VI

VI. MAIZE GENOME DATABASE

mnl.maizegdb.org

Overview

MaizeDB contains over 650,000 records, many with one or more links to an external data repository for primary data source. These links now total some 570,000; and we do not count sites mirrored with GenBank, EMBL and DDBJ. We are greatly indebted to the maize community for making their data available, in particular Dr Marty Sachs of the Maize Genetics Cooperation Stock Center for continued data entry and updates of new genetic stocks.

Other data providers this year:

� DuPont - 10,600 Unigenes, aka Cornsensus sequences, based on public with proprietary sequences. These have been entered into the HTC division of GenBank.

� Incyte Genomics - BAC anchor information and Overgo primers designed from the Cornsensus sequences;

� ZmDB and TIGR - public EST assemblies;

� Gramene - BLAT mappings of the Cornsensus sequences to rice;

� Dr. Cari Soderlund - the FPC computation of contigs, entered into MaizeDB as external database links for BACs and anchoring markers;

� Dr. Marilyn Warburton of CIMMYT - SSR polymorphism;

� Dr. Jeanne Romero-Severson - SSR polymorphism;

� Dr. Mike McMullen of the Maize Mapping Project - SSR data, complete with screening images;

� Dr. Georgia Davis, of the Maize Mapping Project - IBM map coordinates, data, screening images; new set of CORE markers to define the bin edges on the IBM;

� Dr. Dave Selinger, of ChromDB - registry of chromatin gene family names;

� GenBank and SwissProt for email updates of new maize sequences.

Other data acquisition:

We completed bibliographic entry of references back to 1888, with the aid of bibliographies of J. Cunningham in 1948 (for 1888-1916) and 1941 (for 1917-1936). MNL on-line is now retrospective to 1977. Literature citations within MaizeDB are over 100,000, for some 38,000 references.

Genetic Maps

The high resolution IBM map is now entered and includes 1700 loci, complete with probe information, many with links to BAC contigs (WWW FPC). The map is displayed at www.maizemap.org, complete with probe data and links to the evolving physical map. Other sites that display genetic maps extracted from MaizeDB include:

(1) the NCBI, in collaboration with Drs. Brian Smith-White and Tatiana Tatusov; www.ncbi.nlm.nih.gov/cgi-bin/Entrez/map_search? chr=mays.inf;

(2) CUGI, in collaboration with Drs. Cari Soderlund and Rod Wing, www.genome.clemson.edu/projects/maize/fpc/WebChrom/;

(3) Gramene, in collaboration with Drs. Doreen Ware and Lincoln Stein, www.gramene.org.

Map-based strategies, and their caveats for finding BAC clones of interest are described under the sidebar at BACS/YACS, or at www.maizegdb.org/bac.php. Strategies rely on the above resources and also (1) the Mapped Sequence Locator, www.maizemap.org/cgi-bin/zmMSL.cgi, where a BLAST search returns map coordinates and links out various data repositories; (2) various BAC and Probe Lookups based on map coordinates. The basic strategy is to find markers on BACs for your sequence of interest, or which are closely linked.

Coming Soon

Genetic Map Integration

Over the years, some 12,526 loci have been placed to chromosome arm or better. Most mapping experiments have less than 20% overlap of markers; see the MaizeDB report, MNL 71 1997, www.maizegdb.org/mnl/71/maizedb71.html. Because of the high numbers of markers, and maps involved, it is difficult to represent all on a single page or 10, as was the custom for MNL. For this reason one of the main syntheses of MaizeDB has been the bins maps. Thus while the IBM represents 1700 loci, there are an additional 8016 loci that have been placed to a single bin, many with better resolution than represented by the bin. Map based cloning will be supported by a higher resolution integration which we will be presenting on-line this summer, a map at a time, using the IBM map as the frame and supplying the methods of integration. All supporting data and the original maps will be maintained and accessible from the cMAP comparative map display (button in center of MaizeDB home-page).

CIMMYT mirror

We are collaborating with CIMMYT in establishing a mirror site for MaizeDB at CIMMYT that will further enhance access and data acquisition, with CIMMYT storing data directly in validation-readied tables. Anticipated data flow includes polymorphisms and trait studies. Funding for the mirror has been provided directly to CIMMYT by the USDA-ARS.

Submitted May 1, 2002

Ed Coe and Mary Polacco

Please Note: Notes submitted to the Maize Genetics Cooperation Newsletter may be cited only with consent of the authors.

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