Are AFLP markers the best alternative for cultivar identification?

AFLPs have been developed for assessing genetic variability and constructing genetic maps in many species. As a method of multilocus fingerprinting, AFLP seems to be promising for plant variety identification. This technique, which is based on the selective amplification of subsets of genomic restriction fragments, requires a high level of DNA purity. In this work we have compared the AFLP technique with another multilocus fingerprinting method, ISSR, which is faster because there is only one amplification step. The potential of ISSR was assessed with regard to the degree of polymorphism, reproducibility and ability to produce easily scorable patterns. Thirty strawberry cultivars from different geographical and genetic origins, which had been previously described with AFLPs, were tested. A set of 5 ' -anchored ISSRs were designed (based on the variation in a number of selective bases). PCR conditions were optimised to obtain patterns of good quality. Marker reproducibility was tested by analysing different extractions per plant and different organs (e.g. leaves, sepals, rhizomes). Intraclonal variability was assessed using 8-12 plants per clone. The patterns generated were highly reproducible and unlike AFLPs, reproducible patterns were obtained from DNA extracted from rhizomes,. DNA which had failed to give reproducible patterns with AFLPs produced very good results with ISSRs. A total of 96 polymorphic bands were scored among the 30 varieties using four selected primers. The average number of markers generated by each primer was 24, which corresponds to an efficiency similar to AFLPs. Using only one primer, all the varieties were distinguished, including those having common ancestors. Classification of varieties using ISSR markers was consistent with the pedigree data and comparable with the classification obtained from AFLPs. In conclusion, ISSRs can be a good alternative to AFLPs, being cheaper, faster and more reproducible. This was confirmed with preliminary tests on poplar, rose, pea, rapeseed, rye grass and hortensia.