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Arra Y, Auguy F, Stiebner M, Chéron S, Wudick MM, Miras M, Schepler‐Luu V, Köhler S, Cunnac S, Frommer WB, Albar L. Rice Yellow Mottle Virus resistance by genome editing of the Oryza sativa L. ssp. japonica nucleoporin gene OsCPR5.1 but not OsCPR5.2. Plant Biotechnol J 2024; 22:1299-1311. [PMID: 38124291 PMCID: PMC11022797 DOI: 10.1111/pbi.14266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 11/16/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023]
Abstract
Rice yellow mottle virus (RYMV) causes one of the most devastating rice diseases in Africa. Management of RYMV is challenging. Genetic resistance provides the most effective and environment-friendly control. The recessive resistance locus rymv2 (OsCPR5.1) had been identified in African rice (Oryza glaberrima), however, introgression into Oryza sativa ssp. japonica and indica remains challenging due to crossing barriers. Here, we evaluated whether CRISPR/Cas9 genome editing of the two rice nucleoporin paralogs OsCPR5.1 (RYMV2) and OsCPR5.2 can be used to introduce RYMV resistance into the japonica variety Kitaake. Both paralogs had been shown to complement the defects of the Arabidopsis atcpr5 mutant, indicating partial redundancy. Despite striking sequence and structural similarities between the two paralogs, only oscpr5.1 loss-of-function mutants were fully resistant, while loss-of-function oscpr5.2 mutants remained susceptible, intimating that OsCPR5.1 plays a specific role in RYMV susceptibility. Notably, edited lines with short in-frame deletions or replacements in the N-terminal domain (predicted to be unstructured) of OsCPR5.1 were hypersusceptible to RYMV. In contrast to mutations in the single Arabidopsis AtCPR5 gene, which caused severely dwarfed plants, oscpr5.1 and oscpr5.2 single and double knockout mutants showed neither substantial growth defects nor symptoms indicative lesion mimic phenotypes, possibly reflecting functional differentiation. The specific editing of OsCPR5.1, while maintaining OsCPR5.2 activity, provides a promising strategy for generating RYMV-resistance in elite Oryza sativa lines as well as for effective stacking with other RYMV resistance genes or other traits.
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Affiliation(s)
- Yugander Arra
- Faculty of Mathematics and Natural SciencesInstitute for Molecular Physiology, Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Florence Auguy
- IRD, CIRAD, INRAEPHIM Plant Health Institute of Montpellier, Institut Agro, University MontpellierMontpellierFrance
| | - Melissa Stiebner
- Faculty of Mathematics and Natural SciencesInstitute for Molecular Physiology, Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Sophie Chéron
- IRD, CIRAD, INRAEPHIM Plant Health Institute of Montpellier, Institut Agro, University MontpellierMontpellierFrance
| | - Michael M. Wudick
- Faculty of Mathematics and Natural SciencesInstitute for Molecular Physiology, Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Manuel Miras
- Faculty of Mathematics and Natural SciencesInstitute for Molecular Physiology, Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Van Schepler‐Luu
- Faculty of Mathematics and Natural SciencesInstitute for Molecular Physiology, Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Steffen Köhler
- Faculty of Mathematics and Natural SciencesInstitute for Molecular Physiology, Heinrich Heine University DüsseldorfDüsseldorfGermany
- Center for Advanced ImagingHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Sébastien Cunnac
- IRD, CIRAD, INRAEPHIM Plant Health Institute of Montpellier, Institut Agro, University MontpellierMontpellierFrance
| | - Wolf B. Frommer
- Faculty of Mathematics and Natural SciencesInstitute for Molecular Physiology, Heinrich Heine University DüsseldorfDüsseldorfGermany
- Center for Advanced ImagingHeinrich Heine University DüsseldorfDüsseldorfGermany
- Institute of Transformative Bio‐Molecules (ITbM‐WPI)Nagoya UniversityNagoyaJapan
| | - Laurence Albar
- IRD, CIRAD, INRAEPHIM Plant Health Institute of Montpellier, Institut Agro, University MontpellierMontpellierFrance
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Schepler-Luu V, Sciallano C, Stiebner M, Ji C, Boulard G, Diallo A, Auguy F, Char SN, Arra Y, Schenstnyi K, Buchholzer M, Loo EPI, Bilaro AL, Lihepanyama D, Mkuya M, Murori R, Oliva R, Cunnac S, Yang B, Szurek B, Frommer WB. Genome editing of an African elite rice variety confers resistance against endemic and emerging Xanthomonas oryzae pv. oryzae strains. eLife 2023; 12:e84864. [PMID: 37337668 DOI: 10.7554/elife.84864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 06/05/2023] [Indexed: 06/21/2023] Open
Abstract
Bacterial leaf blight (BB) of rice, caused by Xanthomonas oryzae pv. oryzae (Xoo), threatens global food security and the livelihood of small-scale rice producers. Analyses of Xoo collections from Asia, Africa and the Americas demonstrated complete continental segregation, despite robust global rice trade. Here, we report unprecedented BB outbreaks in Tanzania. The causative strains, unlike endemic African Xoo, carry Asian-type TAL effectors targeting the sucrose transporter SWEET11a and iTALes suppressing Xa1. Phylogenomics clustered these strains with Xoo from Southern-China. African rice varieties do not carry effective resistance. To protect African rice production against this emerging threat, we developed a hybrid CRISPR-Cas9/Cpf1 system to edit all known TALe-binding elements in three SWEET promoters of the East African elite variety Komboka. The edited lines show broad-spectrum resistance against Asian and African strains of Xoo, including strains recently discovered in Tanzania. The strategy could help to protect global rice crops from BB pandemics.
