1
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Wang Y, Gao M, Jiang Y, Huang W, Zhao X, Zhu W, Li H, Wang Y, Zeng J, Wu D, Wei Y, Zhou Y, Zheng Y, Zhang P, Chen G, Kang H. Identification of candidate genes for adult plant stripe rust resistance transferred from Aegilops ventricosa 2N vS into wheat via fine mapping and transcriptome analysis. Theor Appl Genet 2024; 137:116. [PMID: 38698276 DOI: 10.1007/s00122-024-04620-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/10/2024] [Indexed: 05/05/2024]
Abstract
KEY MESSAGE An adult plant gene for resistance to stripe rust was narrowed down to the proximal one-third of the 2NvS segment translocated from Aegilops ventricosa to wheat chromosome arm 2AS, and based on the gene expression analysis, two candidate genes were identified showing a stronger response at the adult plant stage compared to the seedling stage. The 2NvS translocation from Aegilops ventricosa, known for its resistance to various diseases, has been pivotal in global wheat breeding for more than three decades. Here, we identified an adult plant resistance (APR) gene in the 2NvS segment in wheat line K13-868. Through fine mapping in a segregating near-isogenic line (NIL) derived population of 6389 plants, the candidate region for the APR gene was narrowed down to between 19.36 Mb and 33 Mb in the Jagger reference genome. Transcriptome analysis in NILs strongly suggested that this APR gene conferred resistance to stripe rust by triggering plant innate immune responses. Based on the gene expression analysis, two disease resistance-associated genes within the candidate region, TraesJAG2A03G00588940 and TraesJAG2A03G00590140, exhibited a stronger response to Puccinia striiformis f. sp. tritici (Pst) infection at the adult plant stage than at the seedling stage, indicating that they could be potential candidates for the resistance gene. Additionally, we developed a co-dominant InDel marker, InDel_31.05, for detecting this APR gene. Applying this marker showed that over one-half of the wheat varieties approved in 2021 and 2022 in Sichuan province, China, carry this gene. Agronomic trait evaluation of NILs indicated that the 2NvS segment effectively mitigated the negative effects of stripe rust on yield without affecting other important agronomic traits. This study provided valuable insights for cloning and breeding through the utilization of the APR gene present in the 2NvS segment.
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Affiliation(s)
- Yuqi Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Plant Breeding Institute, School of Life and Environmental Sciences, The University of Sydney, Cobbitty, NSW, 2570, Australia
| | - Mengru Gao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Wuzhou Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xin Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Wei Zhu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Hao Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yi Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jian Zeng
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Dandan Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yonghong Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Peng Zhang
- Plant Breeding Institute, School of Life and Environmental Sciences, The University of Sydney, Cobbitty, NSW, 2570, Australia.
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Houyang Kang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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Arndell T, Chen J, Sperschneider J, Upadhyaya NM, Blundell C, Niesner N, Outram MA, Wang A, Swain S, Luo M, Ayliffe MA, Figueroa M, Vanhercke T, Dodds PN. Pooled effector library screening in protoplasts rapidly identifies novel Avr genes. Nat Plants 2024; 10:572-580. [PMID: 38409291 PMCID: PMC11035141 DOI: 10.1038/s41477-024-01641-y] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 01/31/2024] [Indexed: 02/28/2024]
Abstract
Crop breeding for durable disease resistance is challenging due to the rapid evolution of pathogen virulence. While progress in resistance (R) gene cloning and stacking has accelerated in recent years1-3, the identification of corresponding avirulence (Avr) genes in many pathogens is hampered by the lack of high-throughput screening options. To address this technology gap, we developed a platform for pooled library screening in plant protoplasts to allow rapid identification of interacting R-Avr pairs. We validated this platform by isolating known and novel Avr genes from wheat stem rust (Puccinia graminis f. sp. tritici) after screening a designed library of putative effectors against individual R genes. Rapid Avr gene identification provides molecular tools to understand and track pathogen virulence evolution via genotype surveillance, which in turn will lead to optimized R gene stacking and deployment strategies. This platform should be broadly applicable to many crop pathogens and could potentially be adapted for screening genes involved in other protoplast-selectable traits.
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Affiliation(s)
- Taj Arndell
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Jian Chen
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Jana Sperschneider
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | | | - Cheryl Blundell
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Nathalie Niesner
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Megan A Outram
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Aihua Wang
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Steve Swain
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Ming Luo
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Michael A Ayliffe
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Melania Figueroa
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Thomas Vanhercke
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia.
| | - Peter N Dodds
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia.
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3
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Li H, Men W, Ma C, Liu Q, Dong Z, Tian X, Wang C, Liu C, Gill HS, Ma P, Zhang Z, Liu B, Zhao Y, Sehgal SK, Liu W. Wheat powdery mildew resistance gene Pm13 encodes a mixed lineage kinase domain-like protein. Nat Commun 2024; 15:2449. [PMID: 38503771 PMCID: PMC10951266 DOI: 10.1038/s41467-024-46814-7] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 03/11/2024] [Indexed: 03/21/2024] Open
Abstract
Wheat powdery mildew is one of the most destructive diseases threatening global wheat production. The wild relatives of wheat constitute rich sources of diversity for powdery mildew resistance. Here, we report the map-based cloning of the powdery mildew resistance gene Pm13 from the wild wheat species Aegilops longissima. Pm13 encodes a mixed lineage kinase domain-like (MLKL) protein that contains an N-terminal-domain of MLKL (MLKL_NTD) domain in its N-terminus and a C-terminal serine/threonine kinase (STK) domain. The resistance function of Pm13 is validated by mutagenesis, gene silencing, transgenic assay, and allelic association analyses. The development of introgression lines with significantly reduced chromosome segments of Ae. longissima encompassing Pm13 enables widespread deployment of this gene into wheat cultivars. The cloning of Pm13 may provide valuable insights into the molecular mechanisms underlying Pm13-mediated powdery mildew resistance and highlight the important roles of kinase fusion proteins (KFPs) in wheat immunity.
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Affiliation(s)
- Huanhuan Li
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, PR China
| | - Wenqiang Men
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, PR China
| | - Chao Ma
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, PR China
| | - Qianwen Liu
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, PR China
| | - Zhenjie Dong
- College of Agronomy, Nanjing Agricultural University, Nanjing, 210000, PR China
| | - Xiubin Tian
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Chaoli Wang
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, PR China
| | - Cheng Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250000, PR China
| | - Harsimardeep S Gill
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Pengtao Ma
- College of Life Sciences, Yantai University, Yantai, 264005, PR China
| | - Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, PR China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, PR China
| | - Yue Zhao
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, PR China.
| | - Sunish K Sehgal
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, 57007, USA.
| | - Wenxuan Liu
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, PR China.
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4
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Edae EA, Kosgey Z, Bajgain P, Ndung'u KC, Gemechu A, Bhavani S, Anderson JA, Rouse MN. The genetics of Ug99 stem rust resistance in spring wheat variety 'Linkert'. Front Plant Sci 2024; 15:1343148. [PMID: 38516672 PMCID: PMC10954791 DOI: 10.3389/fpls.2024.1343148] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/12/2024] [Indexed: 03/23/2024]
Abstract
Wheat stem rust caused by Puccinia graminis f. sp. tritici (Pgt) threatens wheat production worldwide. The objective of this study was to characterize wheat stem rust resistance in 'Linkert', a variety with adult plant resistance effective to emerging wheat stem rust pathogen strain Ug99. Two doubled haploid (DH) populations and one recombinant inbred line (RIL) population were developed with 'Linkert' as a stem rust resistant parent. Hard red spring wheat variety 'Forefront' and genetic stock 'LMPG' were used as stem rust susceptible parents of the DH populations. Breeding line 'MN07098-6' was used as a susceptible parent of the RIL population. Both DH and RIL populations with their parents were evaluated both at the seedling stage and in the field against Pgt races. Genotyping data of the DH populations were generated using the wheat iSelect 90k SNP assay. The RIL population was genotyped by genotyping-by-sequencing. We found QTL consistently associated with wheat stem rust resistance on chromosome 2BS for the Linkert/Forefront DH population and the Linkert/MN07098-6 RIL population both in Ethiopia and Kenya. Additional reliable QTL were detected on chromosomes 5BL (125.91 cM) and 4AL (Sr7a) for the Linkert/LMPG population in Ethiopia and Kenya. Different QTL identified in the populations reflect the importance of examining the genetics of resistance in populations derived from adapted germplasm (Forefront and MN07098-6) in addition to a genetic stock (LMPG). The associated markers in this study could be used to track and select for the identified QTL in wheat breeding programs.
