Sugarcane microsatellites; their use and characteristics

Cultivated sugarcane clones (Saccharum spp., x = 8) are derived from complex interspecific hybridisations between the species S. spontaneum and S. officinarum. To analyse this complex genome, we have investigated the potential of microsatellite sequences as genetic markers in sugarcane with respect to their abundance, variability and ability to detect polymorphisms. From a 50% enriched sugarcane genomic DNA microsatellite library, primer sets were designed and synthesised for over 200 microsatellite sequences and tested over 5 Saccharum genotypes. The number of alleles recorded per marker ranged between 2 to 12 (mean of 8). Markers that show polymorphism had a PIC value of between 0.48 to 0.8 (mean of 0.72). Fluorescently labelled primers for eight of these microsatellite markers were tested on a population of 20 sugarcane varieties and products separated using capillary electrophoresis. Data gathered indicate the ability of these markers to accurately fingerprint genotypes, predict relationships, be used in genetic mapping and assist in selecting specific, genetically diverse parents for use in introgression. In terms of transferability to closely related species or genera, genomic DNA derived microsatellites transfer poorly. In comparison, tests using sugarcane microsatellites derived from EST sequences have a low PIC level (0.23) when tested within cultivars, but show a significantly higher level of polymorphism when applied to progenitor and related species.