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FruitBreedomics KOM 29 03-2011 3 WP1 presentation

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  • 1. WP1: Increase efficiency of (marker assisted) breeding Andrea Patocchi ACW (EVD), Switzerland
  • 2. Objectives
    • Develop more efficient breeding programs applying markers assisted breeding
    • To reach this goal :
      • Selection strategies and schemes will be defined and tested in pilot studies
      • Molecular markers (SNPs) tightly linked to specific major horticultural traits will be developed
      • Cost-efficient MAB pipeline(s) will be implemented and used to genotype the plant material of the pilot studies
  • 3. Approach / Methodology
    • Task 1.1: Breeding strategies (M1-M48)
    • Leaders: INRA-An (apple)-Av (peach) François Laurens and Thierry Pascal
    • Inv. part.: DLO, EVD, UNIBO, UMIL, IRTA, Novadi, B3F, ASF, DRG, DNV
      • Breeding companies and institutes will
      • identify the most important 10-15 biotic/abiotic and fruit quality traits/genes/loci and assign them weights
      • define the ideotype(s) they whish to select in their pilot studies (Task 1.3) [supported by stakeholders]
      • define selection scheme(s) specific for their ideotype(s) and
      • Identify the most cost-efficient time point(s) to apply MAB in their selection strategy(ies)
      • Verify if strategies ( e.g. genome wide selection, GWS) used in other crops can be adapted to apple and peach to increase their breeding efficiencies
  • 4. Milestones and deliverables Task 1
    • Milestones
      • MS1: Description of ideotypes and relative breeding scheme (M12)
      • MS2: Evaluation of applicability of GWS to apple and peach (M12)
      • MS3: Evaluation of breeding strategies used in other crops (M30)
    • Deliverables
      • D1.1 Description of ideotypes and breeding schemes (M12) (INRA-An+Av)
      • D1.2 Evaluation of breeding strategies used in other crops (M30) (DLO)
  • 5. Approach / Methodology
    • Task 1.2: Development and mapping of SNPs tightly associated to selected loci (M1-M24)
    • Leaders: EVD (apple), INRA-Av (peach) Andrea Patocchi and Thierry Pascal
    • Involved partners: ETHZ, UNIBO, JKI, PFR, UMIL, IRTA, INRA-Bo
    • Only done for major genes and QTLs with large effects , mapped before the beginning of the project
    • The goal:
      • 5 SNP markers for the major genes (interval 1cM)
      • 10 SNPs for the QTLs (5 on each side of the QTL peak, interval of 10cM)
    • Traits:
      • Apple:
          • Apple scab ( Vf , Vh2 , Vh4 , Vb , Vbj , Vr2 , Vdurello , Vm , Va1 , QTLs LG17), mildew ( Pl1 and 2 , QTL LG2/13), fire blight (Fb-E, Fb.R5), rosy apple aphid ( Dp-fl )
      • Peach:
          • green peach aphid ( Rm2, QTLs LGs 3/5 ) , powdery mildew ( Vr2 , QTLs LGs 6/8 ), fruit low acidity ( D ), flat/round fruit shape ( S ), peach/nectarine ( G ) yellow/white flesh ( Y ), firm/soft melting flesh ( F/f1/f1 )
  • 6. Milestones and deliverables Task 2
    • Milestones
      • MS4: markers tightly linked to the loci of interest identified (M28)
    • Deliverables
      • D1.3 Submitted manuscripts on the fine mapping of selected major genes or QTLs (M28) (EVD, INRA-Av + all partners involved )
  • 7. Approach / Methodology
    • Task 1.3: Pilot studies (M1-M54)
    • Leaders INRA-An (apple)-Av (peach) François Laurens and Thierry Pascal
    • Involved partners: EVD, UNIBO, Novadi, B3F, UMIL, IRTA, ASF, DRG, DNV
      • Breeding strategies defined in T1.1 will be tested in pilot studies
      • Breeding companies will select among their fruiting populations those that (mostly) match the ideotype(s) defined in T1.1
      • Breeding institutes will perform new crosses according the ideotypes they defined in T1.1
      • The populations should have combinations of traits for which SNPs will be developed (T1.2, T3.2, T3.3 and T4.4)
      • Seg. pops will be genotyped using the genotyping pipeline identified in T6.4 and established in T1.4
      • Validation of MAB: Plants carrying favorable and unfavorable alleles combinations of the traits selected by MAB will be phenotyped to check the correctness of the predictions of the markers
  • 8. Milestones and deliverables Task 3
    • Milestones
      • MS7: Pilot studies performed, including MAB and validation of the results (M54)
    • Deliverables
      • D1.4 Submitted manuscripts of the results of the pilot studies (M54) (INRA-An +Av)
  • 9. Approach / Methodology
    • Task 1.4 : Genotyping pipeline (M23-M30)
    • Leader: UNIBO, Stefano Tartarini
    • Involved partners: EVD, INRA, UMIL, Novadi, B3F, ASF, DRG, DNV, IRTA
      • Optimization, description and test in pilot studies of all the steps necessary to perform MAB (tracking of plants samples, collection of leaf samples, DNA extraction, molecular analysis and scoring)
      • Implementation of the markers (of the traits segregating in the populations) for the genotyping protocol(s) (identified in T6.4) best suited for the breeding strategies tested in the pilot studies
      • Genotyping of the plant material of the pilot studies (fully outsourced)
      • Milestone
      • MS5: Optimized MAB protocol(s) (M24)
  • 10. Approach / Methodology
    • Task 1.5 : Specifications list of the breeder-interface to query the database to foster apple and peach breeding (M1-M30)
    • Leader: UNIBO, Stefano Tartarini
    • Involved partners: ETHZ, EVD, CRA, CRA-W, INRA, JKI, DLO, FEM, UMIL, IRTA, Novadi, B3F, ASF, DRG, DNV
      • Breeders, molecular biologists, statisticians and the programmer of the database (WP7) will prepare the list of specifications of the breeder-interface in order to allow breeders to retrieve the information from the database necessary to select the best parents and to interpret MAB results .
      • Milestone
      • MS6: Specifications of breeder interface defined (M30)
  • 11. Interactions planned with other WPs WP1 WP7 Breeders interface (7.1) WP6 New SNPs on high density array (6.3) MAS protocols (6.4) WP2 Conventional pre-breeding (2.2) Markers associated to genes used in fast-breeding (2.3) WP5 Tools to asses fruit quality (5.2) WP3 “ New” genes/traits mapped (3.2) “ old” genes/traits validated (3.3) WP8 Stakeholders MAB demonstration (8.4) WP4 QTLs detected by GWA (4.4) New traits mapped to be used in the pilot studies How genotype the progenies of the pilot studies How the breeders would like to query the DB Presentation of the results of the pilot studies 5.1 Strategies 5.2 SNP markers 5.3 Pilot studies 5.4 Gen. pipeline 5.5 Specifications
  • 12.
    • Thank you for your attention!