FruitBreedomics KOM 29 03-2011 1 introduction

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FruitBreedomics KOM 29 03-2011 1 introduction

  1. 1. The new EU project Fruit Breedomics *: an integrated approach for increasing breeding efficiency in apple and peach 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, … * FP7 large collaborative Fruit Breedomics
  2. 2. <ul><li>Fruit Breeding programmes </li></ul><ul><ul><li>Numerous </li></ul></ul>Context (1) Fruit Breedomics
  3. 3. <ul><li>Fruit Breeding programmes </li></ul><ul><ul><li>Numerous </li></ul></ul><ul><ul><li>Similar objectives : </li></ul></ul><ul><ul><ul><li>Pest and disease resistance, </li></ul></ul></ul><ul><ul><ul><li>Fruit quality, </li></ul></ul></ul><ul><ul><ul><li>Regular cropping </li></ul></ul></ul><ul><ul><ul><li>.... </li></ul></ul></ul>Context (1) Fruit Breedomics
  4. 4. <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 (1) Fruit Breedomics
  5. 5. <ul><li>Genetic studies </li></ul><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 (2) Fruit Breedomics
  6. 6. Context (3) <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>Fruit Breedomics Fruit Breedomics
  7. 7. <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>Fruit Breedomics’ aims: Fruit Breedomics
  8. 8. <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>Fruit Breedomics’ aims: Fruit Breedomics
  9. 9. Structure of FruitBreedomics 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 Fruit Breedomics
  10. 10. Structure of FruitBreedomics 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 Fruit Breedomics
  11. 11. Structure of FruitBreedomics 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 Fruit Breedomics
  12. 12. Structure of FruitBreedomics 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 Fruit Breedomics WP7 bioinfo FruitBreed DB
  13. 13. Structure of FruitBreedomics 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 Fruit Breedomics WP6 SNP chips Low Medium Low cost MAB High
  14. 14. Structure of FruitBreedomics 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 Fruit Breedomics WP6 SNP chips Low Medium Low cost MAB High WP7 bioinfo FruitBreed DB Tools
  15. 15. Structure of FruitBreedomics 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 Fruit Breedomics WP6 SNP chips Low Medium Low cost MAB High WP7 bioinfo FruitBreed DB Tools Breeding stakeholders Germplasm curators
  16. 16. Interactions within FruitBreedomics 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 Fruit Breedomics
  17. 17. 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) … Fruit Breedomics
  18. 18. <ul><li>/ Scientists : - molecular tools - Better knowledge / genetics + genomics of major agronomic traits + allelic diversity </li></ul>Expected impacts <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>Fruit Breedomics
  19. 19. Acknowledgement to the Fruit Breedomics consortium The most difficult (but the most challenging) is to come!! Fruit Breedomics
  20. 20. Acknowledgement to the Fruit Breedomics consortium The most difficult (but the most challenging) is to come!! Fruit Breedomics
  21. 21. Role of the coordinator <ul><li>His primary roles : </li></ul><ul><ul><li>To represent the Consortium towards the EC </li></ul></ul><ul><ul><li>To promote and supervise the technical and scientific progress of the project </li></ul></ul>
  22. 22. Role of the coordinator <ul><li>He is responsible for : </li></ul><ul><ul><li>Chairing the Executive Committee and the General Assembly => implement decisions from this body </li></ul></ul><ul><ul><li>Ensuring “smooth” operation of the project : work plan maintenance, monitoring project progress, identification of trouble and consequences for future research </li></ul></ul><ul><ul><li>Writing periodic reports </li></ul></ul><ul><ul><li>Submitting all required progress reports, deliverables, financial statements to the EC </li></ul></ul><ul><ul><li>Communicating all information in connection with the project to the EC </li></ul></ul><ul><ul><li>Transferring the advance payments and further payments to the participants … </li></ul></ul>
  23. 23. Role of the European Project Manager <ul><li>He is in charge of: </li></ul><ul><ul><li>the daily management work, </li></ul></ul><ul><ul><li>project administration, </li></ul></ul><ul><ul><li>financial administration, </li></ul></ul><ul><ul><li>consolidation of project reports and handling of the project logistics. </li></ul></ul>

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