Abstract The population structure of crop pathogens such as Puccinia striiformis f. sp. tritici ( Pst ); the cause of wheat stripe rust, is of interest to researchers looking to understand these pathogens on a molecular level, as well as those with an applied focus such as disease epidemiology. Cereal rusts can reproduce sexually or asexually, and the introduction of novel genetic lineages has the potential to cause serious epidemics such as the one caused by ‘Warrior’ lineage in Europe. In a global context, Pst lineages in Canada were not well-characterized and origin of foreign incursions was not known. We used a whole-genome/transcriptome sequencing approach for the Canadian Pst population to identify lineages in a global context, origin, and evidence for foreign incursion. More importantly, for the first time ever, we identified nine alleles of the homeodomain mating-type locus in the worldwide Pst population and show that previously identified lineages generally exhibit a single pair of these alleles. In addition, we find only two pheromone receptor alleles. We show that the recent population shift from the ‘ PstS1’ lineage to the ‘ PstS1-related’ lineage is also associated with the introduction of a novel mating-type allele ( b-3 ) to the Canadian population. We also show evidence for high levels of mating-type diversity in samples associated with the Himalayan center of diversity for Pst , including a single Canadian race previously identified as ‘ PstPr’ (probable recombinant) which we identify as a foreign incursion from China circa. 2010. These data provide comprehensive details on the population biology of Canadian Pst diversity and mating-type alleles in the global Pst population which can be utilized in testing several research questions and hypotheses around sexuality and parasexuality in rust fungi.

Uncovering the history of recombination and population structure in western Canadian stripe rust populations through mating-type alleles