Phylogenetic Analysis of Arabica and Robusta Coffee Using the matK and rbcL Genes

Abstract

Coffee is one of the most traded commodities globally, with Indonesia as one of the major contributors to its production volume. The two most commonly cultivated species in Indonesia are Coffea arabica (arabica) and Coffea canephora (robusta). One notable location for cultivating Arabica and Robusta coffee is the Gayo Experimental Farm in Pondok Gajah, Bener Meriah, Aceh. It is well known that the area has suitable environmental and soil conditions for cultivating both coffee species. Therefore, this study aims to determine the evolutionary relationships between Arabica and Robusta coffee varieties grown at the farm using the matK and rbcL genes. Genomic DNA was extracted using a modified CTAB method and amplified the matK and rbcL genes. Subsequently, DNA sequencing was carried out using BLAST, followed by phylogenetic analysis with Maximum Parsimony. The results showed that the concentration of the extracted genomic DNA ranged from 33.95 to 149.65 ng/µL, and its purity at A260 and A280 was between 1.7 and 1.9. The amplified gene sequences for the matK and rbcL genes were 856–867 bp and 566–657 bp, respectively. In addition, the matK, rbcL, and matK+rbcL genes also showed a genetic distance of 0.001 between Arabica coffee species, Coffea arabica x Coffea canephora, and Coffea eugenioides. The results also indicated that Robusta coffee varieties had a genetic distance of 0.001-0.005 with Coffea canephora. This study's matK and rbcL genes demonstrated the relationship between Arabica and robusta coffee varieties. However, these two genes could not distinguish coffee at the varietal level.