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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] [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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2
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Yu G, Matny O, Gourdoupis S, Rayapuram N, Aljedaani FR, Wang YL, Nürnberger T, Johnson R, Crean EE, Saur IML, Gardener C, Yue Y, Kangara N, Steuernagel B, Hayta S, Smedley M, Harwood W, Patpour M, Wu S, Poland J, Jones JDG, Reuber TL, Ronen M, Sharon A, Rouse MN, Xu S, Holušová K, Bartoš J, Molnár I, Karafiátová M, Hirt H, Blilou I, Jaremko Ł, Doležel J, Steffenson BJ, Wulff BBH. The wheat stem rust resistance gene Sr43 encodes an unusual protein kinase. Nat Genet 2023:10.1038/s41588-023-01402-1. [PMID: 37217714 DOI: 10.1038/s41588-023-01402-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 04/18/2023] [Indexed: 05/24/2023]
Abstract
To safeguard bread wheat against pests and diseases, breeders have introduced over 200 resistance genes into its genome, thus nearly doubling the number of designated resistance genes in the wheat gene pool1. Isolating these genes facilitates their fast-tracking in breeding programs and incorporation into polygene stacks for more durable resistance. We cloned the stem rust resistance gene Sr43, which was crossed into bread wheat from the wild grass Thinopyrum elongatum2,3. Sr43 encodes an active protein kinase fused to two domains of unknown function. The gene, which is unique to the Triticeae, appears to have arisen through a gene fusion event 6.7 to 11.6 million years ago. Transgenic expression of Sr43 in wheat conferred high levels of resistance to a wide range of isolates of the pathogen causing stem rust, highlighting the potential value of Sr43 in resistance breeding and engineering.
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Affiliation(s)
- Guotai Yu
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center for Desert Agriculture, KAUST, Thuwal, Saudi Arabia
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Oadi Matny
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
| | - Spyridon Gourdoupis
- Bioscience Program, Smart Health Initiative, BESE, KAUST, Thuwal, Saudi Arabia
| | - Naganand Rayapuram
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center for Desert Agriculture, KAUST, Thuwal, Saudi Arabia
| | - Fatimah R Aljedaani
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center for Desert Agriculture, KAUST, Thuwal, Saudi Arabia
| | - Yan L Wang
- Department of Plant Biochemistry, Centre of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Thorsten Nürnberger
- Department of Plant Biochemistry, Centre of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Ryan Johnson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
| | - Emma E Crean
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Isabel M-L Saur
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| | - Catherine Gardener
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center for Desert Agriculture, KAUST, Thuwal, Saudi Arabia
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Yajuan Yue
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | | | - Sadiye Hayta
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Mark Smedley
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Wendy Harwood
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Mehran Patpour
- Department of Agroecology, Aarhus University, Slagelse, Denmark
| | - Shuangye Wu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Jesse Poland
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center for Desert Agriculture, KAUST, Thuwal, Saudi Arabia
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | | | - T Lynne Reuber
- 2Blades Foundation, Evanston, IL, USA
- Enko Chem, Mystic, CT, USA
| | - Moshe Ronen
- Institute for Cereal Crops Research, Tel Aviv University, Tel Aviv, Israel
| | - Amir Sharon
- Institute for Cereal Crops Research, and the School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Matthew N Rouse
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
- USDA-ARS, Cereal Disease Laboratory, St. Paul, MN, USA
| | - Steven Xu
- Crop Improvement and Genetics Research Unit, USDA-ARS, Western Regional Research Center, Albany, CA, USA
| | - Kateřina Holušová
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czech Republic
| | - Jan Bartoš
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czech Republic
| | - István Molnár
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czech Republic
- Centre for Agricultural Research, ELKH, Agricultural Institute, Martonvásár, Hungary
| | - Miroslava Karafiátová
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czech Republic
| | - Heribert Hirt
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center for Desert Agriculture, KAUST, Thuwal, Saudi Arabia
| | - Ikram Blilou
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center for Desert Agriculture, KAUST, Thuwal, Saudi Arabia
| | - Łukasz Jaremko
- Bioscience Program, Smart Health Initiative, BESE, KAUST, Thuwal, Saudi Arabia
- Red Sea Research Center, BESE, KAUST, Thuwal, Saudi Arabia
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czech Republic
| | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA.
| | - Brande B H Wulff
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
- Center for Desert Agriculture, KAUST, Thuwal, Saudi Arabia.
- John Innes Centre, Norwich Research Park, Norwich, UK.
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3
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Marchal C, Michalopoulou VA, Zou Z, Cevik V, Sarris PF. Show me your ID: NLR immune receptors with integrated domains in plants. Essays Biochem 2022; 66:527-539. [PMID: 35635051 PMCID: PMC9528084 DOI: 10.1042/ebc20210084] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/27/2022] [Accepted: 05/03/2022] [Indexed: 02/07/2023]
Abstract
Nucleotide-binding and leucine-rich repeat receptors (NLRs) are intracellular plant immune receptors that recognize pathogen effectors secreted into the plant cell. Canonical NLRs typically contain three conserved domains including a central nucleotide binding (NB-ARC) domain, C-terminal leucine-rich repeats (LRRs) and an N-terminal domain. A subfamily of plant NLRs contain additional noncanonical domain(s) that have potentially evolved from the integration of the effector targets in the canonical NLR structure. These NLRs with extra domains are thus referred to as NLRs with integrated domains (NLR-IDs). Here, we first summarize our current understanding of NLR-ID activation upon effector binding, focusing on the NLR pairs Pik-1/Pik-2, RGA4/RGA5, and RRS1/RPS4. We speculate on their potential oligomerization into resistosomes as it was recently shown for certain canonical plant NLRs. Furthermore, we discuss how our growing understanding of the mode of action of NLR-ID continuously informs engineering approaches to design new resistance specificities in the context of rapidly evolving pathogens.
