1. Maps and Markers Gramene SAB Report Jan 2006

2. CMap Improvements Expanded, reorganized and hidden menus New map glyphs –Number of features –Crop map –Magnify map Improved comparative map selection Filtering of features Collapse overlapping features Correspondence aggregation

3. CMap: Reorganized menus

4. CMap: Collapse Features

6. CMap: Filter Features

7. CMap: Crop/Zoom map

8. New & Updated Maps New maps –Rice – Gramene IRGSP Assm 2005 –Maize – Bins –Wheat – Composite 2004 –Wheat – Consensus SSR 2004 –7 OMAP physical maps –3 Rice Class I SSR maps –15 QTL maps Updated TIGR assembly –Gene models –BAC end sequence from wild relatives of rice –Additional markers and ESTs

9. Marker Database Marker TypeMarkers AFLP950 BAC end sequence676,959 Clone602,304 EST2,530,661 EST Cluster601,935 Gene Primer19 mRNA91,074 Primer34 RAPD135 RFLP7,791 SSR16,835 STS65 Tos1718,023 Undefined823 4,547,608 total SpeciesMarkers Barley (Hordeum spp.)535,720 Maize (Zea spp.)1,089,433 Oat (Avena spp.)8,215 Rice (Oryza spp.)1,475,049 Rye (Secale spp.)13,260 Sorghum (Sorghum spp.)260,634 Sugarcane (Saccharum spp.)339,657 Wheat (Triticum spp. + Aegilops spp.) 787,493 Other38,147

10. Marker Search (Users)

11. Marker Admin Tool (Curators)

12. Dataflow Through MarkersDB (I) Gramene-created maps (Genome browser) –Create or update markers in database –Extract marker data –Run through genome pipeline –Update positions in markersDB, Ensembl, CMap

13. Dataflow Through MarkersDB (II) Existing maps (non-Gramene generated) –Enter map positions into database –Reconcile features with markers Marker name, species, type –Create markers if necessary –Output to CMap

14. MarkersDB Issues Improved searches –Marker details –Maps Improved data downloads –Include marker details Marker accession IDs Batch loading of marker data Map load and output scripts Ensure all mapped features (except QTL and genes) have a corresponding marker Reconciliation of new markers with existing ones Continued curation of undefined markers