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Yu Z, Fredua-Agyeman R, Strelkov SE, Hwang SF. RNA-Seq Bulked Segregant Analysis of an Exotic B. napus ssp. napobrassica (Rutabaga) F 2 Population Reveals Novel QTLs for Breeding Clubroot-Resistant Canola. Int J Mol Sci 2024; 25:4596. [PMID: 38731814 PMCID: PMC11083300 DOI: 10.3390/ijms25094596] [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: 03/21/2024] [Revised: 04/16/2024] [Accepted: 04/19/2024] [Indexed: 05/13/2024] Open
Abstract
In this study, a rutabaga (Brassica napus ssp. napobrassica) donor parent FGRA106, which exhibited broad-spectrum resistance to 17 isolates representing 16 pathotypes of Plasmodiophora brassicae, was used in genetic crosses with the susceptible spring-type canola (B. napus ssp. napus) accession FG769. The F2 plants derived from a clubroot-resistant F1 plant were screened against three P. brassicae isolates representing pathotypes 3A, 3D, and 3H. Chi-square (χ2) goodness-of-fit tests indicated that the F2 plants inherited two major clubroot resistance genes from the CR donor FGRA106. The total RNA from plants resistant (R) and susceptible (S) to each pathotype were pooled and subjected to bulked segregant RNA-sequencing (BSR-Seq). The analysis of gene expression profiles identified 431, 67, and 98 differentially expressed genes (DEGs) between the R and S bulks. The variant calling method indicated a total of 12 (7 major + 5 minor) QTLs across seven chromosomes. The seven major QTLs included: BnaA5P3A.CRX1.1, BnaC1P3H.CRX1.2, and BnaC7P3A.CRX1.1 on chromosomes A05, C01, and C07, respectively; and BnaA8P3D.CRX1.1, BnaA8P3D.RCr91.2/BnaA8P3H.RCr91.2, BnaA8P3H.Crr11.3/BnaA8P3D.Crr11.3, and BnaA8P3D.qBrCR381.4 on chromosome A08. A total of 16 of the DEGs were located in the major QTL regions, 13 of which were on chromosome C07. The molecular data suggested that clubroot resistance in FGRA106 may be controlled by major and minor genes on both the A and C genomes, which are deployed in different combinations to confer resistance to the different isolates. This study provides valuable germplasm for the breeding of clubroot-resistant B. napus cultivars in Western Canada.
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Affiliation(s)
| | - Rudolph Fredua-Agyeman
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada; (Z.Y.); (S.-F.H.)
| | - Stephen E. Strelkov
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada; (Z.Y.); (S.-F.H.)
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Hu H, Zhang Y, Yu F. A CRISPR/Cas9-based vector system enables the fast breeding of selection-marker-free canola with Rcr1-rendered clubroot resistance. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1347-1363. [PMID: 37991105 PMCID: PMC10901203 DOI: 10.1093/jxb/erad471] [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: 04/29/2023] [Accepted: 11/20/2023] [Indexed: 11/23/2023]
Abstract
Breeding for disease resistance in major crops is of crucial importance for global food security and sustainability. However, common biotechnologies such as traditional transgenesis or genome editing do not provide an ideal solution, whereas transgenic crops free of selection markers such as cisgenic/intragenic crops might be suitable. In this study, after cloning and functional verification of the Rcr1 gene for resistance to clubroot (Plasmodiophora brassicae), we confirmed that the genes Rcr1, Rcr2, Rcr4, and CRa from Brassica rapa crops and the resistance gene from B. napus oilseed rape cv. 'Mendel' on chromosome A03 were identical in their coding regions. We also determined that Rcr1 has a wide distribution in Brassica breeding materials and renders potent resistance against multiple representative clubroot strains in Canada. We then modified a CRISPR/Cas9-based cisgenic vector system and found that it enabled the fast breeding of selection-marker-free transgenic crops with add-on traits, with selection-marker-free canola (B. napus) germplasms with Rcr1-rendered stable resistance to clubroot disease being successfully developed within 2 years. In the B. napus background, the intragenic vector system was able to remove unwanted residue sequences from the final product with high editing efficiency, and off-target mutations were not detected. Our study demonstrates the potential of applying this breeding strategy to other crops that can be transformed by Agrobacterium. Following the streamlined working procedure, intragenic germplasms can be developed within two generations, which could significantly reduce the breeding time and labor compared to traditional introgression whilst still achieving comparable or even better breeding results.
