Development and use of SNP markers to verify gene haplotypes in sugarcane

Sugarcane cultivars are polyploid, aneuploid, interspecific hybrids between the domesticated species S. officinarum, and a wild relative S. spontaneum. Their chromosome number ranges from 100-130 with approximately 10% contributed by S. spontaneum and ploidy number ranging between 8 and 10. This chromosomal allele complexity limits mapping to dominant single dose DNA markers with multiple dose alleles offering a greater challenge. Verifying haplotypes by SNP marker patterns may offer a solution for this challenge. EST alignments are a rich source for mining SNPs, and the use of pyrosequencing has proved to be a reliable method for measuring the SNP base ratios allowing quantitative SNP allelotyping in sugarcane. Measuring the base ratios at the SNP loci would discriminate single from multiple dose alleles. Verifying the haplotype compositions will genotype the alleles which may provide some information on the phenotypic, genotypic relationship in sugarcane. We have identified SNP haplotypes in isogenes of sucrose phosphate synthase, the sucrose biosynthetic enzyme of sugarcane and are examining these in segregating progeny displaying variation in sucrose accumulation.