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Origin and genetic analysis of stem rust resistance in wheat line Tr129. Sci Rep 2022; 12:4585. [PMID: 35301415 PMCID: PMC8931155 DOI: 10.1038/s41598-022-08681-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/09/2022] [Indexed: 11/16/2022] Open
Abstract
Wheat line Tr129 is resistant to stem rust, caused by Puccinia graminis f. sp. tritici (Pgt). The resistance in Tr129 was reportedly derived from Aegilops triuncialis, but the origin and genetics of resistance have not been confirmed. Here, genomic in situ hybridization (GISH) showed that no Ae. triuncialis chromatin was present in Tr129. Genetic and phenotypic analysis was conducted on F2 and DH populations from the cross RL6071/Tr129. Seedlings were tested with six Pgt races and were genotyped using an Illumina iSelect 90 K SNP array and kompetitive allele specific PCR (KASP) markers. Mapping and phenotyping showed that Tr129 carried four stem rust resistance (Sr) genes on chromosome arms 2BL (Sr9b), 4AL (Sr7b), 6AS (Sr8a), and 6DS (SrTr129). SrTr129 co-segregated with markers for SrCad, however Tr129 has a unique haplotype suggesting the resistance could be new. Analysis of a RL6071/Peace population revealed that like SrTr129, SrCad is ineffective against three North American races. This new understanding of SrCad will guide its use in breeding. Tr129 and the DNA markers reported here are useful resources for improving stem rust resistance in cultivars.
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Luo J, Rouse MN, Hua L, Li H, Li B, Li T, Zhang W, Gao C, Wang Y, Dubcovsky J, Chen S. Identification and characterization of Sr22b, a new allele of the wheat stem rust resistance gene Sr22 effective against the Ug99 race group. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:554-563. [PMID: 34695276 PMCID: PMC8882774 DOI: 10.1111/pbi.13737] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/09/2021] [Accepted: 10/19/2021] [Indexed: 05/09/2023]
Abstract
Wheat stem (or black) rust, caused by Puccinia graminis f. sp. tritici (Pgt), has been historically among the most devastating global fungal diseases of wheat. The recent occurrence and spread of new virulent races such as Ug99 have prompted global efforts to identify and isolate more effective stem rust resistance (Sr) genes. Here, we report the map‐based cloning of the Ug99‐effective SrTm5 gene from diploid wheat Triticum monococcum accession PI 306540 that encodes a typical coiled‐coil nucleotide‐binding leucine‐rich repeat protein. This gene, designated as Sr22b, is a new allele of Sr22 with a rare insertion of a large (13.8‐kb) retrotransposon into its second intron. Biolistic transformation of an ~112‐kb circular bacterial artificial chromosome plasmid carrying Sr22b into the susceptible wheat variety Fielder was sufficient to confer resistance to stem rust. In a survey of 168 wheat genotypes, Sr22b was present only in cultivated T. monococcum subsp. monococcum accessions but absent in all tested tetraploid and hexaploid wheat lines. We developed a diagnostic molecular marker for Sr22b and successfully introgressed a T. monococcum chromosome segment containing this gene into hexaploid wheat to accelerate its deployment and pyramiding with other Sr genes in wheat breeding programmes. Sr22b can be a valuable component of gene pyramids or transgenic cassettes combining different resistance genes to control this devastating disease.