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Affiliation(s)
- Hao Hu
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Yan Zhang
- 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
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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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Jayasinghege CPA, Ozga JA, Manolii VP, Hwang SF, Strelkov SE. Impact of Susceptibility on Plant Hormonal Composition during Clubroot Disease Development in Canola ( Brassica napus). PLANTS (BASEL, SWITZERLAND) 2023; 12:2899. [PMID: 37631111 PMCID: PMC10459861 DOI: 10.3390/plants12162899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/02/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023]
Abstract
Clubroot, caused by Plasmodiophora brassicae, is a soilborne disease of crucifers associated with the formation of large root galls. This root enlargement suggests modulation of plant hormonal networks by the pathogen, stimulating cell division and elongation and influencing host defense. We studied physiological changes in two Brassica napus cultivars, including plant hormone profiles-salicylic acid (SA), jasmonic acid (JA), abscisic acid (ABA), the auxin indole-3-acetic acid (IAA), and the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC)-along with their selected derivatives following inoculation with virulent and avirulent P. brassicae pathotypes. In susceptible plants, water uptake declined from the initial appearance of root galls by 21 days after inoculation, but did not have a significant effect on photosynthetic rate, stomatal conductance, or leaf chlorophyll levels. Nonetheless, a strong increase in ABA levels indicated that hormonal mechanisms were triggered to cope with water stress due to the declining water uptake. The free SA level in the roots increased strongly in resistant interactions, compared with a relatively minor increase during susceptible interactions. The ratio of conjugated SA to free SA was higher in susceptible interactions, indicating that resistant interactions are linked to the plant's ability to maintain higher levels of bioactive free SA. In contrast, JA and its biologically active form JA-Ile declined up to 7-fold in susceptible interactions, while they were maintained during resistant interactions. The ACC level increased in the roots of inoculated plants by 21 days, irrespective of clubroot susceptibility, indicating a role of ethylene in response to pathogen interactions that is independent of disease severity. IAA levels at early and later infection stages were lower only in susceptible plants, suggesting a modulation of auxin homeostasis by the pathogen relative to the host defense system.
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Affiliation(s)
| | - Jocelyn A. Ozga
- Plant BioSystems, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada; (C.P.A.J.); (V.P.M.); (S.-F.H.)
| | | | | | - Stephen E. Strelkov
- Plant BioSystems, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada; (C.P.A.J.); (V.P.M.); (S.-F.H.)
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Improvement of Resistance to Clubroot Disease in the Ogura CMS Restorer Line R2163 of Brassica napus. PLANTS 2022; 11:plants11182413. [PMID: 36145814 PMCID: PMC9504965 DOI: 10.3390/plants11182413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/30/2022] [Accepted: 09/13/2022] [Indexed: 11/30/2022]
Abstract
Oilseed rape (Brassica napus) has significant heterosis and Ogura CMS is a major way to use it. Ogura CMS has the advantages of complete and stable male sterility and easy-to-breed maintainers. Therefore, to breed better restorers has become an important goal for this system. Incidentally, clubroot is a soil-borne disease that is difficult to control by fungicidal chemicals, and it has been the main disease of oilseed rape in recent years in China, severely restricting the development of the oilseed rape industry. At present, the most effective method for controlling clubroot disease is to cultivate resistant varieties. One Ogura CMS restorer line (R2163) has shown much better combining ability, but lacks the clubroot disease resistance. This study was carried out to improve R2163 through marker-assisted backcross breeding (MABB). The resistant locus PbBa8.1 was introduced into the restorer R2163, and we then selected R2163R with clubroot disease resistance. Using the new restorer R2163R as the male parent and the sterile lines 116A and Z11A as the female parent, the improved, new resistant hybrids Kenyouza 741R and Huayouza 706R performed well, providing strong resistance and good agronomic traits. This work advances the utilization of heterosis and breeding for clubroot disease resistance in B. napus.
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Zhu M, Yang L, Zhang Y, Zhuang M, Ji J, Hou X, Li Z, Han F, Fang Z, Lv H, Wang Y. Introgression of clubroot resistant gene into Brassica oleracea L. from Brassica rapa based on homoeologous exchange. HORTICULTURE RESEARCH 2022; 9:uhac195. [PMID: 37180031 PMCID: PMC10167419 DOI: 10.1093/hr/uhac195] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 08/26/2022] [Indexed: 05/15/2023]
Abstract
Clubroot is a soil-borne disease in cabbage (Brassica oleracea L. var. capitata L.) caused by Plasmodiophora brassicae, which poses a great threat to cabbage production. However, clubroot resistance (CR) genes in Brassica rapa could be introduced into the cabbage via breeding to make it clubroot resistant. In this study, CR genes from B. rapa were introduced into the cabbage genome and the mechanism of gene introgression was explored. Two methods were used to create CR materials: (i) The fertility of CR Ogura CMS cabbage germplasms containing CRa was restored by using an Ogura CMS restorer. After cytoplasmic replacement and microspore culture, CRa-positive microspore individuals were obtained. (ii) Distant hybridization was performed between cabbage and B. rapa, which contained three CR genes (CRa, CRb, and Pb8.1). Finally, BC2 individuals containing all three CR genes were obtained. Inoculation results showed that both CRa-positive microspore individuals and BC2 individuals containing three CR genes were resistant to race 4 of P. brassicae. Sequencing results from CRa-positive microspore individuals with specific molecular markers and genome-wide association study (GWAS) showed penetration at the homologous position of the cabbage genome by a 3.42 Mb CRa containing a fragment from B. rapa; indicating homoeologous exchange (HE) as the theoretical basis for the introgression of CR resistance. The successful introduction of CR into the cabbage genome in the present study can provide useful clues for creating introgression lines within other species of interest.
