Genome-wide Profiling and Characterization of Terpene Synthase-linked Simple Sequence Repeats in Coffea canephora Pierre ex A. Froehner for Identification of Potential Markers for Aroma in Philippine-grown Coffee Varieties
Daisy May C. Santos1, Angelo Joshua A. Victoria1,2,
Carla Francesca F. Besa2, and Ernelea P. Cao1
1Institute of Biology, College of Science
2Philippine Genome Center (PGC)
University of the Philippines (UP) Diliman, Quezon City 1101 Philippines
Aroma plays an important role in determining the market value of coffee. The Philippines produces four coffee varieties – namely, Arabica, Robusta, Liberica, and Excelsa for commercial use. In this study, simple sequence repeats (SSRs) linked to terpene synthase (TPS) genes were used to characterize and differentiate the Philippine coffee varieties. SSR loci were mined from the existing sequenced genome of Coffea canephora. Data mining yielded 759,747 perfect SSRs, of which 317 were linked to the aroma. Two hundred were screened using Philippine Arabica, Robusta, Liberica, and Excelsa samples. There were 27 loci that were successfully amplified for all specimens and showed clear polymorphisms. These were used to characterize the coffee varieties based on number of alleles and heterozygosity. The number of alleles ranged from 2 to 8, while the expected heterozygosity ranged from 0.18 to 0.85. There were 26 bands from 17 loci that could differentiate among varieties, of which 15 bands were unique to C. arabica (Arabica variety), three to C. canephora (Robusta variety), three to C. liberica (Liberica and Excelsa varieties), and five that were shared by C. arabica and C. canephora. This study is the first to characterize TPS-linked SSR markers in Philippine grown coffee varieties.
The Philippines is one of the few countries that cultivate four coffee varieties for commercial use. These are the Arabica, Robusta, Liberica, and Excelsa coffee. Coffea arabica (Arabica) is considered as the world’s best coffee due to its superior taste and aroma (Vieira et al. 2010). Coffea canephora (Robusta) accounts for 69% of Philippine coffee production (2017–2022 Philippine Coffee Industry Roadmap). Although inferior to Arabica in terms of taste and aroma, it is of certain advantage because it is high-yielding and tolerant to diseases (Butt and Sultan 2011). Coffea liberica has two varieties – Liberica and Excelsa. Coffea liberica var. liberica (Liberica) is locally known as the “kapeng barako.” It is characterized by its strong, woody, and bitter taste with a pungent aroma (N’Diaye et al. 2005). Coffea liberica var. dewevrei (Excelsa), on the other hand, has a sweet and fruity aroma. . . . read more
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