Population genetics and evolutionary biology of plant pathogenic fungi

Plant pathogens evolve rapidly to overcome the disease control strategies that are deployed against them. Resistance genes often fail within a few years after deployment and fungicide resistance often emerges within a few years after the first spray. Our research is oriented around understanding the processes that drive pathogen evolution with the aim of developing disease management strategies that will remain effective for a long time. Our research is oriented mainly at the level of populations and often includes the individual organisms, but rarely focuses on cellular or molecular processes.

We use many approaches in our research including: experimental evolution in field, greenhouse, and Petri dish settings; comparative genomics based on next-generation sequencing technologies; QTL mapping to identify genes encoding fungicide resistance and pathogen virulence; coalescent analyses of housekeeping genes to reconstruct evolutionary histories of pathogen clades; sequence analyses of genes encoding effectors and other proteins involved in pathogen-plant interactions to identify important mutations; digital image analysis to quantify important quantitative characters.


Recent Publications

  • Morphological changes in response to environmental stresses in the fungal plant pathogen Zymoseptoria tritici
    Francisco, CS; Ma, X; Zwyssig, MM; McDonald, BA; Palma-Guerrero, J
    SCIENTIFIC REPORTS, 9 10.1038/s41598-019-45994-3 JUL 3 2019
  • Wheat blast: from its origins in South America to its emergence as a global threat
    Ceresini, PC; Castroagudin, VL; Rodrigues, FA; Rios, JA; Aucique-Perez, CE; Moreira, SI; Croll, D; Alves, E; de Carvalho, G; Maciel, JLN; McDonald, BA
    MOLECULAR PLANT PATHOLOGY, 20 (2):155-172; 10.1111/mpp.12747 FEB 2019
  • Resistance to host damage is distinct from resistance to pathogen reproduction in the major wheat pathogen Zymoseptoria tritici
    Karisto, P; Yates, S; McDonald, BA; Mikaberidze, A
    PHYTOPATHOLOGY, 108 (10):25-25; S OCT 2018
  • Pan-Parastagonospora Comparative Genome Analysis-Effector Prediction and Genome Evolution
    Syme, RA; Tan, KC; Rybak, K; Friesen, TL; McDonald, BA; Oliver, RP; Hane, JK
    GENOME BIOLOGY AND EVOLUTION, 10 (9):2443-2457; 10.1093/gbe/evy192 SEP 2018
  • Hyperspectral Canopy Sensing of Wheat Septoria Tritici Blotch Disease
    Yu, K; Anderegg, J; Mikaberidze, A; Karisto, P; Mascher, F; McDonald, BA; Walter, A; Hund, A
    FRONTIERS IN PLANT SCIENCE, 9 10.3389/fpls.2018.01195 AUG 17 2018
  • Genome-Wide Detection of Genes Under Positive Selection in Worldwide Populations of the Barley Scald Pathogen
    Mohd-Assaad, N; McDonald, BA; Croll, D
    GENOME BIOLOGY AND EVOLUTION, 10 (5):1315-1332; 10.1093/gbe/evy087 MAY 2018
  • Meiosis Leads to Pervasive Copy-Number Variation and Distorted Inheritance of Accessory Chromosomes of the Wheat Pathogen Zymoseptoria tritici
    Fouche, S; Plissonneau, C; McDonald, BA; Croll, D
    GENOME BIOLOGY AND EVOLUTION, 10 (6):1416-1429; 10.1093/gbe/evy100 JUN 2018
  • Hyperspectral Canopy Sensing of Wheat Septoria Tritici Blotch Disease
    Yu, K; Anderegg, J; Mikaberidze, A; Karisto, P; Mascher, F; McDonald, BA; Walter, A; Hund, A
    FRONTIERS IN PLANT SCIENCE, 9 10.3389/fpls.2018.01195 AUG 17 2018
