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FruitBreedomics KOM 29 03-2011 5 WP3 presentation
FruitBreedomics KOM 29 03-2011 5 WP3 presentation
FruitBreedomics KOM 29 03-2011 5 WP3 presentation
FruitBreedomics KOM 29 03-2011 5 WP3 presentation
FruitBreedomics KOM 29 03-2011 5 WP3 presentation
FruitBreedomics KOM 29 03-2011 5 WP3 presentation
FruitBreedomics KOM 29 03-2011 5 WP3 presentation
FruitBreedomics KOM 29 03-2011 5 WP3 presentation
FruitBreedomics KOM 29 03-2011 5 WP3 presentation
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 <ul><li>Clarify genetics of important traits </li></ul><ul><ul><li>Some major fruit quality traits </li></ul></ul><ul><ul><li>Resistance to some diseases </li></ul></ul><ul><li>in apple: </li></ul><ul><ul><li>Taste </li></ul></ul><ul><ul><ul><li>Firmness </li></ul></ul></ul><ul><ul><ul><li>Juiciness </li></ul></ul></ul><ul><ul><ul><li>Crispness </li></ul></ul></ul><ul><ul><ul><li>Total Sugar </li></ul></ul></ul><ul><ul><ul><li>Acidity </li></ul></ul></ul><ul><ul><li>Storability </li></ul></ul><ul><ul><li>Shelf life </li></ul></ul><ul><ul><li>Harvest date </li></ul></ul><ul><ul><li>Fruit size </li></ul></ul><ul><ul><li>Skin Color </li></ul></ul><ul><ul><li>Chilling requirement </li></ul></ul><ul><ul><li>Resistance to Nectria </li></ul></ul><ul><li>in peach: </li></ul><ul><ul><li>Flowering time </li></ul></ul><ul><ul><li>Maturity time </li></ul></ul><ul><ul><li>Fruit Size </li></ul></ul><ul><ul><li>Skin color </li></ul></ul><ul><ul><li>Firm/soft melting </li></ul></ul><ul><ul><li>Resistance to Monilinia </li></ul></ul>
  • 3. Objectives <ul><ul><li>Indentify and fine-map the genomic regions (QTL) that determine phenotypic variation </li></ul></ul><ul><ul><ul><li>Total number of major genes / QTLs </li></ul></ul></ul><ul><ul><ul><li>Their location on a linkage map </li></ul></ul></ul><ul><ul><li>Characterize these genes/QTL </li></ul></ul><ul><ul><ul><li>Size of their effects </li></ul></ul></ul><ul><ul><ul><li>Their mode of action within a locus ( intra-locus ) </li></ul></ul></ul><ul><ul><ul><ul><li>additive, dominant, over-dominance, recessive? </li></ul></ul></ul></ul><ul><ul><ul><li>Their robustness over genetic background & environments </li></ul></ul></ul><ul><li>Clarify genetics of important traits </li></ul><ul><ul><li>Some major fruit quality traits </li></ul></ul><ul><ul><li>Resistance to some diseases </li></ul></ul>
  • 4. Objectives <ul><li>Establishes a basis for MAB </li></ul><ul><ul><li>QTL-genotype information of cvs & selections </li></ul></ul><ul><ul><li>Identification of 1 st linked markers  WP1 </li></ul></ul><ul><li>Clarify the genetic structure of EU breeding programs </li></ul><ul><ul><li>Genetic diversity explored </li></ul></ul><ul><ul><li>QTL-discovery & validation, allele mining </li></ul></ul><ul><ul><li>Identification of regions under intense selection </li></ul></ul><ul><li>Extend functionalities PBA software </li></ul><ul><li>Clarify genetics of important traits </li></ul><ul><ul><li>Of some major fruit quality traits </li></ul></ul><ul><ul><li>Of resistance to some diseases </li></ul></ul>
