Strategy Sets the Scene: Genetic architecture of linalool resistance in Botrytis cinerea

Abstract Botrytis cinerea is a necrotrophic fungal pathogen that infects thousands of plant species. During infection, these diverse plant hosts produce different specialized metabolites that can inhibit pathogen growth and shape pathogen fitness. However, the genetic architecture of pathogen resistance toward individual host defense metabolites remains poorly understood. To address this question, we exposed 83 B. cinerea isolates to the metabolite linalool and quantified physiological and structural responses. Exposure revealed extensive phenotypic diversity across isolates. Population structure analysis using genome-wide SNP data showed little genetic subdivision despite diverse hosts and geographic location. Genome-wide association identified 98 genes of interest associated with membrane transport and stress response regulation. Genetic associations were stronger for morphological traits than for physiological traits, suggesting that hyphal architecture may have a complex genetic architecture contributing to linalool resistance. Together, these results establish natural variation in linalool response and provide candidate loci for understanding how generalist pathogens respond to host-derived chemical defenses.