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Marone D, Laidò G, Saccomanno A, Petruzzino G, Giaretta Azevedo CV, De Vita P, Mastrangelo AM, Gadaleta A, Ammar K, Bassi FM, Wang M, Chen X, Rubiales D, Matny O, Steffenson BJ, Pecchioni N. Genome-wide association study of common resistance to rust species in tetraploid wheat. FRONTIERS IN PLANT SCIENCE 2024; 14:1290643. [PMID: 38235202 PMCID: PMC10792004 DOI: 10.3389/fpls.2023.1290643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024]
Abstract
Rusts of the genus Puccinia are wheat pathogens. Stem (black; Sr), leaf (brown; Lr), and stripe (yellow; Yr) rust, caused by Puccinia graminis f. sp. tritici (Pgt), Puccinia triticina (Pt), and Puccinia striiformis f. sp. tritici (Pst), can occur singularly or in mixed infections and pose a threat to wheat production globally in terms of the wide dispersal of their urediniospores. The development of durable resistant cultivars is the most sustainable method for controlling them. Many resistance genes have been identified, characterized, genetically mapped, and cloned; several quantitative trait loci (QTLs) for resistance have also been described. However, few studies have considered resistance to all three rust pathogens in a given germplasm. A genome-wide association study (GWAS) was carried out to identify loci associated with resistance to the three rusts in a collection of 230 inbred lines of tetraploid wheat (128 of which were Triticum turgidum ssp. durum) genotyped with SNPs. The wheat panel was phenotyped in the field and subjected to growth chamber experiments across different countries (USA, Mexico, Morocco, Italy, and Spain); then, a mixed linear model (MLM) GWAS was performed. In total, 9, 34, and 5 QTLs were identified in the A and B genomes for resistance to Pgt, Pt, and Pst, respectively, at both the seedling and adult plant stages. Only one QTL on chromosome 4A was found to be effective against all three rusts at the seedling stage. Six QTLs conferring resistance to two rust species at the adult plant stage were mapped: three on chromosome 1B and one each on 5B, 7A, and 7B. Fifteen QTLs conferring seedling resistance to two rusts were mapped: five on chromosome 2B, three on 7B, two each on 5B and 6A, and one each on 1B, 2A, and 7A. Most of the QTLs identified were specific for a single rust species or race of a species. Candidate genes were identified within the confidence intervals of a QTL conferring resistance against at least two rust species by using the annotations of the durum (cv. 'Svevo') and wild emmer wheat ('Zavitan') reference genomes. The 22 identified loci conferring resistance to two or three rust species may be useful for breeding new and potentially durable resistant wheat cultivars.
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Affiliation(s)
- Daniela Marone
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
| | - Giovanni Laidò
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
| | - Antonietta Saccomanno
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Reggio Emilia, Italy
| | - Giuseppe Petruzzino
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
| | - Cleber V. Giaretta Azevedo
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
| | - Pasquale De Vita
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
| | - Anna Maria Mastrangelo
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
| | - Agata Gadaleta
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti (Di.S.S.P.A.), Università di Bari “Aldo Moro”, Bari, Italy
| | - Karim Ammar
- International Maize and Wheat Improvement Centre (CIMMYT), Ciudad de México, Mexico
| | - Filippo M. Bassi
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
- Wheat Health, Genetics, and Quality Research Unit, United States Department of Agriculture - Agriculture Research Service (USDA-ARS), Pullman, WA, United States
| | - Diego Rubiales
- Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas (CSIC), Córdoba, Spain
| | - Oadi Matny
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Brian J. Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Nicola Pecchioni
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Reggio Emilia, Italy
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Arifuzzaman M, Jost M, Wang M, Chen X, Perovic D, Park RF, Rouse M, Forrest K, Hayden M, Khan GA, Dracatos PM. Mining the Australian Grains Gene Bank for Rust Resistance in Barley. Int J Mol Sci 2023; 24:10860. [PMID: 37446042 DOI: 10.3390/ijms241310860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/21/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023] Open
Abstract