  • A fungal avirulence factor encoded in a highly plastic genomic region triggers partial resistance to septoria tritici blotch
    Meile L; Croll D; Brunner PC; Plissonneau C; Hartmann FE; McDonald BA; Sanchez-Vallet A
    NEW PHYTOLOGIST   Volume: 219   Issue: 3 1048-1061 10.1111/nph.15180   AUG 2018
  • Genome-wide evidence for divergent selection between populations of a major agricultural pathogen Molecular Ecology
    Fanny E Hartmann; Bruce A McDonald, Daniel Croll
    MOLECULAR ECOLOGY, 27 (12):2725-2741; 10.1111/mec.14711 JUN 2018
  • Ranking Quantitative Resistance to Septoria tritici Blotch in Elite Wheat Cultivars Using Automated Image Analysis
    Karisto, Petteri; Hund, Andreas; Yu, Kang; Anderegg, Jonas; Walter, Achim; Mascher, Fabio; McDonald, Bruce A.; Mikaberidze, Alexey
    PHYTOPATHOLOGY, 108 (5):568-594; https://doi.org/10.1094/PHYTO-04-17-0163-R MAY 2018
  • Transposable element insertions shape gene regulation and melanin production in a fungal pathogen of wheat
    Krishnan, Parvathy; Meile, Lukas; Plissonneau, Clemence; Ma, Xin; Hartmann, Fanny E; Croll, Daniel; McDonald, Bruce A; Sanchez-Vallet, Andrea
    BMC BIOLOGY   Volume: 16     Article Number: 78  10.1186/s12915-018-0543-2  JUL 16 2018
  • Evidence for local adaptation and pleiotropic effects associated with melanization in a plant pathogenic fungus
    Wen Zhu; Jiasui Zhan; Bruce A. McDonald
    Fungal Genetics and Biology  https://doi.org/10.1016/j.fgb.2018.04.002 JUN 2018
  • Comparative Transcriptomics Reveals How Wheat Responds to Infection by Zymoseptoria tritici
    Ma, Xin; Keller, Beat; McDonald, Bruce A.; Palma-Guerrero, J; Wicker, Thomas
    MOLECULAR PLANT-MICROBE INTERACTIONS  31(4): 420-431 10.1094/MPMI-10-17-0245-R   APR 2018
  • Evolutionary analyses of the avirulence effector AvrStb6 in global populations of Zymoseptoria tritici identify candidate amino acids involved in recognition
    Patrick C. Brunner; Bruce A. McDonald
    Molecular Plant Pathology  https://doi.org/10.1111/mpp.12662 2018-03
  • When resistance gene pyramids are not durable-the role of pathogen diversity 
    Stam, Remco; McDonald, Bruce A. 
    MOLECULAR PLANT PATHOLOGY, 19 (3): 521-524 https://doi.org/10.1111/mpp.12636 MAR 2018
  • Widespread signatures of selection for secreted peptidases in a fungal plant pathogen 
    Krishnan, Parvathy; Ma, Xin; McDonald, Bruce A.; Brunner PC;
    BMC EVOLUTIONARY BIOLOGY, 18:  10.1186/s12862-018-1123-3  JAN 24 2018
  • Quantitative trait locus mapping reveals complex genetic architecture of quantitative virulence in the wheat pathogen Zymoseptoria tritici 
    Stewart, Ethan L.; Croll, Daniel; Lendenmann, Mark H.; et al. 
    MOLECULAR PLANT PATHOLOGY, 19 (1): 201-216 https://doi.org/10.1111/mpp.12515 JAN 2018
McDonald Bruce

Prof. Dr. Bruce McDonald
ETH Zurich
Institute of Integrative Biology
8092 Zurich

Tel: +41 (0)44 632 38 47

Research topics

  • Pathogen origins and pathogen emergence
  • Pathogen evolutionary biology
  • Pathogen population genetics and phylogeography
  • Fungal genomics and effectors
  • Fungicide resistance
  • Deployment of disease resistance genes



  • Sustainable agriculture
  • Plant breeding and crop biotechnology
  • Quantitative genetics
  • World Food System
  • Genetic Diversity Center
  • Comparative genomics