Genetic structure and population diversity of Phytophthora infestans strains in Pacific western Canada.

Late blight caused by Phytophthora infestans is an economically important disease of potato and tomato worldwide. In Canada, an increase in late blight incidence and severity coincided with changes in genetic composition of P. infestans. We monitored late blight incidence on tomato and potato in Pacific western and eastern Canada between 2019 and 2022, identified genotypes of P. infestans, and examined their population genetic diversity. We identified four major existing genotypes US11, US17, US8, and US23 as well as 25 new genotypes. The US11 genotype was dominant in Pacific western Canada, accounting for 59% of the total population. We discovered the US17 genotype for the first time in Canada. We revealed a higher incidence of late blight and quite diverse genotypes of P. infestans in Pacific western Canada than in eastern Canada. We found high genetic diversity of P. infestans population from Pacific western Canada, as evidenced by the high number of multilocus genotypes, high values of genetic diversity indices, and emergence of 25 new genotypes. Considering the number of disease incidence, the detection of diverse known genotypes, the emergence of novel genotypes, and the high number of isolates resistant to metalaxyl-m (95%) from Pacific western Canada, the region could play a role in establishing sexual recombination and diverse populations, which could ultimately pose challenges for late blight management. Therefore, continuous monitoring of P. infestans populations in Pacific western region and across Canada is warranted. KEY POINTS: • Genotypes of P. infestans in Pacific western were quite diverse than in eastern Canada. • We discovered US17 genotype for the first time in Canada and identified 26 novel genotypes. • Approximately 95% of P. infestans isolates were resistant to metalaxyl-m.

Assessing Performance of Spore Samplers in Monitoring Aeromycobiota and Fungal Plant Pathogen Diversity in Canada.

Spore samplers are widely used in pathogen surveillance but not so much for monitoring the composition of aeromycobiota. In Canada, a nationwide spore-sampling network (AeroNet) was established as a pilot project to assess fungal community composition in air and rain samples collected using three different spore samplers in the summers of 2010 and 2011. Metabarcodes of the internal transcribed spacer (ITS) were exhaustively characterized for three of the network sites, in British Columbia (BC), Québec (QC), and Prince Edward Island (PEI), to compare performance of the samplers. Sampler type accounted for ca. 20% of the total explainable variance in aeromycobiota compositional heterogeneity, with air samplers recovering more Ascomycota and rain samplers recovering more Basidiomycota. Spore samplers showed different abilities to collect 27 fungal genera that are plant pathogens. For instance, Cladosporium spp., Drechslera spp., and Entyloma spp. were collected mainly by air samplers, while Fusarium spp., Microdochium spp., and Ustilago spp. were recovered more frequently with rain samplers. The diversity and abundance of some fungi were significantly affected by sampling location and time (e.g., Alternaria and Bipolaris) and weather conditions (e.g., Mycocentrospora and Leptosphaeria), and depended on using ITS1 or ITS2 as the barcoding region (e.g., Epicoccum and Botrytis). The observation that Canada's aeromycobiota diversity correlates with cooler, wetter conditions and northward wind requires support from more long-term data sets. Our vision of the AeroNet network, combined with high-throughput sequencing (HTS) and well-designed sampling strategies, may contribute significantly to a national biovigilance network for protecting plants of agricultural and economic importance in Canada.IMPORTANCE The current study compared the performance of spore samplers for collecting broad-spectrum air- and rain-borne fungal pathogens using a metabarcoding approach. The results provided a thorough characterization of the aeromycobiota in the coastal regions of Canada in relation to the influence of climatic factors. This study lays the methodological basis to eventually develop knowledge-based guidance on pest surveillance by assisting in the selection of appropriate spore samplers.

Proteomics analysis suggests broad functional changes in potato leaves triggered by phosphites and a complex indirect mode of action against Phytophthora infestans.

