Optimisation of random amplified polymorphic DNA (RAPD) protocol for identification of molecular markers in selected wild banana species

Banana (Musa spp) is one of important staple food in the world. But, the disease infected to banana species make the species vulnerable to disease. It is suggested to
plant resistant cultivars rather than using chemical control. The source of resistance plant may be find from wild species. To find the trait of gene must be assist by
molecular marker such as RAPD, AFLP or ISSR. But then, all the assistance of molecular marker need to be optimise to get the best bands. In this study, molecular
techniques specifically RAPD were used to analyse genetic traits. Optimisation of annealing temperature and concentration of MgCl₂ were the focus. Selection of primers also one of the main factors to determine the succesful results. Furthermore, the use of appropriate primer combination could enable the development of DNA
fingerprint for genetic diversity in producing of monomorphic and polymorphic bands. In conclusion, it is suggested to use primer OPJ-04, OPH-09, OPA-06, OPA-19 and OPJ-13 to get the best combination of polymorphic and monomorphic. This research also suggest to use 36.6°C for annealing temperature and 3.0 mM of MgCl₂ concentration as they are the optimum annealing temperature and concentration for all the primers tested.