GDR Newsletter December 2006

Welcome to the sixth issue of the GDR newsletter. This newsletter is issued to inform users about new or updated data and features in GDR and community related news. Please feel free to provide feedback and news either directly by email or via our online form.

What's new at GDR?

• GDR has moved
       GDR has been successfully moved to Washington State University servers. If you have any problems accessing any of the GDR pages, please contact us.
  
• New Unigene
       The Rosaceae&Unigene&Version&3 is now available. All the publicly available Rosaceae ESTs have been assembled using CAP3. Assemblies were also      generated for the EST sets of each genus: Malus, Prunus, Fragaria, Rosa and Pyrus. The contigs and singlets for each assembly have been searched against the      Swissprot and TrEMBL databases, and the homology results are available to search and download.
  
• New Marker/Trait Pages
       A new comprehensive marker and trait search site is now available. Molecular markers can be searched by name, type, species, map position and associated      sequences such as ESTs and BACs. Traits can be searched by name, symbol, taxon, or trait category. Markers are annotated with primer sequences, marker      source, associated BACs or ESTs, map positions and more (eg. BPPCT028, trait flesh adhesion).
  
• Updates to the Comparative Mapping Viewer CMap
       Fifteen new or updated maps
       (peach PxF, Lovell x Nemared, NJ Pillar x KV 77119, Red Raspberry 2006, Diploid Rose D10 x E15, Guardian x Nemaguard 2006, Prunus resistance map,      Prunus transcriptome map, Fiesta x Discovery apple 2006, 815 x 903 BC diploid Fragaria 2006 and FVxFN diploid Fragaria reference map 2006, Bartlett, Housui,      Kinchaku1a, and Kinchaku1b) have been added to the genetic maps available through CMap. This now makes a total of 36 Rosaceae CMaps available through      GDR.
  
• Download page updated
       Available from the updated download page are: all the annotated data of the unigene sets for Rosaceae and each genus, the annotated data for individual EST      projects, and the prunus transcriptome map data (peach ESTs that hybridized to peach BACs, anchored to prunus genetic maps or anchored to peach BAC      contigs).
  
• QTL mailing list available
       The working document for the standard QTL nomenclature has been prepared by Drs Jim Olmstead, Cameron Peace and Eben Oqundiwin. To facilitate      discussions among rosaceae researchers on QTL nomenclature, a specific mailing list has been created. Visit mailing lists page to subscribe and view/search      the list archives.
  
• Additions to the publication database
       The publication database on GDR now contains 2269 relevant publications and can be searched by title, authors, keywords, and date published.
  
• Map/marker annotation effort
       We are making an effort to acquire and annotate publicly available rosaceae maps and markers to upload to CMap and the marker/trait database. A number of      authors responded to our emails asking for map data. We greatly appreciate your interest and help in building this community database!

Community News

• Funding
• The NSF RCN proposal to bring together all the Rosaceae informatics groups to facilitate more collaboration and distribution of GDR work was unsuccessful      this year. We hope to resubmit next year
• In November, a GDR renewal proposal was submitted to the NSF Plant Genome Program. In the meantime, a no-cost extension was granted by the NSF to      allow us to spend out the remainder of funds we had available. Please be aware that we are very limited as to what we can accomplish in GDR over the next six      months while we await the renewal decision and provision of funds if successful.
• The USDA has announced that the CSREES NRI program in 2008 will focus on Rosaceae and Compositae proposals.
  
• Conferences
• Plant and Animal Genome XV Conference, January 13-17th, 2007, events
• A Computer Demonstration of GDR will be provided on Sunday, Jan 14, 3:35pm - 3:55 pm
• GDR will be presented at the Fruit and Nut Workshop and Computer Demos (Part I), and GDR team will be available in all the other Rosaceae events listed      below
• Rosaceae NRI Meeting (open), Friday, Jan 12, 6.00pm - 10.00pm.
• Fruit and Nut Workshop, Saturday, Jan 13 at 8.00am - 12.40pm.
• Citrus Workshop, Saturday, Jan 13 at 1.15pm - 3.25pm.
• US RosEXEC Meeting (open), Sunday, Jan 14, 8.00am - 10.00am.
• Intl Roscaceae Genomics Meeting (open), Sunday, Jan 14, 10.00am - 12.00am.
• A national workshop on \"Plant breeding: A vital capacity for US national goals\" is scheduled for February 8-9, 2007, in Raleigh, NC.
  
• Employment
       Research Opportunities available in the laboratories of Dr. Cameron Peace and Dr. Amit Dhingra at Washington State University. Details are available through the      GDR employment page. Contact us if you would like a Rosaceae job opportunity advertised through GDR.

Subscriptions

Visit our mailing lists be added/removed to the available GDR mailing lists
Once you have registered you may use the mailing lists to send out relevant information the community and it will be stored in searchable web archives. More information is available on each page on how to use them. if you have any difficulties please contact us.
The GDR mailing list.
The International Rosaceae Genomics Community mailing list.
The USA Rosaceae Genomics Community mailing list.

Work in progress

Development of a BAC annotation pipeline
Implementation of a Rosaceae focused metabolic pathways database (MetaCyc)