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Javed MA, Mukhopadhyay S, Normandeau E, Brochu AS, Pérez-López E. Telomere-to-telomere Genome Assembly of the Clubroot Pathogen Plasmodiophora Brassicae. Genome Biol Evol 2024; 16:evae122. [PMID: 38857178 PMCID: PMC11191646 DOI: 10.1093/gbe/evae122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/31/2024] [Accepted: 06/05/2024] [Indexed: 06/12/2024] Open
Abstract
Plasmodiophora brassicae (Woronin, 1877), a biotrophic, obligate parasite, is the causal agent of clubroot disease in brassicas. The clubroot pathogen has been reported in more than 80 countries worldwide, causing economic losses of hundreds of millions every year. Despite its widespread impact, very little is known about the molecular strategies it employs to induce the characteristic clubs in the roots of susceptible hosts during infection, nor about the mechanisms it uses to overcome genetic resistance. Here, we provide the first telomere-to-telomere complete genome of P. brassicae. We generated ∼27 Gb of Illumina, Oxford Nanopore, and PacBio HiFi data from resting spores of strain Pb3A and produced a 25.3 Mb assembly comprising 20 chromosomes, with an N50 of 1.37 Mb. The BUSCO score, the highest reported for any member of the group Rhizaria (Eukaryota: 88.2%), highlights the limitations within the Eukaryota database for members of this lineage. Using available transcriptomic data and protein evidence, we annotated the Pb3A genome, identifying 10,521 protein-coding gene models. This high-quality, complete genome of P. brassicae will serve as a crucial resource for the plant pathology community to advance the much-needed understanding of the evolution of the clubroot pathogen.
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Affiliation(s)
- Muhammad Asim Javed
- Départment de Phytologie, Faculté des sciences de l’agriculture et de l’alimentation, Université Laval, Quebec City, Quebec, Canada
- Centre de recherche et d’innovation sur les végétaux (CRIV), Université Laval, Quebec City, Quebec, Canada
- Plateforme de bio-informatique de l'IBIS (Institut de Biologie Intégrative et des Systèmes), Université Laval, Quebec City, Québec, Canada
- L’Institute EDS, Université Laval, Québec City, Québec, Canada
| | - Soham Mukhopadhyay
- Départment de Phytologie, Faculté des sciences de l’agriculture et de l’alimentation, Université Laval, Quebec City, Quebec, Canada
- Centre de recherche et d’innovation sur les végétaux (CRIV), Université Laval, Quebec City, Quebec, Canada
- Plateforme de bio-informatique de l'IBIS (Institut de Biologie Intégrative et des Systèmes), Université Laval, Quebec City, Québec, Canada
- L’Institute EDS, Université Laval, Québec City, Québec, Canada
| | - Eric Normandeau
- Plateforme de bio-informatique de l'IBIS (Institut de Biologie Intégrative et des Systèmes), Université Laval, Quebec City, Québec, Canada
| | - Anne-Sophie Brochu
- Départment de Phytologie, Faculté des sciences de l’agriculture et de l’alimentation, Université Laval, Quebec City, Quebec, Canada
- Centre de recherche et d’innovation sur les végétaux (CRIV), Université Laval, Quebec City, Quebec, Canada
- Plateforme de bio-informatique de l'IBIS (Institut de Biologie Intégrative et des Systèmes), Université Laval, Quebec City, Québec, Canada
- L’Institute EDS, Université Laval, Québec City, Québec, Canada
| | - Edel Pérez-López
- Départment de Phytologie, Faculté des sciences de l’agriculture et de l’alimentation, Université Laval, Quebec City, Quebec, Canada
- Centre de recherche et d’innovation sur les végétaux (CRIV), Université Laval, Quebec City, Quebec, Canada
- Plateforme de bio-informatique de l'IBIS (Institut de Biologie Intégrative et des Systèmes), Université Laval, Quebec City, Québec, Canada
- L’Institute EDS, Université Laval, Québec City, Québec, Canada
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Musharaf Hossain M, Alinapon CV, Todd CD, Wei Y, Bonham-Smith PC. The Plasmodiophora brassicae Golgi-localized UPF0016 protein PbGDT1 mediates calcium but not manganese transport in yeast and Nicotiana benthamiana. Fungal Genet Biol 2024; 172:103896. [PMID: 38663635 DOI: 10.1016/j.fgb.2024.103896] [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] [Received: 01/12/2024] [Revised: 04/11/2024] [Accepted: 04/23/2024] [Indexed: 05/03/2024]
Abstract
Manganese and calcium homeostasis and signalling, in eukaryotic organisms, are regulated through membrane located pumps, channels and exchangers, including the Mn2+/Ca2+ uncharacterized protein family 0016 (UPF0016). Here we show that Plasmodiophora brassicae PbGDT1 is a member of the UPF0016 and an ortholog of Saccharomyces cerevisiae Gdt1p (GCR Dependent Translation Factor 1) protein involved in manganese homeostasis as well as the calcium mediated stress response in yeast. PbGDT1 complemented the ScGdt1p and ScPMR1 (Ca2+ ATPase) double null mutant under elevated calcium stress but not under elevated manganese conditions. In both yeast and Nicotiana benthamiana, PbGDT1 localizes to the Golgi apparatus, with additional ER association in N. benthamiana. Expression of PbGDT1 in N. benthamiana, suppresses BAX-triggered cell death, further highlighting the importance of calcium homeostasis in maintaining cell physiology and integrity in a stress environment.
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Affiliation(s)
- Md Musharaf Hossain
- Department of Biology, University of Saskatchewan, Saskatoon S7N5E2, Saskatchewan, Canada
| | | | - Christopher D Todd
- Department of Biology, University of Saskatchewan, Saskatoon S7N5E2, Saskatchewan, Canada
| | - Yangdou Wei
- Department of Biology, University of Saskatchewan, Saskatoon S7N5E2, Saskatchewan, Canada
| | - Peta C Bonham-Smith
- Department of Biology, University of Saskatchewan, Saskatoon S7N5E2, Saskatchewan, Canada.
