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Spasibionek S, Mikołajczyk K, Matuszczak M, Kaczmarek J, Ramzi N, Jędryczka M. HO-CR and HOLL-CR: new forms of winter oilseed rape (Brassica napus L.) with altered fatty acid composition and resistance to selected pathotypes of Plasmodiophora brassicae (clubroot). J Appl Genet 2024; 65:439-452. [PMID: 38637489 PMCID: PMC11310246 DOI: 10.1007/s13353-024-00867-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/10/2024] [Indexed: 04/20/2024]
Abstract
The priority in oilseed rape (Brassica napus L.) research and breeding programs worldwide is to combine different features to develop cultivars tailored to specific applications of this crop. In this study, forms with a modified fatty acid composition of seed oil were successfully combined with a source of resistance to Plasmodiophora brassicae Wor., a harmful protist-causing clubroot. Three HO-type recombinants in F6-F12 generations with oleic acid content of 80.2-82.1% and one HOLL-type F6 inbred mutant recombinant (HOmut × LLmut), with a high oleic acid content (80.9%) and reduced linolenic acid content (2.3%), were crossed with the cultivar Tosca, resistant to several pathotypes of P. brassicae. The work involved genotyping with the use of DNA markers specific for allelic variants of desaturase genes responsible for the synthesis of oleic and linolenic fatty acids, CAPS (FAD2 desaturase, C18:1), and SNaPshot (FAD3 desaturase, C18:3), respectively. Of 350 progenies in the F3 generation, 192 (55%) were selected for further studies. Among them, 80 HO (≥ 72%) lines were identified, 10 of which showed resistance to at least one up to four P. brassicae pathotypes. Thirty lines in the selected progeny contained high oleic acid and less than 5% linolenic acid; eight of them belonged to the HOLL type conferring resistance to at least one pathotype. Two HO lines and two HOLL lines were resistant to four pathotypes. The resulting HO-CR and HOLL-CR inbred lines with altered seed oil fatty acid composition and resistance to P. brassicae represent unique oilseed rape material with the desired combination of valuable traits.
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Affiliation(s)
- Stanisław Spasibionek
- Plant Breeding and Acclimatization Institute-National Research Institute, Department of Oilseed Crops, Poznań, Poland
| | - Katarzyna Mikołajczyk
- Plant Breeding and Acclimatization Institute-National Research Institute, Department of Oilseed Crops, Poznań, Poland
| | - Marcin Matuszczak
- Plant Breeding and Acclimatization Institute-National Research Institute, Department of Oilseed Crops, Poznań, Poland
| | - Joanna Kaczmarek
- Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Noor Ramzi
- Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
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Askarian H, Akhavan A, González LG, Hwang SF, Strelkov SE. Genetic Structure of Plasmodiophora brassicae Populations Virulent on Clubroot Resistant Canola ( Brassica napus). PLANT DISEASE 2021; 105:3694-3704. [PMID: 33507096 DOI: 10.1094/pdis-09-20-1980-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Clubroot, caused by Plasmodiophora brassicae Woronin, is a significant threat to the canola (Brassica napus L.) industry in Canada. Clubroot resistance has been overcome in more than 200 fields since 2013, representing one of the biggest challenges to sustainable canola production. The genetic structure of 36 single-spore isolates derived from 12 field isolates of P. brassicae collected before and after the introduction of clubroot resistant (CR) canola cultivars (2005-2014) was evaluated by simple sequence repeat (SSR) marker analysis. Polymorphisms were detected in 32 loci with the identification of 93 distinct alleles. A low level of genetic diversity was found among the single-spore isolates. Haploid linkage disequilibrium and number of migrants suggested that recombination and migration were rare or almost absent in the tested P. brassicae population. A relatively clear relationship was found between the genetic structure and virulence phenotypes of the pathogen as defined on the differential hosts of Somé et al., Williams, and the Canadian Clubroot Differential (CCD) set. Although genetic variability within each pathotype group, as classified on each differential system, was low, significant genetic differentiation was observed among the pathotypes. The highest correlation between genetic structure and virulence was found among matrices produced with genetic data and the hosts of the CCD set, with a threshold index of disease of 50% to distinguish susceptible from resistant reactions. Genetically homogeneous single-spore isolates provided a more complete and clearer picture of the population genetic structure of P. brassicae, and the results suggest some promise for the development of pathotype-specific primers.
