The use of semi-automated fluorescent microsatellite analysis for tomato cultivar identification

The objectives of this study were to evaluate the usefulness of a fluorescent-analysis method for genotyping PCR-based tomato microsatellite markers (Or STMSs) and to establish the value of these markers to generate unique DNA profiles of tomato cultivars. The analyses were performed using forward primers labelled with a fluorochrom and using an ALF express DNA sequencer. In general, analysis of the tomato STMSs revealed distinct allelic peaks. PCR artefacts like stuttering and differential amplification were observed for several tomato STMS markers, but in most cases these artefacts did not seriously hamper allele designation. Comparison of fluorescent and silver-stained allelic profiles revealed a similar distribution of alleles among the test cultivars. Sixteen tomato cultivars were DNA-typed for 20 selected STMS markers using the fluorescent approach. Length polymorphism among the PCR products was detected with 18 of these markers, yielding gene diversity values from 0.06 to 0.74. The number of alleles per microsatellite locus ranged from 2 to 8. As few as four STMSs were sufficient to differentiate between all 16 cultivars. indicating that these markers are especially suitable for a species like tomato which has low levels of variation as detected by other types of markers.