Abstract
Polymerase chain reaction optimization for inter simple sequence repeat primers is a key factor to obtain accurate and reproducible results for gene mapping, studying the genetic structure of populations, plant passporting, phylogenetic analysis. Changing temperature conditions, the amount of amplification cycles and concentration of reaction mixture components is allowed to vary the number of bands obtained by this method. This article is result of preliminary research of method selection for molecular analysis. It is aimed to show how to adjust the profile of inter simple sequence repeat fragments by polymerase chain reaction for four model species Stipa lessingiana, Poa intricata, Equisetum fluviatile and Pteridium aquilinum. The working concentrations of magnesium chloride for primer ((СТС)3GC) and ((АС)8YG) were 2.5 mM for 0.63 units of Taq DNA polymerase and for primer ((СА)6GG) it was 4.5 mM for 1.25 units. Sharply defined banding was observed from the minimal amount of DNA 5 ng per reaction, with primer concentration from 10 to 80 pmol and dNTPs concentration 0.2 mM. Optimal hybridization temperatures were 51.9 °C for primers ((АС)8YG), ((СА)6GG) and 50.0 °C for ((СТС)3GC). The best imaging results were obtained when setting up electrophoresis in 1.9% agarose gel
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