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Affiliation(s)
- Homa Askarian
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Alireza Akhavan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Leonardo Galindo González
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Sheau-Fang Hwang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Stephen E Strelkov
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
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Schwelm A, Ludwig-Müller J. Molecular Pathotyping of Plasmodiophora brassicae-Genomes, Marker Genes, and Obstacles. Pathogens 2021; 10:pathogens10030259. [PMID: 33668372 PMCID: PMC7996130 DOI: 10.3390/pathogens10030259] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/16/2021] [Accepted: 02/21/2021] [Indexed: 11/16/2022] Open
Abstract
Here we review the usefulness of the currently available genomic information for the molecular identification of pathotypes. We focused on effector candidates and genes implied to be pathotype specific and tried to connect reported marker genes to Plasmodiophora brassicae genome information. The potentials for practical applications, current obstacles and future perspectives are discussed.
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Greenhouse Evaluation of Clubroot Resistant- Brassica napus cv. Mendel and Its Efficacy Concerning Virulence and Soil Inoculum Levels of Plasmodiophora brassicae. Pathogens 2021; 10:pathogens10020151. [PMID: 33540852 PMCID: PMC7913074 DOI: 10.3390/pathogens10020151] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/19/2021] [Accepted: 01/27/2021] [Indexed: 11/17/2022] Open
Abstract
Clubroot resistance of oilseed rape (OSR) cultivars frequently relies on a major resistance gene originating from cv. Mendel. The efficacy of this resistance was studied in greenhouse experiments using two Plasmodiophora brassicae isolates, which were either virulent (P1(+)) or avirulent (P1) on Mendel. Seeds of clubroot-susceptible cultivar Visby and clubroot-resistant cultivar Mendel were sown in soil mixtures inoculated with different concentrations of resting spores (101, 103, 105, and 107 resting spores/g soil). Clubroot severity, plant height, shoot and root weight as well as resting spore propagation were assessed for each isolate and cultivar separately at four dates after sowing. The OSR cultivars behaved significantly different in the measured parameters. The threshold of inoculum density to cause disease depended strongly on the virulence of the pathogen and susceptibility of the host plant. In Visby grown in soil infested with P1, clubroot symptoms and increases in root weight and the number of propagated resting spores occurred at inoculum levels of 101 resting spores and higher, whereas Mendel was not affected in soils under the three lowest inoculum densities. In contrast, the P1(+) isolate led to earlier and more severe symptoms, heavier galls, and a significantly higher number of new resting spores in both cultivars.
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The architecture of the Plasmodiophora brassicae nuclear and mitochondrial genomes. Sci Rep 2019; 9:15753. [PMID: 31673019 PMCID: PMC6823432 DOI: 10.1038/s41598-019-52274-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 10/15/2019] [Indexed: 11/09/2022] Open
Abstract
Plasmodiophora brassicae is a soil-borne pathogen that attacks roots of cruciferous plants causing clubroot disease. The pathogen belongs to the Plasmodiophorida order in Phytomyxea. Here we used long-read SMRT technology to clarify the P. brassicae e3 genomic constituents along with comparative and phylogenetic analyses. Twenty contigs representing the nuclear genome and one mitochondrial (mt) contig were generated, together comprising 25.1 Mbp. Thirteen of the 20 nuclear contigs represented chromosomes from telomere to telomere characterized by [TTTTAGGG] sequences. Seven active gene candidates encoding synaptonemal complex-associated and meiotic-related protein homologs were identified, a finding that argues for possible genetic recombination events. The circular mt genome is large (114,663 bp), gene dense and intron rich. It shares high synteny with the mt genome of Spongospora subterranea, except in a unique 12 kb region delimited by shifts in GC content and containing tandem minisatellite- and microsatellite repeats with partially palindromic sequences. De novo annotation identified 32 protein-coding genes, 28 structural RNA genes and 19 ORFs. ORFs predicted in the repeat-rich region showed similarities to diverse organisms suggesting possible evolutionary connections. The data generated here form a refined platform for the next step involving functional analysis, all to clarify the complex biology of P. brassicae.
