Comparative Population Genetics and Fludioxonil Sensitivity of Rhizoctonia solani AG-3 Subgroups from Potato and Tobacco in China

Rhizoctonia solani AG-3 is a major pathogen of solanaceous crops, with subgroups PT, TB, and TM 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, 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 = 0.008-0.033) 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 = 0.005-0.051), and a mixed reproductive mode: Liaoning populations exhibited linkage equilibrium (P > 0.05), while Heilongjiang and Jilin populations showed significant disequilibrium (P < 0.01). High genetic differentiation (F _ST = 0.269-0.549) confirmed PT, TB, and TM as distinct lineages, with PT and TM most closely related. Fludioxonil effectively inhibited all subgroups (mean EC ₅₀ = 0.054-0.090 mg·L ^-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.