Comparative Population Genetics and Fludioxonil Sensitivity of Rhizoctonia solani AG-3 Subgroups from Potato and...

Rhizoctonia solani AG-3 is a major pathogen of solanaceous crops, with subgroups PT (potato type), TB (tobacco type), and TM (tomato type) causing potato black scurf and tobacco target spot in China, yet their population structures remain unexplored. Here, we used microsatellite markers to genotype 160 PT isolates from Northeast China, as well as 189 TB and 124 TM isolates from tobacco-growing areas nationwide, and assessed their baseline sensitivity to fludioxonil. The three subgroups exhibited contrasting structures. PT showed high gene diversity (Hexp = 0.634) but significant linkage disequilibrium and low differentiation (F_ST = 0.008 to 0.033) without isolation-by-distance, suggesting clonal reproduction and dispersal via contaminated seed tubers. TB displayed moderate diversity (Hexp = 0.385), linkage equilibrium, and significant isolation-by-distance, indicating sexual reproduction with gene flow constrained by geography. The Yunnan population may represent a diversity center. TM showed the lowest gene diversity (mean Hexp = 0.273), low differentiation (F_ST = 0.005 to 0.051), and a mixed reproductive mode: Liaoning populations exhibited linkage equilibrium (P > 0.05), whereas Heilongjiang and Jilin populations showed significant disequilibrium (P < 0.01). High genetic differentiation (F_ST = 0.269 to 0.549) confirmed PT, TB, and TM as distinct lineages, with PT and TM most closely related. Fludioxonil effectively inhibited all subgroups (mean EC₅₀ = 0.054 to 0.090 mg·liter^-1), with six resistant isolates detected. Sensitivity was independent of origin or genetic background. This study reveals contrasting population structures among AG-3 subgroups and provides a foundation for subgroup-specific disease management and resistance monitoring.