Global barley production is threatened by plant pathogens, especially the rusts. In this study we used a targeted genotype-by-sequencing (GBS) assisted GWAS approach to identify rust resistance alleles in a collection of 287 genetically distinct diverse barley landraces and historical cultivars available in the Australian Grains Genebank (AGG) and originally sourced from Eastern Europe. The accessions were challenged with seven US-derived cereal rust pathogen races including Puccinia hordei (Ph-leaf rust) race 17VA12C, P. coronata var. hordei (Pch-crown rust) race 91NE9305 and five pathogenically diverse races of P. striiformis f. sp. hordei (Psh-stripe rust) (PSH-33, PSH-48, PSH-54, PSH-72 and PSH-100) and phenotyped quantitatively at the seedling stage. Novel resistance factors were identified on chromosomes 1H, 2H, 4H and 5H in response to Pch, whereas a race-specific QTL on 7HS was identified that was effective only to Psh isolates PSH-72 and PSH-100. A major effect QTL on chromosome 5HL conferred resistance to all Psh races including PSH-72, which is virulent on all 12 stripe rust differential tester lines. The same major effect QTL was also identified in response to leaf rust (17VA12C) suggesting this locus contains several pathogen specific rust resistance genes or the same gene is responsible for both leaf rust and stripe rust resistance. Twelve accessions were highly resistant to both leaf and stripe rust diseases and also carried the 5HL QTL. We subsequently surveyed the physical region at the 5HL locus for across the barley pan genome variation in the presence of known resistance gene candidates and identified a rich source of high confidence protein kinase and antifungal genes in the QTL region.
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Affiliation(s)
- Md Arifuzzaman
- Department of Genetics and Plant Breeding, Hajee Mohammad Danesh Science and Technology University, Dinajpur 5200, Bangladesh
| | - Matthias Jost
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA
- Agricultural Research Service, United States Department of Agriculture Wheat Health, Genetics and Quality Research Unit, Pullman, WA 99164-6430, USA
| | - Dragan Perovic
- Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute, Erwin-Baur-Strasse 27, 06484 Quedlinburg, Germany
| | - Robert F Park
- Plant Breeding Institute, Faculty of Science, The University of Sydney, Cobbitty, NSW 2570, Australia
| | - Matthew Rouse
- USDA-ARS Cereal Disease Laboratory and Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA
| | - Kerrie Forrest
- Agriculture Victoria Research, AgriBio, Melbourne, VIC 3083, Australia
| | - Matthew Hayden
- Agriculture Victoria Research, AgriBio, Melbourne, VIC 3083, Australia
| | - Ghazanfar Abbas Khan
- Department of Animal, Plant and Soil Sciences, La Trobe University, AgriBio, Bundoora, VIC 3086, Australia
| | - Peter M Dracatos
- Department of Animal, Plant and Soil Sciences, La Trobe University, AgriBio, Bundoora, VIC 3086, Australia
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Salotti I, Bove F, Rossi V. Development and Validation of a Mechanistic, Weather-Based Model for Predicting Puccinia graminis f. sp. tritici Infections and Stem Rust Progress in Wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:897680. [PMID: 35693159 PMCID: PMC9184802 DOI: 10.3389/fpls.2022.897680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/09/2022] [Indexed: 05/09/2023]
Abstract
Stem rust (or black rust) of wheat, caused by Puccinia graminis f. sp. tritici (Pgt), is a re-emerging, major threat to wheat production worldwide. Here, we retrieved, analyzed, and synthetized the available information about Pgt to develop a mechanistic, weather-driven model for predicting stem rust epidemics caused by uredospores. The ability of the model to predict the first infections in a season was evaluated using field data collected in three wheat-growing areas of Italy (Emilia-Romagna, Apulia, and Sardinia) from 2016 to 2021. The model showed good accuracy, with a posterior probability to correctly predict infections of 0.78 and a probability that there was no infection when not predicted of 0.96. The model's ability to predict disease progress during the growing season was also evaluated by using published data obtained from trials in Minnesota, United States, in 1968, 1978, and 1979, and in Pennsylvania, United States, in 1986. Comparison of observed versus predicted data generated a concordance correlation coefficient of 0.96 and an average distance between real data and the fitted line of 0.09. The model could therefore be considered accurate and reliable for predicting epidemics of wheat stem rust and could be tested for its ability to support risk-based control of the disease.