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Affiliation(s)
- Mingzhao Zhu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Institute of Vegetable Science, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Limei Yang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yangyong Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Mu Zhuang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jialei Ji
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xilin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Zhansheng Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Fengqing Han
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhiyuan Fang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Honghao Lv
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yong Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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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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Yang Z, Jiang Y, Gong J, Li Q, Dun B, Liu D, Yin F, Yuan L, Zhou X, Wang H, Wang J, Zhan Z, Shah N, Nwafor CC, Zhou Y, Chen P, Zhu L, Li S, Wang B, Xiang J, Zhou Y, Li Z, Piao Z, Yang Q, Zhang C. R gene triplication confers European fodder turnip with improved clubroot resistance. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1502-1517. [PMID: 35445530 PMCID: PMC9342621 DOI: 10.1111/pbi.13827] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 03/30/2022] [Accepted: 04/10/2022] [Indexed: 05/08/2023]
Abstract
Clubroot is one of the most important diseases for many important cruciferous vegetables and oilseed crops worldwide. Different clubroot resistance (CR) loci have been identified from only limited species in Brassica, making it difficult to compare and utilize these loci. European fodder turnip ECD04 is considered one of the most valuable resources for CR breeding. To explore the genetic and evolutionary basis of CR in ECD04, we sequenced the genome of ECD04 using de novo assembly and identified 978 candidate R genes. Subsequently, the 28 published CR loci were physically mapped to 15 loci in the ECD04 genome, including 62 candidate CR genes. Among them, two CR genes, CRA3.7.1 and CRA8.2.4, were functionally validated. Phylogenetic analysis revealed that CRA3.7.1 and CRA8.2.4 originated from a common ancestor before the whole-genome triplication (WGT) event. In clubroot susceptible Brassica species, CR-gene homologues were affected by transposable element (TE) insertion, resulting in the loss of CR function. It can be concluded that the current functional CR genes in Brassica rapa and non-functional CR genes in other Brassica species were derived from a common ancestral gene before WGT. Finally, a hypothesis for CR gene evolution is proposed for further discussion.
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Affiliation(s)
- Zhiquan Yang
- Hubei Key Laboratory of Agricultural BioinformaticsCollege of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Yingfen Jiang
- Institute of Crop ScienceAnhui Academy of Agricultural ScienceHefeiChina
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jianfang Gong
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Qian Li
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Bicheng Dun
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Yangtze River Rare Plant Research InstituteChina Three Gorges CorporationYichangChina
| | - Dongxu Liu
- Hubei Key Laboratory of Agricultural BioinformaticsCollege of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Feifan Yin
- Hubei Key Laboratory of Agricultural BioinformaticsCollege of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Lei Yuan
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Xueqing Zhou
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Huiying Wang
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jing Wang
- Hubei Key Laboratory of Agricultural BioinformaticsCollege of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Zongxiang Zhan
- College of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Nadil Shah
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Chinedu Charles Nwafor
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Yuanwei Zhou
- Yichang Academy of Agricultural ScienceYichangChina
| | - Peng Chen
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Li Zhu
- Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains and College of Biology and Agriculture ResourceHuanggang Normal UniversityHuanggangChina
| | - Shisheng Li
- Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains and College of Biology and Agriculture ResourceHuanggang Normal UniversityHuanggangChina
| | - Bingrui Wang
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Jun Xiang
- Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains and College of Biology and Agriculture ResourceHuanggang Normal UniversityHuanggangChina
| | - Yongming Zhou
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Zaiyun Li
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Zhongyun Piao
- College of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Qingyong Yang
- Hubei Key Laboratory of Agricultural BioinformaticsCollege of InformaticsHuazhong Agricultural UniversityWuhanChina
| | - Chunyu Zhang
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
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Gan C, Yan C, Pang W, Cui L, Fu P, Yu X, Qiu Z, Zhu M, Piao Z, Deng X. Identification of Novel Locus RsCr6 Related to Clubroot Resistance in Radish ( Raphanus sativus L.). FRONTIERS IN PLANT SCIENCE 2022; 13:866211. [PMID: 35665145 PMCID: PMC9161170 DOI: 10.3389/fpls.2022.866211] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/15/2022] [Indexed: 06/15/2023]
Abstract
Clubroot is a devastating disease that causes substantial yield loss worldwide. However, the inheritance and molecular mechanisms of clubroot resistance during pathogen infection in radish remain largely unclear. In this study, we investigated the inheritance of clubroot resistance in the F2 population derived from crossing clubroot-resistant (CR) and clubroot-susceptible inbred lines "GLX" and "XNQ," respectively. Genetic analysis revealed that a single dominant gene controlled the clubroot resistance of "GLX" with a Mendelian ratio of resistance and susceptibility of nearly 3:1. Bulked segregant analysis combined with whole-genome resequencing (BSA-seq) was performed to detect the target region of RsCr6 on chromosome Rs8. Linkage analysis revealed that the RsCr6 locus was located between two markers, HB321 and HB331, with an interval of approximately 92 kb. Based on the outcomes of transcriptome analysis, in the RsCr6 locus, the R120263140 and R120263070 genes with a possible relation to clubroot resistance were considered candidate genes. In addition, three core breeding materials containing the two reported quantitative trait loci (QTLs) and our novel locus RsCr6 targeting clubroot resistance were obtained using marker-assisted selection (MAS) technology. This study reveals a novel locus responsible for clubroot resistance in radishes. Further analysis of new genes may reveal the molecular mechanisms underlying the clubroot resistance of plants and provide a theoretical basis for radish resistance breeding.
