Diversity assessment of Colletotrichum species associated with chilli anthracnose and their characterization via species specific primers

Anthracnose disease caused by Colletotrichum spp. is a major constraint for chilli production and storage throughout the globe. In the present study, diversity analysis and characterization of Colletotrichum species associated with the disease was carried out. Anthracnose infected chilli samples were collected from major chilli growing areas of India and twenty five isolates were selected for species identification. Pathogenicity of all the isolates was confirmed on a susceptible variety K2. The morphological characters viz., colony colour, colony topography, conidial size and shape and size of setae revealed three morphotypes. In contrast to morphological grouping, RAPD based diversity analysis clustered all isolates into two main groups and seven sub-groups. Thereafter, five different species specific primers were employed to characterize different species of Colletotrichum, of which primers specific for C. capsici, C. gloeosporioides and C. acutatum yielded positive results. The phylogenetic analysis based on sequence information of specific region of representative isolates confirmed association of three species with chilli anthracnose. These results have important implications in deciphering species level relationship of Colletotrichum with anthracnose disease in chilli by combined application of species specific PCR assay and morphological character for their routine diagnosis.