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Kim MS, Le VT, Jung YJ, Kang KK, Cho YG. OsPUB9 Gene Edited by CRISPR/Cas9 Enhanced Resistance to Bacterial Leaf Blight in Rice ( Oryza sativa L.). Int J Mol Sci 2024; 25:7145. [PMID: 39000251 PMCID: PMC11241066 DOI: 10.3390/ijms25137145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 06/12/2024] [Accepted: 06/22/2024] [Indexed: 07/16/2024] Open
Abstract
Ubiquitination plays a crucial role in regulating signal pathways during the post-translation stage of protein synthesis in response to various environmental stresses. E3 ubiquitin ligase has been discovered to ultimately control various intracellular activities by imparting specificity to proteins to be degraded. This study was conducted to confirm biological and genetic functions of the U-box type E3 ubiquitin ligase (PUB) gene against biotic stress in rice (Oryza sativa L.). OsPUB9 gene-specific sgRNA were designed and transformants were developed through Agrobacterium-mediated transformation. Deep sequencing using callus was performed to confirm the mutation type of T0 plants, and a total of three steps were performed to select null individuals without T-DNA insertion. In the case of the OsPUB9 gene-edited line, a one bp insertion was generated by gene editing, and it was confirmed that early stop codon and multiple open reading frame (ORF) sites were created by inserting thymine. It is presumed that ubiquitination function also changed according to the change in protein structure of U-box E3 ubiquitin ligase. The OsPUB9 gene-edited null lines were inoculated with bacterial leaf blight, and finally confirmed to have a resistance phenotype similar to Jinbaek, a bacterial blight-resistant cultivar. Therefore, it is assumed that the amino acid sequence derived from the OsPUB9 gene is greatly changed, resulting in a loss of the original protein functions related to biological mechanisms. Comprehensively, it was confirmed that resistance to bacterial leaf blight stress was enhanced when a mutation occurred at a specific site of the OsPUB9 gene.
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Affiliation(s)
- Me-Sun Kim
- Department of Crop Science, College of Agriculture and Life & Environment Sciences, Chungbuk National University, Cheongju 28644, Republic of Korea; (M.-S.K.); (V.T.L.)
| | - Van Trang Le
- Department of Crop Science, College of Agriculture and Life & Environment Sciences, Chungbuk National University, Cheongju 28644, Republic of Korea; (M.-S.K.); (V.T.L.)
| | - Yu Jin Jung
- Division of Horticultural Biotechnology, Hankyong National University, Anseong 17579, Republic of Korea;
| | - Kwon-Kyoo Kang
- Division of Horticultural Biotechnology, Hankyong National University, Anseong 17579, Republic of Korea;
| | - Yong-Gu Cho
- Department of Crop Science, College of Agriculture and Life & Environment Sciences, Chungbuk National University, Cheongju 28644, Republic of Korea; (M.-S.K.); (V.T.L.)
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2
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Li J, Shi X, Wang C, Li Q, Lu J, Zeng D, Xie J, Shi Y, Zhai W, Zhou Y. Genome-Wide Association Study Identifies Resistance Loci for Bacterial Blight in a Collection of Asian Temperate Japonica Rice Germplasm. Int J Mol Sci 2023; 24:ijms24108810. [PMID: 37240156 DOI: 10.3390/ijms24108810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/29/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
Growing resistant rice cultivars is the most effective strategy to control bacterial blight (BB), a devastating disease caused by Xanthomonas oryzae pv. oryzae (Xoo). Screening resistant germplasm and identifying resistance (R) genes are prerequisites for breeding resistant rice cultivars. We conducted a genome-wide association study (GWAS) to detect quantitative trait loci (QTL) associated with BB resistance using 359 East Asian temperate Japonica accessions inoculated with two Chinese Xoo strains (KS6-6 and GV) and one Philippine Xoo strain (PXO99A). Based on the 55K SNPs Array dataset of the 359 Japonica accessions, eight QTL were identified on rice chromosomes 1, 2, 4, 10, and 11. Four of the QTL coincided with previously reported QTL, and four were novel loci. Six R genes were localized in the qBBV-11.1, qBBV-11.2, and qBBV-11.3 loci on chromosome 11 in this Japonica collection. Haplotype analysis revealed candidate genes associated with BB resistance in each QTL. Notably, LOC_Os11g47290 in qBBV-11.3, encoding a leucine-rich repeat receptor-like kinase, was a candidate gene associated with resistance to the virulent strain GV. Knockout mutants of Nipponbare with the susceptible haplotype of LOC_Os11g47290 exhibited significantly improved BB resistance. These results will be useful for cloning BB resistance genes and breeding resistant rice cultivars.
