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Zhao Y, Dong Z, Miao J, Liu Q, Ma C, Tian X, He J, Bi H, Yao W, Li T, Gill HS, Zhang Z, Cao A, Liu B, Li H, Sehgal SK, Liu W. Pm57 from Aegilops searsii encodes a tandem kinase protein and confers wheat powdery mildew resistance. Nat Commun 2024; 15:4796. [PMID: 38839783 PMCID: PMC11153570 DOI: 10.1038/s41467-024-49257-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 05/29/2024] [Indexed: 06/07/2024] Open
Abstract
Powdery mildew is a devastating disease that affects wheat yield and quality. Wheat wild relatives represent valuable sources of disease resistance genes. Cloning and characterization of these genes will facilitate their incorporation into wheat breeding programs. Here, we report the cloning of Pm57, a wheat powdery mildew resistance gene from Aegilops searsii. It encodes a tandem kinase protein with putative kinase-pseudokinase domains followed by a von Willebrand factor A domain (WTK-vWA), being ortholog of Lr9 that mediates wheat leaf rust resistance. The resistance function of Pm57 is validated via independent mutants, gene silencing, and transgenic assays. Stable Pm57 transgenic wheat lines and introgression lines exhibit high levels of all-stage resistance to diverse isolates of the Bgt fungus, and no negative impacts on agronomic parameters are observed in our experimental set-up. Our findings highlight the emerging role of kinase fusion proteins in plant disease resistance and provide a valuable gene for wheat breeding.
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Affiliation(s)
- Yue Zhao
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zhenjie Dong
- College of Agronomy, Nanjing Agricultural University, Nanjing, 210000, China
| | - Jingnan Miao
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Qianwen Liu
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Chao Ma
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiubin Tian
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jinqiu He
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Huihui Bi
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Wen Yao
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Tao Li
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Harsimardeep S Gill
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Aizhong Cao
- College of Agronomy, Nanjing Agricultural University, Nanjing, 210000, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Huanhuan Li
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Sunish K Sehgal
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, 57007, USA.
| | - Wenxuan Liu
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China.
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Sun P, Han X, Milne RJ, Li G. Trans-crop applications of atypical R genes for multipathogen resistance. TRENDS IN PLANT SCIENCE 2024:S1360-1385(24)00122-5. [PMID: 38811244 DOI: 10.1016/j.tplants.2024.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/31/2024]
Abstract
Genetic resistance to plant diseases is essential for global food security. Significant progress has been achieved for plant disease-resistance (R) genes comprising nucleotide-binding domain, leucine-rich repeat-containing receptors (NLRs), and membrane-localized receptor-like kinases or proteins (RLKs/RLPs), which we refer to as typical R genes. However, there is a knowledge gap in how non-receptor-type or atypical R genes contribute to plant immunity. Here, we summarize resources and technologies facilitating the study of atypical R genes, examine diverse atypical R proteins for broad-spectrum resistance, and outline potential approaches for trans-crop applications of atypical R genes. Studies of atypical R genes are important for a holistic understanding of plant immunity and the development of novel strategies in disease control and crop improvement.
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Affiliation(s)
- Peng Sun
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xinyu Han
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ricky J Milne
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia.
| | - Guotian Li
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan, 430070, China.
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3
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Wang Y, Gao M, Jiang Y, Huang W, Zhao X, Zhu W, Li H, Wang Y, Zeng J, Wu D, Wei Y, Zhou Y, Zheng Y, Zhang P, Chen G, Kang H. Identification of candidate genes for adult plant stripe rust resistance transferred from Aegilops ventricosa 2N vS into wheat via fine mapping and transcriptome analysis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:116. [PMID: 38698276 DOI: 10.1007/s00122-024-04620-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/10/2024] [Indexed: 05/05/2024]
Abstract
KEY MESSAGE An adult plant gene for resistance to stripe rust was narrowed down to the proximal one-third of the 2NvS segment translocated from Aegilops ventricosa to wheat chromosome arm 2AS, and based on the gene expression analysis, two candidate genes were identified showing a stronger response at the adult plant stage compared to the seedling stage. The 2NvS translocation from Aegilops ventricosa, known for its resistance to various diseases, has been pivotal in global wheat breeding for more than three decades. Here, we identified an adult plant resistance (APR) gene in the 2NvS segment in wheat line K13-868. Through fine mapping in a segregating near-isogenic line (NIL) derived population of 6389 plants, the candidate region for the APR gene was narrowed down to between 19.36 Mb and 33 Mb in the Jagger reference genome. Transcriptome analysis in NILs strongly suggested that this APR gene conferred resistance to stripe rust by triggering plant innate immune responses. Based on the gene expression analysis, two disease resistance-associated genes within the candidate region, TraesJAG2A03G00588940 and TraesJAG2A03G00590140, exhibited a stronger response to Puccinia striiformis f. sp. tritici (Pst) infection at the adult plant stage than at the seedling stage, indicating that they could be potential candidates for the resistance gene. Additionally, we developed a co-dominant InDel marker, InDel_31.05, for detecting this APR gene. Applying this marker showed that over one-half of the wheat varieties approved in 2021 and 2022 in Sichuan province, China, carry this gene. Agronomic trait evaluation of NILs indicated that the 2NvS segment effectively mitigated the negative effects of stripe rust on yield without affecting other important agronomic traits. This study provided valuable insights for cloning and breeding through the utilization of the APR gene present in the 2NvS segment.
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Affiliation(s)
- Yuqi Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Plant Breeding Institute, School of Life and Environmental Sciences, The University of Sydney, Cobbitty, NSW, 2570, Australia
| | - Mengru Gao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Wuzhou Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xin Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Wei Zhu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Hao Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yi Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jian Zeng
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Dandan Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yonghong Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Peng Zhang
- Plant Breeding Institute, School of Life and Environmental Sciences, The University of Sydney, Cobbitty, NSW, 2570, Australia.
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Houyang Kang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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4
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Mascher M, Marone MP, Schreiber M, Stein N. Are cereal grasses a single genetic system? NATURE PLANTS 2024; 10:719-731. [PMID: 38605239 DOI: 10.1038/s41477-024-01674-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 03/17/2024] [Indexed: 04/13/2024]
Abstract
In 1993, a passionate and provocative call to arms urged cereal researchers to consider the taxon they study as a single genetic system and collaborate with each other. Since then, that group of scientists has seen their discipline blossom. In an attempt to understand what unity of genetic systems means and how the notion was borne out by later research, we survey the progress and prospects of cereal genomics: sequence assemblies, population-scale sequencing, resistance gene cloning and domestication genetics. Gene order may not be as extraordinarily well conserved in the grasses as once thought. Still, several recurring themes have emerged. The same ancestral molecular pathways defining plant architecture have been co-opted in the evolution of different cereal crops. Such genetic convergence as much as cross-fertilization of ideas between cereal geneticists has led to a rich harvest of genes that, it is hoped, will lead to improved varieties.
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Affiliation(s)
- Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
| | - Marina Püpke Marone
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Mona Schreiber
- University of Marburg, Department of Biology, Marburg, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany.
- Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.
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5
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Li M, Zhang H, Xiao H, Zhu K, Shi W, Zhang D, Wang Y, Yang L, Wu Q, Xie J, Chen Y, Qiu D, Guo G, Lu P, Li B, Dong L, Li W, Cui X, Li L, Tian X, Yuan C, Li Y, Yu D, Nevo E, Fahima T, Li H, Dong L, Zhao Y, Liu Z. A membrane associated tandem kinase from wild emmer wheat confers broad-spectrum resistance to powdery mildew. Nat Commun 2024; 15:3124. [PMID: 38600164 PMCID: PMC11006675 DOI: 10.1038/s41467-024-47497-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/04/2024] [Indexed: 04/12/2024] Open
Abstract
Crop wild relatives offer natural variations of disease resistance for crop improvement. Here, we report the isolation of broad-spectrum powdery mildew resistance gene Pm36, originated from wild emmer wheat, that encodes a tandem kinase with a transmembrane domain (WTK7-TM) through the combination of map-based cloning, PacBio SMRT long-read genome sequencing, mutagenesis, and transformation. Mutagenesis assay reveals that the two kinase domains and the transmembrane domain of WTK7-TM are critical for the powdery mildew resistance function. Consistently, in vitro phosphorylation assay shows that two kinase domains are indispensable for the kinase activity of WTK7-TM. Haplotype analysis uncovers that Pm36 is an orphan gene only present in a few wild emmer wheat, indicating its single ancient origin and potential contribution to the current wheat gene pool. Overall, our findings not only provide a powdery mildew resistance gene with great potential in wheat breeding but also sheds light into the mechanism underlying broad-spectrum resistance.
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Affiliation(s)
- Miaomiao Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.
| | - Huaizhi Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Huixin Xiao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Keyu Zhu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wenqi Shi
- Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Dong Zhang
- Beijing PlantTech Biotechnology Co., Ltd., Beijing, China
| | - Yong Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lijun Yang
- Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Qiuhong Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Jingzhong Xie
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Yongxing Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Dan Qiu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Guanghao Guo
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Ping Lu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Beibei Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lei Dong
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wenling Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xuejia Cui
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lingchuan Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiubin Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | | | - Yiwen Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Dazhao Yu
- Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa, Israel
| | - Tzion Fahima
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa, Israel
| | - Hongjie Li
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lingli Dong
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.
| | - Yusheng Zhao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
| | - Zhiyong Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
- Hainan Seed Industry Laboratory, Sanya City, Hainan Province, China.
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6
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Li H, Men W, Ma C, Liu Q, Dong Z, Tian X, Wang C, Liu C, Gill HS, Ma P, Zhang Z, Liu B, Zhao Y, Sehgal SK, Liu W. Wheat powdery mildew resistance gene Pm13 encodes a mixed lineage kinase domain-like protein. Nat Commun 2024; 15:2449. [PMID: 38503771 PMCID: PMC10951266 DOI: 10.1038/s41467-024-46814-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 03/11/2024] [Indexed: 03/21/2024] Open
Abstract
Wheat powdery mildew is one of the most destructive diseases threatening global wheat production. The wild relatives of wheat constitute rich sources of diversity for powdery mildew resistance. Here, we report the map-based cloning of the powdery mildew resistance gene Pm13 from the wild wheat species Aegilops longissima. Pm13 encodes a mixed lineage kinase domain-like (MLKL) protein that contains an N-terminal-domain of MLKL (MLKL_NTD) domain in its N-terminus and a C-terminal serine/threonine kinase (STK) domain. The resistance function of Pm13 is validated by mutagenesis, gene silencing, transgenic assay, and allelic association analyses. The development of introgression lines with significantly reduced chromosome segments of Ae. longissima encompassing Pm13 enables widespread deployment of this gene into wheat cultivars. The cloning of Pm13 may provide valuable insights into the molecular mechanisms underlying Pm13-mediated powdery mildew resistance and highlight the important roles of kinase fusion proteins (KFPs) in wheat immunity.
