Diagnostic SNP Assays to Identify Key Canadian Oat Varieties and Variation Among Seed Sources

Identification of crop varieties using quick, simple assays would benefit breeders and industry. Traditionally, gel-based marker systems such as RFLPs and SSRs have been used for fingerprinting purposes. New SNP-based assays offer diagnostic systems that are faster, more objective, and easier to automate. While many SNPs can be screened using parallel high-throughput platforms, those assays remain too costly for applications that require data from a small set of markers on a large number of samples. KBioscience’s “Kompetitive Allele-Specific PCR” (KASP) is a SNP genotyping system that can be applied more efficiently. We have developed a small but informative set of KASP assays for variety identification of Canadian oat (Avena sativa L.). After consultation with breeders, a set of 24 economically-important varieties was chosen for this study. Primers were designed based on sequences of highly informative SNPs from DArT, EST, and Genotype-by-Sequencing sources. A set of eight markers (PIC≥0.22) was found to distinguish 22 of the varieties studied. Since heterogeneity has been observed within some oat varieties, we are investigating variation that may be present among seed sources and individual seeds of four varieties.