FruitBreedomics 1st Annual meeting 20120208 W4 overview of state of progress
WP4: Exploring the phenotypic and geneticdiversity in European apple and peach germplasmcollections and its exploitation by associationgenetics approach State of progress
State of progress of the ongoing tasks• Task 4.1: Description of available phenotypic and genotypic variability – Creation of a list of peach and apple accessions available in European germplam collections – phenotypic information of peach and apple germplasm, collected through a web-user interface (WP7) or excel templates• Task 4.2: Build apple and peach core collections Peach • 90% of peach germplasm DNA extracted and 9K SNP genotyped • SNP analysis pipeline defined (similar to those in RosBreed)
State of progress of the ongoing tasks Apple • Common SSRs between partners have been identified • Softwares accounting for phenotypic and genetic data (like Darwin and Cervus) will be used for CC definition• Task 4.3: Acquiring new phenotypic data on apple and peach core collections (M13-M46) – List of traits to look at have been defined for both peach and apple
Milestones and Deliverables status• D4.1 (M12): Description of phenotypic and genotypic variability using available data in (i) in 4 peach germplasm collections and (ii) in 5 apple germplasm collections. Postponed to M17• MS14 (M12): Completion of statistical analysis of available phenotypic and genotypic data in peach and apple germplasm
Expected delays and problems• Problem Delay in the analysis of apple phenotypic data. Available phenotypes were not in a digital format, which is taking more time and dedication than expected. Partners involved in this task will dedicate people to enter historical data in an excel template.
Tasks to be done during the AnnualMeeting• Task 4.1: Description of available phenotypic and genotypic variability – Feedback and new options for the web-user interface to enter peach information in a consistent format (partially discussed in the pre-meeting). In the workshop discussion will participate too the database developer. – Possibility of develop a similar tool in apple – Plan schedule for statistic analysis in peach and apple. Common descriptors.
Tasks to be done during the AnnualMeeting• Task 4.2: Build apple and peach core collections – Discuss about the strategy to define peach core collections; in peach discussed in the pre-meeting – In apple establish a strategy for combining SSR marker data – Methodology and plan schedule for to create CC from genotypic and phenotypic data…..• Task 4.3: Acquiring new phenotypic data on apple and peach core collections – Decide the protocol and scales for new peach phenotypic data (decided in the pre-meeting) – In apple, final choice of traits and adequate protocols to be used for 2012
Tasks to be done during the AnnualMeeting• Task T4.4: Genomic location and effect of QTLs detected by genome-wide association (GWA) mapping in apple and peach (M32-M54) – In apple: discuss about the optimal strategy for GW genotyping strategy