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Affiliation(s)
- Huanhuan Li
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, PR China
| | - Wenqiang Men
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, PR China
| | - Chao Ma
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, PR China
| | - Qianwen Liu
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, PR China
| | - Zhenjie Dong
- College of Agronomy, Nanjing Agricultural University, Nanjing, 210000, PR China
| | - Xiubin Tian
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Chaoli Wang
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, PR China
| | - Cheng Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250000, PR China
| | - Harsimardeep S Gill
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Pengtao Ma
- College of Life Sciences, Yantai University, Yantai, 264005, PR China
| | - Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, PR China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, PR China
| | - Yue Zhao
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, PR China.
| | - Sunish K Sehgal
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, 57007, USA.
| | - Wenxuan Liu
- The State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, PR China.
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7
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Edae EA, Kosgey Z, Bajgain P, Ndung'u KC, Gemechu A, Bhavani S, Anderson JA, Rouse MN. The genetics of Ug99 stem rust resistance in spring wheat variety 'Linkert'. FRONTIERS IN PLANT SCIENCE 2024; 15:1343148. [PMID: 38516672 PMCID: PMC10954791 DOI: 10.3389/fpls.2024.1343148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/12/2024] [Indexed: 03/23/2024]
Abstract
Wheat stem rust caused by Puccinia graminis f. sp. tritici (Pgt) threatens wheat production worldwide. The objective of this study was to characterize wheat stem rust resistance in 'Linkert', a variety with adult plant resistance effective to emerging wheat stem rust pathogen strain Ug99. Two doubled haploid (DH) populations and one recombinant inbred line (RIL) population were developed with 'Linkert' as a stem rust resistant parent. Hard red spring wheat variety 'Forefront' and genetic stock 'LMPG' were used as stem rust susceptible parents of the DH populations. Breeding line 'MN07098-6' was used as a susceptible parent of the RIL population. Both DH and RIL populations with their parents were evaluated both at the seedling stage and in the field against Pgt races. Genotyping data of the DH populations were generated using the wheat iSelect 90k SNP assay. The RIL population was genotyped by genotyping-by-sequencing. We found QTL consistently associated with wheat stem rust resistance on chromosome 2BS for the Linkert/Forefront DH population and the Linkert/MN07098-6 RIL population both in Ethiopia and Kenya. Additional reliable QTL were detected on chromosomes 5BL (125.91 cM) and 4AL (Sr7a) for the Linkert/LMPG population in Ethiopia and Kenya. Different QTL identified in the populations reflect the importance of examining the genetics of resistance in populations derived from adapted germplasm (Forefront and MN07098-6) in addition to a genetic stock (LMPG). The associated markers in this study could be used to track and select for the identified QTL in wheat breeding programs.
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Affiliation(s)
- Erena A. Edae
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
| | - Zennah Kosgey
- Kenya Agricultural and Livestock Research Organization (KALRO), Food Crops Research Centre, Njoro, Kenya
| | - Prabin Bajgain
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, United States
| | - Kimani C. Ndung'u
- Kenya Agricultural and Livestock Research Organization (KALRO), Food Crops Research Centre, Njoro, Kenya
| | - Ashenafi Gemechu
- Ethiopian Institute of Agriculture, Debre Zeit Agricultural Research Center, Bishoftu, Ethiopia
| | - Sridhar Bhavani
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - James A. Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, United States
| | - Matthew N. Rouse
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
- Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, Saint Paul, MN, United States
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8
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Liu Y, Hou S, Chen S. Kinase fusion proteins: intracellular R-proteins in plant immunity. TRENDS IN PLANT SCIENCE 2024; 29:278-282. [PMID: 38016865 DOI: 10.1016/j.tplants.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/24/2023] [Accepted: 11/03/2023] [Indexed: 11/30/2023]
Abstract
Resistance (R) genes in the Triticeae tribe include not only genes encoding the canonical intracellular nucleotide-binding leucine-rich-repeat proteins (NLRs) but also genes encoding kinase fusion proteins (KFPs). Exploring these unconventional KFPs may expand the scope of effector-triggered immunity (ETI) and will have significant implications for crop improvement.
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Affiliation(s)
- Yukun Liu
- College of Forestry, Southwest Forestry University, 300 Bailong Si, Kunming, Yunnan 650224, China.
| | - Shuguo Hou
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong 261325, China.
| | - Shisheng Chen
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong 261325, China
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9
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Schreiber M, Jayakodi M, Stein N, Mascher M. Plant pangenomes for crop improvement, biodiversity and evolution. Nat Rev Genet 2024:10.1038/s41576-024-00691-4. [PMID: 38378816 DOI: 10.1038/s41576-024-00691-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2023] [Indexed: 02/22/2024]
Abstract
Plant genome sequences catalogue genes and the genetic elements that regulate their expression. Such inventories further research aims as diverse as mapping the molecular basis of trait diversity in domesticated plants or inquiries into the origin of evolutionary innovations in flowering plants millions of years ago. The transformative technological progress of DNA sequencing in the past two decades has enabled researchers to sequence ever more genomes with greater ease. Pangenomes - complete sequences of multiple individuals of a species or higher taxonomic unit - have now entered the geneticists' toolkit. The genomes of crop plants and their wild relatives are being studied with translational applications in breeding in mind. But pangenomes are applicable also in ecological and evolutionary studies, as they help classify and monitor biodiversity across the tree of life, deepen our understanding of how plant species diverged and show how plants adapt to changing environments or new selection pressures exerted by human beings.
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Affiliation(s)
- Mona Schreiber
- Department of Biology, University of Marburg, Marburg, Germany
| | - Murukarthick Jayakodi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
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10
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Türkösi E, Szakács É, Ivanizs L, Farkas A, Gaál E, Said M, Darkó É, Cséplő M, Mikó P, Doležel J, Molnár-Láng M, Molnár I, Kruppa K. A chromosome arm from Thinopyrum intermedium × Thinopyrum ponticum hybrid confers increased tillering and yield potential in wheat. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:7. [PMID: 38263978 PMCID: PMC10803699 DOI: 10.1007/s11032-024-01439-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 12/25/2023] [Indexed: 01/25/2024]
Abstract
Tiller number is a key component of wheat plant architecture having a direct impact on grain yield. Because of their viability, biotic resistance, and abiotic stress tolerance, wild relative species are a valuable gene source for increasing wheat genetic diversity, including yield potential. Agropyron glael, a perennial hybrid of Thinopyrum intermedium and Th. ponticum, was created in the 1930s. Recent genome analyses identified five evolutionarily distinct subgenomes (J, Jst, Jvs, Jr, and St), making A. glael an important gene source for transferring useful agronomical traits into wheat. During a bread wheat × A. glael crossing program, a genetically stable translocation line, WT153397, was developed. Sequential in situ hybridizations (McGISH) with J-, St-, and D-genomic DNA probes and pSc119.2, Afa family, pTa71, and (GAA)7 DNA repeats, as well as molecular markers specific for the wheat 6D chromosome, revealed the presence of a 6DS.6Jvs Robertsonian translocation in the genetic line. Field trials in low-input and high-input breeding nurseries over four growing seasons demonstrated the Agropyron chromosome arm's high compensating ability for the missing 6DL, as spike morphology and fertility of WT153397 did not differ significantly from those of wheat parents, Mv9kr1 and 'Mv Karizma.' Moreover, the introgressed 6Jvs chromosome arm significantly increased the number of productive tillers, resulting in a significantly higher grain yield potential compared to the parental wheat cultivars. The translocated chromosome could be highly purified by flow cytometric sorting due to the intense fluorescent labeling of (GAA)7 clusters on the Thinopyrum chromosome arm, providing an opportunity to use chromosome genomics to identify Agropyron gene variant(s) responsible for the tillering capacity. The translocation line WT153397 is an important genetic stock for functional genetic studies of tiller formation and useful breeding material for increasing wheat yield potential. The study also discusses the use of the translocation line in wheat breeding. Supplementary information The online version contains supplementary material available at 10.1007/s11032-024-01439-y.
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Affiliation(s)
- Edina Türkösi
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Éva Szakács
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - László Ivanizs
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - András Farkas
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Eszter Gaál
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Mahmoud Said
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, 779 00 Olomouc, Czechia
- Agricultural Research Centre, Field Crops Research Institute, Cairo, Egypt
| | - Éva Darkó
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Mónika Cséplő
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Péter Mikó
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Jaroslav Doležel
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, 779 00 Olomouc, Czechia
| | - Márta Molnár-Láng
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - István Molnár
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
| | - Klaudia Kruppa
- Centre for Agricultural Research, Hungarian Research Network (HUN-REN), 2462 Martonvásár, Hungary
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11
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Chen R, Gajendiran K, Wulff BBH. R we there yet? Advances in cloning resistance genes for engineering immunity in crop plants. CURRENT OPINION IN PLANT BIOLOGY 2024; 77:102489. [PMID: 38128298 DOI: 10.1016/j.pbi.2023.102489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 11/15/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023]
Abstract
Over the past three decades, significant progress has been made in the field of resistance (R) gene cloning. Advances in recombinant DNA technology, genome sequencing, bioinformatics, plant transformation and plant husbandry have facilitated the transition from cloning R genes in model species to crop plants and their wild relatives. To date, researchers have isolated more than 450 R genes that play important roles in plant immunity. The molecular and biochemical mechanisms by which intracellular immune receptors are activated and initiate defense responses are now well understood. These advances present exciting opportunities for engineering disease-resistant crop plants that are protected by genetics rather than pesticides.
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Affiliation(s)
- Renjie Chen
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division (BESE), Center for Desert Agriculture, Thuwal 23955-6900, Saudi Arabia
| | - Karthick Gajendiran
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division (BESE), Center for Desert Agriculture, Thuwal 23955-6900, Saudi Arabia
| | - Brande B H Wulff
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division (BESE), Center for Desert Agriculture, Thuwal 23955-6900, Saudi Arabia.
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12
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Li Y, Wei ZZ, Sela H, Govta L, Klymiuk V, Roychowdhury R, Chawla HS, Ens J, Wiebe K, Bocharova V, Ben-David R, Pawar PB, Zhang Y, Jaiwar S, Molnár I, Doležel J, Coaker G, Pozniak CJ, Fahima T. Dissection of a rapidly evolving wheat resistance gene cluster by long-read genome sequencing accelerated the cloning of Pm69. PLANT COMMUNICATIONS 2024; 5:100646. [PMID: 37415333 PMCID: PMC10811346 DOI: 10.1016/j.xplc.2023.100646] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/10/2023] [Accepted: 07/04/2023] [Indexed: 07/08/2023]
Abstract
Gene cloning in repeat-rich polyploid genomes remains challenging. Here, we describe a strategy for overcoming major bottlenecks in cloning of the powdery mildew resistance gene (R-gene) Pm69 derived from tetraploid wild emmer wheat. A conventional positional cloning approach was not effective owing to suppressed recombination. Chromosome sorting was compromised by insufficient purity. A Pm69 physical map, constructed by assembling Oxford Nanopore Technology (ONT) long-read genome sequences, revealed a rapidly evolving nucleotide-binding leucine-rich repeat (NLR) R-gene cluster with structural variations. A single candidate NLR was identified by anchoring RNA sequencing reads from susceptible mutants to ONT contigs and was validated by virus-induced gene silencing. Pm69 is likely a newly evolved NLR and was discovered in only one location across the wild emmer wheat distribution range in Israel. Pm69 was successfully introgressed into cultivated wheat, and a diagnostic molecular marker was used to accelerate its deployment and pyramiding with other R-genes.
