FruitBreedomics KOM 29 03-2011 6 WP4 presentation
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  • 1. WP4: Exploring the phenotypic and genetic diversity in European apple and peach germplasm collections and its exploitation by association genetics approach Maria José Aranzana IRTA, Spain
  • 2.
    • Association Genetics
    • Method for fine mapping major genes/QTLs and validation of candidate genes (CG)
    • It exploits the variability and low LD level present among unrelated genotypes that have accumulated a large number of recombinations since their very remote common ancestors
  • 3. WP4 Objectives
    • Improve the knowledge of genetic variability
      • Explore diversity available in apple and peach
      • Define subpopulations
      • Survey (LD) in the defined subpopulations
    • Identify genomic regions contributing to the genetic control of major horticultural traits through genome-wide association genetics (LD mapping)
      • Confirm already-known QTL and explore QTL-allele diversity
      • Reduce confidence interval (CI) around QTL
      • Find new QTLs
    • In combination with WP3, supply WP1 with tightly linked molecular markers for implementation into the MAB pipeline.
  • 4. WP4 Approach / Methodology
    • Task T4.1: Description of the phenotypic and genotypic variability in apple and peach cultivars using already available data
      • Selection of cultivars 1900 apple [from North-West, South, South-West Europe and Central Europe], 1250 peach [Italy, France, Spain and China]
      • Collection of available phenotypic and genotypic information
      • Analysis of phenotypic and genotypic information and upload to a database
  • 5.
    • Merge T4.1 information and additional genotypic data to
    • Task T4.2: Build apple and peach core collections
    • Genotypic data
      • Apple: Genotype the 1900 cultivars with 384 SNPs (Illumina)
      • Peach: genotype the 1250 peach cultivars with 9,000 SNPs (Illumina)
    • Analysis
      • Population genetics parameters (allele frequencies, heterozygosity, population struc ture, LD, etc)
    WP4 Approach / Methodology
  • 6.
    • Task T4.3: Acquiring new phenotypic data on apple and peach core collections
      • Phenot ype the CC with additional traits
        • Complete availab le phenotypes
        • Include traits explored in WP5: drought resistance in apple, texture in both apple and peach and resistance to Monilinia storage disease in peach
    WP4 Approach / Methodology
  • 7.
    • Task T4.4: Genomic location and effect of QTLs detected by genome-wide association (GWA) mapping in apple and peach
      • Apple: High density (50K) SNP genotyping apple cultivars
      • Apple and peach: Genome-wide association analysis
    WP4 Approach / Methodology
  • 8. Expected results / outcomes M54 Submit manuscript of genomic location and effect of QTLs detected by GWA mapping in apple and peach. D4.4 M30 Submit manuscript with description and characterization of allelic diversity, population structure and LD in (i) peach (1250 CVs; 9K SNPs) and ii) apple (1900 CVs; 384 SNP) D4.3 M24 Database uploaded with already-available phenotypic characterization of the peach and apple D4.2 M12 Description of variability using available data in (i) 4 peach and (ii) in 5 apple germplasm collections D4.1 Delivery date Deliverable title Deliverable N°
  • 9. Interactions planned with other WPs WP4 Variability and Association mapping WP1 MAB SNPs linked to traits WP3 PBA Complementary approaches WP5 Phenotyping methods Methods to phenotype novel traits WP6 Arrays development 384 and 50K apple SNP array WP7 Database Upload descriptive info WP8 Dissemination Booklets and training
  • 10. Partners involved Apple Peach INRA INRA CRA-W IRTA READING CRA RBIPH ZJU UNIBO UMIL UMIL DLO DLO FEM FEM