With few markers it is possible to calculate and draw the genetic linkage map by hand, however with many markers it is very laborious.

Joinmap 4.1 is Software for the calculation of genetic linkage maps

JoinMap provides high quality tools that allow detailed study of the experimental data and the generation of publication-ready genetic mapcharts. In JoinMap you can perform several diagnostical tests, both before and after the map calculation, and you can remove potentially erroneous loci and individuals from the map calculations by a simple mouse-click. We will practice this with an Arabidopsis data set and a trial version of JoinMap. We will use the demonstration version of Joinmap 4. that has full calculation capabilities but is limited to the construction of only two linkage groups and has less options for exporting of results.

Constructing genetic linkage maps with mapping software Joinmap

In the next section a stepwise procedure leading to the construction of a genetic map is described. Relevant sections of the JoinMap software are introduced and used. In this section underlined parts require an action from you.


Install JoinMap (JM41setup) Regrettably JoinMap cannot be installed if you are not the administrator of the computer you use.

On the desktop of the computer locate the JoinMap icon and double-click with the mouse to start JoinMap 

Open a data file

In the top bar click on the NEW PROJECT icon

A window will open asking where to save your project file

Choose your working directory, then choose a File name for the project 


Use the LOAD DATA icon to import your locus genotype file

Browse through the available files and select the “arabid.loc” file 


This 'loc-file' contains the segregation information of the markers scored in the Arabidopsis population.

These data were collected from a set of 163 Arabidopsis inbred lines. All these Recombinant Inbred Lines (RILs) were obtained by single seed descent for eight generations from the progeny of one cross. The original cross involved two very distinct types of Arabidopsis thaliana. The mother's origin is an accession retrieved in the Cape Verdi Islands, the father is an accession found in Germany. The traits of the parents have been recombined and fixed in the RILs. In total 99 markers were scored in this population. These markers can be used to construct a genetic linkage map of Arabidopsis.

Use the tab-sheets to have a look at the contents of the data file.

Open the tabsheet ‘Data’ and click on the ‘conditional coloring’ button

You should see something like depicted below

Fig 1 Preview Join Map 4.1

Do you understand the way the data are coded? In this example a locus is an SNP marker, each with its own unique code.

Questions Joinmap

5.1         What is the difference between an ‘a’ score and a ‘b’ score?  What does an ‘a’ score mean?

5.2          This is a RIL population, what type of segregation of marker alleles would you expect?

5.3          Open the tabsheet ‘locus Genot Freq and click,on the calculator button to calculate the genotype numbers.

5.4          Some markers have been marked with one or more ‘*’ (asterix) in the column Signific. Can you see why?

5.5          Also additional data in tabsheets can be obtained by selecting the tabsheet and clicking on the calculator button. What information can you obtain by doing this?

5.6          What are the two most similar markers in this dataset?

5.7          What are the two most similar individuals (RILs)?

Grouping markers into linkage groups

Before calculating the map, the markers have to be grouped into separate linkage groups corresponding to the different chromosomes. Arabidopsis has 5 chromosomes, so we should have 5 linkage groups. A linkage group is a group of markers which are significantly linked with each other and together form a (part of) a chromosome. The significance of linkage between two markers is represented by the LOD score. The higher the LOD score of a marker pair, the more likely that these markers are linked. By setting a LOD threshold it is decided which markers belong to the same linkage group and which do not. At a low threshold, all markers will fit in one linkage group. At a high threshold, chromosomes can already fall apart in several linkage groups. It is necessary to find the best LOD threshold at which a chromosome is apart from the rest.

Use the tab-sheets 'LOD groupings' for selecting the 5 linkage groups in the data and create the groups for mapping.

The Demonstration version of Joinmap we use allows us to continue with only 2 groups. Select the first two groups by right-clicking with the mouse on the nodes at LOD=10 (group 1 contains 26 markers and group 2 contains 25 markers).

Constructing the maps of the linkage groups

Select the first linkage group (click with the right side of your mouse to select the group, it becomes red) and calculate the map (click on the ‘map’ icon). 

Either Haldane or Kosambi functions can be used to calculate map distances. In contrast with Kosambi, Haldane does not take chiasma interference (What is that?) into account. Map distances will then be larger because potential double cross-overs are considered.

Question linkage groups.

5.8           Is there significant segregation distortion1 in the map? (Look at the 'Locus Genot. Freq.' tabsheet of the map)

5.9          If so, is that due to one (bad) marker, or is the whole region skewed?

5.10        Can you give a reason for skewness in a mapping population?

The demonstration version does not allow exporting of the results, however the mapping results are present in a usable form in the Joinmap project directory on your computer. If you look for the files with extension ‘.map’ you will find back the mapping results.


To view and print you maps outside of Joinmap and create presentation ready output you may use the free software package Mapchart.

Start up Mapchart (free software after registration)

In mapchart select ‘File’ –‘Open’ and browse to the folder where you saved your mapping results. Open one of the Arabidopsis  .map files Mapchart will display the map.

There are many options to change the looks of the map, the loci etc.


Questions Mapchard

5.11        Print your map