Multiple Trait Mapping

Describe the data set.

% Rmap -i rootmassm.inp -X rootmass -A
% Rcross -i rootmassc.inp -A
% Qstats -A
% LRmapqtl -t 5 -A
% SRmapqtl -A
% Zmapqtl -t 5 -A
% Zmapqtl -t 5 -M 6 -A
% JZmapqtl -t 5 -M 3 -I 14 -A
% Eqtl -S 10.0 -H 14 -A
% mkdir model3
% mv rootmass.z0 rootmass.z1 rootmass.z2 rootmass.z3 rootmass.z4 model3
% cp rootmass.sr model3
% vi rootmass.sr
% JZmapqtl -t 5 -M 6 -I 14 -A
% Eqtl -S 10.0 -H 14 -A

The first six steps should be familiar. Look at the output in each step.

Step seven invokes multitrait mapping with a test for GxE interactions.

Steps 9-12 back up your analysis using interval mapping and prepare for composite interval mapping.

Step 12 requires you to edit the rootmass.sr file. The example uses vi, by you can use any text editor. You should decrease the number of ranked markers in the rootmass.sr file by deleting some of the lines. I would suggest deleting all lines with rank greater than three.