Grey mould, caused by Botrytis cinerea, is a major fungal disease affecting several crops, leading to significant economic losses. Synthetic fungicides, including the phenylpyrrole fludioxonil, remain widely used, yet their precise mode of action and resistance mechanisms in B. cinerea are not fully understood. This study aimed to characterize the transcriptional changes induced by fludioxonil in B. cinerea, identifying differentially expressed genes (DEGs) and metabolic pathways involved in fungicide response and resistance. Two fungal strains, one sensitive and one resistant to fludioxonil, were analysed to elucidate key molecular differences. Illumina sequencing and RNA-Seq were used to assess gene expression changes in B. cinerea strains exposed to fludioxonil at EC50 and EC75. Approximately 91 million short sequence reads were obtained from seven cDNA libraries. DEGs (Fold Change ≥ |6|, RPKM ≥ 5) were identified by comparing treated versus untreated cultures. Functional enrichment analysis was performed to determine the affected biological processes. A total of 930 DEGs were detected in each strain. Redox processes were associated with both up- and down-regulated DEGs. Up-regulated DEGs were linked to biosynthesis of secondary metabolites and modifications of cell wall and surface proteins, while down-regulated DEGs were related to fungal growth, signalling, transmembrane transport, stress responses, and protein metabolism. Membrane-lipid metabolism was up-regulated in the sensitive strain but down-regulated in the resistant one. The mrr1 gene, encoding a transcription factor involved in Multi-Drug Resistance type 1 (MDR1)-related atrB overexpression, was up-regulated in the resistant strain. A single nucleotide polymorphism (SNP) was found in mrr1 in the resistant strain, consistently with other resistant field mutants. Overall, this study provides new insights into B. cinerea responses to fludioxonil, highlighting key resistance mechanisms and contributing to sustainable disease management strategies that minimize environmental impact while preserving fungicide efficacy.
Exploring the effects of phenylpyrrole fungicides in Botrytis cinerea by whole transcriptome analysis
Domenico Di Cosmo
;Rita Milvia De Miccolis Angelini;Caterina Rotolo;Palma Rosa Rotondo;Marco Crudele;Sebastiano Laera;Donato Gerin;Stefania Pollastro;Francesco Faretra
2025-01-01
Abstract
Grey mould, caused by Botrytis cinerea, is a major fungal disease affecting several crops, leading to significant economic losses. Synthetic fungicides, including the phenylpyrrole fludioxonil, remain widely used, yet their precise mode of action and resistance mechanisms in B. cinerea are not fully understood. This study aimed to characterize the transcriptional changes induced by fludioxonil in B. cinerea, identifying differentially expressed genes (DEGs) and metabolic pathways involved in fungicide response and resistance. Two fungal strains, one sensitive and one resistant to fludioxonil, were analysed to elucidate key molecular differences. Illumina sequencing and RNA-Seq were used to assess gene expression changes in B. cinerea strains exposed to fludioxonil at EC50 and EC75. Approximately 91 million short sequence reads were obtained from seven cDNA libraries. DEGs (Fold Change ≥ |6|, RPKM ≥ 5) were identified by comparing treated versus untreated cultures. Functional enrichment analysis was performed to determine the affected biological processes. A total of 930 DEGs were detected in each strain. Redox processes were associated with both up- and down-regulated DEGs. Up-regulated DEGs were linked to biosynthesis of secondary metabolites and modifications of cell wall and surface proteins, while down-regulated DEGs were related to fungal growth, signalling, transmembrane transport, stress responses, and protein metabolism. Membrane-lipid metabolism was up-regulated in the sensitive strain but down-regulated in the resistant one. The mrr1 gene, encoding a transcription factor involved in Multi-Drug Resistance type 1 (MDR1)-related atrB overexpression, was up-regulated in the resistant strain. A single nucleotide polymorphism (SNP) was found in mrr1 in the resistant strain, consistently with other resistant field mutants. Overall, this study provides new insights into B. cinerea responses to fludioxonil, highlighting key resistance mechanisms and contributing to sustainable disease management strategies that minimize environmental impact while preserving fungicide efficacy.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
