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FruitBreedomics 1st Stakeholder Day meeting 20120207 Welcome
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FruitBreedomics 1st Stakeholder Day meeting 20120207 Welcome Presentation Transcript

  • 1. An integrated approach forincreasing breeding efficiency inapple and peachLaurens 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, … EU-FP7 large collaborative project 1 March 2011- 31 August 2015
  • 2. AIMS To fill in the gap between Genetics/Genomics and breeding- Development + use of molecular tools (SNP , Full transcriptchips) /international collaboration- Better knowledge / genetics + genomics of major agronomictraits + allelic diversity  Material + tools + methodologies /breeders (within and outside the consortium)
  • 3. AIMS To fill in the gap between Genetics/Genomics and breeding- Development + use of molecular tools (SNP , Full transcriptchips) /international collaboration- Better knowledge / genetics + genomics of major agronomictraits + allelic diversity  Material + tools + methodologies /breeders (within and outside the consortium)
  • 4. PartnersResearch SMEs1 – INRA 3 – ASF2 – ARO (IL) 4 – B3F5 – CRA-W 7 – DNV6 – CRA 14 – NOVADI8 – ETHZ 17 – RDG9 – EVD10 – FEM Management12 – IRTA 11 – IT 24 China13 – JKI15 – PTP 2116 – RBIPH18 – DLO 18 5 1319 – UMIL 4 1620 – UNIBO21 – READING + in 2012 : KUL, RCL … 1 11 8 922 – ARC (ZA) 323 – PFR (NZ) 19 20 1424 – ZJU (CN) 7 15 17 12 6 10+ close links with : Rosbreed (WSU), SLU (Sweeden) 22 23 2 South Africa NZ Israël
  • 5. Structure WP1 Breeding European Breeding Platform WP2 Pre-BreedingWP9. Management WP8 Dissemination WP6 SNP chips Tools WP7 bioinfo Diversity and QTL mapping WP3 PBA WP5 Trait WP4 LD/GWA knowledge
  • 6. Structure WP1 Breeding European Breeding 1. Breeding strategies Platform 2. Fine mapping 3. Pilot studies 4. Pipeline 5. DB interfaceWP1 leader: A. Patocchi (EVD) - On 10 000 seedlings on apple + 10 000 peach - From commercial selection programmes - Traits : according to the needs of stakeholders - Selection of ind +/ind- - Genotyping pipeline
  • 7. Structure European Breeding WP2 Pre-Breeding Platform 1. Material evaluation 2. Conventional pre breeding 3. Fast prebreeding WP2 leader: A. Peil (JKI)
  • 8. Structure WP1 Breeding European Breeding Platform WP2 Pre-BreedingWP3 leader: E. van de Weg (DLO) Diversity and QTL mapping WP3 PBAPedigree Based Analysis 1. Adaptation Flex WP4 leader: M.J. Aranzana WP4 LD/GA 2. QTL new traits (IRTA) 1. Phen & genet variability Genome Wide 3. QTL Fine mapping Association 2. Core collection 4. Genet. div . in EU Breeding 3. QTL mapping by GWA 5. Wider QTL mining 6. QTL validation
  • 9. Fine Genetic Mapping Allelic diversityPedigree Based Analysis Association Genetics
  • 10. Fine Genetic Mapping Allelic diversityPedigree Based Analysis Association Genetics Objective Find an « association » (correlation) between the variation of a marker and a trait Steps: • Phenotyping • Genotyping • Find out associations markers/phenotypes
