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Li K, Wang K, Shi Y, Liang F, Li X, Bao S, Yesmagul BM, Fatima M, Yu C, Xu A, Zhang X, Fu S, Shi X, Dun X, Zhou Z, Huang Z. BjuA03.BNT1 plays a positive role in resistance to clubroot disease in resynthesized Brassica juncea L. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 349:112268. [PMID: 39313004 DOI: 10.1016/j.plantsci.2024.112268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 09/12/2024] [Accepted: 09/13/2024] [Indexed: 09/25/2024]
Abstract
Clubroot has become a major obstacle in rapeseed production. Breeding varieties resistant to clubroot is the most effective method for disease management. However, the clubroot-resistant germplasm of rapeseed remains limited. To tackle this challenge, we synthesized the clubroot-resistant mustard, CT19, via distant hybridization, and subsequently an F2 segregating population was created by intercrossing CT19 with a clubroot-susceptible germplasm CS15. A major-effect clubroot resistance QTL qCRa3-1 on chromosome A03 was identified through QTL scanning. Transcriptome analyses of CT19 and CS15 revealed that the mechanisms conferring resistance to Plasmodiophora brassica likely involved the regulation of flavonoid metabolism, fatty acid metabolism, and sulfur metabolism. By combining the results from transcriptome, QTL mapping, and gene sequencing, a candidate gene BjuA03.BNT1, encoding NLR (nucleotide-binding domain leucine-rich repeat-containing receptors) protein, was obtained. Intriguingly, comparing with CT19, a base T insertion was discovered in the BjuA03.BNT1 gene's coding sequence in CS15, resulting an alteration within the LRR conserved domain. Overexpression of BjuA03.BNT1 from CT19 notably enhanced the resistance to clubroot in Arabidopsis. Our investigations revealed that BjuA03.BNT1 regulated the resistance to clubroot by modulating fatty acid synthesis and the structure of cell wall. These results are highly relevant for molecular breeding to improve clubroot resistance in rapeseed.
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Affiliation(s)
- Keqi Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Kai Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yiji Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fenghao Liang
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xinru Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shunjun Bao
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Balziya Maratkyzy Yesmagul
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Maliha Fatima
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chengyu Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Aixia Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xingguo Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Sanxiong Fu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Xue Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaoling Dun
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China.
| | - Zhaoyong Zhou
- Information Management Office, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Zhen Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas/College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China.
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Ce F, Mei J, Zhao Y, Li Q, Ren X, Song H, Qian W, Si J. Comparative Analysis of Transcriptomes Reveals Pathways and Verifies Candidate Genes for Clubroot Resistance in Brassica oleracea. Int J Mol Sci 2024; 25:9189. [PMID: 39273138 PMCID: PMC11395044 DOI: 10.3390/ijms25179189] [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: 07/10/2024] [Revised: 08/02/2024] [Accepted: 08/16/2024] [Indexed: 09/15/2024] Open
Abstract
Clubroot, a soil-borne disease caused by Plasmodiophora brassicae, is one of the most destructive diseases of Brassica oleracea all over the world. However, the mechanism of clubroot resistance remains unclear. In this research, transcriptome sequencing was conducted on root samples from both resistant (R) and susceptible (S) B. oleracea plants infected by P. brassicae. Then the comparative analysis was carried out between the R and S samples at different time points during the infection stages to reveal clubroot resistance related pathways and candidate genes. Compared with 0 days after inoculation, a total of 4991 differential expressed genes were detected from the S pool, while only 2133 were found from the R pool. Gene function enrichment analysis found that the effector-triggered immunity played a major role in the R pool, while the pathogen-associated molecular pattern triggered immune response was stronger in the S pool. Simultaneously, candidate genes were identified through weighted gene co-expression network analysis, with Bol010786 (CNGC13) and Bol017921 (SD2-5) showing potential for conferring resistance to clubroot. The findings of this research provide valuable insights into the molecular mechanisms underlying clubroot resistance and present new avenues for further research aimed at enhancing the clubroot resistance of B. oleracea through breeding.
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Affiliation(s)
- Fuquan Ce
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River, Ministry of Education, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Jiaqin Mei
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Chongqing 400716, China
| | - Yu Zhao
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China
| | - Qinfei Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River, Ministry of Education, Chongqing 400716, China
- Chongqing Key Laboratory of Olericulture, Chongqing 400716, China
| | - Xuesong Ren
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River, Ministry of Education, Chongqing 400716, China
- Chongqing Key Laboratory of Olericulture, Chongqing 400716, China
| | - Hongyuan Song
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River, Ministry of Education, Chongqing 400716, China
- Chongqing Key Laboratory of Olericulture, Chongqing 400716, China
| | - Wei Qian
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Chongqing 400716, China
| | - Jun Si
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River, Ministry of Education, Chongqing 400716, China
- Chongqing Key Laboratory of Olericulture, Chongqing 400716, China
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Botero-Ramirez A, Kirk B, Strelkov SE. Optimizing Clubroot Management and the Role of Canola Cultivar Mixtures. Pathogens 2024; 13:640. [PMID: 39204241 PMCID: PMC11357626 DOI: 10.3390/pathogens13080640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/17/2024] [Accepted: 07/29/2024] [Indexed: 09/03/2024] Open
Abstract
The sustainable cultivation of canola is under threat from clubroot disease (Plasmodiophora brassicae). The pathogen's resting spores can survive in the soil for extended periods, complicating disease management. Therefore, effective clubroot control requires a combination of tactics that provide multiple layers of protection. Management strategies have focused on pathogen avoidance and reducing disease levels in infested fields. The sanitation of machinery and field equipment remains the most effective method for preventing the pathogen's introduction into non-infested fields. For disease reduction, crop rotation, liming, chemical control, and host resistance are commonly employed, with the use of clubroot-resistant cultivars being the most effective to date. However, resistance breakdown has been observed within four years of the introduction of new cultivars, jeopardizing the long-term effectiveness of this approach. A promising yet underexplored strategy is the use of cultivar mixtures. This approach leverages mechanisms such as the dilution effect, the barrier effect, induced resistance, disruptive selection, and the compensatory effect to control the disease. Cultivar mixtures have the potential to reduce the impact of clubroot on canola production while preserving pathogen population structure, thereby minimizing the likelihood of resistance breakdown. Given its potential, further research into cultivar mixtures as a management strategy for clubroot disease is warranted.
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Affiliation(s)
- Andrea Botero-Ramirez
- Department of Biological Sciences, Faculty of Arts and Science, MacEwan University, Edmonton, AB T5J 4S2, Canada
| | - Brennon Kirk
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada;
| | - Stephen E. Strelkov
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada;
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Karim MM, Yu F. Identification of QTLs for resistance to 10 pathotypes of Plasmodiophora brassicae in Brassica oleracea cultivar ECD11 through genotyping-by-sequencing. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:249. [PMID: 37982891 PMCID: PMC10661809 DOI: 10.1007/s00122-023-04483-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 10/09/2023] [Indexed: 11/21/2023]
Abstract
KEY MESSAGE Two major quantitative trait loci (QTLs) and five minor QTLs for 10 pathotypes were identified on chromosomes C01, C03, C04 and C08 through genotyping-by-sequencing from Brassica oleracea. Clubroot caused by Plasmodiophora brassicae is an important disease in brassica crops. Managing clubroot disease of canola on the Canadian prairie is challenging due to the continuous emergence of new pathotypes. Brassica oleracea is considered a major source of quantitative resistance to clubroot. Genotyping-by-sequencing (GBS) was performed in the parental lines; T010000DH3 (susceptible), ECD11 (resistant) and 124 BC1 plants. A total of 4769 high-quality polymorphic SNP loci were obtained and distributed on 9 chromosomes of B. oleracea. Evaluation of 124 BC1S1 lines for resistance to 10 pathotypes: 3A, 2B, 5C, 3D, 5G, 3H, 8J, 5K, 5L and 3O of P. brassicae, was carried out. Seven QTLs, 5 originating from ECD11 and 2 from T010000DH3, were detected. One major QTL designated as Rcr_C03-1 on C03 contributed 16.0-65.6% of phenotypic variation explained (PVE) for 8 pathotypes: 2B, 5C, 5G, 3H, 8J, 5K, 5L and 3O. Another major QTL designated as Rcr_C08-1 on C08 contributed 8.3 and 23.5% PVE for resistance to 8J and 5K, respectively. Five minor QTLs designated as Rcr_C01-1, Rcr_C03-2, Rcr_C03-3, Rcr_C04-1 and Rcr_C08-2 were detected on chromosomes C01, C03, C04 and C08 that contributed 8.3-23.5% PVE for 5 pathotypes each of 3A, 2B, 3D, 8J and 5K. There were 1, 10 and 4 genes encoding TIR-NBS-LRR/CC-NBS-LRR class disease resistance proteins in the Rcr_C01-1, Rcr_C03-1 and Rcr_C08-1 flanking regions. The syntenic regions of the two major QTLs Rcr_C03-1 and Rcr_C08-1 in the B. rapa genome 'Chiifu' were searched.
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Affiliation(s)
- Md Masud Karim
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Fengqun Yu
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada.
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5
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Amas JC, Bayer PE, Hong Tan W, Tirnaz S, Thomas WJW, Edwards D, Batley J. Comparative pangenome analyses provide insights into the evolution of Brassica rapa resistance gene analogues (RGAs). PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2100-2112. [PMID: 37431308 PMCID: PMC10502758 DOI: 10.1111/pbi.14116] [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: 02/22/2023] [Revised: 06/11/2023] [Accepted: 06/22/2023] [Indexed: 07/12/2023]
Abstract
Brassica rapa is grown worldwide as economically important vegetable and oilseed crop. However, its production is challenged by yield-limiting pathogens. The sustainable control of these pathogens mainly relies on the deployment of genetic resistance primarily driven by resistance gene analogues (RGAs). While several studies have identified RGAs in B. rapa, these were mainly based on a single genome reference and do not represent the full range of RGA diversity in B. rapa. In this study, we utilized the B. rapa pangenome, constructed from 71 lines encompassing 12 morphotypes, to describe a comprehensive repertoire of RGAs in B. rapa. We show that 309 RGAs were affected by presence-absence variation (PAV) and 223 RGAs were missing from the reference genome. The transmembrane leucine-rich repeat (TM-LRR) RGA class had more core gene types than variable genes, while the opposite was observed for nucleotide-binding site leucine-rich repeats (NLRs). Comparative analysis with the B. napus pangenome revealed significant RGA conservation (93%) between the two species. We identified 138 candidate RGAs located within known B. rapa disease resistance QTL, of which the majority were under negative selection. Using blackleg gene homologues, we demonstrated how these genes in B. napus were derived from B. rapa. This further clarifies the genetic relationship of these loci, which may be useful in narrowing-down candidate blackleg resistance genes. This study provides a novel genomic resource towards the identification of candidate genes for breeding disease resistance in B. rapa and its relatives.