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Affiliation(s)
- Jianmin Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
| | - Xiaorong Shi
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Chunchao Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Quanlin Li
- Institute of Genetics and Developmental Biological, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Jialing Lu
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dan Zeng
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Junping Xie
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Yingyao Shi
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Wenxue Zhai
- Institute of Genetics and Developmental Biological, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Yongli Zhou
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
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3
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Garrett KA, Bebber DP, Etherton BA, Gold KM, Plex Sulá AI, Selvaraj MG. Climate Change Effects on Pathogen Emergence: Artificial Intelligence to Translate Big Data for Mitigation. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:357-378. [PMID: 35650670 DOI: 10.1146/annurev-phyto-021021-042636] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Plant pathology has developed a wide range of concepts and tools for improving plant disease management, including models for understanding and responding to new risks from climate change. Most of these tools can be improved using new advances in artificial intelligence (AI), such as machine learning to integrate massive data sets in predictive models. There is the potential to develop automated analyses of risk that alert decision-makers, from farm managers to national plant protection organizations, to the likely need for action and provide decision support for targeting responses. We review machine-learning applications in plant pathology and synthesize ideas for the next steps to make the most of these tools in digital agriculture. Global projects, such as the proposed global surveillance system for plant disease, will be strengthened by the integration of the wide range of new data, including data from tools like remote sensors, that are used to evaluate the risk ofplant disease. There is exciting potential for the use of AI to strengthen global capacity building as well, from image analysis for disease diagnostics and associated management recommendations on farmers' phones to future training methodologies for plant pathologists that are customized in real-time for management needs in response to the current risks. International cooperation in integrating data and models will help develop the most effective responses to new challenges from climate change.
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Affiliation(s)
- K A Garrett
- Plant Pathology Department, University of Florida, Gainesville, Florida, USA;
- Food Systems Institute, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - D P Bebber
- Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - B A Etherton
- Plant Pathology Department, University of Florida, Gainesville, Florida, USA;
- Food Systems Institute, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - K M Gold
- Plant Pathology and Plant Microbe Biology Section, School of Integrative Plant Sciences, Cornell AgriTech, Cornell University, Geneva, New York, USA
| | - A I Plex Sulá
- Plant Pathology Department, University of Florida, Gainesville, Florida, USA;
- Food Systems Institute, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - M G Selvaraj
- The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia
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Roy S, Mittal P, Tayi L, Bondada S, Ray MK, Patel HK, Sonti RV. Xanthomonas oryzae pv. oryzae Exoribonuclease R Is Required for Complete Virulence in Rice, Optimal Motility, and Growth Under Stress. PHYTOPATHOLOGY 2022; 112:501-510. [PMID: 34384245 DOI: 10.1094/phyto-07-21-0310-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Exoribonuclease R (RNase R) is a 3' hydrolytic exoribonuclease that can degrade structured RNA. Mutation in RNase R affects virulence of certain human pathogenic bacteria. The aim of this study was to determine whether RNase R is necessary for virulence of the phytopathogen that causes bacterial blight in rice, Xanthomonas oryzae pv. oryzae (Xoo). In silico analysis has indicated that RNase R is highly conserved among various xanthomonads. Amino acid sequence alignment of Xoo RNase R with RNase R from various taxa indicated that Xoo RNase R clustered with RNase R of order Xanthomonadales. To study its role in virulence, we generated a gene disruption mutant of Xoo RNase R. The Xoo rnr- mutant is moderately virulence deficient, and the complementing strain (rnr-/pHM1::rnr) rescued the virulence deficiency of the mutant. We investigated swimming and swarming motilities in both nutrient-deficient minimal media and nutrient-optimal media. We observed that RNase R mutation has adversely affected the swimming and swarming motilities of Xoo in optimal media. However, in nutrient-deficient media only swimming motility was noticeably affected. Growth curves in optimal media at suboptimal temperature (15°C cold stress) indicate that the Xoo rnr- mutant grows more slowly than the Xoo wild type and complementing strain (rnr-/pHM1::rnr). Given these findings, we report for the first time that RNase R function is necessary for complete virulence of Xoo in rice. It is also important for motility of Xoo in media and for growth of Xoo at suboptimal temperature.