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Ando S, Otawara S, Tabei Y, Tsushima S. Plasmodiophora brassicae affects host gene expression by secreting the transcription factor-type effector PbZFE1. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:454-467. [PMID: 37738570 DOI: 10.1093/jxb/erad377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 09/20/2023] [Indexed: 09/24/2023]
Abstract
The protist pathogen Plasmodiophora brassicae hijacks the metabolism and development of host cruciferous plants and induces clubroot formation, but little is known about its regulatory mechanisms. Previously, the Pnit2int2 sequence, a sequence around the second intron of the nitrilase gene (BrNIT2) involved in auxin biosynthesis in Brassica rapa ssp. pekinensis, was identified as a specific promoter activated during clubroot formation. In this study, we hypothesized that analysis of the transcriptional regulation of Pnit2int2 could reveal how P. brassicae affects the host gene regulatory system during clubroot development. By yeast one-hybrid screening, the pathogen zinc finger protein PbZFE1 was identified to specifically bind to Pnit2int2. Specific binding of PbZFE1 to Pnit2int2 was also confirmed by electrophoretic mobility shift assay. The binding site of PbZFE1 is essential for promoter activity of Pnit2int2 in clubbed roots of transgenic Arabidopsis thaliana (Pnit2int2-2::GUS), indicating that PbZFE1 is secreted from P. brassicae and functions within plant cells. Ectopic expression of PbZEF1 in A. thaliana delayed growth and flowering time, suggesting that PbZFE1 has significant impacts on host development and metabolic systems. Thus, P. brassicae appears to secrete PbZFE1 into host cells as a transcription factor-type effector during pathogenesis.
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Affiliation(s)
- Sugihiro Ando
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramakiaza-Aoba, Aoba-ku, Sendai, Miyagi 980-8572, Japan
| | - Shinsuke Otawara
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramakiaza-Aoba, Aoba-ku, Sendai, Miyagi 980-8572, Japan
| | - Yutaka Tabei
- Division of Plant Sciences, The Institute of Agrobiological Sciences, NARO (NIAS), 2-1-2 Kan-nondai, Tsukuba, Ibaraki 305-8602, Japan
- Department of Food and Life Sciences, Toyo University, 1-1-1 Izumino, Itakura-machi, Ora-gun, Gunma 374-0193, Japan
| | - Seiya Tsushima
- Strategic Planning Headquarters, National Agriculture and Food Research Organization (NARO), 3-1-1 Kan-nondai, Tsukuba, Ibaraki 305-8517, Japan
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Ochoa JC, Mukhopadhyay S, Bieluszewski T, Jędryczka M, Malinowski R, Truman W. Natural variation in Arabidopsis responses to Plasmodiophora brassicae reveals an essential role for Resistance to Plasmodiophora brasssicae 1 (RPB1). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1421-1440. [PMID: 37646674 DOI: 10.1111/tpj.16438] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/09/2023] [Accepted: 08/16/2023] [Indexed: 09/01/2023]
Abstract
Despite the identification of clubroot resistance genes in various Brassica crops our understanding of the genetic basis of immunity to Plasmodiophora brassicae infection in the model plant Arabidopsis thaliana remains limited. To address this issue, we performed a screen of 142 natural accessions and identified 11 clubroot-resistant Arabidopsis lines. Genome-wide association analysis identified several genetic loci significantly linked with resistance. Three genes from two of these loci were targeted for deletion by CRISPR/Cas9 mutation in resistant accessions Est-1 and Uod-1. Deletion of Resistance to Plasmodiophora brassicae 1 (RPB1) rendered both lines susceptible to the P. brassicae pathotype P1+. Further analysis of rpb1 knock-out Est-1 and Uod-1 lines showed that the RPB1 protein is required for activation of downstream defence responses, such as the expression of phytoalexin biosynthesis gene CYP71A13. RPB1 has recently been shown to encode a cation channel localised in the endoplasmic reticulum. The clubroot susceptible Arabidopsis accession Col-0 lacks a functional RPB1 gene; when Col-0 is transformed with RPB1 expression driven by its native promoter it is capable of activating RPB1 transcription in response to infection, but this is not sufficient to confer resistance. Transient expression of RPB1 in Nicotiana tabacum induced programmed cell death in leaves. We conclude that RPB1 is a critical component of the defence response to P. brassicae infection in Arabidopsis, acting downstream of pathogen recognition but required for the elaboration of effective resistance.
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Affiliation(s)
- Juan Camilo Ochoa
- Institute of Plant Genetics, Polish Academy of Sciences, ul. Strzeszyńska 34, 60-479, Poznań, Poland
| | - Soham Mukhopadhyay
- Institute of Plant Genetics, Polish Academy of Sciences, ul. Strzeszyńska 34, 60-479, Poznań, Poland
| | - Tomasz Bieluszewski
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Małgorzata Jędryczka
- Institute of Plant Genetics, Polish Academy of Sciences, ul. Strzeszyńska 34, 60-479, Poznań, Poland
| | - Robert Malinowski
- Institute of Plant Genetics, Polish Academy of Sciences, ul. Strzeszyńska 34, 60-479, Poznań, Poland
| | - William Truman
- Institute of Plant Genetics, Polish Academy of Sciences, ul. Strzeszyńska 34, 60-479, Poznań, Poland
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Hasan M, Hossain M, Jiang D. New endophytic strains of Trichoderma promote growth and reduce clubroot severity of rapeseed (Brassica napus). PLoS One 2023; 18:e0287899. [PMID: 37906546 PMCID: PMC10617699 DOI: 10.1371/journal.pone.0287899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/15/2023] [Indexed: 11/02/2023] Open
Abstract
Rapeseed (Brassica napus L.) is the world's third most important edible oilseed crop after soybean and palm. The clubroot disease caused by Plasmodiophora brassicae poses a significant risk and causes substantial yield losses in rapeseed. In this study, 13 endophytic fungal strains were isolated from the healthy roots of rapeseed (B. napus) grown in a clubroot-infested field and molecularly identified. Based on germination inhibition of resting spores of P. brassicae, two endophytic fungal antagonists, Trichoderma spp. ReTk1 and ReTv2 were selected to evaluate their potential for plant growth promotion and biocontrol of P. brassicae. The Trichoderma isolates were applied as a soil drench (1×107 spore/g soil) to a planting mix and field soil, in which plants were grown under non-infested and P. brassicae-infested (2×106 spore/g soil) conditions. The endophytic fungi were able to promote plant growth, significantly increasing shoot and root length, leaf diameter, and biomass production (shoots and root weight) both in the absence or presence of P. brassicae. The single and dual treatments with the endophytes were equally effective in significantly decreasing the root-hair infection, root index, and clubroot severity index. Both ReTk1 and ReTv2 inhibited the germination of resting spores of P. brassicae in root exudates. Moreover, the endophytic fungi colonized the roots of rapeseed extensively and possibly induced host resistance by up-regulated expression of defense-related genes involved in jasmonate (BnOPR2), ethylene (BnACO and BnSAM3), phenylpropanoid (BnOPCL and BnCCR), auxin (BnAAO1) and salicylic acid (BnPR2) pathways. Based on these findings, it is evident that the rapeseed root endophytes Trichoderma spp. ReTk1 and ReTv2 could suppress the gall formation on rapeseed roots via antibiosis, induced systemic resistance (ISR), and/or systemic acquired resistance (SAR). According to our knowledge, this is the first report of the endophytic Trichoderma spp. isolated from root tissues of healthy rapeseed plants (B. napus.), promoting plant growth and reducing clubroot severity.
