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.

• A population-level invasion by transposable elements triggers genome expansion in a fungal pathogen
  Oggenfuss, Ursula; Badet, Thomas; Wicker, Thomas; Hartmann, Fanny E.; Singh, Nikhil Kumar; Abraham, Leen; Karisto, Petteri; Vonlanthen, Tiziana; Mundt, Christopher; McDonald, Bruce A.; Croll, Daniel
  Elife 10.7554/eLife.69249 SEP 16 2021
• Population genomics of transposable element activation in the highly repressive genome of an agricultural pathogen
  Pereira, Danilo; Oggenfuss, Ursula; McDonald, Bruce A.; Croll, Daniel
  Microbial Genomics 10.1099/mgen.0.000540  AUG 2021
• Monitoring of Brazilian wheat blast field populations reveals resistance to QoI, DMI, and SDHI fungicides
  Vicentini, Samara N. C.; Casado, Priscila S.; de Carvalho, Giselle; Moreira, Silvino, I; Dorigan, Adriano F.; et al.
  Plant Pathology 10.1111/ppa.13470 SEP 2021
• Genome-wide association study for septoria tritici blotch resistance reveals the occurrence and distribution of Stb6 in a historic Swiss landrace collection (vol 217, 108, 2021)
  Dutta, Anik; Croll, Daniel; McDonald, Bruce A.; Krattinger, Simon G.
  Euphytica 10.1007/s10681-021-02906-9 SEP 2021
• Genome-scale phylogenies reveal relationships among Parastagonospora species infecting domesticated and wild grasses
  Croll, D.; Crous, P. W.; Pereira, D.; Mordecai, E. A.; McDonald, B. A.; Brunner, P. C.
  Persoonia 10.3767/persoonia.2021.46.04 JUN 2021
• Tolerance to oxidative stress is associated with both oxidative stress response and inherent growth in a fungal wheat pathogen
  Zhong, Ziming; McDonald, Bruce A.; Palma-Guerrero, Javier
  Genetics 10.1093/genetics/iyaa022 Published: FEB 2021
• Mapping the adaptive landscape of a major agricultural pathogen reveals evolutionary constraints across heterogeneous environments
  Dutta, Anik; Hartmann, Fanny E.; Francisco, Carolina Sardinha; McDonald, Bruce A.; Croll, Daniel
  Isme Journal, 10.1038/s41396-020-00859-w  MAY 2021
• Mixed infections alter transmission potential in a fungal plant pathogen
  Barrett, Luke G.; Zala, Marcello; Mikaberidze, Alexey; Alassimone, Julien; Ahmad, Muhammad; et al.
  Environmental Microbiology, 10.1111/1462-2920.15417  FEB 2021
• The Genetic Architecture of Emerging Fungicide Resistance in Populations of a Global Wheat Pathogen
  Pereira, Danilo; McDonald, Bruce A.; Croll, Daniel
  Genome Biology And Evolution,  10.1093/gbe/evaa203   DEC 2020
• Widespread distribution of resistance to triazole fungicides in Brazilian populations of the wheat blast pathogen
  Poloni, Nadia Maria; Carvalho, Giselle; Nunes Campos Vicentini, Samara; Francis Dorigan, Adriano; Nunes Maciel, Joao Leodato; et al.
  Plant Pathology  DOI: 10.1111/ppa.13288 OCT 2020
• Maintenance of variation in virulence and reproduction in populations of an agricultural plant pathogen
  Dutta, Anik; Croll, Daniel; McDonald, Bruce A.; Barrett, Luke G.
  Evolutionary Applications  DOI: 10.1111/eva.13117 SEP 2020
• A polyetic modelling framework for plant disease emergence
  Willocquet, Laetitia; Savary, Serge; McDonald, Bruce A.; Mikaberidze, Alexey
  Plant Pathology  DOI: 10.1111/ppa.13249 DEC 2020
• SnToxA,SnTox1, and SnTox3 originated in Parastagonospora nodorum in the Fertile Crescent
  Ghaderi, Fariba; Sharifnabi, Bahram; Javan-Nikkhah, Mohammad; Brunner, Patrick C.; McDonald, Bruce A.
  Plant Pathology  DOI: 10.1111/ppa.13233 OCT 2020
• Natural selection drives population divergence for local adaptation in a wheat pathogen
  Pereira, Danilo; Croll, Daniel; Brunner, Patrick C.; McDonald, Bruce A.
  Fungal Genetics And Biology  DOI: 10.1016/j.fgb.2020.103398  AUG 2020
• A tradeoff between tolerance and resistance to a major fungal pathogen in elite wheat cultivars
  Mikaberidze, Alexey; McDonald, Bruce A.
  New Phytologist  10.1111/nph.16418  MAY 2020
• A 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici
  Badet, Thomas; Oggenfuss, Ursula; Abraham, Leen; McDonald, Bruce A.; Croll, Daniel
  Bmc Biology 18(1) Article Number: 12 DOI: 10.1186/s12915-020-0744-3  FEB 11 2020
• The emergence of the multi-species NIP1 effector in Rhynchosporium was accompanied by high rates of gene duplications and losses
  Mohd-Assaad, N; McDonald, BA; Croll, D
  ENVIRONMENTAL MICROBIOLOGY, 21 (8):2677-2695; 10.1111/1462-2920.14583 AUG 2019
• …

• 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