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Affiliation(s)
- Erena A. Edae
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
| | - Zennah Kosgey
- Kenya Agricultural and Livestock Research Organization (KALRO), Food Crops Research Centre, Njoro, Kenya
| | - Prabin Bajgain
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, United States
| | - Kimani C. Ndung'u
- Kenya Agricultural and Livestock Research Organization (KALRO), Food Crops Research Centre, Njoro, Kenya
| | - Ashenafi Gemechu
- Ethiopian Institute of Agriculture, Debre Zeit Agricultural Research Center, Bishoftu, Ethiopia
| | - Sridhar Bhavani
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - James A. Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, United States
| | - Matthew N. Rouse
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
- Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, Saint Paul, MN, United States
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5
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Norman M, Chen C, Miah H, Patpour M, Sørensen C, Hovmøller M, Forrest K, Kumar S, Prasad P, Gangwar OP, Bhardwaj S, Bariana H, Periyannan S, Bansal U. Sr65: a widely effective gene for stem rust resistance in wheat. Theor Appl Genet 2023; 137:1. [PMID: 38071267 DOI: 10.1007/s00122-023-04507-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 11/15/2023] [Indexed: 12/18/2023]
Abstract
KEY MESSAGE Sr65 in chromosome 1A of Indian wheat landrace Hango-2 is a potentially useful all-stage resistance gene that currently protects wheat from stem rust in Australia, India, Africa and Europe. Stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), threatened global wheat production with the appearance of widely virulent races that included TTKSK and TTRTF. Indian landrace Hango-2 showed resistance to Pgt races in India and Australia. Screening of a Hango-2/Avocet 'S' (AvS) recombinant inbred line population identified two stem rust resistance genes, a novel gene (temporarily named as SrH2) from Hango-2 and Sr26 from AvS. A mapping population segregating for SrH2 alone was developed from two recombinant lines. SrH2 was mapped on the short arm of chromosome 1A, where it was flanked by KASP markers KASP_7944 (proximal) and KASP_12147 (distal). SrH2 was delimited to an interval of 1.8-2.3 Mb on chromosome arm 1AS. The failure to detect candidate genes through MutRenSeq and comparative genomic analysis with the pan-genome dataset indicated the necessity to generate a Hango-2 specific assembly for detecting the gene sequence linked with SrH2 resistance. MutRenSeq however enabled identification of SrH2-linked KASP marker sunCS_265. Markers KASP_12147 and sunCS_265 showed 92% and 85% polymorphism among an Australian cereal cultivar diversity panel and can be used for marker-assisted selection of SrH2 in breeding programs. The effectiveness of SrH2 against Pgt races from Europe, Africa, India, and Australia makes it a valuable resource for breeding stem rust-resistant wheat cultivars. Since no wheat-derived gene was previously located in chromosome arm 1AS, SrH2 represents a new locus and named as SR65.
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Affiliation(s)
- Michael Norman
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Chunhong Chen
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Hanif Miah
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia
| | - Mehran Patpour
- Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Chris Sørensen
- Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Mogens Hovmøller
- Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Kerrie Forrest
- Agriculture Victoria, Department of Energy, Environment and Climate Action, AgriBio, Centre for AgriBioscience, 5 Ring Rd., Bundoora, VIC, 3083, Australia
| | - Subodh Kumar
- Indian Council of Agricultural Research - Indian Institute of Wheat and Barley Research Regional Station, Flowerdale, Shimla, Himachal Pradesh, 171 002, India
| | - Pramod Prasad
- Indian Council of Agricultural Research - Indian Institute of Wheat and Barley Research Regional Station, Flowerdale, Shimla, Himachal Pradesh, 171 002, India
| | - Om Prakash Gangwar
- Indian Council of Agricultural Research - Indian Institute of Wheat and Barley Research Regional Station, Flowerdale, Shimla, Himachal Pradesh, 171 002, India
| | - Subhash Bhardwaj
- Indian Council of Agricultural Research - Indian Institute of Wheat and Barley Research Regional Station, Flowerdale, Shimla, Himachal Pradesh, 171 002, India
| | - Harbans Bariana
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia
- School of Science, Western Sydney University, Bourke Road, Richmond, NSW, 2753, Australia
| | - Sambasivam Periyannan
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, Canberra, ACT, 2601, Australia.
- School of Agriculture and Environmental Science, Centre for Crop Health, University of Southern Queensland, West Street, Toowoomba, QLD, 4350, Australia.
| | - Urmil Bansal
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia.
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6
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Zhang J, Nirmala J, Chen S, Jost M, Steuernagel B, Karafiatova M, Hewitt T, Li H, Edae E, Sharma K, Hoxha S, Bhatt D, Antoniou-Kourounioti R, Dodds P, Wulff BBH, Dolezel J, Ayliffe M, Hiebert C, McIntosh R, Dubcovsky J, Zhang P, Rouse MN, Lagudah E. Single amino acid change alters specificity of the multi-allelic wheat stem rust resistance locus SR9. Nat Commun 2023; 14:7354. [PMID: 37963867 PMCID: PMC10645757 DOI: 10.1038/s41467-023-42747-9] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 10/19/2023] [Indexed: 11/16/2023] Open
Abstract
Most rust resistance genes thus far isolated from wheat have a very limited number of functional alleles. Here, we report the isolation of most of the alleles at wheat stem rust resistance gene locus SR9. The seven previously reported resistance alleles (Sr9a, Sr9b, Sr9d, Sr9e, Sr9f, Sr9g, and Sr9h) are characterised using a synergistic strategy. Loss-of-function mutants and/or transgenic complementation are used to confirm Sr9b, two haplotypes of Sr9e (Sr9e_h1 and Sr9e_h2), Sr9g, and Sr9h. Each allele encodes a highly related nucleotide-binding site leucine-rich repeat (NB-LRR) type immune receptor, containing an unusual long LRR domain, that confers resistance to a unique spectrum of isolates of the wheat stem rust pathogen. The only SR9 protein effective against stem rust pathogen race TTKSK (Ug99), SR9H, differs from SR9B by a single amino acid. SR9B and SR9G resistance proteins are also distinguished by only a single amino acid. The SR9 allelic series found in the B subgenome are orthologs of wheat stem rust resistance gene Sr21 located in the A subgenome with around 85% identity in protein sequences. Together, our results show that functional diversification of allelic variants at the SR9 locus involves single and multiple amino acid changes that recognize isolates of wheat stem rust.
