Characterisation of genetic variation between Vitis vinifera cultivars from central Chile using RAPD and Inter Simple Sequence Repeat markers

The origins and authenticity of many grape cultivars ( Vitis vinifera) used for wine production around the world is unclear and the subject of some controversy. In this study, DNA fingerprints generated by Randomly Amplified Polymorphic DNA (RAPD) and Inter Simple Sequence Repeat Polymerase Chain Reaction (ISSR-PCR) analyses were used to compare the four most widely planted V. vinifera cultivars in Chile (viz. Cabernet Sauvignon, Cabernet Franc, Merlot and Carmenere). Material obtained from France was used as an external reference. Both techniques were able to distinguish between the cultivars studied although the resolving power of ISSR profiles was higher than that of RAPDs, suggesting that the latter would be more suited for use on a wider range of cultivars. Surprisingly, however, variability was observed between clones of Merlot, the original Chilean clone and the representative clone from France. Furthermore, the high degree of divergence between the two sources (64% similarity) suggests that the French Merlot is not even a close relative of the stock in Chile. Interestingly, the latter was derived directly from the original French founder clones of the Merlot cultivar. No variation was found within the Chilean Merlot clone using either ISSR or RAPD analyses. These results indicate that French and Chilean vines grown for Merlot production represent different genotypes. The history of Merlot cultivation and the implications of these findings are explored.