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Affiliation(s)
- Clemence Marchal
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UH, Norwich, United Kingdom
| | - Vassiliki A Michalopoulou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion 70013, Crete, Greece
| | - Zhou Zou
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Bath BA2 7AY, United Kingdom
| | - Volkan Cevik
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Bath BA2 7AY, United Kingdom
| | - Panagiotis F Sarris
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion 70013, Crete, Greece
- Department of Biology, University of Crete, 714 09 Heraklion, Crete, Greece
- Department of Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
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Upadhaya A, Upadhaya SG, Brueggeman R. The Wheat Stem Rust ( Puccinia graminis f. sp. tritici) Population from Washington Contains the Most Virulent Isolates Reported on Barley. PLANT DISEASE 2022; 106:223-230. [PMID: 34546770 DOI: 10.1094/pdis-06-21-1195-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A diverse sexual population of wheat stem rust, Puccinia graminis f. sp. tritici, exists in the Pacific Northwest region of the United States because of the natural presence of Mahonia spp. that serves as alternate hosts to complete its sexual life cycle. The region appears to be a center of stem rust diversity in North America where novel virulence gene combinations can emerge that could overcome deployed barley and wheat stem rust resistances. A total of 100 single pustule isolates derived from stem rust samples collected from barley in Eastern Washington during the 2019 growing season were assayed for virulence on the two known effective barley stem rust resistance genes/loci, Rpg1 and the rpg4/5-mediated resistance locus (RMRL) at the seedling stage. Interestingly, 99% of the P. graminis f. sp. tritici isolates assayed were virulent on barley variety Morex carrying the Rpg1 gene, and 62% of the isolates were virulent on the variety Golden Promise transformant (H228.2c) that carries a single-copy insertion of the Rpg1 gene from Morex and is more resistant than Morex to many Rpg1 avirulent isolates. Also, 16% of the isolates were virulent on the near isogenic line HQ-1, which carries the RMRL introgression from the barley line Q21861 in the susceptible Harrington background. Alarmingly, 10% of the isolates were virulent on barley line Q21861, which contains both Rpg1 and RMRL. Thus, we report on the first P. graminis f. sp. tritici isolates worldwide with virulence on both Rpg1 and RMRL when stacked together, representing the most virulent P. graminis f. sp. tritici isolates reported on barley.
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Affiliation(s)
- Arjun Upadhaya
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164
| | - Sudha Gc Upadhaya
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164
| | - Robert Brueggeman
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164
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5
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Hatta MAM, Arora S, Ghosh S, Matny O, Smedley MA, Yu G, Chakraborty S, Bhatt D, Xia X, Steuernagel B, Richardson T, Mago R, Lagudah ES, Patron NJ, Ayliffe M, Rouse MN, Harwood WA, Periyannan S, Steffenson BJ, Wulff BB. The wheat Sr22, Sr33, Sr35 and Sr45 genes confer resistance against stem rust in barley. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:273-284. [PMID: 32744350 PMCID: PMC7868974 DOI: 10.1111/pbi.13460] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 06/17/2020] [Indexed: 05/16/2023]
Abstract
In the last 20 years, stem rust caused by the fungus Puccinia graminis f. sp. tritici (Pgt), has re-emerged as a major threat to wheat and barley production in Africa and Europe. In contrast to wheat with 60 designated stem rust (Sr) resistance genes, barley's genetic variation for stem rust resistance is very narrow with only ten resistance genes genetically identified. Of these, only one complex locus consisting of three genes is effective against TTKSK, a widely virulent Pgt race of the Ug99 tribe which emerged in Uganda in 1999 and has since spread to much of East Africa and parts of the Middle East. The objective of this study was to assess the functionality, in barley, of cloned wheat Sr genes effective against race TTKSK. Sr22, Sr33, Sr35 and Sr45 were transformed into barley cv. Golden Promise using Agrobacterium-mediated transformation. All four genes were found to confer effective stem rust resistance. The barley transgenics remained susceptible to the barley leaf rust pathogen Puccinia hordei, indicating that the resistance conferred by these wheat Sr genes was specific for Pgt. Furthermore, these transgenic plants did not display significant adverse agronomic effects in the absence of disease. Cloned Sr genes from wheat are therefore a potential source of resistance against wheat stem rust in barley.
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Affiliation(s)
- M. Asyraf Md Hatta
- John Innes CentreNorwich Research ParkNorwichUK
- Department of Agriculture TechnologyFaculty of AgricultureUniversiti Putra MalaysiaSerdangMalaysia
| | - Sanu Arora
- John Innes CentreNorwich Research ParkNorwichUK
| | - Sreya Ghosh
- John Innes CentreNorwich Research ParkNorwichUK
| | - Oadi Matny
- Department of Plant PathologyStakman Borlaug Center for Sustainable Plant HealthUniversity of MinnesotaSt. PaulMNUSA
| | | | - Guotai Yu
- John Innes CentreNorwich Research ParkNorwichUK
| | - Soma Chakraborty
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | - Dhara Bhatt
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | - Xiaodi Xia
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | | | - Terese Richardson
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | - Rohit Mago
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | - Evans S. Lagudah
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | | | - Michael Ayliffe
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | - Matthew N. Rouse
- Department of Plant PathologyStakman Borlaug Center for Sustainable Plant HealthUniversity of MinnesotaSt. PaulMNUSA
- USDA‐ARS Cereal Disease LaboratorySt. PaulMNUSA
| | | | - Sambasivam Periyannan
- Commonwealth Scientific and Industrial Research Organization (CSIRO)Agriculture and FoodCanberraACTAustralia
| | - Brian J. Steffenson
- Department of Plant PathologyStakman Borlaug Center for Sustainable Plant HealthUniversity of MinnesotaSt. PaulMNUSA
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6
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Multiple wheat genomes reveal global variation in modern breeding. Nature 2020; 588:277-283. [PMID: 33239791 PMCID: PMC7759465 DOI: 10.1038/s41586-020-2961-x] [Citation(s) in RCA: 374] [Impact Index Per Article: 93.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 09/09/2020] [Indexed: 12/24/2022]
Abstract
Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome1, and the lack of genome-assembly data for multiple wheat lines2,3. Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses4,5. We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm16, a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars. Comparison of multiple genome assemblies from wheat reveals extensive diversity that results from the complex breeding history of wheat and provides a basis for further potential improvements to this important food crop.
