Simple sequence repeat genotyping of Colletotrichum species associated with soybean anthracnose in Uttarakhand and other states of India

Anthracnose is one of the most devastating diseases affecting soybean (Glycine max L. Merril) in India and is incited by the Colletotrichum truncatum species complex. In this study, 33 isolates of Colletotrichum spp. isolates were collected from major soybean-growing states of India. The cultural, morphological and molecular characteristics (Internal Transcribed Spacer rDNA region) of all isolates were demonstrated. Twelve simple sequence repeat (SSR) markers were selected to amplify the genomic DNA of all isolates, to assess the genetic diversity. On the basis of morpho-cultural and molecular characterization of three different Colletotrichum species, C. truncatum, C. cliviicola and C. cholorophyti were identified. Representative Colletotrichum isolates (Ct-Pant, Ct-Gur and Ct-Gag) from each species group were found pathogenic to susceptible soybean variety (PS 1092) and fulfilled Koch's postulates. The SSR genotyping of 33 isolates revealed that all examined SSR markers exhibited a high degree of polymorphism, as indicated by the mean values of 0.51 for polymorphic information content, 1.97 for marker index and 1.99 for resolving power. For each primer, the average number of alleles per locus was 3.58. The results of Jaccard similarity coefficient-based UPGMA (Un-weighted Pair-Group Method with Arithmetic Mean) cluster analysis and principal component analysis showed that isolates of the same species were clustered together, but no clear-cut grouping was obtained on the basis of geographical distribution. Thus, it can be inferred from the study that C. truncatum accessions obtained from various geographical locations of India exhibit substantial genetic variation and a significant level of relatedness.