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Li H, Luo J, Zhang W, Hua L, Li K, Wang J, Xu B, Yang C, Wang G, Rouse MN, Dubcovsky J, Chen S. High-resolution mapping of SrTm4, a recessive resistance gene to wheat stem rust. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:120. [PMID: 37103626 PMCID: PMC10140103 DOI: 10.1007/s00122-023-04369-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/17/2023] [Indexed: 05/13/2023]
Abstract
KEY MESSAGE The diploid wheat recessive stem rust resistance gene SrTm4 was fine-mapped to a 754-kb region on chromosome arm 2AmL and potential candidate genes were identified. Race Ug99 of Puccinia graminis f. sp. tritici (Pgt), the causal agent of wheat stem (or black) rust is one of the most serious threats to global wheat production. The identification, mapping, and deployment of effective stem rust resistance (Sr) genes are critical to reduce this threat. In this study, we generated SrTm4 monogenic lines and found that this gene confers resistance to North American and Chinese Pgt races. Using a large mapping population (9522 gametes), we mapped SrTm4 within a 0.06 cM interval flanked by marker loci CS4211 and 130K1519, which corresponds to a 1.0-Mb region in the Chinese Spring reference genome v2.1. A physical map of the SrTm4 region was constructed with 11 overlapping BACs from the resistant Triticum monococcum PI 306540. Comparison of the 754-kb physical map with the genomic sequence of Chinese Spring and a discontinuous BAC sequence of DV92 revealed a 593-kb chromosomal inversion in PI 306540. Within the candidate region, we identified an L-type lectin-domain containing receptor kinase (LLK1), which was disrupted by the proximal inversion breakpoint, as a potential candidate gene. Two diagnostic dominant markers were developed to detect the inversion breakpoints. In a survey of T. monococcum accessions, we identified 10 domesticated T. monococcum subsp. monococcum genotypes, mainly from the Balkans, carrying the inversion and showing similar mesothetic resistant infection types against Pgt races. The high-density map and tightly linked molecular markers developed in this study are useful tools to accelerate the deployment of SrTm4-mediated resistance in wheat breeding programs.
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Affiliation(s)
- Hongna Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China
| | - Jing Luo
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China
| | - Wenjun Zhang
- Department of Plant Sciences, University of California, Davis, CA95616, USA
| | - Lei Hua
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China
| | - Kun Li
- Department of Plant Sciences, University of California, Davis, CA95616, USA
| | - Jian Wang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Binyang Xu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chen Yang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guiping Wang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China
| | - Matthew N Rouse
- US Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory and Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA.
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA95616, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
| | - Shisheng Chen
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China.
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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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Li H, Hua L, Rouse MN, Li T, Pang S, Bai S, Shen T, Luo J, Li H, Zhang W, Wang X, Dubcovsky J, Chen S. Mapping and Characterization of a Wheat Stem Rust Resistance Gene in Durum Wheat "Kronos". FRONTIERS IN PLANT SCIENCE 2021; 12:751398. [PMID: 34721479 PMCID: PMC8555631 DOI: 10.3389/fpls.2021.751398] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 09/09/2021] [Indexed: 05/22/2023]
Abstract
Wheat stem (or black) rust is one of the most devastating fungal diseases, threatening global wheat production. Identification, mapping, and deployment of effective resistance genes are critical to addressing this challenge. In this study, we mapped and characterized one stem rust resistance (Sr) gene from the tetraploid durum wheat variety Kronos (temporary designation SrKN). This gene was mapped on the long arm of chromosome 2B and confers resistance to multiple virulent Pgt races, such as TRTTF and BCCBC. Using a large mapping population (3,366 gametes), we mapped SrKN within a 0.29 cM region flanked by the sequenced-based markers pku4856F2R2 and pku4917F3R3, which corresponds to 5.6- and 7.2-Mb regions in the Svevo and Chinese Spring reference genomes, respectively. Both regions include a cluster of nucleotide binding leucine-repeat (NLR) genes that likely includes the candidate gene. An allelism test failed to detect recombination between SrKN and the previously mapped Sr9e gene. This result, together with the similar seedling resistance responses and resistance profiles, suggested that SrKN and Sr9e may represent the same gene. We introgressed SrKN into common wheat and developed completely linked markers to accelerate its deployment in the wheat breeding programs. SrKN can be a valuable component of transgenic cassettes or gene pyramids that includes multiple resistance genes to control this devastating disease.
