Comparison of linkage maps from F2 and three times intermated generations in two populations of European flint maize (Zea mays L.)

Intermated mapping populations are expected to result in high mapping resolution for tightly linked loci. The objectives of our study were to (1) investigate the consequences of constructing linkage maps from intermated populations using mapping methods developed for F2 populations, (2) compare linkage maps constructed from intermated populations (F2Syn3) with maps generated from corresponding F2 and F3 base populations, and (3) investigate the advantages of intermated mapping populations for applications in plant breeding programs. We constructed linkage maps for two European flint maize populations (A x B, C x D) by mapping 105 SSR markers in generations F2 and F2Syn3 of population A x B, and 102 SSR markers in generations F3 and F2Syn3 of population C x D. Maps for F2Syn3 were constructed with mapping methods for F2 populations (Map A) as well as with those specifically developed for intermated populations (Map B). Both methods relate map distances to recombination frequencies in a single meiosis and, therefore, did not show a map expansion in F2Syn3 compared with maps constructed from the respective F2 or F3 base populations. Map A and B differed considerably, presumably because of theoretical shortcomings of Map A. Since loosely linked markers could not unambiguously be mapped in the F2Syn3 populations, they may hamper the construction of linkage maps from intermated populations.