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Affiliation(s)
- Junrey C. Amas
- School of Biological Sciences and the Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - Philipp E. Bayer
- School of Biological Sciences and the Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - Wei Hong Tan
- School of Biological Sciences and the Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - Soodeh Tirnaz
- School of Biological Sciences and the Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - William J. W. Thomas
- School of Biological Sciences and the Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
| | - David Edwards
- School of Biological Sciences and the Centre for Applied BioinformaticsThe University of Western AustraliaCrawleyWAAustralia
| | - Jacqueline Batley
- School of Biological Sciences and the Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
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Adhikary D, Kisiala A, Sarkar A, Basu U, Rahman H, Emery N, Kav NNV. Early-stage responses to Plasmodiophora brassicae at the transcriptome and metabolome levels in clubroot resistant and susceptible oilseed Brassica napus. Mol Omics 2022; 18:991-1014. [PMID: 36382681 DOI: 10.1039/d2mo00251e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Clubroot, a devastating soil-borne root disease, in Brassicaceae is caused by Plasmodiophora brassicae Woronin (P. brassicae W.), an obligate biotrophic protist. Plant growth and development, as well as seed yield of Brassica crops, are severely affected due to this disease. Several reports described the molecular responses of B. napus to P. brassicae; however, information on the early stages of pathogenesis is limited. In this study, we have used transcriptomics and metabolomics to characterize P. brassicae pathogenesis at 1-, 4-, and 7-days post-inoculation (DPI) in clubroot resistant (CR) and susceptible (CS) doubled-haploid (DH) canola lines. When we compared between inoculated and uninoculated groups, a total of 214 and 324 putative genes exhibited differential expression (q-value < 0.05) at one or more time-points in the CR and CS genotypes, respectively. When the inoculated CR and inoculated CS genotypes were compared, 4765 DEGs were differentially expressed (q-value < 0.05) at one or more time-points. Several metabolites related to organic acids (e.g., citrate, pyruvate), amino acids (e.g., proline, aspartate), sugars, and mannitol, were differentially accumulated in roots in response to pathogen infection when the CR and CS genotypes were compared. Several DEGs also corresponded to differentially accumulated metabolites, including pyrroline-5-carboxylate reductase (BnaC04g11450D), citrate synthase (BnaC02g39080D), and pyruvate kinase (BnaC04g23180D) as detected by transcriptome analysis. Our results suggest important roles for these genes in mediating resistance to clubroot disease. To our knowledge, this is the first report of an integrated transcriptome and metabolome analysis aimed at characterizing the molecular basis of resistance to clubroot in canola.
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Affiliation(s)
- Dinesh Adhikary
- Department of Agricultural, Food & Nutritional Sciences, University of Alberta, Edmonton, AB, Canada.
| | - Anna Kisiala
- Biology Department, Trent University, Peterborough, ON, Canada
| | - Ananya Sarkar
- Department of Agricultural, Food & Nutritional Sciences, University of Alberta, Edmonton, AB, Canada.
| | - Urmila Basu
- Department of Agricultural, Food & Nutritional Sciences, University of Alberta, Edmonton, AB, Canada.
| | - Habibur Rahman
- Department of Agricultural, Food & Nutritional Sciences, University of Alberta, Edmonton, AB, Canada.
| | - Neil Emery
- Biology Department, Trent University, Peterborough, ON, Canada
| | - Nat N V Kav
- Department of Agricultural, Food & Nutritional Sciences, University of Alberta, Edmonton, AB, Canada.
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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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8
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Shaw RK, Shen Y, Yu H, Sheng X, Wang J, Gu H. Multi-Omics Approaches to Improve Clubroot Resistance in Brassica with a Special Focus on Brassica oleracea L. Int J Mol Sci 2022; 23:9280. [PMID: 36012543 PMCID: PMC9409056 DOI: 10.3390/ijms23169280] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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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Affiliation(s)
| | | | | | | | | | - Honghui Gu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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9
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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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10
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Adhikary D, Mehta D, Uhrig RG, Rahman H, Kav NNV. A Proteome-Level Investigation Into Plasmodiophora brassicae Resistance in Brassica napus Canola. FRONTIERS IN PLANT SCIENCE 2022; 13:860393. [PMID: 35401597 PMCID: PMC8988049 DOI: 10.3389/fpls.2022.860393] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 02/21/2022] [Indexed: 05/07/2023]
Abstract
Clubroot of Brassicaceae, an economically important soil borne disease, is caused by Plasmodiophora brassicae Woronin, an obligate, biotrophic protist. This disease poses a serious threat to canola and related crops in Canada and around the globe causing significant losses. The pathogen is continuously evolving and new pathotypes are emerging, which necessitates the development of novel resistant canola cultivars to manage the disease. Proteins play a crucial role in many biological functions and the identification of differentially abundant proteins (DAP) using proteomics is a suitable approach to understand plant-pathogen interactions to assist in the development of gene specific markers for developing clubroot resistant (CR) cultivars. In this study, P. brassicae pathotype 3 (P3H) was used to challenge CR and clubroot susceptible (CS) canola lines. Root samples were collected at three distinct stages of pathogenesis, 7-, 14-, and 21-days post inoculation (DPI), protein samples were isolated, digested with trypsin and subjected to liquid chromatography with tandem mass spectrometry (LC-MS/MS) analysis. A total of 937 proteins demonstrated a significant (q-value < 0.05) change in abundance in at least in one of the time points when compared between control and inoculated CR-parent, CR-progeny, CS-parent, CS-progeny and 784 proteins were significantly (q < 0.05) changed in abundance in at least in one of the time points when compared between the inoculated- CR and CS root proteomes of parent and progeny across the three time points tested. Functional annotation of differentially abundant proteins (DAPs) revealed several proteins related to calcium dependent signaling pathways. In addition, proteins related to reactive oxygen species (ROS) biochemistry, dehydrins, lignin, thaumatin, and phytohormones were identified. Among the DAPs, 73 putative proteins orthologous to CR proteins and quantitative trait loci (QTL) associated with eight CR loci in different chromosomes including chromosomes A3 and A8 were identified. Proteins including BnaA02T0335400WE, BnaA03T0374600WE, BnaA03T0262200WE, and BnaA03T0464700WE are orthologous to identified CR loci with possible roles in mediating clubroot responses. In conclusion, these results have contributed to an improved understanding of the mechanisms involved in mediating response to P. brassicae in canola at the protein level.
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Affiliation(s)
- Dinesh Adhikary
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Devang Mehta
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - R. Glen Uhrig
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Habibur Rahman
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Nat N. V. Kav
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
- *Correspondence: Nat N. V. Kav,
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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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Abstract
Broccoli (Brassica oleracea L. var. italica) is one of the most important vegetable crops cultivated worldwide. The market demand for broccoli is still increasing due to its richness in vitamins, anthocyanins, mineral substances, fiber, secondary metabolites and other nutrients. The famous secondary metabolites, glucosinolates, sulforaphane and selenium have protective effects against cancer. Significant progress has been made in fine-mapping and cloning genes that are responsible for important traits; this progress provides a foundation for marker-assisted selection (MAS) in broccoli breeding. Genetic engineering by the well-developed Agrobacterium tumefaciens-mediated transformation in broccoli has contributed to the improvement of quality; postharvest life; glucosinolate and sulforaphane content; and resistance to insects, pathogens and abiotic stresses. Here, we review recent progress in the genetics and molecular breeding of broccoli. Future perspectives for improving broccoli are also briefly discussed.
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13
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Development of a New DNA Marker for Fusarium Yellows Resistance in Brassica rapa Vegetables. PLANTS 2021; 10:plants10061082. [PMID: 34072246 PMCID: PMC8229042 DOI: 10.3390/plants10061082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/19/2021] [Accepted: 05/24/2021] [Indexed: 11/17/2022]
Abstract
In vegetables of Brassica rapa L., Fusarium oxysporum f. sp. rapae (For) or F. oxysporum f. sp. conglutinans (Foc) cause Fusarium yellows. A resistance gene against Foc (FocBr1) has been identified, and deletion of this gene results in susceptibility (focbr1-1). In contrast, a resistance gene against For has not been identified. Inoculation tests showed that lines resistant to Foc were also resistant to For, and lines susceptible to Foc were susceptible to For. However, prediction of disease resistance by a dominant DNA marker on FocBr1 (Bra012688m) was not associated with disease resistance of For in some komatsuna lines using an inoculation test. QTL-seq using four F2 populations derived from For susceptible and resistant lines showed one causative locus on chromosome A03, which covers FocBr1. Comparison of the amino acid sequence of FocBr1 between susceptible and resistant alleles (FocBr1 and FocBo1) showed that six amino acid differences were specific to susceptible lines. The presence and absence of FocBr1 is consistent with For resistance in F2 populations. These results indicate that FocBr1 is essential for For resistance, and changed amino acid sequences result in susceptibility to For. This susceptible allele is termed focbr1-2, and a new DNA marker (focbr1-2m) for detection of the focbr1-2 allele was developed.
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14
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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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15
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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: 15] [Impact Index Per Article: 5.0] [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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16
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Botero-Ramírez A, Laperche A, Guichard S, Jubault M, Gravot A, Strelkov SE, Manzanares-Dauleux MJ. Clubroot Symptoms and Resting Spore Production in a Doubled Haploid Population of Oilseed Rape ( Brassica napus) Are Controlled by Four Main QTLs. FRONTIERS IN PLANT SCIENCE 2020; 11:604527. [PMID: 33391316 PMCID: PMC7773761 DOI: 10.3389/fpls.2020.604527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 11/20/2020] [Indexed: 06/02/2023]
Abstract
Clubroot, caused by Plasmodiophora brassicae Woronin, is one of the most important diseases of oilseed rape (Brassica napus L.). The rapid erosion of monogenic resistance in clubroot-resistant (CR) varieties underscores the need to diversify resistance sources controlling disease severity and traits related to pathogen fitness, such as resting spore production. The genetic control of disease index (DI) and resting spores per plant (RSP) was evaluated in a doubled haploid (DH) population consisting of 114 winter oilseed rape lines, obtained from the cross 'Aviso' × 'Montego,' inoculated with P. brassicae isolate "eH." Linkage analysis allowed the identification of three quantitative trait loci (QTLs) controlling DI (PbBn_di_A02, PbBn_di_A04, and PbBn_di_C03). A significant decrease in DI was observed when combining effects of the three resistance alleles at these QTLs. Only one QTL, PbBn_rsp_C03, was found to control RSP, reducing resting spore production by 40%. PbBn_rsp_C03 partially overlapped with PbBn_di_C03 in a nucleotide-binding leucine-rich repeat (NLR) gene-containing region. Consideration of both DI and RSP in breeding for clubroot resistance is recommended for the long-term management of this disease.
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Affiliation(s)
- Andrea Botero-Ramírez
- Department of Agricultural, Food and Nutritional Sciences, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Anne Laperche
- Institut de Génétique, Environnement et Protection des Plantes, INRAE, Institut Agro, Université de Rennes 1, Le Rheu, France
| | - Solenn Guichard
- Institut de Génétique, Environnement et Protection des Plantes, INRAE, Institut Agro, Université de Rennes 1, Le Rheu, France
| | - Mélanie Jubault
- Institut de Génétique, Environnement et Protection des Plantes, INRAE, Institut Agro, Université de Rennes 1, Le Rheu, France
| | - Antoine Gravot
- Institut de Génétique, Environnement et Protection des Plantes, INRAE, Institut Agro, Université de Rennes 1, Le Rheu, France
| | - Stephen E. Strelkov
- Department of Agricultural, Food and Nutritional Sciences, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Maria J. Manzanares-Dauleux
- Institut de Génétique, Environnement et Protection des Plantes, INRAE, Institut Agro, Université de Rennes 1, Le Rheu, France
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17
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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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18
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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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19
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Ren W, Li Z, Han F, Zhang B, Li X, Fang Z, Yang L, Zhuang M, Lv H, Liu Y, Wang Y, Yu H, Zhang Y. Utilization of Ogura CMS germplasm with the clubroot resistance gene by fertility restoration and cytoplasm replacement in Brassica oleracea L. HORTICULTURE RESEARCH 2020; 7:61. [PMID: 32377352 PMCID: PMC7193625 DOI: 10.1038/s41438-020-0282-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 01/25/2020] [Accepted: 02/24/2020] [Indexed: 06/11/2023]
Abstract
Clubroot disease, a major plant root disease caused by Plasmodiophora brassicae, has become one of the most destructive diseases among cultivated cruciferous vegetables. However, clubroot-resistant Brassica oleracea materials are rare. A few clubroot-resistant cabbage varieties are available on the market, but all are Ogura cytoplasmic male sterile (CMS) types. Therefore, in this study, to reutilize the clubroot-resistant Ogura CMS germplasm of cabbage, a new fertility-restored Ogura CMS material, 16Q2-11, was used as a bridge to transfer the clubroot resistance (CR) gene from the Ogura CMS cytoplasm to the normal cytoplasm by a two-step method (a fertility restoration and cytoplasm replacement method). In the first cross for fertility restoration of Ogura CMS clubroot-resistant cabbage (FRCRC), 16Q2-11 was used as a restorer to cross with Ogura CMS materials containing the CR gene CRb2. Eleven Rfo-positive progenies were generated, of which four contained CRb2: F8-514, F8-620, F8-732 and F8-839. After inoculation with race 4 of P. brassicae, these four CRb2-positive individuals showed resistance. Furthermore, F8-514 and F8-839 were then used as male parents in the second cross of FRCRC to cross with cabbage inbred lines, resulting in the successful introgression of the CRb2 gene into the inbred lines. All offspring produced from this step of cross, which had a normal cytoplasm, showed a high resistance to race 4 of P. brassicae and could be utilized for the breeding of clubroot-resistant cabbage varieties in the future. This is the first time that the Ogura CMS restorer has been used to restore the fertility of Ogura CMS clubroot-resistant cabbages, which could improve germplasm diversity in cabbage and provide a reference method for using CMS germplasm in Brassica crops.
