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

Abstract

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 1 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.

A genetic linkage map of cucumber (Cucumis sativus L) combining SRAP and ISSR markers

“…For example the range of polymorphic bands per primer was 1 -5 with an average of 2 bands, which is relatively smaller compared with the ISSR marker with an average of 4 bands (Figure 1, Tables 3 and 4). Although the advantages of both ISSR and SRAP markers stems from their simplicity and reproducibility, high number of polymorphisms and the fact there is no need for prior knowledge of DNA sequence, their major limitations could be lack of the number of useful primers that could generate useful polymorphism as observed in our studies and supported by Cekic et al (2001) and Nagoaka and Ogihara (1997).…”

Efficacy of random primer-pair arrays in plant genome analysis: a case study of Cucumis (Cucurbitaceae) for identification of wild and cultivated species

“…Identification of the thickness gene for shuck in walnut (Li et al, 2007) and purity testing of F 1 hybrid seed in chili pepper (Capsicum annuum; Jang et al, 2004) have been successfully carried out using RAPD and SCAR markers. The same approach has been adopted by Cekic et al (2001) to demonstrate the potential of ISSR-PCR primer-pair combinations for genetic linkage analysis using the seasonal flowering gene in Fragaria as a model. The primer-pair mixtures have been more frequently used than the conventional RAPD technique in bulk segregant analysis as they generate an extremely large number of markers as was efficiently demonstrated by Sall et al (2000) using two-primer mixtures.…”

The Genetic Relationship Between Some Strawberry Cultivars and F1 Population Derived From These Cultivars

“…ISSR method was used because generated bands are reproducible (reliability) and have high polymorphism (scorability), and also, scanning large number of different locus is possible (Prevost and Wilkinson, 1999;Cekic et al, 2001).…”