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Affiliation(s)
- Jing Luo
- Peking University Institute of Advanced Agricultural SciencesWeifangShandong261000China
| | - Matthew N. Rouse
- USDA‐ARS Cereal Disease Laboratory and Department of Plant PathologyUniversity of MinnesotaSt. PaulMN55108USA
| | - Lei Hua
- Peking University Institute of Advanced Agricultural SciencesWeifangShandong261000China
| | - Hongna Li
- Peking University Institute of Advanced Agricultural SciencesWeifangShandong261000China
| | - Boshu Li
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Genome EditingInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
| | - Tianya Li
- College of Plant ProtectionShenyang Agricultural UniversityShenyangLiaoning110000China
| | - Wenjun Zhang
- Department of Plant SciencesUniversity of CaliforniaDavisCA95616USA
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Genome EditingInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
| | - Yanpeng Wang
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Genome EditingInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
| | - Jorge Dubcovsky
- Department of Plant SciencesUniversity of CaliforniaDavisCA95616USA
- Howard Hughes Medical InstituteChevy ChaseMD20815USA
| | - Shisheng Chen
- Peking University Institute of Advanced Agricultural SciencesWeifangShandong261000China
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Gordon T, Jin Y, Gale S, Rouse M, Stoxen S, Wanyera R, Macharia G, Randhawa M, Bhavani S, Brown-Guedira G, Marshall D, Babiker E, Bockelman H, Bonman JM. Identification of Winter Habit Bread Wheat Landraces in the National Small Grains Collection with Resistance to Emerging Stem Rust Pathogen Variants. PLANT DISEASE 2021; 105:3998-4005. [PMID: 34232053 DOI: 10.1094/pdis-04-21-0743-re] [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: 06/13/2023]
Abstract
Wheat stem rust caused by Puccinia graminis f. sp. tritici is a widespread and recurring threat to wheat production. Emerging P. graminis f. sp. tritici variants are rapidly overcoming major gene resistance deployed in wheat cultivars and new sources of race-nonspecific resistance are urgently needed. The National Small Grains Collection (NSGC) contains thousands of wheat landrace accessions that may harbor unique and broadly effective sources of resistance to emerging P. graminis f. sp. tritici variants. All NSGC available facultative and winter-habit bread wheat landraces were tested in a field nursery in St. Paul, Minnesota, against a bulk collection of six common U.S. P. graminis f. sp. tritici races. Infection response and severity data were collected on 9,192 landrace accessions at the soft-dough stage and resistant accessions were derived from single spikes. Derived accessions were tested in St. Paul a second time to confirm resistance and in a field nursery in Njoro, Kenya against emerging races of P. graminis f. sp. tritici with virulence to many known resistance genes including Sr24, Sr31, Sr38, and SrTmp. Accessions resistant in the St. Paul field were also tested at the seedling stage with up to 13 P. graminis f. sp. tritici races, including TTKSK and TKTTF, and with 19 molecular markers linked with known stem rust resistance genes or genes associated with modern breeding practices. Forty-five accessions were resistant in both U.S. and Kenya field nurseries and lacked alleles linked with known stem rust resistance genes. Accessions with either moderate or strong resistance in the U.S. and Kenya field nurseries and with novel seedling resistance will be prioritized for further study.
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Affiliation(s)
- Tyler Gordon
- U.S. Department of Agriculture, Agricultural Research Service, Small Grains and Potato Germplasm Research, Aberdeen, ID 83210, U.S.A
| | - Yue Jin
- U.S. Department of Agriculture, Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN 55108, U.S.A
| | - Samuel Gale
- U.S. Department of Agriculture, Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN 55108, U.S.A
| | - Matthew Rouse
- U.S. Department of Agriculture, Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN 55108, U.S.A
| | - Samuel Stoxen
- U.S. Department of Agriculture, Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN 55108, U.S.A
| | - Ruth Wanyera
- Kenya Agricultural and Livestock Research Organization, 20107 Njoro, Kenya
| | - Godwin Macharia
- Kenya Agricultural and Livestock Research Organization, 20107 Njoro, Kenya
| | - Mandeep Randhawa
- International Maize and Wheat Improvement Center-Kenya, 1041-00621 Nairobi, Kenya
| | - Sridhar Bhavani
- International Maize and Wheat Improvement Center, El Batán, Texcoco CP 56237, Edo. de México, Mexico
| | - Gina Brown-Guedira
- U.S. Department of Agriculture, Agricultural Research Service, Plant Science Research, Raleigh, NC 27695, U.S.A
| | - David Marshall
- U.S. Department of Agriculture, Agricultural Research Service, Plant Science Research, Raleigh, NC 27695, U.S.A
| | - Ebrahiem Babiker
- U.S. Department of Agriculture, Agricultural Research Service, Small Grains and Potato Germplasm Research, Aberdeen, ID 83210, U.S.A
- U.S. Department of Agriculture, Agricultural Research Service, Southern Horticultural Research Laboratory, Poplarville, MS 39470, U.S.A
| | - Harold Bockelman
