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FruitBreedomics 1st Annual meeting 20120208 WP7 Overview of state of progress
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FruitBreedomics 1st Annual meeting 20120208 WP7 Overview of state of progress

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  • 1. WP7State of progress
  • 2. State of progress of the ongoing tasks• Task 7.1: Structuration/Mirroringof the consensus database (M1– M54) – Applebreedmodelacquired – Schemeof the GDR-FBdbdeveloped – Modulesprogramming – Naturaldiversitymoduleinstalled and tested – Structurefor DB integration• Task 7.2: Constructionofrelational database ofphenotypic data fortargetedtraits (M1– M48) – Database structure developed – Peach and Apple – Interface developed – Peach – Data entry ongoing – Peach – Interface for data retrival - Peach
  • 3. State of progress of the ongoing tasks• Task 7.3: Developmentofpipelinesofanalysis and storageofdetectedgenomicvariation (M8– M36) – Developmentof interface with GDR db – Localgenome browser• Task7.4: Meta-analysis (M24– M48)• Task 7.5: Toolsforfunctional and comparative analysisofidentifiedvariation (M12– M48)
  • 4. Deliverables status• D7.1 (M12) FruitBreedomics database frame – Report • Descriptionof the db structurescheme, DBMS and interface withsequence data• D7.2 (M24): Complete collectionsof trait phenotypic data fromgenetic material available and complete listofidentifiedgenomicvariation – Peachphenotype• D7.3 (M48) Complete operating pipeline for “model” traitsanalysisfor candidate genesdiscovery• D7.4 (M54) Toolsforphenotypic and molecularmarker data analysisfor PBA/LD/MBA integrated in the FruitBreedomics DB.
  • 5. Milestones status• MS34 (M12): Developmentof the consensus database in coordinationwith GDR – DB scheme – Agreement on toolsdevelopment• MS35 (M36): Alfa versionof the integrated database. Developmentofphenotypic data/genetic material network• MS36 (M48): Modellingtraitsstudy• MS37 (M54): Beta versionof the integrated database Correlationofphenotypic/genotypic data for PBA/LD/MBA.
  • 6. Expected delays and problems• Problems: – Some of tripal modules (GDR) stillunderdevelopment • Could cause delays •  corrective action: – Use mySQLbaseddb as a base structure – Automated interface to chado-like structure – Risk:most data willbeadded to dblater •  corrective action: – Use data frompreviousproject (Applebreed) – Start withexample data
  • 7. Tasks to be done during the AnnualMeeting• Task 7.1: Structuration/Mirroringof the consensus database (M1– M54) – Definemarker data input • Input interface and tablesconnections • Define format fordiversity data – Breeder toolbox • Differences and furtherdevelopmentsfromRosBreed BTB• Task 7.2: Constructionofrelational database ofphenotypic data fortargetedtraits (M1– M48) – Definephenotypedescriptorsforapple and relationshipwithaccessions (cultivars) and locations – Fine tuningofphenotypequeriesforpeach
  • 8. Tasks to be done during the AnnualMeeting• Task 7.3: Developmentofpipelinesofanalysis and storageofdetectedgenomicvariation (M8– M36) – Choosedescriptorsfor QTL data • LA and PBA • Peach and apple – Choosedescriptorsforassociationanalysis • Ldanalysis • Peach and Apple• Task 7.5: Toolsforfunctional and comparative analysisofidentifiedvariation (M12– M48) – Agree on fine annotationofidentifiedregionsof interest – Peach and Apple