The value of single nucleotide polymorphism consortium in sugarcane

Single Nucleotide Polymorphism (SNP) markers are key tools in genetics research in many species. Large scale DNA sequencing projects have provided sources of sequence data that can be used to identify SNP’s. The large number of SNP’s in plant genomes means that their analysis requires more effort than may be possible by individual research groups. Consortia of research laboratories have been formed to identify and characterise SNP’s in other plant genomes. Following the Plant and Animal Genome meeting in 2002 a SNP consortium was formed in wheat. This provides a model that might guide the way a consortium could be formed for sugarcane. Centralised alignment of EST contigs has provided a mechanism for allocation of specific sequences to individual collaborating research laboratories. Collaborators take responsibility for confirmation of the presence of a SNP and the analysis of the SNP in a common set of genotypes. These genotypes can include parents used in major international mapping populations. This immediately identifies those SNP’s that can be mapped in existing populations. The availability of large amounts of sugarcane sequence data make a similar approach in sugarcane viable.