Is there any free software anyone could recommend for genotype x environment interaction analysis, Quantitative Trait Loci (QTL) analysis?
I think you are talking about Stability analysis and QTL analysis. For both, R-studio is a very good option. There are simple steps for each of the packages which anyone can learn easily through the tutorials. I will recommend R Statistical packages. Please check R Packages - RStudio.
A QTL x Environment analysis is basically the use of the same QTL model, for single-trait-single-environment, but using the dimensionality of multi-environmental trials. You can, for example, run several QTL models (for each environment), collect the marker effects and build a matrix of marker x environment -- and also check the stability of the QTLs across the environments. All of this is based on linear models, so. you can use any random regression model (in R there are several).
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