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Hernandez J, Del Blanco A, Filichkin T, Fisk S, Gallagher L, Helgerson L, Meints B, Mundt C, Steffenson B, Hayes P. A Genome-Wide Association Study of Resistance to Puccinia striiformis f. sp. hordei and P. graminis f. sp. tritici in Barley and Development of Resistant Germplasm. PHYTOPATHOLOGY 2020; 110:1082-1092. [PMID: 32023173 DOI: 10.1094/phyto-11-19-0415-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Stripe rust (incited by Puccinia striiformis f. sp. hordei) and stem rust (incited by P. graminis f. sp. tritici) are two of the most important diseases affecting barley. Building on prior work involving the introgression of the resistance genes rpg4/Rpg5 into diverse genetic backgrounds and the discovery of additional quantitative trait locus (QTLs) for stem rust resistance, we generated an array of germplasm in which we mapped resistance to stripe rust and stem rust. Stem rust races TTKSK and QCCJB were used for resistance mapping at the seedling and adult plant stages, respectively. Resistance to stripe rust, at the adult plant stage, was determined by QTLs on chromosomes 1H, 4H, and 5H that were previously reported in the literature. The rpg4/Rpg5 complex was validated as a source of resistance to stem rust at the seedling stage. Some parental germplasm, selected as potentially resistant to stem rust or susceptible but having other positive attributes, showed resistance at the seedling stage, which appears to be allelic to rpg4/Rpg5. The rpg4/Rpg5 complex, and this new allele, were not sufficient for adult plant resistance to stem rust in one environment. A QTL on 5H, distinct from Rpg5 and a previously reported resistance QTL, was required for resistance at the adult plant stage in all environments. This QTL is coincident with the QTL for stripe rust resistance. Germplasm with mapped genes/QTLs conferring resistance to stripe and stem rust was identified and is available as a resource to the research and breeding communities.
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Affiliation(s)
- Javier Hernandez
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
| | - Alicia Del Blanco
- Department of Plant Sciences, University of California-Davis, Davis, CA 95616
| | - Tanya Filichkin
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
| | - Scott Fisk
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
| | - Lynn Gallagher
- Department of Plant Sciences, University of California-Davis, Davis, CA 95616
| | - Laura Helgerson
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
| | - Brigid Meints
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
| | - Chris Mundt
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Brian Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Patrick Hayes
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
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8
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Sharma Poudel R, Richards J, Shrestha S, Solanki S, Brueggeman R. Transcriptome-wide association study identifies putative elicitors/suppressor of Puccinia graminis f. sp. tritici that modulate barley rpg4-mediated stem rust resistance. BMC Genomics 2019; 20:985. [PMID: 31842749 PMCID: PMC6915985 DOI: 10.1186/s12864-019-6369-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 12/04/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Stem rust is an economically important disease of wheat and barley. However, studies to gain insight into the molecular basis of these host-pathogen interactions have primarily focused on wheat because of its importance in human sustenance. This is the first extensive study utilizing a transcriptome-wide association mapping approach to identify candidate Puccinia graminis f. sp. tritici (Pgt) effectors/suppressors that elicit or suppress barley stem rust resistance genes. Here we focus on identifying Pgt elicitors that interact with the rpg4-mediated resistance locus (RMRL), the only effective source of Pgt race TTKSK resistance in barley. RESULTS Thirty-seven Pgt isolates showing differential responses on RMRL were genotyped using Restriction Site Associated DNA-Genotyping by Sequencing (RAD-GBS), identifying 24 diverse isolates that were used for transcript analysis during the infection process. In planta RNAseq was conducted with the 24 diverse isolates on the susceptible barley variety Harrington, 5 days post inoculation. The transcripts were mapped to the Pgt race SCCL reference genome identifying 114 K variants in predicted genes that would result in nonsynonymous amino acid substitutions. Transcriptome wide association analysis identified 33 variants across 28 genes that were associated with dominant RMRL virulence, thus, representing candidate suppressors of resistance. Comparative transcriptomics between the 9 RMRL virulent -vs- the 15 RMRL avirulent Pgt isolates identified 44 differentially expressed genes encoding candidate secreted effector proteins (CSEPs), among which 38 were expressed at lower levels in virulent isolates suggesting that they may represent RMRL avirulence genes. Barley transcript analysis after colonization with 9 RMRL virulent and 15 RMRL avirulent isolates inoculated on the susceptible line Harrington showed significantly lower expression of host biotic stress responses specific to RMRL virulent isolates suggesting virulent isolates harbor effectors that suppress resistance responses. CONCLUSIONS This transcriptomic study provided novel findings that help fill knowledge gaps in the understanding of stem rust virulence/avirulence and host resistance in barley. The pathogen transcriptome analysis suggested RMRL virulence might depend on the lack of avirulence genes, but evidence from pathogen association mapping analysis and host transcriptional analysis also suggested the alternate hypothesis that RMRL virulence may be due to the presence of suppressors of defense responses.
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Affiliation(s)
| | - Jonathan Richards
- Department of Plant Pathology and Crop Physiology, Louisiana State University, Baton Rouge, LA, USA
| | - Subidhya Shrestha
- Department of Plant Pathology, North Dakota State University, Fargo, ND, USA
| | - Shyam Solanki
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | - Robert Brueggeman
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA.
