01 introduction-f. laurens-20130221

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01 introduction-f. laurens-20130221

  1. 1. Laurens F., Aranzana M.J., Arus P., Bonany J., Corelli L., Durel C.E., Micheletti D., Patocchi A., Pascal T., Peil, A., Quilot B., Stella A., Troggio M., Troillard V., Velasco R., van de Weg E, … 1 March 2011- 31 August 2015 EU-FP7 large collaborative project www.fruitbreedomics.com2nd annual meeting Lleida
  2. 2. 15 Research 1 – INRA 2 – ARO (IL) 5 – CRA-W 6 – CRA 8 – ETHZ 9 – EVD 10 – FEM 12 – IRTA 13 – JKI 15 – PTP 16 – RBIPH 18 – DLO 19 – UMIL 20 – UNIBO 21 – READING 22 – ARC (ZA) 23 – PFR (NZ) 24 – ZJU (CN) 25 – KUL 26 – RCL SMEs 3 – ASF 4 – B3F 7 – DNV 14 – NOVADI 17 – RDG Management 11 – IT 22 23 24 16 18 19 20 21 3 4 714 17 13 12 10 98 6 5 2 11 IsraëlNZ China South Africa 1 + close links with : Rosbreed (WSU), SLU (Sweeden) Partners 25 + contacts in Russia: VNIISPK (Orel) SKZNIISIV (Krasnodar) North Caucasia
  3. 3. To fill in the gap between Genetics/Genomics and breeding - Development + use of molecular tools (SNP , Full transcript chips) /international collaboration - Better knowledge / genetics + genomics of major agronomic traits + allelic diversity  Material + tools + methodologies /breeders AIMS
  4. 4. WP5 Trait knowledge WP1 Breeding/MAB WP2 Pre-BreedingEuropean Breeding Platform Diversity and QTL mapping WP3 PBA WP4 LD/GWA WP6 SNP chips WP7 bioinfoTools WP8Dissemination WP9.Management A. Patocchi (EVD) A. Peil (JKI) E. van de Weg (DLO) Pedigree Based Analysis Genome Wide Association M.J. Aranzana (IRTA) B. Quilot (INRA) A. Stella (PTP)R. Velasco (FEM) V.Troillard(IT) J.Bonani(IRTA)
  5. 5. Test the efficiency of the use of molecular markers in current breeding programmes WP1 Breeding/MAB
  6. 6. 1. Breeding strategies 2. Fine mapping 3. Pilot studies 4. Pipeline 5. DB interface WP1 highlights 2012 + perspectives 2013 - Apple and peach Questionnaires, meetings  priorities - Breeding criteria - Breeding schemes SNP markers tighted to most of the targeted genes Selection of the apple pilot progenies In progress - Test of SNP based low cost genotyping platforms for MAB and GWS - pipeline… to be discussed at the WP1 workshop Decision to move towards GWS -> MAB for MG -> GWS for Q traits WP1 Breeding/MAB WP8
  7. 7. 1. Breeding strategies 2. Fine mapping 3. Pilot studies 4. Pipeline 5. DB interface WP1 highlights 2012 + perspectives 2013 - Apple and peach Questionnaires, meetings  priorities - Breeding criteria - Breeding schemes SNP Markers tighted to most of the targeted genes Selection of the apple pilot progenies In progress - Test of SNP based low cost genotyping platforms for MAB and GWS - pipeline… to be discussed at the WP1 workshop Decision to move towards GWS -> MAB for MG -> GWS for Q traits WP1 Breeding/MAB  MAB  GWS On apple and peach Ms on fine mapping of selected major genes or QTLs
  8. 8. WP2 Pre-Breeding WP2 highlights 2012 + perspectives 2013 To prepare new genitors (progenitors) for the future breeding programmes  Selection time
  9. 9. 1. Material evaluation 2. Conventional pre breeding 3. Fast prebreeding WP2 highlights 2012 + perspectives 2013 Plant material evaluated for resistance and fruit traits New progenies created to pyramide genes of interest New early apple flowering lines carrying resistance genes (fire blight, powdery mildew) produced and pollinated WP2 Pre-Breeding
  10. 10. 1. Material evaluation 2. Conventional pre breeding 3. Fast prebreeding WP2 highlights 2012 + perspectives 2013 Plant material evaluated for resistance and fruit traits New progenies created to pyramide genes of interest New early apple flowering lines carrying resistance genes (fire blight, powdery mildew) produced and pollinated WP2 Pre-Breeding Phenotype and genotype new progenies Put data in DB Solve some issues about FB early flowering lines