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Affiliation(s)
- Hongna Li
- Peking University Institute of Advanced Agricultural Sciences, Weifang, China
| | - Lei Hua
- Peking University Institute of Advanced Agricultural Sciences, Weifang, China
| | - Matthew N. Rouse
- US Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory and Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Tianya Li
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Shuyong Pang
- Peking University Institute of Advanced Agricultural Sciences, Weifang, China
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Shengsheng Bai
- Peking University Institute of Advanced Agricultural Sciences, Weifang, China
| | - Tao Shen
- Peking University Institute of Advanced Agricultural Sciences, Weifang, China
| | - Jing Luo
- Peking University Institute of Advanced Agricultural Sciences, Weifang, China
| | - Hongyu Li
- Peking University Institute of Advanced Agricultural Sciences, Weifang, China
| | - Wenjun Zhang
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Xiaodong Wang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
- Howard Hughes Medical Institute, Chevy Chase, MD, United States
| | - Shisheng Chen
- Peking University Institute of Advanced Agricultural Sciences, Weifang, China
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Chen S, Hegarty J, Shen T, Hua L, Li H, Luo J, Li H, Bai S, Zhang C, Dubcovsky J. Stripe rust resistance gene Yr34 (synonym Yr48) is located within a distal translocation of Triticum monococcum chromosome 5A mL into common wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2197-2211. [PMID: 33791822 PMCID: PMC8263425 DOI: 10.1007/s00122-021-03816-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/10/2021] [Indexed: 05/24/2023]
Abstract
Key message The stripe rust resistance gene Yr34 was transferred to polyploid wheat chromosome 5AL from T. monococcum and has been used for over two centuries.Wheat stripe (or yellow) rust, caused by Puccinia striiformis f. sp. tritici (Pst), is currently among the most damaging fungal diseases of wheat worldwide. In this study, we report that the stripe rust resistance gene Yr34 (synonym Yr48) is located within a distal segment of the cultivated Triticum monococcum subsp. monococcum chromosome 5AmL translocated to chromosome 5AL in polyploid wheat. The diploid wheat species Triticum monococcum (genome AmAm) is closely related to T. urartu (donor of the A genome to polyploid wheat) and has good levels of resistance against the stripe rust pathogen. When present in hexaploid wheat, the T. monococcum Yr34 resistance gene confers a moderate level of resistance against virulent Pst races present in California and the virulent Chinese race CYR34. In a survey of 1,442 common wheat genotypes, we identified 5AmL translocations of fourteen different lengths in 17.5% of the accessions, with higher frequencies in Europe than in other continents. The old European wheat variety "Mediterranean" was identified as a putative source of this translocation, suggesting that Yr34 has been used for over 200 years. Finally, we designed diagnostic CAPS and sequenced-based markers that will be useful to accelerate the deployment of Yr34 in wheat breeding programs to improve resistance to this devastating pathogen.
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Affiliation(s)
- Shisheng Chen
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, Shandong, China.