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9
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Solanki S, Richards J, Ameen G, Wang X, Khan A, Ali H, Stangel A, Tamang P, Gross T, Gross P, Fetch TG, Brueggeman RS. Characterization of genes required for both Rpg1 and rpg4-mediated wheat stem rust resistance in barley. BMC Genomics 2019; 20:495. [PMID: 31200635 PMCID: PMC6570958 DOI: 10.1186/s12864-019-5858-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 05/29/2019] [Indexed: 01/20/2023] Open
Abstract
Background Puccinia graminis f. sp. tritici (Pgt) race TTKSK and its lineage pose a threat to barley production world-wide justifying the extensive efforts to identify, clone, and characterize the rpg4-mediated resistance locus (RMRL), the only effective resistance to virulent Pgt races in the TTKSK lineage. The RMRL contains two nucleotide-binding domain and leucine-rich repeat (NLR) resistance genes, Rpg5 and HvRga1, which are required for resistance. The two NLRs have head-to-head genome architecture with one NLR, Rpg5, containing an integrated C-terminal protein kinase domain, characteristic of an “integrated sensory domain” resistance mechanism. Fast neutron mutagenesis of line Q21861 was utilized in a forward genetics approach to identify genetic components that function in the RMRL or Rpg1 resistance mechanisms, as Q21861 contains both genes. A mutant was identified that compromises both RMRL and Rpg1-mediated resistances and had stunted seedling roots, designated required for P. graminis resistance 9 (rpr9). Results The rpr9 mutant generated in the Q21861 background was crossed with the Swiss landrace Hv584, which carries RMRL but contains polymorphism across the genome compared to Q21861. To map Rpr9, a Hv584 x rpr9 F6:7 recombinant inbred line (RIL) population was developed. The RIL population was phenotyped with Pgt race QCCJB. The Hv584 x rpr9 RIL population was genotyped with the 9 k Illumina Infinium iSelect marker panel, producing 2701 polymorphic markers. A robust genetic map consisting of 563 noncosegregating markers was generated and used to map Rpr9 to an ~ 3.4 cM region on barley chromosome 3H. The NimbleGen barley exome capture array was utilized to capture rpr9 and wild type Q21861 exons, followed by Illumina sequencing. Comparative analysis, resulting in the identification of a 1.05 Mbp deletion at the chromosome 3H rpr9 locus. The identified deletion contains ten high confidence annotated genes with the best rpr9 candidates encoding a SKP1-like 9 protein and a F-box family protein. Conclusion Genetic mapping and exome capture rapidly identified candidate gene/s that function in RMRL and Rpg1 mediated resistance pathway/s. One or more of the identified candidate rpr9 genes are essential in the only two known effective stem rust resistance mechanisms, present in domesticated barley. Electronic supplementary material The online version of this article (10.1186/s12864-019-5858-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shyam Solanki
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Jonathan Richards
- Department of Plant Pathology and Crop Physiology, Louisiana State University AgCenter, Baton Rouge, LA, 70803, USA
| | - Gazala Ameen
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Xue Wang
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Atiya Khan
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Harris Ali
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Alex Stangel
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Prabin Tamang
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Thomas Gross
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Patrick Gross
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Thomas G Fetch
- Cereal Research Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, R6M 1Y5, Canada
| | - Robert S Brueggeman
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108-6050, USA.
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10
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Hernandez J, Steffenson BJ, Filichkin T, Fisk SP, Helgerson L, Meints B, Vining KJ, Marshall D, Del Blanco A, Chen X, Hayes PM. Introgression of rpg4/ Rpg5 Into Barley Germplasm Provides Insights Into the Genetics of Resistance to Puccinia graminis f. sp. tritici Race TTKSK and Resources for Developing Resistant Cultivars. PHYTOPATHOLOGY 2019; 109:1018-1028. [PMID: 30714882 DOI: 10.1094/phyto-09-18-0350-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Stem rust (incited by Puccinia graminis f. sp. tritici) is a devastating disease of wheat and barley in many production areas. The widely virulent African P. graminis f. sp. tritici race TTKSK is of particular concern, because most cultivars are susceptible. To prepare for the possible arrival of race TTKSK in North America, we crossed a range of barley germplasm-representing different growth habits and end uses-with donors of stem rust resistance genes Rpg1 and rpg4/Rpg5. The former confers resistance to prevalent races of P. graminis f. sp. tritici in North America, and the latter confers resistance to TTKSK and other closely related races from Africa. We produced doubled haploids from these crosses and determined their allele type at the Rpg loci and haplotype at 7,864 single-nucleotide polymorphism loci. The doubled haploids were phenotyped for TTKSK resistance at the seedling stage. Integration of genotype and phenotype data revealed that (i) Rpg1 was not associated with TTKSK resistance, (ii) rpg4/Rpg5 was necessary but was not sufficient for resistance, and (iii) specific haplotypes at two quantitative trait loci were required for rpg4/Rpg5 to confer resistance to TTKSK. To confirm whether lines found resistant to TTKSK at the seedling resistance were also resistant at the adult plant stage, a subset of doubled haploids was evaluated in Kenya. Additionally, adult plant resistance to leaf rust and stripe rust (incited by Puccinia hordei and Puccinia striiformis f. sp. hordei, respectively) was also assessed on the doubled haploids in field trials at three locations in the United States over a 2-year period. Doubled haploids were identified with adult plant resistance to all three rusts, and this germplasm is available to the research and breeding communities.
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Affiliation(s)
- Javier Hernandez
- 1 Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
| | - Brian J Steffenson
- 2 Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Tanya Filichkin
- 1 Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
| | - Scott P Fisk
- 1 Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
| | - Laura Helgerson
- 1 Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
| | - Brigid Meints
- 1 Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
| | - Kelly J Vining
- 3 Department of Horticulture, Oregon State University, Corvallis, OR 97331
| | - David Marshall
- 4 U.S. Department of Agriculture Agricultural Research Service, Raleigh, NC 27695
| | - Alicia Del Blanco
- 5 Department of Plant Sciences, University of California, Davis, CA 95616
| | - Xianming Chen
- 6 U.S. Department of Agriculture Agricultural Research Service Wheat Health, Genetics, and Quality Research Unit and Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430
| | - Patrick M Hayes
- 1 Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
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11
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Sharma Poudel R, Al-Hashel AF, Gross T, Gross P, Brueggeman R. Pyramiding rpg4- and Rpg1-Mediated Stem Rust Resistance in Barley Requires the Rrr1 Gene for Both to Function. FRONTIERS IN PLANT SCIENCE 2018; 9:1789. [PMID: 30568667 PMCID: PMC6290389 DOI: 10.3389/fpls.2018.01789] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 11/19/2018] [Indexed: 05/20/2023]
Abstract
Stem rust, caused by Puccinia graminis f. sp. tritici (Pgt) is an economically important disease of wheat and barley. Rpg1 is the only resistance gene deployed in Midwestern US barley varieties and provides remarkable resistance to most North American races, except Pgt race QCCJB. Rpg1 is also ineffective against Pgt race TTKSK and its lineage that originated in Africa. The barley rpg4-mediated resistance locus (RMRL) conferring resistance to Pgt races QCCJB and TTKSK was isolated from line Q21861, which is resistant to all known Pgt races due to Rpg1 and RMRL. To develop elite barley varieties RMRL was pyramided into the varieties, Pinnacle and Conlon (both contain Rpg1), producing the near isogenic lines (NILs), Pinnacle RMRL-NIL (PRN) and Conlon RMRL-NIL (CRN). The CRN was resistant to Pgt races QCCJB (RMRL specific) and HKHJC (Rpg1 specific) at the seedling stage and Pgt race TTKSK (RMRL specific) at the adult stage. In contrast, PRN was susceptible to QCCJB and HKHJC at the seedling stage and TTKSK at the adult stage. Interestingly, PRN's susceptibility to QCCJB and HKHJC showed that RMRL was non-functional in the Pinnacle background but its presence also suppressed Rpg1-mediated resistance. Thus, in the absence of a gene/s found in the Q21861 background, Rpg1 becomes non-functional if RMRL is present, suggesting that another polymorphic gene, that we designated Rrr1 (required for rpg4-mediated resistance 1), is required for RMRL resistance and Rpg1-mediated resistance in the presence of RMRL. Utilizing a PRN/Q21861 derived recombinant inbred line (RIL) population, Rrr1 was delimited to a ∼0.5 MB physical region, slightly proximal (∼1.8 MB) of RMRL on barley chromosome 5H. A second gene, designated required for Rpg1-mediated resistance 2 (Rrr2), with duplicate gene action to Rrr1 in Rpg1-mediated resistance function, was genetically delimited to a physical region of ∼0.7 MB, slightly distal (∼3.1 MB) to Rpg1 on the short arm of barley chromosome 7H. Thus, Rrr1 is required for RMRL resistance and Rrr1 or Rrr2 is required for functional Rpg1-mediated resistance in the presence of the RMRL introgression. Candidate Rrr1 and Rrr2 genes were identified that need to be considered when pyramiding Rpg1 and RMRL in barley.
