Genotyping of Plasmodiophora brassicae reveals the presence of distinct populations

Holtz, Michael D.; Hwang, Sheau‐Fang; Strelkov, Stephen E.

doi:10.1186/s12864-018-4658-1

Cited by 23 publications

(20 citation statements)

References 45 publications

(77 reference statements)

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“…Only neighbor joining tree was used for further analysis, because the neighbor joining method is optimal for big data sets compared with the maximum likelihood, which is more accurate for very small data sets. In addition, the neighbor joining method is the most commonly used distance method to compute P. brassicae phylogenetic trees [29, 30]. The neighbor joining tree was developed using genome-wide SNPs (total = 10 K SNPs) of 43 strains, which grouped the strains into five clades (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…In addition, P. brassicae may be present as a mixture of pathotypes within a single infected root [27]. Although a few isolates of P. brassicae have been sequenced to date [28–30], study of the genomics and population genetics of P. brassicae is still in its infancy. Analysis of the single-spore isolate e3 from Europe estimated the total genome size of P. brassicae to be 25.5 Mb [27].…”

Section: Introductionmentioning

confidence: 99%

“…When the genomes of six single-spore isolates of pathotypes from Canada were sequenced, pathotypes 2 and 3 were similar, pathotypes 5 and 8 were similar, and pathotype 6 differed from the other isolates but was similar to e3 from Europe [29]. In another study, a field collection of pathotype 6 from vegetables in British Columbia differed substantially from collections from canola in Alberta [30].…”

Section: Introductionmentioning

confidence: 99%

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Whole-genome DNA similarity and population structure of Plasmodiophora brassicae strains from Canada

Sedaghatkish

Gossen

et al. 2019

BMC Genomics

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Background Clubroot is an important disease of brassica crops world-wide. The causal agent, Plasmodiophora brassicae, has been present in Canada for over a century but was first identified on canola (Brassica napus) in Alberta, Canada in 2003. Genetic resistance to clubroot in an adapted canola cultivar has been available since 2009, but resistance breakdown was detected in 2013 and new pathotypes are increasing rapidly. Information on genetic similarity among pathogen populations across Canada could be useful in estimating the genetic variation in pathogen populations, predicting the effect of subsequent selection pressure on changes in the pathogen population over time, and even in identifying the origin of the initial pathogen introduction to canola in Alberta. Results The genomic sequences of 43 strains (34 field collections, 9 single-spore isolates) of P. brassicae from Canada, the United States, and China clustered into five clades based on SNP similarity. The strains from Canada separated into four clades, with two containing mostly strains from the Prairies (provinces of Alberta, Saskatchewan, and Manitoba) and two that were mostly from the rest of Canada or the USA. Several strains from China formed a separate clade. More than one pathotype and host were present in all four Canadian clades. The initial pathotypes from canola on the Prairies clustered separately from the pathotypes on canola that could overcome resistance to the initial pathotypes. Similarly, at one site in central Canada where resistance had broken down, about half of the genes differed (based on SNPs) between strains before and after the breakdown. Conclusion Clustering based on genome-wide DNA sequencing demonstrated that the initial pathotypes on canola on the Prairies clustered separately from the new virulent pathotypes on the Prairies. Analysis indicated that these ‘new’ pathotypes were likely present in the pathogen population at very low frequency, maintained through balancing selection, and increased rapidly in response to selection from repeated exposure to host resistance.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Whole-genome DNA similarity and population structure of Plasmodiophora brassicae strains from Canada

Sedaghatkish

Gossen

et al. 2019

BMC Genomics

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“…It is important that these resistant hybrids not be overused. Frequent cropping of a resistant cultivar in fields with a high spore load produces a strong selection pressure towards virulence in the pathogen population (Holtz et al ., ), which can quickly result in resistance breakdown (Kuginuki et al ., ; Tanaka & Ito, ; Strelkov et al ., ). Therefore, it will be necessary to monitor the response of resistant cultivars to ensure continued resistance to the pathotypes prevalent in Latin America.…”