  11. 11. Diversity and QTL fine mappingWP3 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 Pedigree Based Analysis Genome Wide Association
  12. 12. 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 FlexPedigree Based Analysis Peach progenies genotyped with the 9K IPSC SNP array FlexQTLTM Interface computation time  New functionalities WP3 highlights 2012 + perspectives 2013 first peach QTL mapping analyses in progress Apple 20K SNP array WP6
  13. 13. 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 FlexPedigree Based Analysis Peach progenies genotyped with the 9K IPSC SNP array FlexQTLTM Interface computation time  New functionalities WP3 highlights 2012 + perspectives 2013 Apple 20K SNP array Peach QTL mapping analyses completed Apple QTL mapping analyses Integrated linkage map List of EU-founders and indications on their level of exploitation in breeding. (Del 3.1) WP6 Organization of the PBA training session WP8
  14. 14. WP4 LD/GA Genome Wide Association Genetic structure of apple and peach germplasm. Preliminary GWA studies on peach Apple and peach phenotypic data in FB DB WP4 highlights 2012 + perspectives 2013 WP1 WP7 Define core collection D4.1 Test panel with 48 accessions genotyped with 20K SNP chip WP6
  15. 15. WP4 LD/GA Genome Wide Association Genetic structure of apple and peach germplasm. Preliminary GWA studies on peach Apple and peach phenotypic data in FB DB WP4 highlights 2012 + perspectives 2013 WP1 WP7 Define core collection D4.1 Test panel with 48 accessions genotyped with 20K SNP chip WP6 Peach GWA studies completed Apple genotyping (choice of the genotyping tool) then GWA WP6
  16. 16. WP5 Trait knowledge 1. Biotic stresses: Monilia 2. Fruit quality : texture, fiber 3. Abiotic stresses WP5 highlights 2012 + perspectives 2013 and test of tools and protocols Start transcriptomics approach /Fruit quality
  17. 17. WP5 Trait knowledge 1. Biotic stresses: Monilia 2. Fruit quality : texture, fiber 3. Abiotic stresses WP5 highlights 2012 + perspectives 2013 and test of tools and protocols Start transcriptomics approach /Fruit quality Select highthrouput phenotyping tools Select /stop  New tests in 2013 Analysis of the data
  18. 18. WP6 SNP chips Tools Tests of low density chips for WP1 20k Illumina Infinium Apple SNP Chip available WP6 highlights 2012 + perspectives 2013 Test apple 20k Illumina Infinium on 48 genotypes WP4WP1 WP3
  19. 19. WP6 SNP chips Tools Tests of low density chips for WP1 20k Illumina Infinium Apple SNP Chip available Selection of a genotyping tool for apple WP4 in progress (GBS or arrays ?) WP6 highlights 2012 + perspectives 2013 Test apple 20k Illumina Infinium on 48 genotypes WP4 Protocols to be used for large germplasm genotyping WP1 WP3 WP4 WP4 Final choice = Feb 2013
  20. 20. WP7 bioinfoTools Structure of phenotypic DB for apple and peach completed User Interface completed WP7 highlights 2012 + perspectives 2013 Excel template Apple and peach data in the DB
  21. 21. WP7 bioinfoTools Structure of phenotypic DB for apple and peach completed Need to standardize names (ontology) Search tool in phenotypic database User Interface completed WP7 highlights 2012 + perspectives 2013 Enter and use genotypic data Resequencing data Excel template Apple and peach data in the DB
  22. 22. WP8 Dissemination WP8 highlights 2012 + perspectives 2013 Design and management of the Website Contacts with stakeholders (meetings, questionnaires) 1st Newsletter
  23. 23. Training sessions WP8 Dissemination WP8 highlights 2012 + perspectives 2013 Design and management of the Website Contacts with stakeholders (meetings, questionnaires) 1st Newsletter 2nd Newsletter Transfer of technology to stakeholders

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