MapChart is a free software to plot publishing quality genetic maps as well as QTL data. This software was developed by Roeland E. Voorrips at Wageningen University and can be downloaded at this link .

In this tutorial, I will show how to prepare input files and plot the genetic map in the MapChart software. For detail information, please read this article at this link. The software also contains a descriptive manual, please consult it for detailed information.

Step 1: Preparing the Input file

In MS Excel or any relevant software, create the input file as shown in the image below. Please Note third column is optional, which can be used to color code the marker names and position. In this example, I have used C2 to color some markers in the red.

Input File

Step 2: Running the MapChart software

1.1 Importing input file

Open MapChart and copy the input data from MS Excel, and paste in the window as shown below. Please note, if you have data for multiple linkage groups or chromosomes then in the same window add those information starting from different line and make sure to have the correct the chromosome number for each Group.

Import data

Step: 1.2 Plot maps

Once the input data are loaded, click chart to plot the map. Follow the steps shown in the below figure to run this step. Once the plot is generated, it can be copied and pasted or saved as a desired format.


Step: 1.3 Formating the plot (optional)

Under the Tools click chart options one can format the plot by choosing the given parameters.


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Thank you for reading this tutorial. If you have any questions or comments, please let me know in the comment section below or send me an email.

Happy plott-ing !


Voorrips, R. E. "MapChart: software for the graphical presentation of linkage maps and QTLs." Journal of heredity 93.1 (2002): 77-78.