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Affiliation(s)
- Wenjing Ren
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081 China
| | - Zhiyuan Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081 China
| | - Fengqing Han
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081 China
| | - Bin Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081 China
| | - Xing Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081 China
| | - Zhiyuan Fang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081 China
| | - Limei Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081 China
| | - Mu Zhuang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081 China
| | - Honghao Lv
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081 China
| | - Yumei Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081 China
| | - Yong Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081 China
| | - Hailong Yu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081 China
| | - Yangyong Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, #12 Zhong Guan Cun Nandajie Street, Beijing, 100081 China
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Lv H, Fang Z, Yang L, Zhang Y, Wang Y. An update on the arsenal: mining resistance genes for disease management of Brassica crops in the genomic era. HORTICULTURE RESEARCH 2020; 7:34. [PMID: 32194970 PMCID: PMC7072071 DOI: 10.1038/s41438-020-0257-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 01/12/2020] [Accepted: 01/15/2020] [Indexed: 05/18/2023]
Abstract
Brassica species include many economically important crops that provide nutrition and health-promoting substances to humans worldwide. However, as with all crops, their production is constantly threatened by emerging viral, bacterial, and fungal diseases, whose incidence has increased in recent years. Traditional methods of control are often costly, present limited effectiveness, and cause environmental damage; instead, the ideal approach is to mine and utilize the resistance genes of the Brassica crop hosts themselves. Fortunately, the development of genomics, molecular genetics, and biological techniques enables us to rapidly discover and apply resistance (R) genes. Herein, the R genes identified in Brassica crops are summarized, including their mapping and cloning, possible molecular mechanisms, and application in resistance breeding. Future perspectives concerning how to accurately discover additional R gene resources and efficiently utilize these genes in the genomic era are also discussed.
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Affiliation(s)
- Honghao Lv
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12# Zhongguancun South Street, Beijing, 100081 China
| | - Zhiyuan Fang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12# Zhongguancun South Street, Beijing, 100081 China
| | - Limei Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12# Zhongguancun South Street, Beijing, 100081 China
| | - Yangyong Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12# Zhongguancun South Street, Beijing, 100081 China
| | - Yong Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12# Zhongguancun South Street, Beijing, 100081 China
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Farid M, Yang RC, Kebede B, Rahman H. Evaluation of Brassica oleracea accessions for resistance to Plasmodiophora brassicae and identification of genomic regions associated with resistance. Genome 2020; 63:91-101. [DOI: 10.1139/gen-2019-0098] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Clubroot disease caused by Plasmodiophora brassicae is a challenge to Brassica crop production. Breakdown of resistance controlled by major genes of the Brassica A genome has been reported. Therefore, identification of resistance in the Brassica C genome is needed to broaden the genetic base of resistance in Brassica napus canola. In this study, we evaluated 135 Brassica oleracea accessions, belonging to eight variants of this species to identify resistant accessions as well as to identify the genomic regions associated with resistance to two recently evolved P. brassicae pathotypes, F3-14 (3A) and F-359-13 (5X L-G2). Resistance to these pathotypes was observed more frequently in var. acephala (kale) followed by var. capitata (cabbage); few accessions also carried resistance to both pathotypes. Association mapping using single nucleotide polymorphism (SNP) markers developed through genotyping by sequencing technique identified 10 quantitative trait loci (QTL) from six C-genome chromosomes to be associated with resistance to these pathotypes; among these, two QTL associated with resistance to 3A and one QTL associated with resistance to 5X L-G2 carried ≥3 SNP markers. The 10 QTL identified in this study individually accounted for 8%–18% of the total phenotypic variance. Thus, the results from this study can be used in molecular breeding of Brassica crops for resistance to this disease.
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Affiliation(s)
- Mehdi Farid
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Rong-Cai Yang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Berisso Kebede
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Habibur Rahman
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
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iTRAQ-based quantitative analysis reveals proteomic changes in Chinese cabbage (Brassica rapa L.) in response to Plasmodiophora brassicae infection. Sci Rep 2019; 9:12058. [PMID: 31427711 PMCID: PMC6700187 DOI: 10.1038/s41598-019-48608-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 08/07/2019] [Indexed: 01/07/2023] Open
Abstract
Clubroot disease is one of the major diseases affecting Brassica crops, especially Chinese cabbage (Brassica rapa L. ssp. pekinensis), which is known to be highly susceptible to the disease. In this study, the obligate biotrophic protist Plasmodiophora brassicae Woronin was used to infect the roots of Chinese cabbage seedlings. The disease symptoms were noticeable at 28 and 35 days after inoculation (DAI) in the susceptible (CM) line. Using isobaric tags for relative and absolute quantitation (iTRAQ) analysis, a total of 5,003 proteins of differential abundance were identified in the resistant/susceptible lines, which could be quantitated by dipeptide or polypeptide segments. Gene ontology (GO) analysis indicated that the differentially expressed proteins (DEPs) between the susceptible (CM) and resistant (CCR) lines were associated with the glutathione transferase activity pathway, which could catalyze the combination of glutathione and other electrophilic compounds to protect plants from disease. In addition, the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the DEPs may be significantly enriched cytokinin signaling or arginine biosynthesis pathways, both of which are responses to stimuli and are plant defense reactions. The cytokinins may facilitate cell division in the shoot, resulting in the hypertrophy and formation of galls and the presentation of typical clubroot symptoms. In this study, the proteomic results provide a new perspective for creating germplasm resistance to P. brassicae, as well as a genetic basis for breeding to improve Chinese cabbage.
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Hejna O, Havlickova L, He Z, Bancroft I, Curn V. Analysing the genetic architecture of clubroot resistance variation in Brassica napus by associative transcriptomics. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2019; 39:112. [PMID: 31396013 PMCID: PMC6647481 DOI: 10.1007/s11032-019-1021-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/08/2019] [Indexed: 06/01/2023]
Abstract
Clubroot is a destructive soil-borne pathogen of Brassicaceae that causes significant recurrent reductions in yield of cruciferous crops. Although there is some resistance in oilseed rape (a crop type of the species Brassica napus), the genetic basis of that resistance is poorly understood. In this study, we used an associative transcriptomics approach to elucidate the genetic basis of resistance to clubroot pathotype ECD 17/31/31 across a genetic diversity panel of 245 accessions of B. napus. A single nucleotide polymorphism (SNP) association analysis was performed with 256,397 SNPs distributed across the genome of B. napus and combined with transcript abundance data of 53,889 coding DNA sequence (CDS) gene models. The SNP association analysis identified two major loci (on chromosomes A2 and A3) controlling resistance and seven minor loci. Within these were a total of 86 SNP markers. Altogether, 392 genes were found in these regions. Another 21 genes were implicated as potentially involved in resistance using gene expression marker (GEM) analysis. After GO enrichment analysis and InterPro functional analysis of the identified genes, 82 candidate genes were identified as having roles in clubroot resistance. These results provide useful information for marker-assisted breeding which could lead to acceleration of pyramiding of multiple clubroot resistance genes in new varieties.
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Affiliation(s)
- Ondrej Hejna
- Biotechnological Centre, Faculty of Agriculture, University of South Bohemia, Studentska, 1668 Ceske Budejovice, Czech Republic
- Department of Biology, University of York, Heslington, York, YO10 5DD UK
| | - Lenka Havlickova
- Department of Biology, University of York, Heslington, York, YO10 5DD UK
| | - Zhesi He
- Department of Biology, University of York, Heslington, York, YO10 5DD UK
| | - Ian Bancroft
- Department of Biology, University of York, Heslington, York, YO10 5DD UK
| | - Vladislav Curn
- Biotechnological Centre, Faculty of Agriculture, University of South Bohemia, Studentska, 1668 Ceske Budejovice, Czech Republic
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Chang A, Lamara M, Wei Y, Hu H, Parkin IAP, Gossen BD, Peng G, Yu F. Clubroot resistance gene Rcr6 in Brassica nigra resides in a genomic region homologous to chromosome A08 in B. rapa. BMC PLANT BIOLOGY 2019; 19:224. [PMID: 31142280 PMCID: PMC6542104 DOI: 10.1186/s12870-019-1844-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 05/22/2019] [Indexed: 05/24/2023]
Abstract
BACKGROUND Clubroot, caused by Plasmodiophora brassicae Woronin, is a very important disease of Brassica species. Management of clubroot relies heavily on genetic resistance. In a cross of Brassica nigra lines PI 219576 (highly resistant, R) × CR2748 (highly susceptible, S) to clubroot, all F1 plants were resistant to clubroot. There was a 1:1 ratio of R:S in the BC1 and 3R:1S in the F2, which indicated that a single dominant gene controlled clubroot resistance in PI 219576. This gene was designated Rcr6. Mapping of Rcr6 was performed using genome sequencing information from A-genome of B. rapa and B-genome of B. nigra though bulked segregant RNA sequencing (BSR-Seq) and further mapping with Kompetitive Allele Specific PCR (KASP) analysis. RESULTS Reads of R and S bulks from BSR-Seq were initially aligned onto B. rapa (A-genome; B. nigra has the B-genome) where Rcr6 was associated with chromosome A08. KASP analysis showed that Rcr6 was flanked by SNP markers homologous to the region of 14.8-15.4 Mb of chromosome A08. There were 190 genes annotated in this region, with five genes (Bra010552, Bra010588, Bra010589, Bra010590 and Bra010663) identified as encoding the toll-interleukin-1 receptor / nucleotide-binding site / leucine-rich-repeat (TIR-NBS-LRR; TNL) class of proteins. The reads from BSR-Seq were then aligned into a draft B-genome of B. nigra, where Rcr6 was mapped on chromosome B3. KASP analysis indicated that Rcr6 was located on chromosome B3 in a 0.5 Mb region from 6.1-6.6 Mb. Only one TNL gene homologous to the B. rapa gene Bra010663 was identified in the target region. This gene is a likely candidate for Rcr6. Subsequent analysis of the Rcr6 equivalent region based on a published B. nigra genome was performed. This gene is located into chromosome B7 of the published B-genome, homologous to BniB015819. CONCLUSION Rcr6 was the first gene identified and mapped in the B-genome of Brassica species. It resides in a genomic region homologous to chromosome A08 of A-genome. Based on this finding, it could possibly integrate into A08 of B. napus using marker assisted selection with SNP markers tightly linked to Rcr6 developed in this study.