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Affiliation(s)
- Mahmodol Hasan
- Plant Pathology Laboratory, Department of Agronomy and Agricultural Extension, University of Rajshahi, Rajshahi, Bangladesh
| | - Motaher Hossain
- Department of Plant Pathology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Daohong Jiang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, PR China
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Garvetto A, Murúa P, Kirchmair M, Salvenmoser W, Hittorf M, Ciaghi S, Harikrishnan SL, Gachon CMM, Burns JA, Neuhauser S. Phagocytosis underpins the biotrophic lifestyle of intracellular parasites in the class Phytomyxea (Rhizaria). THE NEW PHYTOLOGIST 2023; 238:2130-2143. [PMID: 36810975 PMCID: PMC10953367 DOI: 10.1111/nph.18828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 02/06/2023] [Indexed: 05/04/2023]
Abstract
Phytomyxea are intracellular biotrophic parasites infecting plants and stramenopiles, including the agriculturally impactful Plasmodiophora brassicae and the brown seaweed pathogen Maullinia ectocarpii. They belong to the clade Rhizaria, where phagotrophy is the main mode of nutrition. Phagocytosis is a complex trait of eukaryotes, well documented for free-living unicellular eukaryotes and specific cellular types of animals. Data on phagocytosis in intracellular, biotrophic parasites are scant. Phagocytosis, where parts of the host cell are consumed at once, is seemingly at odds with intracellular biotrophy. Here we provide evidence that phagotrophy is part of the nutritional strategy of Phytomyxea, using morphological and genetic data (including a novel transcriptome of M. ectocarpii). We document intracellular phagocytosis in P. brassicae and M. ectocarpii by transmission electron microscopy and fluorescent in situ hybridization. Our investigations confirm molecular signatures of phagocytosis in Phytomyxea and hint at a small specialized subset of genes used for intracellular phagocytosis. Microscopic evidence confirms the existence of intracellular phagocytosis, which in Phytomyxea targets primarily host organelles. Phagocytosis seems to coexist with the manipulation of host physiology typical of biotrophic interactions. Our findings resolve long debated questions on the feeding behaviour of Phytomyxea, suggesting an unrecognized role for phagocytosis in biotrophic interactions.
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Affiliation(s)
- Andrea Garvetto
- Institute of MicrobiologyUniversity of InnsbruckTechnikerstraße 25Innsbruck6020TyrolAustria
| | - Pedro Murúa
- Laboratorio de Macroalgas, Instituto de AcuiculturaUniversidad Austral de ChilePuerto Montt5480000Chile
| | - Martin Kirchmair
- Institute of MicrobiologyUniversity of InnsbruckTechnikerstraße 25Innsbruck6020TyrolAustria
| | - Willibald Salvenmoser
- Institute of ZoologyUniversity of InnsbruckTechnikerstraße 25Innsbruck6020TyrolAustria
| | - Michaela Hittorf
- Institute of MicrobiologyUniversity of InnsbruckTechnikerstraße 25Innsbruck6020TyrolAustria
| | - Stefan Ciaghi
- Institute of MicrobiologyUniversity of InnsbruckTechnikerstraße 25Innsbruck6020TyrolAustria
| | - Srilakshmy L. Harikrishnan
- Centre for Plant Systems BiologyVIBZwijnaarde 71Ghent9052Belgium
- Department of Plant Biotechnology and BioinformaticsGhent UniversityZwijnaarde 71Ghent9052Belgium
| | - Claire M. M. Gachon
- Muséum National d'Histoire Naturelle, UMR 7245, CNRS CP 2657 rue Cuvier75005ParisFrance
- Scottish Association for Marine ScienceScottish Marine InstituteDunbegObanPA37 1QAUK
| | - John A. Burns
- Bigelow Laboratory for Ocean Sciences60 Bigelow Dr.East BoothbayME04544USA
| | - Sigrid Neuhauser
- Institute of MicrobiologyUniversity of InnsbruckTechnikerstraße 25Innsbruck6020TyrolAustria
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Vañó MS, Nourimand M, MacLean A, Pérez-López E. Getting to the root of a club - Understanding developmental manipulation by the clubroot pathogen. Semin Cell Dev Biol 2023; 148-149:22-32. [PMID: 36792438 DOI: 10.1016/j.semcdb.2023.02.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023]
Abstract
Plasmodiophora brassicae Wor., the clubroot pathogen, is the perfect example of an "atypical" plant pathogen. This soil-borne protist and obligate biotrophic parasite infects the roots of cruciferous crops, inducing galls or clubs that lead to wilting, loss of productivity, and plant death. Unlike many other agriculturally relevant pathosystems, research into the molecular mechanisms that underlie clubroot disease and Plasmodiophora-host interactions is limited. After release of the first P. brassicae genome sequence and subsequent availability of transcriptomic data, the clubroot research community have implicated the involvement of phytohormones during the clubroot pathogen's manipulation of host development. Herein we review the main events leading to the formation of root galls and describe how modulation of select phytohormones may be key to modulating development of the plant host to the benefit of the pathogen. Effector-host interactions are at the base of different strategies employed by pathogens to hijack plant cellular processes. This is how we suspect the clubroot pathogen hijacks host plant metabolism and development to induce nutrient-sink roots galls, emphasizing a need to deepen our understanding of this master manipulator.
