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Ayala FM, Hernández-Sánchez IE, Chodasiewicz M, Wulff BBH, Svačina R. Engineering a One Health Super Wheat. ANNUAL REVIEW OF PHYTOPATHOLOGY 2024; 62:193-215. [PMID: 38857542 DOI: 10.1146/annurev-phyto-121423-042128] [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: 06/12/2024]
Abstract
Wheat is the predominant crop worldwide, contributing approximately 20% of protein and calories to the human diet. However, the yield potential of wheat faces limitations due to pests, diseases, and abiotic stresses. Although conventional breeding has improved desirable traits, the use of modern transgenesis technologies has been limited in wheat in comparison to other crops such as maize and soybean. Recent advances in wheat gene cloning and transformation technology now enable the development of a super wheat consistent with the One Health goals of sustainability, food security, and environmental stewardship. This variety combines traits to enhance pest and disease resistance, elevate grain nutritional value, and improve resilience to climate change. In this review, we explore ways to leverage current technologies to combine and transform useful traits into wheat. We also address the requirements of breeders and legal considerations such as patents and regulatory issues.
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Affiliation(s)
- Francisco M Ayala
- Bioceres Crop Solutions, Rosario, Santa Fe, Argentina
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; ,
| | - Itzell Eurídice Hernández-Sánchez
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; ,
| | - Monika Chodasiewicz
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; ,
| | - Brande B H Wulff
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; ,
| | - Radim Svačina
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; ,
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Zdrzałek R, Xi Y, Langner T, Bentham AR, Petit-Houdenot Y, De la Concepcion JC, Harant A, Shimizu M, Were V, Talbot NJ, Terauchi R, Kamoun S, Banfield MJ. Bioengineering a plant NLR immune receptor with a robust binding interface toward a conserved fungal pathogen effector. Proc Natl Acad Sci U S A 2024; 121:e2402872121. [PMID: 38968126 PMCID: PMC11252911 DOI: 10.1073/pnas.2402872121] [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: 02/11/2024] [Accepted: 05/21/2024] [Indexed: 07/07/2024] Open
Abstract
Bioengineering of plant immune receptors has emerged as a key strategy for generating novel disease resistance traits to counteract the expanding threat of plant pathogens to global food security. However, current approaches are limited by rapid evolution of plant pathogens in the field and may lack durability when deployed. Here, we show that the rice nucleotide-binding, leucine-rich repeat (NLR) immune receptor Pik-1 can be engineered to respond to a conserved family of effectors from the multihost blast fungus pathogen Magnaporthe oryzae. We switched the effector binding and response profile of the Pik NLR from its cognate rice blast effector AVR-Pik to the host-determining factor pathogenicity toward weeping lovegrass 2 (Pwl2) by installing a putative host target, OsHIPP43, in place of the native integrated heavy metal-associated domain (generating Pikm-1OsHIPP43). This chimeric receptor also responded to other PWL alleles from diverse blast isolates. The crystal structure of the Pwl2/OsHIPP43 complex revealed a multifaceted, robust interface that cannot be easily disrupted by mutagenesis, and may therefore provide durable, broad resistance to blast isolates carrying PWL effectors in the field. Our findings highlight how the host targets of pathogen effectors can be used to bioengineer recognition specificities that have more robust properties compared to naturally evolved disease resistance genes.
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Affiliation(s)
- Rafał Zdrzałek
- Department of Biochemistry and Metabolism, John Innes Centre, NorwichNR4 7UH, United Kingdom
| | - Yuxuan Xi
- Department of Biochemistry and Metabolism, John Innes Centre, NorwichNR4 7UH, United Kingdom
| | - Thorsten Langner
- The Sainsbury Laboratory, University of East Anglia, NorwichNR4 7UH, United Kingdom
| | - Adam R. Bentham
- Department of Biochemistry and Metabolism, John Innes Centre, NorwichNR4 7UH, United Kingdom
- The Sainsbury Laboratory, University of East Anglia, NorwichNR4 7UH, United Kingdom
| | | | - Juan Carlos De la Concepcion
- Department of Biochemistry and Metabolism, John Innes Centre, NorwichNR4 7UH, United Kingdom
- The Sainsbury Laboratory, University of East Anglia, NorwichNR4 7UH, United Kingdom
| | - Adeline Harant
- The Sainsbury Laboratory, University of East Anglia, NorwichNR4 7UH, United Kingdom
| | - Motoki Shimizu
- Division of Genomics and Breeding, Iwate Biotechnology Research Center, Iwate024-0003, Japan
| | - Vincent Were
- The Sainsbury Laboratory, University of East Anglia, NorwichNR4 7UH, United Kingdom
| | - Nicholas J. Talbot
- The Sainsbury Laboratory, University of East Anglia, NorwichNR4 7UH, United Kingdom
| | - Ryohei Terauchi
- Division of Genomics and Breeding, Iwate Biotechnology Research Center, Iwate024-0003, Japan
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Kyoto606-8501, Japan
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, NorwichNR4 7UH, United Kingdom
| | - Mark J. Banfield
- Department of Biochemistry and Metabolism, John Innes Centre, NorwichNR4 7UH, United Kingdom
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Wang Z, Kim W, Wang YW, Yakubovich E, Dong C, Trail F, Townsend JP, Yarden O. The Sordariomycetes: an expanding resource with Big Data for mining in evolutionary genomics and transcriptomics. FRONTIERS IN FUNGAL BIOLOGY 2023; 4:1214537. [PMID: 37746130 PMCID: PMC10512317 DOI: 10.3389/ffunb.2023.1214537] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 06/06/2023] [Indexed: 09/26/2023]
Abstract