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Affiliation(s)
- Sharmila Roy
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana State, India 500007
| | - Pragya Mittal
- MRC Human Genetics Unit, University of Edinburgh, Crewe Road South, Edinburgh, UK, EH4 2XU
| | - Lavanya Tayi
- Center for Plant Molecular Biology, Osmania University, Tarnaka, Hyderabad, Telangana State, India 500007
| | - Sahitya Bondada
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana State, India 500007
| | - Malay K Ray
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana State, India 500007
| | - Hitendra K Patel
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana State, India 500007
| | - Ramesh V Sonti
- Indian Institute of Science Education and Research, Tirupati, Andhra Pradesh, India 517507
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5
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Xu Z, Xu X, Wang Y, Liu L, Li Y, Yang Y, Liu L, Zou L, Chen G. A varied AvrXa23-like TALE enables the bacterial blight pathogen to avoid being trapped by Xa23 resistance gene in rice. J Adv Res 2022; 42:263-272. [PMID: 36513417 PMCID: PMC9788936 DOI: 10.1016/j.jare.2022.01.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/12/2022] [Accepted: 01/15/2022] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Xa23 as an executor mediates broad-spectrum resistance to Xanthomonas oryzae pv. oryzae (Xoo), which contains a matching avirulence gene avrXa23, in rice for bacterial leaf blight (BLB). avrXa23 encodes a transcription activator-like effector (TALE) protein which binds to the EBE (effector-binding element) of the Xa23 promoter. It is unclear whether the considerable pressure of Xa23 leads to an emerging Xoo strain that overcomes Xa23 resistance. OBJECTIVES This study aimed to uncover new Xoo isolate(s) that overcome Xa23-mediated resistance and to investigate how the pathogen evades the resistance. METHODS Totally 185 Xoo isolates were used to screen possibly compatible strain(s) with Xa23-containing rice CBB23 by pathogenicity test. Genome Sequencing, Southern blot, tal gene cloning, Western blot, qRT-PCR and electrophoretic mobility shift assays (EMSA) were conducted to determine the mechanism of one Xoo isolate being compatible with Xa23-containing rice. RESULTS One isolate AH28 from Anhui province is compatible with CBB23. AH28 strain contains an ortholog of avrXa23, tal7b and has 17 tal genes. The 4th RVD (repeat-variable diresidue) in Tal7b are missed and the 5th and 8th RVDs changed from NG and NS to NS and S*, respectively. These alternations made Tal7b unable to bind to the EBE of Xa23 promoter to activate the expression of Xa23 in rice. The ectopic expression of tal7b in a tal-free mutant PH of PXO99A did not alter the virulence of the strain PH, whereas avrXa23 made AH28 from compatibility to incompatibility with Xa23 rice. CONCLUSION Best to our knowledge, this is the first insight of a naturally-emerging Xoo isolate that overcomes the broad-spectrum resistance of Xa23 by the variable AvrXa23-like TALE Tal7b. The RVD alteration in AvrXa23 may be a common strategy for the pathogen evolution to avoid being "trapped" by the executor R gene.
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Affiliation(s)
- Zhengyin Xu
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China,State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiameng Xu
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China,State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yijie Wang
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Linlin Liu
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China,State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ying Li
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China,State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yangyang Yang
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Liang Liu
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lifang Zou
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China,State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Gongyou Chen
- Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China,State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China,Corresponding author.
