ITS-Based molecular diversity and population structure of potato-associated Rhizoctonia solani in the Southern Colombian Andes

Rhizoctonia solani is an important soilborne pathogen of potato, yet its molecular diversity and spatial organization remain insufficiently characterized in potato-producing areas of the southern Colombian Andes. This study characterized the phylogenetic identity, spatial and cultivar-associated internal transcribed spacer (ITS) variation, and haplotype diversity of potato-associated R. solani isolates collected across major potato-producing municipalities of Nariño, Colombia. Of 50 isolates initially obtained, 47 yielded ITS sequences that were retained after quality control. Maximum-likelihood phylogenetic inference assigned 45 isolates (95.7%) to anastomosis group 3 potato type (AG-3 PT) and two to AG-2-1. Within AG-3 PT, genetic distance was not associated with geographic distance (Mantel ρ = −0.066, P  = 0.1609), and permutational multivariate analysis of variance (PERMANOVA) detected no significant ITS differentiation by municipality or potato cultivar. This absence of cultivar-associated differentiation remained consistent when permutations were restricted within municipality. Analysis of the curated 43-isolate dataset identified 16 ITS haplotypes, with relatively high haplotype diversity ( Hd  = 0.796) but low nucleotide diversity (π = 0.00411). Two dominant haplotypes accounted for 62.8% of isolates and were broadly distributed across municipalities and five potato cultivars. Overall, AG-3 PT was the predominant R. solani subgroup associated with potato in Nariño, while ITS variation was characterized by numerous closely related sequence variants rather than robust geographic or cultivar-associated subdivision. These findings provide a regional baseline for understanding R. solani diversity and support the use of higher-resolution genomic approaches to investigate finer-scale population structure and epidemiological connectivity.