The complex genetic structure of sugarcane limits identification of additional SNP-defined simplex alleles in microsatellite loci.

Cultivated sugarcane possesses a large number of chromosomes (typically >80) which can be organised into eight homology groups, each containing approximately 12 homo(eo)logous chromosomes. Currently, microsatellite (SSR) markers are the most easily used markers for marker-assisted selection and other genetic applications. However, only SSR alleles that segregate as simplex and duplex markers can be incorporated into sugarcane maps using populations of ∼300 progeny. Consequently only a subset of possible alleles have been mapped for a given SSR locus and are available for subsequent QTL analyses. Three sugarcane SSR loci, mSSCIR8, mSSCIR17 and mSSCIR18, were amplified, cloned and sequenced from the parents of an Australian sugarcane mapping population, IJ76-514 and Open image in new window . The sequences were examined to identify nucleotide sequence polymorphisms in the flanking regions that could provide additional simplex SSR allele markers. Alignment of the sequences revealed SNP, indel and repeat length variation and the pattern of sequence variation suggested multiple alleles for each SSR, including all of the alleles previously scored by fragment length. While the flanking regions of the SSR loci contained numerous SNPs and indels, none defined new simplex alleles within multiplex fragments and no new SSR simplex alleles were mapped. Furthermore, many of the sequence-defined alleles appear to be spurious and may have arisen from PCR-mediated recombination. These results confirm the difficulties associated with characterising allelic diversity in a polyploid species and the complexity of mapping in sugarcane.