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6
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Dossa GS, Quibod I, Atienza-Grande G, Oliva R, Maiss E, Vera Cruz C, Wydra K. Rice pyramided line IRBB67 (Xa4/Xa7) homeostasis under combined stress of high temperature and bacterial blight. Sci Rep 2020; 10:683. [PMID: 31959799 PMCID: PMC6971257 DOI: 10.1038/s41598-020-57499-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 12/21/2019] [Indexed: 01/03/2023] Open
Abstract
Rice bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) implies substantial yield loss to rice. In times of climate change, increasing temperatures are observed and further acceleration is expected worldwide. Increasing temperature often turns into inhibition of host plant defense to pathogens. Recently, a reduced resistance in rice IRBB4 carrying Xa4, but an increase in resistance in IRBB7 carrying Xa7 resistance by increasing temperature has been reported. Influence of high temperature on both R genes (Xa4+Xa7) combined in IRBB67 was analyzed under growth chamber conditions and transcriptomic analysis performed. The pyramided line IRBB67 showed no differences in lesion length between both temperature regimes, demonstrating that non-effectiveness of Xa4 at high temperature did not affect IRBB67 resistance. Moreover, Xa4 complements Xa7 resistance with no Xoo spread in planta beyond the symptomatic area under both temperature regimes in IRBB67. Time course transcriptomic analysis revealed that temperature enhanced IRBB67 resistance to combined heat and Xoo. Our findings highlight altered cellular compartments and point at a role of the cell wall involved in Xoo resistance and heat stress tolerance in both susceptible (IR24) and the resistant (IRBB67) NILs. Interestingly, up-regulation of trehalose-6-phosphatase gene and low affinity cation transporter in IRBB67 suggest that IRBB67 maintained a certain homeostasis under high temperature which may have enhanced its resistance. The interplay of both heat stress and Xoo responses as determined by up-regulated and down-regulated genes demonstrates how resistant plants cope with combined biotic and abiotic stresses.
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Affiliation(s)
- Gerbert Sylvestre Dossa
- International Rice Research Institute, Los Baños, Philippines.
- Department of Phytomedicine, Leibniz Universität Hannover, Hannover, Germany.
- Food and Agriculture Organization, Sub Regional Office for Central Africa, PO. Box 2643, Libreville, Gabon.
| | - Ian Quibod
- International Rice Research Institute, Los Baños, Philippines
| | - Genelou Atienza-Grande
- International Rice Research Institute, Los Baños, Philippines
- College of Agriculture and Food Science, University of the Philippines, Los Baños, Philippines
| | - Ricardo Oliva
- International Rice Research Institute, Los Baños, Philippines
| | - Edgar Maiss
- Department of Phytomedicine, Leibniz Universität Hannover, Hannover, Germany
| | | | - Kerstin Wydra
- Department of Phytomedicine, Leibniz Universität Hannover, Hannover, Germany
- Plant Production and Climate Change, Erfurt University of Applied Sciences, Erfurt, Germany
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7
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Eom JS, Luo D, Atienza-Grande G, Yang J, Ji C, Thi Luu V, Huguet-Tapia JC, Char SN, Liu B, Nguyen H, Schmidt SM, Szurek B, Vera Cruz C, White FF, Oliva R, Yang B, Frommer WB. Diagnostic kit for rice blight resistance. Nat Biotechnol 2019; 37:1372-1379. [PMID: 31659338 PMCID: PMC6831515 DOI: 10.1038/s41587-019-0268-y] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 08/28/2019] [Indexed: 11/09/2022]
Abstract
Blight-resistant rice lines are the most effective solution for bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo). Key resistance mechanisms involve SWEET genes as susceptibility factors. Bacterial transcription activator-like (TAL) effectors bind to effector-binding elements (EBEs) in SWEET gene promoters and induce SWEET genes. EBE variants that cannot be recognized by TAL effectors abrogate induction, causing resistance. Here we describe a diagnostic kit to enable analysis of bacterial blight in the field and identification of suitable resistant lines. Specifically, we include a SWEET promoter database, RT–PCR primers for detecting SWEET induction, engineered reporter rice lines to visualize SWEET protein accumulation and knock-out rice lines to identify virulence mechanisms in bacterial isolates. We also developed CRISPR–Cas9 genome-edited Kitaake rice to evaluate the efficacy of EBE mutations in resistance, software to predict the optimal resistance gene set for a specific geographic region, and two resistant ‘mega’ rice lines that will empower farmers to plant lines that are most likely to resist rice blight. Strategic deployment of blight-resistant rice lines is enabled by a molecular diagnostic kit.
