Methods for studying population structure, including sensitivity to the fungicide silthiofam, of the cereal take-all fungus, Gaeumannomyces graminis var. tritici

Field isolates (n = 144) of the wheat take-all fungus Gaeumannomyces graminis var. tritici (Ggt) were tested for sensitivity to silthiofam, a take-all-specific fungicide used as a seed treatment, and identified as A- or B-type by PCR-RFLP analysis of nuclear rDNA. A possible association was identified between polymorphisms in ITS2 of the nuclear rDNA and sensitivity to silthiofam. A Ggt-specific PCR assay was developed which simultaneously identified isolates of Ggt as A- or B-type, based on the polymorphisms in the nuclear rDNA. A highly significant correlation between Ggt type using the PCR assay and sensitivity to silthiofam was demonstrated in a collection of 358 isolates from three field experiments designed to test the effects of seed-treatment fungicides on take-all and Ggt populations in winter wheat. In one experiment the percentages of silthiofam-sensitive and B-type isolates were significantly less in populations from plots sown with silthiofam-treated seed in two consecutive years than in populations from plots sown with nontreated seed. However, silthiofam still provided a significant amount of control of take-all. The natural occurrence of fungicide-insensitive isolates, up to about 30% in soils in which the fungicide had never been used, is unusual. The new PCR assay provides a useful tool for studying the population structure of Ggt, and may provide a novel method for assessing the incidence of insensitivity to silthiofam (the target site for which has not yet been identified) in field populations of Ggt.