The high annealing temperature random amplified polymorphic DNA (HAT-RAPD) method can be used to generate highly polymorphic data from PCR amplification of DNA samples to determine relatedness in plant cultivars. Using the HAT-RAPD method, we created a fingerprint database of tropical plants for fourteen subspecies of Dimocarpus longan Lour., twelve subspecies of Litchi chinensis Sonn., and seven distinct varieties of the genus Peuraria, two of which were previously uncharacterized. Out of a total of 22 distinct primer sets, a subset of primers with reproducible DNA band patterns was characterized for each species. From this data, we developed a web-accessible database that both graphically and quantitatively depicts the existent bands and species phylogenies using character state data generated from the banding patterns. Using historical and geographic data for these plant species and subspecies, the generated phylogenies support the currently accepted species relationships for D. longan and L. chinensis and characterize the unidentified varieties of Peuraria. The HAT-RAPD experimental method combined with band pattern recognition is a cost effective and easily characterized methodology that can be used to identify plant varieties, as well as to advance the knowledge of biodiversity in previously uncharacterized species.
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