Retrotransposon-based ISAP markers in the analysis of Rosa L. in the Sirius Federal Territory and adjacent areas

Background. Rosaceae is among the top five most significant families in the Caucasus, where the genus Rosa L. is represented by nine species. This genus is polytypic, which complicates species identification; roses easily run wild under cultivation and readily produce hybrid forms. Therefore, it is quite problematic to study visually similar populations solely on the basis of their morphological characters, so the use of molecular markers seems highly relevant. Additionally, molecular markers can be used to monitor biodiversity in anthropogenically modified areas, such as the Sirius Federal Territory.

Materials and methods. This study employed new ISAP markers (ROSE-CL0, ROSE-CL3, ROSE-CL6, and ROSE-CL7) based on the analysis of polymorphisms in the genomic localization of SINE retrotransposons. A total of 132 rose samples from 16 different locations within the Sirius Federal Territory and adjacent areas were studied.

Results. The ISAP analysis revealed high levels of polymorphism across all calculated parameters. In total, 127 different amplicons were identified in the samples, with a mean of 31.8 per marker. The average number of effective Ne alleles for all primers was 11.9, with the polymorphism index P% = 100% for the studied subset, MI = 1.41, and Dj = 0.96. Comparing subpopulations from locations #2, #3, #4, #7, #8, #9 and #13 showed that they differed in their unique characteristics both in terms of calculated polymorphism indices and allelic composition. Samples from location #8 proved to be almost homogeneous, suggesting that their reproduction at this site may have occurred vegetatively. Ward’s clustering made it possible to divide the samples into three clusters, with some geographic affinity.

Conclusion. The ISAP analysis of polymorphism in roses confirmed high effectiveness of this new type of retrotransposon-based markers. The method can be recommended for use in population genetics and for assessing the biodiversity of wild roses and rose cultivars.

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