| | - Joshua Hegarty
- Department of Plant Sciences, University of California, Davis, CA95616, USA
| | - Tao Shen
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, Shandong, China
| | - Lei Hua
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, Shandong, China
| | - Hongna Li
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, Shandong, China
| | - Jing Luo
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, Shandong, China
| | - Hongyu Li
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, Shandong, China
| | - Shengsheng Bai
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, Shandong, China
| | - Chaozhong Zhang
- Department of Plant Sciences, University of California, Davis, CA95616, USA
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA95616, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
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Chen S, Rouse MN, Zhang W, Zhang X, Guo Y, Briggs J, Dubcovsky J. Wheat gene Sr60 encodes a protein with two putative kinase domains that confers resistance to stem rust. THE NEW PHYTOLOGIST 2020; 225:948-959. [PMID: 31487050 DOI: 10.1111/nph.16169] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 08/28/2019] [Indexed: 05/18/2023]
Abstract
Wheat stem rust, caused by Puccinia graminis Pers. f. sp. tritici (Pgt), is a devastating fungal disease threatening global wheat production. The present paper reports the identification of stem rust resistance gene Sr60, a race-specific gene from diploid wheat Triticum monococcum L. that encodes a protein with two putative kinase domains. This gene, designated as WHEAT TANDEM KINASE 2 (WTK2), confers intermediate levels of resistance to Pgt. WTK2 was identified by map-based cloning and validated by transformation of a c.10-kb genomic sequence including WTK2 into susceptible common wheat variety Fielder (Triticum aestivum L.). Transformation of Fielder with WTK2 was sufficient to confer Pgt resistance. Sr60 transcripts were transiently upregulated 1 d post-inoculation with Pgt, but not in mock-inoculated plants. The upregulation of Sr60 was associated with stable upregulation of several pathogenesis-related genes. The Sr60-resistant haplotype found in T. monococcum was not found in polyploid wheat, suggesting an opportunity to introduce a novel resistance gene. Sr60 was successfully introgressed into hexaploid wheat, and we developed a diagnostic molecular marker to accelerate its deployment and pyramiding with other resistance genes. The cloned Sr60 also can be a useful component of transgenic cassettes including other resistance genes with complementary resistance profiles.
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Affiliation(s)
- Shisheng Chen
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, 261000, China
| | - Matthew N Rouse
- USDA-ARS Cereal Disease Laboratory and Department of Plant Pathology, University of Minnesota, St Paul, MN, 55108, USA
| | - Wenjun Zhang
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Xiaoqin Zhang
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Yan Guo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Jordan Briggs
- USDA-ARS Cereal Disease Laboratory and Department of Plant Pathology, University of Minnesota, St Paul, MN, 55108, USA
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
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Sharma JS, Zhang Q, Rouse MN, Klindworth DL, Friesen TL, Long Y, Olivera PD, Jin Y, McClean PE, Xu SS, Faris JD. Mapping and characterization of two stem rust resistance genes derived from cultivated emmer wheat accession PI 193883. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:3177-3189. [PMID: 31494680 DOI: 10.1007/s00122-019-03417-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/27/2019] [Indexed: 05/13/2023]
Abstract
Two stem rust resistance genes identified on chromosome arms 2BL and 6AL of the cultivated emmer wheat accession PI 193883 can be used for protecting modern varieties against Ug99 strains. The wheat research community consistently strives to identify new genes that confer resistance to stem rust caused by the fungal pathogen Puccinia graminis f. sp. tritici Eriks & E. Henn (Pgt). In the current study, our objective was to identify and genetically characterize the stem rust resistance derived from the cultivated emmer accession PI 193883. A recombinant inbred line population developed from a cross between the susceptible durum wheat line Rusty and PI 193883 was genotyped and evaluated for reaction to Pgt races TTKSK, TRTTF, and TMLKC. Two QTLs conferring resistance were identified on chromosome arms 2BL (QSr.fcu-2B) and 6AL (QSr.fcu-6A). The stem rust resistance gene (Sr883-2B) underlying QSr.fcu-2B was recessive, and based on its physical location it is located proximal to the Sr9 region. QSr.fcu-6A was located in the Sr13 region, but PI 193883 is known to carry the susceptible haplotype S4 for Sr13, indicating that the gene underlying QSr.fcu-6A (Sr883-6A) is likely a new allele of Sr13 or a gene residing close to Sr13. Three IWGSC scaffold-based simple sequence repeat (SSR) and two SNP-based semi-thermal asymmetric reverse PCR (STARP) markers were developed for the Sr883-2B region, and one STARP marker was developed for Sr883-6A. Sr883-2B was epistatic to Sr883-6A for reaction to TTKSK and TRTTF, and the two genes had additive effects for TMLKC. These two genes and the markers developed in this research provide additional resources and tools for the improvement in stem rust resistance in durum and common wheat breeding programs.