Phosphite (salts of phosphorous acid; Phi)-based fungicides are increasingly used in controlling oomycete pathogens, such as the late blight agent Phytophthora infestans. In plants, low amounts of Phi induce pathogen resistance through an indirect mode of action. We used iTRAQ-based quantitative proteomics to investigate the effects of phosphite on potato plants before and after infection with P. infestans. Ninety-three (62 up-regulated and 31 down-regulated) differentially regulated proteins, from a total of 1172 reproducibly identified proteins, were identified in the leaf proteome of Phi-treated potato plants. Four days post-inoculation with P. infestans, 16 of the 31 down-regulated proteins remained down-regulated and 42 of the 62 up-regulated proteins remained up-regulated, including 90% of the defense proteins. This group includes pathogenesis-related, stress-responsive, and detoxification-related proteins. Callose deposition and ultrastructural analyses of leaf tissues after infection were used to complement the proteomics approach. This study represents the first comprehensive proteomics analysis of the indirect mode of action of Phi, demonstrating broad effects on plant defense and plant metabolism. The proteomics data and the microscopy study suggest that Phi triggers a hypersensitive response that is responsible for induced resistance of potato leaves against P. infestans. BIOLOGICAL SIGNIFICANCE: Phosphie triggers complex functional changes in potato leaves that are responsible for the induced resistance against Phytophthora infestans. This article is part of a Special Issue entitled: Translational Plant Proteomics.

Protein profiling in potato (Solanum tuberosum L.) leaf tissues by differential centrifugation.

Foliar diseases, such as late blight, result in serious threats to potato production. As such, potato leaf tissue becomes an important substrate to study biological processes, such as plant defense responses to infection. Nonetheless, the potato leaf proteome remains poorly characterized. Here, we report protein profiling of potato leaf tissues using a modified differential centrifugation approach to separate the leaf tissues into cell wall and cytoplasmic fractions. This method helps to increase the number of identified proteins, including targeted putative cell wall proteins. The method allowed for the identification of 1484 nonredundant potato leaf proteins, of which 364 and 447 were reproducibly identified proteins in the cell wall and cytoplasmic fractions, respectively. Reproducibly identified proteins corresponded to over 70% of proteins identified in each replicate. A diverse range of proteins was identified based on their theoretical pI values, molecular masses, functional classification, and biological processes. Such a protein extraction method is effective for the establishment of a highly qualified proteome profile.

Genetic Composition of Phytophthora infestans in Canada Reveals Migration and Increased Diversity.

A dramatic increase in the incidence of late blight and changes within populations of Phytophthora infestans have been observed in various regions of Canada. In this study, the occurrence of several new genotypes of the pathogen was documented with associated phenotypes that dominated pathogen populations. Genotype US-23, previously detected only among isolates from the United States, dominated in the western Canadian provinces of British Columbia, Alberta (AB), Saskatchewan, and Manitoba (MB). Although isolates of US-23 infect both potato and tomato, these isolates were the only genotype recovered from commercial garden centers in Canada. Isolates of genotype US-8, previously dominant throughout Canada, represented the only genotype detected from the eastern Canadian provinces of New Brunswick and Prince Edward Island. Isolates of other genotypes detected in Canada included US-11 in AB, US-24 in MB, and US-22 in Ontario (ON). An additional genotype was detected in ON which appears to be a derivative of US-22 that may have arisen through sexual reproduction. However, evidence of clonal reproduction dominated among the isolates collected, and opportunities for sexual reproduction were probably limited because of a surprising geographic separation of the A1 and A2 mating types in Canada. Sensitivity of the US-22, US-23, and US-24 isolates to the fungicide metalaxyl, movement of potato seed and transplants, and weather conditions may have contributed to reduced opportunities for contact between the mating types in fields in Canada. All P. infestans isolates were readily distinguished from other related oomycetes with RG57 restriction fragment length polymorphism analysis. Long-distance movement in seed tubers and garden center transplants may have contributed to the rapid spread of the P. infestans genotypes across Canada. Tracking pathogen movement and population composition should improve the ability to predict the genotypes expected each year in different regions of Canada.

