Population structure and fungicide resistance in Botrytis fragariae from strawberry fields in the Eastern U.S.
- 1Department of Plant Science and Landscape Architecture, University of Maryland
Abstract
Introduction: Botrytis fragariae has been frequently recovered from strawberry fields in the eastern United States and differs from B. cinerea in fungicide sensitivity, yet its population structure and genomic variation associated with resistance remain poorly understood.
Methods: We analyzed 105 B. fragariae isolates from nine eastern U.S. states collected across seven sampling years to characterize population structure, fungicide-resistance profiles, and candidate genomic regions associated with fludioxonil resistance. Resistance to 10 fungicides representing seven chemical classes was evaluated, and whole-genome sequencing data were used for phylogenetic, principal component, admixture, and genome-wide differentiation analyses.
Results: Phylogenetic analysis identified five clades, broadly supported by principal component analysis, while admixture analysis showed greater mixed ancestry in the two major clades than in the three smaller clades. Geographic origin and collection year did not strictly explain clade membership, with closely related isolates found across states and years, indicating broad distribution and persistence of multiple genetic backgrounds. Resistance to multiple chemical classes of fungicides, including fludioxonil, occurred more frequently in recent collections of isolates in different clades, indicating that resistance may have evolved independently. Furthermore, genome-wide weighted F ST and nucleotide-diversity scans comparing 65 fludioxonil-resistant and 40 sensitive isolates identified 15 outlier windows that merged into eight candidate genomic regions relating to the resistance. Seven of these regions contained 39 predicted genes, including genes encoding MFS/MDR transporters, cytochrome P450 proteins, transcription factors, an iron transporter, and proteins involved in membrane and redox-related processes.
Discussion: Together, these findings provided a comprehensive population-genomic characterization of B. fragariae in Eastern U.S. strawberry fields and identified candidate genomic regions for subsequent functional investigation of fludioxonil resistance.
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BibTeX
@article{lu2026population,
title = {{Population structure and fungicide resistance in Botrytis fragariae from strawberry fields in the Eastern U.S.}},
author = {Hongjin Lu and Mengjun Hu},
journal = {Frontiers in Plant Science},
year = {2026},
month = oct,
doi = {10.3389/fpls.2026.1983036},
url = {https://www.frontiersin.org/articles/10.3389/fpls.2026.1983036/full},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Population structure and fungicide resistance in Botrytis fragariae from strawberry fields in the Eastern U.S.
AU - Hongjin Lu
AU - Mengjun Hu
PY - 2026
DA - 2026/10/19
JO - Frontiers in Plant Science
DO - 10.3389/fpls.2026.1983036
UR - https://www.frontiersin.org/articles/10.3389/fpls.2026.1983036/full
AB - Introduction: Botrytis fragariae has been frequently recovered from strawberry fields in the eastern United States and differs from B. cinerea in fungicide sensitivity, yet its population structure and genomic variation associated with resistance remain poorly understood. Methods: We analyzed 105 B. fragariae isolates from nine eastern U.S. states collected across seven sampling years to characterize population structure, fungicide-resistance profiles, and candidate genomic regions associated with fludioxonil resistance. Resistance to 10 fungicides representing seven chemical classes was evaluated, and whole-genome sequencing data were used for phylogenetic, principal component, admixture, and genome-wide differentiation analyses. Results: Phylogenetic analysis identified five clades, broadly supported by principal component analysis, while admixture analysis showed greater mixed ancestry in the two major clades than in the three smaller clades. Geographic origin and collection year did not strictly explain clade membership, with closely related isolates found across states and years, indicating broad distribution and persistence of multiple genetic backgrounds. Resistance to multiple chemical classes of fungicides, including fludioxonil, occurred more frequently in recent collections of isolates in different clades, indicating that resistance may have evolved independently. Furthermore, genome-wide weighted F ST and nucleotide-diversity scans comparing 65 fludioxonil-resistant and 40 sensitive isolates identified 15 outlier windows that merged into eight candidate genomic regions relating to the resistance. Seven of these regions contained 39 predicted genes, including genes encoding MFS/MDR transporters, cytochrome P450 proteins, transcription factors, an iron transporter, and proteins involved in membrane and redox-related processes. Discussion: Together, these findings provided a comprehensive population-genomic characterization of B. fragariae in Eastern U.S. strawberry fields and identified candidate genomic regions for subsequent functional investigation of fludioxonil resistance.
SN - 1664-462X
ER -