Pathogenic and Genetic Diversity of Sclerotium rolfsii, the Causal Agent of Southern Blight of Common Bean in Uganda

<i>Sclerotium rolfsii</i> Sacc. is a soil-borne fungus that causes southern blight on many crops in the tropical and subtropical regions. In 2018, southern blight was reported as the most prevalent bean root rot in Uganda. Earlier studies ascertained the morphological and pathogenic diversity of <i>S. rolfsii</i>, but a limited understanding of its genetic diversity exists. Knowledge of <i>S. rolfsii</i> genetic diversity is a critical resource for pathogen surveillance and developing common bean varieties with durable resistance. A total of 188 <i>S. rolfsii</i> strains from infected common bean plants were collected from seven agro-ecological zones of Uganda in 2013, 2020 and 2021, and characterized morphologically and pathogenically. The genetic diversity of the strains was assessed using single-nucleotide polymorphisms (SNPs) obtained from whole-genome sequencing. The growth rate of the strains ranged between 1.1 and 3.6 cm per day, while the number of sclerotia produced ranged from 0 to 543 per strain. The strains had fluffy, fibrous, and compact colony texture. The strains were pathogenic on common bean and caused disease severity indices ranging from 10.1% to 93.3%. Average polymorphic information content across all chromosomes was 0.27. Population structure analysis identified five genetically distinct clusters. The results of analysis of molecular variance revealed that 54% of the variation was between clusters while 46% of variation was within clusters. Pairwise comparison of Wright's fixation indices between genetic clusters ranged from 0.31 to 0.78. The findings of this study revealed moderate genetic diversity among <i>S. rolfsii</i> strains, which should be taken into consideration when selecting strains for germplasm screening.