The potential of ISSR-PCR primer-pair combinations for genetic linkage analysis using the seasonal flowering locus in Fragaria as a model

ISSR-PCR has been widely used for genetic distance analysis and DNA fingerprinting but has been less well utilised for mapping purposes. A key limitation lies in the small number of primer designs available to generate useful polymorphisms. In this study, the potential of paired combinations of ISSR primers is evaluated using a test cross mapping population of 168 BC, individuals between Fragaria vesca f. vesca and a closely related line F. vesca f. semperflorens. Ten ISSR primers and all possible pairwise combinations between them were used to generate markers potentially linked to the locus controlling seasonal flowering in F. vesca. Band profiles of individual primers were found to be highly reproducible for band position and intensity, and only minor variation was noted in band intensity (but not in position) between different constituent mixes of primer-pair combinations. Overall, ISSR primers used in isolation produced 85 markers of which only five were specific to F. vesca. None of these markers were linked to the seasonal flowering locus. In contrast, the primer-pair combinations yielded 493 markers, including 14 specific to F. vesca. These markers included two located within 2.2 cM of the seasonality locus. The strengths and limitations of using pairs of ISSR primers in combination for mapping and other genetic analyses are briefly explored.