Genotyping by sequencing suggests overwintering of Peronospora destructor in southwestern Québec, Canada

Abstract

Several Peronospora species are carried by wind over short and long distances, from warmer climates where they survive on living plants to cooler climates. In eastern Canada, this annual flow of sporangia was thought to be the main source of Peronospora destructor responsible for onion downy mildew. However, the results of a recent study showed that the increasing frequency of onion downy mildew epidemics in eastern Canada is associated with warmer autumns, milder winters, and previous year disease severity, suggesting overwintering of the inoculum in an area where the pathogen is not known to be endogenous. In this study, genotyping by sequencing was used to investigate the population structure of P. destructor at the landscape scale. The study focused on a particular region of southwestern Québec—Les Jardins de Napierville—to determine if the populations were clonal and regionally differentiated. The data were characterized by a high level of linkage disequilibrium, characteristic of clonal organisms. Consequently, the null hypothesis of random mating was rejected when tested on predefined or nonpredefined populations, indicating that linkage disequilibrium was not a function of population structure and suggesting a mixed reproduction mode. Discriminant analysis of principal components performed with predefined population assignment allowed grouping P. destructor isolates by geographical regions, while analysis of molecular variance confirmed that this genetic differentiation was significant at the regional level. Without using a priori population assignment, isolates were clustered into four genetic clusters. These results represent a baseline estimate of the genetic diversity and population structure of P. destructor.

Oomycete communities are influenced by land use and disease status in Christmas tree production in Southern Québec, Canada

“…The pipeline used for quality filtering, ITS1 extraction, and generation of the representative sequence data is available via the GitHub page: https://github.com/duceppemo/QIIME2_ITS. Additional scripts used to analyze the data, as well as the data converted into a single phyloseq object, are available through GitHub (https://github.com/hvanderheyden/cimdec_phytophthora) and FASTQ files and R‐codes through Figshare (Van Der Heyden et al., 2023, 2024).…”

Attack of the clones: Population genetics reveals clonality of Colletotrichum lupini, the causal agent of lupin anthracnose

“…Population genetics offers great potential to get insight in the evolutionary processes that affect genetic diversity and population structure of fungal plant pathogens (McDonald & Linde, 2002 ). In many important fungal and oomycete plant pathogens, such as Peronospora destructor on onion (Van der Heyden et al, 2022 ), Fusarium oxysporum on cotton (Halpern et al, 2020 ), and Colletotrichum graminicola on maize (Rogério et al, 2023 ), population genetics provided essential information on pathogen evolution and diversity. Knowledge on pathogen population structure is crucial for developing long‐term disease management strategies as was pointed out by Wallace et al ( 2020 ) for Pseudoperonospora cubensis on Cucurbitaceae.…”