Genetic Diversity and Evolution of Puccinia striiformis in Canada
Bibliographic record
Abstract
Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), poses a significant threat to global wheat production. Additional forms of this pathogen affect barley and other grasses, complicating management efforts. This thesis presents a comprehensive analysis of the Canadian Pst population by integrating field surveys, virulence characterization, and genomic studies to understand both temporal evolution and host-associated variation. Disease surveys conducted in southern Alberta from 2020 to 2023, together with samples from eastern Canada, indicated that climatic conditions significantly influence the prevalence of Pst. Cool and humid years promote disease development, whereas extreme heat and dryness suppress outbreaks. Predominant North American races (C-41 and C-17) remain widespread, yet isolates from Quebec display greater race diversity, indicating ongoing adaptation. The breakdown of key resistance genes, such as Yr6, Yr7, Yr10, Yr17, Yr18, and Yr27, alongside the continued effectiveness of Yr1-highlights regional differences in virulence dynamics. Virulence patterns were influenced by regional variation in wheat differential sets, underscoring the need for expanded resistance screening. In addition, barley stripe rust isolates exhibit virulence on several Yr genes in the wheat host, raising concerns about the emergence of novel pathotypes. For the first time, a mutation in the CYP51 gene (Y135F) was identified in Canadian P. striiformis isolates collected from barley and foxtail barley. This mutation, previously reported in Chinese and New Zealand Pst isolates, had not been previously documented in North America. Its occurrence in Canada suggests selection pressure from repeated fungicide applications, necessitating further investigation into fungicide tolerance in stripe rust populations. Comprehensive genomic analyses of P. striiformis isolates collected from 1984 to 2023 provided insights into the evolutionary history of the pathogen lineages in Canada. We conducted Simple-sequence repeat (SSR) genotyping and mating-type allele analyses for this population to trace changes in the lineages over time and region. We found a transition from the old lineage PstS0, which was predominant in Canada and the USA pre-2000, to PstS1-related lineages post-2010. Lineage analysis of four isolates collected between 2000 and 2010 identified two isolates as belonging to the South African lineage and two as PstPr (a probable recombinant). The South African lineage, distinguished by its unique Pst_b1*-HD, Pst_b1-HD, and Pst_b2-HD alleles, likely contributed to the incursion of heat tolerant virulent races in the early 2000s. In contrast, PstPr was previously suggested to be a new recombinant lineage in Canada derived from a hybrid between the pre-existing PstS0 lineage and an European lineage. However, based on the MAT alleles carried by the pathogen population in this study, we demonstrated that this lineage is indeed a hybrid, but likely between PstS0 and a South African lineage. We also suggest that PstS1-related lineages likely result from a recombination between PstS1 and other lineages, probably PstPr. In addition, isolates collected in 2022 and 2023 from eastern Canada appear to belong to a novel lineage, designated here as PstC2022, with the presence of Pst_b8-HD. This is likely a recombinant lineage between PstS1 and a foreign lineage, possibly from East Africa, Europe, China or Pakistan. The PstC2022 lineage was also confirmed with the variants callings, which revealed distinct genetic clusters corresponding to collection periods and lineage classifications rather than geographic origin, highlighting the pathogen’s capacity for long-distance dispersal. Genome analysis confirmed that Pst has an open pangenome structure, characterized by a small core gene set and a large number of accessory genes. This genome structure suggests gene flow and adaptive potential. A high percentage of transposable elements, particularly Copia, Gypsy, and Helitrons, may play a crucial role in driving genome variation. Collectively, our findings provide a comprehensive overview of the dynamic nature of P. striiformis populations in Canada over the past 40 years, highlighting significant changes in stripe rust virulence and lineage evolution. By generating extensive genomic data for pathogen collections made over four decades, we offer a valuable resource for the research community to investigate pathogen evolution, including shifts in virulence and adaptation. These results of this study underscore the importance of continued pathogen surveillance, particularly on non-wheat hosts, alongside studies evaluating fungicide tolerance and genetic variation to trace pathogen incursions and local adaptation. Such efforts are crucial for guiding resistance breeding strategies and mitigating the ongoing threat of stripe rust in wheat and barley production.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.002 | 0.003 |
| Science and technology studies | 0.002 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".