Optimal positioning of markers to control genetic background in marker-assisted backcrossing

Molecular markers are commonly used in backcross breeding programs in plants. As genetic maps contain more and more markers, it is of interest to determine which markers are to be used for selection. Here we describe how one can compute an optimal positioning of markers resulting in a maximization of the expected proportion of recipient genome. This criterion allows us to take selection into account and to produce relevant results regarding the final efficiency of background selection in backcross programs.