Solanum section Petota, the potato and its wild relatives, contains over 200 wild species distributed from the southwestern United States to central Argentina and adjacent Chile. Many taxa are similar morphologically and may be conspecific. We tested the phylogenetic utility of microsatellites in Solanum tuberosum, the source of the microsatellite primers, and in Mexican diploid species, the most distant clade to Solanum tuberosum in sect. Petota. We used both an infinite allele model and a step-wise mutation model with many tree building methods. The infinite allele model and Neighbor Joining produced trees most closely matching species boundaries and hypotheses of relationships, but clustered taxa very poorly in the Mexican diploids. We sequenced three microsatellite fragments from three species, and compared these to sequences of S. tuberosum. There were many cases of divergence among priming sites that explained some cases of non-amplification. There also was much divergence of microsatellite flanking sequences, showing non-homology of fragment sizes, explaining their reduced phylogenetic utility in the Mexican diploids.

Key words: microsatellites, Petota, sequence, Solanaceae, Solanum, SSR