Structural Variability of Subtelomeres Applied for Genotyping of Selected Potato Varieties

Subtelomeric regions reveal a relatively high degree of polymorphism due to the increased frequency of recombination events in these chromosome loci. In a search for molecular markers applicable to genotyping of potato varieties, we focused on two possible sources of polymorphism occurring in this region: (i) arrangement of blocks of subtelomeric chromatin; (ii) structure of telomere-subtelomere boundary. Analysis of the internal arrangement of subtelomeric sequences showed several types of cultivar-specific spectra of PCR products arising from the variant orientation of sequence units of the ST3-subtelomeric sequence, or from different lengths of regions linking the individual sequence units. Further, the telomere-subtelomere boundary sequences were amplified using telomeric and ST3-specific primers and the obtained products were cloned. Sequence analysis of the clones resulted in characterisation of a novel telomere-associated sequence (FIN2). Primers derived from this sequence were then used alone or in combination with telomeric or ST3-specific primers to generate cultivar-specific spectra of PCR products. The described combinations of sequence-specific primers may be used for the fast, cheap and reproducible PCR-genotyping of selected potato varieties.