Section: Clubroot Management In Latin Americamentioning

confidence: 99%

Clubroot disease in Latin America: distribution and management strategies

et al. 2019

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Clubroot caused by Plasmodiophora brassicae is an important disease of cruciferous crops worldwide. In Latin America (from Mexico to Chile, including the Caribbean), most of the area in cruciferous crops is devoted to oilseed rape (Brassica napus; c. 230 600 ha) in Brazil, Chile, Paraguay, Uruguay and Argentina, while cruciferous vegetables such as cabbage, cauliflower, broccoli and Brussels sprouts (40 900 ha) are cropped intensively on small acreages across the region. Although clubroot is present in most Latin American countries, there have been very few studies of P. brassicae. Clubroot research in Latin America has focused mainly on adapting disease management strategies developed in temperate climates to tropical climates, including liming, biological control and genetic resistance. This review summarizes the management strategies used in Latin America to reduce the impact of clubroot, including novel strategies when compared with temperate regions, such as a crop rotation with aromatic plant species and the use of biological control with Trichoderma spp. Latin America has unique characteristics relative to temperate countries such as high humidity, warm temperatures and acidic soil that impact the interaction between P. brassicae and its plant hosts, so more research is required.

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“…P. brassicae populations in the fields are often a mixture of different pathotypes (Xue et al 2008). P. brassicae is a highly variable pathogen and its genotyping revealed the presence of distinct populations (Holtz et al 2018). Due to the continuous cropping of a single resistant cultivar, the virulent pathotypes are likely to be selected and then compromise the resistance (Tanaka et al 2013).…”

Section: Introductionmentioning

confidence: 99%

Genes for defense response to Plasmodiophora brassicae during late infection in small spheroid galls of Brassica rapa

Yang¹,

Fang²,

Wang³

et al. 2020

Biol. plant.

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Plasmodiophora brassicae is a biotrophic pathogen causing clubroots of cruciferous crops. The Brassica rapa accession T1-145 has an ability to produce small spheroid galls (SSGs), which represent neither a fully compatible interaction nor a complete resistance. To explore the defense response in SSGs induced by P. brassicae infection, global transcriptome profiling SSGs was performed at different time points. By comparing gene expression patterns, we identified many defense related genes. The first group included genes encoding receptor-like protein/kinases, such as cysteine-rich receptor-like protein kinases, receptor-like proteins, phloem intercalated with xylem/tracheary element differentiation inhibitory factor receptor (PXY/TDR), PXY-correlated 1, wall-associated kinases, nuclear shuttle protein-interacting kinase, lectin receptorlike kinases, and flagelin-sensitive 2, which might activate a basal defense. The second group involved robust effectortriggered immunity response genes such as resistance to leptosphaeria maculans 1B, constitutive shade-avoidance 1, target of avirulence B operation 1, ribosomal protein of the small subunit 6, resistance to Pseudomonas maculicola 1-interacting protein 4, enhanced disease resistance 2L, and recognition of Peronospora parasitica 13-like protein 4. The third group included genes encoding secondary cell wall formation related protein/s, a nodulin-like protein, a germin-like protein, a jacalin-related lectin, a defensin-like protein, tumor inhibitors, and sugars will eventually be exported transporter, which might contribute to quantitative resistance against P. brassicae. The gene expressions were the highest at the late stage of infection. To our knowledge, it is the first report on exploring defense response genes during SSG occurrence by a transcriptome analysis. Our data would provide useful information to further explore molecular mechanisms of the incomplete resistance.

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Genotyping of Plasmodiophora brassicae reveals the presence of distinct populations

Cited by 23 publications

References 45 publications

Whole-genome DNA similarity and population structure of Plasmodiophora brassicae strains from Canada

Whole-genome DNA similarity and population structure of Plasmodiophora brassicae strains from Canada

Clubroot disease in Latin America: distribution and management strategies

Genes for defense response to Plasmodiophora brassicae during late infection in small spheroid galls of Brassica rapa

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