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Affiliation(s)
- Jianping Zhang
- CSIRO Agriculture & Food, Canberra, ACT, 2601, Australia
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, 2570, Australia
- State Key Laboratory of Wheat and Maize Crop Science, National Wheat Innovation Centre, Centre for Crop Genome Engineering, and College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, 450046, China
| | | | - Shisheng Chen
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, 261000, China
| | - Matthias Jost
- CSIRO Agriculture & Food, Canberra, ACT, 2601, Australia
| | | | - Mirka Karafiatova
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, 77900, Olomouc, Czech Republic
| | - Tim Hewitt
- CSIRO Agriculture & Food, Canberra, ACT, 2601, Australia
| | - Hongna Li
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, 261000, China
| | - Erena Edae
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Keshav Sharma
- US Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN, 55108, USA
| | - Sami Hoxha
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, 2570, Australia
| | - Dhara Bhatt
- CSIRO Agriculture & Food, Canberra, ACT, 2601, Australia
| | - Rea Antoniou-Kourounioti
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Peter Dodds
- CSIRO Agriculture & Food, Canberra, ACT, 2601, Australia
| | - Brande B H Wulff
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Centre for Desert Agriculture, KAUST, Thuwal, 23955-6900, Saudi Arabia
| | - Jaroslav Dolezel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, 77900, Olomouc, Czech Republic
| | | | - Colin Hiebert
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, 101 Route 100, Morden, MB, R6M 1Y5, Canada
| | - Robert McIntosh
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, 2570, Australia
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Peng Zhang
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, 2570, Australia.
| | - Matthew N Rouse
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA.
- US Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN, 55108, USA.
| | - Evans Lagudah
- CSIRO Agriculture & Food, Canberra, ACT, 2601, Australia.
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, 2570, Australia.
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7
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Jost M, Outram MA, Dibley K, Zhang J, Luo M, Ayliffe M. Plant and pathogen genomics: essential approaches for stem rust resistance gene stacks in wheat. Front Plant Sci 2023; 14:1223504. [PMID: 37727853 PMCID: PMC10505659 DOI: 10.3389/fpls.2023.1223504] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/27/2023] [Indexed: 09/21/2023]
Abstract
The deployment of disease resistance genes is currently the most economical and environmentally sustainable method of crop protection. However, disease resistance genes can rapidly break down because of constant pathogen evolution, particularly when they are deployed singularly. Polygenic resistance is, therefore, considered the most durable, but combining and maintaining these genes by breeding is a laborious process as effective genes are usually unlinked. The deployment of polygenic resistance with single-locus inheritance is a promising innovation that overcomes these difficulties while enhancing resistance durability. Because of major advances in genomic technologies, increasing numbers of plant resistance genes have been cloned, enabling the development of resistance transgene stacks (RTGSs) that encode multiple genes all located at a single genetic locus. Gene stacks encoding five stem rust resistance genes have now been developed in transgenic wheat and offer both breeding simplicity and potential resistance durability. The development of similar genomic resources in phytopathogens has advanced effector gene isolation and, in some instances, enabled functional validation of individual resistance genes in RTGS. Here, the wheat stem rust pathosystem is used as an illustrative example of how host and pathogen genomic advances have been instrumental in the development of RTGS, which is a strategy applicable to many other agricultural crop species.
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Affiliation(s)
| | | | | | | | | | - Michael Ayliffe
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Canberra, ACT, Australia
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Liu S, Liu D, Zhang C, Zhang W, Wang X, Mi Z, Gao X, Ren Y, Lan C, Liu X, Zhao Z, Liu J, Li H, Yuan F, Su B, Kang Z, Li C, Han D, Wang C, Cao X, Wu J. Slow stripe rusting in Chinese wheat Jimai 44 conferred by Yr29 in combination with a major QTL on chromosome arm 6AL. Theor Appl Genet 2023; 136:175. [PMID: 37498321 DOI: 10.1007/s00122-023-04420-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 07/05/2023] [Indexed: 07/28/2023]
Abstract
YrJ44, a more effective slow rusting gene than Yr29, was localized to a 3.5-cM interval between AQP markers AX-109373479 and AX-109563479 on chromosome 6AL. "Slow rusting" (SR) is a type of adult plant resistance (APR) that can provide non-specific durable resistance to stripe rust in wheat. Chinese elite wheat cultivar Jimai 44 (JM44) has maintained SR to stripe rust in China since its release despite exposure to a changing and variable pathogen population. An F2:6 population comprising 295 recombinant inbred lines (RILs) derived from a cross between JM44 and susceptible cultivar Jimai 229 (JM229) was used in genetic analysis of the SR. The RILs and parental lines were evaluated for stripe rust response in five field environments and genotyped using the Affymetrix Wheat55K SNP array and 13 allele-specific quantitative PCR-based (AQP) markers. Two stable QTL on chromosome arms 1BL and 6AL were identified by inclusive composite interval mapping. The 1BL QTL was probably the pleiotropic gene Lr46/Yr29/Sr58. QYr.nwafu-6AL (hereafter named YrJ44), mapped in a 3.5-cM interval between AQP markers AX-109373479 and AX-109563479, was more effective than Yr29 in reducing disease severity and relative area under the disease progress curve (rAUDPC). RILs harboring both YrJ44 and Yr29 displayed levels of SR equal to the resistant parent JM44. The AQP markers linked with YrJ44 were polymorphic and significantly correlated with stripe rust resistance in a panel of 1,019 wheat cultivars and breeding lines. These results suggested that adequate SR resistance can be obtained by combining YrJ44 and Yr29 and the AQP markers can be used in breeding for durable stripe rust resistance.
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Affiliation(s)
- Shengjie Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Dan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Chuanliang Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Wenjing Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Xiaoting Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Zhiwen Mi
- Key Laboratory of Agricultural Internet of Things, Ministry of Agriculture and Rural Affairs, Laboratory of Agricultural Information Perception and Intelligent Services, College of Mechanical and Electronic Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Xin Gao
- Crop Research Institute, Key Laboratory of Wheat Biology and Genetic Improvement in North Yellow and Huai River Valley, Ministry of Agriculture /Shandong Provincial Technology Innovation Center for Wheat, Shandong Academy of Agricultural Sciences / National Engineering Research Center for Wheat and Maize, Jinan, 250100, China
| | - Yong Ren
- Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Province, Mianyang Institute of Agricultural Science, Mianyang, 621023, Sichuan, China
| | - Caixia Lan
- College of Plant Science and Technology, Huazhong Agricultural University/Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Xiukun Liu
- Crop Research Institute, Key Laboratory of Wheat Biology and Genetic Improvement in North Yellow and Huai River Valley, Ministry of Agriculture /Shandong Provincial Technology Innovation Center for Wheat, Shandong Academy of Agricultural Sciences / National Engineering Research Center for Wheat and Maize, Jinan, 250100, China
| | - Zhendong Zhao
- Crop Research Institute, Key Laboratory of Wheat Biology and Genetic Improvement in North Yellow and Huai River Valley, Ministry of Agriculture /Shandong Provincial Technology Innovation Center for Wheat, Shandong Academy of Agricultural Sciences / National Engineering Research Center for Wheat and Maize, Jinan, 250100, China
| | - Jianjun Liu
- Crop Research Institute, Key Laboratory of Wheat Biology and Genetic Improvement in North Yellow and Huai River Valley, Ministry of Agriculture /Shandong Provincial Technology Innovation Center for Wheat, Shandong Academy of Agricultural Sciences / National Engineering Research Center for Wheat and Maize, Jinan, 250100, China
| | - Haosheng Li
- Crop Research Institute, Key Laboratory of Wheat Biology and Genetic Improvement in North Yellow and Huai River Valley, Ministry of Agriculture /Shandong Provincial Technology Innovation Center for Wheat, Shandong Academy of Agricultural Sciences / National Engineering Research Center for Wheat and Maize, Jinan, 250100, China
| | - Fengping Yuan
- State Key Laboratory of Crop Stress Biology for Arid Areas, Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Baofeng Su
- Key Laboratory of Agricultural Internet of Things, Ministry of Agriculture and Rural Affairs, Laboratory of Agricultural Information Perception and Intelligent Services, College of Mechanical and Electronic Engineering, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Chunlian Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Changfa Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
| | - Xinyou Cao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
- Crop Research Institute, Key Laboratory of Wheat Biology and Genetic Improvement in North Yellow and Huai River Valley, Ministry of Agriculture /Shandong Provincial Technology Innovation Center for Wheat, Shandong Academy of Agricultural Sciences / National Engineering Research Center for Wheat and Maize, Jinan, 250100, China.
