Population biology and genetics of Rhizoctonia solani anastomosis group 3 (AG-3)

Abstract

Anastomosis group 3 (AG-3) of Rhizoctonia solani is frequently associated with diseases of potato and tobacco. Although isolates from the two hosts are taxonomically related, previous studies have shown differences in their biology, fatty acid composition, pathogenicity and ribosomal DNA. However, the genetic diversity of populations of R. solani AG-3 from potato and tobacco are not known. In this study, the genetic diversity of field populations of R. solani AG-3 from potato and tobacco in North Carolina were examined using somatic compatibility and amplified fragment length polymorphisms (AFLP). A sample of 32 isolates from potato and 36 from tobacco were paired in all possible combinations on PDA plus activated charcoal and glass slides and examined for somatic interactions. Approximately 5% of tobacco isolates and less than 0.5% of potato isolates were somatically compatible. Twenty-eight and eight distinct somatic compatibility groups (SCG) were identified in the potato and tobacco samples, respectively. AFLP analyses indicated that the potato sample of R. solani AG-3 was more genetically diverse (32 AFLP patterns) than the tobacco sample (26 AFLP patterns). None of the potato or tobacco isolates were somatically compatible or shared a common AFLP pattern. Clones (i.e., cases where two or more isolates were somatically compatible and shared the same AFLP pattern) were identified only in the tobacco sample. Eight clones of R. solani AG-3 from tobacco represented 22% of the total sample. All eight SCG of R. solani AG-3 from tobacco were associated with more than one AFLP pattern. Compatible interactions between potato isolates only occurred between isolates from the same field (two isolates in each of four different fields), with similar but not identical AFLP pattern. For analysis of the population structure of R. solani AG-3 from potato, a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was used to identify and differentiate genotypes. A population sample of 104 isolates from five counties in eastern NC was analyzed using polymorphic codominant single-locus PCR-RFLP markers identified after sequencing and screening anonymous DNA from a fungal genomic library. Multilocus genotypes were determined screening isolates using combinations of PCR product/polymorphic enzyme for each locus, generating seven PCR-RFLP markers. There was evidence for high levels of gene flow between populations of R. solani AG-3. The five samples were genetically similar with one another. When data was clone-corrected and samples pooled into one single population from NC, random associations of alleles within and between loci were found for all the loci or pairs of loci, indicating random mating. However, when all genotype were analyzed the observed genotypic diversity deviated from panmixia and alleles within and between loci were not randomly associated. These findings support a model of population structure for R. solani AG-3 on potato that includes both recombination and clonality. This study describes the application of a population genetics-based statistical method for detecting migration in populations of R. solani AG-3 from potato using multilocus PCR-RFLP genotypes. The effect of migration from source populations of the pathogen on potato seed tuber on the magnitude of gene flow with a recipient (soil population) in NC was also examined. Analysis of genetic data indicated that the NC population of R. solani AG-3 has experienced recent migration. There was also an indication of high levels of gene flow between the source and the recipient population. Unidirectional migration from source population(s) followed by establishment of migrant genotypes in the recipient population, through colonization, is postulated to explain the high level of gene flow observed.