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Affiliation(s)
- Irene Salotti
- Department of Sustainable Crop Production (DI.PRO.VES.), Università Cattolica del Sacro Cuore, Piacenza, Italy
| | | | - Vittorio Rossi
- Department of Sustainable Crop Production (DI.PRO.VES.), Università Cattolica del Sacro Cuore, Piacenza, Italy
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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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Henningsen EC, Omidvar V, Della Coletta R, Michno JM, Gilbert E, Li F, Miller ME, Myers CL, Gordon SP, Vogel JP, Steffenson BJ, Kianian SF, Hirsch CD, Figueroa M. Identification of Candidate Susceptibility Genes to Puccinia graminis f. sp. tritici in Wheat. FRONTIERS IN PLANT SCIENCE 2021; 12:657796. [PMID: 33968112 PMCID: PMC8097158 DOI: 10.3389/fpls.2021.657796] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 03/22/2021] [Indexed: 05/30/2023]
Abstract
Wheat stem rust disease caused by Puccinia graminis f. sp. tritici (Pgt) is a global threat to wheat production. Fast evolving populations of Pgt limit the efficacy of plant genetic resistance and constrain disease management strategies. Understanding molecular mechanisms that lead to rust infection and disease susceptibility could deliver novel strategies to deploy crop resistance through genetic loss of disease susceptibility. We used comparative transcriptome-based and orthology-guided approaches to characterize gene expression changes associated with Pgt infection in susceptible and resistant Triticum aestivum genotypes as well as the non-host Brachypodium distachyon. We targeted our analysis to genes with differential expression in T. aestivum and genes suppressed or not affected in B. distachyon and report several processes potentially linked to susceptibility to Pgt, such as cell death suppression and impairment of photosynthesis. We complemented our approach with a gene co-expression network analysis to identify wheat targets to deliver resistance to Pgt through removal or modification of putative susceptibility genes.
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Affiliation(s)
- Eva C. Henningsen
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Vahid Omidvar
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Rafael Della Coletta
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, United States
| | - Jean-Michel Michno
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN, United States
| | - Erin Gilbert
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Feng Li
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Marisa E. Miller
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Chad L. Myers
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN, United States
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, United States
| | | | - John P. Vogel
- Joint Genome Institute, Walnut Creek, CA, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Brian J. Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Shahryar F. Kianian
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
- USDA-ARS Cereal Disease Laboratory, St. Paul, MN, United States
| | - Cory D. Hirsch
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
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Emerging infectious diseases threatening food security and economies in Africa. GLOBAL FOOD SECURITY 2021. [DOI: 10.1016/j.gfs.2020.100479] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Henningsen E, Sallam AH, Matny O, Szinyei T, Figueroa M, Steffenson BJ. Rpg7: A New Gene for Stem Rust Resistance from Hordeum vulgare ssp. spontaneum. PHYTOPATHOLOGY 2021; 111:548-558. [PMID: 32880513 DOI: 10.1094/phyto-08-20-0325-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: 06/11/2023]
Abstract
Wheat stem rust (causal organism: Puccinia graminis f. sp. tritici) is an important fungal disease that causes significant yield losses in barley. The deployment of resistant cultivars is the most effective means of controlling this disease. Stem rust evaluations of a diverse collection of wild barley (Hordeum vulgare ssp. spontaneum) identified two Jordanian accessions (WBDC094 and WBDC238) with resistance to a virulent pathotype (P. graminis f. sp. tritici HKHJC) from the United States. To elucidate the genetics of stem rust resistance, both accessions were crossed to the susceptible landrace Hiproly. Segregation ratios of F2 and F3 progeny indicated that a single dominant gene confers resistance to P. graminis f. sp. tritici HKHJC. Molecular mapping of the resistance locus was performed in the Hiproly/WBDC238 F2 population based on 3,329 single-nucleotide polymorphism markers generated by genotyping-by-sequencing. Quantitative trait locus analysis positioned the resistance gene to the long arm of chromosome 3H between the physical/genetic positions of 683.8 Mbp/172.9 cM and 693.7 Mbp/176.0 cM. Because this resistance gene is novel, it was assigned the new gene locus symbol of Rpg7 with a corresponding allele symbol of Rpg7.i. At the seedling stage, Rpg7 confers resistance against a number of other important P. graminis f. sp. tritici pathotypes from the United States (MCCFC, QCCJB, and TTTTF) and Africa (TTKSK) as well as an isolate (92-MN-90) of the rye stem rust pathogen (P. graminis f. sp. secalis) from Minnesota. The resistance conferred by Rpg7 can be readily transferred into breeding programs because of its simple inheritance and clear phenotypic expression.