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
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Ni F, Zheng Y, Liu X, Yu Y, Zhang G, Epstein L, Mao X, Wu J, Yuan C, Lv B, Yu H, Li J, Zhao Q, Yang Q, Liu J, Qi J, Fu D, Wu J. Sequencing trait-associated mutations to clone wheat rust-resistance gene YrNAM. Nat Commun 2023; 14:4353. [PMID: 37468469 PMCID: PMC10356923 DOI: 10.1038/s41467-023-39993-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 07/06/2023] [Indexed: 07/21/2023] Open
Abstract
Stripe (yellow) rust, caused by Puccinia striiformis f. sp. tritici (Pst), can significantly affect wheat production. Cloning resistance genes is critical for efficient and effective breeding of stripe rust resistant wheat cultivars. One resistance gene (Yr10CG) underlying the Pst resistance locus Yr10 has been cloned. However, following haplotype and linkage analyses indicate the presence of additional Pst resistance gene(s) underlying/near Yr10 locus. Here, we report the cloning of the Pst resistance gene YrNAM in this region using the method of sequencing trait-associated mutations (STAM). YrNAM encodes a non-canonical resistance protein with a NAM domain and a ZnF-BED domain. We show that both domains are required for resistance. Transgenic wheat harboring YrNAM gene driven by its endogenous promoter confers resistance to stripe rust races CYR32 and CYR33. YrNAM is an ancient gene and present in wild wheat species Aegilops longissima and Ae. sharonensis; however, it is absent in most wheat cultivars, which indicates its breeding value.
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Affiliation(s)
- Fei Ni
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Yanyan Zheng
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China
- Zhoucun District Agricultural Technology Service Center, Zibo, Shandong, 255300, China
| | - Xiaoke Liu
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Yang Yu
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Guangqiang Zhang
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China
- College of Agriculture and Bioengineering, Heze University, Heze, Shandong, 274015, China
| | - Lynn Epstein
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA
| | - Xue Mao
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Jingzheng Wu
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China
- Zhejiang Pharmaceutical University, Ningbo, Zhejiang, 315000, China
| | - Cuiling Yuan
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China
- Shandong Peanut Research Institute, Qingdao, Shandong, 266100, China
| | - Bo Lv
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Haixia Yu
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Jinlong Li
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Qi Zhao
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Qiyu Yang
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Jiajun Liu
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Juan Qi
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Daolin Fu
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China.
- Spring Valley Agriscience Co., Ltd., Jinan, Shandong, 250300, China.
| | - Jiajie Wu
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China.
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Tamborski J, Seong K, Liu F, Staskawicz BJ, Krasileva KV. Altering Specificity and Autoactivity of Plant Immune Receptors Sr33 and Sr50 Via a Rational Engineering Approach. Mol Plant Microbe Interact 2023; 36:434-446. [PMID: 36867580 PMCID: PMC10561695 DOI: 10.1094/mpmi-07-22-0154-r] [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] [Indexed: 08/15/2023]
Abstract
Many resistance genes deployed against pathogens in crops are intracellular nucleotide-binding (NB) leucine-rich repeat (LRR) receptors (NLRs). The ability to rationally engineer the specificity of NLRs will be crucial in the response to newly emerging crop diseases. Successful attempts to modify NLR recognition have been limited to untargeted approaches or depended on previously available structural information or knowledge of pathogen-effector targets. However, this information is not available for most NLR-effector pairs. Here, we demonstrate the precise prediction and subsequent transfer of residues involved in effector recognition between two closely related NLRs without their experimentally determined structure or detailed knowledge about their pathogen effector targets. By combining phylogenetics, allele diversity analysis, and structural modeling, we successfully predicted residues mediating interaction of Sr50 with its cognate effector AvrSr50 and transferred recognition specificity of Sr50 to the closely related NLR Sr33. We created synthetic versions of Sr33 that contain amino acids from Sr50, including Sr33syn, which gained the ability to recognize AvrSr50 with 12 amino-acid substitutions. Furthermore, we discovered that sites in the LRR domain needed to transfer recognition specificity to Sr33 also influence autoactivity in Sr50. Structural modeling suggests these residues interact with a part of the NB-ARC domain, which we named the NB-ARC latch, to possibly maintain the inactive state of the receptor. Our approach demonstrates rational modifications of NLRs, which could be useful to enhance existing elite crop germplasm. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Janina Tamborski
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, U.S.A
| | - Kyungyong Seong
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, U.S.A
| | - Furong Liu
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, U.S.A
- Innovative Genomics Institute, University of California Berkeley, 2151 Berkeley Way, Berkeley, CA 94720, U.S.A
| | - Brian J. Staskawicz
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, U.S.A
- Innovative Genomics Institute, University of California Berkeley, 2151 Berkeley Way, Berkeley, CA 94720, U.S.A
| | - Ksenia V. Krasileva
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, U.S.A
- Innovative Genomics Institute, University of California Berkeley, 2151 Berkeley Way, Berkeley, CA 94720, U.S.A
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11
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Thatcher S, Leonard A, Lauer M, Panangipalli G, Norman B, Hou Z, Llaca V, Hu WN, Qi X, Jaqueth J, Severns D, Whitaker D, Wilson B, Tabor G, Li B. The northern corn leaf blight resistance gene Ht1 encodes an nucleotide-binding, leucine-rich repeat immune receptor. Mol Plant Pathol 2023; 24:758-767. [PMID: 36180934 DOI: 10.1111/mpp.13267] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 06/11/2023]
Abstract
Northern corn leaf blight, caused by the fungal pathogen Exserohilum turcicum, is a major disease of maize. The first major locus conferring resistance to E. turcicum race 0, Ht1, was identified over 50 years ago, but the underlying gene has remained unknown. We employed a map-based cloning strategy to identify the Ht1 causal gene, which was found to be a coiled-coil nucleotide-binding, leucine-rich repeat (NLR) gene, which we named PH4GP-Ht1. Transgenic testing confirmed that introducing the native PH4GP-Ht1 sequence to a susceptible maize variety resulted in resistance to E. turcicum race 0. A survey of the maize nested association mapping genomes revealed that susceptible Ht1 alleles had very low to no expression of the gene. Overexpression of the susceptible B73 allele, however, did not result in resistant plants, indicating that sequence variations may underlie the difference between resistant and susceptible phenotypes. Modelling of the PH4GP-Ht1 protein indicated that it has structural homology to the Arabidopsis NLR resistance gene ZAR1, and probably forms a similar homopentamer structure following activation. RNA sequencing data from an infection time course revealed that 1 week after inoculation there was a threefold reduction in fungal biomass in the PH4GP-Ht1 transgenic plants compared to wild-type plants. Furthermore, PH4GP-Ht1 transgenics had significantly more inoculation-responsive differentially expressed genes than wild-type plants, with enrichment seen in genes associated with both defence and photosynthesis. These results demonstrate that the NLR PH4GP-Ht1 is the causal gene underlying Ht1, which represents a different mode of action compared to the previously reported wall-associated kinase northern corn leaf blight resistance gene Htn1/Ht2/Ht3.
