A Global Meta-analysis of the Host Range, Diversity and Evolution of <em>Rhizoctonia solani</em>

Rhizoctonia solani is a soil-borne fungal pathogen with substantial adverse effects on global agriculture. The pathogen causes plant diseases in staple crops such as black scurf in potatoes, root rot in soybeans, and sheath blight in rice. This fungal species is characterized by its genetic diversity, which has been historically assessed based on morphology and hyphal fusion, leading to the identification of 14 anastomosis groups (AGs). Besides being genetically different, each AG exhibits distinct host range association, lifestyle, and pathogenicity. To better understand the ecology and evolution of R. solani, questions regarding the fundamentals underlying the genetic differentiation among these AGs and evolutionary history of interactions with host plants should be addressed. The primary objective of this study was to determine how host association drives adaptation and diversity in R. solani. A combination of phylogenetics, host transition estimation, and population structure analyses were employed on a publicly available global dataset containing 4,119 rDNA-ITS sequences of R. solani isolates collected in the last 70 years and newly sequenced isolates from Nebraska. Our phylogenetic analyses suggest the reported AGs are mostly consistent with monophyletic placement. Since the majority of R. solani populations behave like generalists by exhibiting a wide host range, while others are often associated with a narrower host range, we studied host transitions using a Bayesian Inference approach. Results suggested the temporary host transition and extensive gene flow drive genetic differentiation in generalist populations, while host drives genetic differentiation among specialist populations, with AG-3 representing the population with the narrowest host range (Solanaceae). To improve detection efforts of this specialist population, we developed a quantitative PCR (qPCR) assay with 99% efficiency and very sensitive detection (2 x 10-4 ng/µL), and low likelihood of off-target amplification. The findings of this study provide insights into the evolutionary pressures among R. solani populations and set foundations for developing long-lasting disease management strategies.\nAdvisor: Teddy Garcia-Aroca