  • 5. Approach I: clarifying genetics of traits <ul><li>Use of multiple breeding families </li></ul><ul><ul><li>From multiple programs/sites </li></ul></ul><ul><li>QTL–analyses with PBA software </li></ul><ul><ul><li>FlexQTL TM : QTL-discovery </li></ul></ul><ul><ul><li>Genstat: Robustness over genetic backgrounds & environments </li></ul></ul><ul><ul><li>Pedimap: Visualization </li></ul></ul><ul><li>Use of available phenotypic data </li></ul><ul><ul><li>New phenotyping only for some specific new traits </li></ul></ul><ul><li>SNP genotyping (± 9K-arrays) </li></ul><ul><ul><li>Conversion to SNP haplotypes  multi-allelic markers </li></ul></ul><ul><li>Results: </li></ul><ul><ul><li>New QTL discovered </li></ul></ul><ul><ul><li>known QTL are fine mapped </li></ul></ul>
  • 6. Approach II: Genetic structure of breeding programs <ul><li>Breeding progr. with deep pedigrees </li></ul><ul><ul><li>Breeders interests has to be raised to collaborate ! </li></ul></ul><ul><li>Assess pedigrees of their germplasm </li></ul><ul><li>Phenotype pedigrees </li></ul><ul><li>SNP genotype </li></ul><ul><ul><li>Analyses of allele representation: Signature of breeding? </li></ul></ul><ul><li>QTL-analyses: </li></ul><ul><ul><li>QTL validation </li></ul></ul><ul><ul><li>Allele mining </li></ul></ul><ul><ul><li>Robustness over environments </li></ul></ul>
  • 7. Tasks <ul><li>T1: Extension of PBA-software for application </li></ul><ul><li> to high density SNP- genotyping (M1-M24) </li></ul>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 <ul><li>D1: List of EU-founders & indications on their level of exploitation in breeding. M10 </li></ul>D2: New version of FlexQTL TM software M24 <ul><li>D3: Scientific Papers on </li></ul><ul><ul><ul><li>1. QTL for Nectria resistance in apple M36 </li></ul></ul></ul><ul><ul><ul><li>2. Some QTLs in peach. M36 </li></ul></ul></ul>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 <ul><li>WP6 - Use of SNP array developed in WP6 </li></ul><ul><li> - Defining requirements new apple array </li></ul><ul><ul><ul><ul><li>Test performance 8K RosBREED array </li></ul></ul></ul></ul><ul><ul><ul><ul><ul><li>% good SNP (call, parent-offspring (duplications!) </li></ul></ul></ul></ul></ul><ul><ul><ul><ul><ul><li>transferability of SNP to founders germplasm-wide </li></ul></ul></ul></ul></ul><ul><ul><ul><ul><ul><li>Reliability of methodology, Defining minimum size </li></ul></ul></ul></ul></ul><ul><ul><ul><li>- WP5 Runs the arrays, checks scores </li></ul></ul></ul>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 <ul><li>Apple </li></ul><ul><ul><li>Performance </li></ul></ul><ul><ul><ul><li>DLO-PRI </li></ul></ul></ul><ul><ul><ul><li>INRA </li></ul></ul></ul><ul><ul><ul><li>UMIL </li></ul></ul></ul><ul><ul><ul><li>UNIBO </li></ul></ul></ul><ul><ul><ul><li>ARC – SA </li></ul></ul></ul><ul><ul><li>Background </li></ul></ul><ul><ul><ul><li>JKI </li></ul></ul></ul><ul><ul><ul><li>RIPF </li></ul></ul></ul><ul><ul><ul><li>SGGW </li></ul></ul></ul><ul><ul><li>Extensions </li></ul></ul><ul><ul><ul><li>IASMA </li></ul></ul></ul><ul><ul><ul><li>KUL ? </li></ul></ul></ul><ul><ul><ul><li>RC-Laimburg ? </li></ul></ul></ul><ul><li>Peach </li></ul><ul><ul><li>IRTA </li></ul></ul><ul><ul><li>INRA </li></ul></ul><ul><ul><li>UMIL </li></ul></ul><ul><ul><li>CRA </li></ul></ul><ul><ul><li>PTP </li></ul></ul><ul><ul><li>DLO-PRI </li></ul></ul>Kick-off Meeting

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