- U.S. Department of Agriculture, Agricultural Research Service, Small Grains and Potato Germplasm Research, Aberdeen, ID 83210, U.S.A
| | - J Michael Bonman
- U.S. Department of Agriculture, Agricultural Research Service, Small Grains and Potato Germplasm Research, Aberdeen, ID 83210, U.S.A
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Edae EA, Rouse MN. Association mapping of resistance to emerging stem rust pathogen races in spring wheat using genotyping-by-sequencing. THE PLANT GENOME 2020; 13:e20050. [PMID: 33217214 DOI: 10.1002/tpg2.20050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 06/27/2020] [Accepted: 06/29/2020] [Indexed: 06/11/2023]
Abstract
The identification and characterization of resistance genes should outpace the rapid emergence of new P. graminis f. sp. tritici races, such as TTRTF and TTKTT, to mitigate stem rust damage to wheat. The objective of the current study was to identify and characterize P. graminis f. sp. tritici race resistance association signals. A total of 250 North American spring wheat lines were evaluated at the seedling stage with a total of seven isolates including TKKTP, TKTTF, TKTTF, TRTTF, TTRTF, TTKSK, and TTKTT. The lines were genotyped by a GBS platform and 9,042 SNPs were used for identification of chromosome regions associated with resistance against the seven isolates. Strong association signals were detected on chromosomes 6BL (Sr11 gene region) and 4AL, likely Sr7a, for resistance against both TKKTP and TKTTF. Similarly, association signals were also detected on chromosomes 4AL (race TTRTF resistance) and 4BS (race TTKSK and TTKTT resistance). Association analysis based on mean phenotypic differences between closely related isolates identified QTL that were not elucidated by direct association mapping of the responses, individually. Overall, with the exception of race TRTTF, each race shared at least one association signal with another race. However, the number of race-specific association signals are larger than that of association signals common among races suggesting the need for identifying and characterizing QTL/genes for newly emerging stem rust pathogen races. There was also high concordance between PCA-based GWAS association signals and association signals from that of both single and multi-locus mixed models.
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Affiliation(s)
- Erena A Edae
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55018, USA
| | - Matthew N Rouse
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55018, USA
- USDA-ARS, Cereal Disease Laboratory, 1551 Lindig Street, St. Paul, MN, 55018, USA
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Improving grain yield, stress resilience and quality of bread wheat using large-scale genomics. Nat Genet 2019; 51:1530-1539. [DOI: 10.1038/s41588-019-0496-6] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 08/13/2019] [Indexed: 01/11/2023]
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Edae EA, Pumphrey MO, Rouse MN. A Genome-Wide Association Study of Field and Seedling Response to Individual Stem Rust Pathogen Races Reveals Combinations of Race-Specific Genes in North American Spring Wheat. FRONTIERS IN PLANT SCIENCE 2018; 9:52. [PMID: 29441083 PMCID: PMC5797647 DOI: 10.3389/fpls.2018.00052] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 01/10/2018] [Indexed: 05/22/2023]
Abstract
Stem rust of wheat caused by the fungal pathogen Puccinia graminis f. sp. tritici historically caused major yield losses of wheat worldwide. To understand the genetic basis of stem rust resistance in contemporary North American spring wheat, genome-wide association analysis (GWAS) was conducted on an association mapping panel comprised of 250 elite lines. The lines were evaluated in separate nurseries each inoculated with a different P. graminis f. sp. tritici race for 3 years (2013, 2015, and 2016) at Rosemount, Minnesota allowing the evaluation of race-specificity separate from the effect of environment. The lines were also challenged with the same four races at the seedling stage in a greenhouse facility at the USDA-ARS Cereal Disease Laboratory. A total of 22,310 high-quality SNPs obtained from the Infinium 90,000 SNPs chip were used to perform association analysis. We observed often negative and sometimes weak correlations between responses to different races that highlighted the abundance of race-specific resistance and the inability to predict the response of the lines across races. Markers strongly associated with resistance to the four races at seedling and field environments were identified. At the seedling stage, the most significant marker-trait associations were detected in the regions of known major genes (Sr6, Sr7a, and Sr9b) except for race QFCSC where a strong association was detected on chromosome arm 1AL. We postulated the presence of Sr2, Sr6, Sr7a, Sr8a, Sr9b, Sr11, Sr12, Sr24, Sr25, Sr31, and Sr57 (Lr34) in this germplasm based on phenotypic and marker data. We found over half of the panel possessed three or more Sr genes, and most commonly included various combinations of Sr6, Sr7a, Sr8a, Sr9b, Sr11, Sr12, and Sr57. Most of these genes confer resistance to specific P. graminis f. sp. tritici races accounting for the prevalent stem rust resistance in North American spring wheat.
