Pathogen Evolutionary Ecology

Plant pathogens are notorious for their propensity to evolve rapidly to overcome control strategies based on major resistance genes and fungicides. Knowledge of pathogen ecology and evolutionary biology can be very useful for designing effective and lasting disease management strategies. We use tools of population genetics, phylogeography and phylogenetics to infer the where, when and how of pathogen emergence and origins with the aim of achieving a better understanding of the ecological and evolutionary factors driving pathogen evolution. Our analyses inform the development of sustainable disease control based on improving the effectiveness of quarantines, resistance breeding, fungicide deployment, biological control agents and crop rotations.

Our past research utilized RFLPs, microsatellites (SSRs), DNA sequences and the genomic toolbox to elucidate the population genetics, phylogeography, global movement and origins of the fungal pathogens Zymoseptoria tritici (formerly Mycosphaerella graminicola, Septoria tritici blotch on wheat), Parastagonospora nodorum (formerly Phaeosphaeria nodorum, leaf and glume blotch on wheat), Pyricularia tritici (wheat blast), Rhynchosporium commune (formerly Rhynchosporium secalis, scald on barley), and Rhizoctonia solani AG1-IA which causes sheath blight on rice. We conducted experimental evolution studies across several spatial and temporal scales, including the laboratory bench (in vitro, 3 months), the greenhouse (in planta controlled environment, 12 months), and the field plot (in planta uncontrolled environment, multiyear) for several of these pathogenic fungi. Current research focuses on understanding the connection between diversity for ecologically relevant quantitative characters and diversity for DNA-based genetic marker systems (QST/FST comparisons), and using QTL mapping and population genomics to identify key genes involved in virulence, fungicide resistance and thermal adaptation. We also seek to better understand and measure the trade-offs and fitness costs associated with evolution of virulence and fungicide resistance.

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