Genetic profiles of three Cinchona species in Junghuhn Natural Reserve, Indonesia

Abstract

Cinchona species were widely used as ancient medicines for different diseases because they contain the active component quinine and its derivatives. However, studies on the molecular aspects of cinchona, including its genetic diversity, have not been reported because most previous works focused on the administration of the antimalarial cinchona alkaloid. Quinine is also being tested as alternative compound for the treatment of Covid-19. The Junghuhn Natural Reserve in Indonesia contains three different types of cinchona plants, namely, Cinchona calisaya, Cinchona pubescens, and Cinchona sp. Given that the genetic diversity and kinship of these species have never been studied, collecting data on the cinchona gene pool has become imperative. This study analyzed the genetic diversity of the cinchona species in the Junghuhn Natural Reserve, Indonesia, by using eight RAPD markers, i.e., OPA-2, OPA-9, OPB-02, OPB-03, OPB-04, OPB-05, OPB-7, and OPJ-07, during 2020 at the University of Jenderal Soedirman, Purwokerto-Indonesia. Polymorphic band data were obtained. Then, phenogram analysis was conducted by using UPGMA and maximum parsimony with MEGA7. The RAPD profiles of Cinchona species (C. calisaya, C. pubescent, and Cinchona sp.) revealed polymorphism with different markers, i.e., OPA-2 (90%), OPB-2 (75%), OPB-5 (75%), OPB-3 (66.66%), OPB-4 (66.66%), OPB-7 (66.66%), OPJ-7 (66.66%), and OPA-9 (58.33%) sequentially with total polymorphism (70.62%). C. calisaya was identified as the most distinctive species. UPGMA yielded a coefficient of 0.200 and two distinctive groups: Group I, which comprised C. pubescens and Cinchona sp. with the p-distance value of 0.333, and Group II, which contained C. calisaya. Ixora sp. was treated as an outgroup plant. The topology of the dendrogram was consistent with that of the UPGMA dendrogram. Results may be used for the further exploration of the genetic diversity of cinchona species.