Advances in genomics and transcriptomics accompanying the rapid accumulation of omics data have provided new tools that have transformed and expanded the traditional concepts of model fungi. Evolutionary genomics and transcriptomics have flourished with the use of classical and newer fungal models that facilitate the study of diverse topics encompassing fungal biology and development. Technological advances have also created the opportunity to obtain and mine large datasets. One such continuously growing dataset is that of the Sordariomycetes, which exhibit a richness of species, ecological diversity, economic importance, and a profound research history on amenable models. Currently, 3,574 species of this class have been sequenced, comprising nearly one-third of the available ascomycete genomes. Among these genomes, multiple representatives of the model genera Fusarium, Neurospora, and Trichoderma are present. In this review, we examine recently published studies and data on the Sordariomycetes that have contributed novel insights to the field of fungal evolution via integrative analyses of the genetic, pathogenic, and other biological characteristics of the fungi. Some of these studies applied ancestral state analysis of gene expression among divergent lineages to infer regulatory network models, identify key genetic elements in fungal sexual development, and investigate the regulation of conidial germination and secondary metabolism. Such multispecies investigations address challenges in the study of fungal evolutionary genomics derived from studies that are often based on limited model genomes and that primarily focus on the aspects of biology driven by knowledge drawn from a few model species. Rapidly accumulating information and expanding capabilities for systems biological analysis of Big Data are setting the stage for the expansion of the concept of model systems from unitary taxonomic species/genera to inclusive clusters of well-studied models that can facilitate both the in-depth study of specific lineages and also investigation of trait diversity across lineages. The Sordariomycetes class, in particular, offers abundant omics data and a large and active global research community. As such, the Sordariomycetes can form a core omics clade, providing a blueprint for the expansion of our knowledge of evolution at the genomic scale in the exciting era of Big Data and artificial intelligence, and serving as a reference for the future analysis of different taxonomic levels within the fungal kingdom.
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Affiliation(s)
- Zheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
| | - Wonyong Kim
- Korean Lichen Research Institute, Sunchon National University, Suncheon, Republic of Korea
| | - Yen-Wen Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
| | - Elizabeta Yakubovich
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Caihong Dong
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Frances Trail
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Jeffrey P. Townsend
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
- Department of Ecology and Evolutionary Biology, Program in Microbiology, and Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, United States
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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Rosa SB, Humphreys G, Langille L, Voldeng H, Henriquez MA, Burt AJ, Randhawa HS, Fetch T, Hiebert CW, Blackwell B, Zegeye T, Cummiskey A, Fortier E, Scheeren PL, Turra C, McCallum B. Characterization of Brazilian spring wheat germplasm and its potential for increasing wheat genetic diversity in Canada. Front Genet 2023; 14:1125940. [PMID: 37007938 PMCID: PMC10063806 DOI: 10.3389/fgene.2023.1125940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/06/2023] [Indexed: 03/19/2023] Open
Abstract
In the present era of climate instability, Canadian wheat production has been frequently affected by abiotic stresses and by dynamic populations of pathogens and pests that are more virulent and aggressive over time. Genetic diversity is fundamental to guarantee sustainable and improved wheat production. In the past, the genetics of Brazilian cultivars, such as Frontana, have been studied by Canadian researchers and consequently, Brazilian germplasm has been used to breed Canadian wheat cultivars. The objective of this study was to characterize a collection of Brazilian germplasm under Canadian growing conditions, including the reaction of the Brazilian germplasm to Canadian isolates/pathogens and to predict the presence of certain genes in an effort to increase genetic diversity, improve genetic gain and resilience of Canadian wheat. Over 100 Brazilian hard red spring wheat cultivars released from 1986 to 2016 were evaluated for their agronomic performance in eastern Canada. Some cultivars showed good adaptability, with several cultivars being superior or statistically equal to the highest yielding Canadian checks. Several Brazilian cultivars had excellent resistance to leaf rust, even though only a few of these tested positive for the presence of either Lr34 or Lr16, two of the most common resistance genes in Canadian wheat. Resistance for stem rust, stripe rust and powdery mildew was variable among the Brazilian cultivars. However, many Brazilian cultivars had high levels of resistance to Canadian and African - Ug99 strains of stem rust. Many Brazilian cultivars had good Fusarium head blight (FHB) resistance, which appears to be derived from Frontana. In contrast FHB resistance in Canadian wheat is largely based on the Chinese variety, Sumai-3. The Brazilian germplasm is a valuable source of semi-dwarf (Rht) genes, and 75% of the Brazilian collection possessed Rht-B1b. Many cultivars in the Brazilian collection were found to be genetically distinct from Canadian wheat, making them a valuable resource to increase the disease resistance and genetic variability in Canada and elsewhere.
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Affiliation(s)
- Silvia Barcellos Rosa
- Centre de recherche sur les grains (CÉROM), Saint-Mathieu-de-Beloeil, QC, Canada
- *Correspondence: Silvia Barcellos Rosa,
| | - Gavin Humphreys
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Linda Langille
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Harvey Voldeng
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Maria Antonia Henriquez
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Andrew James Burt
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Harpinder Singh Randhawa
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Tom Fetch
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB, Canada
| | - Colin W. Hiebert
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Barbara Blackwell
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Taye Zegeye
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Allan Cummiskey
- Charlottetown Research and Development Center, Agriculture and Agri-Food Canada, Charlottetown, PEI, Canada
| | - Eric Fortier
- Centre de recherche sur les grains (CÉROM), Saint-Mathieu-de-Beloeil, QC, Canada
| | - Pedro Luiz Scheeren
- Empresa Brasileira de Pesquisa Agropecuaria (EMBRAPA) Trigo, Passo Fundo, Brazil
| | - Camila Turra
- OR Melhoramento de Sementes, Passo Fundo, Brazil
| | - Brent McCallum
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
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