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Affiliation(s)
- Shawn Thatcher
- Department of Biotechnology, Corteva Agriscience, Johnston, Iowa, USA
| | - April Leonard
- Department of Biotechnology, Corteva Agriscience, Johnston, Iowa, USA
| | - Marianna Lauer
- Department of Biotechnology, Corteva Agriscience, Johnston, Iowa, USA
- Oxford, Pennsylvania, USA
| | | | - Bret Norman
- Department of Biotechnology, Corteva Agriscience, Johnston, Iowa, USA
| | - Zhenglin Hou
- Department of Biotechnology, Corteva Agriscience, Johnston, Iowa, USA
| | - Victor Llaca
- Department of Biotechnology, Corteva Agriscience, Johnston, Iowa, USA
| | - Wang-Nan Hu
- Department of Biotechnology, Corteva Agriscience, Johnston, Iowa, USA
- Kissimmee, Florida, USA
| | - Xiuli Qi
- Department of Biotechnology, Corteva Agriscience, Johnston, Iowa, USA
| | - Jennifer Jaqueth
- Department of Biotechnology, Corteva Agriscience, Johnston, Iowa, USA
| | - Dina Severns
- Department of Seed Product Development, Corteva Agriscience, Windfall, Indiana, USA
| | - David Whitaker
- Department of Seed Product Development, Corteva Agriscience, New Holland, Pennsylvania, USA
| | - Bill Wilson
- Department of Seed Product Development, Corteva Agriscience, Windfall, Indiana, USA
| | - Girma Tabor
- Department of Biotechnology, Corteva Agriscience, Johnston, Iowa, USA
| | - Bailin Li
- Department of Biotechnology, Corteva Agriscience, Johnston, Iowa, USA
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12
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Kou H, Zhang Z, Yang Y, Wei C, Xu L, Zhang G. Advances in the Mining of Disease Resistance Genes from Aegilops tauschii and the Utilization in Wheat. Plants (Basel) 2023; 12:plants12040880. [PMID: 36840228 PMCID: PMC9966637 DOI: 10.3390/plants12040880] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/01/2022] [Accepted: 12/07/2022] [Indexed: 06/02/2023]
Abstract
Aegilops tauschii is one of the malignant weeds that affect wheat production and is also the wild species ancestor of the D genome of hexaploid wheat (Triticum aestivum, AABBDD). It contains many disease resistance genes that have been lost in the long-term evolution of wheat and is an important genetic resource for the mining and utilization of wheat disease resistance genes. In recent years, the genome sequence of Aegilops tauschii has been preliminarily completed, which has laid a good foundation for the further exploration of wheat disease resistance genes in Aegilops tauschii. There are many studies on disease resistance genes in Aegilops tauschii; in order to provide better help for the disease resistance breeding of wheat, this paper analyzes and reviews the relationship between Aegilops tauschii and wheat, the research progress of Aegilops tauschii, the discovery of disease resistance genes from Aegilops tauschii, and the application of disease resistance genes from Aegilops tauschii to modern wheat breeding, providing a reference for the further exploration and utilization of Aegilops tauschii in wheat disease resistance breeding.
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Affiliation(s)
- Hongyun Kou
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China
| | - Zhenbo Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China
| | - Yu Yang
- College of Agriculture and Bioengineering, Heze University, Heze 274015, China
| | - Changfeng Wei
- College of Agriculture and Bioengineering, Heze University, Heze 274015, China
| | - Lili Xu
- College of Agriculture and Bioengineering, Heze University, Heze 274015, China
| | - Guangqiang Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China
- College of Agriculture and Bioengineering, Heze University, Heze 274015, China
- Shandong Shofine Seed Technology Co., Ltd., Jining 272400, China
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13
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Park RF, Boshoff WHP, Cabral AL, Chong J, Martinelli JA, McMullen MS, Fetch JWM, Paczos-Grzęda E, Prats E, Roake J, Sowa S, Ziems L, Singh D. Breeding oat for resistance to the crown rust pathogen Puccinia coronata f. sp. avenae: achievements and prospects. Theor Appl Genet 2022; 135:3709-3734. [PMID: 35665827 PMCID: PMC9729147 DOI: 10.1007/s00122-022-04121-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 05/01/2022] [Indexed: 05/05/2023]
Abstract
Crown rust, caused by Puccinia coronata f. sp. avenae (Pca), is a significant impediment to global oat production. Some 98 alleles at 92 loci conferring resistance to Pca in Avena have been designated; however, allelic relationships and chromosomal locations of many of these are unknown. Long-term monitoring of Pca in Australia, North America and elsewhere has shown that it is highly variable even in the absence of sexual recombination, likely due to large pathogen populations that cycle between wild oat communities and oat crops. Efforts to develop cultivars with genetic resistance to Pca began in the 1950s. Based almost solely on all all-stage resistance, this has had temporary benefits but very limited success. The inability to eradicate wild oats, and their common occurrence in many oat growing regions, means that future strategies to control Pca must be based on the assumption of a large and variable prevailing pathogen population with high evolutionary potential, even if cultivars with durable resistance are deployed and grown widely. The presence of minor gene, additive APR to Pca in hexaploid oat germplasm opens the possibility of pyramiding several such genes to give high levels of resistance. The recent availability of reference genomes for diploid and hexaploid oat will undoubtedly accelerate efforts to discover, characterise and develop high throughput diagnostic markers to introgress and pyramid resistance to Pca in high yielding adapted oat germplasm.
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Affiliation(s)
- R F Park
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia.
| | - W H P Boshoff
- Department of Plant Sciences, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - A L Cabral
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, Canada
| | - J Chong
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, Canada
| | - J A Martinelli
- Department of Crop Science, Agronomy School, Federal University of Rio Grande Do Sul (UFRGS), Av. Bento Gonçalves, 7712, Porto Alegre, RS, 91501-970, Brazil
| | - M S McMullen
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58105-5051, USA
| | - J W Mitchell Fetch
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, Canada
| | - E Paczos-Grzęda
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, 20-950, Lublin, Poland
| | - E Prats
- CSIC-Institute for Sustainable Agriculture, Avda. Menéndez Pidal s/n. , 14004, Córdoba, Spain
| | - J Roake
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
| | - S Sowa
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, 20-950, Lublin, Poland
| | - L Ziems
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
| | - D Singh
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
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14
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Mapuranga J, Zhang N, Zhang L, Liu W, Chang J, Yang W. Harnessing genetic resistance to rusts in wheat and integrated rust management methods to develop more durable resistant cultivars. Front Plant Sci 2022; 13:951095. [PMID: 36311120 PMCID: PMC9614308 DOI: 10.3389/fpls.2022.951095] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Wheat is one of the most important staple foods on earth. Leaf rust, stem rust and stripe rust, caused by Puccini triticina, Puccinia f. sp. graminis and Puccinia f. sp. striiformis, respectively, continue to threaten wheat production worldwide. Utilization of resistant cultivars is the most effective and chemical-free strategy to control rust diseases. Convectional and molecular biology techniques identified more than 200 resistance genes and their associated markers from common wheat and wheat wild relatives, which can be used by breeders in resistance breeding programmes. However, there is continuous emergence of new races of rust pathogens with novel degrees of virulence, thus rendering wheat resistance genes ineffective. An integration of genomic selection, genome editing, molecular breeding and marker-assisted selection, and phenotypic evaluations is required in developing high quality wheat varieties with resistance to multiple pathogens. Although host genotype resistance and application of fungicides are the most generally utilized approaches for controlling wheat rusts, effective agronomic methods are required to reduce disease management costs and increase wheat production sustainability. This review gives a critical overview of the current knowledge of rust resistance, particularly race-specific and non-race specific resistance, the role of pathogenesis-related proteins, non-coding RNAs, and transcription factors in rust resistance, and the molecular basis of interactions between wheat and rust pathogens. It will also discuss the new advances on how integrated rust management methods can assist in developing more durable resistant cultivars in these pathosystems.