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Affiliation(s)
- Jyoti S Sharma
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 100, Morden, MB, R6M 1Y5, Canada
| | - Qijun Zhang
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Matthew N Rouse
- USDA-ARS, Cereal Disease Laboratory and Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Daryl L Klindworth
- USDA-ARS, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, 1616 Albrecht Blvd. North, Fargo, ND, 58102-2765, USA
| | - Timothy L Friesen
- USDA-ARS, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, 1616 Albrecht Blvd. North, Fargo, ND, 58102-2765, USA
| | - Yunming Long
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Pablo D Olivera
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Yue Jin
- USDA-ARS, Cereal Disease Laboratory and Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Phillip E McClean
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Steven S Xu
- USDA-ARS, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, 1616 Albrecht Blvd. North, Fargo, ND, 58102-2765, USA
| | - Justin D Faris
- USDA-ARS, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, 1616 Albrecht Blvd. North, Fargo, ND, 58102-2765, USA.
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Kishii M. An Update of Recent Use of Aegilops Species in Wheat Breeding. FRONTIERS IN PLANT SCIENCE 2019; 10:585. [PMID: 31143197 PMCID: PMC6521781 DOI: 10.3389/fpls.2019.00585] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 04/18/2019] [Indexed: 05/16/2023]
Abstract
Aegilops species have significantly contributed to wheat breeding despite the difficulties involved in the handling of wild species, such as crossability and incompatibility. A number of biotic resistance genes have been identified and incorporated into wheat varieties from Aegilops species, and this genus is also contributing toward improvement of complex traits such as yield and abiotic tolerance for drought and heat. The D genome diploid species of Aegilops tauschii has been utilized most often in wheat breeding programs. Other Aegilops species are more difficult to utilize in the breeding because of lower meiotic recombination frequencies; generally they can be utilized only after extensive and time-consuming procedures in the form of translocation/introgression lines. After the emergence of Ug99 stem rust and wheat blast threats, Aegilops species gathered more attention as a form of new resistance sources. This article aims to update recent progress on Aegilops species, as well as to cover new topics around their use in wheat breeding.
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Affiliation(s)
- Masahiro Kishii
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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Chen S, Guo Y, Briggs J, Dubach F, Chao S, Zhang W, Rouse MN, Dubcovsky J. Mapping and characterization of wheat stem rust resistance genes SrTm5 and Sr60 from Triticum monococcum. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:625-635. [PMID: 29164273 PMCID: PMC5814525 DOI: 10.1007/s00122-017-3024-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 11/17/2017] [Indexed: 05/24/2023]
Abstract
KEY MESSAGE The new stem rust resistance gene Sr60 was fine-mapped to the distal region of chromosome arm 5AmS, and the TTKSK-effective gene SrTm5 could be a new allele of Sr22. The emergence and spread of new virulent races of the wheat stem rust pathogen (Puccinia graminis f. sp. tritici; Pgt), including the Ug99 race group, is a serious threat to global wheat production. In this study, we mapped and characterized two stem rust resistance genes from diploid wheat Triticum monococcum accession PI 306540. We mapped SrTm5, a previously postulated gene effective to Ug99, on chromosome arm 7AmL, completely linked to Sr22. SrTm5 displayed a different race specificity compared to Sr22 indicating that they are distinct. Sequencing of the Sr22 homolog in PI 306540 revealed a novel haplotype. Characterization of the segregating populations with Pgt race QFCSC revealed an additional resistance gene on chromosome arm 5AmS that was assigned the official name Sr60. This gene was also effective against races QTHJC and SCCSC but not against TTKSK (a Ug99 group race). Using two large mapping populations (4046 gametes), we mapped Sr60 within a 0.44 cM interval flanked by sequenced-based markers GH724575 and CJ942731. These two markers delimit a 54.6-kb region in Brachypodium distachyon chromosome 4 and a 430-kb region in the Chinese Spring reference genome. Both regions include a leucine-rich repeat protein kinase (LRRK123.1) that represents a potential candidate gene. Three CC-NBS-LRR genes were found in the colinear Brachypodium region but not in the wheat genome. We are currently developing a Bacterial Artificial Chromosome library of PI 306540 to determine which of these candidate genes are present in the T. monococcum genome and to complete the cloning of Sr60.
