How could I analyse agronomic and marker data using principal components analysis (PCA)?

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M. Humberto Reyes-Valdes

Why PCA? Since marker data are categorical, I find PCA rather ill-defined. It would be good to know for what purpose you wan to use this technique. I have used multidimensional scaling (MDS) instead, based on the distance matrix. If you combine marker and agronomic traits, you can use Gower distance.