G x E Analysis

One special case of G x E analysis has been incorporated into JZmapqtl, namely the situation where a set of genotypes is raised in more than one environment. The value of the trait in each environment is treated as a separate trait for the common genotype. For this type of data, use hypothesis 14 or 34 to invoke the G x E analysis. Hypothesis 14 is for data with two marker genotypes, while 34 is for three marker genotypes. There will be an extra column in the output that give a likelihood ratio for a G x E effect versus no effect. When running Eqtl subsequent to doing a G x E analysis, be sure to specify the same hypothesis test.