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Affiliation(s)
- Shisheng Chen
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Yan Guo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Jordan Briggs
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Felix Dubach
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Shiaoman Chao
- USDA-ARS Biosciences Research Laboratory, 1605 Albrecht Blvd. N., Fargo, ND, 58102, USA
| | - Wenjun Zhang
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Matthew N Rouse
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
- USDA-ARS Cereal Disease Laboratory, St. Paul, MN, 55108, USA
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
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Uauy C, Wulff BB, Dubcovsky J. Combining Traditional Mutagenesis with New High-Throughput Sequencing and Genome Editing to Reveal Hidden Variation in Polyploid Wheat. Annu Rev Genet 2017; 51:435-454. [DOI: 10.1146/annurev-genet-120116-024533] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Brande B.H. Wulff
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Jorge Dubcovsky
- Howard Hughes Medical Institute and Department of Plant Sciences, University of California, Davis, California 95616, USA
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Muleta KT, Rouse MN, Rynearson S, Chen X, Buta BG, Pumphrey MO. Characterization of molecular diversity and genome-wide mapping of loci associated with resistance to stripe rust and stem rust in Ethiopian bread wheat accessions. BMC PLANT BIOLOGY 2017; 17:134. [PMID: 28778144 PMCID: PMC5545024 DOI: 10.1186/s12870-017-1082-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 07/21/2017] [Indexed: 05/06/2023]
Abstract
BACKGROUND The narrow genetic basis of resistance in modern wheat cultivars and the strong selection response of pathogen populations have been responsible for periodic and devastating epidemics of the wheat rust diseases. Characterizing new sources of resistance and incorporating multiple genes into elite cultivars is the most widely accepted current mechanism to achieve durable varietal performance against changes in pathogen virulence. Here, we report a high-density molecular characterization and genome-wide association study (GWAS) of stripe rust and stem rust resistance in 190 Ethiopian bread wheat lines based on phenotypic data from multi-environment field trials and seedling resistance screening experiments. A total of 24,281 single nucleotide polymorphism (SNP) markers filtered from the wheat 90 K iSelect genotyping assay was used to survey Ethiopian germplasm for population structure, genetic diversity and marker-trait associations. RESULTS Upon screening for field resistance to stripe rust in the Pacific Northwest of the United States and Ethiopia over multiple growing seasons, and against multiple races of stripe rust and stem rust at seedling stage, eight accessions displayed resistance to all tested races of stem rust and field resistance to stripe rust in all environments. Our GWAS results show 15 loci were significantly associated with seedling and adult plant resistance to stripe rust at false discovery rate (FDR)-adjusted probability (P) <0.10. GWAS also detected 9 additional genomic regions significantly associated (FDR-adjusted P < 0.10) with seedling resistance to stem rust in the Ethiopian wheat accessions. Many of the identified resistance loci were mapped close to previously identified rust resistance genes; however, three loci on the short arms of chromosomes 5A and 7B for stripe rust resistance and two on chromosomes 3B and 7B for stem rust resistance may be novel. CONCLUSION Our results demonstrate that considerable genetic variation resides within the landrace accessions that can be utilized to broaden the genetic base of rust resistance in wheat breeding germplasm. The molecular markers identified in this study should be useful in efficiently targeting the associated resistance loci in marker-assisted breeding for rust resistance in Ethiopia and other countries.
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Affiliation(s)
- Kebede T Muleta
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
| | - Matthew N Rouse
- USDA-ARS Cereal Disease Laboratory, Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Sheri Rynearson
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
| | - Xianming Chen
- USDA-ARS, Wheat Health, Genetics, and Quality Research Unit, and Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, Pullman, WA, 99164-6430, USA
| | - Bedada G Buta
- Ethiopian Institute of Agricultural Research, Kulumsa Agricultural Research Center, P. O. Box 489, Assela, Ethiopia
| | - Michael O Pumphrey
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA.
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