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Sedaghatkish A, Gossen BD, Yu F, Torkamaneh D, McDonald MR. Whole-genome DNA similarity and population structure of Plasmodiophora brassicae strains from Canada. BMC Genomics 2019; 20:744. [PMID: 31619176 PMCID: PMC6794840 DOI: 10.1186/s12864-019-6118-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/20/2019] [Indexed: 11/28/2022] Open
Abstract
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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Affiliation(s)
- Afsaneh Sedaghatkish
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada.,Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Bruce D Gossen
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada.
| | - Fengqun Yu
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Davoud Torkamaneh
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada.,Département de Phytologie, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Mary Ruth McDonald
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada
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Holtz MD, Hwang SF, Strelkov SE. Genotyping of Plasmodiophora brassicae reveals the presence of distinct populations. BMC Genomics 2018; 19:254. [PMID: 29661147 PMCID: PMC5902848 DOI: 10.1186/s12864-018-4658-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 04/10/2018] [Indexed: 11/21/2022] Open
Abstract
Background Plasmodiophora brassicae is a soilborne pathogen of the family Brassicaceae and the causal agent of clubroot disease. In Canada, P. brassicae is now one of the most important constraints to canola (Brassica napus) production, and is managed mainly by the deployment of resistant cultivars. In recent years, however, new strains of the pathogen have emerged that are capable of overcoming host resistance, posing new challenges for disease management. Despite its economic significance, molecular studies of P. brassicae are rare, mainly because this microorganism cannot be cultured outside of its host. Results Restriction site-associated DNA sequencing (RADseq) was used to examine the genetic diversity within P. brassicae single-spore and field isolates collected from across Canada. The isolates included individuals that were either capable or incapable of causing disease on clubroot resistant canola cultivars. Over 8750 variants were identified through RADseq. Population analysis indicated that most isolates belonged to one of two distinct populations, corresponding with the ability of isolates to cause disease on resistant cultivars. Within each population, there were low levels of genetic diversity. One thousand and fifty of the genetic variants that distinguished the two populations were nonsynonymous, altering the coding sequences of genes. Conclusion The application of RADseq revealed two distinct populations of P. brassicae in Canada, suggesting multiple introductions of the pathogen into the country. The genetic variation found here will be important for future research and monitoring of the pathogen. Electronic supplementary material The online version of this article (10.1186/s12864-018-4658-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michael D Holtz
- Alberta Agriculture and Forestry, Field Crop Development Centre, Lacombe, Alberta, Canada
| | - Sheau-Fang Hwang
- Alberta Agriculture and Forestry, Crop Diversification Centre North, Edmonton, Alberta, Canada
| | - Stephen E Strelkov
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada.
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Schwelm A, Berney C, Dixelius C, Bass D, Neuhauser S. The Large Subunit rDNA Sequence of Plasmodiophora brassicae Does not Contain Intra-species Polymorphism. Protist 2016; 167:544-554. [PMID: 27750174 PMCID: PMC5221739 DOI: 10.1016/j.protis.2016.08.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 08/24/2016] [Accepted: 08/28/2016] [Indexed: 12/02/2022]
Abstract
Clubroot disease caused by Plasmodiophora brassicae is one of the most important diseases of cultivated brassicas. P. brassicae occurs in pathotypes which differ in the aggressiveness towards their Brassica host plants. To date no DNA based method to distinguish these pathotypes has been described. In 2011 polymorphism within the 28S rDNA of P. brassicae was reported which potentially could allow to distinguish pathotypes without the need of time-consuming bioassays. However, isolates of P. brassicae from around the world analysed in this study do not show polymorphism in their LSU rDNA sequences. The previously described polymorphism most likely derived from soil inhabiting Cercozoa more specifically Neoheteromita-like glissomonads. Here we correct the LSU rDNA sequence of P. brassicae. By using FISH we demonstrate that our newly generated sequence belongs to the causal agent of clubroot disease.
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Affiliation(s)
- Arne Schwelm
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, P.O. Box 7080, SE-75007 Uppsala, Sweden; University of Innsbruck, Institute of Microbiology, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Cédric Berney
- Division of Genomics and Microbial Diversity, Dept of Life Sciences, Natural History Museum London, Cromwell Road, SW7 5BD, UK; Groupe Evolution des Protistes et Ecosystèmes Pélagiques, UMR 7144, CNRS & Université Pierre et Marie Curie, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Christina Dixelius
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, P.O. Box 7080, SE-75007 Uppsala, Sweden
| | - David Bass
- Division of Genomics and Microbial Diversity, Dept of Life Sciences, Natural History Museum London, Cromwell Road, SW7 5BD, UK; Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, The Nothe, Weymouth, DT4 8UB, UK
| | - Sigrid Neuhauser
- University of Innsbruck, Institute of Microbiology, Technikerstraße 25, 6020 Innsbruck, Austria; Division of Genomics and Microbial Diversity, Dept of Life Sciences, Natural History Museum London, Cromwell Road, SW7 5BD, UK.
