Genetic and phenotypic diversity and random association of DNA markers of isolates of the fungal plant pathogen Sclerotinia sclerotiorum from soil on a fine geographic scale

Sclerotia of the soil-borne plant pathogen Sclerotinia sclerotiorum were collected from 1 m2 area of the top 1.27 cm layer of soil in an alfalfa field in southeastern Washington state of the US. Out of 272 sclerotia collected, 40 were randomly selected and analyzed for genetic diversity in terms of microsatellite loci, mycelial compatibility groups (MCGs) and phenotypic diversity using five phenotypic traits (fungicide sensitivity, oxalic acid production, growth rate, colony color and virulence). Sixteen microsatellite haplotypes and 15 MCGs were found among the 40 isolates. The isolates showed three colony colors (beige, dark and white) on Difco PDA and exhibited significant differences in growth rate, oxalic acid production, and sensitivity to three fungicides, benomyl, fluazinam and iprodione. However, these isolates did not show differences in their ability to colonize detached pea leaves. No apparent relationship among the neutral genetic markers and the phenotypic traits was detected. Two of the haplotypes accounted 40% of the isolates, suggesting isolates of these haplotypes might be better adapted to the environmental conditions in this alfalfa field. Several lines of evidence indicated high levels of genetic diversity and potential outcrossing within the population of S. sclerotiorum: 1) high likelihood of five genetic populations based on Bayesian probability and the presence of admixed isolates; 2) random association of alleles in every pair-wise linkage disequilibrium test among eight independent microsatellite loci; 3) discordances between microsatellite haplotypes and MCGs and 4) lack of correspondence among the genetic markers and phenotypic traits. Multilocus Index of Association test suggested that outcrossing occurs only within interbreeding subpopulations of S. sclerotiorum. ⺠We study diversity of the soil-borne fungal plant pathogen Sclerotinia sclerotiorum. ⺠We sample sclerotia of Sclerotinia sclerotiorum directly from soil in a 1 m2 area. ⺠Soil harbors high levels of genetic and phenotypic diversity and population subdivision. ⺠Genetic recombination occurs in interbreeding subpopulations of the pathogen.