Sequence Analysis of Select Terpene Synthase Genes in Philippine Coffee

Abstract

Aroma is one of the factors used to evaluate coffee quality. Aroma profile differences between coffee varieties are dictated by the unique and diverse combination of volatiles, such as terpenes. Several studies have elucidated the phylogenetic relationships of coffee varieties using various DNA markers; however, this is the first study to directly compare the DNA sequences of their terpene synthase (TPS) genes, specifically in Philippine coffee samples. Primers were designed for select TPS genes, and phylogenetic relationships were analyzed through the neighbor-joining (NJ) method. The NJ tree successfully distinguished between the three coffee species: Coffea arabica, C. canephora, and C. liberica. A 10-base-pair (bp) indel in CofarTPS8 is present in Arabica but absent in the other varieties, while a 14-bp indel in CofTPS24 was found to be present in Robusta, Liberica, and Excelsa but absent in Arabica. Both indels occur in the intron regions of their respective genes, which may or may not have an indirect effect on the final product. Future studies may look into these particular genes to determine if there are marked differences in their respective products.