Performance Story: A pilot project to study pathogen diversity directly from field samples and determine their adaptation to host varieties
Dr. Randy Kutcher, University of Saskatchewan
The project addressed the challenge in rapid characterization of wheat rust pathogen populations by utilizing a DNA sequencing approach called ‘field pathogenomics’, an approach previously employed in Europe to characterize wheat stripe rust populations from commercial crops.
The purpose of the project was to collect rust infected leaves from field plots and perform sequencing directly from the samples and identify genetic groups (termed as lineages) the samples belong to. The method is quick as compared to classical methods (such as race characterization or genotyping with molecular markers) for pathogen population characterization. We collected 85 samples of stripe rust, leaf rust, stem rust, and leaf spotting pathogens from western Canada (mainly Alberta and Saskatchewan) which were subjected to ‘field pathogenomic’ analyses. ‘Field pathogenomics’ is a quick method of generating genetic information on rust pathogen populations, i.e., this pilot project studying the feasibility was very successful.
Stripe rust and leaf rust pathogen populations in Western Canada have very low genetic diversity i.e. only a few genetic lineages are prevalent in western Canada. However, this low genetic diversity does not mean low virulence diversity i.e. multiple pathogen races can belong to the same genetic lineage but may not be virulent on the same set of varieties. There is a need for establishing a better base knowledge of the existing genetic lineages of these pathogens and it is important to keep tracking the populations of pathogens to trace origin and evolution, possibly new introductions of pathogens, which will help researchers direct their efforts on disease management.
These results are important for wheat breeders as they can keep in mind the existing pathogen populations while breeding for resistance. With classical methods, it is hard to determine the prevalent lineages or diversity in pathogen population within a year of sample collection; however, with ‘field pathogenomics’, we can overcome that limitation. This approach will likely be adopted by other research groups for pathogen characterization on regular basis.
We are now improving the method to cut-short time from one year to even further by using ultra-modern portable genome sequencers. In an effort to do so, we have submitted a follow-up research project for funding in 2020 to Agriculture Development Fund as well as other funders on the prairies. In addition, from existing 2019 data, we are trying to improve the method so as to characterize pathogens other than rusts.