Using Genotyping-By-Sequencing to Study the Population Genomics of the Plant Pathogen Fusarium graminearum

Fusarium graminearum, a haploid filamentous fungus, is the predominant causal agent of Fusarium head blight (FHB) disease on wheat and barley in most of the world. The disease leads to major economic losses due to decreased yield and the contamination of grain with toxic secondary metabolites, such as trichothecenes. Previous population genetic studies of this species have found evidence for frequent outcrossing in this species capable of self-fertilization as well as genetic clustering into populations associated with genotypes at the trichothecene gene cluster. Recently, the sequencing of its genome has revealed how the genome is functionally organized and which regions are most dense with polymorphisms. However, no study has used sequence-based markers on a genome-wide scale to describe patterns of variation along chromosomes and among different geographical regions.

Here, we report our population genomic analyses using genotyping by sequencing. Though our sample is still expanding, we have revisited population structure with nearly 300 isolates and asked how it relates to isolate collection location and trichothecene genotype. Our GBS markers let us investigate how patterns of genetic differentiation between populations vary across the genome, identifying candidates for local adaptation. To determine whether genome-wide association studies are feasible, we have characterized the decay of linkage disequilibrium with distance along chromosomes and how this varies by genome location. Finally, we are scanning the genome to determine whether footprints of selection support the hypothesis that genetic changes at the FHB-related trichothecene loci have spread due to selection acting directly on them.