Identification of DNA Mutations in Coffea liberica from Kepulauan Meranti Using Next Generation Sequencing Tisha Melia, Fatayat, Ninik Nihayatul Wahibah and Siti Fatonah
Faculty of Mathematics and Natural Sciences, Universitas Riau
Abstract
Coffee is Indonesia^s most prominent agricultural product, cultivated primarily as either robusta (Coffea canephora Pierre ex A. Froehner) or arabica (Coffea arabica L.). It is unfortunate that these two coffee species are not well suited for cultivation on peatlands. The Ministry of Agriculture has introduced two superior varieties, Liberoid Meranti 1 (Lim 1) and Liberoid Meranti 2 (Lim 2), derived from the Coffea liberica species found in Kepulauan Meranti. These two varieties offer the dual benefit of being suitable for planting on peatlands and exhibiting resistance to leaf rust disease. Unfortunately, scientific studies on these two coffee varieties are currently limited to the investigation of disease resistance genes. Consequently, there is a necessity for scientific studies to gather genetic data from Lim 1 and Lim 2 with the objective of investigating their high adaptability in peatlands. The DNA was extracted and subsequently sequenced using next-generation sequencing technology, allowing for the reading of DNA sequences from six plants. Three plants were selected from each variety for analysis. A total of 414 million sequencing reads were successfully mapped to the C. canephora genome, with an average of 69 million mapped reads per sample. The mapped reads were used to identify single nucleotide polymorphisms (SNPs) and small indels. Many of the identified DNA mutations were specific to each variety, thus making them suitable for use as variety identification markers. The study provides a comprehensive investigation into the DNA mutations present in Lim 1 and Lim 2. This will not only enrich the genetic data in public databases, but also provide a foundation for investigating the evolution and habitat adaptation of these two varieties.
