Molecular characterization and genetic structure analysis of Coffea arabica and Coffea canephora cultivars from India using SCoT markers

Abstract

Coffee is the second most traded community after oil and provides a livelihood for more than 125 million people worldwide. It is cultivated in 80 countries spreading over Africa, Asia and Latin America. In recent years, there is an increasing demand for high quality planting material because of the changing dynamics of pests and disease occurrence possibly triggered by climate change. This calls for a better understanding of the existing genetic diversity and its utilization in the breeding program. In this study, we investigated the molecular characterization and genetic structure of twenty coffee cultivars predominantly bred and cultivated in India using Start Codon Targeted (SCoT) molecular markers. Thirty-six SCoT primers amplified 368 bands of which 192 (52.17%) are polymorphic. The mean values of PIC, Resolving power (RP), mean effective multiplex ratio (EMR) and marker index (MI) were 0.27, 16.04, 3.26 and 1.12 respectively indicating the usefulness of these markers for the genetic analysis of coffee cultivars. Four cultivars produced 17 unique bands due to their specific genetic constituents and these bands could be useful for fingerprinting diagnostics. UPGMA clustering based on SCoT markers separated the accessions into two major clusters which accommodated five sub-clusters which are supported by the principal coordinate analysis (PCoA). The STRUCTURE analysis showed K = 5 as the optimum number of groups and completely separated the cultivars mainly according to their development and genetic constitution. Our results represent the first-of-its-kind attempt to shed light on the genetic diversity among coffee cultivars grown in India using the functional marker.