Note that for CMap, a map set corresponds to a map, a map to a chromosome and a feature to a gene, a marker, a QTL or any other element positioned on a map.

QTLs and genes/markers are positioned on physical or genetic maps that can be seen using CMap. Two options are possible to display the maps:
- From the link http://gohelle.cirad.fr/cgi-bin/cmap_euroot click on "Map viewer", choose the species and click on "change species". Then choose the map and click on "show the selected set maps".
Then choose the chromosome and click on "draw selected maps". The map will appear showing the chromosome with its markers and genes and the QTLs with their confidence intervals.

- From individual genes or QTLs in results of a query in the EURoot interface. For a given QTL/gene, pass the mouse on a QTL/gene name; a popup will appear then click on "CMAP-QTL" (QTL) or on "CMAP-marker" (gene) in the popup. The map will appear directly with the initial QTL/gene highlighted in a yellow box.

Below the graph but often unnoticed, "Map options", "Features options", "Correspondence options" and "Display options" are available that enables to zoom on an interesting segment and to display a subset of information.

Comparison between maps
To make comparisons between maps having common genes/markers, make sure a map (initial map) is displayed and unfold the "Map options". In the box that will appear, click on "Add maps right" (or "Add maps left"). If map(s) have genes/markers in common with the initial map, another box will be displayed where you will have to choose a map set in the "Add map set" drop-down list. After you selected a map set, a list of the map(s) where there are matching genes/markers is shown where you can make a single or multiple selections. Click on "Add maps" to visualize all the maps you have added.

Method used for rice-maize comparisons
To establish bridges between the rice and maize physical maps, data on syntenic regions between the two species were recovered from the CoGe comparative genomic system (https://genomevolution.org/CoGe/) using the SynMap application on CDS with the masked option (Schnable and Lyons 2011). The application provides a robust method to identify true orthologous genes based on the conservation of gene order between genomic regions related by common descent. The bridges encompass approximately 19,000 genes in 727 syntenic blocks and cover about 98% of the genomes. The positions of the limit of the syntenic blocks in rice and maize are used in CMap to display the syntenic relationships between the two species (marker names starting with "B" as "Bridge").

Schnable JC, Lyons E (2011) Comparative genomics with maize and other grasses: from genes to genomes. Maydica 56-1763