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Affiliation(s)
- Yinghui Li
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa 3498838, Israel; The Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa 3498838, Israel
| | - Zhen-Zhen Wei
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa 3498838, Israel; The Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa 3498838, Israel; The Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Hanan Sela
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa 3498838, Israel; The Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa 3498838, Israel
| | - Liubov Govta
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa 3498838, Israel; The Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa 3498838, Israel
| | - Valentyna Klymiuk
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa 3498838, Israel; The Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa 3498838, Israel; Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Rajib Roychowdhury
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa 3498838, Israel; The Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa 3498838, Israel
| | - Harmeet Singh Chawla
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Jennifer Ens
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Krystalee Wiebe
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Valeria Bocharova
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa 3498838, Israel; The Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa 3498838, Israel
| | - Roi Ben-David
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa 3498838, Israel; The Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa 3498838, Israel; Department of Vegetables and Field Crops, Institute of Plant Sciences, Agricultural Research Organization (ARO) - Volcani Center, Rishon Lezion 7505101, Israel
| | - Prerna B Pawar
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa 3498838, Israel; The Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa 3498838, Israel
| | - Yuqi Zhang
- Department of Crop Genomics and Bioinformatics, China Agricultural University, Beijing 100094, China
| | - Samidha Jaiwar
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa 3498838, Israel; The Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa 3498838, Israel
| | - István Molnár
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Gitta Coaker
- Plant Pathology Department, University of California, Davis, Davis, CA 95616, USA
| | - Curtis J Pozniak
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Tzion Fahima
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa 3498838, Israel; The Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa 3498838, Israel.
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13
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Norman M, Chen C, Miah H, Patpour M, Sørensen C, Hovmøller M, Forrest K, Kumar S, Prasad P, Gangwar OP, Bhardwaj S, Bariana H, Periyannan S, Bansal U. Sr65: a widely effective gene for stem rust resistance in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 137:1. [PMID: 38071267 DOI: 10.1007/s00122-023-04507-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 11/15/2023] [Indexed: 12/18/2023]
Abstract
KEY MESSAGE Sr65 in chromosome 1A of Indian wheat landrace Hango-2 is a potentially useful all-stage resistance gene that currently protects wheat from stem rust in Australia, India, Africa and Europe. Stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), threatened global wheat production with the appearance of widely virulent races that included TTKSK and TTRTF. Indian landrace Hango-2 showed resistance to Pgt races in India and Australia. Screening of a Hango-2/Avocet 'S' (AvS) recombinant inbred line population identified two stem rust resistance genes, a novel gene (temporarily named as SrH2) from Hango-2 and Sr26 from AvS. A mapping population segregating for SrH2 alone was developed from two recombinant lines. SrH2 was mapped on the short arm of chromosome 1A, where it was flanked by KASP markers KASP_7944 (proximal) and KASP_12147 (distal). SrH2 was delimited to an interval of 1.8-2.3 Mb on chromosome arm 1AS. The failure to detect candidate genes through MutRenSeq and comparative genomic analysis with the pan-genome dataset indicated the necessity to generate a Hango-2 specific assembly for detecting the gene sequence linked with SrH2 resistance. MutRenSeq however enabled identification of SrH2-linked KASP marker sunCS_265. Markers KASP_12147 and sunCS_265 showed 92% and 85% polymorphism among an Australian cereal cultivar diversity panel and can be used for marker-assisted selection of SrH2 in breeding programs. The effectiveness of SrH2 against Pgt races from Europe, Africa, India, and Australia makes it a valuable resource for breeding stem rust-resistant wheat cultivars. Since no wheat-derived gene was previously located in chromosome arm 1AS, SrH2 represents a new locus and named as SR65.
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Affiliation(s)
- Michael Norman
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Chunhong Chen
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Hanif Miah
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia
| | - Mehran Patpour
- Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Chris Sørensen
- Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Mogens Hovmøller
- Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Kerrie Forrest
- Agriculture Victoria, Department of Energy, Environment and Climate Action, AgriBio, Centre for AgriBioscience, 5 Ring Rd., Bundoora, VIC, 3083, Australia
| | - Subodh Kumar
- Indian Council of Agricultural Research - Indian Institute of Wheat and Barley Research Regional Station, Flowerdale, Shimla, Himachal Pradesh, 171 002, India
| | - Pramod Prasad
- Indian Council of Agricultural Research - Indian Institute of Wheat and Barley Research Regional Station, Flowerdale, Shimla, Himachal Pradesh, 171 002, India
| | - Om Prakash Gangwar
- Indian Council of Agricultural Research - Indian Institute of Wheat and Barley Research Regional Station, Flowerdale, Shimla, Himachal Pradesh, 171 002, India
| | - Subhash Bhardwaj
- Indian Council of Agricultural Research - Indian Institute of Wheat and Barley Research Regional Station, Flowerdale, Shimla, Himachal Pradesh, 171 002, India
| | - Harbans Bariana
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia
- School of Science, Western Sydney University, Bourke Road, Richmond, NSW, 2753, Australia
| | - Sambasivam Periyannan
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, Canberra, ACT, 2601, Australia.
- School of Agriculture and Environmental Science, Centre for Crop Health, University of Southern Queensland, West Street, Toowoomba, QLD, 4350, Australia.
| | - Urmil Bansal
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia.
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14
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Zhao P, Ma X, Zhang R, Cheng M, Niu Y, Shi X, Ji W, Xu S, Wang X. Integration of genome-wide association study, linkage analysis, and population transcriptome analysis to reveal the TaFMO1-5B modulating seminal root growth in bread wheat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1385-1400. [PMID: 37713270 DOI: 10.1111/tpj.16432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/10/2023] [Accepted: 08/12/2023] [Indexed: 09/16/2023]
Abstract
Bread wheat, one of the keystone crops for global food security, is challenged by climate change and resource shortage. The root system plays a vital role in water and nutrient absorption, making it essential for meeting the growing global demand. Here, using an association-mapping population composed of 406 accessions, we identified QTrl.Rs-5B modulating seminal root development with a genome-wide association study and validated its genetic effects with two F5 segregation populations. Transcriptome-wide association study prioritized TaFMO1-5B, a gene encoding the flavin-containing monooxygenases, as the causal gene for QTrl.Rs-5B, whose expression levels correlate negatively with the phenotyping variations among our population. The lines silenced for TaFMO1-5B consistently showed significantly larger seminal roots in different genetic backgrounds. Additionally, the agriculture traits measured in multiple environments showed that QTrl.Rs-5B also affects yield component traits and plant architecture-related traits, and its favorable haplotype modulates these traits toward that of modern cultivars, suggesting the application potential of QTrl.Rs-5B for wheat breeding. Consistently, the frequency of the favorable haplotype of QTrl.Rs-5B increased with habitat expansion and breeding improvement of bread wheat. In conclusion, our findings identified and demonstrated the effects of QTrl.Rs-5B on seminal root development and illustrated that it is a valuable genetic locus for wheat root improvement.
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Affiliation(s)
- Peng Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiuyun Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ruize Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Mingzhu Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yaxin Niu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xue Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Wanquan Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Shengbao Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaoming Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
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15
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Farkas A, Gaál E, Ivanizs L, Blavet N, Said M, Holušová K, Szőke-Pázsi K, Spitkó T, Mikó P, Türkösi E, Kruppa K, Kovács P, Darkó É, Szakács É, Bartoš J, Doležel J, Molnár I. Chromosome genomics facilitates the marker development and selection of wheat-Aegilops biuncialis addition, substitution and translocation lines. Sci Rep 2023; 13:20499. [PMID: 37993509 PMCID: PMC10665447 DOI: 10.1038/s41598-023-47845-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/19/2023] [Indexed: 11/24/2023] Open
Abstract
The annual goatgrass, Aegilops biuncialis is a rich source of genes with considerable agronomic value. This genetic potential can be exploited for wheat improvement through interspecific hybridization to increase stress resistance, grain quality and adaptability. However, the low throughput of cytogenetic selection hampers the development of alien introgressions. Using the sequence of flow-sorted chromosomes of diploid progenitors, the present study enabled the development of chromosome-specific markers. In total, 482 PCR markers were validated on wheat (Mv9kr1) and Ae. biuncialis (MvGB642) crossing partners, and 126 on wheat-Aegilops additions. Thirty-two markers specific for U- or M-chromosomes were used in combination with GISH and FISH for the screening of 44 Mv9kr1 × Ae. biuncialis BC3F3 genotypes. The predominance of chromosomes 4M and 5M, as well as the presence of chromosomal aberrations, may indicate that these chromosomes have a gametocidal effect. A new wheat-Ae. biuncialis disomic 4U addition, 4M(4D) and 5M(5D) substitutions, as well as several introgression lines were selected. Spike morphology and fertility indicated that the Aegilops 4M or 5M compensated well for the loss of 4D and 5D, respectively. The new cytogenetic stocks represent valuable genetic resources for the introgression of key genes alleles into wheat.