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Affiliation(s)
| | | | | | | | - Robert Brueggeman
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
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12
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Case AJ, Bhavani S, Macharia G, Pretorius Z, Coetzee V, Kloppers F, Tyagi P, Brown-Guedira G, Steffenson BJ. Mapping adult plant stem rust resistance in barley accessions Hietpas-5 and GAW-79. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2245-2266. [PMID: 30109391 DOI: 10.1007/s00122-018-3149-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/23/2018] [Indexed: 06/08/2023]
Abstract
Key message Major stem rust resistance QTLs proposed to be Rpg2 from Hietpas-5 and Rpg3 from GAW-79 were identified in chromosomes 2H and 5H, respectively, and will enhance the diversity of stem rust resistance in barley improvement programs. Stem rust is a devastating disease of cereal crops worldwide. In barley (Hordeum vulgare ssp. vulgare), the disease is caused by two pathogens: Puccinia graminis f. sp. secalis (Pgs) and Puccinia graminis f. sp. tritici (Pgt). In North America, the stem rust resistance gene Rpg1 has protected barley from serious losses for more than 60 years; however, widely virulent Pgt races from Africa in the Ug99 group threaten the crop. The accessions Hietpas-5 (CIho 7124) and GAW-79 (PI 382313) both possess moderate-to-high levels of adult plant resistance to stem rust and are the sources of the resistance genes Rpg2 and Rpg3, respectively. To identify quantitative trait loci (QTL) for stem rust resistance in Hietpas-5 and GAW-79, two biparental populations were developed with Hiproly (PI 60693), a stem rust-susceptible accession. Both populations were phenotyped to the North American Pgt races of MCCFC, QCCJB, and HKHJC in St. Paul, Minnesota, and to African Pgt races (predominately TTKSK in the Ug99 group) in Njoro, Kenya. In the Hietpas-5/Hiproly population, a major effect QTL was identified in chromosome 2H, which is proposed as the location for Rpg2. In the GAW-79/Hiproly population, a major effect QTL was identified in chromosome 5H and is the proposed location for Rpg3. These QTLs will enhance the diversity of stem rust resistance in barley improvement programs.
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Affiliation(s)
- Austin J Case
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
| | - Sridhar Bhavani
- Centro Internacional de Mejoramiento de Maíz y Trigo (CIMMYT), Nairobi, Kenya
| | - Godwin Macharia
- Kenya Agriculture and Livestock Research Organization (KALRO), Njoro, Kenya
| | - Zacharias Pretorius
- Department of Plant Sciences, University of the Free State, Bloemfontein, Republic of South Africa
| | - Vicky Coetzee
- Pannar Seed (Pyt) Ltd, Greytown, Republic of South Africa
| | | | - Priyanka Tyagi
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | | | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA.
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13
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Xing L, Hu P, Liu J, Witek K, Zhou S, Xu J, Zhou W, Gao L, Huang Z, Zhang R, Wang X, Chen P, Wang H, Jones JDG, Karafiátová M, Vrána J, Bartoš J, Doležel J, Tian Y, Wu Y, Cao A. Pm21 from Haynaldia villosa Encodes a CC-NBS-LRR Protein Conferring Powdery Mildew Resistance in Wheat. MOLECULAR PLANT 2018; 11:874-878. [PMID: 29567451 DOI: 10.1016/j.molp.2018.02.013] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 02/28/2018] [Accepted: 02/28/2018] [Indexed: 05/18/2023]
Affiliation(s)
- Liping Xing
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China.
| | - Ping Hu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China
| | - Jiaqian Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China
| | - Kamil Witek
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UK
| | - Shuang Zhou
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China
| | - Jiefei Xu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China
| | - Weihao Zhou
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China
| | - Li Gao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China
| | - Zhenpu Huang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China
| | - Ruiqi Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China
| | - Xiue Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China
| | - Peidu Chen
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China
| | - Haiyan Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China
| | | | - Miroslava Karafiátová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371 Olomouc, Czech Republic
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371 Olomouc, Czech Republic
| | - Jan Bartoš
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371 Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 78371 Olomouc, Czech Republic
| | - Yuanchun Tian
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China
| | - Yufeng Wu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China
| | - Aizhong Cao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China.
