Evaluation of microsatellites (simple sequence repeats) as genetic markers in sugarcane

Cultivated sugarcane genotypes (Saccharum spp.) are derived from complex interspecific hybridizations between the species S. spontaneum and S. officinarum. To analyse this complex genome, we have investigated the potential of sugarcane microsatellite sequences as genetic markers in terms of their abundance, variability and ability to detect polymorphisms. From an enriched sugarcane genomic DNA microsatellite library, primer sets were designed and synthesized for over 200 microsatellite sequences. These were tested over five Saccharum genotypes. The number of alleles recorded per marker ranged between 2 and 12 (mean of 8). Markers that showed polymorphism had a Polymorphism Information Content (or PIC, where a value of 0=monomorphic and 1=highly polymorphic) value between 0.48 and 0.8 (mean of 0.72). Fluorescently labelled primers for eight of these microsatellite markers were tested on a population of 20 sugarcane cultivars. Results indicated 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. However, these genomic DNA derived microsatellites transferred poorly to related genera. By comparison, sugarcane microsatellites derived from expressed sequence tag sequences had a low PIC level when tested within cultivars, but a significantly higher level of polymorphism when applied to progenitor and related species.