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Sclerotinia trifoliorum Erikks is an ascomycete fungus that causes rot in red clover crops, a disease difficult to control as no completely resistant red clover varieties
are available. Breeding programs aimed at improving the resistance of red clover varieties are hindered by insufficient knowledge about the genetic diversity of S. trifoliorum in Europe. Therefore, the genetic diversity among 192 Sclerotinia isolates from red clover crops from 12 European countries was investigated using
mycelial compatibility grouping and AFLP analysis. Phylogenetic analysis revealed that two Sclerotinia species are present on red clover: S. trifoliorum in most locations and S. sclerotiorum in 2 out of 25 locations. Species identification was confirmed using a test based on the ß-tubulin gene we constructed. No subpopulations within the S. trifoliorum species were found, nor correlation between genetic and geographical distance. Most of the total variation (79.2%) was detected within S. trifoliorum populations, whereas a lower variation (20.8%) occurred among populations. The average FST value was 0.208, indicating that S. trifoliorum isolates from red clover should be regarded as one population close to panmixis with a very low degree of population differentiation. Future research would be useful to compare the aggressiveness of S. trifoliorum and S. sclerotiorum on red clover plants and to determine the correlation between the isolates’ aggressiveness and their genetic diversity.