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Affiliation(s)
- Adrian Chang
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, SK S7N 0X2 Canada
| | - Mebarek Lamara
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, SK S7N 0X2 Canada
| | - Yangdou Wei
- Department of Biology, University of Saskatchewan, Saskatoon, SK S7N 5E2 Canada
| | - Hao Hu
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, SK S7N 0X2 Canada
| | - Isobel A. P. Parkin
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, SK S7N 0X2 Canada
| | - Bruce D. Gossen
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, SK S7N 0X2 Canada
| | - Gary Peng
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, SK S7N 0X2 Canada
| | - Fengqun Yu
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, SK S7N 0X2 Canada
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Fu Y, Zhang Y, Mason AS, Lin B, Zhang D, Yu H, Fu D. NBS-Encoding Genes in Brassica napus Evolved Rapidly After Allopolyploidization and Co-localize With Known Disease Resistance Loci. FRONTIERS IN PLANT SCIENCE 2019; 10:26. [PMID: 30761170 PMCID: PMC6363714 DOI: 10.3389/fpls.2019.00026] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 01/09/2019] [Indexed: 05/19/2023]
Abstract
Genes containing nucleotide-binding sites (NBS) play an important role in pathogen resistance in plants. However, the evolutionary fate of NBS-encoding genes after formation of allotetraploid Brassica napus (AnAnCnCn, 2n = 38) is still unknown. We performed a genome-wide comparison of putatively functional NBS-encoding genes in B. napus and its progenitor species Brassica rapa (ArAr, 2n = 20) and Brassica oleracea (CoCo, 2n = 18), identifying 464, 202, and 146 putatively functional NBS-encoding genes respectively, with genes unevenly distributed in several clusters. The An-subgenome of B. napus possessed similar numbers of NBS-encoding genes (191 genes) to the Ar genome of B. rapa (202 genes) and similar clustering patterns. However, the Cn genome of B. napus had many more genes (273) than the B. oleracea Co genome (146), with different clustering trends. Only 97 NBS-encoding genes (66.4%) in B. oleracea were homologous with NBS-encoding genes in B. napus, while 176 NBS-encoding genes (87.1%) were homologous between B. rapa and B. napus. These results suggest a greater diversification of NBS-encoding genes in the C genome may have occurred after formation of B. napus. Although most NBS-encoding genes in B. napus appeared to derive from the progenitors, the birth and death of several NBS-encoding genes was also putatively mediated by non-homologous recombination. The Ka/Ks values of most homologous pairs between B. napus and the progenitor species were less than 1, suggesting purifying selection during B. napus evolution. The majority of NBS-encoding genes (60% in all species) showed higher expression levels in root tissue (out of root, leaf, stem, seed and flower tissue types). Comparative analysis of NBS-encoding genes with mapped resistance QTL against three major diseases of B. napus (blackleg, clubroot and Sclerotinia stem rot) found 204 NBS-encoding genes in B. napus located within 71 resistance QTL intervals. The majority of NBS-encoding genes were co-located with resistance QTLs against a single disease, while 47 genes were co-located with QTLs against two diseases and 3 genes were co-located with QTLs against all three. Our results revealed significant variation as well as interesting evolutionary trajectories of NBS-encoding genes in the different Brassica subgenomes, while co-localization of NBS-encoding genes and resistance QTL may facilitate resistance breeding in oilseed rape.
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Affiliation(s)
- Ying Fu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yaofeng Zhang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Annaliese S. Mason
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Giessen, Germany
| | - Baogang Lin
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Dongqing Zhang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Huasheng Yu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- *Correspondence: Huasheng Yu, Donghui Fu,
| | - Donghui Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, China
- *Correspondence: Huasheng Yu, Donghui Fu,
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26
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Peng L, Zhou L, Li Q, Wei D, Ren X, Song H, Mei J, Si J, Qian W. Identification of Quantitative Trait Loci for Clubroot Resistance in Brassica oleracea With the Use of Brassica SNP Microarray. FRONTIERS IN PLANT SCIENCE 2018; 9:822. [PMID: 29967632 PMCID: PMC6015909 DOI: 10.3389/fpls.2018.00822] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 05/28/2018] [Indexed: 05/27/2023]
Abstract
Increasing clubroot resistance (CR) of Brassica oleracea by ascertaining the molecular mechanisms has been the key focus in modern B. oleracea breeding. In order to identify the quantitative trait loci (QTLs) associated with CR in B. oleracea, 94 F2 vegetative lines which were developed by tissue culture of selfed seeds from the F1 generation between a clubroot-resistant B. oleracea inbred line and a susceptible line, were identified for disease incidence and six CR-associated traits under a lab inoculation by Plasmodiophora brassicae and were genotyped with the 60K Brassica SNP array. Significant correlations were detected for numbers of fibrous roots and P. brassicae content in roots with disease incidence. Nine linkage groups were constructed from 565 bins which covered around 3,000 SNPs, spanning 1,028 cM of the B. oleracea genome with an average distance of 1.82 cM between adjacent bins. A total of 23 QTLs were identified for disease incidence and the other two correlated traits, individually explaining 6.1-17.8% of the phenotypic variation. Several overlaps were detected among traits, including one three-traits-overlapped locus on linkage group C08 and two important overlapped regions between the two CR-associated traits on C06. The QTLs were compared with known CR loci/genes and the novelty of our QTLs was discussed.
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Affiliation(s)
- Lisha 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
- Chongqing Yudongnan Academy of Agricultural Sciences, Chongqing, China
| | - Lili Zhou
- 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
| | - 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
| | - Dayong Wei
- 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
| | - 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
| | - Jiaqin Mei
- College of Agronomy and Biotechnology, Southwest University, 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
| | - Wei Qian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
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Shea DJ, Tomaru Y, Itabashi E, Nakamura Y, Miyazaki T, Kakizaki T, Naher TN, Shimizu M, Fujimoto R, Fukai E, Okazaki K. The production and characterization of a BoFLC2 introgressed Brassica rapa by repeated backcrossing to an F 1. BREEDING SCIENCE 2018; 68:316-325. [PMID: 30100798 PMCID: PMC6081295 DOI: 10.1270/jsbbs.17115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 02/13/2018] [Indexed: 05/25/2023]
Abstract
Flowering time is an important agronomic trait for Brassica rapa crops, and previous breeding work in Brassica has successfully transmitted other important agronomic traits from donor species. However, there has been no previous attempts to produce hybrids replacing the original Brassica FLC alleles with alien FLC alleles. In this paper, we introduce the creation of a chromosome substitution line (CSSL) containing a homozygous introgression of Flowering Locus C from Brassica oleracea (BoFLC2) into a B. rapa genomic background, and characterize the CSSL line with respect to the parental cultivars. The preferential transmission of alien chromosome inheritance and the pattern of transmission observed during the production of the CSSLs are also discussed.
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Affiliation(s)
- Daniel J. Shea
- Laboratory of Plant Breeding, Graduate School of Science and Technology, Niigata University,
2-8050 Ikarashi, Nishi-ku, Niigata 950-2181,
Japan
| | - Yuki Tomaru
- Laboratory of Plant Breeding, Graduate School of Science and Technology, Niigata University,
2-8050 Ikarashi, Nishi-ku, Niigata 950-2181,
Japan
| | - Etsuko Itabashi
- National Institute of Vegetable and Tea Science,
360 Kusawa, Ano, Tsu, Mie 514-2392,
Japan
| | - Yuri Nakamura
- Laboratory of Plant Breeding, Graduate School of Science and Technology, Niigata University,
2-8050 Ikarashi, Nishi-ku, Niigata 950-2181,
Japan
| | - Toshio Miyazaki
- Nippon Norin Seed Co.,
6-6-5 Takinogawa, Kita-ku, Tokyo 114-0023,
Japan
| | - Tomohiro Kakizaki
- National Institute of Vegetable and Tea Science,
360 Kusawa, Ano, Tsu, Mie 514-2392,
Japan
| | | | - Motoki Shimizu
- Iwate Biotechnology Research Center,
22-174-4 Narita, Kitakami, Iwate 024-0003,
Japan
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University,
Rokkodai, Nada-ku, Kobe, Hyogo 657-8501,
Japan
| | - Eigo Fukai
- Laboratory of Plant Breeding, Graduate School of Science and Technology, Niigata University,
2-8050 Ikarashi, Nishi-ku, Niigata 950-2181,
Japan
| | - Keiichi Okazaki
- Laboratory of Plant Breeding, Graduate School of Science and Technology, Niigata University,
2-8050 Ikarashi, Nishi-ku, Niigata 950-2181,
Japan
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28
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Pérez-López E, Waldner M, Hossain M, Kusalik AJ, Wei Y, Bonham-Smith PC, Todd CD. Identification of Plasmodiophora brassicae effectors - A challenging goal. Virulence 2018; 9:1344-1353. [PMID: 30146948 PMCID: PMC6177251 DOI: 10.1080/21505594.2018.1504560] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 07/18/2018] [Indexed: 11/06/2022] Open
Abstract
Clubroot is an economically important disease affecting Brassica plants worldwide. Plasmodiophora brassicae is the protist pathogen associated with the disease, and its soil-borne obligate parasitic nature has impeded studies related to its biology and the mechanisms involved in its infection of the plant host. The identification of effector proteins is key to understanding how the pathogen manipulates the plant's immune response and the genes involved in resistance. After more than 140 years studying clubroot and P. brassicae, very little is known about the effectors playing key roles in the infection process and subsequent disease progression. Here we analyze the information available for identified effectors and suggest several features of effector genes that can be used in the search for others. Based on the information presented in this review, we propose a comprehensive bioinformatics pipeline for effector identification and provide a list of the bioinformatics tools available for such.
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Affiliation(s)
- Edel Pérez-López
- Department of Biology, University of Saskatchewan, Saskatoon, Canada
| | - Matthew Waldner
- Department of Computer Science, University of Saskatchewan, Saskatoon, Canada
| | - Musharaf Hossain
- Department of Biology, University of Saskatchewan, Saskatoon, Canada
| | - Anthony J. Kusalik
- Department of Computer Science, University of Saskatchewan, Saskatoon, Canada
| | - Yangdou Wei
- Department of Biology, University of Saskatchewan, Saskatoon, Canada
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29
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Neik TX, Barbetti MJ, Batley J. Current Status and Challenges in Identifying Disease Resistance Genes in Brassica napus. FRONTIERS IN PLANT SCIENCE 2017; 8:1788. [PMID: 29163558 PMCID: PMC5681527 DOI: 10.3389/fpls.2017.01788] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 10/02/2017] [Indexed: 05/18/2023]
Abstract
Brassica napus is an economically important crop across different continents including temperate and subtropical regions in Europe, Canada, South Asia, China and Australia. Its widespread cultivation also brings setbacks as it plays host to fungal, oomycete and chytrid pathogens that can lead to serious yield loss. For sustainable crop production, identification of resistance (R) genes in B. napus has become of critical importance. In this review, we discuss four key pathogens affecting Brassica crops: Clubroot (Plasmodiophora brassicae), Blackleg (Leptosphaeria maculans and L. biglobosa), Sclerotinia Stem Rot (Sclerotinia sclerotiorum), and Downy Mildew (Hyaloperonospora parasitica). We first review current studies covering prevalence of these pathogens on Brassica crops and highlight the R genes and QTL that have been identified from Brassica species against these pathogens. Insights into the relationships between the pathogen and its Brassica host, the unique host resistance mechanisms and how these affect resistance outcomes is also presented. We discuss challenges in identification and deployment of R genes in B. napus in relation to highly specific genetic interactions between host subpopulations and pathogen pathotypes and emphasize the need for common or shared techniques and research materials or tighter collaboration between researchers to reconcile the inconsistencies in the research outcomes. Using current genomics tools, we provide examples of how characterization and cloning of R genes in B. napus can be carried out more effectively. Lastly, we put forward strategies to breed resistant cultivars through introgressions supported by genomic approaches and suggest prospects that can be implemented in the future for a better, pathogen-resistant B. napus.
