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FruitBreedomics KOM 29 03-2011 5 WP3 presentation
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FruitBreedomics KOM 29 03-2011 5 WP3 presentation

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  • 1. Eric van de Weg DLO - PRI , The Netherlands WP3: Identification & characterisation of QTL for fruit quality & disease resistance by Pedigree Based Analysis
  • 2. Objectives
    • Clarify genetics of important traits
      • Some major fruit quality traits
      • Resistance to some diseases
    • in apple:
      • Taste
        • Firmness
        • Juiciness
        • Crispness
        • Total Sugar
        • Acidity
      • Storability
      • Shelf life
      • Harvest date
      • Fruit size
      • Skin Color
      • Chilling requirement
      • Resistance to Nectria
    • in peach:
      • Flowering time
      • Maturity time
      • Fruit Size
      • Skin color
      • Firm/soft melting
      • Resistance to Monilinia
  • 3. Objectives
      • Indentify and fine-map the genomic regions (QTL) that determine phenotypic variation
        • Total number of major genes / QTLs
        • Their location on a linkage map
      • Characterize these genes/QTL
        • Size of their effects
        • Their mode of action within a locus ( intra-locus )
          • additive, dominant, over-dominance, recessive?
        • Their robustness over genetic background & environments
    • Clarify genetics of important traits
      • Some major fruit quality traits
      • Resistance to some diseases
  • 4. Objectives
    • Establishes a basis for MAB
      • QTL-genotype information of cvs & selections
      • Identification of 1 st linked markers  WP1
    • Clarify the genetic structure of EU breeding programs
      • Genetic diversity explored
      • QTL-discovery & validation, allele mining
      • Identification of regions under intense selection
    • Extend functionalities PBA software
    • Clarify genetics of important traits
      • Of some major fruit quality traits
      • Of resistance to some diseases
  • 5. Approach I: clarifying genetics of traits
    • Use of multiple breeding families
      • From multiple programs/sites
    • QTL–analyses with PBA software
      • FlexQTL TM : QTL-discovery
      • Genstat: Robustness over genetic backgrounds & environments
      • Pedimap: Visualization
    • Use of available phenotypic data
      • New phenotyping only for some specific new traits
    • SNP genotyping (± 9K-arrays)
      • Conversion to SNP haplotypes  multi-allelic markers
    • Results:
      • New QTL discovered
      • known QTL are fine mapped
  • 6. Approach II: Genetic structure of breeding programs
    • Breeding progr. with deep pedigrees
      • Breeders interests has to be raised to collaborate !
    • Assess pedigrees of their germplasm
    • Phenotype pedigrees
    • SNP genotype
      • Analyses of allele representation: Signature of breeding?
    • QTL-analyses:
      • QTL validation
      • Allele mining
      • Robustness over environments
  • 7. Tasks
    • T1: Extension of PBA-software for application
    • to high density SNP- genotyping (M1-M24)
    T2: Identification of QTL for new traits by classical QTL mapping (M11-M54) T3: Identification and fine-mapping of QTL by the PBA-approach (M11-M54) T4: Assessment of genetic diversity within European breeding programmes (M1-M48) T5: Mining apple QTL-alleles in breeding germplasm (M12-M48) T6: Robustness apple QTL over environments (M25-M54)
  • 8. Deliverables
    • D1: List of EU-founders & indications on their level of exploitation in breeding. M10
    D2: New version of FlexQTL TM software M24
    • D3: Scientific Papers on
        • 1. QTL for Nectria resistance in apple M36
        • 2. Some QTLs in peach. M36
    D4: Paper on the genetic diversity as exploited in EU apple & peach breeding M48 D5: Paper on some QTLs in apple M52 D6: Report on identified QTL: Location, mode of action, sources, stability & linked markers. M54
  • 9. Interactions planned with other WPs
    • WP6 - Use of SNP array developed in WP6
    • - Defining requirements new apple array
          • Test performance 8K RosBREED array
            • % good SNP (call, parent-offspring (duplications!)
            • transferability of SNP to founders germplasm-wide
            • Reliability of methodology, Defining minimum size
        • - WP5 Runs the arrays, checks scores
    WP8 Workshops on PBA based QTL analyses WP4 - Genetic diversity old & recent cultivars - Platform for validation LD-discovered genes WP1 New QTL/’genes’ for adaptation to MAB WP5 Use of new WP5-phenotyping methods for QTL-mapping of new traits (few progenies) WP7 Support design conceptual model FB-DB
  • 10. Partners involved
    • Apple
      • Performance
        • DLO-PRI
        • INRA
        • UMIL
        • UNIBO
        • ARC – SA
      • Background
        • JKI
        • RIPF
        • SGGW
      • Extensions
        • IASMA
        • KUL ?
        • RC-Laimburg ?
    • Peach
      • IRTA
      • INRA
      • UMIL
      • CRA
      • PTP
      • DLO-PRI
    Kick-off Meeting