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Affiliation(s)
- Joon-Seob Eom
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University of Düsseldorf, Düsseldorf, Germany.,Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Dangping Luo
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Genelou Atienza-Grande
- International Rice Research Institute, Metro Manila, Philippines.,College of Agriculture and Food Science, University of the Philippines, Los Baños, Philippines
| | - Jungil Yang
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University of Düsseldorf, Düsseldorf, Germany.,Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Chonghui Ji
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Van Thi Luu
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University of Düsseldorf, Düsseldorf, Germany.,Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | - Si Nian Char
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Bo Liu
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Hanna Nguyen
- International Rice Research Institute, Metro Manila, Philippines
| | - Sarah Maria Schmidt
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University of Düsseldorf, Düsseldorf, Germany.,Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Boris Szurek
- IRD, CIRAD, Université Montpellier, IPME, Montpellier, France
| | | | - Frank F White
- Department of Plant Pathology, University of Florida, Gainesville, FL, USA
| | - Ricardo Oliva
- International Rice Research Institute, Metro Manila, Philippines
| | - Bing Yang
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA. .,Donald Danforth Plant Science Center, St. Louis, MO, USA.
| | - Wolf B Frommer
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University of Düsseldorf, Düsseldorf, Germany. .,Max Planck Institute for Plant Breeding Research, Cologne, Germany. .,Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Aichi, Japan.
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8
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Chukwu SC, Rafii MY, Ramlee SI, Ismail SI, Oladosu Y, Okporie E, Onyishi G, Utobo E, Ekwu L, Swaray S, Jalloh M. Marker-assisted selection and gene pyramiding for resistance to bacterial leaf blight disease of rice (Oryza sativa L.). BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1584054] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Samuel Chibuike Chukwu
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Selangor, Malaysia
- Department of Crop Production and Landscape Management, Faculty of Agriculture and Natural Resources Management, Ebonyi State University, Abakaliki, Nigeria
| | - Mohd Y. Rafii
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Selangor, Malaysia
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia (UPM), Selangor, Malaysia
| | - Shairul Izan Ramlee
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia (UPM), Selangor, Malaysia
| | - Siti Izera Ismail
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia (UPM), Selangor, Malaysia
| | - Yussuf Oladosu
- Department of Crop Science and Technology, School of Agriculture and Agricultural Technology, Federal University of Technology, Owerri, Nigeria
| | - Emmanuel Okporie
- Department of Crop Production and Landscape Management, Faculty of Agriculture and Natural Resources Management, Ebonyi State University, Abakaliki, Nigeria
| | - Godwin Onyishi
- Department of Crop Science and Technology, School of Agriculture and Agricultural Technology, Federal University of Technology, Owerri, Nigeria
| | - Emeka Utobo
- Department of Crop Production and Landscape Management, Faculty of Agriculture and Natural Resources Management, Ebonyi State University, Abakaliki, Nigeria
| | - Lynda Ekwu
- Department of Crop Production and Landscape Management, Faculty of Agriculture and Natural Resources Management, Ebonyi State University, Abakaliki, Nigeria
| | - Senesie Swaray
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Selangor, Malaysia
| | - Momodu Jalloh
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Selangor, Malaysia
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9
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Garrett KA, Andersen KF, Asche F, Bowden RL, Forbes GA, Kulakow PA, Zhou B. Resistance Genes in Global Crop Breeding Networks. PHYTOPATHOLOGY 2017; 107:1268-1278. [PMID: 28742460 DOI: 10.1094/phyto-03-17-0082-fi] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Resistance genes are a major tool for managing crop diseases. The networks of crop breeders who exchange resistance genes and deploy them in varieties help to determine the global landscape of resistance and epidemics, an important system for maintaining food security. These networks function as a complex adaptive system, with associated strengths and vulnerabilities, and implications for policies to support resistance gene deployment strategies. Extensions of epidemic network analysis can be used to evaluate the multilayer agricultural networks that support and influence crop breeding networks. Here, we evaluate the general structure of crop breeding networks for cassava, potato, rice, and wheat. All four are clustered due to phytosanitary and intellectual property regulations, and linked through CGIAR hubs. Cassava networks primarily include public breeding groups, whereas others are more mixed. These systems must adapt to global change in climate and land use, the emergence of new diseases, and disruptive breeding technologies. Research priorities to support policy include how best to maintain both diversity and redundancy in the roles played by individual crop breeding groups (public versus private and global versus local), and how best to manage connectivity to optimize resistance gene deployment while avoiding risks to the useful life of resistance genes. [Formula: see text] Copyright © 2017 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
