Most plants face attacks by fungal pathogens. In agriculture, outbreaks of diseases are frequent and pose a significant threat to sustainable food production. What enables pathogens to overcome host defenses and cause damage is poorly understood. A key evolutionary step for pathogens is to evolve effectors that specifically target and disable the plant immune system.

Our group uses experimental and population genomics tools to analyze the rapid emergence of pathogens. A major focus is to use genome-wide association studies (GWAS) to directly identify the genes in pathogen genomes linked to the breakdown of host resistance. We also assemble complete genomes to analyze mechanisms that generate high degrees of sequence polymorphism. We are particularly interested in the action of transposable elements (selfish elements in the genome) and the evolution of gene regulation. Our group also conducts population genomic studies to analyze the process of adaptive evolution in natural field populations.

• Wheat Blast: Past, Present, and Future
  Ceresini, PC; Castroagudin, VL; Rodrigues, FA; Rios, JA; Aucique-Perez, CE; Moreira, SI; Alves, E; Croll, D; Maciel, JLN
  Edited by: Leach JE; Lindow SE
  ANNUAL REVIEW OF PHYTOPATHOLOGY, VOL 56, 56 427-456; 10.1146/annurev-phyto-080417-050036 2018
• The Genome Biology of Effector Gene Evolution in Filamentous Plant Pathogens
  Sanchez-Vallet, A; Fouche, S; Fudal, I; Hartmann, FE; Soyer, JL; Tellier, A; Croll, D Edited by: Leach JE; Lindow SE
  ANNUAL REVIEW OF PHYTOPATHOLOGY, VOL 56, 56 21-40; 10.1146/annurev-phyto-080516-035303 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
• 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
• 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
• 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
• A monothiol glutaredoxin is required for iron homeostasis and virulence in the AIDS-associated pathogen Cryptococcus neoformans
  Hu, GG; Attarian, R; Do, E; Croll, D; Caza, M; Bach, H; Missall, TA; Lodge, J; Jung, WH; Kronstad, JW
  MEDICAL MYCOLOGY, 56 S124-S124; 2 JUN 2018
• Comparative Genomics of Smut Pathogens: Insights From Orphans and Positively Selected Genes Into Host Specialization
  Benevenuto, J; Teixeira-Silva, NS; Kuramae, EE; Croll, D; Monteiro-Vitorello, CB
  FRONTIERS IN MICROBIOLOGY, 9 https://doi.org/10.3389/fmicb.2018.00660 APR 6 2018
• Population genomics analyses of European ibex species show lower diversity and higher inbreeding in reintroduced populations 
  Grossen, Christine; Biebach, Iris; Angelone-Alasaad, Samer; et al. 
  EVOLUTIONARY APPLICATIONS, 11 (2): 123-139  https://doi.org/10.1111/eva.12490   FEB 2018 
• Acetate provokes mitochondrial stress and cell death in Ustilago maydis 
  Kretschmer, Matthias; Lambie, Scott; Croll, Daniel; et al. 
  MOLECULAR MICROBIOLOGY, 107 (4): 488-507 https://doi.org/10.1111/mmi.13894 FEB 2018
• Pangenome analyses of the wheat pathogen Zymoseptoria tritici reveal the structural basis of a highly plastic eukaryotic genome 
  Plissonneau, Clemence; Hartmann, Fanny E.; Croll, Daniel 
  BMC BIOLOGY, 16: https://doi.org/10.1186/s12915-017-0457-4 JAN 11 2018
• Nature's genetic screens: using genome-wide association studies for effector discovery 
  Sanchez-Vallet, Andrea; Hartmann, Fanny E.; Marcel, Thierry C.; et al. 
  MOLECULAR PLANT PATHOLOGY, 19 (1): 3-6 https://doi.org/10.1111/mpp.12592 JAN 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

• Genetic basis of pathogen virulence
• Ecological genomics and local adaptation of pathogens
• Population genomics of pathogen outbreaks
• Structure and evolution of pathogen genomes
• Transposable elements and the evolution of gene regulation

• Crop resistance breeding
• Bioinformatics and genome assembly
• Molecular plant pathology
• Fungal community analyses
• Genome-wide association mapping (GWAS)