RAPD primer screening for amplification on Katokkon pepper from Toraja, South Sulawesi, Indonesia

Abstract

Abstract Random amplified polymorphic DNA (RAPD) is a well-known molecular marker that extensively applied to the genetic diversity analysis among species in the populations. Here, this marker was utilized in Katokkon pepper ( Capsicum chinense Jacq.), a highland pepper and having unique characteristics cultivated in specific regions (Tana Toraja and North Toraja), on preliminary primer screening using 30 RAPD primer pairs. A total of eight primers (OPA-02, OPAE-11, OPG-09, M-29, OPP-08, OPG-19, OPZ-05, and OPD-20) could produce polymorphic bands on twelve randomly selected DNA samples. OPA-02, OPP-08, OPG-19, OPZ-05, and OPD-20 generated polymorphic bands on all twelve evaluated samples, yet OPZ-05 was excluded in further analysis due to producing unclear bands. Clear and polymorphic bands were formed by OPAE-11 on eleven samples, whilst OPG-09 and M-29 only produced bands on ten samples. The primers are suitable to be used for amplifying DNA and determining the genetic diversity of Katokkon pepper in further analyses.

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