Validating single nucleotide polymorphisms as a new marker system for understanding the saccharum genome

A pilot study was undertaken to determine the value of Single Nucleotide Polymorphisms as an informative marker system for understanding the complex sugarcane genome. 100 EST clusters aligned using the software program CAP3, and derived from ESTs belonging to the FAPESP collection were examined for SNPs. From just over 100 potential SNP sites identified, SNP detection primers and/or PCR primers could be designed to 38. Of these 20 amplified product useful for analysis through Pyrosequencing™. These markers were tested on 42 varied genotypes that included progeny and parents of two mapping populations, ancestral species and cultivars. The indications are that SNPs in sugarcane will be suited for fingerprinting and assessments of phylogenetic and germplasm population relationships. Single dose markers were also identified and show the expected segregation pattern in progeny, indicating the potential of these markers for use in mapping. High throughput detection is straightforward and achievable using the pyrosequencer and the system is repeatable, with a 3 - 5% variation call on the proportion of each SNP present.