MaizeGDB
jobs | upcoming events | sitemap
 | docs | bulk data | browse data | tools | login / register | links 
homeA popup window providing help for using the search form to the right  

Map Data In MaizeGDB

Simple Map Search | Advanced Map Search | Map Reports, Tools, & Map Score Downloads | Discussion of Map Data for the General Public


Simple Map Search

Updated! Handy reference for determining what are the most current maps and for understanding the content of the various Neighbors maps.

If you are looking for particular map markers, use the locus search.

This search form allows you to just enter basic name info to quickly retrieve the desired map. Use % as a wild card.

(see a sample map query)

Other interesting searches include Genetic (locates our genetic maps) and SSR (finds maps assembled using SSRs)

This search can be executed on every page on the site by utilizing the form in the upper right corner. Choose "map" from the drop-down menu, enter your search term in the field, and hit return to find the map you're looking for.


Advanced Map Search

Are you looking for core bin markers?

Set Up Search Criteria

Check the boxes next to the fields you want to search; by setting a criterion, the box will be checked for you. Only checked boxes will have that criterion evaluated.

that contain (for example, you could find maps with kn1)
that contain (for example, you could find maps with tub1)
that contain
of :
from :
from :
 

Map Reports & Tools

Composite Genotype Finder: This tool allows you to search for particular genotypes at loci of interest, browse genotype data from different genetic maps, and obtain stocks that have desired genotypes.

New! Incongruencies between B73 RefGen_v2 and ISU Integrated IBM 2009 map : This tool lists loci that are placed on B73 RefGen_v2 by sequence similarity (via BLAST), and compares that position to their predicted genomic position based on their genetic position on the ISU Integrated IBM 2009 map.

A list of all maps can be found here: Full List (chrom. 1 2 3 4 5 6 7 8 9 10 )

Here are some of the more popular complete maps.

UMC 98 (chrom. 1 2 3 4 5 6 7 8 9 10): Considered to be a standard reference map for maize
Genetic (2008) (chrom. 1 2 3 4 5 6 7 8 9 10): Derived in 2008 from retrospective data
NAM (chrom. 1 2 3 4 5 6 7 8 9 10): Nested Association Mapping (NAM) for maize

IBM2 (chrom. 1 2 3 4 5 6 7 8 9 10): Intermated B73/Mo17, a high resolution genetic map
IBM2 2008 Neighbors Frame (chrom. 1 2 3 4 5 6 7 8 9 10): Most recent version of the IBM2 Neighbors Frame Map
IBM2 2008 Neighbors (chrom. 1 2 3 4 5 6 7 8 9 10): Most recent version of the IBM2 Neighbors Map

ISU IBM Map4 (chrom. 1 2 3 4 5 6 7 8 9 10): Map combining data from ISU Maize Genetic Mapping Project and the Missouri Mapping Project (MMP).
ISU IBM Map7 (chrom. 1 2 3 4 5 6 7 8 9 10): Map from ISU Maize Genetic Mapping Project. New Indels.

LHRF Gnp2004 (chrom. 1 2 3 4 5 6 7 8 9 10): High-resolution genetic map from Genoplante.
IBM GNP2004 (chrom. 1 2 3 4 5 6 7 8 9 10): Genetic map from Genoplante.

B73 BAC (chrom. 1 2 3 4 5 6 7 8 9 10): sequenced B73 BACs, derived from the maize sequencing project, the physical map at Arizona and GenBank. Updated monthly.

Physical Map: View the physical map from the Maize Mapping Project (at www.genome.arizona.edu)
Recombination Nodule Maps: Map containing data on the distribution of recombination nodules along pachytene synaptonemal complexes can be used to predict cytological locations of genetically mapped loci and vice versa using the Morgan2McClintock Translator

Map Score Downloads
IBM 94 population list of lines, cIBM map scores (on-frame only), IBM GNP 2004 map scores (complete set), and a MapMaker infile (which includes all markers in MaizeGDB that have been mapped using the IBM 94 population and also includes the ISU-IBM Map4 IDP markers).
IBM 302 population list of lines, map scores, and QTL Cartographer files.


Discussion of Map Data for the General Public

What is a map?

The basic information that describes each organism is stored on several long strands of DNA, called chromosomes. Loci (plural for locus) are specific points on these chromosomes.

Thus, a map is the description of the relative positions of loci on a chromosome. Thus, by determining where a particular locus is in respect to a few other loci, we can easily determine where the locus is in respect to many other loci by using a map.

What value does studying map data have?

When we know the relative closeness of various loci to each other, we can then tell how often they will be inherited together, as loci that are closer together are more often inherited together. Thus, map data can improve breeding experiments.

What is the connection between corn and map data?

Map data can provide the backbone for the selection of various traits in corn breeding experiments, resulting in better, hardier hybrids with more nutrition.

What are the defintions of the Map terms?

Definitions for the map terms can be found here.


Return to the homepage

Last updated 11:01 am, Sep 02, 2011.

home  

Please cite us!

This page is HTML 4.01 valid!