Assessment of the Suitability of Molecular SCoT Markers for Genetic Analysis of Coffee Species

Abstract Start codon targeted polymorphism (SCoT), a novel and gene-targeted marker, has recently become the marker of choice in genetic diversity studies. In the present study, 31 SCoT primers were tested for their suitability in the genetic analysis of 21 coffee genotypes representing 18 species. A total of 647 distinct PCR amplified fragments were produced with a mean of 20.9 fragments per primer and 80.80% of which were polymorphic. The polymorphic information content of SCoT primers ranged from 0.16 to 0.86, with a mean value of 0.63. Resolving power ranged from 6.19 to 28.29, with a mean value of 20.2. Species-specific unique PCR amplified fragments were identified for 16 species, which could be used as genetic fingerprints. The genetic similarity among various coffee species calculated using the Dice similarity coefficient ranged between 0.60 and 0.89. The dendrogram constructed using the unweighted pair group of arithmetic means (UPGMA) clustered the 21 coffee genotypes into two major groups. The study revealed that Coffea jenkinsii, an indigenous species from India, showed the highest similarity with C. arabica, which is of Ethiopian origin. The results proved the suitability of SCoT markers in genetic analysis of coffee genotypes.