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Affiliation(s)
- Marina Silvestre Vañó
- Départment de phytologie, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Quebec City, Quebec, Canada; Centre de recherche et d'innovation sur les végétaux (CRIV), Université Laval, Quebec City, Quebec, Canada; Institute de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
| | - Maryam Nourimand
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Allyson MacLean
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
| | - Edel Pérez-López
- Départment de phytologie, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Quebec City, Quebec, Canada; Centre de recherche et d'innovation sur les végétaux (CRIV), Université Laval, Quebec City, Quebec, Canada; Institute de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada.
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Bíbová J, Kábrtová V, Večeřová V, Kučerová Z, Hudeček M, Plačková L, Novák O, Strnad M, Plíhal O. The Role of a Cytokinin Antagonist in the Progression of Clubroot Disease. Biomolecules 2023; 13:biom13020299. [PMID: 36830668 PMCID: PMC9953476 DOI: 10.3390/biom13020299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/31/2023] [Accepted: 02/03/2023] [Indexed: 02/08/2023] Open
Abstract
Plasmodiophora brassicae is an obligate biotrophic pathogen causing clubroot disease in cruciferous plants. Infected plant organs are subject to profound morphological changes, the roots form characteristic galls, and the leaves are chlorotic and abscise. The process of gall formation is governed by timely changes in the levels of endogenous plant hormones that occur throughout the entire life cycle of the clubroot pathogen. The homeostasis of two plant hormones, cytokinin and auxin, appears to be crucial for club development. To investigate the role of cytokinin and auxin in gall formation, we used metabolomic and transcriptomic profiling of Arabidopsis thaliana infected with clubroot, focusing on the late stages of the disease, where symptoms were more pronounced. Loss-of-function mutants of three cytokinin receptors, AHK2, AHK3, and CRE1/AHK4, were employed to further study the homeostasis of cytokinin in response to disease progression; ahk double mutants developed characteristic symptoms of the disease, albeit with varying intensity. The most susceptible to clubroot disease was the ahk3 ahk4 double mutant, as revealed by measuring its photosynthetic performance. Quantification of phytohormone levels and pharmacological treatment with the cytokinin antagonist PI-55 showed significant changes in the levels of endogenous cytokinin and auxin, which was manifested by both enhanced and reduced development of disease symptoms in different genotypes.
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Affiliation(s)
- Jana Bíbová
- Laboratory of Growth Regulators, Faculty of Science, Institute of Experimental Botany of the Czech Academy of Sciences, Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic
| | - Veronika Kábrtová
- Laboratory of Growth Regulators, Faculty of Science, Institute of Experimental Botany of the Czech Academy of Sciences, Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic
| | - Veronika Večeřová
- Laboratory of Growth Regulators, Faculty of Science, Institute of Experimental Botany of the Czech Academy of Sciences, Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic
| | - Zuzana Kučerová
- Department of Biophysics, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic
| | - Martin Hudeček
- Laboratory of Growth Regulators, Faculty of Science, Institute of Experimental Botany of the Czech Academy of Sciences, Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic
| | - Lenka Plačková
- Laboratory of Growth Regulators, Faculty of Science, Institute of Experimental Botany of the Czech Academy of Sciences, Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic
| | - Ondřej Novák
- Laboratory of Growth Regulators, Faculty of Science, Institute of Experimental Botany of the Czech Academy of Sciences, Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Faculty of Science, Institute of Experimental Botany of the Czech Academy of Sciences, Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic
- Correspondence: (M.S.); (O.P.)
| | - Ondřej Plíhal
- Laboratory of Growth Regulators, Faculty of Science, Institute of Experimental Botany of the Czech Academy of Sciences, Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic
- Correspondence: (M.S.); (O.P.)
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Javed MA, Schwelm A, Zamani‐Noor N, Salih R, Silvestre Vañó M, Wu J, González García M, Heick TM, Luo C, Prakash P, Pérez‐López E. The clubroot pathogen Plasmodiophora brassicae: A profile update. MOLECULAR PLANT PATHOLOGY 2023; 24:89-106. [PMID: 36448235 PMCID: PMC9831288 DOI: 10.1111/mpp.13283] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 05/13/2023]
Abstract
BACKGROUND Plasmodiophora brassicae is the causal agent of clubroot disease of cruciferous plants and one of the biggest threats to the rapeseed (Brassica napus) and brassica vegetable industry worldwide. DISEASE SYMPTOMS In the advanced stages of clubroot disease wilting, stunting, yellowing, and redness are visible in the shoots. However, the typical symptoms of the disease are the presence of club-shaped galls in the roots of susceptible hosts that block the absorption of water and nutrients. HOST RANGE Members of the family Brassicaceae are the primary host of the pathogen, although some members of the family, such as Bunias orientalis, Coronopus squamatus, and Raphanus sativus, have been identified as being consistently resistant to P. brassicae isolates with variable virulence profile. TAXONOMY Class: Phytomyxea; Order: Plasmodiophorales; Family: Plasmodiophoraceae; Genus: Plasmodiophora; Species: Plasmodiophora brassicae (Woronin, 1877). DISTRIBUTION Clubroot disease is spread worldwide, with reports from all continents except Antarctica. To date, clubroot disease has been reported in more than 80 countries. PATHOTYPING Based on its virulence on different hosts, P. brassicae is classified into pathotypes or races. Five main pathotyping systems have been developed to understand the relationship between P. brassicae and its hosts. Nowadays, the Canadian clubroot differential is extensively used in Canada and has so far identified 36 different pathotypes based on the response of a set of 13 hosts. EFFECTORS AND RESISTANCE After the identification and characterization of the clubroot pathogen SABATH-type methyltransferase PbBSMT, several other effectors have been characterized. However, no avirulence gene is known, hindering the functional characterization of the five intercellular nucleotide-binding (NB) site leucine-rich-repeat (LRR) receptors (NLRs) clubroot resistance genes validated to date. IMPORTANT LINK Canola Council of Canada is constantly updating information about clubroot and P. brassicae as part of their Canola Encyclopedia: https://www.canolacouncil.org/canola-encyclopedia/diseases/clubroot/. PHYTOSANITARY CATEGORIZATION PLADBR: EPPO A2 list; Annex designation 9E.
