Despite numerous recent studies using inter-simple sequence repeat (ISSR) markers, there have been no comprehensive studies examining homology among ISSR fragments. In this study, we are assessing homology among ISSR fragments by southern hybridization. Thirty two taxa, representing a wide sampling among the Lamiales, with a focus on Penstemon subg. Dasanthera were chosen for study. Three ISSR primers representing different repeat motifs have been used for DNA amplification. Southern blots were performed for all three primers of interest. Probes for southern hybridization were generated from three taxa (Penstemon cardwellii, Hyobanche glabrata, and Scrophularia scopoli) for all three primers by PCR cloning. Each ISSR band was hybridized separately to the appropriate primer blot and visualized using the ECL non-radioactive labeling kit. Preliminary data suggest that comigrating fragments represent homologous fragments among closely-related taxa, but homology assessment is more complicated among distantly-related taxa. In addition, some ISSR bands have been demonstrated to hybridize with multiple bands generated by the same primer, especially among closely-related taxa. This could be the result of tandemly-repeated SSRs of the same di- or trinucleotide repeat. Comparisons are being made for genetic diversity statistics estimated including all bands visualized using ethidium bromide-stained agarose gels and only bands that are determined to be independent based on southern hybridization. In addition, a new strategy for developing microsatellite loci from ISSR fragments will be discussed.

Key words: ISSR band homology, microsatellite development, Scrophulariaceae, southern hybridization