Symptoms of Botrytis blight, a disease caused by the ubiquitous fungal plant pathogen Botrytis cinerea, include leaf spots, rot, damping off, and blight of petioles, flowers, leaves, and stems of ornamental crops. B. cinerea is regarded as the second most important fungal plant pathogen in the world partly due to its ability to cause extensive pre- and post- harvest losses in hundreds of economically valuable fruit, vegetable, and ornamental crops. Fungicides are important for Botrytis blight control and represent 10% of the global fungicide market. B. cinerea isolates (386) obtained from herbaceous ornamentals growing in Michigan greenhouses exhibited widespread multifungicide resistance; 63.5% were resistant to four or more site-specific fungicide classes and only 2.3% were sensitive to all fungicides. Resistance profiles of individual isolates were diverse (48 phenotypes). The most common profile (8.7%) demonstrated resistance to all site-specific fungicide classes including thiophanate-methyl (FRAC 1), fenhexamid (FRAC 17), iprodione (FRAC 2), fludioxonil (FRAC 12), boscalid/fluopyram (FRAC 7), cyprodinil (FRAC 9), and pyraclostrobin (FRAC 11). Resistance frequencies and profiles were not associated with location, year, or host. Whole-genome sequencing was performed on 276 single-spored B. cinerea isolates from petunia, geranium, or poinsettia in 11 greenhouses during two growing cycles. De novo assembly and functional annotation were performed with isolates resistant (5) or sensitive (2) to all fungicides. Publicly available assemblies and corresponding annotation data are a resource for research on fungicide resistance, genetic relatedness among global crops and regions, and other Botrytis genomics-related studies. Reference-guided assembly of 276 isolate genomes enabled analyses of i) population structure stratified by multifungicide resistance, ii) novel genomic regions associated with multifungicide resistance, iii) mating type characterization, and iv) other measurements of genetic differentiation based on fungicide resistance, crop, location, and other factors. Isolates with resistance to multiple fungicides (0-7) impacted population structure and were genetically differentiated as indicated by discriminant analyses of principal components, fixation index values, and analyses of molecular variance. A quantitative trait genome-wide association study identified genomic regions significantly associated with multifungicide resistance, including putative efflux pump genes. To date, this is the largest study of B. cinerea population genomics, prompting new questions and highlighting the need for novel management tools due to widespread fungicide resistance.
Read