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Affiliation(s)
- Ting Xiang Neik
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | - Martin J. Barbetti
- School of Agriculture and Environment and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
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Yu F, Zhang X, Peng G, Falk KC, Strelkov SE, Gossen BD. Genotyping-by-sequencing reveals three QTL for clubroot resistance to six pathotypes of Plasmodiophora brassicae in Brassica rapa. Sci Rep 2017; 7:4516. [PMID: 28674416 PMCID: PMC5495781 DOI: 10.1038/s41598-017-04903-2] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 05/22/2017] [Indexed: 12/20/2022] Open
Abstract
Clubroot, caused by Plasmodiophora brassicae, is an important disease of Brassica crops worldwide. F1 progeny from the Brassica rapa lines T19 (resistant) × ACDC (susceptible) were backcrossed with ACDC, then self-pollinated to produce BC1S1 lines, From genotyping-by-sequencing (GBS) of the parental lines and BC1 plants, about 1.32 M sequences from T19 were aligned into the reference genome of B. rapa with 0.4-fold coverage, and 1.77 M sequences with 0.5-fold coverage in ACDC. The number of aligned short reads per plant in the BC1 ranged from 0.07 to 1.41 M sequences with 0.1-fold coverage. A total of 1584 high quality SNP loci were obtained, distributed on 10 chromosomes. A single co-localized QTL, designated as Rcr4 on chromosome A03, conferred resistance to pathotypes 2, 3, 5, 6 and 8. The peak was at SNP locus A03_23710236, where LOD values were 30.3 to 38.8, with phenotypic variation explained (PVE) of 85-95%. Two QTLs for resistance to a novel P. brassicae pathotype 5x, designated Rcr8 on chromosome A02 and Rcr9 on A08, were detected with 15.0 LOD and 15.8 LOD, and PVE of 36% and 39%, respectively. Bulked segregant analysis was performed to examine TIR-NBS-LRR proteins in the regions harboring the QTL.
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Affiliation(s)
- Fengqun Yu
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK, S7N OX2, Canada.
| | - Xingguo Zhang
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK, S7N OX2, Canada
| | - Gary Peng
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK, S7N OX2, Canada
| | - Kevin C Falk
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK, S7N OX2, Canada
| | - 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
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Laperche A, Aigu Y, Jubault M, Ollier M, Guichard S, Glory P, Strelkov SE, Gravot A, Manzanares-Dauleux MJ. Clubroot resistance QTL are modulated by nitrogen input in Brassica napus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:669-684. [PMID: 28050618 DOI: 10.1007/s00122-016-2842-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 12/10/2016] [Indexed: 05/25/2023]
Abstract
Nitrogen levels can modulate the effectiveness of clubroot resistance in an isolate- and host-specific manner. While the same QTL were detected under high and low nitrogen, their effects were altered. Clubroot, caused by Plasmodiophora brassicae, is one of the most damaging diseases of oilseed rape and is known to be affected by nitrogen fertilization. However, the genetic factors involved in clubroot resistance have not been characterized under nitrogen-limiting conditions. This study aimed to assess the variability of clubroot resistance under different nitrogen levels and to characterize the impact of nitrogen supply on genetic resistance factors. Linkage analyses and a genome-wide association study were conducted to detect QTL for clubroot resistance and evaluate their sensitivity to nitrogen. The clubroot response of a set of 92 diverse oilseed rape accessions and 108 lines derived from a cross between 'Darmor-bzh' (resistant) and 'Yudal' (susceptible) was studied in the greenhouse under high- and low-nitrogen conditions, following inoculation with the P. brassicae isolates eH and K92-16. Resistance to each isolate was controlled by a major QTL and a few small-effects QTL. While the same QTL were detected under both high and low nitrogen, their effects were altered. Clubroot resistance to isolate eH, but not K92-16, was greater under a low-N supply versus a high-N supply. New sources of resistance were found among the oilseed rape accessions under both low and high-N conditions. The results are discussed relative to the literature and from a crop improvement perspective.
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Affiliation(s)
- A Laperche
- IGEPP, AGROCAMPUS OUEST, INRA, Université de Rennes 1, 35650, Le Rheu, France
| | - Y Aigu
- IGEPP, AGROCAMPUS OUEST, INRA, Université de Rennes 1, 35650, Le Rheu, France
| | - M Jubault
- IGEPP, AGROCAMPUS OUEST, INRA, Université de Rennes 1, 35650, Le Rheu, France
| | - M Ollier
- IGEPP, AGROCAMPUS OUEST, INRA, Université de Rennes 1, 35650, Le Rheu, France
| | - S Guichard
- IGEPP, AGROCAMPUS OUEST, INRA, Université de Rennes 1, 35650, Le Rheu, France
| | - P Glory
- IGEPP, AGROCAMPUS OUEST, INRA, Université de Rennes 1, 35650, Le Rheu, France
| | - S E Strelkov
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - A Gravot
- IGEPP, AGROCAMPUS OUEST, INRA, Université de Rennes 1, 35650, Le Rheu, France
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Li L, Luo Y, Chen B, Xu K, Zhang F, Li H, Huang Q, Xiao X, Zhang T, Hu J, Li F, Wu X. A Genome-Wide Association Study Reveals New Loci for Resistance to Clubroot Disease in Brassica napus. FRONTIERS IN PLANT SCIENCE 2016; 7:1483. [PMID: 27746804 PMCID: PMC5044777 DOI: 10.3389/fpls.2016.01483] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 09/20/2016] [Indexed: 05/19/2023]
Abstract
Rapeseed (Brassica napus L.) is one of the most important oil crops in the world. However, the yield and quality of rapeseed were largely decreased by clubroot (Plasmodiophora brassicae Woronin). Therefore, it is of great importance for screening more resistant germplasms or genes and improving the resistance to P. brassicae in rapeseed breeding. In this study, a massive resistant identification for a natural global population was conducted in two environments with race/pathotype 4 of P. brassicae which was the most predominant in China, and a wide range of phenotypic variation was found in the population. In addition, a genome-wide association study of 472 accessions for clubroot resistance (CR) was performed with 60K Brassica Infinium SNP arrays for the first time. In total, nine QTLs were detected, seven of which were novel through integrative analysis. Furthermore, additive effects in genetic control of CR in rapeseed among the above loci were found. By bioinformatic analyses, the candidate genes of these loci were predicted, which indicated that TIR-NBS gene family might play an important role in CR. It is believable that the results presented in our study could provide valuable information for understanding the genetic mechanism and molecular regulation of CR.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Xiaoming Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute – Chinese Academy of Agricultural SciencesWuhan, China
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Li L, Luo Y, Chen B, Xu K, Zhang F, Li H, Huang Q, Xiao X, Zhang T, Hu J, Li F, Wu X. A Genome-Wide Association Study Reveals New Loci for Resistance to Clubroot Disease in Brassica napus. FRONTIERS IN PLANT SCIENCE 2016; 7:1483. [PMID: 27746804 DOI: 10.3389/fpls.2015.01483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 09/20/2016] [Indexed: 05/26/2023]
Abstract
Rapeseed (Brassica napus L.) is one of the most important oil crops in the world. However, the yield and quality of rapeseed were largely decreased by clubroot (Plasmodiophora brassicae Woronin). Therefore, it is of great importance for screening more resistant germplasms or genes and improving the resistance to P. brassicae in rapeseed breeding. In this study, a massive resistant identification for a natural global population was conducted in two environments with race/pathotype 4 of P. brassicae which was the most predominant in China, and a wide range of phenotypic variation was found in the population. In addition, a genome-wide association study of 472 accessions for clubroot resistance (CR) was performed with 60K Brassica Infinium SNP arrays for the first time. In total, nine QTLs were detected, seven of which were novel through integrative analysis. Furthermore, additive effects in genetic control of CR in rapeseed among the above loci were found. By bioinformatic analyses, the candidate genes of these loci were predicted, which indicated that TIR-NBS gene family might play an important role in CR. It is believable that the results presented in our study could provide valuable information for understanding the genetic mechanism and molecular regulation of CR.
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Affiliation(s)
- Lixia Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute - Chinese Academy of Agricultural Sciences Wuhan, China
| | - Yujie Luo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute - Chinese Academy of Agricultural Sciences Wuhan, China
| | - Biyun Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute - Chinese Academy of Agricultural Sciences Wuhan, China
| | - Kun Xu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute - Chinese Academy of Agricultural Sciences Wuhan, China
| | - Fugui Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute - Chinese Academy of Agricultural Sciences Wuhan, China
| | - Hao Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute - Chinese Academy of Agricultural Sciences Wuhan, China
| | - Qian Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute - Chinese Academy of Agricultural Sciences Wuhan, China
| | - Xin Xiao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute - Chinese Academy of Agricultural Sciences Wuhan, China
| | - Tianyao Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute - Chinese Academy of Agricultural Sciences Wuhan, China
| | - Jihong Hu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute - Chinese Academy of Agricultural Sciences Wuhan, China
| | - Feng Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute - Chinese Academy of Agricultural Sciences Wuhan, China
| | - Xiaoming Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crop Research Institute - Chinese Academy of Agricultural Sciences Wuhan, China
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Hasan MJ, Rahman H. Genetics and molecular mapping of resistance to Plasmodiophora brassicae pathotypes 2, 3, 5, 6, and 8 in rutabaga (Brassica napus var. napobrassica). Genome 2016; 59:805-815. [PMID: 27549861 DOI: 10.1139/gen-2016-0034] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Clubroot disease, caused by Plasmodiophora brassicae, is a threat to the production of Brassica crops including oilseed B. napus. In Canada, several pathotypes of this pathogen, such as pathotypes 2, 3, 5, 6, and 8, were identified, and resistance to these pathotypes was found in a rutabaga (B. napus var. napobrassica) genotype. In this paper, we report the genetic basis and molecular mapping of this resistance by use of F2, backcross (BC1), and doubled haploid (DH) populations generated from crossing of this rutabaga line to a susceptible spring B. napus canola line. The F1, F2, and BC1 populations were evaluated for resistance to pathotype 3, and the DH population was evaluated for resistance to pathotypes 2, 3, 5, 6, and 8. A 3:1 segregation in F2 and a 1:1 segregation in BC1 were found for resistance to pathotype 3, and a 1:1 segregation was found in the DH population for resistance to all pathotypes. Molecular mapping by using the DH population identified a genomic region on chromosome A8 carrying resistance to all five pathotypes. This suggests that a single gene or a cluster of genes, located in this genomic region, is involved in the control of resistance to these pathotypes.
