Characterization of the genetic variation and fungicide resistance in Botrytis cinerea populations on rooibos seedlings in the Western Cape of South Africa

Botrytis cinerea causes severe losses of rooibos seedlings in the Clanwilliam region of the Western Cape of South Africa. A total of 207 isolates were collected from diseased seedlings representing five nurseries. The cryptic species status of these isolates was determined with restriction enzyme analysis of the Bc-hch gene with 206 of the isolates identified as B. cinerea and one isolate as B. pseudocinerea. Analysis of the B. cinerea populations using seven microsatellite loci revealed a high total gene diversity (H), with a mean of 0.67. Analysis of molecular variance indicated that 97 % of the total genetic variation is distributed within subpopulations. Genotype flow was evident between nurseries indicated by shared occurrence of clonal lineages, in agreement with the relatively low but significant population differentiation between nurseries (mean F _ST?=?0.030, P?=?0.001). The distribution of the mating type alleles MAT1-1 and MAT1-2 differed significantly from the ratio of 1:1 for the total population and in two of the five nursery subpopulations. Together with significant linkage disequilibrium found, populations appear to mainly reproduce asexually. Fungicide resistance frequency against iprodione for 198 of the genotyped isolates, showed highly varying levels of resistance between the nurseries. The mean incidence of resistance towards iprodione was 44 % in total, ranging from 0 % to 81 % for the five nurseries. This study has shown an adaptive capacity to overcome current chemical means of control in the studied B. cinerea population.