Plant & Animal Genomes XIV Conference

January 14-18, 2006
Town & Country Convention Center
San Diego, CA

SNP Analysis Tools For Functional Analysis Of Sugarcane Genes

Giovanni M. Cordeiro , Frances Eliott , Brett Kennedy , Robert J. Henry

  Southern Cross University Centre for Plant Conservation Genetics PO Box 157 LISMORE NSW 2480 Australia

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.