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Genome-Wide Association and Selective Sweep Studies Reveal the Complex Genetic Architecture of DMI Fungicide Resistance in Cercospora beticola

Rebecca Spanner1, Demetris Taliadoros2, Jonathan Richards3, Viviana Rivera-Varas4, Jonathan Neubauer5, Mari Natwick5, Olivia Hamilton4, Niloofar Vaghefi6, Sarah Pethybridge7, Gary A Secor4, Timothy L Friesen5, Eva H Stukenbrock8, Melvin D Bolton4,5

1Northern Crop Science Laboratory, United States Department of Agriculture, Fargo, North Dakota, USA Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, USA.  Present addresses: Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile; ANID—Millennium Science Initiative—Millennium Institute for Integrative Biology (iBIO), Santiago, Chil. 2Environmental Genomics Group, Max Planck Institute for Evolutionary Biology, Plön, Germany Christian-Albrechts University of Kiel, Germany. 3Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA.  4Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, USA. 5Northern Crop Science Laboratory, United States Department of Agriculture, Fargo, North Dakota, USA. 6Centre for Crop Health, University of Southern Queensland, Toowoomba, Queensland, Australia. 7School of Integrative Plant Science, Cornell University, Geneva, New York, USA. 8Botanical Institute, Christian-Albrechts University of Kiel, Kiel, Germany Max Planck Institute for Evolutionary Biology, Plön, Germany.

Corresponding Author(s): Melvin D. Bolton ([email protected])


The rapid and widespread evolution of fungicide resistance remains a challenge for crop disease management. The demethylation inhibitor (DMI) class of fungicides is a widely used chemistry for managing disease, but there has been a gradual decline in efficacy in many crop pathosystems. Reliance on DMI fungicides has increased resistance in populations of the plant pathogenic fungus Cercospora beticola worldwide. To better understand the genetic and evolutionary basis for DMI resistance in C. beticola, a genome-wide association study (GWAS) and selective sweep analysis were conducted for the first time in this species. We performed whole-genome resequencing of 190 C. beticola isolates infecting sugar beet (Beta vulgaris ssp. vulgaris). All isolates were phenotyped for sensitivity to the DMI tetraconazole. Intragenic markers on chromosomes 1, 4, and 9 were significantly associated with DMI fungicide resistance, including a polyketide synthase gene and the gene encoding the DMI target CbCYP51. Haplotype analysis of CbCYP51 identified a synonymous mutation (E170) and nonsynonymous mutations (L144F, I387M, and Y464S) associated with DMI resistance. Genome-wide scans of selection showed that several of the GWAS mutations for fungicide resistance resided in regions that have recently undergone a selective sweep. Using radial plate growth on selected media as a fitness proxy, we did not find a trade-off associated with DMI fungicide resistance. Taken together, we show that population genomic data from a crop pathogen can allow the identification of mutations conferring fungicide resistance and inform about their origins in the pathogen population.

This work is written by (a) US Government employee(s) and is in the public domain in the US.
Author: Spanner et al.
Publication: Genome Biology and Evolution
Publisher: Oxford University Press
Date: 2021-09-09

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