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Karelov A, Kozub N, Sozinova O, Pirko Y, Sozinov I, Yemets A, Blume Y. Wheat Genes Associated with Different Types of Resistance against Stem Rust ( Puccinia graminis Pers.). Pathogens 2022; 11:pathogens11101157. [PMID: 36297214 PMCID: PMC9608978 DOI: 10.3390/pathogens11101157] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/25/2022] [Accepted: 10/05/2022] [Indexed: 11/13/2022] Open
Abstract
Stem rust is one wheat's most dangerous fungal diseases. Yield losses caused by stem rust have been significant enough to cause famine in the past. Some races of stem rust are considered to be a threat to food security even nowadays. Resistance genes are considered to be the most rational environment-friendly and widely used way to control the spread of stem rust and prevent yield losses. More than 60 genes conferring resistance against stem rust have been discovered so far (so-called Sr genes). The majority of the Sr genes discovered have lost their effectiveness due to the emergence of new races of stem rust. There are some known resistance genes that have been used for over 50 years and are still effective against most known races of stem rust. The goal of this article is to outline the different types of resistance against stem rust as well as the effective and noneffective genes, conferring each type of resistance with a brief overview of their origin and usage.
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Affiliation(s)
- Anatolii Karelov
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 04123 Kyiv, Ukraine
- Institute of Plant Protection, National Academy of Agrarian Sciences of Ukraine, 03022 Kyiv, Ukraine
- Correspondence: (A.K.); (Y.B.)
| | - Natalia Kozub
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 04123 Kyiv, Ukraine
- Institute of Plant Protection, National Academy of Agrarian Sciences of Ukraine, 03022 Kyiv, Ukraine
| | - Oksana Sozinova
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 04123 Kyiv, Ukraine
- Institute of Plant Protection, National Academy of Agrarian Sciences of Ukraine, 03022 Kyiv, Ukraine
| | - Yaroslav Pirko
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 04123 Kyiv, Ukraine
| | - Igor Sozinov
- Institute of Plant Protection, National Academy of Agrarian Sciences of Ukraine, 03022 Kyiv, Ukraine
| | - Alla Yemets
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 04123 Kyiv, Ukraine
| | - Yaroslav Blume
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 04123 Kyiv, Ukraine
- Correspondence: (A.K.); (Y.B.)
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16
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Förderer A, Li E, Lawson AW, Deng YN, Sun Y, Logemann E, Zhang X, Wen J, Han Z, Chang J, Chen Y, Schulze-Lefert P, Chai J. A wheat resistosome defines common principles of immune receptor channels. Nature 2022; 610:532-539. [PMID: 36163289 PMCID: PMC9581773 DOI: 10.1038/s41586-022-05231-w] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 08/11/2022] [Indexed: 01/17/2023]
Abstract
Plant intracellular nucleotide-binding leucine-rich repeat receptors (NLRs) detect pathogen effectors to trigger immune responses1. Indirect recognition of a pathogen effector by the dicotyledonous Arabidopsis thaliana coiled-coil domain containing NLR (CNL) ZAR1 induces the formation of a large hetero-oligomeric protein complex, termed the ZAR1 resistosome, which functions as a calcium channel required for ZAR1-mediated immunity2-4. Whether the resistosome and channel activities are conserved among plant CNLs remains unknown. Here we report the cryo-electron microscopy structure of the wheat CNL Sr355 in complex with the effector AvrSr356 of the wheat stem rust pathogen. Direct effector binding to the leucine-rich repeats of Sr35 results in the formation of a pentameric Sr35-AvrSr35 complex, which we term the Sr35 resistosome. Wheat Sr35 and Arabidopsis ZAR1 resistosomes bear striking structural similarities, including an arginine cluster in the leucine-rich repeats domain not previously recognized as conserved, which co-occurs and forms intramolecular interactions with the 'EDVID' motif in the coiled-coil domain. Electrophysiological measurements show that the Sr35 resistosome exhibits non-selective cation channel activity. These structural insights allowed us to generate new variants of closely related wheat and barley orphan NLRs that recognize AvrSr35. Our data support the evolutionary conservation of CNL resistosomes in plants and demonstrate proof of principle for structure-based engineering of NLRs for crop improvement.
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Affiliation(s)
- Alexander Förderer
- Institute of Biochemistry, University of Cologne, Cologne, Germany
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ertong Li
- Institute of Biochemistry, University of Cologne, Cologne, Germany
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Aaron W Lawson
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ya-Nan Deng
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yue Sun
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Elke Logemann
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Xiaoxiao Zhang
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jie Wen
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Zhifu Han
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Junbiao Chang
- Henan Key Laboratory of Organic Functional Molecules and Drug Innovation, Henan Normal University, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Yuhang Chen
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
| | | | - Jijie Chai
- Institute of Biochemistry, University of Cologne, Cologne, Germany.
- Max Planck Institute for Plant Breeding Research, Cologne, Germany.
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China.
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17
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Zhang X, Li J, Ge Y, Guan H, Li G, Zhang S, Wang X, Li X, Chang Z, Zhang P, Jia J, Liu C. Molecular cytogenetic characterization of a new wheat- Thinopyrum intermedium homoeologous group-6 chromosome disomic substitution line with resistance to leaf rust and stripe rust. Front Plant Sci 2022; 13:1006281. [PMID: 36147230 PMCID: PMC9486089 DOI: 10.3389/fpls.2022.1006281] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 08/12/2022] [Indexed: 06/16/2023]
Abstract
Thinopyrum intermedium (JJJsJsStSt, 2n = 6x = 42), a member of tertiary gene pool of hexaploid wheat (Triticum aestivum L., AABBDD, 2n = 6x = 42), provides several beneficial genes for wheat improvement. In this study, line CH51 was developed from the BC1F8 progeny of a partial wheat-Th. intermedium amphiploid TAI8335 (2n = 56) and wheat cultivar (cv.) Jintai 170. Somatic metaphase chromosome counting showed that CH51 had stable 42 chromosomes. Genomic in situ hybridization (GISH) analysis showed that CH51 had 40 wheat chromosomes and two Th. intermedium chromosomes involving translocation between Js- and St-genome chromosomes. Non-denaturing fluorescence in situ hybridization (ND-FISH) analysis revealed that CH51 lacked a pair of wheat chromosome 6B. Wheat 55K SNP array analysis verified that chromosome 6B had the highest percentage of missing SNP loci in both CH51 and Chinese Spring (CS) nullisomic 6B-tetrasomic 6D (CS-N6BT6D) and had the highest percentage of polymorphic SNP loci between CH51 and cv. Jintai 170. We identified that CH51 was a wheat-Th. intermedium T6StS.6JsL (6B) disomic substitution line. Disease resistance assessment showed that CH51 exhibited high levels of resistance to the prevalent Chinese leaf rust and stripe rust races in the field. Therefore, the newly developed line CH51 can be utilized as a potential germplasm in wheat disease resistance breeding.
