfo FruitBreed DB Breeding stakeholders
  17. 17. WP8 Dissemination WP9. Management WP5 Trait knowledge 1. Biotic stresses 2. Fruit quality 3. Abiotic stresses WP1 Breeding 1. Breeding strategies 2. Fine mapping 3. Pilot studies 4. Pipeline 5. DB interface WP2 Pre-Breeding 1. Material evaluation 2. Conventional pre breeding 3. Fast prebreeding European Breeding Platform Diversity and QTL mapping WP3 PBA 3. QTL Fine mapping 2. QTL new traits 5. Wider QTL mining 4. Genet. div . in EU Breeding 6. QTL validation 1. Adaptation Flex WP4 LD/GA 1. Phen & genet variability 2. Core collection 3. QTL mapping by GWA WP6 SNP chips Low Medium Low cost MAB High WP7 bioinfo FruitBreed DB Tools
  18. 18. 15 22 23 24 16 18 19 20 21 3 4 7 14 17 13 12 10 9 8 6 5 2 11 Israël NZ Chine Afrique du Sud 1 + close links with : Rosbreed (WSU) KUL, RCL … Fruit Breedomics
  19. 19. <ul><li>/ Scientists : - molecular tools - Better knowledge / genetics + genomics of major agronomic traits + allelic diversity </li></ul><ul><li>Germplasm curators: </li></ul><ul><li>access to tools + information on the genetic diversity </li></ul><ul><li>Breeders (within + outside the project) </li></ul><ul><li>access to data, material (wider diversity), tools, methodologies </li></ul>Expected Impact
  20. 20. <ul><li>WP1 . Availability of molecular markers /pilot studies </li></ul><ul><li>Links with stakeholders </li></ul><ul><li>WP2 . Availability of prebreeding material / stakeholders </li></ul><ul><li>WP3. Peach -> changes ? </li></ul><ul><li>Apple: chip: RosBREED 9K?, FBO 3-9K? </li></ul><ul><li>WP4. Apple: new strategy: 384 -> 50K : save time and money </li></ul><ul><li>WP5. Workplan OK </li></ul><ul><li>WP6. Peach: RosBREED 9K = OK </li></ul><ul><li>Apple: European resequencing strategy: FEM, PRI, INRA </li></ul><ul><li>chips: 50K, medium: RosBREED 9K?, FBO 3-9K? </li></ul><ul><li>WP7. Clearer strategy /DB: proposal to RosBREED … soon. </li></ul><ul><li>WP8. New logo; website and dissemination stuff… </li></ul><ul><li>Agenda /stakeholder contacts </li></ul>Some feedback from the last 2 days
  21. 21. <ul><li>In April … </li></ul><ul><li>Status of Invited Partners </li></ul><ul><li>Status and availability of prebreeding material </li></ul><ul><li>End of June: </li></ul><ul><li>Formalised links with RosBREED </li></ul>Next changes in the consortium agreement
  22. 22. <ul><li>Need to get closer connections with stakeholders! </li></ul>
  23. 23. Stakeholder Advisory Board <ul><li>Composition of the Fruit Breedomics Stakeholder Advisory Board (SAB) </li></ul><ul><ul><li>The Fruit Breedomics SAB is composed of 6 members: international leading scientific experts, and representatives of the fruit breeding sector. </li></ul></ul><ul><ul><li>The SAB membership can be modified during the lifetime of the project, especially, to include, if needed, other groups of stakeholders such as food processing and retail industry and representatives of the civil society. </li></ul></ul><ul><li>Activities of the SAB </li></ul><ul><ul><li>The SAB provides the Coordinator and the ExCom of Fruit Breedomics with scientific and strategic feedback from stakeholders regarding the project’s progress. </li></ul></ul><ul><ul><li>The SAB contributes to the overall fine-tuning of the project to improve outputs and to ensure that they are compatible with stakeholder needs and priorities, be they technical, commercial and economic or societal. </li></ul></ul><ul><li>Meetings of the SAB </li></ul><ul><ul><li>It will meet jointly with the ExCom at least once per year. </li></ul></ul><ul><ul><li>Members of the SAB will be invited to participate to the Annual meeting of the project. </li></ul></ul><ul><li>Intellectual and Property Rights issues </li></ul><ul><ul><li>Prior to the beginning of its activity, each SAB member will enter into a non disclosure agreement regarding confidential information that could be exchanged during the meeting they will attend. </li></ul></ul>
  24. 24. Stakeholder Platform <ul><li>Expected role in the project (Cf Dow): </li></ul><ul><ul><li>The objectives of the Stakeholder Platform are: </li></ul></ul><ul><ul><ul><li>to provide preferential contact for the dissemination of the project’s outcomes to society, </li></ul></ul></ul><ul><ul><ul><li>to discuss the most promising results and how they should be transferred. </li></ul></ul></ul><ul><ul><ul><li>To listen to European fruit chain problems and request </li></ul></ul></ul><ul><ul><li>The Stakeholder Platform will gather representatives of all players intervening in the supply chain from scientists, breeders, germplasm collection curators, nurserymen, to cooperatives, and growers. </li></ul></ul><ul><ul><li>Targeting primarily the apple and peach sectors, it will be opened up to stakeholders of all the Rosacae species. </li></ul></ul>FruitBreedomics-Stakeholders : reciprocal relationship
  25. 25. Stakeholder Platform <ul><ul><li>Actions planned: </li></ul></ul><ul><ul><li>- 31/03/2011: stakeholder day </li></ul></ul><ul><ul><li>- 2011-2012: updating lists and develop contacts: </li></ul></ul><ul><ul><li>Focus 1= breeders (Task1.1) </li></ul></ul><ul><ul><li>Focus 2 = germplasm curators </li></ul></ul><ul><ul><li>Focus 3= fruit chain </li></ul></ul><ul><li>2012: thinking about a European Breeding platform </li></ul><ul><li>FruitBreedomics benefits: </li></ul><ul><li>Links with the European breeders and the fruit chain </li></ul><ul><li>Stakeholder benefits: </li></ul><ul><li>- Participation to the annual stakeholder day </li></ul><ul><li>For some, participation to T3.5 </li></ul><ul><li>Participation to the training sessions (PBA software, DB, pre-breeding material, new traits and tools, new genotyping tools, MAB protocols) </li></ul>
  26. 26. Breeding Stakeholder Platform <ul><ul><li>Actions planned for 2011: </li></ul></ul><ul><ul><li>31/03/2011 : stakeholder day </li></ul></ul><ul><ul><li>April 2011 . François + WP8 : leaflet/ presentation of the project for the breeders: what can the project bring to the breeders? </li></ul></ul><ul><ul><li>May 2011 . Preparation of a questionnaire: Francois, WP1, WP2, WP3, WP8 </li></ul></ul>
  27. 27. Coordination and Governance

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