Different parameters for the -M option allow for the analysis of the data assuming different models. See the Zmapqtl man page for explanations of models 3 and 6. These are the main analysis models available in JZmapqtl. You can also use model 9, which prepares an input file for use in MultiRegress. Mainly, it calculates the expected genotypes at the sites where it would have done analyses. The expected genotypes are calculated according to table 3.7 from the QTL Cartographer manual.