Novel genomic regions associated with multifungicide resistance in <i>Botrytis cinerea</i> and factors impacting greenhouse population structure

The fungal plant pathogen <i>Botrytis cinerea</i> affects hundreds of valuable crops including fruits, vegetables, and ornamental plants. In greenhouse production systems, <i>B. cinerea</i> disease management largely depends on the use of fungicides; however, the emergence of resistance to multiple fungicide classes has become a major challenge. An improved understanding of <i>B. cinerea</i> populations can contribute to the development of resistance management strategies. In this study, isolates (n=276) of <i>B. cinerea</i> were collected from ornamental production greenhouses in Michigan and whole-genome resequencing was performed to evaluate genetic differentiation among hosts, locations, growing cycles, and fungicide resistance. Discriminant analyses of principal components and analyses of molecular variance revealed limited genetic differentiation among isolates from different hosts, greenhouses, and year of isolate collection. In contrast, the same analyses alongside pairwise fixation indexes and an evaluation of population structure indicated significant genetic differentiation among isolates based on the number of fungicides to which they are resistant. There are two described mechanisms that confer resistance to multiple fungicides at the same time, both of which are mediated by efflux pumps. Results from a quantitative trait genome-wide association study revealed novel genomic regions associated with multifungicide resistance, including two genes that encode putative efflux pumps. An understanding of fungicide resistance patterns is essential for developing durable disease control measures. Our results highlight the importance of continued monitoring of <i>B. cinerea</i> populations, as the observed genetic differentiation linked to fungicide resistance emphasizes their ability to adapt to selection pressure.