Construction of a genetic linkage map in tetraploid species using molecular markers

This article presents methodology for the construction of a linkage map in an autotetraploid species, using either codominant or dominant molecular ma rkers scored on two parents and their full-sib progeny. The steps of the an alysis are as follows: identification of parental genotypes from the parent al and offspring phenotypes; testing for independent segregation of markers ; partition of markers into linkage groups using cluster analysis; maximum- likelihood estimation of the phase, recombination frequency, and LOD score for all pairs of markers in the same linkage group using the EM algorithm; ordering the markers and estimating distances between them; and reconstruct ing their linkage phases. The information from different marker configurati ons about the recombination frequency is examined and found to vary conside rably, depending on the number of different alleles, the number of alleles shared by the parents, and the phase of the markers. The methods are applie d to a simulated data set and to a small set of SSR and AFLP markers scored in a full-sib population of tetraploid potato.