Molecular genetic characterization of fungal isolates representing biogeographic diversity in the colletotrichum-bean pathosystem

Colletotrichum lindemuthianum is a pathogen of Phaseolus vulgaris (common bean) causing anthracnose disease and poses a threat to food security. The aim of the study was to advance understanding of genotype-phenotype-environmental interactions in Colletotrichum spp. through biomolecular approaches including multilocus molecular phylogenetic analysis, AP-PCR and morphological diversity assessment. Following initial screening five loci were selected for further investigation including ribosomal RNA gene block internal transcribed spacer (ITS), tubulin (TUB), glyceraldehyde phosphate dehydrogenase, glutamine synthetase, and the mating type gene. Study included 18 Colletotrichum isolates representing wide biogeographic diversity. Two isolates were identified as C. gloeosporioides and C. truncatum, which are not commonly known bean pathogens and this needs further research. The TUB marker was the most conserved amongst the C. lindemuthianum isolates. Universal marker ITS distinguished 5 haplotypes; concatenated sequence data provided the highest resolution with 7 haplotypes. AP-PCR differentiated between 5-9 haplotypes and appeared more suitable for local population monitoring purposes. Variability in growth rate, sporulation and colony morphology was observed among the Colletotrichum spp. isolates. The study would serve as a platform for genome sequencing based studies into environmental change adaptation in Colletotrichum spp. particularly C. lindemuthianum using isolates representing historical and contemporary populations.