Construction of a genetically anchored physical map of the potato genome

We are well underway with the construction of a genome-wide physical map of potato. For this goal a two-enzyme, 70,000 BAC library has been constructed of the heterozygous diploid genotype RH89-039-16. This library has an average insert size of over 120 kbp and has an expected coverage of 9-10 genome equivalents. The BACs have been fingerprinted by non-selective AFLP PCR and capillary electrophoresis on a MegaBACE sequencer. Physical map contigs will be constructed using two independent approaches. Firstly, BACs will be grouped into contigs using the computer program FPC (Soderlund et al., CABIOS 13:523-535). A draft first version of the physical map based on this analysis will be presented. Secondly, contigs will be identified using AFLP markers from the ultra dense genetic map of potato (http://potatodbase.dpw.wau.nl/UHDdata.html). In this second approach, selective (+3/+3 Eco/Mse) AFLP markers, made visible in fingerprints of BAC pools, will be compared with co-migrating non-selective (+0/+0 Eco/Mse) markers in the individual BAC fingerprints. In this way, an extensive integration of the physical map and the genetic map of potato will be achieved. This integrated map will serve as a source for map-based cloning of genes for disease resistance and tuber quality traits.