Spontaneous and fungicide-induced genomic variation in Sclerotinia sclerotiorum

Authors: GAMBHIR, NIKITA - University Of Nebraska; KAMVAR, ZHIAN - University Of Nebraska; HIGGINS, REBECCA - University Of Nebraska; AMARADASA, B. SAJEEWA - University Of Nebraska; EVERHART, SYDNEY - University Of Nebraska

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/30/2020
Publication Date: 1/29/2021
Citation: Gambhir, N., Kamvar, Z.N., Higgins, R., Amaradasa, B.S., Everhart, S.E. 2021. Spontaneous and fungicide-induced genomic variation in Sclerotinia sclerotiorum. Phytopathology. 111:160-169. https://doi.org/10.1094/PHYTO-10-20-0471-FI.
DOI: https://doi.org/10.1094/PHYTO-10-20-0471-FI

Interpretive Summary: Fungicides play a central role in crop protection against several fungal pathogens. Unfortunately, fungicide resistance can develop in pathogen populations, as a result of random genetic mutations, especially when sublethal doses of fungicide are applied. To better understand the development of fungicide resistance in the white mold pathogen, Sclerotinia sclerotiorum, we exposed strains of this fungus to sublethal doses of four fungicides and looked for evidence of genetic mutations in the pathogen. We found that insertions or deletions of nucleotides in the genetic sequence were increased in two of the strains, while other types of mutations were found in all the strains studied. Understanding the factors that affect mutations in the white mold pathogen will assist farmers in their disease management strategies. This will help delay the development of fungicide resistance and prolong the life of currently used fungicides.

Technical Abstract: Stress from exposure to sublethal fungicide doses may cause genomic instability in fungal plant pathogens, which may accelerate the emergence of fungicide resistance or other adaptive traits. In a previous study, five strains of Sclerotinia sclerotiorum were exposed to sublethal doses of four fungicides with different modes of action, and genotyping showed that such exposure induced mutations. The goal of the present study was to characterize genome-wide mutations in response to sublethal fungicide stress in S. sclerotiorum and study the effect of genomic background on the mutational repertoire. The objectives were to determine the effect of sublethal dose exposure and genomic background on mutation frequency/type, distribution of mutations, and fitness costs. Fifty-five S. sclerotiorum genomes were sequenced and aligned to the reference genome. Variants were called and quality filtered to obtain high confidence calls for single nucleotide polymorphisms (SNPs), insertions/deletions (INDELs), copy number variants, and transposable element (TE) insertions. Results suggest that sublethal fungicide exposure significantly increased the frequency of INDELs in two strains from one genomic background (P value = 0.05), while TE insertions were generally repressed for all genomic backgrounds and under all fungicide exposures. The frequency and/or distribution of SNPs, INDELs, and TE insertions varied with genomic background. A propensity for large duplications on chromosome 7 and aneuploidy of this chromosome were observed in the S. sclerotiorum genome. Mutation accumulation did not significantly affect the overall in planta strain aggressiveness (P value > 0.05). Understanding factors that affect pathogen mutation rates can inform disease management strategies that delay resistance evolution.