  • 11. Fine Genetic Mapping Allelic diversity Pedigree Based Analysis Association Genetics MAPPING POPULATIONS CULTIVARS RallsJan Delicious Fuji X-3318 X-3143 Winesap PRI668-100 X-2771 I_J01 Crandall RomBeauty X-6398 Jonathan PRI14-126 Galarina X-3177 X-3263 M_PRI668-100 PRI14-152 12_F01 X-6564 X-6683 GoldenDel RedWinterX3177 Idared PRI612-1 F2_26829-2-2 X-3305 X-6820 12_J01 RedWinter KidsOrRed Florina Wagenerap Gala X-4598 12_I01 Prima Baujade I_W01 Cox Z185 X-6681 I_CC03 X-4355 F_X-4598 X-3259 X-2599 Anta34.16 I_M01 12_K01 X-6799 F_X-4355 Chantecler X-3188 X-6679 Jefferies Ill_#2 12_L01 PRI830-101 12_N01 Coop-17 PRI672-3 Clochard Rubinette Dorianne 12_O03 ReiDuMans X-6823 12_P01 GranSmith X-6417 X-4638 X-6808 I_BB02 F_Ill_#2 TN_R10A8 O53T136 Apple Peach Apple Peach 30 progenies 30 progenies 20-50K SNP chip 9K SNP chip?9-20K? SNP chip 9K SNP chip 4 CC 4 CC
  • 12. Structure WP1 Breeding European Breeding Platform WP2 Pre-Breeding Diversity and QTL mapping WP3 PBA1. Adaptation FlexQTL2. QTL new traits3. QTL Fine mapping4. Genet. div . in EU Breeding5. Wider QTL mining6. QTL validation
  • 13. StructureWP1 Breeding European Breeding Platform WP2 Pre-Breeding Diversity and QTL mapping WP4 LD/GWA 1. Phen & genet variability 2. Core collection 3. QTL mapping by GWA
  • 14. Structure WP5 Trait knowledge WP5 leader: B. Quilot (INRA) 1. Biotic stresses: Monilia
  • 15. Structure- Set up infection tests- Assessment of fruit physical andbiochemical characteristics- Different sources of resistance- Modeling /fruit growth WP5 Trait knowledge WP5 leader: B. Quilot (INRA) 1. Biotic stresses: Monilia
  • 16. Structure Cell wall biochemical Transcriptomics analyses WP5 Trait knowledge 2. Fruit quality : texture, fiber
  • 17. StructureSet up tests to :- Predict chilling and heat requirement WP5 Trait knowledge- Evaluate responses to water scarcity 3. Abiotic stresses:
  • 18. Structure WP1 Breeding European Breeding 1. Breeding strategies Platform WP2 Pre-Breeding 1. Material evaluation 2. Fine mapping 2. Conventional pre breeding 3. Pilot studies 3. Fast prebreeding 4. Pipeline 5. DB interface WP6 SNP chips PFR WP6 leader: R. Velasco RosBREED Low Medium High ARC FEM Low cost MAB Diversity and QTL mapping WP3 PBA1. Adaptation Flex WP5 Trait WP4 LD/GWA knowledge2. QTL new traits 1. Phen & genet variability 1. Biotic stresses3. QTL Fine mapping 2. Core collection 2. Fruit quality4. Genet. div . in EU Breeding 3. QTL mapping by GWA 3. Abiotic stresses5. Wider QTL mining6. QTL validation
  • 19. Structure WP1 Breeding European Breeding 1. Breeding strategies Platform WP2 Pre-Breeding 1. Material evaluation 2. Fine mapping 2. Conventional pre breeding 3. Pilot studies 3. Fast prebreeding 4. Pipeline 5. DB interface WP7 bioinfo WP7 leader: A. Stella GDR (PTP) FruitBreed DB RosBREED (US) Diversity and QTL mapping WP3 PBA1. Adaptation Flex WP5 Trait WP4 LD/GWA knowledge2. QTL new traits 1. Phen & genet variability 1. Biotic stresses3. QTL Fine mapping 2. Core collection 2. Fruit quality4. Genet. div . in EU Breeding 3. QTL mapping by GWA 3. Abiotic stresses5. Wider QTL mining6. QTL validation
  • 20. Structure WP1 Breeding European Breeding 1. Breeding strategies Platform WP2 Pre-Breeding 1. Material evaluation WP9 leader: V. Troillard (IT) WP8 leader: J. Bonany (IRTA) 2. Fine mapping 2. Conventional pre breedingWP9. Management WP8 Dissemination 3. Pilot studies 3. Fast prebreeding 4. Pipeline 5. DB interface WP6 SNP chips Tools WP7 bioinfo Low Medium High FruitBreed DB Low cost MAB Diversity and QTL mapping WP3 PBA 1. Adaptation Flex WP5 Trait WP4 LD/GWA knowledge 2. QTL new traits 1. Phen & genet variability 1. Biotic stresses 3. QTL Fine mapping 2. Core collection 2. Fruit quality 4. Genet. div . in EU Breeding 3. QTL mapping by GWA 3. Abiotic stresses 5. Wider QTL mining 6. QTL validation