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Affiliation(s)
- Eva Henningsen
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Ahmad H Sallam
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Oadi Matny
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Tamas Szinyei
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, ACT 2601, Australia
| | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
- Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, MN 55108, U.S.A
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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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Hernandez J, Meints B, Hayes P. Introgression Breeding in Barley: Perspectives and Case Studies. FRONTIERS IN PLANT SCIENCE 2020; 11:761. [PMID: 32595671 PMCID: PMC7303309 DOI: 10.3389/fpls.2020.00761] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 05/13/2020] [Indexed: 05/04/2023]
Abstract
Changing production scenarios resulting from unstable climatic conditions are challenging crop improvement efforts. A deeper and more practical understanding of plant genetic resources is necessary if these assets are to be used effectively in developing improved varieties. In general, current varieties and potential varieties have a narrow genetic base, making them prone to suffer the consequences of new and different abiotic and biotic stresses that can reduce crop yield and quality. The deployment of genomic technologies and sophisticated statistical analysis procedures has generated a dramatic change in the way we characterize and access genetic diversity in crop plants, including barley. Various mapping strategies can be used to identify the genetic variants that lead to target phenotypes and these variants can be assigned coordinates in reference genomes. In this way, new genes and/or new alleles at known loci present in wild ancestors, germplasm accessions, land races, and un-adapted introductions can be located and targeted for introgression. In principle, the introgression process can now be streamlined and linkage drag reduced. In this review, we present an overview of (1) past and current efforts to identify diversity that can be tapped to improve barley yield and quality, and (2) case studies of our efforts to introgress resistance to stripe and stem rust from un-adapted germplasm. We conclude with a description of a modified Nested Association Mapping (NAM) population strategy that we are implementing for the development of multi-use naked barley for organic systems and share perspectives on the use of genome editing in introgression breeding.
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Affiliation(s)
- Javier Hernandez
- Department Crop and Soil Science, Oregon State University, Corvallis, OR, United States
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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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11
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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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12
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Solanki S, Ameen G, Borowicz P, Brueggeman RS. Shedding Light on Penetration of Cereal Host Stomata by Wheat Stem Rust Using Improved Methodology. Sci Rep 2019; 9:7939. [PMID: 31138873 PMCID: PMC6538696 DOI: 10.1038/s41598-019-44280-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 05/08/2019] [Indexed: 11/09/2022] Open
Abstract
Asexual urediniospore infection of primary cereal hosts by Puccinia graminis f. sp. tritici (Pgt), the wheat stem rust pathogen, was considered biphasic. The first phase, spore germination and appressoria formation, requires a dark period and moisture. The second phase, host entry by the penetration peg originating from the appressoria formed over the guard cells, was thought to require light to induce natural stomata opening. Previous studies concluded that inhibition of colonization by the dark was due to lack of penetration through closed stomata. A sensitive WGA-Alexa Fluor 488 fungal staining, surface creation and biovolume analysis method was developed enabling visualization and quantification of fungal growth in planta at early infection stages surpassing visualization barriers using previous methods. The improved method was used to investigate infection processes of Pgt during stomata penetration and colonization in barley and wheat showing that penetration is light independent. Based on the visual growth and fungal biovolume analysis it was concluded that the differences in pathogen growth dynamics in both resistant and susceptible genotypes was due to light induced pathogen growth after penetration into the substomatal space. Thus, light induced plant or pathogen cues triggers pathogen growth in-planta post penetration.