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Affiliation(s)
- Caixia Gan
- Hubei Key Laboratory of Vegetable Germplasm Enhancement and Genetic Improvement, Institute of Economic Crops, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Chenghuan Yan
- Hubei Key Laboratory of Vegetable Germplasm Enhancement and Genetic Improvement, Institute of Economic Crops, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Wenxing Pang
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Lei Cui
- Hubei Key Laboratory of Vegetable Germplasm Enhancement and Genetic Improvement, Institute of Economic Crops, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Pengyu Fu
- College of Chemistry and Life Science, Chifeng University, Chifeng, China
| | - Xiaoqing Yu
- Hubei Key Laboratory of Vegetable Germplasm Enhancement and Genetic Improvement, Institute of Economic Crops, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Zhengming Qiu
- Hubei Key Laboratory of Vegetable Germplasm Enhancement and Genetic Improvement, Institute of Economic Crops, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Meiyu Zhu
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Zhongyun Piao
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Xiaohui Deng
- Hubei Key Laboratory of Vegetable Germplasm Enhancement and Genetic Improvement, Institute of Economic Crops, Hubei Academy of Agricultural Sciences, Wuhan, China
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Yu F, Zhang Y, Wang J, Chen Q, Karim MM, Gossen BD, Peng G. Identification of Two Major QTLs in Brassica napus Lines With Introgressed Clubroot Resistance From Turnip Cultivar ECD01. FRONTIERS IN PLANT SCIENCE 2022; 12:785989. [PMID: 35095960 PMCID: PMC8790046 DOI: 10.3389/fpls.2021.785989] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/02/2021] [Indexed: 05/31/2023]
Abstract
Plasmodiophora brassicae causes clubroot disease in brassica crops worldwide. Brassica rapa, a progenitor of Brassica napus (canola), possesses important sources for resistance to clubroot. A doubled haploid (DH) population consisting of 84 DH lines were developed from a Backcross2 (BC2) plant through an interspecific cross of B. rapa turnip cv. ECD01 (resistant, R) with canola line DH16516 (susceptible, S) and then backcrossed with DH16516 as the recurrent parent. The DH lines and their parental lines were tested for resistance to four major pathotypes (3A, 3D, 3H, and 5X) of P. brassicae identified from canola. The R:S segregation ratio for pathotype 3A was 1:3, and 3:1 for pathotypes 3D, 3H, and 5X. From genotyping by sequencing (GBS), a total of 355.3 M short reads were obtained from the 84 DH lines, ranging from 0.81 to 11.67 M sequences per line. The short reads were aligned into the A-genome of B. napus "Darmor-bzh" version 4.1 with a total of 260 non-redundant single-nucleotide polymorphism (SNP) sites. Two quantitative trait loci (QTLs), Rcr10 ECD01 and Rcr9 ECD01 , were detected for the pathotypes in chromosomes A03 and A08, respectively. Rcr10 ECD01 and Rcr9 ECD01 were responsible for resistance to 3A, 3D, and 3H, while only one QTL, Rcr9 ECD01 , was responsible for resistance to pathotype 5X. The logarithm of the odds (LOD) values, phenotypic variation explained (PVE), additive (Add) values, and confidence interval (CI) from the estimated QTL position varied with QTL, with a range of 5.2-12.2 for LOD, 16.2-43.3% for PVE, 14.3-25.4 for Add, and 1.5-12.0 cM for CI. The presence of the QTLs on the chromosomes was confirmed through the identification of the percentage of polymorphic variants using bulked-segregant analysis. There was one gene encoding a disease resistance protein and 24 genes encoding proteins with function related to plant defense response in the Rcr10 ECD01 target region. In the Rcr9 ECD01 region, two genes encoded disease resistance proteins and 10 genes encoded with defense-related function. The target regions for Rcr10 ECD01 and Rcr9 ECD01 in B. napus were homologous to the 11.0-16.0 Mb interval of chromosome A03 and the 12.0-14.5 Mb interval of A08 in B. rapa "Chiifu" reference genome, respectively.
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11
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Ce F, Mei J, He H, Zhao Y, Hu W, Yu F, Li Q, Ren X, Si J, Song H, Qian W. Identification of Candidate Genes for Clubroot-Resistance in Brassica oleracea Using Quantitative Trait Loci-Sequencing. FRONTIERS IN PLANT SCIENCE 2021; 12:703520. [PMID: 34868102 PMCID: PMC8635040 DOI: 10.3389/fpls.2021.703520] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 10/19/2021] [Indexed: 05/27/2023]
Abstract
Clubroot caused by Plasmodiophora brassicae is a devastating disease of cabbage (Brassica oleracea). To identify quantitative trait loci (QTLs) for clubroot resistance (CR) in B. oleracea, genomic resequencing was carried out in two sets of extreme pools, group I and group II, which were constructed separately from 110 and 74 F2 cloned lines derived from the cross between clubroot-resistant (R) cabbage "GZ87" (against race 4) and susceptible (S) cabbage "263." Based on the QTL-sequencing (QTL-Seq) analysis of group I and group II, three QTLs (i.e., qCRc7-2, qCRc7-3, and qCRc7-4) were determined on the C07 chromosome. RNA-Seq and qRT-PCR were conducted in the extreme pools of group II before and after inoculation, and two potential candidate genes (i.e., Bol037115 and Bol042270), which exhibiting upregulation after inoculation in the R pool but downregulation in the S pool, were identified from the three QTLs on C07. A functional marker "SWU-OA" was developed from qCRc7-4 on C07, exhibiting ∼95% accuracy in identifying CR in 56 F2 lines. Our study will provide valuable information on resistance genes against P. brassicae and may accelerate the breeding process of B. oleracea with CR.
