Cross infection and molecular characterization of Colletotrichum spp. infecting coffee and black pepper

Abstract Anthracnose caused by Colletotrichum species is an economically important fungal disease in both coffee and black pepper leading to substantial crop losses. In India, coffee is cultivated under natural shade conditions and black pepper is grown as an inter-crop. Since Colletotrichum species can infect a broad range of host plants, there is an apprehension of the spread of anthracnose from coffee to black pepper and vice versa. Because of this, it is essential to identify the Colletotrichum strains infecting coffee and black pepper as an aid in developing effective control measure strategies. Cross-infection studies using the strain isolated from coffee and black pepper failed to infect each other. However, the ITS sequence of Colletotrichum spp. isolated from coffee and black pepper shared a similarity of 96.45% and placed both the strains under Colletotrichum gloeosporioides. The genetic variability between both strains was studied using 20 SRAP and 15 SCoT polymorphic molecular markers. The average polymorphism information content (PIC) and resolving power (Rp) of the 20 SRAP primer combinations were 0.52 and 14.65 and for SCoT primers it was 0.39 and 12.27 respectively. The UPGMA dendrogram and principal coordinate analysis divided the Colletotrichum species into two clusters and placed them in two different coordinates. Based on the Jacquard coefficient index, the similarity between the two strains was 31.0% using SRAP and 60.0% using SCoT markers whereas using SRAP and SCoT combined assay it was 43.0%. The study showed that the two Colletotrichum strains infecting coffee and black pepper are genetically distinct.