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Affiliation(s)
- Muhammad Jakir Hasan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Agriculture/Forestry Centre, Edmonton, AB T6G 2P5, Canada.,Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Agriculture/Forestry Centre, Edmonton, AB T6G 2P5, Canada
| | - Habibur Rahman
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Agriculture/Forestry Centre, Edmonton, AB T6G 2P5, Canada.,Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Agriculture/Forestry Centre, Edmonton, AB T6G 2P5, Canada
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35
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Yu F, Zhang X, Huang Z, Chu M, Song T, Falk KC, Deora A, Chen Q, Zhang Y, McGregor L, Gossen BD, McDonald MR, Peng G. Identification of Genome-Wide Variants and Discovery of Variants Associated with Brassica rapa Clubroot Resistance Gene Rcr1 through Bulked Segregant RNA Sequencing. PLoS One 2016; 11:e0153218. [PMID: 27078023 DOI: 10.1371/journal.pone.00153218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 03/27/2016] [Indexed: 05/26/2023] Open
Abstract
Clubroot, caused by Plasmodiophora brassicae, is an important disease on Brassica species worldwide. A clubroot resistance gene, Rcr1, with efficacy against pathotype 3 of P. brassicae, was previously mapped to chromosome A03 of B. rapa in pak choy cultivar "Flower Nabana". In the current study, resistance to pathotypes 2, 5 and 6 was shown to be associated with Rcr1 region on chromosome A03. Bulked segregant RNA sequencing was performed and short read sequences were assembled into 10 chromosomes of the B. rapa reference genome v1.5. For the resistant (R) bulks, a total of 351.8 million (M) sequences, 30,836.5 million bases (Mb) in length, produced 120-fold coverage of the reference genome. For the susceptible (S) bulks, 322.9 M sequences, 28,216.6 Mb in length, produced 109-fold coverage. In total, 776.2 K single nucleotide polymorphisms (SNPs) and 122.2 K insertion / deletion (InDels) in R bulks and 762.8 K SNPs and 118.7 K InDels in S bulks were identified; each chromosome had about 87% SNPs and 13% InDels, with 78% monomorphic and 22% polymorphic variants between the R and S bulks. Polymorphic variants on each chromosome were usually below 23%, but made up 34% of the variants on chromosome A03. There were 35 genes annotated in the Rcr1 target region and variants were identified in 21 genes. The numbers of poly variants differed significantly among the genes. Four out of them encode Toll-Interleukin-1 receptor / nucleotide-binding site / leucine-rich-repeat proteins; Bra019409 and Bra019410 harbored the higher numbers of polymorphic variants, which indicates that they are more likely candidates of Rcr1. Fourteen SNP markers in the target region were genotyped using the Kompetitive Allele Specific PCR method and were confirmed to associate with Rcr1. Selected SNP markers were analyzed with 26 recombinants obtained from a segregating population consisting of 1587 plants, indicating that they were completely linked to Rcr1. Nine SNP markers were used for marker-assisted introgression of Rcr1 into B. napus canola from B. rapa, with 100% accuracy in this study.
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Affiliation(s)
- Fengqun Yu
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Xingguo Zhang
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Zhen Huang
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Mingguang Chu
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Tao Song
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Kevin C Falk
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Abhinandan Deora
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, Canada
| | - Qilin Chen
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Yan Zhang
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Linda McGregor
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Bruce D Gossen
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Mary Ruth McDonald
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, Canada
| | - Gary Peng
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
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Identification of Genome-Wide Variants and Discovery of Variants Associated with Brassica rapa Clubroot Resistance Gene Rcr1 through Bulked Segregant RNA Sequencing. PLoS One 2016; 11:e0153218. [PMID: 27078023 PMCID: PMC4831815 DOI: 10.1371/journal.pone.0153218] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 03/27/2016] [Indexed: 11/19/2022] Open
Abstract
Clubroot, caused by Plasmodiophora brassicae, is an important disease on Brassica species worldwide. A clubroot resistance gene, Rcr1, with efficacy against pathotype 3 of P. brassicae, was previously mapped to chromosome A03 of B. rapa in pak choy cultivar “Flower Nabana”. In the current study, resistance to pathotypes 2, 5 and 6 was shown to be associated with Rcr1 region on chromosome A03. Bulked segregant RNA sequencing was performed and short read sequences were assembled into 10 chromosomes of the B. rapa reference genome v1.5. For the resistant (R) bulks, a total of 351.8 million (M) sequences, 30,836.5 million bases (Mb) in length, produced 120-fold coverage of the reference genome. For the susceptible (S) bulks, 322.9 M sequences, 28,216.6 Mb in length, produced 109-fold coverage. In total, 776.2 K single nucleotide polymorphisms (SNPs) and 122.2 K insertion / deletion (InDels) in R bulks and 762.8 K SNPs and 118.7 K InDels in S bulks were identified; each chromosome had about 87% SNPs and 13% InDels, with 78% monomorphic and 22% polymorphic variants between the R and S bulks. Polymorphic variants on each chromosome were usually below 23%, but made up 34% of the variants on chromosome A03. There were 35 genes annotated in the Rcr1 target region and variants were identified in 21 genes. The numbers of poly variants differed significantly among the genes. Four out of them encode Toll-Interleukin-1 receptor / nucleotide-binding site / leucine-rich-repeat proteins; Bra019409 and Bra019410 harbored the higher numbers of polymorphic variants, which indicates that they are more likely candidates of Rcr1. Fourteen SNP markers in the target region were genotyped using the Kompetitive Allele Specific PCR method and were confirmed to associate with Rcr1. Selected SNP markers were analyzed with 26 recombinants obtained from a segregating population consisting of 1587 plants, indicating that they were completely linked to Rcr1. Nine SNP markers were used for marker-assisted introgression of Rcr1 into B. napus canola from B. rapa, with 100% accuracy in this study.
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Lv H, Wang Q, Liu X, Han F, Fang Z, Yang L, Zhuang M, Liu Y, Li Z, Zhang Y. Whole-Genome Mapping Reveals Novel QTL Clusters Associated with Main Agronomic Traits of Cabbage (Brassica oleracea var. capitata L.). FRONTIERS IN PLANT SCIENCE 2016; 7:989. [PMID: 27458471 PMCID: PMC4933720 DOI: 10.3389/fpls.2016.00989] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/22/2016] [Indexed: 05/06/2023]
Abstract
We describe a comprehensive quantitative trait locus (QTL) analysis for 24 main agronomic traits of cabbage. Field experiments were performed using a 196-line double haploid population in three seasons in 2011 and 2012 to evaluate important agronomic traits related to plant type, leaf, and head traits. In total, 144 QTLs with LOD threshold >3.0 were detected for the 24 agronomic traits: 25 for four plant-type-related traits, 64 for 10 leaf-related traits, and 55 for 10 head-related traits; each QTL explained 6.0-55.7% of phenotype variation. Of the QTLs, 95 had contribution rates higher than 10%, and 51 could be detected in more than one season. Major QTLs included Ph 3.1 (max R (2) = 55.7, max LOD = 28.2) for plant height, Ll 3.2 (max R (2) = 31.7, max LOD = 13.95) for leaf length, and Htd 3.2 (max R (2) = 28.5, max LOD = 9.49) for head transverse diameter; these could all be detected in more than one season. Twelve QTL clusters were detected on eight chromosomes, and the most significant four included Indel481-scaffold18376 (3.20 Mb), with five QTLs for five traits; Indel64-scaffold35418 (2.22 Mb), six QTLs for six traits; scaffold39782-Indel84 (1.78 Mb), 11 QTLs for 11 traits; and Indel353-Indel245 (9.89 Mb), seven QTLs for six traits. Besides, most traits clustered within the same region were significantly correlated with each other. The candidate genes at these regions were also discussed. Robust QTLs and their clusters obtained in this study should prove useful for marker-assisted selection (MAS) in cabbage breeding and in furthering our understanding of the genetic control of these traits.
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Affiliation(s)
- Honghao Lv
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Qingbiao Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
| | - Xing Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, 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 SciencesBeijing, 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 SciencesBeijing, 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 SciencesBeijing, 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 SciencesBeijing, China
| | - Yumei Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, 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 SciencesBeijing, 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 SciencesBeijing, China
- *Correspondence: Yangyong Zhang
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Lee J, Izzah NK, Choi BS, Joh HJ, Lee SC, Perumal S, Seo J, Ahn K, Jo EJ, Choi GJ, Nou IS, Yu Y, Yang TJ. Genotyping-by-sequencing map permits identification of clubroot resistance QTLs and revision of the reference genome assembly in cabbage (Brassica oleracea L.). DNA Res 2015; 23:29-41. [PMID: 26622061 PMCID: PMC4755525 DOI: 10.1093/dnares/dsv034] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Accepted: 10/28/2015] [Indexed: 12/22/2022] Open
Abstract
Clubroot is a devastating disease caused by Plasmodiophora brassicae and results in severe losses of yield and quality in Brassica crops. Many clubroot resistance genes and markers are available in Brassica rapa but less is known in Brassica oleracea. Here, we applied the genotyping-by-sequencing (GBS) technique to construct a high-resolution genetic map and identify clubroot resistance (CR) genes. A total of 43,821 SNPs were identified using GBS data for two parental lines, one resistant and one susceptible lines to clubroot, and 18,187 of them showed >5× coverage in the GBS data. Among those, 4,103 were credibly genotyped for all 78 F2 individual plants. These markers were clustered into nine linkage groups spanning 879.9 cM with an average interval of 1.15 cM. Quantitative trait loci (QTLs) survey based on three rounds of clubroot resistance tests using F2:3 progenies revealed two and single major QTLs for Race 2 and Race 9 of P. brassicae, respectively. The QTLs show similar locations to the previously reported CR loci for Race 4 in B. oleracea but are in different positions from any of the CR loci found in B. rapa. We utilized two reference genome sequences in this study. The high-resolution genetic map developed herein allowed us to reposition 37 and 2 misanchored scaffolds in the 02–12 and TO1000DH genome sequences, respectively. Our data also support additional positioning of two unanchored 3.3 Mb scaffolds into the 02–12 genome sequence.
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Affiliation(s)
- Jonghoon Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea
| | - Nur Kholilatul Izzah
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea Indonesian Research Institute for Industrial and Beverage Crops (IRIIBC), Pakuwon, Sukabumi, Indonesia
| | - Beom-Soon Choi
- Phyzen Genomics Institute, Seoul 151-836, Republic of Korea
| | - Ho Jun Joh
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea
| | - Sang-Choon Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea
| | - Sampath Perumal
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea
| | - Joodeok Seo
- Joeun Seed, Goesan-Gun, Chungcheongbuk-Do 367-833, Republic of Korea
| | - Kyounggu Ahn
- Joeun Seed, Goesan-Gun, Chungcheongbuk-Do 367-833, Republic of Korea
| | - Eun Ju Jo
- Research Center for Biobased Chemistry, Korea Research Institute of Chemical Technology, Daejeon 305-600, Republic of Korea
| | - Gyung Ja Choi
- Research Center for Biobased Chemistry, Korea Research Institute of Chemical Technology, Daejeon 305-600, Republic of Korea
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, Suncheon 540-950, Republic of Korea
| | - Yeisoo Yu
- Phyzen Genomics Institute, Seoul 151-836, Republic of Korea
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang 232-916, Republic of Korea
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Su Y, Liu Y, Li Z, Fang Z, Yang L, Zhuang M, Zhang Y. QTL Analysis of Head Splitting Resistance in Cabbage (Brassica oleracea L. var. capitata) Using SSR and InDel Makers Based on Whole-Genome Re-Sequencing. PLoS One 2015; 10:e0138073. [PMID: 26406606 PMCID: PMC4583274 DOI: 10.1371/journal.pone.0138073] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 08/26/2015] [Indexed: 11/19/2022] Open
Abstract
Head splitting resistance (HSR) in cabbage is an important trait closely related to both quality and yield of head. However, the genetic control of this trait remains unclear. In this study, a doubled haploid (DH) population derived from an intra-cross between head splitting-susceptible inbred cabbage line 79-156 and resistant line 96-100 was obtained and used to analyze inheritance and detect quantitative trait loci (QTLs) for HSR using a mixed major gene/polygene inheritance analysis and QTL mapping. HSR can be attributed to additive-epistatic effects of three major gene pairs combined with those of polygenes. Negative and significant correlations were also detected between head Hsr and head vertical diameter (Hvd), head transverse diameter (Htd) and head weight (Hw). Using the DH population, a genetic map was constructed with simple sequence repeat (SSR) and insertion-deletion (InDel) markers, with a total length of 1065.9 cM and average interval length of 4.4 cM between adjacent markers. Nine QTLs for HSR were located on chromosomes C3, C4, C7, and C9 based on 2 years of phenotypic data using both multiple-QTL mapping and inclusive composite interval mapping. The identified QTLs collectively explained 39.4 to 59.1% of phenotypic variation. Three major QTLs (Hsr 3.2, 4.2, 9.2) showing a relatively larger effect were robustly detected in different years or with different mapping methods. The HSR trait was shown to have complex genetic mechanisms. Results from QTL mapping and classical genetic analysis were consistent. The QTLs obtained in this study should be useful for molecular marker-assisted selection in cabbage breeding and provide a foundation for further research on HSR genetic regulation.
