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Zhou X, Zhong T, Wu M, Li Q, Yu W, Gan L, Xiang X, Zhang Y, Shi Y, Zhou Y, Chen P, Zhang C. Multiomics analysis of a resistant European turnip ECD04 during clubroot infection reveals key hub genes underlying resistance mechanism. FRONTIERS IN PLANT SCIENCE 2024; 15:1396602. [PMID: 38845850 PMCID: PMC11153729 DOI: 10.3389/fpls.2024.1396602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 04/29/2024] [Indexed: 06/09/2024]
Abstract
The clubroot disease has become a worldwide threat for crucifer crop production, due to its soil-borne nature and difficulty to eradicate completely from contaminated field. In this study we used an elite resistant European fodder turnip ECD04 and investigated its resistance mechanism using transcriptome, sRNA-seq, degradome and gene editing. A total of 1751 DEGs were identified from three time points after infection, among which 7 hub genes including XTH23 for cell wall assembly and two CPK28 genes in PTI pathways. On microRNA, we identified 17 DEMs and predicted 15 miRNA-target pairs (DEM-DEG). We validated two pairs (miR395-APS4 and miR160-ARF) by degradome sequencing. We investigated the miR395-APS4 pair by CRISPR-Cas9 mediated gene editing, the result showed that knocking-out APS4 could lead to elevated clubroot resistance in B. napus. In summary, the data acquired on transcriptional response and microRNA as well as target genes provide future direction especially gene candidates for genetic improvement of clubroot resistance on Brassica species.
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Affiliation(s)
- Xueqing Zhou
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ting Zhong
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Meixiu Wu
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qian Li
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Wenlin Yu
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Longcai Gan
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xianyu Xiang
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yunyun Zhang
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Yaru Shi
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yuanwei Zhou
- Rice and Oil Research Institute, Yichang Academy of Agricultural Science, Yichang, China
| | - Peng Chen
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chunyu Zhang
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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Xi DD, Gao L, Miao LM, Ge LA, Zhang DY, Zhang ZH, Li XF, Zhu YY, Shen HB, Zhu HF. Changes in Diversity and Composition of Rhizosphere Bacterial and Fungal Community between Resistant and Susceptible Pakchoi under Plasmodiophora brassicae. Int J Mol Sci 2023; 24:16779. [PMID: 38069101 PMCID: PMC10706474 DOI: 10.3390/ijms242316779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
Plasmodiophora brassicae (P. brassicae) is a soil-born pathogen worldwide and can infect most cruciferous plants, which causes great yield decline and economic losses. It is not well known how microbial diversity and community composition change during P. brassicae infecting plant roots. Here, we employed a resistant and a susceptible pakchoi cultivar with and without inoculation with P. brassicae to analyze bacterial and fungal diversity using 16S rRNA V3-V4 and ITS_V1 regions, respectively. 16S rRNA V3-V4 and ITS_V1 regions were amplified and sequenced separately. Results revealed that both fungal and bacterial diversity increased, and composition was changed in the rhizosphere soil of the susceptible pakchoi compared with the resistant cultivar. In the four groups of R_mock, S_mock, R_10d, and S_10d, the most relatively abundant bacterium and fungus was Proteobacteria, accounting for 61.92%, 58.17%, 48.64%, and 50.00%, respectively, and Ascomycota, accounting for 75.11%, 63.69%, 72.10%, and 90.31%, respectively. A total of 9488 and 11,914 bacteria were observed uniquely in the rhizosphere soil of resistant and susceptible pakchoi, respectively, while only 80 and 103 fungi were observed uniquely in the correlated soil. LefSe analysis showed that 107 and 49 differentially abundant taxa were observed in bacteria and fungi. Overall, we concluded that different pakchoi cultivars affect microbial diversity and community composition, and microorganisms prefer to gather around the rhizosphere of susceptible pakchoi. These findings provide a new insight into plant-microorganism interactions.
