GDR Newsletter May 2006
Welcome to the fifh issue of the GDR newsletter. This newsletter is 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. The online version can be found
at
http://www.mainlab.clemson.edu/gdr/newsletter/newsletter0506.shtml
Attached is the pdf version of this newsletter.
Community News
White Paper
The US National Rosaceae Genomic, Genetics and Breeding Executive
Committee have completed the US white paper on Rosaceae Genomics. It can
be downloaded from GDR and any comments can be addressed to the executive
committee chair, Dr Amy Iezonni.
Funding
1. A US based proposal, supported by strong international collaboration,
is being submitted to the NSF Plant Genome Comparative Sequencing program
in June. We are proposing to sequence the peach genome as a reference for
Rosaceae, with skim sequencing of strawberry and apple, and targeted deep
coverage of selected loci across multiple species. For more information
contact Bryon Sosinski of NC State.
2. A US based proposal is being submitted to the NSF Networking program in
June to fund a Rosaceae Informatics Network where international
bioinformatics researchers will meet regularly and develop a collaborative
bioinformatics infrastructure for the community database. For more
information contact Dorrie Main or Bert Abbott.
Conferences
The 3rd International Rosaceae Genomics Conference was held March 19-22,
2006, in Napier, New Zealand. Download the conference outcomes and the
abstracts from this meeting. The 4th International Rosaceae Genomics
Conference is scheduled to be held in Pućon, Chile in March 2008.
More details will be posted in the GDR conferences page as they become
available.
Employment
A faculty position in plant breeding is available at the Pontificia
Universidas Catolica de Chile.
What's new at GDR?
1. SNPs (Single Nucleotide Polymorphisms)
2. Updates to the peach physical map
3. Updates to the Comparative Mapping Viewer CMap
4. Marker/Map data template available
5. Rosaceae Genomics White papers
6. Species page/Project page
7. New header bar
8. Community pages and mailing lists
9. New publication from GDR
10. Additions to the publication database
1. SNPs (Single Nucleotide Polymorphisms)
The new Fragaria, Malus, Prunus, Pyrus, and Rosa unigenes have been
searched for SNPs using the software package AutoSNP. A total of 14,801
SNPs are available to be viewed and searched, including 10426 SNPs from
Malus, 3776 from Prunus, 316 from Rosa, and 283 from Fragaria.
2. Updates to the peach physical map
The latest peach physical map contains 18387 BACs and 1367 contigs.
Physical length of the contigs is appoximately 210-230Mb and that of the
anchored contigs is 33Mb. WebFPC / WebChrom displays the peach physical
map. Anchored peach BAC contigs can be accessed directly from the prunus
reference TxE map from the GDR map viewer.
3. Updates to the Comparative Mapping Viewer CMap
Four new maps (Apricot GxV F1 2002, Apricot LxL F2 2003, Peach AxJ 2005
and 815x903BC diploid Fragaria 2006) have been added to the genetic maps
available through CMap. This now makes a total of 24 Rosaceae CMaps are
available through CMap at GDR.
These include:
Prunus: Prunus bin map 2005, TxE almond x peach F2 2004, Myrobalan Plum
x Almond- Peach hybrid 2004, GxN almond x peach F2 2001
Peach: Peach AxJ 2005, Peach PMP2 2005, Peach peach x P. ferganensis BC1
PxF 2001, Peach JxF 2004, Peach Sc x B 1998
Apricot: Apricot GxV F1 2002, Apricot LxL F2 2003
Almond: Almond FxT 2000, Almond FxB F1 1998
Sour Cherry: PcerasusEB, PcerasusRS
Strawberry: FVxFN diploid Fragaria reference map, 815x903BC diploid
Fragaria 2006
Apple: MNY75441-58, MNY75441-67, MWijcik_McIntosh, MRomeBeauty,
MRomeBeauty_2, MWhiteAngel, MWhiteAngel_2
If you have mapping data that we can add, please contact us and we will
work with you to make your data available via GDR.
4. Marker/Map data template available
Efforts are underway to curate more extensive genetics data to GDR, and
data templates for map/marker/trait/polymorphism/gene/QTL/Diversity are
available.
5. Rosaceae Genomics White papers
The US National Rosaceae Genomic, Genetics and Breeding Executive
Committee have completed the US white paper on Rosaceae Genomics. They can
be downloaded from GDR and any comments can be submitted to the executive
committee chair, Dr Amy Iezonni.
6. Species page/Project page
GDR has been reorganized to enhance navigation in the website. We have
created specific species pages, under each genus where you can access all
the information related to that species in GDR. Go to apple, prunus,
almond, apricot, cherry, peach, rose, strawberry pages for all GDR
structural genomics, functional genomics and funded project information.
7. New header bar
Dropdown and left side navigation bars remodeled to enhance ease of access
to GDR data.
8. Community pages and mailing lists
The community page at GDR has been modified to make it easier to access
the community pages of interest. In addition new International and US
communication pages have been added, with new mailing lists to join (via a
web form). We encourage you to join the appropriate mailing lists and use
them to communicate to the community using these tools.
9. New publication from GDR
Synteny conservation between the Prunus genome and both the present and
ancestral Arabidopsis genomes. Sook Jung, Dorrie Main, Margaret Staton,
Ilhyung Cho, Tatyana Zhebentyayeva, Pere Arus and Albert Abbott. BMC
Genomics 2006, 7:81
10. Additions to the publication database
The publication database on GDR now contains publication data from
Agricola, the catalog of articles maintained by the National Agricultural
Library. 564 relevant publications are online and can be searched by
title, authors, keywords, and date published.
Subscription
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
1. Efforts to integrate more extensive map/marker data
We are updating our map/marker database structure to integrate the details
of molecular marker data such as primer sequences, source BAC/ESTs,
produce size and much more.
2. Creation of other databases within GDR
We are also creating new database modules such as gene, trait loci, QTL,
polymorphism/allele, germplasm, and diversity data.
