Population genomic analyses reveal geographic structure in Rhizoctonia solani AG1-IA isolates associated with different crops in the USA and the Caribbean

Soilborne fungi threaten food security, but limited knowledge of their population biology, including genetic variability and structure, hinders the development of effective strategies to prevent crop losses. Rhizoctonia solani AG-1 (Basidiomycota: Agaricomycetes) is a significant soilborne pathogen worldwide, divided into subgroups based on host range and molecular diversity. Rhizoctonia solani AG1-IA causes sheath blight in rice and aerial blight in soybean, two devastating diseases in these economically important crops. Rice and soybean are often used in rotation, increasing inoculum in the fields over cropping seasons. Monitoring genetic variability and structure in R. solani AG1-IA is critical to understand the population biology of the pathogen and aid in disease management practices, including screening and developing new resistant cultivars. A total of 145 isolates of R. solani collected between 1993 and 2022 from different hosts and states in the USA were sequenced. The population genetic structure was inferred with clustering approaches based on approximately two million biallelic single nucleotide polymorphisms (SNPs). Rhizoctonia solani AG1-IA showed relatively high genetic diversity and little departure from mutation-drift equilibrium, pointing to an ancient, widespread, indigenous pathogen in the USA. While populations had a clear geographic structure, they lacked host specialization, suggesting dispersal is mainly distance limited. Shared ancestry between populations and the discovery of clonal lineages, however, indicated recent connections between geographic areas. Our work provides valuable insights into the evolutionary history and population biology of R. solani AG1-IA, offering a foundation for developing targeted management strategies and resistant crop varieties.