In-Furrow Applications of Metalaxyl and Phosphite for Control of Pink Rot (Phytophthora erythroseptica) of Potato in New Brunswick, Canada.

The efficacy of metalaxyl-m (Ridomil Gold 480EC) and phosphite (Phostrol) applied at planting in-furrow against pink rot (Phytophthora erythroseptica) of potato (Solanum tuberosum) 'Shepody' and 'Russet Burbank' was evaluated in field trials conducted in 2005 and 2006 in Florenceville, New Brunswick, Canada. Inoculum made from a metalaxyl-m-sensitive isolate of P. erythroseptica from New Brunswick was applied either in-furrow as a vermiculite slurry at planting or as a zoospore drench in soils adjacent to potato plants in late August. After harvest, the number and weight of tubers showing pink rot symptoms were assessed and expressed as percentages of the total tuber number and total weight of tubers. Metalaxyl-m applied in-furrow was significantly more effective against pink rot than phosphite. The mean percentage of diseased tubers as a percentage of total tuber weight was 1.5% (2005) and 1.2% (2006) for metalaxyl-m-treated plots and 9.6% (2005) and 2.8% (2006) for phosphite-treated plots, a percentage similar to that obtained in inoculated control plots with no fungicide treatment. The mean percentage of diseased tubers expressed as a percentage of the total number of tubers was 1.7% (2005) and 1.3% (2006) for metalaxyl-m-treated plots and 10.1% (2005) and 3.1% (2006) for phosphite-treated plots. Disease incidence was significantly higher using the late-season inoculation technique (respective means in 2005 and 2006 were 9.9 and 3.8% diseased tubers, by weight, and 10.6 and 3.9%, by number) than with the in-furrow inoculation method (respective means in 2005 and 2006 were 3.3 and 0.7% by weight, and 3.7 and 1.3%, by number). The potato cv. Shepody was significantly more susceptible to pink rot (9.9 and 3.3% diseased tubers, by weight, in 2005 and 2006, respectively, and 10.6 and 3.9%, by number) than Russet Burbank (respective means in 2005 and 2006 were 3.4,% and 1.2%, by weight, and 3.7,% and 1.2%, by number). Our findings indicate that metalaxyl applied in-furrow at planting is a viable option for control of pink rot caused by metalaxyl-sensitive strains of P. erythroseptica, whereas phosphite was ineffective.

Limited Genetic Diversity in North American Isolates of Phytophthora erythroseptica Pathogenic to Potato Based on RAPD Analysis.

Pink rot of potato (Solanum tuberosum), caused by Phytophthora erythroseptica, is found wherever potatoes are grown, and in the last decade, it has reemerged as an economically important disease in Canada and the United States. A selection of isolates of P. erythroseptica from major potato-growing regions in North America, namely Prince Edward Island and New Brunswick, Canada, and Maine and Idaho, U.S.A., was assessed for genetic diversity with randomly chosen decanucleotide primers which were used to amplify regions of DNA to reveal polymorphisms among templates (random amplified polymorphic DNA [RAPD]). The isolates varied in their geographic origin as well as in their sensitivity to mefenoxam, as determined by an in vitro assay. In three separate RAPD screens (I, II, and III) with 23 isolates of P. erythroseptica chosen from a larger collection, 1,410, 369, and 316 robust, scorable bands were amplified, respectively. However, among the bands amplified in screens I, II, and III, only 3, 1, and 3 bands, respectively, were polymorphic. When three primers yielding polymorphisms were used to screen 106 isolates from Prince Edward Island and New Brunswick, or a representative collection of 32 isolates from Prince Edward Island, New Brunswick, Maine, and Idaho, no major variation was discovered. RAPD markers were not correlated with geographic origin or mefenoxam sensitivity of the isolates. From an evolutionary standpoint, the absence of genetic diversity among the isolates of P. erythroseptica we examined may be attributable to the relatively recent introduction of a small founding population of the pathogen in North America.