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Affiliation(s)
- Fuquan Ce
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Jiaqin Mei
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing, China
| | - Haiyan He
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing, China
- Chongqing Key Laboratory of Olericulture, Chongqing, China
| | - Yu Zhao
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing, China
| | - Wenhui Hu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing, China
- Chongqing Key Laboratory of Olericulture, Chongqing, China
| | - Fengqun Yu
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Center, Saskatoon, SK, Canada
| | - Qinfei Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing, China
- Chongqing Key Laboratory of Olericulture, Chongqing, China
| | - Xuesong Ren
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing, China
- Chongqing Key Laboratory of Olericulture, Chongqing, China
| | - Jun Si
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing, China
- Chongqing Key Laboratory of Olericulture, Chongqing, China
| | - Hongyuan Song
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing, China
- Chongqing Key Laboratory of Olericulture, Chongqing, China
| | - Wei Qian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing, China
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12
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Park SG, Noh E, Choi S, Choi B, Shin IG, Yoo SI, Lee DJ, Ji S, Kim HS, Hwang YJ, Kim JS, Batley J, Lim YP, Edwards D, Hong CP. Draft Genome Assembly and Transcriptome Dataset for European Turnip ( Brassica rapa L. ssp. rapifera), ECD4 Carrying Clubroot Resistance. Front Genet 2021; 12:651298. [PMID: 34276765 PMCID: PMC8285094 DOI: 10.3389/fgene.2021.651298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 06/01/2021] [Indexed: 12/15/2022] Open
Affiliation(s)
| | - Eonji Noh
- Theragen Bio Co., Ltd., Suwon, South Korea
| | - SuRyun Choi
- Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon, South Korea
| | - Boram Choi
- Theragen Bio Co., Ltd., Suwon, South Korea
| | | | | | | | - Sumin Ji
- Theragen Bio Co., Ltd., Suwon, South Korea
| | | | - Yoon-Jung Hwang
- Department of Chemistry Life Science, Sahmyook University, Seoul, South Korea
| | - Jung Sun Kim
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Yong Pyo Lim
- Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon, South Korea
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
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Li Q, Xu B, Du Y, Peng A, Ren X, Si J, Song H. Development of Ogura CMS restorers in Brassica oleracea subspecies via direct Rfo B gene transformation. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1123-1132. [PMID: 33404672 DOI: 10.1007/s00122-020-03757-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 12/19/2020] [Indexed: 06/12/2023]
Abstract
The Ogura CMS RfoB restorer developing via RfoB gene transformation was utilized to produce specific morphological Ogura CMS restorers and clubroot resistance lines in Brassica oleracea subspecies. Brassica oleracea vegetables including cabbage, cauliflower, kohlrabi, Brussels sprouts and Chinese kale are morphologically very different despite being members of the same species. The Ogura cytoplasmic male sterility (CMS) system is the most stable strategy for the hybrid breeding of these species. However, this limits the utilization of some excellent genes due to the lack of fertile restorer genes in the system. Herein, to efficaciously use Ogura CMS, the Ogura CMS RfoB restorer was produced by transforming the modified RfoB restorer gene into the Ogura CMS line 'CMS2016' of B. oleracea var. capitata. This gene was shown to recover fertility of natural Ogura CMS lines in B. oleracea subspecies and create transient Ogura CMS RfoB restorers such as the clubroot resistance Ogura CMS RfoB restorer. Interestingly, clubroot resistant individuals without transgenic elements were screened in the progenies of hybrids between B. oleracea inbred lines and the clubroot resistance Ogura CMS RfoB restorer. In addition, 18 different morphological Ogura CMS restorers were developed to specifically recover fertile of Ogura CMS cultivars in B. oleracea subspecies.
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Affiliation(s)
- Qinfei Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing, China
- Chongqing Key Laboratory of Olericulture, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Bingbing Xu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing, China
- Chongqing Key Laboratory of Olericulture, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Yangmei Du
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing, China
- Chongqing Key Laboratory of Olericulture, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Ao Peng
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing, China
- Chongqing Key Laboratory of Olericulture, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Xuesong Ren
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing, China
- Chongqing Key Laboratory of Olericulture, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Jun Si
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing, China
- Chongqing Key Laboratory of Olericulture, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Hongyuan Song
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China.
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing, China.
- Chongqing Key Laboratory of Olericulture, Chongqing, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing, China.
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14
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Hasan J, Megha S, Rahman H. Clubroot in Brassica: recent advances in genomics, breeding, and disease management. Genome 2021; 64:735-760. [PMID: 33651640 DOI: 10.1139/gen-2020-0089] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Clubroot disease, caused by Plasmodiophora brassicae, affects Brassica oilseed and vegetable production worldwide. This review is focused on various aspects of clubroot disease and its management, including understanding the pathogen and resistance in the host plants. Advances in genetics, molecular biology techniques, and omics research have helped to identify several major loci, QTL, and genes from the Brassica genomes involved in the control of clubroot resistance. Transcriptomic studies have helped to extend our understanding of the mechanism of infection by the pathogen and the molecular basis of resistance/susceptibility in the host plants. A comprehensive understanding of the clubroot disease and host resistance would allow developing a better strategy by integrating the genetic resistance with cultural practices to manage this disease from a long-term perspective.