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Affiliation(s)
- András Farkas
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Eszter Gaál
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary.
| | - László Ivanizs
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Nicolas Blavet
- Institute for Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, 779 00, Olomouc, Czech Republic
| | - Mahmoud Said
- Institute for Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, 779 00, Olomouc, Czech Republic
- Field Crops Research Institute, Agricultural Research Centre, 9 Gamma Street, Giza, Cairo, 12619, Egypt
| | - Kateřina Holušová
- Institute for Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, 779 00, Olomouc, Czech Republic
| | - Kitti Szőke-Pázsi
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Tamás Spitkó
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Péter Mikó
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Edina Türkösi
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Klaudia Kruppa
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Péter Kovács
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Éva Darkó
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Éva Szakács
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
| | - Jan Bartoš
- Institute for Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, 779 00, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute for Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, 779 00, Olomouc, Czech Republic
| | - István Molnár
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Lóránd Research Network, Martonvásár, 2462, Hungary
- Institute for Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, 779 00, Olomouc, Czech Republic
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16
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Zhang J, Nirmala J, Chen S, Jost M, Steuernagel B, Karafiatova M, Hewitt T, Li H, Edae E, Sharma K, Hoxha S, Bhatt D, Antoniou-Kourounioti R, Dodds P, Wulff BBH, Dolezel J, Ayliffe M, Hiebert C, McIntosh R, Dubcovsky J, Zhang P, Rouse MN, Lagudah E. Single amino acid change alters specificity of the multi-allelic wheat stem rust resistance locus SR9. Nat Commun 2023; 14:7354. [PMID: 37963867 PMCID: PMC10645757 DOI: 10.1038/s41467-023-42747-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 10/19/2023] [Indexed: 11/16/2023] Open
Abstract
Most rust resistance genes thus far isolated from wheat have a very limited number of functional alleles. Here, we report the isolation of most of the alleles at wheat stem rust resistance gene locus SR9. The seven previously reported resistance alleles (Sr9a, Sr9b, Sr9d, Sr9e, Sr9f, Sr9g, and Sr9h) are characterised using a synergistic strategy. Loss-of-function mutants and/or transgenic complementation are used to confirm Sr9b, two haplotypes of Sr9e (Sr9e_h1 and Sr9e_h2), Sr9g, and Sr9h. Each allele encodes a highly related nucleotide-binding site leucine-rich repeat (NB-LRR) type immune receptor, containing an unusual long LRR domain, that confers resistance to a unique spectrum of isolates of the wheat stem rust pathogen. The only SR9 protein effective against stem rust pathogen race TTKSK (Ug99), SR9H, differs from SR9B by a single amino acid. SR9B and SR9G resistance proteins are also distinguished by only a single amino acid. The SR9 allelic series found in the B subgenome are orthologs of wheat stem rust resistance gene Sr21 located in the A subgenome with around 85% identity in protein sequences. Together, our results show that functional diversification of allelic variants at the SR9 locus involves single and multiple amino acid changes that recognize isolates of wheat stem rust.
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Affiliation(s)
- Jianping Zhang
- CSIRO Agriculture & Food, Canberra, ACT, 2601, Australia
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, 2570, Australia
- State Key Laboratory of Wheat and Maize Crop Science, National Wheat Innovation Centre, Centre for Crop Genome Engineering, and College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, 450046, China
| | | | - Shisheng Chen
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, 261000, China
| | - Matthias Jost
- CSIRO Agriculture & Food, Canberra, ACT, 2601, Australia
| | | | - Mirka Karafiatova
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, 77900, Olomouc, Czech Republic
| | - Tim Hewitt
- CSIRO Agriculture & Food, Canberra, ACT, 2601, Australia
| | - Hongna Li
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, 261000, China
| | - Erena Edae
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Keshav Sharma
- US Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN, 55108, USA
| | - Sami Hoxha
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, 2570, Australia
| | - Dhara Bhatt
- CSIRO Agriculture & Food, Canberra, ACT, 2601, Australia
| | - Rea Antoniou-Kourounioti
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Peter Dodds
- CSIRO Agriculture & Food, Canberra, ACT, 2601, Australia
| | - Brande B H Wulff
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Centre for Desert Agriculture, KAUST, Thuwal, 23955-6900, Saudi Arabia
| | - Jaroslav Dolezel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, 77900, Olomouc, Czech Republic
| | | | - Colin Hiebert
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, 101 Route 100, Morden, MB, R6M 1Y5, Canada
| | - Robert McIntosh
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, 2570, Australia
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Peng Zhang
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, 2570, Australia.
| | - Matthew N Rouse
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA.
- US Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN, 55108, USA.
| | - Evans Lagudah
- CSIRO Agriculture & Food, Canberra, ACT, 2601, Australia.
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, 2570, Australia.
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17
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Wang Z, Miao L, Chen Y, Peng H, Ni Z, Sun Q, Guo W. Deciphering the evolution and complexity of wheat germplasm from a genomic perspective. J Genet Genomics 2023; 50:846-860. [PMID: 37611848 DOI: 10.1016/j.jgg.2023.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/29/2023] [Accepted: 08/09/2023] [Indexed: 08/25/2023]
Abstract
Bread wheat provides an essential fraction of the daily calorific intake for humanity. Due to its huge and complex genome, progress in studying on the wheat genome is substantially trailed behind those of the other two major crops, rice and maize, for at least a decade. With rapid advances in genome assembling and reduced cost of high-throughput sequencing, emerging de novo genome assemblies of wheat and whole-genome sequencing data are leading to a paradigm shift in wheat research. Here, we review recent progress in dissecting the complex genome and germplasm evolution of wheat since the release of the first high-quality wheat genome. New insights have been gained in the evolution of wheat germplasm during domestication and modern breeding progress, genomic variations at multiple scales contributing to the diversity of wheat germplasm, and complex transcriptional and epigenetic regulations of functional genes in polyploid wheat. Genomics databases and bioinformatics tools meeting the urgent needs of wheat genomics research are also summarized. The ever-increasing omics data, along with advanced tools and well-structured databases, are expected to accelerate deciphering the germplasm and gene resources in wheat for future breeding advances.
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Affiliation(s)
- Zihao Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Lingfeng Miao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yongming Chen
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
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18
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Adhikari L, Raupp J, Wu S, Koo DH, Friebe B, Poland J. Genomic characterization and gene bank curation of Aegilops: the wild relatives of wheat. FRONTIERS IN PLANT SCIENCE 2023; 14:1268370. [PMID: 37915516 PMCID: PMC10616851 DOI: 10.3389/fpls.2023.1268370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 09/25/2023] [Indexed: 11/03/2023]
Abstract
Genetic diversity found in crop wild relatives is critical to preserve and utilize for crop improvement to achieve sustainable food production amid climate change and increased demand. We genetically characterized a large collection of 1,041 Aegilops accessions distributed among 23 different species using more than 45K single nucleotide polymorphisms identified by genotyping-by-sequencing. The Wheat Genetics Resource Center (WGRC) Aegilops germplasm collection was curated through the identification of misclassified and redundant accessions. There were 49 misclassified and 28 sets of redundant accessions within the four diploid species. The curated germplasm sets now have improved utility for genetic studies and wheat improvement. We constructed a phylogenetic tree and principal component analysis cluster for all Aegilops species together, giving one of the most comprehensive views of Aegilops. The Sitopsis section and the U genome Aegilops clade were further scrutinized with in-depth population analysis. The genetic relatedness among the pair of Aegilops species provided strong evidence for the species evolution, speciation, and diversification. We inferred genome symbols for two species Ae. neglecta and Ae. columnaris based on the sequence read mapping and the presence of segregating loci on the pertinent genomes as well as genetic clustering. The high genetic diversity observed among Aegilops species indicated that the genus could play an even greater role in providing the critical need for untapped genetic diversity for future wheat breeding and improvement. To fully characterize these Aegilops species, there is an urgent need to generate reference assemblies for these wild wheats, especially for the polyploid Aegilops.
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Affiliation(s)
- Laxman Adhikari
- Plant Breeding and Genetics Lab, Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - John Raupp
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Shuangye Wu
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Dal-Hoe Koo
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Bernd Friebe
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Jesse Poland
- Plant Breeding and Genetics Lab, Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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19
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Dracatos PM, Lu J, Sánchez‐Martín J, Wulff BB. Resistance that stacks up: engineering rust and mildew disease control in the cereal crops wheat and barley. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1938-1951. [PMID: 37494504 PMCID: PMC10502761 DOI: 10.1111/pbi.14106] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 07/28/2023]
Abstract
Staying ahead of the arms race against rust and mildew diseases in cereal crops is essential to maintain and preserve food security. The methodological challenges associated with conventional resistance breeding are major bottlenecks for deploying resistance (R) genes in high-yielding crop varieties. Advancements in our knowledge of plant genomes, structural mechanisms, innovations in bioinformatics, and improved plant transformation techniques have alleviated this bottleneck by permitting rapid gene isolation, functional studies, directed engineering of synthetic resistance and precise genome manipulation in elite crop cultivars. Most cloned cereal R genes encode canonical immune receptors which, on their own, are prone to being overcome through selection for resistance-evading pathogenic strains. However, the increasingly large repertoire of cloned R genes permits multi-gene stacking that, in principle, should provide longer-lasting resistance. This review discusses how these genomics-enabled developments are leading to new breeding and biotechnological opportunities to achieve durable rust and powdery mildew control in cereals.
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Affiliation(s)
- Peter M. Dracatos
- La Trobe Institute for Sustainable Agriculture & Food (LISAF)Department of Animal, Plant and Soil SciencesLa Trobe UniversityVIC 3086Australia
| | - Jing Lu
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
- Center for Desert AgricultureKAUSTThuwalSaudi Arabia
- College of Life SciencesSichuan UniversityChengduChina
- Chengdu Institute of Biology, Chinese Academy of SciencesChengduChina
| | - Javier Sánchez‐Martín
- Department of Microbiology and Genetics, Spanish‐Portuguese Agricultural Research Center (CIALE)University of SalamancaSalamancaSpain
| | - Brande B.H. Wulff
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
- Center for Desert AgricultureKAUSTThuwalSaudi Arabia
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20
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Li H, Hua L, Zhao S, Hao M, Song R, Pang S, Liu Y, Chen H, Zhang W, Shen T, Gou JY, Mao H, Wang G, Hao X, Li J, Song B, Lan C, Li Z, Deng XW, Dubcovsky J, Wang X, Chen S. Cloning of the wheat leaf rust resistance gene Lr47 introgressed from Aegilops speltoides. Nat Commun 2023; 14:6072. [PMID: 37770474 PMCID: PMC10539295 DOI: 10.1038/s41467-023-41833-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/20/2023] [Indexed: 09/30/2023] Open
Abstract
Leaf rust, caused by Puccinia triticina Eriksson (Pt), is one of the most severe foliar diseases of wheat. Breeding for leaf rust resistance is a practical and sustainable method to control this devastating disease. Here, we report the identification of Lr47, a broadly effective leaf rust resistance gene introgressed into wheat from Aegilops speltoides. Lr47 encodes a coiled-coil nucleotide-binding leucine-rich repeat protein that is both necessary and sufficient to confer Pt resistance, as demonstrated by loss-of-function mutations and transgenic complementation. Lr47 introgression lines with no or reduced linkage drag are generated using the Pairing homoeologous1 mutation, and a diagnostic molecular marker for Lr47 is developed. The coiled-coil domain of the Lr47 protein is unable to induce cell death, nor does it have self-protein interaction. The cloning of Lr47 expands the number of leaf rust resistance genes that can be incorporated into multigene transgenic cassettes to control this devastating disease.
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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 Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Lei Hua
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Shuqing Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, 071000, Baoding, Hebei, China
| | - Ming Hao
- Triticeae Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Rui Song
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Shuyong Pang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, 071000, Baoding, Hebei, China
| | - Yanna Liu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Hong Chen
- Triticeae Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Wenjun Zhang
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Tao Shen
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Jin-Ying Gou
- Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, 100193, Beijing, China
| | - Hailiang Mao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, China
| | - Guiping Wang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Xiaohua Hao
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Jian Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Baoxing Song
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Caixia Lan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, China
| | - Zaifeng Li
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, 071000, Baoding, Hebei, China
| | - Xing Wang Deng
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Xiaodong Wang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, 071000, Baoding, Hebei, China.
| | - Shisheng Chen
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China.