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Affiliation(s)
- Yanbin Su
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, People’s Republic of China
- Beijing Zhongnong Futong Horticulture Corporation Limited, Beijing 100083, People’s Republic of China
| | - Yumei Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, People’s Republic of China
| | - Zhansheng Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, People’s Republic of China
| | - Zhiyuan Fang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, People’s Republic of China
| | - Limei Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, People’s Republic of China
| | - Mu Zhuang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, People’s Republic of China
| | - Yangyong Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, People’s Republic of China
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Zhang H, Feng J, Zhang S, Zhang S, Li F, Strelkov SE, Sun R, Hwang SF. Resistance to Plasmodiophora brassicae in Brassica rapa and Brassica juncea genotypes From China. PLANT DISEASE 2015; 99:776-779. [PMID: 30699533 DOI: 10.1094/pdis-08-14-0863-re] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Clubroot disease, caused by Plasmodiophora brassicae Woronin, has become a major problem in cruciferous crops worldwide. Chinese cabbage (Brassica rapa), pak choi (B. rapa), and mustard (B. juncea) are important vegetable crops in China. Development of clubroot-resistant cultivars of these crops is urgently needed. In this study, 71 B. rapa and B. juncea genotypes from China, including cultivars and inbred lines, were evaluated for resistance to three P. brassicae pathotypes. A significant interaction was observed between the P. brassicae pathotypes and the Brassica genotypes. Pathotype 3, as defined on the differentials of Williams, exhibited the weakest virulence on all plant material. By contrast, pathotypes 5 and 6 were both highly pathogenic on most of the tested genotypes. In all, 10 of the 14 Chinese cabbage cultivars were resistant to all three pathotypes, while 4 were resistant only to a specific pathotype. Seven of eight progenies obtained from the selfing of Chinese cabbage cultivars were resistant to pathotype 3 but most were susceptible to pathotypes 5 and 6. Most inbred lines of Chinese cabbage and all inbred lines of pak choi and mustard were susceptible to all three pathotypes but their susceptibility was lower to pathotype 3 than to pathotypes 5 and 6.
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Affiliation(s)
- Hui Zhang
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, and Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
| | - Jie Feng
- Crop Diversification Centre North, Alberta Agriculture and Rural Development, Edmonton, Alberta T5Y 6H3, Canada
| | - Shujiang Zhang
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing
| | - Shifan Zhang
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing
| | - Fei Li
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing
| | - Stephen E Strelkov
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton
| | - Rifei Sun
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081
| | - Sheau-Fang Hwang
- Crop Diversification Centre North, Alberta Agriculture and Rural Development, Edmonton
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41
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Shimizu M, Pu ZJ, Kawanabe T, Kitashiba H, Matsumoto S, Ebe Y, Sano M, Funaki T, Fukai E, Fujimoto R, Okazaki K. Map-based cloning of a candidate gene conferring Fusarium yellows resistance in Brassica oleracea. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:119-30. [PMID: 25351523 DOI: 10.1007/s00122-014-2416-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 10/11/2014] [Indexed: 05/13/2023]
Abstract
We identified the candidate gene conferring yellow wilt resistance (YR) in B. oleracea . This work will facilitate YR breeding programs for B. oleracea and its closely related species. Yellow wilt disease is one of the most serious diseases of cabbage worldwide. Type A resistance to the disease is controlled by a single dominant gene that is used in cabbage breeding. Our previous QTL study identified the FocBo1 locus controlling type A resistance. In this study, the FocBo1 locus was fine-mapped by using 139 recombinant F2 plants derived from resistant cabbage (AnjuP01) and susceptible broccoli (GCP04) DH lines. As a result, we successfully delimited the location of FocBo1 within 1.00 cM between markers, BoInd 2 and BoInd 11. Analysis of BAC and cosmid sequences corresponding to the FocBo1 locus identified an orthologous gene of Bra012688 that was recently identified as an candidate gene that confers yellows resistance in Chinese cabbage. The candidate gene-specific DNA markers and phenotypes in F1 cabbage cultivars and their selfed F2 populations showed a perfect correlation. Our identification of the candidate gene for FocBo1 will assist introduction of fusarium resistance into B. oleracea cultivars and contribute further understanding of interaction between Brassica plants and fusarium.
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Affiliation(s)
- Motoki Shimizu
- Laboratory of Plant Breeding, Graduate School of Science and Technology, Faculty of Agriculture, Niigata University, 2-8050, Ikarashi, Nishi-ku, Niigata, 950-2181, Japan
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42
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Brown AF, Yousef GG, Chebrolu KK, Byrd RW, Everhart KW, Thomas A, Reid RW, Parkin IAP, Sharpe AG, Oliver R, Guzman I, Jackson EW. High-density single nucleotide polymorphism (SNP) array mapping in Brassica oleracea: identification of QTL associated with carotenoid variation in broccoli florets. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:2051-64. [PMID: 25119868 DOI: 10.1007/s00122-014-2360-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 07/13/2014] [Indexed: 05/19/2023]
Abstract
A high-resolution genetic linkage map of B. oleracea was developed from a B. napus SNP array. The work will facilitate genetic and evolutionary studies in Brassicaceae. A broccoli population, VI-158 × BNC, consisting of 150 F2:3 families was used to create a saturated Brassica oleracea (diploid: CC) linkage map using a recently developed rapeseed (Brassica napus) (tetraploid: AACC) Illumina Infinium single nucleotide polymorphism (SNP) array. The map consisted of 547 non-redundant SNP markers spanning 948.1 cM across nine chromosomes with an average interval size of 1.7 cM. As the SNPs are anchored to the genomic reference sequence of the rapid cycling B. oleracea TO1000, we were able to estimate that the map provides 96 % coverage of the diploid genome. Carotenoid analysis of 2 years data identified 3 QTLs on two chromosomes that are associated with up to half of the phenotypic variation associated with the accumulation of total or individual compounds. By searching the genome sequences of the two related diploid species (B. oleracea and B. rapa), we further identified putative carotenoid candidate genes in the region of these QTLs. This is the first description of the use of a B. napus SNP array to rapidly construct high-density genetic linkage maps of one of the constituent diploid species. The unambiguous nature of these markers with regard to genomic sequences provides evidence to the nature of genes underlying the QTL, and demonstrates the value and impact this resource will have on Brassica research.
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Affiliation(s)
- Allan F Brown
- Department of Horticultural Science, Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, 28081, USA,
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Sharma A, Li X, Lim YP. Comparative genomics of Brassicaceae crops. BREEDING SCIENCE 2014; 64:3-13. [PMID: 24987286 PMCID: PMC4031108 DOI: 10.1270/jsbbs.64.3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 02/16/2014] [Indexed: 06/03/2023]
Abstract
The family Brassicaceae is one of the major groups of the plant kingdom and comprises diverse species of great economic, agronomic and scientific importance, including the model plant Arabidopsis. The sequencing of the Arabidopsis genome has revolutionized our knowledge in the field of plant biology and provides a foundation in genomics and comparative biology. Genomic resources have been utilized in Brassica for diversity analyses, construction of genetic maps and identification of agronomic traits. In Brassicaceae, comparative sequence analysis across the species has been utilized to understand genome structure, evolution and the detection of conserved genomic segments. In this review, we focus on the progress made in genetic resource development, genome sequencing and comparative mapping in Brassica and related species. The utilization of genomic resources and next-generation sequencing approaches in improvement of Brassica crops is also discussed.
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Affiliation(s)
- Ashutosh Sharma
- Graduate School of Agricultural Science, Tohoku University,
Aoba, Sendai, Miyagi 981-8555,
Japan
- Present address: Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Xiaonan Li
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University,
Daejeon 305-764,
Republic of Korea
| | - Yong Pyo Lim
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University,
Daejeon 305-764,
Republic of Korea
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Liu XY, Min Y, Wang KM, Wan ZY, Zhang ZG, Cao CX, Zhou RH, Jiang AB, Liu CJ, Zhang GY, Cheng XL, Zhang W, Yang ZW. Draft genome sequence of Bacillus amyloliquefaciens HB-26. Stand Genomic Sci 2014; 9:775-82. [PMID: 25197462 PMCID: PMC4149015 DOI: 10.4056/sigs.4978673] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Bacillus amyloliquefaciens HB-26, a Gram-positive bacterium was isolated from soil in China. SDS-PAGE analysis showed this strain secreted six major protein bands of 65, 60, 55, 34, 25 and 20 kDa. A bioassay of this strain reveals that it shows specific activity against P. brassicae and nematode. Here we describe the features of this organism, together with the draft genome sequence and annotation. The 3,989,358 bp long genome (39 contigs) contains 4,001 protein-coding genes and 80 RNA genes.
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Affiliation(s)
- Xiao-Yan Liu
- National Biopesticide Engineering Technology Research Center, Hubei Biopesticide Engineering Research Center, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Yong Min
- National Biopesticide Engineering Technology Research Center, Hubei Biopesticide Engineering Research Center, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Kai-Mei Wang
- National Biopesticide Engineering Technology Research Center, Hubei Biopesticide Engineering Research Center, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Zhong-Yi Wan
- National Biopesticide Engineering Technology Research Center, Hubei Biopesticide Engineering Research Center, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Zhi-Gang Zhang
- National Biopesticide Engineering Technology Research Center, Hubei Biopesticide Engineering Research Center, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Chun-Xia Cao
- National Biopesticide Engineering Technology Research Center, Hubei Biopesticide Engineering Research Center, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Rong-Hua Zhou
- National Biopesticide Engineering Technology Research Center, Hubei Biopesticide Engineering Research Center, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Ai-Bing Jiang
- National Biopesticide Engineering Technology Research Center, Hubei Biopesticide Engineering Research Center, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Cui-Jun Liu
- National Biopesticide Engineering Technology Research Center, Hubei Biopesticide Engineering Research Center, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Guang-Yang Zhang
- National Biopesticide Engineering Technology Research Center, Hubei Biopesticide Engineering Research Center, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Xian-Liang Cheng
- National Biopesticide Engineering Technology Research Center, Hubei Biopesticide Engineering Research Center, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Wei Zhang
- Department of Horticulture, Hubei Vocational College of Bio-technology, Wuhan 430070, China
| | - Zi-Wen Yang
- National Biopesticide Engineering Technology Research Center, Hubei Biopesticide Engineering Research Center, Hubei Academy of Agricultural Sciences, Wuhan, China
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45
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Chen J, Jing J, Zhan Z, Zhang T, Zhang C, Piao Z. Identification of novel QTLs for isolate-specific partial resistance to Plasmodiophora brassicae in Brassica rapa. PLoS One 2013; 8:e85307. [PMID: 24376876 PMCID: PMC3869933 DOI: 10.1371/journal.pone.0085307] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 11/25/2013] [Indexed: 11/21/2022] Open
Abstract
Plasmodiophora brassicae, the causal agent of clubroot disease of the Brassica crops, is widespread in the world. Quantitative trait loci (QTLs) for partial resistance to 4 different isolates of P. brassicae (Pb2, Pb4, Pb7, and Pb10) were investigated using a BC1F1 population from a cross between two subspecies of Brassica rapa, i.e. Chinese cabbage inbred line C59-1 as a susceptible recurrent parent and turnip inbred line ECD04 as a resistant donor parent. The BC1F2 families were assessed for resistance under controlled conditions. A linkage map constructed with simple sequence repeats (SSR), unigene-derived microsatellite (UGMS) markers, and specific markers linked to published clubroot resistance (CR) genes of B. rapa was used to perform QTL mapping. A total of 6 QTLs residing in 5 CR QTL regions of the B. rapa chromosomes A01, A03, and A08 were identified to account for 12.2 to 35.2% of the phenotypic variance. Two QTL regions were found to be novel except for 3 QTLs in the respective regions of previously identified Crr1, Crr2, and Crr3. QTL mapping results indicated that 1 QTL region was common for partial resistance to the 2 isolates of Pb2 and Pb7, whereas the others were specific for each isolate. Additionally, synteny analysis between B. rapa and Arabidopsis thaliana revealed that all CR QTL regions were aligned to a single conserved crucifer blocks (U, F, and R) on 3 Arabidopsis chromosomes where 2 CR QTLs were detected in A. thaliana. These results suggest that some common ancestral genomic regions were involved in the evolution of CR genes in B. rapa.