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14
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Case AJ, Bhavani S, Macharia G, Steffenson BJ. Genome-wide association study of stem rust resistance in a world collection of cultivated barley. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:107-126. [PMID: 29177535 DOI: 10.1007/s00122-017-2989-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 09/19/2017] [Indexed: 05/20/2023]
Abstract
QTL conferring a 14-40% reduction in adult plant stem rust severity to multiple races of Pgt were found on chromosome 5H and will be useful in barley breeding. Stem rust, caused by Puccinia graminis f. sp. tritici (Pgt) is an important disease of barley. The resistance gene Rpg1 has protected the crop against stem rust losses for over 70 years in North America, but is not effective against the African Pgt race TTKSK (and its variants) nor the domestic race QCCJB. To identify resistance to these Rpg1-virulent races, the Barley iCore Collection, held by the United States Department of Agriculture-Agricultural Research Service National Small Grains Collection was evaluated for adult plant resistance (APR) and seedling resistance to race TTKSK and APR to race QCCJB and the Pgt TTKSK composite of races TTKSK, TTKST, TTKTK, and TTKTT. Using a genome-wide association study approach based on 6224 single nucleotide polymorphic markers, seven significant loci for stem rust resistance were identified on chromosomes 1H, 2H, 3H, and 5H. The most significant markers detected were 11_11355 and SCRI_RS_177017 at 71-75 cM on chromosome 5H, conferring APR to QCCJB and TTKSK composite. Significant markers were also detected for TTKSK seedling resistance on chromosome 5H. All markers detected on 5H were independent of the rpg4/Rpg5 complex at 152-168 cM. This study verified the importance of the 11_11355 locus in conferring APR to races QCCJB and TTKSK and suggests that it may be effective against other races in the Ug99 lineage.
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Affiliation(s)
- Austin J Case
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
| | - Sridhar Bhavani
- Centro Internacional de Mejoramiento de Maíz y Trigo (CIMMYT), Nairobi, Kenya
| | - Godwin Macharia
- Kenya Agriculture Livestock Research Organization (KALRO), Njoro, Kenya
| | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA.
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15
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Steffenson BJ, Case AJ, Pretorius ZA, Coetzee V, Kloppers FJ, Zhou H, Chai Y, Wanyera R, Macharia G, Bhavani S, Grando S. Vulnerability of Barley to African Pathotypes of Puccinia graminis f. sp. tritici and Sources of Resistance. PHYTOPATHOLOGY 2017; 107:950-962. [PMID: 28398875 DOI: 10.1094/phyto-11-16-0400-r] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The emergence of widely virulent pathotypes (e.g., TTKSK in the Ug99 race group) of the stem rust pathogen (Puccinia graminis f. sp. tritici) in Africa threatens wheat production on a global scale. Although intensive research efforts have been advanced to address this threat in wheat, few studies have been conducted on barley, even though pathotypes such as TTKSK are known to attack the crop. The main objectives of this study were to assess the vulnerability of barley to pathotype TTKSK and identify possible sources of resistance. From seedling evaluations of more than 1,924 diverse cultivated barley accessions to pathotype TTKSK, more than 95% (1,844) were found susceptible. A similar high frequency (910 of 934 = 97.4%) of susceptibility was found for the wild progenitor (Hordeum vulgare subsp. spontaneum) of cultivated barley. Additionally, 55 barley lines with characterized or putative introgressions from various wild Hordeum spp. were also tested against pathotype TTKSK but none was found resistant. In total, more than 96% of the 2,913 Hordeum accessions tested were susceptible as seedlings, indicating the extreme vulnerability of the crop to the African pathotypes of P. graminis f. sp. tritici. In total, 32 (1.7% of accessions evaluated) and 13 (1.4%) cultivated and wild barley accessions, respectively, exhibited consistently highly resistant to moderately resistant reactions across all experiments. Molecular assays were conducted on these resistant accessions to determine whether they carried rpg4/Rpg5, the only gene complex known to be highly effective against pathotype TTKSK in barley. Twelve of the 32 (37.5%) resistant cultivated accessions and 11 of the 13 (84.6%) resistant wild barley accessions tested positive for a functional Rpg5 gene, highlighting the narrow genetic base of resistance in Hordeum spp. Other resistant accessions lacking the rpg4/Rpg5 complex were discovered in the evaluated germplasm and may possess useful resistance genes. Combining rpg4/Rpg5 with resistance genes from these other sources should provide more durable resistance against the array of different virulence types in the Ug99 race group.
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Affiliation(s)
- B J Steffenson
- First, second, sixth, and seventh authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; third author: Department of Plant Sciences, University of The Free State, Bloemfontein, Republic of South Africa 9300; fourth and fifth authors: Pannar Seed (Pty) Ltd., P.O. Box 19, Greytown, Republic of South Africa 3250; eighth and ninth authors: Kenyan Agricultural and Livestock Research Organization, Njoro, Kenya; tenth author: International Maize and Wheat Improvement Center, Apdo. Postal, 6-641, 06600, Mexico, D.F.; and eleventh author: International Center for Agricultural Research in the Dry Areas, P.O. Box 114/5055, Beirut, Lebanon 1108-2010
| | - A J Case
- First, second, sixth, and seventh authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; third author: Department of Plant Sciences, University of The Free State, Bloemfontein, Republic of South Africa 9300; fourth and fifth authors: Pannar Seed (Pty) Ltd., P.O. Box 19, Greytown, Republic of South Africa 3250; eighth and ninth authors: Kenyan Agricultural and Livestock Research Organization, Njoro, Kenya; tenth author: International Maize and Wheat Improvement Center, Apdo. Postal, 6-641, 06600, Mexico, D.F.; and eleventh author: International Center for Agricultural Research in the Dry Areas, P.O. Box 114/5055, Beirut, Lebanon 1108-2010
| | - Z A Pretorius
- First, second, sixth, and seventh authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; third author: Department of Plant Sciences, University of The Free State, Bloemfontein, Republic of South Africa 9300; fourth and fifth authors: Pannar Seed (Pty) Ltd., P.O. Box 19, Greytown, Republic of South Africa 3250; eighth and ninth authors: Kenyan Agricultural and Livestock Research Organization, Njoro, Kenya; tenth author: International Maize and Wheat Improvement Center, Apdo. Postal, 6-641, 06600, Mexico, D.F.; and eleventh author: International Center for Agricultural Research in the Dry Areas, P.O. Box 114/5055, Beirut, Lebanon 1108-2010
| | - V Coetzee
- First, second, sixth, and seventh authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; third author: Department of Plant Sciences, University of The Free State, Bloemfontein, Republic of South Africa 9300; fourth and fifth authors: Pannar Seed (Pty) Ltd., P.O. Box 19, Greytown, Republic of South Africa 3250; eighth and ninth authors: Kenyan Agricultural and Livestock Research Organization, Njoro, Kenya; tenth author: International Maize and Wheat Improvement Center, Apdo. Postal, 6-641, 06600, Mexico, D.F.; and eleventh author: International Center for Agricultural Research in the Dry Areas, P.O. Box 114/5055, Beirut, Lebanon 1108-2010
