Simple sequence repeat DNA fragments (SSRs) have been suggested as the method of choice for DNA fingerprinting of grape cultivars. Nevertheless, the use of SSRs as a practical fingerprinting method is not without its pitfalls. For example, when the polymerase chain reaction is used to amplify SSR sequences, potentially confusing “stutter” bands may occur, or there may be non-template directed addition of an “A” to the end of synthesized fragments, or other artifactual amplification products may be produced. Since we would like to fingerprint our entire cold-hardy grape collection of ≈1300 cultivars, we decided to conduct a blind test to determine if SSR fingerprinting actually would be practical in our circumstances. First, SSR fingerprints were established for 45 commercially important cool-climate grape cultivars, the known standards. Then, SSR fingerprints were produced for 44 “unknown” cultivars grown in the Finger Lakes Region of New York. The identities of these were known only to the third author. To independently identity these “unknowns,” their fingerprints were compared to those of the known standards. By this means, 42 of the 44 “unknowns” were immediately correctly identified. The identity of one of the two remaining unknowns was truly not known to the vineyard owner; it was identified as Cabernet Franc, a grape commonly grown in the region. The final “unknown” was a plant of Pinot Blanc, whose fingerprint matched those of both the known and the unknown Pinot Gris and Pinot Noir plants, but did not match that of the Pinot Blanc plants used as standards. This was surprising, since all three Pinot's varieties are simply fruit color mutants of the same genotype. Further investigation revealed that the known plants of “Pinot Blanc” had been misidentified, and actually were the cultivar Melon. Thus, identification of the “unknown” Pinot Blanc as Pinot Noir or Pinot Gris was correct, as were the identifications of the 43 other `unknowns.”
This study confirmed that SSR fingerprinting is a practical method for identifying cool-climate grape cultivars.
SSR fingerprinting of raspberry cultivars traded in Germany clearly showed that certainty about the genotype authenticity is a prerequisite for any horticultural experiment
