A comparison between two recently developed, PCR-based DNA marker technologies (amplified fragment length polymorphism, AFLP; inverse sequence-lagged repeat analysis, ISTR) was carried out in a group of 19 Vitis vinifera L. accessions, including 13 putative Sangiovese-related grapevines and 6 ''coloured'' ecotypes whose fruits are of importance for conferring intense red colour to the wine. A large amount of polymorphic DNA fragments was revealed by both molecular techniques: 8 different AFLP and 5 ISTR primer combinations generated 264 and 249 polymorphic markers, respectively. Similarity relationships among the accessions were described by cluster analysis. The AFLP analysis revealed the existence of a uniform group for the Sangiovese (SG) ecotypes showing a high degree of genetic relatedness for the members of this cultivar. Among the coloured ecotypes (CLR), variability was more evident. Only the so called Colorino americano ecotype significantly diverged from both groups. ISTR analysis confirmed the genetic dissimilarity of Colorino americano and the existence of the SG and CLR groups, but in addition detected a higher proportion of polymorphism among the Sangiovese accessions compared to AFLP analysis. Sangiovese forte and Saragiolo apparently differed from the other SG-related grapevines in agreement with AFLP results. It is possible that the observed genetic dissimilarity between Sangiovese forte, Saragiolo and other SG-related types could be interpreted by the putative polyclonal origin of many grapevine cultivars, a concept which is generally accepted by the grapevine research community. Both AFLP and ISTR appear to represent innovative, efficient and sensitive molecular tools for investigating genetic diversity among Vitis vinifera ecotypes and for the eventual identification of clones
