Characterisation of microsatellite markers from Sugarcane ( Saccharum sp.) a highly polyploid species

Abstract Cultivated sugarcane varieties ( Saccharum spp) are derived from complex interspecific hybridisations between the species S. spontaneum (2 n =40–128) and S. officinarum (2 n =60 or 80). To analyse this complex genome, the potential of microsatellite repeats as genetic markers in sugarcane with respect to their abundance, variability and ability to detect polymorphisms was investigated. A set of microsatellite markers for genome analysis in cultivated sugarcane was identified from an enriched genomic DNA library constructed from Saccharum sp. cv Q124. Sequencing of 798 sugarcane genomic DNA clones from an enriched microsatellite library, yielded 457 inserts containing microsatellite repeat motifs. Just over 84% of the microsatellites contained dinucleotide or trinucleotide repeats averaging 15 and 13 repeat motifs, respectively. Primer sets were designed and synthesised for over 100 microsatellite sequences and tested on a set of five sugarcane cultivars. Both, heterozygosity as witnessed by the number of alleles, and length polymorphisms as seen in the differences in PCR product size for a particular allele were observed. Microsatellite markers are likely to have many applications in sugarcane genetics and breeding including germplasm analysis, cultivar identification, parent evaluation and marker assisted breeding.