Cultivar-specific fungicide resistance emerges during a growing season in field populations of Zymoseptoria tritici

Zymoseptoria tritici causes the most damaging wheat disease in Europe, septoria tritici blotch (STB). In Europe, STB is controlled mainly by fungicides and fungicide resistance is frequently reported. While fungicide resistance is thought to emerge mainly from standing genetic variation within field populations of Z. tritici, few studies have attempted to quantify the degree of fungicide resistance occurring at the field scale and to measure changes in frequencies of resistant strains following fungicide applications during a single growing season. Even fewer studies have considered the effects of different wheat cultivars on the emergence of fungicide resistance. We measured EC50 values for 1005 strains of Z. tritici sampled at two time points from 17 different wheat cultivars growing in a replicated field experiment that was treated with combinations of five different fungicides three times during the growing season. We found that field populations of Z. tritici can maintain a very high diversity in fungicide sensitivity phenotypes despite three fungicide treatments, with as much diversity found within a single field during a single growing season as has been described across all of Europe over several years. Multidrug resistance to two or more fungicides was found in 18.9% of the tested strains. We discovered that wheat cultivars that were more resistant to STB tended to be colonized by Z. tritici strains that exhibited higher fungicide resistance. We also found that specific wheat cultivars selected for resistance to specific active ingredients. Overall, our findings illustrate the many challenges associated with designing fungicide treatment programs that aim to reduce selection for fungicide resistance when confronted with a pathogen like Z. tritici that has a very high evolutionary potential.