Fungicide Resistance: Surveillance, Risk Assessment and Evolution in Two Soil-Borne Pathogens

Authors

Nikita Gambhir, University of Nebraska-LincolnFollow

First Advisor

Sydney E. Everhart

Date of this Version

Fall 12-2020

Document Type

Dissertation

Citation

Gambhir, N. 2020. Fungicide Resistance: Surveillance, Risk Assessment and Evolution in Two Soil-Borne Pathogens. Doctoral Dissertation. University of Nebraska, Lincoln.

Comments

A DISSERTATION Presented to the Faculty of The Graduate College at the University of Nebraska In Partial Fulfillment of Requirements For the Degree of Doctor of Philosophy, Major: Agronomy and Horticulture (Plant Pathology), Under the Supervision of Professor Sydney E. Everhart. Lincoln, Nebraska: December, 2020

Copyright © 2020 Nikita Gambhir

Abstract

Fungicide-resistant pathogens are an increasing threat to fungicide efficacy and plant health. The goal of this dissertation was to advance the foundational knowledge required to prevent and detect fungicide resistance development in the seedling disease pathogen, Rhizoctonia zeae and the white-mold pathogen, Sclerotinia sclerotiorum. Corn and soybean fields in 12 states (IA, IL, IN, KS, KY, MI, MN, MO, ND, NE, SD, and WI) were surveyed for R. zeae. In vitro fungicide sensitivity was determined for 91 isolates to fludioxonil, sedaxane, and/or prothioconazole. Rhizoctonia zeae was sensitive to all fungicides (EC₅₀ < 3 µg/ml) except azoxystrobin (EC₅₀ > 100 µg/ml). In planta application of azoxystrobin did not significantly change the disease severity or total dry weight of soybean plants (P > 0.05), suggesting ineffective control. To understand the intrinsic risk of resistance development in R. zeae, the genetic structure of R. zeae populations was characterized. Six microsatellite markers were designed for genotyping 200 R. zeae isolates. Results showed that the population has a mixed mode of reproduction and is genetically differentiated according to geographic region and year, suggesting limited dispersal and an intermediate risk of resistance development. To prevent fungicide resistance, it is also important to understand the fungicide-risk factors to develop resistance. Sublethal fungicide stress may cause genomic instability in fungal plant pathogens, which may accelerate the emergence of resistance. Genome-wide mutations were characterized in 55 S. sclerotiorum genomes after sublethal fungicide exposure. Results showed that sublethal fungicide exposure increased the frequency of insertions/deletions in one genomic background of S. sclerotiorum. The frequency and distribution of mutations varied with genomic background. Understanding factors that increase pathogen mutation rates can inform disease management strategies that delay resistance evolution. On examining the evolutionary role of hypermutators in fungal pathogen populations, the literature reviewed suggested that hypermutators may be a new factor to consider in fungicide resistance development. Overall, this dissertation will advance the knowledge on fungicide- and pathogen-risk factors to develop resistance, which can inform fungicide resistance management.

Advisor: Sydney E. Everhart