Which method to use?

Either of these methods are perfectly legitimate to use for Marker-Assisted Breeding. The results should be quite similar. For MAB, in the end what is needed is a marker to use to track the QTL or trait; it doesn’t really matter which method or software program you use to arrive at that point. However, for using a marker identified by someone else in your own work, you would of course want to know the methods and statistical levels they used so you can feel comfortable using the marker(s) in your work.