SNP discovery from amphidiploid species and transferability across the Brassicaceae

Single Nucleotide Polymorphisms (SNPs) are the most abundant genetic marker and predominate applications in modern plant genetic analysis, such as diversity analysis, genetic trait mapping, association studies, and marker assisted selection. SNPs are direct markers, as the sequence information provides the exact nature of the allelic variants. Furthermore, this sequence variation can have a major impact on how the organism develops and responds to the environment. Here we present the discovery of SNPs from diploid and amphidiploid Brassica species using GAIIx sequence data, and validation using an Illumina GoldenGate assay. These SNPs have been applied for cross-amplification in Brassica species and wild relatives from an international germplasm collection. Genotyping across diverse Brassica species can be used to assign lines and populations to heterotic groups; to study the evolutionary history of wild relatives; to verify pedigrees and fill in the gaps in incomplete pedigree or selection history, to monitor changes in allele frequencies in cultivars or populations and to help narrow the search for new alleles at loci of interest.