Genetic diversity of Colletotrichum lindemuthianum races based on ITS-rDNA regions

Colletotrichum lindemuthianum is the causal agent of anthracnose in common bean. Favorable conditions for this disease might result in up to 100% yield losses. One of the main challenges for common bean producers and breeders still remains the management disease, since this pathogen exhibits a wide genetic variability probably due to its recombination sexual reproduction. The 5·8S gene and the flanking internal transcribed spacer regions (ITS1 and ITS2) of 40 different isolates of C. lindemuthianum collected in Brazil were amplified by PCR, and sequenced in order to determine genetic variability. The results revealed that 46.88% of SNPs were detected in the ITS1 region, while 53.12% of them were located in the ITS2 region. The genetic distance ranged from 0.000 to 0.169 between races. The greatest distance was observed between the races 10 and 73 with a value of 0.169, indicating a wide genetic variability between them. The phylogenetic tree was composed of three groups. Group I had five subgroups. Similar results were also observed through population structure analysis, which revealed the presence of three clusters. These results suggest that sequence analysis of ITS rDNA regions of C. lindemuthianum may be a valuable tool to identify this pathogen through design of specific primers.