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Affiliation(s)
- Shyam Solanki
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Gazala Ameen
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Pawel Borowicz
- Department of Animal Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Robert S Brueggeman
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108-6050, USA.
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13
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Pretorius ZA, Booysen GJ, Boshoff WHP, Joubert JH, Maree GJ, Els J. Additive Manufacturing of Devices Used for Collection and Application of Cereal Rust Urediniospores. FRONTIERS IN PLANT SCIENCE 2019; 10:639. [PMID: 31156688 PMCID: PMC6530045 DOI: 10.3389/fpls.2019.00639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 04/29/2019] [Indexed: 06/01/2023]
Abstract
Optimized inoculation procedures are an important consideration in achieving repeatable plant infection when working with biotrophic rust fungi. Several plant pathology laboratories specializing in rust research employ a system where the collection and application of fungal spores are accomplished using an exchangeable gelatin capsule. Urediniospores are collected from erumpent pustules on plant surfaces into a capsule fitted to a cyclone collector controlled by a vacuum pump. By adding light mineral oil to the same capsule, the spore suspension is then sprayed onto plants by means of a dedicated atomizer (inoculator) connected to an air pressure source. Although devices are not commercially available, modern day technologies provide an opportunity to efficiently design and manufacture collectors and inoculators. Using a process called Additive Manufacturing (AM), also known as "3D printing," the bodies of a collector and inoculator were digitally designed and then laser-sintered in nylon. Depending on availability, copper or aluminum tubes were fitted to the bodies of both devices afterward to either facilitate directed collection of spores from rust pustules on plant surfaces or act as a siphon tube to deliver the spore suspension contained in the capsule. No statistical differences were found between AM and metal inoculators for spray delivery time or spore deposition per unit area. In replicated collection and inoculation tests of wheat seedlings with urediniospore bulks or single pustule collections of Puccinia triticina and P. graminis f. sp. tritici, the causal organisms of leaf rust and stem rust, consistent and satisfactory infection levels were achieved. Immersing used devices in acetone for 60 s followed by a 2 h heat treatment at 75°C produced no contaminant infection in follow-up tests.
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Affiliation(s)
| | - Gerrie J. Booysen
- Centre for Rapid Prototyping and Manufacturing, Central University of Technology, Bloemfontein, South Africa
| | - Willem H. P. Boshoff
- Department of Plant Sciences, University of the Free State, Bloemfontein, South Africa
| | - Jozua H. Joubert
- Product Development Technology Station, Central University of Technology, Bloemfontein, South Africa
| | - Gerrie J. Maree
- Department of Plant Sciences, University of the Free State, Bloemfontein, South Africa
| | - Johan Els
- Centre for Rapid Prototyping and Manufacturing, Central University of Technology, Bloemfontein, South Africa
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14
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Dracatos PM, Haghdoust R, Singh RP, Huerta Espino J, Barnes CW, Forrest K, Hayden M, Niks RE, Park RF, Singh D. High-Density Mapping of Triple Rust Resistance in Barley Using DArT-Seq Markers. FRONTIERS IN PLANT SCIENCE 2019; 10:467. [PMID: 31105717 PMCID: PMC6498947 DOI: 10.3389/fpls.2019.00467] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 03/28/2019] [Indexed: 05/31/2023]
Abstract
The recent availability of an assembled and annotated genome reference sequence for the diploid crop barley (Hordeum vulgare L.) provides new opportunities to study the genetic basis of agronomically important traits such as resistance to stripe [Puccinia striiformis f. sp. hordei (Psh)], leaf [P. hordei (Ph)], and stem [P. graminis f. sp. tritici (Pgt)] rust diseases. The European barley cultivar Pompadour is known to possess high levels of resistance to leaf rust, predominantly due to adult plant resistance (APR) gene Rph20. We developed a barley recombinant inbred line (RIL) population from a cross between Pompadour and the leaf rust and stripe rust susceptible selection Biosaline-19 (B-19), and genotyped this population using DArT-Seq genotyping by sequencing (GBS) markers. In the current study, we produced a high-density linkage map comprising 8,610 (SNP and in silico) markers spanning 5957.6 cM, with the aim of mapping loci for resistance to leaf rust, stem rust, and stripe rust. The RIL population was phenotyped in the field with Psh (Mexico and Ecuador) and Ph (Australia) and in the greenhouse at the seedling stage with Australian Ph and Pgt races, and at Wageningen University with a European variant of Psh race 24 (PshWUR). For Psh, we identified a consistent field QTL on chromosome 2H across all South American field sites and years. Two complementary resistance genes were mapped to chromosomes 1H and 4H at the seedling stage in response to PshWUR, likely to be the loci rpsEm1 and rpsEm2 previously reported from the cultivar Emir from which Pompadour was bred. For leaf rust, we determined that Rph20 in addition to two minor-effect QTL on 1H and 3H were effective at the seedling stage, whilst seedling resistance to stem rust was due to QTL on chromosomes 3H and 7H conferred by Pompadour and B-19, respectively.
