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Gladieux P, van Oosterhout C, Fairhead S, Jouet A, Ortiz D, Ravel S, Shrestha RK, Frouin J, He X, Zhu Y, Morel JB, Huang H, Kroj T, Jones JDG. Extensive immune receptor repertoire diversity in disease-resistant rice landraces. Curr Biol 2024; 34:3983-3995.e6. [PMID: 39146939 DOI: 10.1016/j.cub.2024.07.061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/19/2024] [Accepted: 07/16/2024] [Indexed: 08/17/2024]
Abstract
Plants have powerful defense mechanisms and extensive immune receptor repertoires, yet crop monocultures are prone to epidemic diseases. Rice (Oryza sativa) is susceptible to many diseases, such as rice blast caused by Magnaporthe oryzae. Varietal resistance of rice to blast relies on intracellular nucleotide binding, leucine-rich repeat (NLR) receptors that recognize specific pathogen molecules and trigger immune responses. In the Yuanyang terraces in southwest China, rice landraces rarely show severe losses to disease whereas commercial inbred lines show pronounced field susceptibility. Here, we investigate within-landrace NLR sequence diversity of nine rice landraces and eleven modern varieties using complexity reduction techniques. We find that NLRs display high sequence diversity in landraces, consistent with balancing selection, and that balancing selection at NLRs is more pervasive in landraces than modern varieties. Notably, modern varieties lack many ancient NLR haplotypes that are retained in some landraces. Our study emphasizes the value of standing genetic variation that is maintained in farmer landraces as a resource to make modern crops and agroecosystems less prone to disease. The conservation of landraces is, therefore, crucial for ensuring food security in the face of dynamic biotic and abiotic threats.
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Affiliation(s)
- Pierre Gladieux
- Plant Health Institute Montpellier, University of Montpellier, INRAE, CIRAD, IRD, Institut Agro, 34398 Montpellier, France.
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Sebastian Fairhead
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Agathe Jouet
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Diana Ortiz
- Plant Health Institute Montpellier, University of Montpellier, INRAE, CIRAD, IRD, Institut Agro, 34398 Montpellier, France
| | - Sebastien Ravel
- Plant Health Institute Montpellier, University of Montpellier, INRAE, CIRAD, IRD, Institut Agro, 34398 Montpellier, France
| | - Ram-Krishna Shrestha
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Julien Frouin
- CIRAD, UMR AGAP Institut, 34398 Montpellier, France; UMR AGAP Institut, Université de Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France
| | - Xiahong He
- School of Landscape and Horticulture, Southwest Forestry University, Kunming 650233, China
| | - Youyong Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming 650201, China
| | - Jean-Benoit Morel
- Plant Health Institute Montpellier, University of Montpellier, INRAE, CIRAD, IRD, Institut Agro, 34398 Montpellier, France
| | - Huichuan Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming 650201, China.
| | - Thomas Kroj
- Plant Health Institute Montpellier, University of Montpellier, INRAE, CIRAD, IRD, Institut Agro, 34398 Montpellier, France.
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK.
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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 BIOTECHNOLOGY JOURNAL 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] [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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Pidon H, Ruge-Wehling B, Will T, Habekuß A, Wendler N, Oldach K, Maasberg-Prelle A, Korzun V, Stein N. High-resolution mapping of Ryd4 Hb, a major resistance gene to Barley yellow dwarf virus from Hordeum bulbosum. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:60. [PMID: 38409375 PMCID: PMC10896957 DOI: 10.1007/s00122-024-04542-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 01/05/2024] [Indexed: 02/28/2024]
Abstract
KEY MESSAGE We mapped Ryd4Hb in a 66.5 kbp interval in barley and dissociated it from a sublethality factor. These results will enable a targeted selection of the resistance in barley breeding. Virus diseases are causing high yield losses in crops worldwide. The Barley yellow dwarf virus (BYDV) complex is responsible for one of the most widespread and economically important viral diseases of cereals. While no gene conferring complete resistance (immunity) has been uncovered in the primary gene pool of barley, sources of resistance were searched and identified in the wild relative Hordeum bulbosum, representing the secondary gene pool of barley. One such locus, Ryd4Hb, has been previously introgressed into barley, and was allocated to chromosome 3H, but is tightly linked to a sublethality factor that prevents the incorporation and utilization of Ryd4Hb in barley varieties. To solve this problem, we fine-mapped Ryd4Hb and separated it from this negative factor. We narrowed the Ryd4Hb locus to a corresponding 66.5 kbp physical interval in the barley 'Morex' reference genome. The region comprises a gene from the nucleotide-binding and leucine-rich repeat immune receptor family, typical of dominant virus resistance genes. The closest homolog to this Ryd4Hb candidate gene is the wheat Sr35 stem rust resistance gene. In addition to the fine mapping, we reduced the interval bearing the sublethality factor to 600 kbp in barley. Aphid feeding experiments demonstrated that Ryd4Hb provides a resistance to BYDV rather than to its vector. The presented results, including the high-throughput molecular markers, will permit a more targeted selection of the resistance in breeding, enabling the use of Ryd4Hb in barley varieties.