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21
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Escudero-Martinez C, Bulgarelli D. Engineering the Crop Microbiota Through Host Genetics. ANNUAL REVIEW OF PHYTOPATHOLOGY 2023; 61:257-277. [PMID: 37196364 DOI: 10.1146/annurev-phyto-021621-121447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The microbiota populating the plant-soil continuum defines an untapped resource for sustainable crop production. The host plant is a driver for the taxonomic composition and function of these microbial communities. In this review, we illustrate how the host genetic determinants of the microbiota have been shaped by plant domestication and crop diversification. We discuss how the heritable component of microbiota recruitment may represent, at least partially, a selection for microbial functions underpinning the growth, development, and health of their host plants and how the magnitude of this heritability is influenced by the environment. We illustrate how host-microbiota interactions can be treated as an external quantitative trait and review recent studies associating crop genetics with microbiota-based quantitative traits. We also explore the results of reductionist approaches, including synthetic microbial communities, to establish causal relationships between microbiota and plant phenotypes. Lastly, we propose strategies to integrate microbiota manipulation into crop selection programs. Although a detailed understanding of when and how heritability for microbiota composition can be deployed for breeding purposes is still lacking, we argue that advances in crop genomics are likely to accelerate wider applications of plant-microbiota interactions in agriculture.
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Affiliation(s)
| | - Davide Bulgarelli
- Plant Sciences, School of Life Sciences, University of Dundee, Dundee, United Kingdom; ,
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22
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Jost M, Outram MA, Dibley K, Zhang J, Luo M, Ayliffe M. Plant and pathogen genomics: essential approaches for stem rust resistance gene stacks in wheat. FRONTIERS IN PLANT SCIENCE 2023; 14:1223504. [PMID: 37727853 PMCID: PMC10505659 DOI: 10.3389/fpls.2023.1223504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/27/2023] [Indexed: 09/21/2023]
Abstract
The deployment of disease resistance genes is currently the most economical and environmentally sustainable method of crop protection. However, disease resistance genes can rapidly break down because of constant pathogen evolution, particularly when they are deployed singularly. Polygenic resistance is, therefore, considered the most durable, but combining and maintaining these genes by breeding is a laborious process as effective genes are usually unlinked. The deployment of polygenic resistance with single-locus inheritance is a promising innovation that overcomes these difficulties while enhancing resistance durability. Because of major advances in genomic technologies, increasing numbers of plant resistance genes have been cloned, enabling the development of resistance transgene stacks (RTGSs) that encode multiple genes all located at a single genetic locus. Gene stacks encoding five stem rust resistance genes have now been developed in transgenic wheat and offer both breeding simplicity and potential resistance durability. The development of similar genomic resources in phytopathogens has advanced effector gene isolation and, in some instances, enabled functional validation of individual resistance genes in RTGS. Here, the wheat stem rust pathosystem is used as an illustrative example of how host and pathogen genomic advances have been instrumental in the development of RTGS, which is a strategy applicable to many other agricultural crop species.
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Affiliation(s)
| | | | | | | | | | - Michael Ayliffe
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Canberra, ACT, Australia
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23
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Page R, Huang S, Ronen M, Sela H, Sharon A, Shrestha S, Poland J, Steffenson BJ. Genome-wide association mapping of rust resistance in Aegilops longissima. FRONTIERS IN PLANT SCIENCE 2023; 14:1196486. [PMID: 37575932 PMCID: PMC10413114 DOI: 10.3389/fpls.2023.1196486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 06/30/2023] [Indexed: 08/15/2023]
Abstract
The rust diseases, including leaf rust caused by Puccinia triticina (Pt), stem rust caused by P. graminis f. sp. tritici (Pgt), and stripe rust caused by P. striiformis f. sp. tritici (Pst), are major limiting factors in wheat production worldwide. Identification of novel sources of rust resistance genes is key to developing cultivars resistant to rapidly evolving pathogen populations. Aegilops longissima is a diploid wild grass native to the Levant and closely related to the modern bread wheat D subgenome. To explore resistance genes in the species, we evaluated a large panel of Ae. longissima for resistance to several races of Pt, Pgt, and Pst, and conducted a genome-wide association study (GWAS) to map rust resistance loci in the species. A panel of 404 Ae. longissima accessions, mostly collected from Israel, were screened for seedling-stage resistance to four races of Pt, four races of Pgt, and three races of Pst. Out of the 404 accessions screened, two were found that were resistant to all 11 races of the three rust pathogens screened. The percentage of all accessions screened that were resistant to a given rust pathogen race ranged from 18.5% to 99.7%. Genotyping-by-sequencing (GBS) was performed on 381 accessions of the Ae. longissima panel, wherein 125,343 single nucleotide polymorphisms (SNPs) were obtained after alignment to the Ae. longissima reference genome assembly and quality control filtering. Genetic diversity analysis revealed the presence of two distinct subpopulations, which followed a geographic pattern of a northern and a southern subpopulation. Association mapping was performed in the genotyped portion of the collection (n = 381) and in each subpopulation (n = 204 and 174) independently via a single-locus mixed-linear model, and two multi-locus models, FarmCPU, and BLINK. A large number (195) of markers were significantly associated with resistance to at least one of 10 rust pathogen races evaluated, nine of which are key candidate markers for further investigation due to their detection via multiple models and/or their association with resistance to more than one pathogen race. The novel resistance loci identified will provide additional diversity available for use in wheat breeding.
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Affiliation(s)
- Rae Page
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
| | - Shuyi Huang
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
| | - Moshe Ronen
- Institute for Cereal Crops Research, Tel Aviv University, Tel Aviv, Israel
| | - Hanan Sela
- Institute for Cereal Crops Research, Tel Aviv University, Tel Aviv, Israel
| | - Amir Sharon
- Institute for Cereal Crops Research, Tel Aviv University, Tel Aviv, Israel
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Sandesh Shrestha
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Jesse Poland
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- KAUST Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Brian J. Steffenson
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
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24
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Gao Z, Bian J, Lu F, Jiao Y, He H. Triticeae crop genome biology: an endless frontier. FRONTIERS IN PLANT SCIENCE 2023; 14:1222681. [PMID: 37546276 PMCID: PMC10399237 DOI: 10.3389/fpls.2023.1222681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/04/2023] [Indexed: 08/08/2023]
Abstract
Triticeae, the wheatgrass tribe, includes several major cereal crops and their wild relatives. Major crops within the Triticeae are wheat, barley, rye, and oat, which are important for human consumption, animal feed, and rangeland protection. Species within this tribe are known for their large genomes and complex genetic histories. Powered by recent advances in sequencing technology, researchers worldwide have made progress in elucidating the genomes of Triticeae crops. In addition to assemblies of high-quality reference genomes, pan-genome studies have just started to capture the genomic diversities of these species, shedding light on our understanding of the genetic basis of domestication and environmental adaptation of Triticeae crops. In this review, we focus on recent signs of progress in genome sequencing, pan-genome analyses, and resequencing analysis of Triticeae crops. We also propose future research avenues in Triticeae crop genomes, including identifying genome structure variations, the association of genomic regions with desired traits, mining functions of the non-coding area, introgression of high-quality genes from wild Triticeae resources, genome editing, and integration of genomic resources.
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Affiliation(s)
- Zhaoxu Gao
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Jianxin Bian
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong, China
| | - Fei Lu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yuling Jiao
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory for Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Hang He
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong, China
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25
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Ni F, Zheng Y, Liu X, Yu Y, Zhang G, Epstein L, Mao X, Wu J, Yuan C, Lv B, Yu H, Li J, Zhao Q, Yang Q, Liu J, Qi J, Fu D, Wu J. Sequencing trait-associated mutations to clone wheat rust-resistance gene YrNAM. Nat Commun 2023; 14:4353. [PMID: 37468469 PMCID: PMC10356923 DOI: 10.1038/s41467-023-39993-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 07/06/2023] [Indexed: 07/21/2023] Open
Abstract
Stripe (yellow) rust, caused by Puccinia striiformis f. sp. tritici (Pst), can significantly affect wheat production. Cloning resistance genes is critical for efficient and effective breeding of stripe rust resistant wheat cultivars. One resistance gene (Yr10CG) underlying the Pst resistance locus Yr10 has been cloned. However, following haplotype and linkage analyses indicate the presence of additional Pst resistance gene(s) underlying/near Yr10 locus. Here, we report the cloning of the Pst resistance gene YrNAM in this region using the method of sequencing trait-associated mutations (STAM). YrNAM encodes a non-canonical resistance protein with a NAM domain and a ZnF-BED domain. We show that both domains are required for resistance. Transgenic wheat harboring YrNAM gene driven by its endogenous promoter confers resistance to stripe rust races CYR32 and CYR33. YrNAM is an ancient gene and present in wild wheat species Aegilops longissima and Ae. sharonensis; however, it is absent in most wheat cultivars, which indicates its breeding value.
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Affiliation(s)
- Fei Ni
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Yanyan Zheng
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China
- Zhoucun District Agricultural Technology Service Center, Zibo, Shandong, 255300, China
| | - Xiaoke Liu
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Yang Yu
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Guangqiang Zhang
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China
- College of Agriculture and Bioengineering, Heze University, Heze, Shandong, 274015, China
| | - Lynn Epstein
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA
| | - Xue Mao
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Jingzheng Wu
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China
- Zhejiang Pharmaceutical University, Ningbo, Zhejiang, 315000, China
| | - Cuiling Yuan
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China
- Shandong Peanut Research Institute, Qingdao, Shandong, 266100, China
| | - Bo Lv
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Haixia Yu
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Jinlong Li
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Qi Zhao
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Qiyu Yang
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Jiajun Liu
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Juan Qi
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Daolin Fu
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China.
- Spring Valley Agriscience Co., Ltd., Jinan, Shandong, 250300, China.
| | - Jiajie Wu
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China.
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26
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Minter F, Saunders DGO. Safeguarding wheat yields from cereal fungal invaders in the postgenomic era. Curr Opin Microbiol 2023; 73:102310. [PMID: 37018996 DOI: 10.1016/j.mib.2023.102310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/05/2023] [Accepted: 03/08/2023] [Indexed: 04/05/2023]
Abstract
Wheat production is under constant threat from pests and pathogens, with fungal foliar diseases causing considerable annual yield losses. However, recent improvements in genomic tools and resources provide an unprecedented opportunity to enhance wheat's resilience in the face of these biotic constraints. Here, we discuss the impact of these advances on three key areas of managing fungal diseases of wheat: (i) enhancing the abundance of resistance traits available for plant breeding, (ii) accelerating the identification of novel fungicide targets and (iii) developing better tools for disease diagnostics and surveillance. Embracing these new genomics-led technological innovations in crop protection could revolutionise our wheat production system to improve resilience and prevent yield losses.