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Affiliation(s)
- Van Schepler-Luu
- Institute for Molecular Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Coline Sciallano
- Plant Health Institute of Montpellier, Université Montpellier, Montpellier, France
| | - Melissa Stiebner
- Institute for Molecular Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Chonghui Ji
- Division of Plant Science and Technology, University of Missouri, Columbia, United States
| | - Gabriel Boulard
- Plant Health Institute of Montpellier, Université Montpellier, Montpellier, France
| | - Amadou Diallo
- Plant Health Institute of Montpellier, Université Montpellier, Montpellier, France
| | - Florence Auguy
- Plant Health Institute of Montpellier, Université Montpellier, Montpellier, France
| | - Si Nian Char
- Division of Plant Science and Technology, University of Missouri, Columbia, United States
| | - Yugander Arra
- Institute for Molecular Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Kyrylo Schenstnyi
- Institute for Molecular Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Marcel Buchholzer
- Institute for Molecular Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Eliza P I Loo
- Institute for Molecular Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Atugonza L Bilaro
- Tanzania Agricultural Research Institute (TARI)-Uyole Centre, Mbeya, United Republic of Tanzania
| | - David Lihepanyama
- Tanzania Agricultural Research Institute (TARI)-Uyole Centre, Mbeya, United Republic of Tanzania
| | - Mohammed Mkuya
- Eastern and Southern Africa Region, International Rice Research Institute, Nairobi, Kenya
| | - Rosemary Murori
- Africa Regional Office, International Rice Research Institute, Nairobi, Kenya
| | | | - Sebastien Cunnac
- Plant Health Institute of Montpellier, Université Montpellier, Montpellier, France
| | - Bing Yang
- Division of Plant Science and Technology, University of Missouri, Columbia, United States
| | - Boris Szurek
- Plant Health Institute of Montpellier, Université Montpellier, Montpellier, France
| | - Wolf B Frommer
- Institute for Molecular Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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Luu VT, Stiebner M, Maldonado PE, Valdés S, Marín D, Delgado G, Laluz V, Wu LB, Chavarriaga P, Tohme J, Slamet-Loedin IH, Frommer WB. Efficient Agrobacterium-mediated Transformation of The Elite- Indica Rice Variety Komboka. Bio Protoc 2020; 10:e3739. [PMID: 33659399 DOI: 10.21769/bioprotoc.3739] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/27/2020] [Accepted: 06/29/2020] [Indexed: 11/02/2022] Open
Abstract
Genetic transformation is crucial for both investigating gene functions and for engineering of crops to introduce new traits. Rice (Oryza sativa L.) is an important model in plant research, since it is the staple food for more than half of the world's population. As a result, numerous transformation methods have been developed for both indica and japonica rice. Since breeders continuously develop new rice varieties, transformation protocols have to be adapted for each new variety. Here we provide an optimized transformation protocol with detailed tips and tricks for a new African variety Komboka using immature embryos. In Komboka, we obtained an apparent transformation rate of up to 48% for GUS/GFP reporter gene constructs using this optimized protocol. This protocol is also applicable for use with other elite indica rice varieties.
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Affiliation(s)
- Van T Luu
- Institute for Molecular Physiology, Heinrich Heine University of Düsseldorf (HHU), Düsseldorf, Germany.,Max-Planck-Institute for Plant Breeding Research (MPI), Köln, Germany
| | - Melissa Stiebner
- Institute for Molecular Physiology, Heinrich Heine University of Düsseldorf (HHU), Düsseldorf, Germany
| | - Paula Emmerich Maldonado
- Institute for Molecular Physiology, Heinrich Heine University of Düsseldorf (HHU), Düsseldorf, Germany
| | - Sandra Valdés
- International Center for Tropical Agriculture (CIAT), PO Box 6713, Cali, Colombia
| | - Didier Marín
- International Center for Tropical Agriculture (CIAT), PO Box 6713, Cali, Colombia
| | - Gerardo Delgado
- International Center for Tropical Agriculture (CIAT), PO Box 6713, Cali, Colombia.,International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Virginia Laluz
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Lin-Bo Wu
- Institute for Molecular Physiology, Heinrich Heine University of Düsseldorf (HHU), Düsseldorf, Germany.,Max-Planck-Institute for Plant Breeding Research (MPI), Köln, Germany
| | - Paul Chavarriaga
- International Center for Tropical Agriculture (CIAT), PO Box 6713, Cali, Colombia
| | - Joe Tohme
- International Center for Tropical Agriculture (CIAT), PO Box 6713, Cali, Colombia
| | - Inez H Slamet-Loedin
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Wolf B Frommer
- Institute for Molecular Physiology, Heinrich Heine University of Düsseldorf (HHU), Düsseldorf, Germany.,Max-Planck-Institute for Plant Breeding Research (MPI), Köln, Germany.,Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Aichi 464-8602, Japan
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