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: 11/13/2020
Publication Date: 12/15/2020
Citation: Gambhir, N., Kamvar, Z.N., Higgins, R., Amaradasa, B., Everhart, S.E. 2020. 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: Fungal pathogens that cause disease in crop plants can usually be controlled by appropriate fungicides administered at a proper dose. However, when fungicide applications are below recommended rates, the fungus is not killed, and it has the possibility to adapt to the fungicide through induced genetic modifications. This can result in new fungal strains that are resistant to the fungicide. In this study, sublethal doses of fungicide were applied to different strains of the white mold pathogen, Sclerotinia sclerotiorum, to monitor changes in its genetic structure. Sublethal fungicide exposure increased the frequency of insertions or deletions of DNA segments in the genome of the fungus in two strains. Other genetic changes, including single DNA base changes, were seen in all the strains tested. Understanding the factors that affect pathogen mutation rates can inform disease management strategies that could delay fungicide resistance.

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.