Map Curation on GrainGenes Victoria Carollo, Gerard Lazo, David Matthews, Olin Anderson Biological Databases Curators Meeting October 2003

The Maps and Map Data page has links to articles, raw data and line maps

‘Map’ of CS x Cheyenne Disomic Substitution

Raw Mapping data of CS x Cheyenne Disomic Substitution

The Maps and Map Data page has links to articles, raw data and line maps

Web Summary of Interactive Maps links to the GrainGenes database

Flavors of GrainGenes Maps Genetic: Loci mapped by recombination frequency in Synthetic x Opata

Flavors of GrainGenes Maps Highlighted loci have best BLAST hits. Consensus: combined maps of hexaploid wheat by Sorrells et al.

0 100, , , , , ,000 May-00 Sep-00 Jan-01 May-01 Sep-01 Jan-02 May-02 Sep-02 Jan-03 May-03 Sep-03 Date Number of ESTs Wheat Barley Wheat and Barley Public EST Resources

Flavors of GrainGenes Maps Physical: loci mapped by physical placement on a chromosome. This is a deletion map from the U.S. wheat genome project.

Sequence Records from the NSF ESTs contain the supporting data and links to maps supported by other projects:

QTL map from a barley malting quality study

Interactive Map Construction 1.Identify relevant maps from the literature, usually from Theoretical and Applied Genetics find Reference Keyword=map* & Year=2002 results in 186 objects 2.Contact authors to acquire raw data and a spreadsheet with loci and chromosome positions

3.Convert locus names to GrainGenes standardized nomenclature

4.Check all loci to be sure a probe record exists 5.Create probe records for new loci involves going to references within the paper contact with authors can be very time consuming!!! 6.Create other object records genes, germplasm, colleague, reference etc. A map set takes ~ a week if all goes smoothly and authors cooperate.

The Genome Browser (GBrowse) is a new map viewing tool.

Click on a Bin bar to see all loci mapped to that region

Click on a Probe ESTs link to access query features on wEST

The CMAP viewer will allow users to compare maps.

NCBI is importing GrainGenes records for the Entrez Map View Tool.

Maps for Education

In-Depth pages will provide links to PubMed literature searches, NCBI, GrainGenes, etc.