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Affiliation(s)
- Jingjing Chen
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Jing Jing
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Zhongxiang Zhan
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Teng Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Chunyu Zhang
- National Key Laboratory of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- * E-mail: (ZP); (CZ)
| | - Zhongyun Piao
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- * E-mail: (ZP); (CZ)
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Guo S, Zou J, Li R, Long Y, Chen S, Meng J. A genetic linkage map of Brassica carinata constructed with a doubled haploid population. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:1113-24. [PMID: 22669300 DOI: 10.1007/s00122-012-1898-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Accepted: 05/11/2012] [Indexed: 05/11/2023]
Abstract
Brassica carinata is an important oilseed crop with unique favourable traits that are desirable for other Brassica crops. However, given the limited research into genetic resources in B. carinata, knowledge of the genetic structure of this species is relatively poor. Nine homozygous, genetically distinct accessions of B. carinata were obtained via microspore culture, from which two divergent doubled haploid (DH) lines were used to develop a DH mapping population that consisted of 183 lines. The mapping population showed segregation of multiple traits of interest. A genetic map was constructed with PCR-based markers, and a total of 212 loci, which covered 1,703 cM, were assigned to eight linkage groups in the B genome and nine linkage groups in the C genome, which allowed comparison with genetic maps of other important Brassica species that contain the B/C genome(s). Loci for two Mendelian-inherited traits related to pigmentation (petal and anther tip colour) and one quantitative trait (seed coat colour) were identified using the linkage map. The significance of the mapping population in the context of genetic improvement of Brassica crops is discussed.
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Affiliation(s)
- Shaomin Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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Kato T, Hatakeyama K, Fukino N, Matsumoto S. Identificaiton of a clubroot resistance locus conferring resistance to a Plasmodiophora brassicae classified into pathotype group 3 in Chinese cabbage (Brassica rapa L.). BREEDING SCIENCE 2012; 62:282-7. [PMID: 23226089 PMCID: PMC3501946 DOI: 10.1270/jsbbs.62.282] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 04/19/2012] [Indexed: 05/24/2023]
Abstract
In Chinese cabbage (Brassica rapa), the clubroot resistance (CR) genes Crr1 and Crr2 are effective against the mild Plasmodiophora brassicae isolate Ano-01 and the more virulent isolate Wakayama-01, but not against isolate No. 14, classified into pathotype group 3. 'Akiriso', a clubroot-resistant F(1) cultivar, showed resistance to isolate No. 14. To increase the durability of resistance, we attempted to identify the CR locus in 'Akiriso'. CR in 'Akiriso' segregated as a single dominant gene and was linked to several molecular markers that were also linked to CRb, a CR locus from cultivar 'CR Shinki'. We developed additional markers around CRb and constructed partial genetic maps of this region in 'Akiriso' and 'CR Shinki'. The positions and order of markers in the genetic maps of the two cultivars were very similar. The segregation ratios for resistance to isolate No. 14 in F(2) populations derived from each of the two cultivars were also very similar. These results suggest that the CR locus in 'Akiriso' is CRb or a tightly linked locus. The newly developed markers in this study were more closely linked to CRb than previously reported markers and will be useful for marker-assisted selection of CRb in Chinese cabbage breeding.
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Affiliation(s)
- Takeyuki Kato
- Graduate School of Bioresources, Mie University, 1577 Kurima-machiya, Tsu, Mie 514-8507, Japan
- NARO Institute of Vegetable and Tea Science, 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Katsunori Hatakeyama
- NARO Institute of Vegetable and Tea Science, 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Nobuko Fukino
- NARO Institute of Vegetable and Tea Science, 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Satoru Matsumoto
- NARO Institute of Vegetable and Tea Science, 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
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Nukui S, Kitamura S, Hioki T, Ootsuka H, Miyoshi K, Satou T, Takatori Y, Oomiya T, Okazaki K. N(2)O induces mitotic polyploidization in anther somatic cells and restores fertility in sterile interspecific hybrid lilies. BREEDING SCIENCE 2011; 61:327-37. [PMID: 23136469 PMCID: PMC3406768 DOI: 10.1270/jsbbs.61.327] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 08/02/2011] [Indexed: 05/18/2023]
Abstract
Fertile plants undergoing male gametogenesis can be treated with nitrous oxide (N(2)O) gas to obtain 2n male gametes. N(2)O treatment is also expected to restore the fertility of interspecific hybrids through meiotic restitution or mitotic amphidiploidization. However, this technique has few applications to date, and it is un-known how N(2)O treatment restores fertility in sterile hybrids. To establish optimal N(2)O treatment conditions and determine its cytological mechanism of action, we treated various sized floral buds with N(2)O gas at different anther developmental stages from fertile and sterile hybrid lilies. N(2)O treatment using the optimal 1-4 mm floral buds induced mitotic polyploidization of male archesporial cells to produce 2n pollen in fertile hybrid lilies. In sterile hybrid lilies, N(2)O treatment doubled the chromosome number in male archesporial cells followed by homologous chromosome pairing and normal meiosis in pollen mother cells (PMC), resulting in restoration of pollen fertility. Backcrossing the resultant fertile pollen to Lilium × formolongi produced many triploid BC(1) plants. Thus N(2)O treatment at the archesporial cell proliferating stage effectively overcame pollen sterility in hybrid lilies, resulting in fertile, 2n pollen grains that could produce progeny. The procedure presented here will promote interspecific or interploidy hybridization of lilies.
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Affiliation(s)
- Shotarou Nukui
- The Graduate School of Science and Technology, Niigata University, Nishi, Ikarashi, Niigata 950-2181, Japan
| | - Satomi Kitamura
- The Graduate School of Science and Technology, Niigata University, Nishi, Ikarashi, Niigata 950-2181, Japan
- Kaneko Seeds, Co., Ltd., 1-50-12 Furuichi, Maebashi, Gunma 371-8503, Japan
| | - Tomoyo Hioki
- The Graduate School of Science and Technology, Niigata University, Nishi, Ikarashi, Niigata 950-2181, Japan
| | - Hideaki Ootsuka
- Niigata Agricultural Research Institute Horticultural Research Center, 177 Mano, Seiro, Niigata 957-0111, Japan
| | - Kazumitsu Miyoshi
- Faculty of Bioresources and Sciences, Akita Prefectural University, 241-438 Shimoshinjyo, Akita 010-0195, Japan
| | - Takao Satou
- Akita Prefectural Agriculture, Forestry and Fisheries Research Center, Agricultural Experiment Station, 34-1 Yuwaaikawa, Akita 010-1231, Japan
| | - Yuka Takatori
- Saga Prefectural Agriculture Research Center, 1088 Kawasoe, Saga 840-2205, Japan
| | - Tomo Oomiya
- Hokkaido Ornamental Plants and Vegetables Research Center, 735 Higashitakikawa, Takikawa, Hokkaido 073-0026, Japan
| | - Keiichi Okazaki
- The Graduate School of Science and Technology, Niigata University, Nishi, Ikarashi, Niigata 950-2181, Japan
- Corresponding author (e-mail: )
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Björkman M, Klingen I, Birch ANE, Bones AM, Bruce TJA, Johansen TJ, Meadow R, Mølmann J, Seljåsen R, Smart LE, Stewart D. Phytochemicals of Brassicaceae in plant protection and human health--influences of climate, environment and agronomic practice. PHYTOCHEMISTRY 2011; 72:538-56. [PMID: 21315385 DOI: 10.1016/j.phytochem.2011.01.014] [Citation(s) in RCA: 165] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 12/13/2010] [Accepted: 01/11/2011] [Indexed: 05/18/2023]
Abstract
In this review, we provide an overview of the role of glucosinolates and other phytochemical compounds present in the Brassicaceae in relation to plant protection and human health. Current knowledge of the factors that influence phytochemical content and profile in the Brassicaceae is also summarized and multi-factorial approaches are briefly discussed. Variation in agronomic conditions (plant species, cultivar, developmental stage, plant organ, plant competition, fertilization, pH), season, climatic factors, water availability, light (intensity, quality, duration) and CO(2) are known to significantly affect content and profile of phytochemicals. Phytochemicals such as the glucosinolates and leaf surface waxes play an important role in interactions with pests and pathogens. Factors that affect production of phytochemicals are important when designing plant protection strategies that exploit these compounds to minimize crop damage caused by plant pests and pathogens. Brassicaceous plants are consumed increasingly for possible health benefits, for example, glucosinolate-derived effects on degenerative diseases such as cancer, cardiovascular and neurodegenerative diseases. Thus, factors influencing phytochemical content and profile in the production of brassicaceous plants are worth considering both for plant and human health. Even though it is known that factors that influence phytochemical content and profile may interact, studies of plant compounds were, until recently, restricted by methods allowing only a reductionistic approach. It is now possible to design multi-factorial experiments that simulate their combined effects. This will provide important information to ecologists, plant breeders and agronomists.
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Affiliation(s)
- Maria Björkman
- Norwegian Institute for Agricultural and Environmental Research (Bioforsk), Plant Health and Plant Protection Division, Høgskoleveien 7, N-1432 Ås, Norway
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50
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Saito M, Kubo N, Matsumoto S, Suwabe K, Tsukada M, Hirai M. Fine mapping of the clubroot resistance gene, Crr3, in Brassica rapa. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 114:81-91. [PMID: 17039346 DOI: 10.4141/cjps10073] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2006] [Accepted: 09/08/2006] [Indexed: 05/26/2023]
Abstract
A linkage map of Chinese cabbage (Brassica rapa) was constructed to localize the clubroot resistance (CR) gene, Crr3. Quantitative trait loci analysis using an F(3) population revealed a sharp peak in the logarithm of odds score around the sequence-tagged site (STS) marker, OPC11-2S. Therefore, this region contained Crr3. Nucleotide sequences of OPC11-2S and its proximal markers showed homology to sequences in the top arm of Arabidopsis chromosome 3, suggesting a synteny between the two species. For fine mapping of Crr3, a number of STS markers were developed based on genomic information from Arabidopsis. We obtained polymorphisms in 23 Arabidopsis-derived STS markers, 11 of which were closely linked to Crr3. The precise position of Crr3 was determined using a population of 888 F(2) plants. Eighty plants showing recombination around Crr3 locus were selected and used for the mapping. A fine map of 4.74 cM was obtained, in which two markers (BrSTS-41 and BrSTS-44) and three markers (OPC11-2S, BrSTS-54 and BrSTS-61) were cosegregated. Marker genotypes of the 21 selected F(2) families and CR tests of their progenies strongly suggested that the Crr3 gene is located in a 0.35 cM segment between the two markers, BrSTS-33 and BrSTS-78.
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Affiliation(s)
- M Saito
- Graduate School of Agriculture, Kyoto Prefectural University, Kyoto Prefectural Institute of Agricultural Biotechnology, 74 Oji, Kitainayazuma, Seika, Soraku, Kyoto, 619-0244, Japan
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