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Affiliation(s)
- Dan-Dan Xi
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Zhuanghang Comprehensive Experiment Station, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (D.-D.X.); (L.G.); (L.-M.M.); (D.-Y.Z.); (Z.-H.Z.); (X.-F.L.); (Y.-Y.Z.); (H.-B.S.)
| | - Lu Gao
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Zhuanghang Comprehensive Experiment Station, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (D.-D.X.); (L.G.); (L.-M.M.); (D.-Y.Z.); (Z.-H.Z.); (X.-F.L.); (Y.-Y.Z.); (H.-B.S.)
| | - Li-Ming Miao
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Zhuanghang Comprehensive Experiment Station, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (D.-D.X.); (L.G.); (L.-M.M.); (D.-Y.Z.); (Z.-H.Z.); (X.-F.L.); (Y.-Y.Z.); (H.-B.S.)
| | - Li-Ao Ge
- Jinshan Agricultural Technology Extension Center, Shanghai 201599, China;
| | - Ding-Yu Zhang
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Zhuanghang Comprehensive Experiment Station, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (D.-D.X.); (L.G.); (L.-M.M.); (D.-Y.Z.); (Z.-H.Z.); (X.-F.L.); (Y.-Y.Z.); (H.-B.S.)
| | - Zhao-Hui Zhang
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Zhuanghang Comprehensive Experiment Station, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (D.-D.X.); (L.G.); (L.-M.M.); (D.-Y.Z.); (Z.-H.Z.); (X.-F.L.); (Y.-Y.Z.); (H.-B.S.)
| | - Xiao-Feng Li
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Zhuanghang Comprehensive Experiment Station, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (D.-D.X.); (L.G.); (L.-M.M.); (D.-Y.Z.); (Z.-H.Z.); (X.-F.L.); (Y.-Y.Z.); (H.-B.S.)
| | - Yu-Ying Zhu
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Zhuanghang Comprehensive Experiment Station, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (D.-D.X.); (L.G.); (L.-M.M.); (D.-Y.Z.); (Z.-H.Z.); (X.-F.L.); (Y.-Y.Z.); (H.-B.S.)
| | - Hai-Bin Shen
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Zhuanghang Comprehensive Experiment Station, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (D.-D.X.); (L.G.); (L.-M.M.); (D.-Y.Z.); (Z.-H.Z.); (X.-F.L.); (Y.-Y.Z.); (H.-B.S.)
| | - Hong-Fang Zhu
- Shanghai Key Laboratory of Protected Horticultural Technology, Horticultural Research Institute, Zhuanghang Comprehensive Experiment Station, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (D.-D.X.); (L.G.); (L.-M.M.); (D.-Y.Z.); (Z.-H.Z.); (X.-F.L.); (Y.-Y.Z.); (H.-B.S.)
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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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Pang W, Zhang X, Ma Y, Wang Y, Zhan Z, Piao Z. Fine mapping and candidate gene analysis of CRA3.7 conferring clubroot resistance in Brassica rapa. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:4541-4548. [PMID: 36243892 DOI: 10.1007/s00122-022-04237-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 10/09/2022] [Indexed: 06/16/2023]
Abstract
In this study, we fine-mapped a clubroot resistance gene CRA3.7 in Chinese cabbage and developed its closely linked marker syau-InDel3008 for marker-assisted selection in CR cultivars breeding. Chinese cabbage is an important leafy vegetable rich in many nutrients widely grown in China. Clubroot disease caused by an obligate biotrophic pathogen Plasmodiophora brassicae was rapidly spread and challenged to Chinese cabbage production. A clubroot resistance (CR) gene, CRA3.7, was mapped on chromosome A03 of Brassica rapa. A Chinese cabbage line 'CR510', which harbor homozygous resistance locus CRA3.7 was selected from a BC4F3 family. 'CR510' was crossed with a clubroot susceptible Chinese cabbage inbred line '59-1'. Total 51 recombinant plants were identified from an F2 population including 3000 individuals. These recombinants were selfed and the clubroot resistance of F2/3 families was evaluated. Finally, a clubroot resistance gene CRA3.7 was fine-mapped to an interval of approximately 386 kb between marker syau-InDel3024 and syau-InDel3008. According to the reference genome, total 54 genes including five encoding the TIR-NBS-LRR proteins was annotated in the fine-mapped region. Further, nine candidate's gene expression in parental lines at 7, 14 and 21 days after inoculation of P. brassicae were evaluated. Bra019376, Bra019401, Bra019403 and Bra019410 are highly expressed in 'CR510' than '59-1'. Gene sequence of Bra019410 from 'CR510' was cloned and identified different from CRa. Therefore, Bra019376, Bra019401, Bra019403 and Bra019410 are the most likely candidates for CRA3.7. Our research provides a valuable germplasm resource against P. brassicae Pb3 and CRA3.7 closely linked marker for marker-assisted selection in CR cultivars breeding.
