Optimization of rapd method and its application for the analysis of genetic variability in cultivated and wild Indian sesame

The importance of the oilseed crop sesame in agro-based industry has challenged the improvement of its population selection, as it takes longer time by traditional methods. The selection period can be reduced by the application of Random Amplified Polymorphic DNA(RAPD) technique.There are factors influencing the results of RAPD, such as Concentration of Mg²⁺, dNTPs, DNAtemplate, Taq polymerase, Annealing temperature etc. These conditions for RAPD were optimized for the molecular characterization of some of the cultivated and wild sesame (Sesamum indicum, S. mulayanum). The influence of various factors like concentration of Mg²⁺, DNAtemplate, primer, Taq polymerase, dNTPs, phases and the number of PCR cycles were determined and optimized for Random Amplified Polymorphic DNA (RAPD) analysis of sesame A combination of Mg²⁺ at 3.0 mM, primer at 0.8 μM (Operon Biotechnologies), dNTPs at 0.12 μM (SibEnzyme), genomic DNAat 50 ng, Taq polymerase 1.5 U (SibEnzyme) in 25 l reaction mixture with 45 PCR cycles was best for RAPD amplification. Application of these optimized conditions for RAPD analysis for genetic diversity assessment of Sesamum spp. showed enormous diversity among cultivated and wild sesame accessions. This study provides an enriched RAPD protocol suitable for molecular analysis of sesame and helpful for breeding.