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Kim H, Jo EJ, Choi YH, Jang KS, Choi GJ. Pathotype Classification of Plasmodiophora brassicae Isolates Using Clubroot-Resistant Cultivars of Chinese Cabbage. THE PLANT PATHOLOGY JOURNAL 2016; 32:423-430. [PMID: 27721692 PMCID: PMC5051561 DOI: 10.5423/ppj.oa.04.2016.0081] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Revised: 07/05/2016] [Accepted: 07/07/2016] [Indexed: 05/02/2023]
Abstract
Clubroot disease caused by Plasmodiophora brassicae is one of the most serious diseases in Brassica crops worldwide. In this study, the pathotypes of 12 Korean P. brassicae field isolates were determined using various Chinese cabbage including 22 commercial cultivars from Korea, China, and Japan, and 15 inbred lines. All P. brassicae isolates exhibited the typical clubroot disease on non-clubroot resistant cultivar, indicating that the isolates were highly pathogenic. According to the reactions on the Williams' hosts, the 12 field isolates were initially classified into five races. However, when these isolates were inoculated onto clubroot-resistant (CR) cultivars of Chinese cabbage, several isolates led to different disease responses even though the isolates have been assigned to the same race by the Williams' host responses. Based on the pathogenicity results, the 12 field isolates were reclassified into four different groups: pathotype 1 (GN1, GN2, GS, JS, and HS), 2 (DJ and KS), 3 (HN1, PC, and YC), and 4 (HN2 and SS). In addition, the CR cultivars from Korea, China, and Japan exhibited distinguishable disease responses to the P. brassicae isolates, suggesting that the 22 cultivars used in this study, including the non-CR cultivars, are classified into four different host groups based on their disease resistance. Combining these findings, the four differential hosts of Chinese cabbage and four pathotype groups of P. brassicae might provide an efficient screening system for resistant cultivars and a new foundation of breeding strategies for CR Chinese cabbage.
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Affiliation(s)
- Hun Kim
- Center for Eco-friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon 34114,
Korea
- Department of Green Chemistry and Environmental Biotechnology, Korea University of Science and Technology, Daejeon 34113,
Korea
| | - Eun Ju Jo
- Center for Eco-friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon 34114,
Korea
| | - Yong Ho Choi
- Center for Eco-friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon 34114,
Korea
| | - Kyoung Soo Jang
- Center for Eco-friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon 34114,
Korea
| | - Gyung Ja Choi
- Center for Eco-friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon 34114,
Korea
- Department of Green Chemistry and Environmental Biotechnology, Korea University of Science and Technology, Daejeon 34113,
Korea
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Strehlow B, de Mol F, Struck C. Risk Potential of Clubroot Disease on Winter Oilseed Rape. PLANT DISEASE 2015; 99:667-675. [PMID: 30699684 DOI: 10.1094/pdis-05-14-0482-re] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Clubroot disease caused by Plasmodiophora brassicae is an important disease of cruciferous plants. Although the pathogen is widespread and has been reported to cause high yield losses, the impact on winter oilseed rape (OSR) has not been experimentally verified. To quantify the risk potential of P. brassicae, we conducted two closely linked experiments. A semicontrolled experiment used artificial soil infestation at inoculum densities between 106 and 108 spores liter-1 of soil to detect the impact on seed yield and yield components of a susceptible and resistant OSR cultivar. A greenhouse experiment was implemented using the soil of the semicontrolled experiment after cropping the two cultivars to quantify the influence of cultivar resistance on soil inoculum. According to cumulative link mixed models, disease rating was positively correlated with the amount of inoculum. Linear regression analyses revealed a negative correlation between seed yield and inoculum density. Yield losses of 60% already appeared at the lowest inoculum density. Plant losses and reduced seed per pod were accountable for yield losses. Although the resistant cultivar showed clubroot symptoms, seed yield was not affected by the pathogen. The greenhouse experiment revealed that clubroot severity in subsequent OSR was reduced after cropping the resistant cultivar. This study showed significant yield damage of P. brassicae already at low infestation levels.
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Affiliation(s)
- Becke Strehlow
- Group Crop Health, Faculty of Agricultural and Environmental Sciences, University of Rostock, 18059 Germany
| | - Friederike de Mol
- Group Crop Health, Faculty of Agricultural and Environmental Sciences, University of Rostock, 18059 Germany
| | - Christine Struck
- Group Crop Health, Faculty of Agricultural and Environmental Sciences, University of Rostock, 18059 Germany
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