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Affiliation(s)
- Muhammad Asim Javed
- Départment de phytologie, Faculté des sciences de l'agriculture et de l'alimentationUniversité LavalQuebec CityQuebecCanada
- Centre de recherche et d'innovation sur les végétauxUniversité LavalQuebec CityQuebecCanada
- Institute de Biologie Intégrative et des Systèmes, Université LavalQuebec CityQuebecCanada
| | - Arne Schwelm
- Department of Plant ScienceWageningen University and ResearchWageningenNetherlands
- Teagasc, Crops Research CentreCarlowIreland
| | - Nazanin Zamani‐Noor
- Julius Kühn‐Institute, Institute for Plant Protection in Field Crops and GrasslandBraunschweigGermany
| | - Rasha Salih
- Départment de phytologie, Faculté des sciences de l'agriculture et de l'alimentationUniversité LavalQuebec CityQuebecCanada
- Centre de recherche et d'innovation sur les végétauxUniversité LavalQuebec CityQuebecCanada
- Institute de Biologie Intégrative et des Systèmes, Université LavalQuebec CityQuebecCanada
| | - Marina Silvestre Vañó
- Départment de phytologie, Faculté des sciences de l'agriculture et de l'alimentationUniversité LavalQuebec CityQuebecCanada
- Centre de recherche et d'innovation sur les végétauxUniversité LavalQuebec CityQuebecCanada
- Institute de Biologie Intégrative et des Systèmes, Université LavalQuebec CityQuebecCanada
| | - Jiaxu Wu
- Départment de phytologie, Faculté des sciences de l'agriculture et de l'alimentationUniversité LavalQuebec CityQuebecCanada
- Centre de recherche et d'innovation sur les végétauxUniversité LavalQuebec CityQuebecCanada
- Institute de Biologie Intégrative et des Systèmes, Université LavalQuebec CityQuebecCanada
| | - Melaine González García
- Départment de phytologie, Faculté des sciences de l'agriculture et de l'alimentationUniversité LavalQuebec CityQuebecCanada
- Centre de recherche et d'innovation sur les végétauxUniversité LavalQuebec CityQuebecCanada
- Institute de Biologie Intégrative et des Systèmes, Université LavalQuebec CityQuebecCanada
| | | | - Chaoyu Luo
- Départment de phytologie, Faculté des sciences de l'agriculture et de l'alimentationUniversité LavalQuebec CityQuebecCanada
- College of Agronomy and BiotechnologySouthwest UniversityChongqingChina
| | - Priyavashini Prakash
- Départment de phytologie, Faculté des sciences de l'agriculture et de l'alimentationUniversité LavalQuebec CityQuebecCanada
- K. S. Rangasamy College of TechnologyNamakkalIndia
| | - Edel Pérez‐López
- Départment de phytologie, Faculté des sciences de l'agriculture et de l'alimentationUniversité LavalQuebec CityQuebecCanada
- Centre de recherche et d'innovation sur les végétauxUniversité LavalQuebec CityQuebecCanada
- Institute de Biologie Intégrative et des Systèmes, Université LavalQuebec CityQuebecCanada
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10
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Decroës A, Mahillon M, Genard M, Lienard C, Lima-Mendez G, Gilmer D, Bragard C, Legrève A. Rhizomania: Hide and Seek of Polymyxa betae and the Beet Necrotic Yellow Vein Virus with Beta vulgaris. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:989-1005. [PMID: 35816413 DOI: 10.1094/mpmi-03-22-0063-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The molecular interactions between Polymyxa betae, the protist vector of sugar beet viruses, beet necrotic yellow vein virus (BNYVV), the causal agent of rhizomania, and Beta vulgaris have not been extensively studied. Here, the transmission of BNYVV to sugar beet by P. betae zoospores was optimized using genetically characterized organisms. Molecular interactions of aviruliferous and viruliferous protist infection on sugar beet were highlighted by transcriptomic analysis. P. betae alone induced limited gene expression changes in sugar beet, as a biotrophic asymptomatic parasite. Most differentially expressed plant genes were down-regulated and included resistance gene analogs and cell wall peroxidases. Several enzymes involved in stress regulation, such as the glutathione-S-transferases, were significantly induced. With BNYVV, the first stages of the P. betae life cycle on sugar beet were accelerated with a faster increase of relative protist DNA level and an earlier appearance of sporangia and sporosori in plants roots. A clear activation of plant defenses and the modulation of genes involved in plant cell wall metabolism were observed. The P. betae transcriptome in the presence of BNYVV revealed induction of genes possibly involved in the switch to the survival stage. The interactions were different depending on the presence or absence of the virus. P. betae alone alleviates plant defense response, playing hide-and-seek with sugar beet and allowing for their mutual development. Conversely, BNYVV manipulates plant defense and promotes the rapid invasion of plant roots by P. betae. This accelerated colonization is accompanied by the development of thick-walled resting spores, supporting the virus survival. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Alain Decroës
- Phytopathology-Applied Microbiology, Earth and Life Institute, UCLouvain, Louvain-la-Neuve, 1348, Belgium
| | | | - Margaux Genard
- Phytopathology-Applied Microbiology, Earth and Life Institute, UCLouvain, Louvain-la-Neuve, 1348, Belgium
| | - Charlotte Lienard
- Phytopathology-Applied Microbiology, Earth and Life Institute, UCLouvain, Louvain-la-Neuve, 1348, Belgium
| | - Gipsi Lima-Mendez
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Louvain-la-Neuve, 1348, Belgium
| | - David Gilmer
- Institut de biologie moléculaire des plantes, CNRS UPR2357, Université de Strasbourg, Strasbourg, 67084, France
| | - Claude Bragard
- Phytopathology-Applied Microbiology, Earth and Life Institute, UCLouvain, Louvain-la-Neuve, 1348, Belgium
| | - Anne Legrève
- Phytopathology-Applied Microbiology, Earth and Life Institute, UCLouvain, Louvain-la-Neuve, 1348, Belgium