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Affiliation(s)
- Hélène Pidon
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France.
| | - Brigitte Ruge-Wehling
- Julius Kühn Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Agricultural Crops, Sanitz, Germany
| | - Torsten Will
- Julius Kühn Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Antje Habekuß
- Julius Kühn Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | | | | | | | | | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
- Center for Integrated Breeding Research (CiBreed), Georg-August University, Göttingen, Germany.
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Greenwood JR, Zhang X, Rathjen JP. Precision genome editing of crops for improved disease resistance. Curr Biol 2023; 33:R650-R657. [PMID: 37279695 DOI: 10.1016/j.cub.2023.04.058] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Genome editing (GE) technologies allow rapid trait manipulation in crop plants. Disease resistance is one of the best test cases for this technology because it is usually monogenic and under constant challenge by rapidly evolving pathogens. Classical methods suffer from severe bottlenecks in discovery of new resistance (R) genes and their incorporation into elite varieties, largely because they are identified in landraces and species with limited sexual compatibility, and may last only a few years before losing effectiveness. Most plant R genes encode receptors located externally on the plasma membrane (receptor proteins and receptor kinases) or internally as NOD-like receptors (NLR). Both have well defined molecular interactions with activating pathogen ligands which are virulence proteins known as effectors. As structural data for R-effector interactions accumulate, promising strategies for rational manipulation of binding specificities are emerging. This offers the potential to change elite varieties directly rather than through 10-20 years of crossing. Successful application of GE is already evident in mutation of susceptibility (S) genes required for infection. GE is in its infancy with only four modified organisms grown currently in the US. The Anglosphere and Japan seem more open to deployment of these technologies, with the European Union, Switzerland and New Zealand being notably more conservative. Consumers are not well informed on the differences between GE and classical genetic modification (GM). The possibility that minor GE changes will not be regulated as GM offers the hope that current bottlenecks to resistance breeding can be eased.
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Affiliation(s)
- Julian R Greenwood
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT 2601, Australia
| | - Xiaoxiao Zhang
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT 2601, Australia
| | - John P Rathjen
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT 2601, Australia.
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Dossou L, Pinel-Galzi A, Aribi J, Poulicard N, Albar L, Fatogoma S, Ndjiondjop MN, Koné D, Hébrard E. Molecular Tools to Infer Resistance-Breaking Abilities of Rice Yellow Mottle Virus Isolates. Viruses 2023; 15:v15040959. [PMID: 37112939 PMCID: PMC10144094 DOI: 10.3390/v15040959] [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: 03/10/2023] [Revised: 03/31/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Rice yellow mottle virus (RYMV) is a major biotic constraint to rice cultivation in Africa. RYMV shows a high genetic diversity. Viral lineages were defined according to the coat protein (CP) phylogeny. Varietal selection is considered as the most efficient way to manage RYMV. Sources of high resistance were identified mostly in accessions of the African rice species, Oryza glaberrima. Emergence of resistance-breaking (RB) genotypes was observed in controlled conditions. The RB ability was highly contrasted, depending on the resistance sources and on the RYMV lineages. A molecular marker linked to the adaptation to susceptible and resistant O. glaberrima was identified in the viral protein genome-linked (VPg). By contrast, as no molecular method was available to identify the hypervirulent lineage able to overcome all known resistance sources, plant inoculation assays were still required. Here, we designed specific RT-PCR primers to infer the RB abilities of RYMV isolates without greenhouse experiments or sequencing steps. These primers were tested and validated on 52 isolates, representative of RYMV genetic diversity. The molecular tools described in this study will contribute to optimizing the deployment strategy of resistant lines, considering the RYMV lineages identified in fields and their potential adaptability.
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Affiliation(s)
- Laurence Dossou
- AfricaRice Center, M'bé Research Station, Bouaké 01 BP 2551, Côte d'Ivoire
- WASCAL/CEA-CCBAD, Université Félix Houphouët-Boigny, Abidjan 01 BP V 34, Côte d'Ivoire
| | - Agnès Pinel-Galzi
- PHIM, Plant Health Institute, University Montpellier, IRD, INRAE, CIRAD, SupAgro, 911 Avenue Agropolis, 34394 Montpellier, France
| | - Jamel Aribi
- PHIM, Plant Health Institute, University Montpellier, IRD, INRAE, CIRAD, SupAgro, 911 Avenue Agropolis, 34394 Montpellier, France
| | - Nils Poulicard
- PHIM, Plant Health Institute, University Montpellier, IRD, INRAE, CIRAD, SupAgro, 911 Avenue Agropolis, 34394 Montpellier, France
| | - Laurence Albar
- PHIM, Plant Health Institute, University Montpellier, IRD, INRAE, CIRAD, SupAgro, 911 Avenue Agropolis, 34394 Montpellier, France
| | - Sorho Fatogoma
- WASCAL/CEA-CCBAD, Université Félix Houphouët-Boigny, Abidjan 01 BP V 34, Côte d'Ivoire
| | | | - Daouda Koné
- WASCAL/CEA-CCBAD, Université Félix Houphouët-Boigny, Abidjan 01 BP V 34, Côte d'Ivoire
| | - Eugénie Hébrard
- PHIM, Plant Health Institute, University Montpellier, IRD, INRAE, CIRAD, SupAgro, 911 Avenue Agropolis, 34394 Montpellier, France
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