Page 172 - Plant Canada 2024 Proceeding

PLANT CANADA 2024

Identifying and characterizing effectors secreted by P. brassicae will enhance our understanding of its
infection mechanisms to help guide future management practices.

*[O135] GENOMIC ANALYSIS OF THE PUCCINIA STRIIFORMIS F.SP TRITICI POPULATIONS
CAUSING STRIPE RUST IN CANADA. Bohan Wei , Ryan Gourlie , Rodrigo Ortega Polo , Nathaniel
1
1
1,2
1
1
Zhin-Loong Lim , Rhodesia Celoy , Stephen Strelkov , and Reem Aboukhaddour . Lethbridge Research
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1 1
and Development Centre, Agriculture and Agri-Food Canada, 5403 1 Ave S, Lethbridge, AB, Canada,
T1J 4B1; and Department of Agriculture, Food and Nutritional Science, University of Alberta, 116 St & 85
2
Ave, Edmonton, AB, Canada T6G 2R3
Correspondence to: reem.aboukhaddour@agr.gc.ca

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), significantly impacts global wheat production.
Other forms of this pathogen can infect barley and other grasses, contributing to the complexity of stripe
rust management. Despite its global importance, the genomic evolution of Pst in Canada remains
underexplored. This study aims to fill this gap by analyzing temporal genomic changes in Pst populations
from Canada, focusing on their evolution and adaptation mechanisms. We conducted whole-genome
Illumina short-read sequencing (NovaSeq, Génome Québec) and de novo assembly (MaSuRCA) of 27 P.
striiformis isolates collected between 1984 and 2023 from wheat, barley, and foxtail barley across Alberta,
Quebec, and PEI. Assemblies were annotated with the FunGAP or Funnanotate pipelines utilizing RNA
reads from Pst CYR34 urediniospores. Four previously published isolates from the UK and USA were
also included in downstream analysis. To explore genetic diversity and relatedness reads we conducted
variant calling. Reads were quality-checked with FASTQC, and SAMtools was used to sort and align
reads to the reference genome PST-130. Variant calling was performed with HaplotypeCaller and
GenotypeGVCF from Genome Analysis Toolkit. SNPs were filtered for quality and depth, converted to
phylip format, and a maximum-likelihood tree was generated using RAxML and visualized with IToL. The
phylogenetic tree revealed four major branches encompassing all isolates, with Canadian isolates distinct
from those in the UK and USA. Significant genomic differences were observed between pre-2000 and
post-2010 collections, and between samples from 2022-2023. Our next steps involve using Pangloss to
create a pangenome and analyze core and accessory genes between pre-2000 and post-2010 groups to
uncover evolutionary patterns and adaptation mechanisms in the Canadian Pst population. Preliminary
results will be presented. We will also investigate genes related to host specificity, focusing on wheat,
barley, and foxtail barley. Tracing gene changes from 1984 to 2023 will enhance our understanding of
core gene involvement in stripe rust virulence in Canada, providing insights into future disease
management strategies. Our data reveals new insights into the evolution of diverse Pst phenotypes over
different periods, highlighting pathogen adaptation dynamics and informing predictive models for disease
management.

*[O136] DEVELOPMENT OF A KASP ASSAY FOR DETECTION OF SUCCINATE DEHYDROGENASE
MUTATIONS ASSOCIATED WITH SDHI RESISTANCE IN STEMPHYLIUM VESICARIUM. Julia
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Scicluna , Emily McFaul , Afsaneh Sedaghatkish , Bruce D. Gossen , and Mary Ruth McDonald .
1 Department of Plant Agriculture, University of Guelph, 50 Stone Rd E, Guelph, ON, Canada, N1G 2W1;
2
and Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science
Place, Saskatoon, SK, Canada, S7N 0X2
Correspondence to: mrmcdona@uoguelph.ca

Stemphylium leaf blight (SLB) caused by Stemphylium vesicarium is the most common foliar disease of
onion in Ontario. SLB management relies on repeated fungicide applications each year and most
fungicides contain succinate dehydrogenase inhibitor (SDHI) active ingredients. Resistance to the SDHI
active ingredients fluxapyroxad and penflufen has increased since 2012 in Ontario and SDHIs have poor
efficacy in the field. Isolates of S. vesicarium from New York State classified as highly resistant to SDHI
fungicides frequently had one of three mutations (G79R, H134R and C135R) in the gene encoding
succinate dehydrogenase subunit C (sdhC). In the current study, a Kompetitive Allele Specific PCR
(KASP) assay was designed to detect the single nucleotide polymorphisms (SNPs) of G79R, H134R and
C135R in sdhC. The assay was tested on 70 S. vesicarium isolates collected in Ontario from 2012-2023
that were classified as either sensitive or resistant to fluxapyroxad and penflufen based on mycelial
growth assays. The C135R and G79R mutations were identified in 4% and 11% of isolates resistant to
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