SNP analysis tools for functional analysis of sugarcane genes

Single nucleotide polymorphism (SNP) analysis in polyploid genomes such as sugarcane requires the application of tools that allow quantitative analysis of mixed alleles even when analysing DNA from a single genotype. We have developed several techniques and adapted them to analysis of sugarcane SNP. Association of SNP or the numbers of homeologous alleles defined by a SNP is required to associate allele dose with phenotype in sugarcane. Protocols for ecotilling using an ABI Genetic Analyzer platform for capillary electrophoresis have been optimised for use in SNP discovery. Sequenom analysis allows efficient quantitative analysis of known SNP in association studies. Novel chemistries for RT PCR based upon Locked Nucleic Acid (LNA) strand displacement probes provide new options for analysis of sugarcane SNP.