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Affiliation(s)
- Peter M. Dracatos
- Plant Breeding Institute Cobbitty, Sydney Institute of Agriculture, The University of Sydney, Sydney, NSW, Australia
| | - Rouja Haghdoust
- Plant Breeding Institute Cobbitty, Sydney Institute of Agriculture, The University of Sydney, Sydney, NSW, Australia
| | - Ravi P. Singh
- International Maize and Wheat Improvement Center, Texcoco, Mexico
- Campo Experimental Valle de México, INIFAP, Chapingo, Mexico
| | - Julio Huerta Espino
- International Maize and Wheat Improvement Center, Texcoco, Mexico
- Campo Experimental Valle de México, INIFAP, Chapingo, Mexico
| | - Charles W. Barnes
- Instituto Nacional de Investigaciones Agropecuarias (INIAP), Quito, Ecuador
| | - Kerrie Forrest
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, La Trobe University, Melbourne, VIC, Australia
| | - Matthew Hayden
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, La Trobe University, Melbourne, VIC, Australia
| | - Rients E. Niks
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Robert F. Park
- Plant Breeding Institute Cobbitty, Sydney Institute of Agriculture, The University of Sydney, Sydney, NSW, Australia
| | - Davinder Singh
- Plant Breeding Institute Cobbitty, Sydney Institute of Agriculture, The University of Sydney, Sydney, NSW, Australia
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15
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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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16
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Lewis CM, Persoons A, Bebber DP, Kigathi RN, Maintz J, Findlay K, Bueno-Sancho V, Corredor-Moreno P, Harrington SA, Kangara N, Berlin A, García R, Germán SE, Hanzalová A, Hodson DP, Hovmøller MS, Huerta-Espino J, Imtiaz M, Mirza JI, Justesen AF, Niks RE, Omrani A, Patpour M, Pretorius ZA, Roohparvar R, Sela H, Singh RP, Steffenson B, Visser B, Fenwick PM, Thomas J, Wulff BBH, Saunders DGO. Potential for re-emergence of wheat stem rust in the United Kingdom. Commun Biol 2018; 1:13. [PMID: 30271900 PMCID: PMC6053080 DOI: 10.1038/s42003-018-0013-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 01/11/2018] [Indexed: 12/05/2022] Open
Abstract
Wheat stem rust, a devastating disease of wheat and barley caused by the fungal pathogen Puccinia graminis f. sp. tritici, was largely eradicated in Western Europe during the mid-to-late twentieth century. However, isolated outbreaks have occurred in recent years. Here we investigate whether a lack of resistance in modern European varieties, increased presence of its alternate host barberry and changes in climatic conditions could be facilitating its resurgence. We report the first wheat stem rust occurrence in the United Kingdom in nearly 60 years, with only 20% of UK wheat varieties resistant to this strain. Climate changes over the past 25 years also suggest increasingly conducive conditions for infection. Furthermore, we document the first occurrence in decades of P. graminis on barberry in the UK . Our data illustrate that wheat stem rust does occur in the UK and, when climatic conditions are conducive, could severely harm wheat and barley production.
