PubMed Nucleotide Protein Genome Structure Taxonomy

Zea mays genome data and search tips Revised May 21, 2003

The Map Viewer help document describes how to use the Map Viewer software. This page describes the data available for Zea mays (corn), and the search tips specific to that organism. You may return to the Zea mays genome overview page to follow links to on-line help for Zea mays bioinformatics. The Map Viewer home page allows you to search the genome data of any organism represented in MapViewer.

  1. Scope of Data
  2. Available Maps
  3. Constructing Queries
  4. Constructing URLs

Scope of Data back to contents

Three points about genetic maps need to be emphasized. First, genetic maps usually are generated as a close-ended project. When the map is offered to the public there is little refinement afterwards. Second, the unit of a genetic map is the cM, computed from the frequency of recombination between two segregating loci. Thus the determined size of a chromosome, in cM, depends upon the extent of the chromosome between the most separated markers and may vary between different genetic maps. Third, correlation between genetic maps is only possible to the extent of comparison between the loci common to the maps under comparison. To facilitate comparison between genetic maps, MapViewer can graphically indicate a locus that is common to adjacent maps. This capability is user-controlled via the "Display settings" link at the top of the MapView page. Checking (mouse clicking) the "Show connections" option in the "Display settings" dialog box invokes the capability. The order of genetic map presentation (left to right across the window) is also chosen in the "Display settings" dialog box.

The "Verbose" mode, chosen in the "Display settings" dialog box, shows the GenBank accession(s) associated with the molecular probe.


Frequency of Updates to Map Viewer Data back to contents

The Emerson, Beadle, Fraser map from 1935 is a completed endeavor. The MW99 map is the maize genetic map reported in Wilson, (1999). This genetic map is a completed endeavor and thus will have no updates. The IBM map is the most current map from the Maize Mapping Project. This project is focused upon producing a genetic map with as great a density of loci as possible. Also from Maize DB is the UMC 98 map. This map is a completed endeavor.

Available Maps back to contents

Currently seven maps are available. As other map data is acquired, these maps will be noted as being available.

Emerson, Beadle, Fraser; 1935 back to contents
This data was previously published, Emerson RA et al. 1935 Cornell Univ Agric Exp Stn Memoir 180:1-83. The data was provided by MaizeDB and is currently available from MaizeGDB. Map units are cM.

IBM back to contents
There are two IBM maps. Both are from the Maize Mapping project of intermating the B73 and Mo 17 R1 lines. One, IBM_00 is an interim product. This work was reported by G. Davis et al. at the Maize Genetics Conference, 2000. The other, IBM_02, is a more recent consolidation of multiple independent maps and the introduction of new loci. The details are provided by Maize Mapping Project, Lee M et al. Plant Molecular Biology 2002; 48:453-461 and Sharopova N et al. Plant Molecular Biology 2002; 463-481. Map units are cM.

MW99 back to contents
This is the most recent mapping data from Cornell University using the T232/CM37 recombinant inbred lines developed at the Brookhaven National Laboratory. The data for this map was published elsewhere, Wilson et al., (1999). The data was collected in two stages. The initial data was provided by RiceGenes. Following RiceGenes going dark, MaizeDB was the source for the necessary data. The map data is currently available from MaizeGDB. Map units are cM.

UMC 98 back to contents
This map was developed over 4 years using an immortalized Tx303 x CO159 F2 population. The map was intitially presented in Gardiner, J et al., (1993). This map is the reference for the framework loci that define intervals in the maps of bin-mapped loci and QTLs. Map units are cM.

Bin-mapped loci back to contents
Bin-mapped loci are those particulate, Mendelian genetic entities whose mapped location is no more precise than between two particular framework markers (see UMC 98 map for details). The framework loci were first described in Gardiner, J et al., (1993). Map units are cM.

QTL map back to contents
A quantitative trait locus (QTL) is defined as a genetic interval demonstrating a partial influence upon the measured trait/phenotype. The ends of a QTL are framework loci from UMC98. Map units are cM.

Constructing queries back to contents

Searchable Terms back to contents

Text terms back to contents

The current version implements searching of flat files. The viewer supports searching on any text term that may describe an element on the map. These include:

  • locus mnemonics
  • alternate mnemonics
    A search for 'cdo507' or '*ant' will retrieve the locus named 'cdo507(ant)'. Both terms, "cdo507" and "ant", refer to the same genetic entity. The terms are therefore considered synonyms and either term will retrieve the same information for viewing.
  • current names or text words that are part of names
    A search for '*do*' will retrieve those map objects containing 'do' anywhere as part of their descriptions.
The specific terms available for each map are:
  • IBM Map
      • locus mnemonic, alternate name, corresponding GenBank accession
  • MW99 Map
      • locus mnemonic, alternate name, corresponding GenBank accession
  • UMC 98 Map
      • locus mnemonic, alternate name, corresponding GenBank accession
  • Emerson, Beadle, Fraser Map
      • locus mnemonic, alternate name, corresponding GenBank accession
  • Bin-mapped Loci Map
      • locus mnemonic, alternate name, corresponding GenBank accession
  • QTL Map
      • locus mnemonic, alternate name, corresponding GenBank accession

The search program looks for the query term in the maps mentioned above. The search is case-insensitive - thus "CDO*" and "cdo*" will identify the same genetic sites.

Truncation back to contents

Search terms can also be truncated using an asterisk (*) as a wild card to represent zero to many characters. For example "rz*" will locate all of the loci with "rz" as the first two characters - i.e. rz672a, rz251a and others. To locate sites using a search string that is embedded in the target, for example "uaz*" and "rz*" using 'z', the search string needs an asterick (*) as the leading character - i.e. *z* will locate both "uza*" and "rz*". Searches of adjacent terms, adjacency searches, are not supported at present. See the truncation section of the general Map Viewer Help document for more details.

Map Positions back to contents

As noted in the Search By Position section of the Entrez Map Viewer general help document, there are three main ways to search by map position from the Map View of a chromosome:
  1. enter a range of interest in the Region text boxes in side bar
  2. click on the region of interest in the chromosome thumbnail graphic in the sidebar
  3. click on a region of interest in the enlarged Map View of the chromosome

For Zea mays, the following types of map positions can be entered in the Region text boxes noted in option 1:
  • symbols - you can enter gene symbols, marker names, or alternate symbols or marker names to display a region of the chromosome between those mapped elements. Note that both elements must be present on the map in order for the range search to work properly.

Query options back to contents

Boolean Operators back to contents

Boolean operators in a query are not currently supported.

Advanced Search Page back to contents

The Advanced Search page is currently under development.

Constructing URLs that link to Map Viewer back to contents

If you would like to create WWW links to the Map Viewer, the instructions for constructing URLs are given in the general Map Viewer Help document. You can construct URLs that either perform a search or display a specific mapped object or chromosomal region.

Questions or comments:
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