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11
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Ludwig-Müller J. What Can We Learn from -Omics Approaches to Understand Clubroot Disease? Int J Mol Sci 2022; 23:ijms23116293. [PMID: 35682976 PMCID: PMC9180986 DOI: 10.3390/ijms23116293] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/31/2022] [Accepted: 06/02/2022] [Indexed: 02/04/2023] Open
Abstract
Clubroot is one of the most economically significant diseases worldwide. As a result, many investigations focus on both curing the disease and in-depth molecular studies. Although the first transcriptome dataset for the clubroot disease describing the clubroot disease was published in 2006, many different pathogen-host plant combinations have only recently been investigated and published. Articles presenting -omics data and the clubroot pathogen Plasmodiophora brassicae as well as different host plants were analyzed to summarize the findings in the richness of these datasets. Although genome data for the protist have only recently become available, many effector candidates have been identified, but their functional characterization is incomplete. A better understanding of the life cycle is clearly required to comprehend its function. While only a few proteome studies and metabolome analyses were performed, the majority of studies used microarrays and RNAseq approaches to study transcriptomes. Metabolites, comprising chemical groups like hormones were generally studied in a more targeted manner. Furthermore, functional approaches based on such datasets have been carried out employing mutants, transgenic lines, or ecotypes/cultivars of either Arabidopsis thaliana or other economically important host plants of the Brassica family. This has led to new discoveries of potential genes involved in disease development or in (partial) resistance or tolerance to P. brassicae. The overall contribution of individual experimental setups to a larger picture will be discussed in this review.
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12
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Control Strategies of Clubroot Disease Caused by Plasmodiophora brassicae. Microorganisms 2022; 10:microorganisms10030620. [PMID: 35336194 PMCID: PMC8949847 DOI: 10.3390/microorganisms10030620] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/17/2022] [Accepted: 03/11/2022] [Indexed: 12/04/2022] Open
Abstract
The clubroot disease caused by the soil-borne pathogen Plasmodiophora brassicae is one of the most important diseases of cruciferous crops worldwide. As with many plant pathogens, the spread is closely related to the cultivation of suitable host plants. In addition, temperature and water availability are crucial determinants for the occurrence and reproduction of clubroot disease. Current global changes are contributing to the widespread incidence of clubroot disease. On the one hand, global trade and high prices are leading to an increase in the cultivation of the host plant rapeseed worldwide. On the other hand, climate change is improving the living conditions of the pathogen P. brassicae in temperate climates and leading to its increased occurrence. Well-known ways to control efficiently this disease include arable farming strategies: growing host plants in wide crop rotations, liming the contaminated soils, and using resistant host plants. Since chemical control of the clubroot disease is not possible or not ecologically compatible, more and more alternative control options are being investigated. In this review, we address the challenges for its control, with a focus on biological control options.
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13
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Ma Y, Choi SR, Wang Y, Chhapekar SS, Zhang X, Wang Y, Zhang X, Zhu M, Liu D, Zuo Z, Yan X, Gan C, Zhao D, Liang Y, Pang W, Lim YP. Starch content changes and metabolism-related gene regulation of Chinese cabbage synergistically induced by Plasmodiophora brassicae infection. HORTICULTURE RESEARCH 2022; 9:uhab071. [PMID: 35043157 PMCID: PMC9015896 DOI: 10.1093/hr/uhab071] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/31/2021] [Indexed: 05/10/2023]
Abstract
Clubroot is one of the major diseases adversely affecting Chinese cabbage (Brassica rapa) yield and quality. To precisely characterize the Plasmodiophora brassicae infection on Chinese cabbage, we developed a dual fluorescent staining method for simultaneously examining the pathogen, cell structures, and starch grains. The number of starch (amylopectin) grains increased in B. rapa roots infected by P. brassicae, especially from 14 to 21 days after inoculation. Therefore, the expression levels of 38 core starch metabolism genes were investigated by quantitative real-time PCR. Most genes related to starch synthesis were up-regulated at seven days after the P. brassicae inoculation, whereas the expression levels of the starch degradation-related genes increased at 14 days after the inoculation. Then genes encoding the core enzymes involved in starch metabolism were investigated by assessing their chromosomal distributions, structures, duplication events, and synteny among Brassica species. Genome comparisons indicated that 38 non-redundant genes belonging to six core gene families related to starch metabolism are highly conserved among Arabidopsis thaliana, B. rapa, Brassica nigra, and Brassica oleracea. Genome sequencing projects have revealed that P. brassicae obtained host nutrients by manipulating plant metabolism. Starch may serve as a carbon source for P. brassicae colonization as indicated by the histological observation and transcriptomic analysis. Results of this study may elucidate the evolution and expression of core starch metabolism genes and provide researchers with novel insights into the pathogenesis of clubroot in B. rapa.