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Affiliation(s)
- Xiaojun Zhang
- College of Agriculture, Shanxi Agricultural University, Taiyuan, Shanxi, China
| | - Jianbo Li
- College of Agriculture, Shanxi Agricultural University, Taiyuan, Shanxi, China
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
- Plant Breeding Institute, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Yudi Ge
- School of Life Sciences, Shanxi University, Taiyuan, Shanxi, China
| | - Haixia Guan
- Plant Breeding Institute, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Guangrong Li
- School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Shuwei Zhang
- College of Agriculture, Shanxi Agricultural University, Taiyuan, Shanxi, China
| | - Xiaolu Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
| | - Xin Li
- College of Agriculture, Shanxi Agricultural University, Taiyuan, Shanxi, China
| | - Zhijian Chang
- College of Agriculture, Shanxi Agricultural University, Taiyuan, Shanxi, China
| | - Peng Zhang
- Plant Breeding Institute, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Juqing Jia
- College of Agriculture, Shanxi Agricultural University, Taiyuan, Shanxi, China
| | - Cheng Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
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18
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Li J, Bao Y, Han R, Wang X, Xu W, Li G, Yang Z, Zhang X, Li X, Liu A, Li H, Liu J, Zhang P, Liu C. Molecular and Cytogenetic Identification of Stem Rust Resistant Wheat- Thinopyrum intermedium Introgression Lines. Plant Dis 2022; 106:2447-2454. [PMID: 35196099 DOI: 10.1094/pdis-10-21-2274-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Thinopyrum intermedium (JJJsJsStSt, 2n = 6x = 42), a wild relative of common wheat, possesses many desirable agronomic genes for wheat improvement. The production of wheat-Thinopyrum intermedium introgression lines is a key step for transferring these beneficial genes into wheat. In this study, we characterized three wheat-Thinopyrum intermedium introgression lines TA3681, TA5566, and TA5567 using non-denaturing fluorescence in situ hybridization, genomic in situ hybridization, PCR-based landmark unique gene, and intron targeting markers. Our results showed that TA3681 is a wheat-Thinopyrum intermedium 1St disomic addition line, TA5566 is a wheat-Thinopyrum intermedium non-Robertsonian translocation line carrying two pairs of 3A-7Js translocation chromosomes, and that TA5567 is a wheat-Thinopyrum intermedium non-Robertsonian translocation line carrying a pair of 3A-7Js translocation chromosomes. We developed 13, 36, and 15 Thinopyrum intermedium chromosome-specific markers for detecting the introgressed Thinopyrum chromosomes in TA3681, TA5566, and TA5567, respectively. Stem rust assessment revealed that TA3681 exhibited a high level of seedling resistance to Chinese-prevalent Puccinia graminis f. sp. tritici pathotypes, and both TA5566 and TA5567 were highly resistant to Australian P. graminis f. sp. tritici pathotypes, indicating that Thinopyrum intermedium chromosomes 1St and 7Js might carry new stem rust resistance genes. Therefore, the new identified introgression lines may be useful for improving wheat stem rust resistance.
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Affiliation(s)
- Jianbo Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Huang and Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat and Maize, Jinan, Shandong 250100, China
- Plant Breeding Institute, School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2570, Australia
| | - Yinguang Bao
- Agronomy College, Shandong Agricultural University, Taian, Shandong 271002, China
| | - Ran Han
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Huang and Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat and Maize, Jinan, Shandong 250100, China
| | - Xiaolu Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Huang and Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat and Maize, Jinan, Shandong 250100, China
| | - Wenjing Xu
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Huang and Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat and Maize, Jinan, Shandong 250100, China
| | - Guangrong Li
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, China
| | - Zujun Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, China
| | - Xiaojun Zhang
- College of Agriculture, Shanxi Agricultural University, Taigu, Jinzhong 030810, China
| | - Xin Li
- College of Agriculture, Shanxi Agricultural University, Taigu, Jinzhong 030810, China
| | - Aifeng Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Huang and Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat and Maize, Jinan, Shandong 250100, China
| | - Haosheng Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Huang and Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat and Maize, Jinan, Shandong 250100, China
| | - Jianjun Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Huang and Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat and Maize, Jinan, Shandong 250100, China
| | - Peng Zhang
- Plant Breeding Institute, School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2570, Australia
| | - Cheng Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences/Key Laboratory of Wheat Biology and Genetic Improvement in the North Huang and Huai River Valley, Ministry of Agriculture/National Engineering Laboratory for Wheat and Maize, Jinan, Shandong 250100, China
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19
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Kale SM, Schulthess AW, Padmarasu S, Boeven PHG, Schacht J, Himmelbach A, Steuernagel B, Wulff BBH, Reif JC, Stein N, Mascher M. A catalogue of resistance gene homologs and a chromosome-scale reference sequence support resistance gene mapping in winter wheat. Plant Biotechnol J 2022; 20:1730-1742. [PMID: 35562859 PMCID: PMC9398310 DOI: 10.1111/pbi.13843] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/06/2022] [Accepted: 04/23/2022] [Indexed: 06/15/2023]
Abstract
A resistance gene atlas is an integral component of the breeder's arsenal in the fight against evolving pathogens. Thanks to high-throughput sequencing, catalogues of resistance genes can be assembled even in crop species with large and polyploid genomes. Here, we report on capture sequencing and assembly of resistance gene homologs in a diversity panel of 907 winter wheat genotypes comprising ex situ genebank accessions and current elite cultivars. In addition, we use accurate long-read sequencing and chromosome conformation capture sequencing to construct a chromosome-scale genome sequence assembly of cv. Attraktion, an elite variety representative of European winter wheat. We illustrate the value of our resource for breeders and geneticists by (i) comparing the resistance gene complements in plant genetic resources and elite varieties and (ii) conducting genome-wide associations scans (GWAS) for the fungal diseases yellow rust and leaf rust using reference-based and reference-free GWAS approaches. The gene content under GWAS peaks was scrutinized in the assembly of cv. Attraktion.
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Affiliation(s)
- Sandip M. Kale
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
| | - Albert W. Schulthess
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
| | - Sudharsan Padmarasu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
| | | | | | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
| | | | - Brande B. H. Wulff
- John Innes CentreNorwich Research ParkNorwichUK
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - Jochen C. Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
- Center for Integrated Breeding Research (CiBreed)Georg‐August‐University GöttingenGöttingenGermany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
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20
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Ortiz D, Chen J, Outram MA, Saur IM, Upadhyaya NM, Mago R, Ericsson DJ, Cesari S, Chen C, Williams SJ, Dodds PN. The stem rust effector protein AvrSr50 escapes Sr50 recognition by a substitution in a single surface-exposed residue. New Phytol 2022; 234:592-606. [PMID: 35107838 PMCID: PMC9306850 DOI: 10.1111/nph.18011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 07/26/2021] [Accepted: 01/12/2022] [Indexed: 05/28/2023]
Abstract
Pathogen effectors are crucial players during plant colonisation and infection. Plant resistance mostly relies on effector recognition to activate defence responses. Understanding how effector proteins escape from plant surveillance is important for plant breeding and resistance deployment. Here we examined the role of genetic diversity of the stem rust (Puccinia graminis f. sp. tritici (Pgt)) AvrSr50 gene in determining recognition by the corresponding wheat Sr50 resistance gene. We solved the crystal structure of a natural variant of AvrSr50 and used site-directed mutagenesis and transient expression assays to dissect the molecular mechanisms explaining gain of virulence. We report that AvrSr50 can escape recognition by Sr50 through different mechanisms including DNA insertion, stop codon loss or by amino-acid variation involving a single substitution of the AvrSr50 surface-exposed residue Q121. We also report structural homology of AvrSr50 to cupin superfamily members and carbohydrate-binding modules indicating a potential role in binding sugar moieties. This study identifies key polymorphic sites present in AvrSr50 alleles from natural stem rust populations that play important roles to escape from Sr50 recognition. This constitutes an important step to better understand Pgt effector evolution and to monitor AvrSr50 variants in natural rust populations.