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27
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Yu G, Matny O, Gourdoupis S, Rayapuram N, Aljedaani FR, Wang YL, Nürnberger T, Johnson R, Crean EE, Saur IML, Gardener C, Yue Y, Kangara N, Steuernagel B, Hayta S, Smedley M, Harwood W, Patpour M, Wu S, Poland J, Jones JDG, Reuber TL, Ronen M, Sharon A, Rouse MN, Xu S, Holušová K, Bartoš J, Molnár I, Karafiátová M, Hirt H, Blilou I, Jaremko Ł, Doležel J, Steffenson BJ, Wulff BBH. The wheat stem rust resistance gene Sr43 encodes an unusual protein kinase. Nat Genet 2023:10.1038/s41588-023-01402-1. [PMID: 37217714 DOI: 10.1038/s41588-023-01402-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 04/18/2023] [Indexed: 05/24/2023]
Abstract
To safeguard bread wheat against pests and diseases, breeders have introduced over 200 resistance genes into its genome, thus nearly doubling the number of designated resistance genes in the wheat gene pool1. Isolating these genes facilitates their fast-tracking in breeding programs and incorporation into polygene stacks for more durable resistance. We cloned the stem rust resistance gene Sr43, which was crossed into bread wheat from the wild grass Thinopyrum elongatum2,3. Sr43 encodes an active protein kinase fused to two domains of unknown function. The gene, which is unique to the Triticeae, appears to have arisen through a gene fusion event 6.7 to 11.6 million years ago. Transgenic expression of Sr43 in wheat conferred high levels of resistance to a wide range of isolates of the pathogen causing stem rust, highlighting the potential value of Sr43 in resistance breeding and engineering.
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Affiliation(s)
- Guotai Yu
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center for Desert Agriculture, KAUST, Thuwal, Saudi Arabia
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Oadi Matny
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
| | - Spyridon Gourdoupis
- Bioscience Program, Smart Health Initiative, BESE, KAUST, Thuwal, Saudi Arabia
| | - Naganand Rayapuram
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center for Desert Agriculture, KAUST, Thuwal, Saudi Arabia
| | - Fatimah R Aljedaani
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center for Desert Agriculture, KAUST, Thuwal, Saudi Arabia
| | - Yan L Wang
- Department of Plant Biochemistry, Centre of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Thorsten Nürnberger
- Department of Plant Biochemistry, Centre of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Ryan Johnson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
| | - Emma E Crean
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Isabel M-L Saur
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| | - Catherine Gardener
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center for Desert Agriculture, KAUST, Thuwal, Saudi Arabia
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Yajuan Yue
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | | | - Sadiye Hayta
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Mark Smedley
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Wendy Harwood
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Mehran Patpour
- Department of Agroecology, Aarhus University, Slagelse, Denmark
| | - Shuangye Wu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Jesse Poland
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center for Desert Agriculture, KAUST, Thuwal, Saudi Arabia
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | | | - T Lynne Reuber
- 2Blades Foundation, Evanston, IL, USA
- Enko Chem, Mystic, CT, USA
| | - Moshe Ronen
- Institute for Cereal Crops Research, Tel Aviv University, Tel Aviv, Israel
| | - Amir Sharon
- Institute for Cereal Crops Research, and the School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Matthew N Rouse
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
- USDA-ARS, Cereal Disease Laboratory, St. Paul, MN, USA
| | - Steven Xu
- Crop Improvement and Genetics Research Unit, USDA-ARS, Western Regional Research Center, Albany, CA, USA
| | - Kateřina Holušová
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czech Republic
| | - Jan Bartoš
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czech Republic
| | - István Molnár
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czech Republic
- Centre for Agricultural Research, ELKH, Agricultural Institute, Martonvásár, Hungary
| | - Miroslava Karafiátová
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czech Republic
| | - Heribert Hirt
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center for Desert Agriculture, KAUST, Thuwal, Saudi Arabia
| | - Ikram Blilou
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center for Desert Agriculture, KAUST, Thuwal, Saudi Arabia
| | - Łukasz Jaremko
- Bioscience Program, Smart Health Initiative, BESE, KAUST, Thuwal, Saudi Arabia
- Red Sea Research Center, BESE, KAUST, Thuwal, Saudi Arabia
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czech Republic
| | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA.
| | - Brande B H Wulff
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
- Center for Desert Agriculture, KAUST, Thuwal, Saudi Arabia.
- John Innes Centre, Norwich Research Park, Norwich, UK.
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28
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Wang Y, Abrouk M, Gourdoupis S, Koo DH, Karafiátová M, Molnár I, Holušová K, Doležel J, Athiyannan N, Cavalet-Giorsa E, Jaremko Ł, Poland J, Krattinger SG. An unusual tandem kinase fusion protein confers leaf rust resistance in wheat. Nat Genet 2023:10.1038/s41588-023-01401-2. [PMID: 37217716 DOI: 10.1038/s41588-023-01401-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 04/18/2023] [Indexed: 05/24/2023]
Abstract
The introgression of chromosome segments from wild relatives is an established strategy to enrich crop germplasm with disease-resistance genes1. Here we use mutagenesis and transcriptome sequencing to clone the leaf rust resistance gene Lr9, which was introduced into bread wheat from the wild grass species Aegilops umbellulata2. We established that Lr9 encodes an unusual tandem kinase fusion protein. Long-read sequencing of a wheat Lr9 introgression line and the putative Ae. umbellulata Lr9 donor enabled us to assemble the ~28.4-Mb Lr9 translocation and to identify the translocation breakpoint. We likewise cloned Lr58, which was reportedly introgressed from Aegilops triuncialis3, but has an identical coding sequence compared to Lr9. Cytogenetic and haplotype analyses corroborate that the two genes originate from the same translocation event. Our work sheds light on the emerging role of kinase fusion proteins in wheat disease resistance, expanding the repertoire of disease-resistance genes for breeding.
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Affiliation(s)
- Yajun Wang
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Michael Abrouk
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Spyridon Gourdoupis
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Dal-Hoe Koo
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Miroslava Karafiátová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - István Molnár
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Kateřina Holušová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Naveenkumar Athiyannan
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Emile Cavalet-Giorsa
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Łukasz Jaremko
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jesse Poland
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Simon G Krattinger
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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29
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Annan EN, Huang L. Molecular Mechanisms of the Co-Evolution of Wheat and Rust Pathogens. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091809. [PMID: 37176866 PMCID: PMC10180972 DOI: 10.3390/plants12091809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023]
Abstract
Wheat (Triticum spp.) is a cereal crop domesticated >8000 years ago and the second-most-consumed food crop nowadays. Ever since mankind has written records, cereal rust diseases have been a painful awareness in antiquity documented in the Old Testament (about 750 B.C.). The pathogen causing the wheat stem rust disease is among the first identified plant pathogens in the 1700s, suggesting that wheat and rust pathogens have co-existed for thousands of years. With advanced molecular technologies, wheat and rust genomes have been sequenced, and interactions between the host and the rust pathogens have been extensively studied at molecular levels. In this review, we summarized the research at the molecular level and organized the findings based on the pathogenesis steps of germination, penetration, haustorial formation, and colonization of the rusts to present the molecular mechanisms of the co-evolution of wheat and rust pathogens.
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Affiliation(s)
- Emmanuel N Annan
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717-3150, USA
| | - Li Huang
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717-3150, USA
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30
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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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31
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Norman M, Bariana H, Bansal U, Periyannan S. The Keys to Controlling Wheat Rusts: Identification and Deployment of Genetic Resistance. PHYTOPATHOLOGY 2023; 113:667-677. [PMID: 36897760 DOI: 10.1094/phyto-02-23-0041-ia] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Rust diseases are among the major constraints for wheat production worldwide due to the emergence and spread of highly destructive races of Puccinia. The most common approach to minimize yield losses due to rust is to use cultivars that are genetically resistant. Modern wheat cultivars, landraces, and wild relatives can contain undiscovered resistance genes, which typically encode kinase or nucleotide-binding site leucine rich repeat (NLR) domain containing receptor proteins. Recent research has shown that these genes can provide either resistance in all growth stages (all-stage resistance; ASR) or specially in later growth stages (adult-plant resistance; APR). ASR genes are pathogen and race-specific, meaning can function against selected races of the Puccinia fungus due to the necessity to recognize specific avirulence molecules in the pathogen. APR genes are either pathogen-specific or multipathogen resistant but often race-nonspecific. Prediction of resistance genes through rust infection screening alone remains complex when more than one resistance gene is present. However, breakthroughs during the past half century such as the single-nucleotide polymorphism-based genotyping techniques and resistance gene isolation strategies like mutagenesis, resistance gene enrichment, and sequencing (MutRenSeq), mutagenesis and chromosome sequencing (MutChromSeq), and association genetics combined with RenSeq (AgRenSeq) enables rapid transfer of resistance from source to modern cultivars. There is a strong need for combining multiple genes for better efficacy and longer-lasting resistance. Hence, techniques like gene cassette creation speeds up the gene combination process, but their widespread adoption and commercial use is limited due to their transgenic nature.
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Affiliation(s)
- Michael Norman
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, NSW 2570, Australia
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, Canberra, ACT 2601, Australia
| | - Harbans Bariana
- School of Science, Western Sydney University, Bourke Road, Richmond, NSW 2753, Australia
| | - Urmil Bansal
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, NSW 2570, Australia
| | - Sambasivam Periyannan
- School of Agriculture and Environmental Science & Centre for Crop Health, University of Southern Queensland, Toowoomba, Qld 4350, Australia
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32
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Kou H, Zhang Z, Yang Y, Wei C, Xu L, Zhang G. Advances in the Mining of Disease Resistance Genes from Aegilops tauschii and the Utilization in Wheat. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12040880. [PMID: 36840228 PMCID: PMC9966637 DOI: 10.3390/plants12040880] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/01/2022] [Accepted: 12/07/2022] [Indexed: 06/02/2023]
Abstract
Aegilops tauschii is one of the malignant weeds that affect wheat production and is also the wild species ancestor of the D genome of hexaploid wheat (Triticum aestivum, AABBDD). It contains many disease resistance genes that have been lost in the long-term evolution of wheat and is an important genetic resource for the mining and utilization of wheat disease resistance genes. In recent years, the genome sequence of Aegilops tauschii has been preliminarily completed, which has laid a good foundation for the further exploration of wheat disease resistance genes in Aegilops tauschii. There are many studies on disease resistance genes in Aegilops tauschii; in order to provide better help for the disease resistance breeding of wheat, this paper analyzes and reviews the relationship between Aegilops tauschii and wheat, the research progress of Aegilops tauschii, the discovery of disease resistance genes from Aegilops tauschii, and the application of disease resistance genes from Aegilops tauschii to modern wheat breeding, providing a reference for the further exploration and utilization of Aegilops tauschii in wheat disease resistance breeding.