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Affiliation(s)
- Yinbo Ma
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon 305-764, Republic of Korea
| | - Su Ryun Choi
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon 305-764, Republic of Korea
| | - Yu Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Sushil Satish Chhapekar
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon 305-764, Republic of Korea
| | - Xue Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Yingjun Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Xueying Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Meiyu Zhu
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Di Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Zhennan Zuo
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Xinyu Yan
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Caixia Gan
- Cash Crops Research Institute, Hubei Academy of Agricultural Sciences, Hubei Key Laboratory of Vegetable Germplasm Enhancement and Genetic Improvement, Wuhan 430070, China
| | - Di Zhao
- Analytical and Testing Center, Shenyang Agricultural University, Shenyang 110866, China
| | - Yue Liang
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Wenxing Pang
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Yong Pyo Lim
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon 305-764, Republic of Korea
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14
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A Novel Target (Oxidation Resistant 2) in Arabidopsis thaliana to Reduce Clubroot Disease Symptoms via the Salicylic Acid Pathway without Growth Penalties. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae8010009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The clubroot disease (Plasmodiophora brassicae) is one of the most damaging diseases worldwide among brassica crops. Its control often relies on resistant cultivars, since the manipulation of the disease hormones, such as salicylic acid (SA) alters plant growth negatively. Alternatively, the SA pathway can be increased by the addition of beneficial microorganisms for biocontrol. However, this potential has not been exhaustively used. In this study, a recently characterized protein Oxidation Resistant 2 (OXR2) from Arabidopsis thaliana is shown to increase the constitutive pathway of SA defense without decreasing plant growth. Plants overexpressing AtOXR2 (OXR2-OE) show strongly reduced clubroot symptoms with improved plant growth performance, in comparison to wild type plants during the course of infection. Consequently, oxr2 mutants are more susceptible to clubroot disease. P. brassicae itself was reduced in these galls as determined by quantitative real-time PCR. Furthermore, we provide evidence for the transcriptional downregulation of the gene encoding a SA-methyltransferase from the pathogen in OXR2-OE plants that could contribute to the phenotype.
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15
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Anjali A, Fatima U, Senthil-Kumar M. The ins and outs of SWEETs in plants: Current understanding of the basics and their prospects in crop improvement. J Biosci 2021. [DOI: 10.1007/s12038-021-00227-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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16
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Pérez-López E, Hossain MM, Wei Y, Todd CD, Bonham-Smith PC. A clubroot pathogen effector targets cruciferous cysteine proteases to suppress plant immunity. Virulence 2021; 12:2327-2340. [PMID: 34515618 PMCID: PMC8451464 DOI: 10.1080/21505594.2021.1968684] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Plant pathogen effector proteins are key to pathogen virulence. In susceptible host Brassicas, the clubroot pathogen, Plasmodiophora brassicae, induces the production of nutrient-sink root galls, at the site of infection. Among a list of 32 P. brassiae effector candidates previously reported by our group, we identified SSPbP53 as a putative apoplastic cystatin-like protein highly expressed during the secondary infection. Here we found that SSPbP53 encoding gene is conserved among several P. brassicae pathotypes and that SSPbP53 is an apoplastic protein able to directly interact with and inhibit cruciferous papain-like cysteine proteases (PLCPs), specifically Arabidopsis XYLEM CYSTEINE PEPTIDASE 1 (AtXCP1). The severity of clubroot disease is greatly reduced in the Arabidopsis xcp1 null mutant (AtΔxcp1) after infection with P. brassicae resting spores, indicating that the interaction of P. brassicae SSPbP53 with XCP1 is important to clubroot susceptibility. SSPbP53 is the first cystatin-like effector identified and characterized for a plant pathogenic protist.
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Affiliation(s)
- Edel Pérez-López
- Department of Biology, University of Saskatchewan, Saskatoon, Canada.,Department of Plant Sciences, University Laval, Criv, Quebec City, Canada
| | | | - Yangdou Wei
- Department of Biology, University of Saskatchewan, Saskatoon, Canada
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17
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Stefanowicz K, Szymanska-Chargot M, Truman W, Walerowski P, Olszak M, Augustyniak A, Kosmala A, Zdunek A, Malinowski R. Plasmodiophora brassicae-Triggered Cell Enlargement and Loss of Cellular Integrity in Root Systems Are Mediated by Pectin Demethylation. FRONTIERS IN PLANT SCIENCE 2021; 12:711838. [PMID: 34394168 PMCID: PMC8359924 DOI: 10.3389/fpls.2021.711838] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/05/2021] [Indexed: 05/24/2023]
Abstract
Gall formation on the belowground parts of plants infected with Plasmodiophora brassicae is the result of extensive host cellular reprogramming. The development of these structures is a consequence of increased cell proliferation followed by massive enlargement of cells colonized with the pathogen. Drastic changes in cellular growth patterns create local deformities in the roots and hypocotyl giving rise to mechanical tensions within the tissue of these organs. Host cell wall extensibility and recomposition accompany the growth of the gall and influence pathogen spread and also pathogen life cycle progression. Demethylation of pectin within the extracellular matrix may play an important role in P. brassicae-driven hypertrophy of host underground organs. Through proteomic analysis of the cell wall, we identified proteins accumulating in the galls developing on the underground parts of Arabidopsis thaliana plants infected with P. brassicae. One of the key proteins identified was the pectin methylesterase (PME18); we further characterized its expression and conducted functional and anatomic studies in the knockout mutant and used Raman spectroscopy to study the status of pectin in P. brassicae-infected galls. We found that late stages of gall formation are accompanied with increased levels of PME18. We have also shown that the massive enlargement of cells colonized with P. brassicae coincides with decreases in pectin methylation. In pme18-2 knockout mutants, P. brassicae could still induce demethylation; however, the galls in this line were smaller and cellular expansion was less pronounced. Alteration in pectin demethylation in the host resulted in changes in pathogen distribution and slowed down disease progression. To conclude, P. brassicae-driven host organ hypertrophy observed during clubroot disease is accompanied by pectin demethylation in the extracellular matrix. The pathogen hijacks endogenous host mechanisms involved in cell wall loosening to create an optimal cellular environment for completion of its life cycle and eventual release of resting spores facilitated by degradation of demethylated pectin polymers.
