Development of SNP markers for mapping and allelotyping in sugarcane

The highly complex and polyploid genome of sugarcane provides challenges to nearly all technologies developed to analyse diploid genomes. In cultivated clones, chromosome numbers vary in excess of 100, and the ploidy number between loci can vary from 8 and 14 within an individual. This restricts mapping to simplex (single dose) DNA markers; and makes it impossible to determine potential ‘active’ gene haplotypes. SNP markers offer the best solution to overcome many of the difficulties, although it is in itself a challenge to develop for this complex genome. The recent release of a large scale sugarcane EST sequencing project into the public databases has provided a means of identifying potential SNPs for development into markers that can be used for mapping, cultivar identification and potentially, gene haplotype discrimination. We outline the methods we have used to measure SNP base ratios to allow quantitative SNP allelotyping in sugarcane that will allow mapping of single dose markers and potentially identify gene haplotypes linked to phenotypes