Generation of a large set of microsatellites markers for Phytophthora infestans by mining sequence data

Microsatellite or simple-sequence repeat (SSR) markers are extremely useful in population studies particularly in diploid species. So far, however, only a limited number of informative microsatellite loci have been identified in the potato late blight pathogen Phytophthora infestans and none have been mapped. To identify additional polymorphic SSR loci, genomic and EST sequences were scanned for the presence of di- and trinucleotide units that are repeated six or more times. We identified 333 unique SSR loci using an automated software pipeline. Primers flanking these SSRs were developed and tested on a set of ten previously characterized P. infestans field isolates. Of the 300 primers pairs tested, 203 pairs generated a clear fragment of the expected length. More than half of these amplified microsatellites (110) showed length differences among the different isolates. Some microsatellites seemed to be very variable in the P. infestans population with up to 9 different alleles detected in the ten genotypes. The most informative microsatellites are currently being positioned on the genetic linkage map of cross 71 (80029 x 88133). The genomic and EST sequences (xgi.ncgr.org/spc/; Randall et al., 2005 MPMI in press) proved to be an excellent source for new microsatellites. We anticipate that these SSR markers will be instrumental for efficient analyses of P. infestans populations and will facilitate integration of the various genetic datasets available for this important plant pathogen.