Our main goal will be to understand the genetic architecture of virulence and fungicide resistance in our "pet fungus" Zymoseptoria tritici (a common pathogen of wheat). We will use genome-wide association studies across populations and in experimental crosses to identify quantitative trait loci contributing to important phenotypic traits of the pathogen. In collaboration with others, we aim to validate our candidates through molecular genetics and transcriptome analyses.
A second goal is to understand the standing genetic variation in pathogen populations by comparing genomes of hundreds of isolates. We are particularly interested in presence-absence polymorphisms of genes and chromosomal regions related to virulence. This may lead us to discover trade-offs between infection strategies maintained through balancing selection.
Populations of plant pathogenic fungi can show extraordinary plasticity in the number and lengths of chromosomes. Z. tritici offers a fantastic insight into the dynamics of ongoing chromosomal rearrangements. We already documented large insertions and rearrangements occurring in a single population (see our PLOS Genetics paper), but we suspect that we are only looking at the tip of the iceberg. We aim to (nearly) fully assemble chromosomes of various isolates to retrace the sequence of events that generated the chromosomal polymorphism in the pathogen.
I will update this with more info in the near future.