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Affiliation(s)
- Hongyun Kou
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China
| | - Zhenbo Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China
| | - Yu Yang
- College of Agriculture and Bioengineering, Heze University, Heze 274015, China
| | - Changfeng Wei
- College of Agriculture and Bioengineering, Heze University, Heze 274015, China
| | - Lili Xu
- College of Agriculture and Bioengineering, Heze University, Heze 274015, China
| | - Guangqiang Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China
- College of Agriculture and Bioengineering, Heze University, Heze 274015, China
- Shandong Shofine Seed Technology Co., Ltd., Jining 272400, China
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Zhang X, Wang H, Sun H, Li Y, Feng Y, Jiao C, Li M, Song X, Wang T, Wang Z, Yuan C, Sun L, Lu R, Zhang W, Xiao J, Wang X. A chromosome-scale genome assembly of Dasypyrum villosum provides insights into its application as a broad-spectrum disease resistance resource for wheat improvement. MOLECULAR PLANT 2023; 16:432-451. [PMID: 36587241 DOI: 10.1016/j.molp.2022.12.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 11/27/2022] [Accepted: 12/29/2022] [Indexed: 06/17/2023]
Abstract
Dasypyrum villosum is one of the most valuable gene resources in wheat improvement, especially for disease resistance. The mining of favorable genes from D. villosum is frustrated by the lack of a whole genome sequence. In this study, we generated a doubled-haploid line, 91C43DH, using microspore culture and obtained a 4.05-GB high-quality, chromosome-scale genome assembly for D. villosum. The assembly contains39 727 high-confidence genes, and 85.31% of the sequences are repetitive. Two reciprocal translocation events were detected, and 7VS-4VL is a unique translocation in D. villosum. The prolamin seed storage protein-coding genes were found to be duplicated; in particular, the genes encoding low-molecular-weight glutenin at the Glu-V3 locus were significantly expanded. RNA sequencing (RNA-seq) analysis indicated that, after Blumeria graminearum f.sp tritici (Bgt) inoculation, there were more upregulated genes involved in the pattern-triggered immunity and effector-triggered immunity defense pathways in D. villosum than in Triticum urartu. MNase hypersensitive sequencing (MH-seq) identified two Bgt-inducible MH sites (MHSs), one in the promoter and one in the 3' terminal region of the powdery mildew resistance (Pm) gene NLR1-V. Each site had two subpeaks and they were termed MHS1 (MHS1.1/1.2) and MHS2 (MHS2.1/2.2). Bgt-inducible MHS2.2 was uniquely present in D. villosum, and MHS1.1 was more inducible in D. villosum than in wheat, suggesting that MHSs may be critical for regulation of NLR1-V expression and plant defense. In summary, this study provides a valuable genome resource for functional genomics studies and wheat-D. villosum introgression breeding. The identified regulatory mechanisms may also be exploited to develop new strategies for enhancing Pm resistance by optimizing gene expression in wheat.
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Affiliation(s)
- Xu Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Haiyan Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Haojie Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Yingbo Li
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Yilong Feng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Chengzhi Jiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Mengli Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Xinying Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Tong Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Zongkuan Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Chunxia Yuan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Li Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Ruiju Lu
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Wenli Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Jin Xiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China.
| | - Xiue Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China.
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Marone MP, Singh HC, Pozniak CJ, Mascher M. A technical guide to TRITEX, a computational pipeline for chromosome-scale sequence assembly of plant genomes. PLANT METHODS 2022; 18:128. [PMID: 36461065 PMCID: PMC9719158 DOI: 10.1186/s13007-022-00964-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND As complete and accurate genome sequences are becoming easier to obtain, more researchers wish to get one or more of them to support their research endeavors. Reliable and well-documented sequence assembly workflows find use in reference or pangenome projects. RESULTS We describe modifications to the TRITEX genome assembly workflow motivated by the rise of fast and easy long-read contig assembly of inbred plant genomes and the routine deployment of the toolchains in pangenome projects. New features include the use as surrogates of or complements to dense genetic maps and the introduction of user-editable tables to make the curation of contig placements easier and more intuitive. CONCLUSION Even maximally contiguous sequence assemblies of the telomere-to-telomere sort, and to a yet greater extent, the fragmented kind require validation, correction, and comparison to reference standards. As pangenomics is burgeoning, these tasks are bound to become more widespread and TRITEX is one tool to get them done. This technical guide is supported by a step-by-step computational tutorial accessible under https://tritexassembly.bitbucket.io/ . The TRITEX source code is hosted under this URL: https://bitbucket.org/tritexassembly .
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Affiliation(s)
- Marina Püpke Marone
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Seeland, Germany
- Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas, Campinas, Brazil
| | - Harmeet Chawla Singh
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
- Department of Plant Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Curtis J Pozniak
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Martin Mascher
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Seeland, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
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Gruner P, Witzke A, Flath K, Eifler J, Schmiedchen B, Schmidt M, Gordillo A, Siekmann D, Fromme FJ, Koch S, Piepho HP, Miedaner T. Studying Stem Rust and Leaf Rust Resistances of Self-Fertile Rye Breeding Populations. Int J Mol Sci 2022; 23:ijms232213674. [PMID: 36430155 PMCID: PMC9692268 DOI: 10.3390/ijms232213674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/02/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022] Open
Abstract
Stem rust (SR) and leaf rust (LR) are currently the two most important rust diseases of cultivated rye in Central Europe and resistant cultivars promise to prevent yield losses caused by those pathogens. To secure long-lasting resistance, ideally pyramided monogenic resistances and race-nonspecific resistances are applied. To find respective genes, we screened six breeding populations and one testcross population for resistance to artificially inoculated SR and naturally occurring LR in multi-environmental field trials. Five populations were genotyped with a 10K SNP marker chip and one with DArTseqTM. In total, ten SR-QTLs were found that caused a reduction of 5-17 percentage points in stem coverage with urediniospores. Four QTLs thereof were mapped to positions of already known SR QTLs. An additional gene at the distal end of chromosome 2R, Pgs3.1, that caused a reduction of 40 percentage points SR infection, was validated. One SR-QTL on chromosome 3R, QTL-SR4, was found in three populations linked with the same marker. Further QTLs at similar positions, but from different populations, were also found on chromosomes 1R, 4R, and 6R. For SR, additionally seedling tests were used to separate between adult-plant and all-stage resistances and a statistical method accounting for the ordinal-scaled seedling test data was used to map seedling resistances. However, only Pgs3.1 could be detected based on seedling test data, even though genetic variance was observed in another population, too. For LR, in three of the populations, two new large-effect loci (Pr7 and Pr8) on chromosomes 1R and 2R were mapped that caused 34 and 21 percentage points reduction in leaf area covered with urediniospores and one new QTL on chromosome 1R causing 9 percentage points reduction.
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Affiliation(s)
- Paul Gruner
- State Plant Breeding Institute, University of Hohenheim, 70593 Stuttgart, Germany
| | - Anne Witzke
- Julius Kuehn-Institute, Institute for Plant Protection in Field Crops and Grassland, 14532 Kleinmachnow, Germany
| | - Kerstin Flath
- Julius Kuehn-Institute, Institute for Plant Protection in Field Crops and Grassland, 14532 Kleinmachnow, Germany
| | | | | | | | | | | | | | - Silvia Koch
- State Plant Breeding Institute, University of Hohenheim, 70593 Stuttgart, Germany
| | - Hans-Peter Piepho
- Biostatistics Unit, Institute of Crop Science, University of Hohenheim, 70593 Stuttgart, Germany
| | - Thomas Miedaner
- State Plant Breeding Institute, University of Hohenheim, 70593 Stuttgart, Germany
- Correspondence:
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Mapuranga J, Zhang N, Zhang L, Liu W, Chang J, Yang W. Harnessing genetic resistance to rusts in wheat and integrated rust management methods to develop more durable resistant cultivars. FRONTIERS IN PLANT SCIENCE 2022; 13:951095. [PMID: 36311120 PMCID: PMC9614308 DOI: 10.3389/fpls.2022.951095] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Wheat is one of the most important staple foods on earth. Leaf rust, stem rust and stripe rust, caused by Puccini triticina, Puccinia f. sp. graminis and Puccinia f. sp. striiformis, respectively, continue to threaten wheat production worldwide. Utilization of resistant cultivars is the most effective and chemical-free strategy to control rust diseases. Convectional and molecular biology techniques identified more than 200 resistance genes and their associated markers from common wheat and wheat wild relatives, which can be used by breeders in resistance breeding programmes. However, there is continuous emergence of new races of rust pathogens with novel degrees of virulence, thus rendering wheat resistance genes ineffective. An integration of genomic selection, genome editing, molecular breeding and marker-assisted selection, and phenotypic evaluations is required in developing high quality wheat varieties with resistance to multiple pathogens. Although host genotype resistance and application of fungicides are the most generally utilized approaches for controlling wheat rusts, effective agronomic methods are required to reduce disease management costs and increase wheat production sustainability. This review gives a critical overview of the current knowledge of rust resistance, particularly race-specific and non-race specific resistance, the role of pathogenesis-related proteins, non-coding RNAs, and transcription factors in rust resistance, and the molecular basis of interactions between wheat and rust pathogens. It will also discuss the new advances on how integrated rust management methods can assist in developing more durable resistant cultivars in these pathosystems.
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Karelov A, Kozub N, Sozinova O, Pirko Y, Sozinov I, Yemets A, Blume Y. Wheat Genes Associated with Different Types of Resistance against Stem Rust ( Puccinia graminis Pers.). Pathogens 2022; 11:pathogens11101157. [PMID: 36297214 PMCID: PMC9608978 DOI: 10.3390/pathogens11101157] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/25/2022] [Accepted: 10/05/2022] [Indexed: 11/13/2022] Open
Abstract
Stem rust is one wheat's most dangerous fungal diseases. Yield losses caused by stem rust have been significant enough to cause famine in the past. Some races of stem rust are considered to be a threat to food security even nowadays. Resistance genes are considered to be the most rational environment-friendly and widely used way to control the spread of stem rust and prevent yield losses. More than 60 genes conferring resistance against stem rust have been discovered so far (so-called Sr genes). The majority of the Sr genes discovered have lost their effectiveness due to the emergence of new races of stem rust. There are some known resistance genes that have been used for over 50 years and are still effective against most known races of stem rust. The goal of this article is to outline the different types of resistance against stem rust as well as the effective and noneffective genes, conferring each type of resistance with a brief overview of their origin and usage.
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Affiliation(s)
- Anatolii Karelov
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 04123 Kyiv, Ukraine
- Institute of Plant Protection, National Academy of Agrarian Sciences of Ukraine, 03022 Kyiv, Ukraine
- Correspondence: (A.K.); (Y.B.)
| | - Natalia Kozub
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 04123 Kyiv, Ukraine
- Institute of Plant Protection, National Academy of Agrarian Sciences of Ukraine, 03022 Kyiv, Ukraine
| | - Oksana Sozinova
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 04123 Kyiv, Ukraine
- Institute of Plant Protection, National Academy of Agrarian Sciences of Ukraine, 03022 Kyiv, Ukraine
| | - Yaroslav Pirko
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 04123 Kyiv, Ukraine
| | - Igor Sozinov
- Institute of Plant Protection, National Academy of Agrarian Sciences of Ukraine, 03022 Kyiv, Ukraine
| | - Alla Yemets
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 04123 Kyiv, Ukraine
| | - Yaroslav Blume
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 04123 Kyiv, Ukraine
- Correspondence: (A.K.); (Y.B.)
