Development of a Robust and Rapid In-House Cultivar Identification Method and Its Application to Japanese Local Cultivars of Unknown Origin

Abstract

Cultivar identification is essential for many purposes. The most common method depends on allele differences detected through electrophoresis. Potato is an autotetraploid with four alleles per locus; therefore, in this study, allele dosage was assessed using real-time PCR. Seventeen markers, which detect dosages at 13 SNP loci, one insertion/deletion, and three resistance genes, uniquely identified 183 cultivars and breeding clones, excluding six mutational variants. This method was applied to 71 local cultivars of unknown origin, excluding five duplicates collected by different collectors. Of these, 14 were synonyms of 10 existing cultivars, while seven were uniquely identified. The remaining 50 cultivars were classified into five synonym groups of unknown origin, at least one of which is likely a remnant of the first European potatoes. This real-time PCR method proved to be a reliable and efficient in-house identification technique, taking only three hours from DNA extraction to final report.