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

Spanner, Rebecca and Taliadoros, Demetris and Richards, Jonathan and Rivera-Varas, Viviana and Neubauer, Jonathan and Natwick, Mari and Hamilton, Olivia and Vaghefi, Niloofar ORCID: https://orcid.org/0000-0003-0430-4856 and Pethybridge, Sarah and Secor, Gary A. and Friesen, Timothy L. and Stukenbrock, Eva H. and Bolton, Melvin D. (2021) Genome-Wide Association and Selective Sweep Studies Reveal the Complex Genetic Architecture of DMI Fungicide Resistance in Cercospora beticola. Genome Biology and Evolution, 13 (9):evab209. pp. 1-17. ISSN 1759-6653


Abstract

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.


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Item Type: Article (Commonwealth Reporting Category C)
Refereed: Yes
Item Status: Live Archive
Faculty/School / Institute/Centre: Current - Institute for Life Sciences and the Environment - Centre for Crop Health (24 Mar 2014 -)
Faculty/School / Institute/Centre: Current - Institute for Life Sciences and the Environment - Centre for Crop Health (24 Mar 2014 -)
Date Deposited: 02 Nov 2021 04:02
Last Modified: 09 Nov 2021 00:35
Uncontrolled Keywords: GWAS, CYP51, azole, synonymous mutation, antifungal, selection
Fields of Research (2008): 06 Biological Sciences > 0607 Plant Biology > 060705 Plant Physiology
06 Biological Sciences > 0604 Genetics > 060408 Genomics
Fields of Research (2020): 31 BIOLOGICAL SCIENCES > 3108 Plant biology > 310805 Plant pathology
31 BIOLOGICAL SCIENCES > 3105 Genetics > 310509 Genomics
30 AGRICULTURAL, VETERINARY AND FOOD SCIENCES > 3004 Crop and pasture production > 300409 Crop and pasture protection (incl. pests, diseases and weeds)
Socio-Economic Objectives (2008): D Environment > 96 Environment > 9604 Control of Pests, Diseases and Exotic Species > 960413 Control of Plant Pests, Diseases and Exotic Species in Farmland, Arable Cropland and Permanent Cropland Environments
E Expanding Knowledge > 97 Expanding Knowledge > 970106 Expanding Knowledge in the Biological Sciences
Identification Number or DOI: https://doi.org/10.1093/gbe/evab209
URI: http://eprints.usq.edu.au/id/eprint/43877

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