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 Annual
Meeting
• 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 Annual
Meeting
• 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
