New high throughput DNA technologies resulted in a disproportion between the high number of scored markers for the mapping populations and relatively small sizes of the genotyped populations. Correspondingly, the number of markers may, by orders of magnitude, exceed the threshold of recombination resolution achievable for a given population size. Hence, only a small part of markers can be genuinely ordered in the map. The question is how to choose the most informative markers for building such a reliable “skeleton” map. We believe that our approach provides a solution to this difficult problem due to: a) powerful tools of discrete optimization for multilocus ordering;b) a verification procedure, which is impossible without fast and high-quality optimization, to control the map quality based on re-sampling techniques;c) an interactive algorithm of marker clustering in complicated situations caused by significant deviation of recombination rates between markers of non-homologous chromosomes from the expected 50% (referred to as quasi-linkage or pseudo-linkage);and d) an algorithm for detection and removing excessive markers to increase the stability of multilocus ordering.
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