Structure of microsatellite loci for genetic analysis of Ukrainian hazelnut varieties

DOI: https://doi.org/10.7124/visnyk.utgis.23.1-2.1776
Keywords: hazelnut, Corylus, SSR markers, nucleotide sequence

Abstract

The aim of this study was to investigate the structural organization of nine microsatellite loci used for the characterization of Ukrainian hazelnut varieties, based on the analysis of PCR product sequencing data and sequences deposited in the NCBI GenBank database. Methods. PCR amplification with specific primers, cloning and sequencing of PCR products, bioinformatic analysis. Results. Four SSR loci were amplified and the obtained PCR products were cloned and sequenced. A search for allelic variants of nine SSR loci was also performed for five Corylus species. The structural organization and variability of the repetitive regions of these loci were investigated, and the frequency distribution of allelic variants was analyzed. Most loci have a conservative sequence and contain simple trinucleotide repeats; the number of repeat units determines the size of the corresponding variants. Three loci were found to have combined dinucleotide and trinucleotide repeats or interrupted repeats, and some of the variants were found to have deletions and insertions. These structural features determine the complex nature of the size distribution of these loci variants. Conclusions. The structural organization of nine simple sequence repeat (SSR) loci, which have been proposed for identifying Ukrainian hazelnut varieties, was identified. These features should be considered when interpreting the PCR analysis results.

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