| | - F J Kloppers
- First, second, sixth, and seventh authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; third author: Department of Plant Sciences, University of The Free State, Bloemfontein, Republic of South Africa 9300; fourth and fifth authors: Pannar Seed (Pty) Ltd., P.O. Box 19, Greytown, Republic of South Africa 3250; eighth and ninth authors: Kenyan Agricultural and Livestock Research Organization, Njoro, Kenya; tenth author: International Maize and Wheat Improvement Center, Apdo. Postal, 6-641, 06600, Mexico, D.F.; and eleventh author: International Center for Agricultural Research in the Dry Areas, P.O. Box 114/5055, Beirut, Lebanon 1108-2010
| | - H Zhou
- First, second, sixth, and seventh authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; third author: Department of Plant Sciences, University of The Free State, Bloemfontein, Republic of South Africa 9300; fourth and fifth authors: Pannar Seed (Pty) Ltd., P.O. Box 19, Greytown, Republic of South Africa 3250; eighth and ninth authors: Kenyan Agricultural and Livestock Research Organization, Njoro, Kenya; tenth author: International Maize and Wheat Improvement Center, Apdo. Postal, 6-641, 06600, Mexico, D.F.; and eleventh author: International Center for Agricultural Research in the Dry Areas, P.O. Box 114/5055, Beirut, Lebanon 1108-2010
| | - Y Chai
- First, second, sixth, and seventh authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; third author: Department of Plant Sciences, University of The Free State, Bloemfontein, Republic of South Africa 9300; fourth and fifth authors: Pannar Seed (Pty) Ltd., P.O. Box 19, Greytown, Republic of South Africa 3250; eighth and ninth authors: Kenyan Agricultural and Livestock Research Organization, Njoro, Kenya; tenth author: International Maize and Wheat Improvement Center, Apdo. Postal, 6-641, 06600, Mexico, D.F.; and eleventh author: International Center for Agricultural Research in the Dry Areas, P.O. Box 114/5055, Beirut, Lebanon 1108-2010
| | - R Wanyera
- First, second, sixth, and seventh authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; third author: Department of Plant Sciences, University of The Free State, Bloemfontein, Republic of South Africa 9300; fourth and fifth authors: Pannar Seed (Pty) Ltd., P.O. Box 19, Greytown, Republic of South Africa 3250; eighth and ninth authors: Kenyan Agricultural and Livestock Research Organization, Njoro, Kenya; tenth author: International Maize and Wheat Improvement Center, Apdo. Postal, 6-641, 06600, Mexico, D.F.; and eleventh author: International Center for Agricultural Research in the Dry Areas, P.O. Box 114/5055, Beirut, Lebanon 1108-2010
| | - G Macharia
- First, second, sixth, and seventh authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; third author: Department of Plant Sciences, University of The Free State, Bloemfontein, Republic of South Africa 9300; fourth and fifth authors: Pannar Seed (Pty) Ltd., P.O. Box 19, Greytown, Republic of South Africa 3250; eighth and ninth authors: Kenyan Agricultural and Livestock Research Organization, Njoro, Kenya; tenth author: International Maize and Wheat Improvement Center, Apdo. Postal, 6-641, 06600, Mexico, D.F.; and eleventh author: International Center for Agricultural Research in the Dry Areas, P.O. Box 114/5055, Beirut, Lebanon 1108-2010
| | - S Bhavani
- First, second, sixth, and seventh authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; third author: Department of Plant Sciences, University of The Free State, Bloemfontein, Republic of South Africa 9300; fourth and fifth authors: Pannar Seed (Pty) Ltd., P.O. Box 19, Greytown, Republic of South Africa 3250; eighth and ninth authors: Kenyan Agricultural and Livestock Research Organization, Njoro, Kenya; tenth author: International Maize and Wheat Improvement Center, Apdo. Postal, 6-641, 06600, Mexico, D.F.; and eleventh author: International Center for Agricultural Research in the Dry Areas, P.O. Box 114/5055, Beirut, Lebanon 1108-2010
| | - S Grando
- First, second, sixth, and seventh authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; third author: Department of Plant Sciences, University of The Free State, Bloemfontein, Republic of South Africa 9300; fourth and fifth authors: Pannar Seed (Pty) Ltd., P.O. Box 19, Greytown, Republic of South Africa 3250; eighth and ninth authors: Kenyan Agricultural and Livestock Research Organization, Njoro, Kenya; tenth author: International Maize and Wheat Improvement Center, Apdo. Postal, 6-641, 06600, Mexico, D.F.; and eleventh author: International Center for Agricultural Research in the Dry Areas, P.O. Box 114/5055, Beirut, Lebanon 1108-2010
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Ivaschuk BV, Samofalova DO, Pirko YV, Fedak G, Blume YB. The homologous identification of the stem rust resistance genes Rpg5, Adf3 and RGA1 in the relatives of barley. CYTOL GENET+ 2016. [DOI: 10.3103/s0095452716020055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Dracatos P, Singh D, Fetch T, Park R. Resistance to Puccinia graminis f. sp. avenae in Barley Is Associated with the Rpg5 Locus. PHYTOPATHOLOGY 2015; 105:490-494. [PMID: 25870923 DOI: 10.1094/phyto-08-14-0224-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In barley, gene Rpg5 was first identified for providing resistance to the rye stem rust pathogen (Puccinia graminis f. sp. secalis). A subsequent study determined that Rpg5 is required for rpg4-mediated resistance to the wheat stem rust pathogen (P. graminis f. sp. tritici) including pathotype TTKSK ("Ug99"), which poses a major threat to global wheat and barley production. Based on the effectiveness of Rpg5 against P. graminis f. sp. tritici and P. graminis f. sp. secalis, we assessed whether it also conferred resistance to the oat stem rust pathogen (P. graminis f. sp. avenae). A barley F8 recombinant inbred line (RIL) population was produced by crossing 'Q21861' (Rpg1 and Rpg5) with '73-G1' (Rpg1), which is susceptible to P. graminis f. sp. avenae, P. graminis f. sp. secalis, and some pathotypes of P. graminis f. sp. tritici. Seedling tests were performed on the F8 RIL population using Australian pathotypes of P. graminis f. sp. tritici, P. graminis f. sp. secalis, P. graminis f. sp. avenae, and a putative somatic hybrid between P. graminis f. sp. tritici and P. graminis f. sp. secalis known as the 'Scabrum' rust. Segregation in the responses to all rust isolates for the RILs was identical (50 resistant: 52 susceptible), and fitted a 1:1 ratio (X2=0.039, P=0.843), indicating that resistance to all isolates was monogenetically inherited. Screening of the RILs and the parental lines with perfect markers for the functional Rpg1 and Rpg5 resistance alleles indicated that Rpg1 was fixed, while Rpg5 was positive in all resistant lines and negative in all susceptible lines. This suggests that different formae speciales of P. graminis may share common effectors, and that the Rpg5 locus confers resistance to both P. graminis f. sp. tritici and P. graminis f. sp. secalis and the heterologous formae speciales of P. graminis, P. graminis f. sp. avenae.
