Location: Plant Genetics Research
Title: MaizeGDB as Chromosome Walking Companion Authors
Submitted to: American Society of Plant Biologists Annual Meeting
Publication Type: Abstract Only
Publication Acceptance Date: April 4, 2008
Publication Date: June 1, 2008
Citation: Schaeffer, M.L., Campbell, D.A., Harper, E.C., Seigfried, T.E., Sen, T.Z., Lawrence, C.J. 2008. MaizeGDB as Chromosome Walking Companion. American Society of Plant Biologists Annual Meeting. p.106. Technical Abstract: MaizeGDB, www.maizegdb.org, is the primary repository for genetic and cytogenetic maps, with many details about chromosome markers, genes, QTL, phenotypic variations, and sequences. It links these data to various external resources: GenBank; the EST and GSS contigs at PlantGDB, www.plantgdb.org and Dana Farber (previously at TIGR), compbio.dfci.harvard.edu; the FPC BAC contig assemblies at Arizona, www.genome.arizona.edu and their sequenced counterpart at the Maize Sequencing Project, www.maizesequence.org; and the SNP allele alignments at Panzea, www.panzea.org. The focus of this poster is usage examples, targeting groups interested in chromosome walking to sequences encoding a phenotypic trait of interest and groups that use reverse genetics to discover function. The examples use the current tools, although we are working to add a sequence-based genome browser shortly after the B73 sequencing project is completed this year. Based on a community survey, we will be using GBrowse, also recently adapted by TAIR. In addition we summarize recently added genetic and cytogenetic map data, which include the first new generation SNP maps from the Maize Diversity Project; additional INDEL mappings from Pat Schnable; data from the TILLING Project; and RNAi resources and data from the Maize Chromatin Project. Researchers are invited to add their own data using our community curation tools. Assistance in using MaizeGDB is available by on-line tutorials, or direct contact. Email inqueries are typically answered within 24 hours. In addition, researchers may request a MaizeGDB site visit for more extensive assistance; we currently schedule 3 visits/year from an expert curator for this purpose.