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Affiliation(s)
- Wenxing Pang
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China.
| | - Xue Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yinbo Ma
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Yingjun Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Zongxiang Zhan
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Zhongyun Piao
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China.
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Germplasm Enhancement and Identification of Loci Conferring Resistance against Plasmodiophora brassicae in Broccoli. Genes (Basel) 2022; 13:genes13091600. [PMID: 36140766 PMCID: PMC9498593 DOI: 10.3390/genes13091600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/03/2022] [Accepted: 09/06/2022] [Indexed: 11/30/2022] Open
Abstract
In order to breed broccoli and other Brassica materials to be highly resistant to clubroot disease, 41 Brassicaceae varieties were developed and identified between 2020 and 2021. Seven known clubroot genes were used for screening these materials. In addition, the resistant and susceptible broccoli cultivars were designed for observing their differences in the infection process with Plasmodiophora brassicae. The results showed that 90% of total materials had carried more than two clubroot resistance genes: one material carried two disease resistance genes, four materials carried seven genes for clubroot resistance, two materials carried six genes for clubroot resistance, and in total 32% of these materials carried five genes for clubroot resistance. As a result, several new genotypes of Brassicaceae germplasm were firstly created and obtained based on distant hybridization and identification of loci conferring resistance against Plasmodiophora brassicae in this study. We found and revealed that similar infection models of Plasmodiophora brassicae occurred in susceptible and resistant cultivars of broccoli, but differences in infection efficiency of Plasmodiophora brassicae also existed in both materials. For resistant broccoli plants, a small number of conidia formed in the root hair, and only a few spores could enter the cortex without forming sporangia while sporangia could form in susceptible plants. Our study could provide critical Brassica materials for breeding resistant varieties and new insight into understanding the mechanism of plant resistance.
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Multi-Omics Approaches to Improve Clubroot Resistance in Brassica with a Special Focus on Brassica oleracea L. Int J Mol Sci 2022; 23:ijms23169280. [PMID: 36012543 PMCID: PMC9409056 DOI: 10.3390/ijms23169280] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/04/2022] [Accepted: 08/13/2022] [Indexed: 11/17/2022] Open
Abstract
Brassica oleracea is an agronomically important species of the Brassicaceae family, including several nutrient-rich vegetables grown and consumed across the continents. But its sustainability is heavily constrained by a range of destructive pathogens, among which, clubroot disease, caused by a biotrophic protist Plasmodiophora brassicae, has caused significant yield and economic losses worldwide, thereby threatening global food security. To counter the pathogen attack, it demands a better understanding of the complex phenomenon of Brassica-P. brassicae pathosystem at the physiological, biochemical, molecular, and cellular levels. In recent years, multiple omics technologies with high-throughput techniques have emerged as successful in elucidating the responses to biotic and abiotic stresses. In Brassica spp., omics technologies such as genomics, transcriptomics, ncRNAomics, proteomics, and metabolomics are well documented, allowing us to gain insights into the dynamic changes that transpired during host-pathogen interactions at a deeper level. So, it is critical that we must review the recent advances in omics approaches and discuss how the current knowledge in multi-omics technologies has been able to breed high-quality clubroot-resistant B. oleracea. This review highlights the recent advances made in utilizing various omics approaches to understand the host resistance mechanisms adopted by Brassica crops in response to the P. brassicae attack. Finally, we have discussed the bottlenecks and the way forward to overcome the persisting knowledge gaps in delivering solutions to breed clubroot-resistant Brassica crops in a holistic, targeted, and precise way.
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