The construction of an ultra-dense genetic linkage map of potato

An ultra-dense genetic linkage map with nearly 10,000 AFLP loci was constructed from a heterozygous diploid potato population. It is among the densest meiotic maps ever constructed. A fast marker ordering algorithm was used in combination with genotyping error-detection software to obtain "skeleton bin maps". A "bin" is a position on the genetic map with a unique segregation pattern and separated from adjacent bins by a single recombination event. Subsequently all marker loci were assigned to the bins on the map by maximum likelihood based on their original segregation pattern. From the markers that were heterozygous in either the maternal or paternal parent, 98% could be fit in the bins. Of the markers that were heterozygous in both parents (bridge markers), only 79% could be fit. In both parental maps the twelve chromosomes could be identified. In addition, the paternal map includes a small unassigned linkage group with a severe segregation distortion. Recombination frequencies or marker positions are non-randomly distributed across the map. Putative centromeric regions showed extensive marker clustering while putative recombination hot spots resulted in large intervals up to 15 cM without markers. The markers derived from EcoRI/MseI and SacI/MseI primer combinations clustered more frequently than those derived from PstI/MseI primer combinations. The distribution of recombination events per chromatid indicated an overall absence of the occurrence of 0 chiasmata and excluded absolute chiasma interference within arms. The ultra-high density map has been used for anchoring of BAC-contigs for a sequence ready potato physical map and gene cloning.