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Affiliation(s)
- Peter Dracatos
- First, second, and fourth authors: The University of Sydney, Plant Breeding Institute Cobbitty, Private Bag 4011, Narellan, NSW, 2567, Australia; and third author: Cereal Research Centre, Agriculture & Agri-Food Canada, Winnipeg, MB, Canada
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Mamo BE, Smith KP, Brueggeman RS, Steffenson BJ. Genetic Characterization of Resistance to Wheat Stem Rust Race TTKSK in Landrace and Wild Barley Accessions Identifies the rpg4/Rpg5 Locus. PHYTOPATHOLOGY 2015; 105:99-109. [PMID: 25084303 DOI: 10.1094/phyto-12-13-0340-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Race TTKSK of the wheat stem rust pathogen (Puccinia graminis f. sp. tritici) threatens the production of wheat and barley worldwide because of its broad-spectrum virulence on many widely grown cultivars. Sources of resistance against race TTKSK were recently identified in several barley landraces (Hordeum vulgare subsp. vulgare) and wild barley accessions (H. vulgare subsp. spontaneum). The objectives of this study were to characterize the inheritance of resistance to wheat stem rust race TTKSK in four barley landraces (Hv501, Hv545, Hv602, and Hv612) and two wild barley (WBDC213 and WBDC345) accessions, map the resistance genes, and determine the allelic relationships among the genes in these accessions and the previously described rpg4/Rpg5 locus. Resistant accessions were crossed with the susceptible cv. Steptoe and resulting F3 populations were evaluated for resistance to race TTKSK at the seedling stage. Segregation of F3 families in populations involving the resistance sources of Hv501, Hv545, Hv612, WBDC213, and WBDC345 fit a 1:2:1 ratio for homozygous resistant (HR)/segregating (SEG)/homozygous susceptible (HS) progenies (with χ2=2.27 to 5.87 and P=0.053 to 0.321), indicating that a single gene confers resistance to race TTKSK. Segregation of F3 families in cross Steptoe/Hv602 did not fit a 1:2:1 ratio (HR/SEG/HS of 20:47:43 with χ2=11.95 and P=0.003), indicating that more than one gene is involved in imparting resistance to race TTKSK. Bulked segregant analysis using >1,500 single-nucleotide polymorphism markers positioned a resistance locus in all six populations on chromosome 5HL in very close proximity to the known location of the rpg4/Rpg5 complex locus. Allelism tests were conducted by making crosses among resistant accessions Hv501, Hv545, and Hv612 and also Q21861 with the rpg4/Rpg5 complex. No segregation was observed in F2 families inoculated with race TTKSK, demonstrating that all Hv lines carry the same allele for resistance and that it resides at or very near the rpg4/Rpg5 locus. Phenotype evaluations of the six barley accessions with wheat stem rust race QCCJ revealed resistant infection types (ITs) at a low incubation temperature and susceptible ITs at a high incubation temperature, similar to Q21861, which carries the temperature-sensitive gene rpg4. The accessions also exhibited low ITs against the rye stem rust isolate 92-MN-90, suggesting that they also carry Rpg5. This result was confirmed through molecular analysis, which revealed that all six barley accessions contain the serine threonine protein kinase domain that confers Rpg5 resistance. These results indicate that cultivated barley is extremely vulnerable to African stem rust races such as TTKSK because even these diverse selections of landrace and wild barley accessions carry only one locus for resistance.
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Derevnina L, Fetch T, Singh D, Brueggeman R, Dong C, Park RF. Analysis of Stem Rust Resistance in Australian Barley Cultivars. PLANT DISEASE 2014; 98:1485-1493. [PMID: 30699785 DOI: 10.1094/pdis-11-13-1174-re] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Eighty-two Australian and five exotic barley cultivars were evaluated at the seedling stage for resistance to the Australian stem rust pathotype 98-1,2,3,5,6. Although most of these cultivars exhibited mesothetic (mixed infection type) reactions that were associated with a high level of chlorosis, two ('O'Connor' and 'Pacific Ranger') were highly resistant. Marker analysis indicated that four Australian cultivars ('Empress', 'Vlamingh', Pacific Ranger, and 'Yerong') possess the stem rust resistance gene Rpg1. Tests conducted using North American Puccinia graminis f. sp. tritici pathotypes MCCJ and QCCJ supported marker results and indicated that 'Pacific Ranger' and 'Vlamingh' likely carry additional stem rust resistance genes. Based on pedigree information and results from multipathotype tests, these genes are believed to be uncharacterized and, therefore, new. The resistance in Australian barley 'Franklin' conferred resistance against all pathotypes tested in this study. Studies of inheritance to MCCJ revealed that it possessed an unknown seedling resistance, which was independent of and displayed additivity to Rpg1.
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Affiliation(s)
- L Derevnina
- University of Sydney, Plant Breeding Institute, Private Bag 4011, Narellan, NSW, 2567, Australia
| | - T Fetch
- Cereal Research Centre, Winnipeg, Manitoba R3T 2M9, Canada
| | - D Singh
- University of Sydney, Plant Breeding Institute
| | - R Brueggeman
- Department of Plant Pathology, North Dakota State University, Fargo 58102
| | - C Dong
- University of Sydney, Plant Breeding Institute
| | - R F Park
- University of Sydney, Plant Breeding Institute
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