  • 21. Structure WP1 Breeding European Breeding 1. Breeding strategies Platform WP2 Pre-Breeding 1. Material evaluation 2. Fine mapping 2. Conventional pre breedingWP9. Management WP8 Dissemination 3. Pilot studies 3. Fast prebreeding 4. Pipeline Breeding stakeholders 5. DB interface WP6 SNP chips Tools WP7 bioinfo Low Medium High FruitBreed DB Low cost MAB Diversity and QTL mapping WP3 PBA 1. Adaptation Flex WP5 Trait WP4 LD/GWA knowledge 2. QTL new traits 1. Phen & genet variability 1. Biotic stresses 3. QTL Fine mapping 2. Core collection 2. Fruit quality 4. Genet. div . in EU Breeding 3. QTL mapping by GWA 3. Abiotic stresses 5. Wider QTL mining Germplasm 6. QTL validation curators
  • 22. Contacts with breeding stakeholders Objective:to establish collaborations with all EU apple and peachbreeding programs to improve our understanding onvarious genetic aspects of breedingThen, extension to non EU countries and other Rosaceaespecies Steps:1- Registration to the stakeholder platform2- Questionnaire/breeding programmes3- Invitation letter to participate to some research (WP3)4- Questionnaire on Database/Breeder interface Not yet started
  • 23. Contacts with breeding stakeholders Questionnaire• General information• Selection criteria/ objectives of selection• Methodology/cycle of selection• Database/ Breeder interface• Genitors, funders, genealogy• ….
  • 24. Contacts with breeding stakeholders Invitation for participation in some research of FruitBreedomics (WP3)Your requested input:1- Providing genealogy information on your germplasm.2-(later), providing young leaves of some selected pedigreed germplasm (for DNAisolation) plus related phenotypic data for some selected traitsIn WP3, FruitBreedomics will provide you with:- Level of representation of your founders in available European breeding germplasm- Genetic relationships within your germplasm (Pedimap software WUR-DLO)- Detailed marker data (SNP markers ) on your material- Report on (in)-consistencies between genealogy and marker data on your material- Presence and absence of QTL-alleles (identified and characterised in other parts ofFruitBreedomics)- Functionality of these QTLs in your environment and genetic backgrounds- Participation in a workshop on Pedigree Based Analyses
  • 25. Contacts with breeding stakeholders General output for the breeders• Access to relevant information on the development of the project• Be eligible for funds to attend training activities and workshops organized by FruitBreedomics on: – MAB protocols (WP1, WP6), – characteristics of new breeding lines or populations made available (WP2), – PBA software: FlexQTL (WP3), Spring 2013 – genetic resources available for fruit breeding (WP4), – assessment of new traits (WP5), – bioinformatics tools (WP7)• Access to the Database and the Breeder interface (when completed)• Invitation to the annual stakeholder seminars of the project
  • 26. Acknowledgement tothe FruitBreedomics consortium
  • 27. Go on www.fruitbreedomics.com to get the last news of the project francois.laurens@angers.inra.fr