Polymorphic primer identification and annealing temperature optimization of dominant markers for two species of Syzygium from UNHAS Educational Forest

Abstract

Abstract Primers that produce polymorphic bands and appropriate annealing temperatures are two crucial factors in genetic diversity analysis. This study aims to identify polymorphic primers and determine an optimal annealing temperature for Syzygium cumini and S. nervosum . Two types of dominant markers were used, ten primers for Inter Simple Sequence Repeat (ISSR) and fourteen primers for Random Amplified Polymorphic DNA (RAPD). A temperature gradient was performed at the annealing stage to determine the optimal temperature for each primer evaluated. ISSR primers produced more polymorphic bands on S. nervosum DNA samples compared to S. cumini . Seven out of ten ISSR primers produced polymorphic bands on S. cumini DNA samples, and three primers produced monomorphic bands. While in S. nervosum , nine ISSR primers produced polymorphic bands, and one primer was not amplified. All RAPD primers evaluated successfully amplified S. cumini DNA, but only nine primers produced polymorphic bands, while five primers produced monomorphic bands. On the other hand, in S. nervosum, six RAPD primers produced polymorphic bands, six primers did not produce any bands, and three primers produced monomorphic bands. The optimal temperature ranges for ISSR primers were from 41.5°C to 54.0°C, and for RAPD primers, from 31.4°C to 45.8°C. The results of this study are expected to serve as a reference for selecting primers to be used in genetic diversity analyses of S. cumini and S. nervosum .

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