This document provides a status update on tasks within Work Package 4, which aims to explore phenotypic and genetic diversity in European apple and peach germplasm collections. It outlines progress made so far in describing variability, building core collections for apple and peach, and acquiring new phenotypic data. Key tasks to be discussed and planned during an upcoming annual meeting include finalizing tools and protocols for phenotypic data collection and analysis, defining strategies for building core collections and genome-wide association mapping in apple and peach.

1. WP4: Exploring the phenotypic and genetic
diversity in European apple and peach germplasm
collections and its exploitation by association
genetics approach State of progress

2. 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)

3. 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

4. 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

5. 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.

6. Tasks to be done during the Annual
Meeting
• 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.

7. Tasks to be done during the Annual
Meeting
• 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

8. Tasks to be done during the Annual
Meeting
• 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