WP 5 - Bioinformatics
WP Leader: Dr. Klaus Mayer (HMGU, E-mail: k.mayer@helmholtz-muenchen.de)
Large amounts of physical map information and BAC end sequences (WP1), genetic mapping and molecular markers data (WP2), and genomic sequences from targeted regions (WP3) will be produced during the TriticeaeGenome project.
WP5 aims at developing new tools to structure, relate, and analyse these data comprehensively. A first task is to build a conceptual database and a web interface to store and display physical maps integrated with genetic maps through molecular markers and sequence data. This “TriticeaeGenome platform” will capture and integrate publicly available data from related national and international efforts. Since no database has been established for the wheat or barley international consortia thus far, this platform can be proposed as a reference for the Triticeae physical maps and sequence collections that will be generated by the other international projects.
During the first year, databases at INRA and HGMU were optimized to prepare their implementation with marker data that will be useful for the physical map anchoring and map-based cloning projects. Marker types and common exchange format were agreed. In addition, a new analytical framework for Linear Topology Contig (LTC) assembly has been developed and its elements have been tested on data from the wheat 3B physical map.
Deliverables:
D5.1: TriticeaeGenome database & web interface : maps; sequences, genomic, genetic resources and SNP data integration and display (June 2010)
D5.2: Prototype implementation of Triticeae online structural analysis tool (June 2009) available
D5.3: GnpMap graphical interface MapComparator improvement to display physical maps and develop comparative and integrative maps for different mapping populations (June 2010)
D5.4: Adaptive assembly algorithm for physical mapping with regulated stringency of clustering and verification of the resulted contigs and clone orders within contigs (November 2010)
D5.5: Comparative Triticeae map and genome platform and referencing to suitable reference and model genomes (July 2011)
Other WPs:
- WP1 - Establishment of genomic resources for physical mapping of wheat
- WP2 - Construction of anchored chromosome- and genomic physical maps of wheat and barley
- WP3 - Gene isolation and new allele discovery
- WP4 - Markers for molecular breeding
- WP6 - Dissemination, Technology Transfer and training
- WP7 - Management
This project is supported by the European Commission under the 7th Framework Programme
for Research and Technological Development