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Affiliation(s)
- Jakir Hasan
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture/Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada.,Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture/Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Swati Megha
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture/Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada.,Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture/Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Habibur Rahman
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture/Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada.,Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture/Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
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15
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Ma Y, Chhapekar SS, Lu L, Oh S, Singh S, Kim CS, Kim S, Choi GJ, Lim YP, Choi SR. Genome-wide identification and characterization of NBS-encoding genes in Raphanus sativus L. and their roles related to Fusarium oxysporum resistance. BMC PLANT BIOLOGY 2021; 21:47. [PMID: 33461498 PMCID: PMC7814608 DOI: 10.1186/s12870-020-02803-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 12/16/2020] [Indexed: 05/21/2023]
Abstract
BACKGROUND The nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes are important for plant development and disease resistance. Although genome-wide studies of NBS-encoding genes have been performed in several species, the evolution, structure, expression, and function of these genes remain unknown in radish (Raphanus sativus L.). A recently released draft R. sativus L. reference genome has facilitated the genome-wide identification and characterization of NBS-encoding genes in radish. RESULTS A total of 225 NBS-encoding genes were identified in the radish genome based on the essential NB-ARC domain through HMM search and Pfam database, with 202 mapped onto nine chromosomes and the remaining 23 localized on different scaffolds. According to a gene structure analysis, we identified 99 NBS-LRR-type genes and 126 partial NBS-encoding genes. Additionally, 80 and 19 genes respectively encoded an N-terminal Toll/interleukin-like domain and a coiled-coil domain. Furthermore, 72% of the 202 NBS-encoding genes were grouped in 48 clusters distributed in 24 crucifer blocks on chromosomes. The U block on chromosomes R02, R04, and R08 had the most NBS-encoding genes (48), followed by the R (24), D (23), E (23), and F (17) blocks. These clusters were mostly homogeneous, containing NBS-encoding genes derived from a recent common ancestor. Tandem (15 events) and segmental (20 events) duplications were revealed in the NBS family. Comparative evolutionary analyses of orthologous genes among Arabidopsis thaliana, Brassica rapa, and Brassica oleracea reflected the importance of the NBS-LRR gene family during evolution. Moreover, examinations of cis-elements identified 70 major elements involved in responses to methyl jasmonate, abscisic acid, auxin, and salicylic acid. According to RNA-seq expression analyses, 75 NBS-encoding genes contributed to the resistance of radish to Fusarium wilt. A quantitative real-time PCR analysis revealed that RsTNL03 (Rs093020) and RsTNL09 (Rs042580) expression positively regulates radish resistance to Fusarium oxysporum, in contrast to the negative regulatory role for RsTNL06 (Rs053740). CONCLUSIONS The NBS-encoding gene structures, tandem and segmental duplications, synteny, and expression profiles in radish were elucidated for the first time and compared with those of other Brassicaceae family members (A. thaliana, B. oleracea, and B. rapa) to clarify the evolution of the NBS gene family. These results may be useful for functionally characterizing NBS-encoding genes in radish.
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Affiliation(s)
- Yinbo Ma
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon, 34134 Republic of Korea
| | - Sushil Satish Chhapekar
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon, 34134 Republic of Korea
| | - Lu Lu
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon, 34134 Republic of Korea
| | - Sangheon Oh
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon, 34134 Republic of Korea
| | - Sonam Singh
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon, 34134 Republic of Korea
| | - Chang Soo Kim
- Department of Crop Science, College of Agricultural and Life Sciences, Chungnam National University, Daejeon, 34134 Republic of Korea
| | - Seungho Kim
- Neo Seed Co., 256-45 Jingeonjung-gil, Gongdo-eup, Anseong, Gyeonggi Province 17565 Republic of Korea
| | - Gyung Ja Choi
- Center for Eco-friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon, 34114 Republic of Korea
| | - Yong Pyo Lim
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon, 34134 Republic of Korea
| | - Su Ryun Choi
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon, 34134 Republic of Korea
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Zhou Q, Galindo-González L, Manolii V, Hwang SF, Strelkov SE. Comparative Transcriptome Analysis of Rutabaga ( Brassica napus) Cultivars Indicates Activation of Salicylic Acid and Ethylene-Mediated Defenses in Response to Plasmodiophora brassicae. Int J Mol Sci 2020; 21:ijms21218381. [PMID: 33171675 PMCID: PMC7664628 DOI: 10.3390/ijms21218381] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/01/2020] [Accepted: 11/04/2020] [Indexed: 01/04/2023] Open
Abstract
Clubroot, caused by Plasmodiophora brassicae Woronin, is an important soilborne disease of Brassica napus L. and other crucifers. To improve understanding of the mechanisms of resistance and pathogenesis in the clubroot pathosystem, the rutabaga (B. napus subsp. rapifera Metzg) cultivars ‘Wilhelmsburger’ (resistant) and ‘Laurentian’ (susceptible) were inoculated with P. brassicae pathotype 3A and their transcriptomes were analyzed at 7, 14, and 21 days after inoculation (dai) by RNA sequencing (RNA-seq). Thousands of transcripts with significant changes in expression were identified in each host at each time-point in inoculated vs. non-inoculated plants. Molecular responses at 7 and 14 dai supported clear differences in the clubroot response mechanisms of the two genotypes. Both the resistant and the susceptible cultivars activated receptor-like protein (RLP) genes, resistance (R) genes, and genes involved in salicylic acid (SA) signaling as clubroot defense mechanisms. In addition, genes related to calcium signaling and genes encoding leucine-rich repeat (LRR) receptor kinases, the respiratory burst oxidase homolog (RBOH) protein, and transcription factors such as WRKYs, ethylene responsive factors, and basic leucine zippers (bZIPs), appeared to be upregulated in ‘Wilhelmsburger’ to restrict P. brassicae development. Some of these genes are essential components of molecular defenses, including ethylene (ET) signaling and the oxidative burst. Our study highlights the importance of activation of genes associated with SA- and ET-mediated responses in the resistant cultivar. A set of candidate genes showing contrasting patterns of expression between the resistant and susceptible cultivars was identified and includes potential targets for further study and validation through approaches such as gene editing.