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Affiliation(s)
- Erena A. Edae
- Cereal Disease Laboratory, United States Department of Agriculture - Agricultural Research Service (USDA ARS), St. Paul, MN, United States
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Michael O. Pumphrey
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Matthew N. Rouse
- Cereal Disease Laboratory, United States Department of Agriculture - Agricultural Research Service (USDA ARS), St. Paul, MN, United States
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
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Zurn JD, Rouse MN, Chao S, Aoun M, Macharia G, Hiebert CW, Pretorius ZA, Bonman JM, Acevedo M. Dissection of the multigenic wheat stem rust resistance present in the Montenegrin spring wheat accession PI 362698. BMC Genomics 2018; 19:67. [PMID: 29357813 PMCID: PMC5776780 DOI: 10.1186/s12864-018-4438-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 01/04/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Research to identify and characterize stem rust resistance genes in common wheat, Triticum aestivum, has been stimulated by the emergence of Ug99-lineage races of the wheat stem rust pathogen, Puccinia graminis f. sp. tritici (Pgt), in Eastern Africa. The Montenegrin spring wheat landrace PI 362698 was identified as a source of Pgt resistance. This accession exhibits resistance to multiple Ug99-lineage and North American Pgt races at seedling and adult-plant stages. A recombinant inbred population was developed by crossing the susceptible line LMPG-6 with a single plant selection of PI 362698. A genetic map was constructed using the Illumina iSelect 90 K wheat assay and the markers csLv34, NB-LRR3, and wMAS000003 and quantitative trait locus (QTL) analysis was performed. RESULTS QTL analysis identified five significant QTLs (α = 0.05) on chromosomes 2B, 3B, 6A, 6D, and 7A associated with wheat stem rust resistance. The QTL on chromosome 3B was identified using both field data from Kenya (Pgt Ug99-lineage races) and seedling data from Pgt race MCCF. This QTL potentially corresponds to Sr12 or a new allele of Sr12. The multi-pathogen resistance gene Sr57 located on chromosome 7D is present in PI 362698 according to the diagnostic markers csLv34 and wMAS000003, however a significant QTL was not detected at this locus. The QTLs on chromosomes 2B, 6A, and 6D were identified during seedling trials and are thought to correspond to Sr16, Sr8a, and Sr5, respectively. The QTL identified on chromosome 7A was detected using MCCF seedling data and may be Sr15 or a potentially novel allele of recently detected Ug99 resistance QTLs. CONCLUSIONS The combination of resistance QTLs found in PI 362698 is like the resistance gene combination present in the broadly resistant cultivar Thatcher. As such, PI 362698 may not be a landrace as previously thought. PI 362698 has been crossed with North Dakota wheat germplasm for future breeding efforts. Additional work is needed to fully understand why the combination of genes present in PI 362698 and 'Thatcher' provide such durable resistance.
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Affiliation(s)
- Jason D Zurn
- Department of Plant Pathology, North Dakota State University, Fargo, ND, USA
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, OR, USA
| | - Matthew N Rouse
- USDA-ARS, Cereal Disease Laboratory, and Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
| | - Shiaoman Chao
- USDA-ARS, Cereal Crops Research Unit, Fargo, ND, USA
| | - Meriem Aoun
- Department of Plant Pathology, North Dakota State University, Fargo, ND, USA
| | - Godwin Macharia
- Kenya Agricultural and Livestock Research Organization, Njoro, Kenya
| | | | - Zacharias A Pretorius
- Department of Plant Sciences, University of the Free State, Bloemfontein, South Africa
| | - J Michael Bonman
- USDA-ARS, Small Grains and Potato Germplasm Research Unit, Aberdeen, ID, USA
| | - Maricelis Acevedo
- Department of Plant Pathology, North Dakota State University, Fargo, ND, USA.
