SCAMing: an efficient high throughput approach to discovery and analysis of Snps for genotyping of tropical crop species

Model organisms have well established genetic marker tools. However, genotyping of the wide range of agricultural and food species requires the discovery of genetic variations in each species that can be used to distinguish genotypes. Single Nucleotide Polymorphisms (SNPs) are the basis of most high throughput genetic analysis technologies. We have developed a generic approach to the discovery and analysis of SNPs in non-model organisms. SNP Characterisation and Mapping in Genomes (SCAMinG) has been developed from mutation detection based on enzymatic cleavage of DNA heteroduplexes as applied to naturally occurring genetic variation (ecoTILLinG). Our protocol involves application of high throughput capillary electrophoresis to provide efficient discovery of SNPs. SNPs discovered in this way are then available for analysis by other high throughput methods such as mass spectrometry using the mass array platform (Sequenom). These methods can be combined to map SNPs in the genome and to associate SNPs with key traits. The combined approach provides an efficient strategy for SNP genotyping in agricultural species.