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17
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Neik TX, Amas J, Barbetti M, Edwards D, Batley J. Understanding Host-Pathogen Interactions in Brassica napus in the Omics Era. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1336. [PMID: 33050509 PMCID: PMC7599536 DOI: 10.3390/plants9101336] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/02/2020] [Accepted: 10/06/2020] [Indexed: 12/12/2022]
Abstract
Brassica napus (canola/oilseed rape/rapeseed) is an economically important crop, mostly found in temperate and sub-tropical regions, that is cultivated widely for its edible oil. Major diseases of Brassica crops such as Blackleg, Clubroot, Sclerotinia Stem Rot, Downy Mildew, Alternaria Leaf Spot and White Rust have caused significant yield and economic losses in rapeseed-producing countries worldwide, exacerbated by global climate change, and, if not remedied effectively, will threaten global food security. To gain further insights into the host-pathogen interactions in relation to Brassica diseases, it is critical that we review current knowledge in this area and discuss how omics technologies can offer promising results and help to push boundaries in our understanding of the resistance mechanisms. Omics technologies, such as genomics, proteomics, transcriptomics and metabolomics approaches, allow us to understand the host and pathogen, as well as the interaction between the two species at a deeper level. With these integrated data in multi-omics and systems biology, we are able to breed high-quality disease-resistant Brassica crops in a more holistic, targeted and accurate way.
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Affiliation(s)
- Ting Xiang Neik
- Sunway College Kuala Lumpur, Bandar Sunway 47500, Selangor, Malaysia;
| | - Junrey Amas
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth 6009, Australia; (J.A.); (D.E.)
| | - Martin Barbetti
- School of Agriculture and Environment and Institute of Agriculture, The University of Western Australia, Perth 6009, Australia;
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth 6009, Australia; (J.A.); (D.E.)
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth 6009, Australia; (J.A.); (D.E.)
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18
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Ton LB, Neik TX, Batley J. The Use of Genetic and Gene Technologies in Shaping Modern Rapeseed Cultivars ( Brassica napus L.). Genes (Basel) 2020; 11:E1161. [PMID: 33008008 PMCID: PMC7600269 DOI: 10.3390/genes11101161] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/27/2020] [Accepted: 09/27/2020] [Indexed: 12/20/2022] Open
Abstract
Since their domestication, Brassica oilseed species have undergone progressive transformation allied with the development of breeding and molecular technologies. The canola (Brassica napus) crop has rapidly expanded globally in the last 30 years with intensive innovations in canola varieties, providing for a wider range of markets apart from the food industry. The breeding efforts of B. napus, the main source of canola oil and canola meal, have been mainly focused on improving seed yield, oil quality, and meal quality along with disease resistance, abiotic stress tolerance, and herbicide resistance. The revolution in genetics and gene technologies, including genetic mapping, molecular markers, genomic tools, and gene technology, especially gene editing tools, has allowed an understanding of the complex genetic makeup and gene functions in the major bioprocesses of the Brassicales, especially Brassica oil crops. Here, we provide an overview on the contributions of these technologies in improving the major traits of B. napus and discuss their potential use to accomplish new improvement targets.
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Affiliation(s)
- Linh Bao Ton
- School of Biological Science, The University of Western Australia, Perth, WA 6009, Australia;
| | - Ting Xiang Neik
- Sunway College Kuala Lumpur, No. 2, Jalan Universiti, Bandar Sunway, Selangor 47500, Malaysia;
| | - Jacqueline Batley
- School of Biological Science, The University of Western Australia, Perth, WA 6009, Australia;
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19
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Karim MM, Dakouri A, Zhang Y, Chen Q, Peng G, Strelkov SE, Gossen BD, Yu F. Two Clubroot-Resistance Genes, Rcr3 and Rcr9wa, Mapped in Brassica rapa Using Bulk Segregant RNA Sequencing. Int J Mol Sci 2020; 21:ijms21145033. [PMID: 32708772 PMCID: PMC7404267 DOI: 10.3390/ijms21145033] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/13/2020] [Accepted: 07/14/2020] [Indexed: 11/24/2022] Open
Abstract
Genetic resistance is widely used to manage clubroot (Plasmodiophora brassicae) in brassica crops, but new pathotypes have recently been identified on canola (Brassica napus) on the Canadian prairies. Resistance effective against both the most prevalent pathotype (3H, based on the Canadian Clubroot Differential system) and the new pathotypes is needed. BC1 plants of Brassica rapa from a cross of line 96-6990-2 (clubroot resistance originating from turnip cultivar ‘Waaslander’) and a susceptible doubled-haploid line, ACDC, exhibited a 1:1 segregation for resistance against pathotypes 3H and 5X. A resistance gene designated as Rcr3 was mapped initially based on the percentage of polymorphic variants using bulked segregant RNA sequencing (BSR-Seq) and further mapped using Kompetitive Allele Specific PCR. DNA variants were identified by assembling short reads against a reference genome of B. rapa. Rcr3 was mapped into chromosome A08. It was flanked by single nucleotide polymorphisms (SNP) markers (A90_A08_SNP_M12 and M16) between 10.00 and 10.23 Mb, in an interval of 231.6 Kb. There were 32 genes in the Rcr3 interval. Three genes (Bra020951, Bra020974, and Bra020979) were annotated with disease resistance mechanisms, which are potential candidates for Rcr3. Another resistance gene, designated as Rcr9wa, for resistance to pathotype 5X was mapped, with the flanking markers (A90_A08_SNP_M28 and M79) between 10.85 and 11.17 Mb using the SNP sites identified through BSR-Seq for Rcr3. There were 44 genes in the Rcr9wa interval, three of which (Bra020827, Bra020828, Bra020814) were annotated as immune-system-process related genes, which are potential candidates for Rcr9wa.