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Affiliation(s)
- K A Garrett
- First and second authors: Plant Pathology Department, Emerging Pathogens Institute, and Institute for Sustainable Food Systems, University of Florida, Gainesville 32611; third author: School of Forest Resources and Conservation and Institute for Sustainable Food Systems, University of Florida, Gainesville; fourth author: United States Department of Agriculture-Agricultural Research Service Hard Winter Wheat Genetics Research Unit, 4008 Throckmorton Hall, Kansas State University, Manhattan 66506; fifth author: International Potato Center, Lima, Peru; sixth author: International Institute of Tropical Agriculture, Ibadan, Nigeria; and seventh author: International Rice Research Institute, Manila, Philippines
| | - K F Andersen
- First and second authors: Plant Pathology Department, Emerging Pathogens Institute, and Institute for Sustainable Food Systems, University of Florida, Gainesville 32611; third author: School of Forest Resources and Conservation and Institute for Sustainable Food Systems, University of Florida, Gainesville; fourth author: United States Department of Agriculture-Agricultural Research Service Hard Winter Wheat Genetics Research Unit, 4008 Throckmorton Hall, Kansas State University, Manhattan 66506; fifth author: International Potato Center, Lima, Peru; sixth author: International Institute of Tropical Agriculture, Ibadan, Nigeria; and seventh author: International Rice Research Institute, Manila, Philippines
| | - F Asche
- First and second authors: Plant Pathology Department, Emerging Pathogens Institute, and Institute for Sustainable Food Systems, University of Florida, Gainesville 32611; third author: School of Forest Resources and Conservation and Institute for Sustainable Food Systems, University of Florida, Gainesville; fourth author: United States Department of Agriculture-Agricultural Research Service Hard Winter Wheat Genetics Research Unit, 4008 Throckmorton Hall, Kansas State University, Manhattan 66506; fifth author: International Potato Center, Lima, Peru; sixth author: International Institute of Tropical Agriculture, Ibadan, Nigeria; and seventh author: International Rice Research Institute, Manila, Philippines
| | - R L Bowden
- First and second authors: Plant Pathology Department, Emerging Pathogens Institute, and Institute for Sustainable Food Systems, University of Florida, Gainesville 32611; third author: School of Forest Resources and Conservation and Institute for Sustainable Food Systems, University of Florida, Gainesville; fourth author: United States Department of Agriculture-Agricultural Research Service Hard Winter Wheat Genetics Research Unit, 4008 Throckmorton Hall, Kansas State University, Manhattan 66506; fifth author: International Potato Center, Lima, Peru; sixth author: International Institute of Tropical Agriculture, Ibadan, Nigeria; and seventh author: International Rice Research Institute, Manila, Philippines
| | - G A Forbes
- First and second authors: Plant Pathology Department, Emerging Pathogens Institute, and Institute for Sustainable Food Systems, University of Florida, Gainesville 32611; third author: School of Forest Resources and Conservation and Institute for Sustainable Food Systems, University of Florida, Gainesville; fourth author: United States Department of Agriculture-Agricultural Research Service Hard Winter Wheat Genetics Research Unit, 4008 Throckmorton Hall, Kansas State University, Manhattan 66506; fifth author: International Potato Center, Lima, Peru; sixth author: International Institute of Tropical Agriculture, Ibadan, Nigeria; and seventh author: International Rice Research Institute, Manila, Philippines
| | - P A Kulakow
- First and second authors: Plant Pathology Department, Emerging Pathogens Institute, and Institute for Sustainable Food Systems, University of Florida, Gainesville 32611; third author: School of Forest Resources and Conservation and Institute for Sustainable Food Systems, University of Florida, Gainesville; fourth author: United States Department of Agriculture-Agricultural Research Service Hard Winter Wheat Genetics Research Unit, 4008 Throckmorton Hall, Kansas State University, Manhattan 66506; fifth author: International Potato Center, Lima, Peru; sixth author: International Institute of Tropical Agriculture, Ibadan, Nigeria; and seventh author: International Rice Research Institute, Manila, Philippines
| | - B Zhou
- First and second authors: Plant Pathology Department, Emerging Pathogens Institute, and Institute for Sustainable Food Systems, University of Florida, Gainesville 32611; third author: School of Forest Resources and Conservation and Institute for Sustainable Food Systems, University of Florida, Gainesville; fourth author: United States Department of Agriculture-Agricultural Research Service Hard Winter Wheat Genetics Research Unit, 4008 Throckmorton Hall, Kansas State University, Manhattan 66506; fifth author: International Potato Center, Lima, Peru; sixth author: International Institute of Tropical Agriculture, Ibadan, Nigeria; and seventh author: International Rice Research Institute, Manila, Philippines
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