Expressed sequence tags (ESTs) in the sugarcane (Saccharum spp) database (SUCEST) were electronically searched and 402 microsatellites identified. Various dinucleotide and trinucleotide simple sequence repeat (SSR) motifs were found, with these being more frequently observed in ESTs obtained from flower cDNA libraries. PCR primers were designed for 20 of these SSRs and were tested on eight sugarcane genotypes, the sequences of these primers and a list of known sugarcane genes containing SSR motifs being presented in this paper. Polymorphisms were evident both at the cultivar level and between Saccharum species. These results show that EST-derived SSRs in Saccharum species are useful because they are polymorphic and transferable. The large number of microsatellites that will eventually be available from the SUCEST database (containing 295,000 submitted reads) will have many potential applications in linkage mapping and the planning of crosses
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