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Affiliation(s)
- Md. Masud Karim
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N OX2, Canada; (M.M.K.); (A.D.); (Y.Z.); (Q.C.); (G.P.); (B.D.G.)
| | - Abdulsalam Dakouri
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N OX2, Canada; (M.M.K.); (A.D.); (Y.Z.); (Q.C.); (G.P.); (B.D.G.)
| | - Yan Zhang
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N OX2, Canada; (M.M.K.); (A.D.); (Y.Z.); (Q.C.); (G.P.); (B.D.G.)
| | - Qilin Chen
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N OX2, Canada; (M.M.K.); (A.D.); (Y.Z.); (Q.C.); (G.P.); (B.D.G.)
| | - Gary Peng
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N OX2, Canada; (M.M.K.); (A.D.); (Y.Z.); (Q.C.); (G.P.); (B.D.G.)
| | - Stephen E. Strelkov
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada;
| | - Bruce D. Gossen
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N OX2, Canada; (M.M.K.); (A.D.); (Y.Z.); (Q.C.); (G.P.); (B.D.G.)
| | - Fengqun Yu
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N OX2, Canada; (M.M.K.); (A.D.); (Y.Z.); (Q.C.); (G.P.); (B.D.G.)
- Correspondence:
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Quantitative Trait Locus Mapping of Clubroot Resistance and Plasmodiophora brassicae Pathotype Banglim-Specific Marker Development in Brassica rapa. Int J Mol Sci 2020; 21:ijms21114157. [PMID: 32532118 PMCID: PMC7312193 DOI: 10.3390/ijms21114157] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/28/2020] [Accepted: 06/06/2020] [Indexed: 12/12/2022] Open
Abstract
Clubroot resistance is an economically important trait in Brassicaceae crops. Although many quantitative trait loci (QTLs) for clubroot resistance have been identified in Brassica, disease-related damage continues to occur owing to differences in host variety and constant pathogen variation. Here, we investigated the inheritance of clubroot resistance in a double haploid population developed by crossing clubroot resistant and susceptible lines "09CR500" and "09CR501", respectively. The resistance of "09CR500" to Plasmodiophora brassicae pathotype "Banglim" was controlled as a single dominant gene, with the segregation of resistance and susceptibility being nearly 1:1. PbBrA08Banglim was identified as having a logarithm of odds value of 7.9-74.8, and a phenotypic variance of 26.0-97.1% with flanking marker "09CR.11390652" in A08. After aligning QTL regions to the B. rapa reference genome, 11 genes were selected as candidates. PbBrA08Banglim was located near Crr1, CRs, and Rcr9 loci, but differences were validated by marker analysis, gene structural variations, and gene expression levels, as well as phenotypic responses to the pathotype. Genotyping using the "09CR.11390652" marker accurately distinguished the Banglim-resistance phenotypes in the double haploid population. Thus, the developed marker will be useful in Brassica breeding programs, marker-assisted selection, and gene pyramiding to identify and develop resistant cultivars.
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Genetics of Clubroot and Fusarium Wilt Disease Resistance in Brassica Vegetables: The Application of Marker Assisted Breeding for Disease Resistance. PLANTS 2020; 9:plants9060726. [PMID: 32526827 PMCID: PMC7355935 DOI: 10.3390/plants9060726] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/12/2020] [Accepted: 05/27/2020] [Indexed: 01/29/2023]
Abstract
The genus Brassica contains important vegetable crops, which serve as a source of oil seed, condiments, and forages. However, their production is hampered by various diseases such as clubroot and Fusarium wilt, especially in Brassica vegetables. Soil-borne diseases are difficult to manage by traditional methods. Host resistance is an important tool for minimizing disease and many types of resistance (R) genes have been identified. More than 20 major clubroot (CR) disease-related loci have been identified in Brassica vegetables and several CR-resistant genes have been isolated by map-based cloning. Fusarium wilt resistant genes in Brassica vegetables have also been isolated. These isolated R genes encode the toll-interleukin-1 receptor/nucleotide-binding site/leucine-rice-repeat (TIR-NBS-LRR) protein. DNA markers that are linked with disease resistance allele have been successfully applied to improve disease resistance through marker-assisted selection (MAS). In this review, we focused on the recent status of identifying clubroot and Fusarium wilt R genes and the feasibility of using MAS for developing disease resistance cultivars in Brassica vegetables.
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