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Affiliation(s)
- Clare M Lewis
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | | | - Rose N Kigathi
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
- Pwani University, 195-80108, Kilifi, Kenya
| | - Jens Maintz
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Kim Findlay
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | | | | | | | - Anna Berlin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden
| | - Richard García
- Instituto Nacional de Investigación Agropecuaria (INIA) La Estanzuela, Mailbox 39173, Colonia, Uruguay
| | - Silvia E Germán
- Instituto Nacional de Investigación Agropecuaria (INIA) La Estanzuela, Mailbox 39173, Colonia, Uruguay
| | - Alena Hanzalová
- Crop Research Institute, Ruzyně, 161 06 Praha 6, Czech Republic
| | - David P Hodson
- International Maize and Wheat Improvement Center (CIMMYT), 5689, Addis Ababa, Ethiopia
| | | | | | | | - Javed Iqbal Mirza
- Crop Disease Research Program, National Agriculture Research Center, Islamabad, 44000, Pakistan
| | | | - Rients E Niks
- Wageningen University, Wageningen, 6700, The Netherlands
| | - Ali Omrani
- Faculty of Agriculture, Department of Plant Breeding and Biotechnology, University of Tabriz, Tabriz, 5166616471, Iran
| | | | | | - Ramin Roohparvar
- Seed and Plant Improvement Institute, Agricultural Research, Education and Extension Organization (AREEO), 4119, Karaj, Iran
| | - Hanan Sela
- Tel Aviv University, Tel Aviv, 69978, Israel
| | - Ravi P Singh
- CIMMYT, Apdo. Postal 6-641, D. F. México, 06600, Mexico
| | | | - Botma Visser
- University of the Free State, Bloemfontein, 9301, South Africa
| | | | - Jane Thomas
- National Institute of Agricultural Botany, Cambridge, CB3 0LE, UK
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17
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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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18
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Sallam AH, Tyagi P, Brown-Guedira G, Muehlbauer GJ, Hulse A, Steffenson BJ. Genome-Wide Association Mapping of Stem Rust Resistance in Hordeum vulgare subsp. spontaneum. G3 (BETHESDA, MD.) 2017; 7:3491-3507. [PMID: 28855281 PMCID: PMC5633397 DOI: 10.1534/g3.117.300222] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 08/24/2017] [Indexed: 01/06/2023]
Abstract
Stem rust was one of the most devastating diseases of barley in North America. Through the deployment of cultivars with the resistance gene Rpg1, losses to stem rust have been minimal over the past 70 yr. However, there exist both domestic (QCCJB) and foreign (TTKSK aka isolate Ug99) pathotypes with virulence for this important gene. To identify new sources of stem rust resistance for barley, we evaluated the Wild Barley Diversity Collection (WBDC) (314 ecogeographically diverse accessions of Hordeum vulgare subsp. spontaneum) for seedling resistance to four pathotypes (TTKSK, QCCJB, MCCFC, and HKHJC) of the wheat stem rust pathogen (Puccinia graminis f. sp. tritici, Pgt) and one isolate (92-MN-90) of the rye stem rust pathogen (P. graminis f. sp. secalis, Pgs). Based on a coefficient of infection, the frequency of resistance in the WBDC was low ranging from 0.6% with HKHJC to 19.4% with 92-MN-90. None of the accessions was resistant to all five cultures of P. graminis A genome-wide association study (GWAS) was conducted to map stem rust resistance loci using 50,842 single-nucleotide polymorphic markers generated by genotype-by-sequencing and ordered using the new barley reference genome assembly. After proper accounting for genetic relatedness and structure among accessions, 45 quantitative trait loci were identified for resistance to P. graminis across all seven barley chromosomes. Three novel loci associated with resistance to TTKSK, QCCJB, MCCFC, and 92-MN-90 were identified on chromosomes 5H and 7H, and two novel loci associated with resistance to HKHJC were identified on chromosomes 1H and 3H. These novel alleles will enhance the diversity of resistance available for cultivated barley.
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Affiliation(s)
- Ahmad H Sallam
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108
| | - Priyanka Tyagi
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, North Carolina 27695
| | - Gina Brown-Guedira
- United States Department of Agriculture-Agricultural Research Service, Raleigh, North Carolina 27695
| | - Gary J Muehlbauer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Alex Hulse
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108
| | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108
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