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Gramene Diversity Module

Gramene Diversity Module. Dan Born, Peter Bradbury, Ed Buckler Payan Canaran, Terry Casstevens , Dallas Kroon, Dave Matthews, Susan McCouch, Junjian Ni, Isaak Yosief Tecle, Doreen Ware, Immanuel Yap, Frank You, Ken Youens-Clark, Wei Zhao. Current Status of Most Diversity Informatics. Collect

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Gramene Diversity Module

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  1. Gramene Diversity Module Dan Born, Peter Bradbury, Ed Buckler Payan Canaran, Terry Casstevens, Dallas Kroon, Dave Matthews, Susan McCouch, Junjian Ni, Isaak Yosief Tecle, Doreen Ware, Immanuel Yap, Frank You, Ken Youens-Clark, Wei Zhao

  2. Current Status of Most Diversity Informatics Collect Data Analyze Data Publish Results • QTL locations published • Sometime gets into DB • Segregation data often lost • Reanalysis nearly impossible

  3. Panzea Web Data Access Alignment & SNP Display Upload Tools Display GDPDM Gramene Panzea (Maize) Rice Evol. GDPC Data Browser GDPC Other Analysis Tools TASSEL Germinate GRIN DBs Middleware Analysis

  4. Specific Aim #3: Develop data models and query tools to manage natural variation in monocot varietiesFinal Objectives for Nov 2007: • Create data model • Done; Revised in 2006; maize, wheat and rice proj. DBs live in Gramene • Aid in curation • Pedigree parser done; Excel upload for traits; project specific for other genotypes • Interfaces • Dataset download – Done (GDPC; web interfaces) • Need to instantiate wheat and rice web interface • Pedigree Display – Alpha Complete • To do: Add trait and genotype • Haplotype viewer – To Do • GIS display – To Do

  5. 2005 Goals • Fuse and instantiate project DBs into Gramene • Complete upload tools; train key curators • Complete GDPC browser; Complete Germinate connection; Write GRIN connection • Start pedigree interface browser

  6. 1. Fuse and instantiate project DBs into Gramene • DB revised in light of more input. Frozen in May 2005 • Maize: Millions of curated phenotypic and genotypic data points have been included (Data from NSF “Maize molecular and functional diversity” project). • Curator Qi Sun and Jeff Glaubitz • Live through www.panzea.org

  7. 1. Fuse and instantiate project DBs into Gramene • Rice: Allelic data on 234 accessions with 169 genome-wide SSRs. Contains passport, taxonomic data, and links to IRRI/IRIS and GRIN. (Data from NRI "Molecular Evaluation of Rice Germplasm using microsatellite markers"project) • Curator: Isaak Yosief Tecle • Wheat: 48 taxa and 6000+ SNP assays (Data from NSF “Haplotype polymorphism in polyploidy wheats and their diploid ancestors”) • Curator: Frank You • Live on dev site

  8. Gramene General Search • Searches all tables for name or value • Developed by Ken Youens-Clark • On dev site.

  9. Panzea Web Interface • Search by topic area • SNP viewer • Several outputs formats Developed by Payan Canaran, Wei Zhao, and Doreen Ware with maize project

  10. 2. Complete upload tools; train key curators • Excel upload for phenotypes complete • Pedigree parser and upload for rice pedigrees • Project specific upload tools have been developed • Community genotype and passport may not be trivial. They will probably need to go through curators. • Core mapping and association panels will facilitate sharing • We can make specific spreadsheets for these easily

  11. 3. Complete GDPC browser; Complete Germinate connection; Write GRIN connection • Numerous improvements in GDPC • Mapped and currently accesses: Gramene (Maize, wheat, and rice); Panzea (Maize); Germinate (Pea); and GRIN (passport data) • Full integration with TASSEL (leading association tool) • Need to do phenotypes for Germinate and GRIN

  12. 3. Complete GDPC browser; Complete Germinate connection; Write GRIN connection • Numerous improvements in GDPC • Mapped and currently accesses: Gramene (Maize, wheat, and rice); Panzea (Maize); Germinate (Pea); and GRIN (passport data) • Full integration with TASSEL (leading association tool) • Need to do phenotypes for Germinate and GRIN

  13. 4. Start pedigree interface browser • Connects to GDPC • Draws clean pedigrees • Runs as an applet http://www.maizegenetics.net/gdpc/browser/pedigree_applet.html

  14. B7 B3 B73 B732 B731 B734 Taxon Flowering Homestead, 2003 Flowering Homestead, 2004 PZA0001.1 PZA0002.1 Flowering Clayton, 2003 Flowering Ithaca, 2005 PZA0004.1 PZA0005.1 4. Pedigree Vision • Marker based-minimum spanning networks • Phenotypic and genotypic connection to GDPC • Estimates of breeding values • Highlight key polymorphisms

  15. 2006 Goals • Migrate Panzea tools to Gramene; make rice and wheat live • Optimize GDPC for large data sets; Further GRIN & Germinate connections • Complete pedigree interface browser • Start geography and haplotype viewers

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