- International Programs, College of Agriculture and Life Sciences, Cornell University, Mann Library B-75, Ithaca, NY, 14853, USA.
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Nirmala J, Saini J, Newcomb M, Olivera P, Gale S, Klindworth D, Elias E, Talbert L, Chao S, Faris J, Xu S, Jin Y, Rouse MN. Discovery of a Novel Stem Rust Resistance Allele in Durum Wheat that Exhibits Differential Reactions to Ug99 Isolates. G3 (BETHESDA, MD.) 2017; 7:3481-3490. [PMID: 28855282 PMCID: PMC5633396 DOI: 10.1534/g3.117.300209] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 08/24/2017] [Indexed: 11/18/2022]
Abstract
Wheat stem rust, caused by Puccinia graminis f. sp. tritici Eriks. & E. Henn, can incur yield losses in susceptible cultivars of durum wheat, Triticum turgidum ssp. durum (Desf.) Husnot. Although several durum cultivars possess the stem rust resistance gene Sr13, additional genes in durum wheat effective against emerging virulent races have not been described. Durum line 8155-B1 confers resistance against the P. graminis f. sp. tritici race TTKST, the variant race of the Ug99 race group with additional virulence to wheat stem rust resistance gene Sr24 However, 8155-B1 does not confer resistance to the first-described race in the Ug99 race group: TTKSK. We mapped a single gene conferring resistance in 8155-B1 against race TTKST, Sr8155B1, to chromosome arm 6AS by utilizing Rusty/8155-B1 and Rusty*2/8155-B1 populations and the 90K Infinium iSelect Custom bead chip supplemented by KASP assays. One marker, KASP_6AS_IWB10558, cosegregated with Sr8155B1 in both populations and correctly predicted Sr8155B1 presence or absence in 11 durum cultivars tested. We confirmed the presence of Sr8155B1 in cultivar Mountrail by mapping in the population Choteau/Mountrail. The marker developed in this study could be used to predict the presence of resistance to race TTKST in uncharacterized durum breeding lines, and also to combine Sr8155B1 with resistance genes effective to Ug99 such as Sr13 The map location of Sr8155B1 cannot rule out the possibility that this gene is an allele at the Sr8 locus. However, race specificity indicates that Sr8155B1 is different from the known alleles Sr8a and Sr8b.
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Affiliation(s)
- Jayaveeramuthu Nirmala
- Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, Saint Paul, Minnesota 55108
- Department of Plant Pathology, University of Minnesota, Saint Paul, Minnesota 55108
| | - Jyoti Saini
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota 58108
| | - Maria Newcomb
- The School of Plant Sciences, University of Arizona, Tucson, Arizona 85721
| | - Pablo Olivera
- Department of Plant Pathology, University of Minnesota, Saint Paul, Minnesota 55108
| | - Sam Gale
- Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, Saint Paul, Minnesota 55108
| | - Daryl Klindworth
- Cereal Crops Research, United States Department of Agriculture-Agricultural Research Service, Fargo, North Dakota 58102
| | - Elias Elias
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota 58108
| | - Luther Talbert
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, Montana 59717
| | - Shiaoman Chao
- Cereal Crops Research, United States Department of Agriculture-Agricultural Research Service, Fargo, North Dakota 58102
| | - Justin Faris
- Cereal Crops Research, United States Department of Agriculture-Agricultural Research Service, Fargo, North Dakota 58102
| | - Steven Xu
- Cereal Crops Research, United States Department of Agriculture-Agricultural Research Service, Fargo, North Dakota 58102
| | - Yue Jin
- Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, Saint Paul, Minnesota 55108
- Department of Plant Pathology, University of Minnesota, Saint Paul, Minnesota 55108
| | - Matthew N Rouse
- Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, Saint Paul, Minnesota 55108
- Department of Plant Pathology, University of Minnesota, Saint Paul, Minnesota 55108
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