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Kroupin PY, Badaeva ED, Sokolova VM, Chikida NN, Belousova MK, Surzhikov SA, Nikitina EA, Kocheshkova AA, Ulyanov DS, Ermolaev AS, Khuat TML, Razumova OV, Yurkina AI, Karlov GI, Divashuk MG. Aegilops crassa Boiss. repeatome characterized using low-coverage NGS as a source of new FISH markers: Application in phylogenetic studies of the Triticeae. FRONTIERS IN PLANT SCIENCE 2022; 13:980764. [PMID: 36325551 PMCID: PMC9621091 DOI: 10.3389/fpls.2022.980764] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/29/2022] [Indexed: 06/13/2023]
Abstract
Aegilops crassa Boiss. is polyploid grass species that grows in the eastern part of the Fertile Crescent, Afghanistan, and Middle Asia. It consists of tetraploid (4x) and hexaploid (6x) cytotypes (2n = 4x = 28, D1D (Abdolmalaki et al., 2019) XcrXcr and 2n = 6x = 42, D1D (Abdolmalaki et al., 2019) XcrXcrD2D (Adams and Wendel, 2005), respectively) that are similar morphologically. Although many Aegilops species were used in wheat breeding, the genetic potential of Ae. crassa has not yet been exploited due to its uncertain origin and significant genome modifications. Tetraploid Ae. crassa is thought to be the oldest polyploid Aegilops species, the subgenomes of which still retain some features of its ancient diploid progenitors. The D1 and D2 subgenomes of Ae. crassa were contributed by Aegilops tauschii (2n = 2x = 14, DD), while the Xcr subgenome donor is still unknown. Owing to its ancient origin, Ae. crassa can serve as model for studying genome evolution. Despite this, Ae. crassa is poorly studied genetically and no genome sequences were available for this species. We performed low-coverage genome sequencing of 4x and 6x cytotypes of Ae. crassa, and four Ae. tauschii accessions belonging to different subspecies; diploid wheatgrass Thinopyrum bessarabicum (Jb genome), which is phylogenetically close to D (sub)genome species, was taken as an outgroup. Subsequent data analysis using the pipeline RepeatExplorer2 allowed us to characterize the repeatomes of these species and identify several satellite sequences. Some of these sequences are novel, while others are found to be homologous to already known satellite sequences of Triticeae species. The copy number of satellite repeats in genomes of different species and their subgenome (D1 or Xcr) affinity in Ae. crassa were assessed by means of comparative bioinformatic analysis combined with quantitative PCR (qPCR). Fluorescence in situ hybridization (FISH) was performed to map newly identified satellite repeats on chromosomes of common wheat, Triticum aestivum, 4x and 6x Ae. crassa, Ae. tauschii, and Th. bessarabicum. The new FISH markers can be used in phylogenetic analyses of the Triticeae for chromosome identification and the assessment of their subgenome affinities and for evaluation of genome/chromosome constitution of wide hybrids or polyploid species.
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Affiliation(s)
- Pavel Yu. Kroupin
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Ekaterina D. Badaeva
- N.I.Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Victoria M. Sokolova
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Nadezhda N. Chikida
- All-Russian Institute of Plant Genetic Resources (VIR), Department of Wheat Genetic Resources, St. Petersburg, Russia
| | - Maria Kh. Belousova
- All-Russian Institute of Plant Genetic Resources (VIR), Department of Wheat Genetic Resources, St. Petersburg, Russia
| | - Sergei A. Surzhikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina A. Nikitina
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Alina A. Kocheshkova
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Daniil S. Ulyanov
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Aleksey S. Ermolaev
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Thi Mai Luong Khuat
- Agricultural Genetics Institute, Department of Molecular Biology, Hanoi, Vietnam
| | - Olga V. Razumova
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Anna I. Yurkina
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Gennady I. Karlov
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
| | - Mikhail G. Divashuk
- All-Russia Research Institute of Agricultural Biotechnology, Kurchatov Genomics Centre – ARRIAB, Moscow, Russia
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Said M, Cápal P, Farkas A, Gaál E, Ivanizs L, Friebe B, Doležel J, Molnár I. Flow karyotyping of wheat- Aegilops additions facilitate dissecting the genomes of Ae. biuncialis and Ae. geniculata into individual chromosomes. FRONTIERS IN PLANT SCIENCE 2022; 13:1017958. [PMID: 36262648 PMCID: PMC9575658 DOI: 10.3389/fpls.2022.1017958] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 09/09/2022] [Indexed: 06/13/2023]
Abstract
Breeding of wheat adapted to new climatic conditions and resistant to diseases and pests is hindered by a limited gene pool due to domestication and thousands of years of human selection. Annual goatgrasses (Aegilops spp.) with M and U genomes are potential sources of the missing genes and alleles. Development of alien introgression lines of wheat may be facilitated by the knowledge of DNA sequences of Aegilops chromosomes. As the Aegilops genomes are complex, sequencing relevant Aegilops chromosomes purified by flow cytometric sorting offers an attractive route forward. The present study extends the potential of chromosome genomics to allotetraploid Ae. biuncialis and Ae. geniculata by dissecting their M and U genomes into individual chromosomes. Hybridization of FITC-conjugated GAA oligonucleotide probe to chromosomes suspensions of the two species allowed the application of bivariate flow karyotyping and sorting some individual chromosomes. Bivariate flow karyotype FITC vs. DAPI of Ae. biuncialis consisted of nine chromosome-populations, but their chromosome content determined by microscopic analysis of flow sorted chromosomes indicated that only 7Mb and 1Ub could be sorted at high purity. In the case of Ae. geniculata, fourteen chromosome-populations were discriminated, allowing the separation of nine individual chromosomes (1Mg, 3Mg, 5Mg, 6Mg, 7Mg, 1Ug, 3Ug, 6Ug, and 7Ug) out of the 14. To sort the remaining chromosomes, a partial set of wheat-Ae. biuncialis and a whole set of wheat-Ae. geniculata chromosome addition lines were also flow karyotyped, revealing clear separation of the GAA-rich Aegilops chromosomes from the GAA-poor A- and D-genome chromosomes of wheat. All of the alien chromosomes represented by individual addition lines could be isolated at purities ranging from 74.5% to 96.6% and from 87.8% to 97.7%, respectively. Differences in flow karyotypes between Ae. biuncialis and Ae. geniculata were analyzed and discussed. Chromosome-specific genomic resources will facilitate gene cloning and the development of molecular tools to support alien introgression breeding of wheat.
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Affiliation(s)
- Mahmoud Said
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
- Field Crops Research Institute, Agricultural Research Centre, Cairo, Egypt
| | - Petr Cápal
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - András Farkas
- Agricultural Institute, Centre for Agricultural Research, Eötvös Lóránd Kutatási Hálózat (ELKH), Martonvásár, Hungary
| | - Eszter Gaál
- Agricultural Institute, Centre for Agricultural Research, Eötvös Lóránd Kutatási Hálózat (ELKH), Martonvásár, Hungary
| | - László Ivanizs
- Agricultural Institute, Centre for Agricultural Research, Eötvös Lóránd Kutatási Hálózat (ELKH), Martonvásár, Hungary
| | - Bernd Friebe
- Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, United States
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - István Molnár
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
- Agricultural Institute, Centre for Agricultural Research, Eötvös Lóránd Kutatási Hálózat (ELKH), Martonvásár, Hungary
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Wheat genomic study for genetic improvement of traits in China. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1718-1775. [PMID: 36018491 DOI: 10.1007/s11427-022-2178-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/10/2022] [Indexed: 01/17/2023]
Abstract
Bread wheat (Triticum aestivum L.) is a major crop that feeds 40% of the world's population. Over the past several decades, advances in genomics have led to tremendous achievements in understanding the origin and domestication of wheat, and the genetic basis of agronomically important traits, which promote the breeding of elite varieties. In this review, we focus on progress that has been made in genomic research and genetic improvement of traits such as grain yield, end-use traits, flowering regulation, nutrient use efficiency, and biotic and abiotic stress responses, and various breeding strategies that contributed mainly by Chinese scientists. Functional genomic research in wheat is entering a new era with the availability of multiple reference wheat genome assemblies and the development of cutting-edge technologies such as precise genome editing tools, high-throughput phenotyping platforms, sequencing-based cloning strategies, high-efficiency genetic transformation systems, and speed-breeding facilities. These insights will further extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process, ultimately contributing to more sustainable agriculture in China and throughout the world.
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Sinha A, Singh L, Rawat N. Current understanding of atypical resistance against fungal pathogens in wheat. CURRENT OPINION IN PLANT BIOLOGY 2022; 68:102247. [PMID: 35716636 DOI: 10.1016/j.pbi.2022.102247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/05/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
Pathogens and pests are a major challenge to global food security. Around one hundred different pests and pathogens challenge wheat, one of the most important food crops in the world. Traditional worldwide use of a few key resistance genes in wheat cultivars has necessitated a diversification of the toolbox of resistance genes in wheat varieties over the coming decades to meet the global production demands. Recent advances in gene discovery and functional characterization of genetic resistance mechanisms in wheat reveal great diversity in the types and effectiveness of the underlying resistance genes. This article summarizes the recent developments in the discovery of non-traditional "atypical" resistance genes in wheat against diverse fungal pathogens.
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Affiliation(s)
- Arunima Sinha
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
| | - Lovepreet Singh
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
| | - Nidhi Rawat
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA.
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Unconventional R proteins in the botanical tribe Triticeae. Essays Biochem 2022; 66:561-569. [PMID: 35670039 DOI: 10.1042/ebc20210081] [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: 02/01/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 11/17/2022]
Abstract
Plant immunity is triggered following the perception of pathogen-derived molecules by plant receptor proteins. Two protein families, membrane-localized receptor-like kinases (RLK) and intracellular nucleotide-binding leucine-rich repeat (NLR) receptors, play key roles in pathogen perception and in the initiation of downstream signaling cascades that lead to defense responses. In addition to RLKs and NLRs, recent research has identified additional protein families that function as plant resistance (R) proteins. In particular, the botanical tribe Triticeae, which includes the globally important crop species wheat and barley, has played a significant role in the discovery of 'unconventional' R proteins. In this review, we will summarize the current knowledge on unconventional R genes in Triticeae and the proteins they encode. The knowledge on unconventional R proteins will not only broaden our understanding of plant-pathogen interactions but also have great implications for disease resistance breeding in crops.
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