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Affiliation(s)
| | | | - William Truman
- Institute of Plant Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Piotr Walerowski
- Institute of Plant Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Marcin Olszak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Adam Augustyniak
- Centre for Advanced Technology, Adam Mickiewicz University, Poznan, Poland
| | - Arkadiusz Kosmala
- Institute of Plant Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Artur Zdunek
- Institute of Agrophysics, Polish Academy of Sciences, Lublin, Poland
| | - Robert Malinowski
- Institute of Plant Genetics, Polish Academy of Sciences, Poznan, Poland
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18
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Kopec PM, Mikolajczyk K, Jajor E, Perek A, Nowakowska J, Obermeier C, Chawla HS, Korbas M, Bartkowiak-Broda I, Karlowski WM. Local Duplication of TIR-NBS-LRR Gene Marks Clubroot Resistance in Brassica napus cv. Tosca. FRONTIERS IN PLANT SCIENCE 2021; 12:639631. [PMID: 33936130 PMCID: PMC8082685 DOI: 10.3389/fpls.2021.639631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/09/2021] [Indexed: 06/12/2023]
Abstract
Clubroot, caused by Plasmodiophora brassicae infection, is a disease of growing importance in cruciferous crops, including oilseed rape (Brassica napus). The affected plants exhibit prominent galling of the roots that impairs their capacity for water and nutrient uptake, which leads to growth retardation, wilting, premature ripening, or death. Due to the scarcity of effective means of protection against the pathogen, breeding of resistant varieties remains a crucial component of disease control measures. The key aspect of the breeding process is the identification of genetic factors associated with variable response to the pathogen exposure. Although numerous clubroot resistance loci have been described in Brassica crops, continuous updates on the sources of resistance are necessary. Many of the resistance genes are pathotype-specific, moreover, resistance breakdowns have been reported. In this study, we characterize the clubroot resistance locus in the winter oilseed rape cultivar "Tosca." In a series of greenhouse experiments, we evaluate the disease severity of P. brassicae-challenged "Tosca"-derived population of doubled haploids, which we genotype with Brassica 60 K array and a selection of SSR/SCAR markers. We then construct a genetic map and narrow down the resistance locus to the 0.4 cM fragment on the A03 chromosome, corresponding to the region previously described as Crr3. Using Oxford Nanopore long-read genome resequencing and RNA-seq we review the composition of the locus and describe a duplication of TIR-NBS-LRR gene. Further, we explore the transcriptomic differences of the local genes between the clubroot resistant and susceptible, inoculated and control DH lines. We conclude that the duplicated TNL gene is a promising candidate for the resistance factor. This study provides valuable resources for clubroot resistance breeding programs and lays a foundation for further functional studies on clubroot resistance.
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Affiliation(s)
- Piotr M. Kopec
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University Poznan, Poznan, Poland
| | - Katarzyna Mikolajczyk
- Department of Genetics and Breeding of Oilseed Crops, Plant Breeding and Acclimatization Institute-National Research Institute, Poznan, Poland
| | - Ewa Jajor
- Institute of Plant Protection - National Research Institute, Poznan, Poland
| | - Agnieszka Perek
- Institute of Plant Protection - National Research Institute, Poznan, Poland
| | - Joanna Nowakowska
- Department of Genetics and Breeding of Oilseed Crops, Plant Breeding and Acclimatization Institute-National Research Institute, Poznan, Poland
| | - Christian Obermeier
- Department of Plant Breeding, Justus-Liebig-Universitaet Giessen, Giessen, Germany
| | - Harmeet Singh Chawla
- Department of Plant Breeding, Justus-Liebig-Universitaet Giessen, Giessen, Germany
- Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Marek Korbas
- Institute of Plant Protection - National Research Institute, Poznan, Poland
| | - Iwona Bartkowiak-Broda
- Department of Genetics and Breeding of Oilseed Crops, Plant Breeding and Acclimatization Institute-National Research Institute, Poznan, Poland
| | - Wojciech M. Karlowski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University Poznan, Poznan, Poland
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19
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Czubatka-Bieńkowska A, Kaczmarek J, Marzec-Schmidt K, Nieróbca A, Czajka A, Jędryczka M. Country-Wide qPCR Based Assessment of Plasmodiophora brassicae Spread in Agricultural Soils and Recommendations for the Cultivation of Brassicaceae Crops in Poland. Pathogens 2020; 9:pathogens9121070. [PMID: 33419297 PMCID: PMC7766057 DOI: 10.3390/pathogens9121070] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/17/2020] [Accepted: 12/17/2020] [Indexed: 11/16/2022] Open
Abstract
Clubroot is a damaging disease of oilseed rape and vegetable brassicas worldwide, caused by the soil-borne protist Plasmodiophora brassicae Wor. Due to the long life of resting spores, the assessment of the pathogen abundance in agricultural fields can serve as a guideline for disease control at the country-wide level or the regional scale. Between 2013 and 2019, we collected 431 soil samples from fields cultivated with Brassicaceae crops throughout 16 provinces of Poland. The samples were subjected to qPCR based analysis of P. brassicae DNA concentration. From these data, the spore loads and gene copies g−1 soil were calculated and used to produce an assessment of the current clubroot risk potential at a country-wide and regional scale. The country-wide map, showing the spread of the pathogen in agricultural soils, was made using ArcGis software package implementing the interpolation with the Inverse Distance Weight method. The calculation of gene copies specific to P. brassicae helped to formulate the recommendations for farmers in respect to the cultivation guidelines. It showed a high risk of yield losses in defined regions of north, south-west and central Poland and an urgent need to undertake intensive preventative measures.
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Affiliation(s)
- Anna Czubatka-Bieńkowska
- Department of Vegetable and Ornamental Plants Protection, Research Institute of Horticulture, Kościuszki 2, 96-100 Skierniewice, Poland; (A.C.-B.); (A.C.)
| | - Joanna Kaczmarek
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, 60-479 Poznań, Poland;
| | - Katarzyna Marzec-Schmidt
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Gråbrödragatan19, 532 31 Skara, Sweden;
| | - Anna Nieróbca
- Department of Agriculture, Pope John Paul II State School of Higher Education, ul. Sidorska 95/97, 21-500 Biała Podlaska, Poland;
- Institute of Soil Science and Plant Cultivation, State Research Institute, Czartoryskich 8, 24‑100 Puławy, Poland
| | - Agnieszka Czajka
- Department of Vegetable and Ornamental Plants Protection, Research Institute of Horticulture, Kościuszki 2, 96-100 Skierniewice, Poland; (A.C.-B.); (A.C.)
| | - Małgorzata Jędryczka
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, 60-479 Poznań, Poland;
- Correspondence: ; Tel.: +48-61-655-0271
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20
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Biocontrol arsenals of bacterial endophyte: An imminent triumph against clubroot disease. Microbiol Res 2020; 241:126565. [DOI: 10.1016/j.micres.2020.126565] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 07/20/2020] [Accepted: 07/23/2020] [Indexed: 11/18/2022]
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