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Affiliation(s)
- Diana Ortiz
- Agriculture and FoodCommonwealth Scientific and Industrial Research OrganisationCanberraACT2601Australia
- National Research Institute for AgricultureFood and Environment, Genetics and Breeding of Fruit and Vegetables UnitMontfavet84143France
| | - Jian Chen
- Agriculture and FoodCommonwealth Scientific and Industrial Research OrganisationCanberraACT2601Australia
- Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
| | - Megan A. Outram
- Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
| | - Isabel M.L. Saur
- Department of Plant–Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologne50829Germany
- University of Plant SciencesUniversity of CologneCologne50674Germany
- Cluster of Excellence on Plant SciencesCologne50674Germany
| | - Narayana M. Upadhyaya
- Agriculture and FoodCommonwealth Scientific and Industrial Research OrganisationCanberraACT2601Australia
| | - Rohit Mago
- Agriculture and FoodCommonwealth Scientific and Industrial Research OrganisationCanberraACT2601Australia
| | - Daniel J. Ericsson
- Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
- Australian SynchrotronMacromolecular CrystallographyClaytonVic.3168Australia
| | - Stella Cesari
- PHIM Plant Health InstituteUniversité de MontpellierINRAE, CIRADInstitut AgroIRDMontpellier34980France
| | - Chunhong Chen
- Agriculture and FoodCommonwealth Scientific and Industrial Research OrganisationCanberraACT2601Australia
| | - Simon J. Williams
- Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
| | - Peter N. Dodds
- Agriculture and FoodCommonwealth Scientific and Industrial Research OrganisationCanberraACT2601Australia
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21
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Yu G, Matny O, Champouret N, Steuernagel B, Moscou MJ, Hernández-Pinzón I, Green P, Hayta S, Smedley M, Harwood W, Kangara N, Yue Y, Gardener C, Banfield MJ, Olivera PD, Welchin C, Simmons J, Millet E, Minz-Dub A, Ronen M, Avni R, Sharon A, Patpour M, Justesen AF, Jayakodi M, Himmelbach A, Stein N, Wu S, Poland J, Ens J, Pozniak C, Karafiátová M, Molnár I, Doležel J, Ward ER, Reuber TL, Jones JDG, Mascher M, Steffenson BJ, Wulff BBH. Aegilops sharonensis genome-assisted identification of stem rust resistance gene Sr62. Nat Commun 2022; 13:1607. [PMID: 35338132 DOI: 10.1038/s41467-022-29132-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 02/24/2022] [Indexed: 02/06/2023] Open
Abstract
The wild relatives and progenitors of wheat have been widely used as sources of disease resistance (R) genes. Molecular identification and characterization of these R genes facilitates their manipulation and tracking in breeding programmes. Here, we develop a reference-quality genome assembly of the wild diploid wheat relative Aegilops sharonensis and use positional mapping, mutagenesis, RNA-Seq and transgenesis to identify the stem rust resistance gene Sr62, which has also been transferred to common wheat. This gene encodes a tandem kinase, homologues of which exist across multiple taxa in the plant kingdom. Stable Sr62 transgenic wheat lines show high levels of resistance against diverse isolates of the stem rust pathogen, highlighting the utility of Sr62 for deployment as part of a polygenic stack to maximize the durability of stem rust resistance. Aegilops sharonensis is a wild diploid relative of wheat. Here, the authors assemble the genome of Ae. sharonensis and use the assembly as an aid to clone the Ae. sharonensis-derived stem rust resistance gene Sr62 in the allohexaploid genome of wheat.
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22
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Qian LH, Wang Y, Chen M, Liu J, Lu RS, Zou X, Sun XQ, Zhang YM. Genome-wide Identification and Evolutionary Analysis of NBS-LRR Genes From Secale cereale. Front Genet 2021; 12:771814. [PMID: 34858486 PMCID: PMC8630680 DOI: 10.3389/fgene.2021.771814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 10/25/2021] [Indexed: 11/14/2022] Open
Abstract
Secale cereale is an important crop in the Triticeae tribe of the Poaceae family, and it has unique agronomic characteristics and genome properties. It possesses resistance to many diseases and serves as an important resource for the breeding of other Triticeae crops. We performed a genome-wide study on S. cereale to identify the largest group of plant disease resistance genes (R genes), the nucleotide-binding site-leucine-rich repeat receptor (NBS-LRR) genes. In its genome, 582 NBS-LRR genes were identified, including one from the RNL subclass and 581 from the CNL subclass. The NBS-LRR gene number in the S. cereale genome is greater than that in barley and the diploid wheat genomes. S. cereale chromosome 4 contains the largest number of NBS-LRR genes among the seven chromosomes, which is different from the pattern in barley and the genomes B and D of wheat but similar to that in the genome A of wheat. Further synteny analysis suggests that more NBS-LRR genes on chromosome 4 have been inherited from a common ancestor by S. cereale and the wheat genome A than the wheat genomes B and D. Phylogenetic analysis revealed that at least 740 NBS-LRR lineages are present in the common ancestor of S. cereale, Hordeum vulgare and Triticum urartu. However, most of them have only been inherited by one or two species, with only 65 of them preserved in all three species. The S. cereale genome inherited 382 of these ancestral NBS-LRR lineages, but 120 of them have been lost in both H. vulgare and T. urartu. This study provides the full NBS-LRR profile of the S. cereale genome, which is a resource for S. cereale breeding and indicates that S. cereale can be an important material for the molecular breeding of other Triticeae crops.
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Affiliation(s)
- Lan-Hua Qian
- Suzhou Polytechnic Institute of Agriculture, Suzhou, China
| | - Yue Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Min Chen
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Jia Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Rui-Sen Lu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Xin Zou
- Seed Administrative Station of Suzhou, Suzhou, China
| | - Xiao-Qin Sun
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Yan-Mei Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
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23
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Upadhyaya NM, Mago R, Panwar V, Hewitt T, Luo M, Chen J, Sperschneider J, Nguyen-Phuc H, Wang A, Ortiz D, Hac L, Bhatt D, Li F, Zhang J, Ayliffe M, Figueroa M, Kanyuka K, Ellis JG, Dodds PN. Genomics accelerated isolation of a new stem rust avirulence gene-wheat resistance gene pair. Nat Plants 2021; 7:1220-1228. [PMID: 34294906 DOI: 10.1038/s41477-021-00971-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 06/18/2021] [Indexed: 06/13/2023]
Abstract
Stem rust caused by the fungus Puccinia graminis f. sp. tritici (Pgt) is a devastating disease of the global staple crop wheat. Although this disease was largely controlled in the latter half of the twentieth century, new virulent strains of Pgt, such as Ug99, have recently evolved1,2. These strains have caused notable losses worldwide and their continued spread threatens global wheat production. Breeding for disease resistance provides the most cost-effective control of wheat rust diseases3. A number of rust resistance genes have been characterized in wheat and most encode immune receptors of the nucleotide-binding leucine-rich repeat (NLR) class4, which recognize pathogen effector proteins known as avirulence (Avr) proteins5. However, only two Avr genes have been identified in Pgt so far, AvrSr35 and AvrSr50 (refs. 6,7), and none in other cereal rusts8,9. The Sr27 resistance gene was first identified in a wheat line carrying an introgression of the 3R chromosome from Imperial rye10. Although not deployed widely in wheat, Sr27 is widespread in the artificial crop species Triticosecale (triticale), which is a wheat-rye hybrid and is a host for Pgt11,12. Sr27 is effective against Ug99 (ref. 13) and other recent Pgt strains14,15. Here, we identify both the Sr27 gene in wheat and the corresponding AvrSr27 gene in Pgt and show that virulence to Sr27 can arise experimentally and in the field through deletion mutations, copy number variation and expression level polymorphisms at the AvrSr27 locus.
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Affiliation(s)
- Narayana M Upadhyaya
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Rohit Mago
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Vinay Panwar
- Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Tim Hewitt
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Ming Luo
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Jian Chen
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Jana Sperschneider
- Biological Data Science Institute, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Hoa Nguyen-Phuc
- Department of Ecology and Evolutionary Biology, Vietnam National University, Ho Chi Minh, Vietnam
| | - Aihua Wang
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Diana Ortiz
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
- Génétique et Amélioration des Fruits et Légumes, INRA, Montfavet Cedex, France
| | - Luch Hac
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Dhara Bhatt
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Feng Li
- Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Jianping Zhang
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Michael Ayliffe
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Kostya Kanyuka
- Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Jeffrey G Ellis
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Peter N Dodds
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia.
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