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Tong J, Zhao C, Liu D, Jambuthenne DT, Sun M, Dinglasan E, Periyannan SK, Hickey LT, Hayes BJ. Genome-wide atlas of rust resistance loci in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:179. [PMID: 38980436 PMCID: PMC11233289 DOI: 10.1007/s00122-024-04689-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 06/29/2024] [Indexed: 07/10/2024]
Abstract
Rust diseases, including leaf rust, stripe/yellow rust, and stem rust, significantly impact wheat (Triticum aestivum L.) yields, causing substantial economic losses every year. Breeding and deployment of cultivars with genetic resistance is the most effective and sustainable approach to control these diseases. The genetic toolkit for wheat breeders to select for rust resistance has rapidly expanded with a multitude of genetic loci identified using the latest advances in genomics, mapping and cloning strategies. The goal of this review was to establish a wheat genome atlas that provides a comprehensive summary of reported loci associated with rust resistance. Our atlas provides a summary of mapped quantitative trait loci (QTL) and characterised genes for the three rusts from 170 publications over the past two decades. A total of 920 QTL or resistance genes were positioned across the 21 chromosomes of wheat based on the latest wheat reference genome (IWGSC RefSeq v2.1). Interestingly, 26 genomic regions contained multiple rust loci suggesting they could have pleiotropic effects on two or more rust diseases. We discuss a range of strategies to exploit this wealth of genetic information to efficiently utilise sources of resistance, including genomic information to stack desirable and multiple QTL to develop wheat cultivars with enhanced resistance to rust disease.
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Affiliation(s)
- Jingyang Tong
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Cong Zhao
- National Wheat Improvement Centre, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Dan Liu
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Dilani T Jambuthenne
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Mengjing Sun
- National Wheat Improvement Centre, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Eric Dinglasan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia.
| | - Sambasivam K Periyannan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia.
- School of Agriculture and Environmental Science and Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, 4350, Australia.
| | - Lee T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia.
| | - Ben J Hayes
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia.
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Jin Y, Feng G, Luo J, Yan H, Sun M, Jing T, Yang Y, Jia J, Zhu X, Wang X, Zhang X, Huang L. Combined Genome-Wide Association Study and Transcriptome Analysis Reveal Candidate Genes for Resistance to Rust ( Puccinia graminis) in Dactylis glomerata. PLANT DISEASE 2024; 108:2197-2205. [PMID: 38956749 DOI: 10.1094/pdis-02-24-0360-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
Rust disease is a common plant disease that can cause wilting, slow growth of plant leaves, and even affect the growth and development of plants. Orchardgrass (Dactylis glomerata L.) is native to temperate regions of Europe, which has been introduced as a superior forage grass in temperate regions worldwide. Orchardgrass has rich genetic diversity and is widely distributed in the world, which may contain rust resistance genes not found in other crops. Therefore, we collected a total of 333 orchardgrass accessions from different regions around the world. Through a genome-wide association study (GWAS) analysis conducted in four different environments, 91 genes that overlap or are adjacent to significant single nucleotide polymorphisms (SNPs) were identified as potential rust disease resistance genes. Combining transcriptome data from susceptible (PI292589) and resistant (PI251814) accessions, the GWAS candidate gene DG5C04160.1 encoding glutathione S-transferase (GST) was found to be important for orchardgrass rust (Puccinia graminis) resistance. Interestingly, by comparing the number of GST gene family members in seven species, it was found that orchardgrass has the most GST gene family members, containing 119 GST genes. Among them, 23 GST genes showed significant differential expression after inoculation with the rust pathogen in resistant and susceptible accessions; 82% of the genes still showed significantly increased expression 14 days after inoculation in resistant accessions, while the expression level significantly decreased in susceptible accessions. These results indicate that GST genes play an important role in orchardgrass resistance to rust (P. graminis) stress by encoding GST to reduce its oxidative stress response.
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Affiliation(s)
- Yarong Jin
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Guangyan Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jinchan Luo
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Haidong Yan
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Department of Genetics, University of Georgia, Athens, GA 30602, U.S.A
| | - Min Sun
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Tingting Jing
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yuchen Yang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiyuan Jia
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xin Zhu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoshan Wang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xinquan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
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Xiao B, Qie Y, Jin Y, Yu N, Sun N, Liu W, Wang X, Wang J, Qian Z, Zhao Y, Yuan T, Li L, Wang F, Liu C, Ma P. Genetic basis of an elite wheat cultivar Guinong 29 with harmonious improvement between multiple diseases resistance and other comprehensive traits. Sci Rep 2024; 14:14336. [PMID: 38906938 PMCID: PMC11192888 DOI: 10.1038/s41598-024-64998-2] [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: 01/25/2024] [Accepted: 06/14/2024] [Indexed: 06/23/2024] Open
Abstract
Fungal diseases, such as powdery mildew and rusts, significantly affect the quality and yield of wheat. Pyramiding diverse types of resistance genes into cultivars represents the preferred strategy to combat these diseases. Moreover, achieving collaborative improvement between diseases resistance, abiotic stress, quality, and agronomic and yield traits is difficult in genetic breeding. In this study, the wheat cultivar, Guinong 29 (GN29), showed high resistance to powdery mildew and stripe rust at both seedling and adult plant stages, and was susceptible to leaf rust at the seedling stage but slow resistance at the adult-plant stage. Meanwhile, it has elite agronomic and yield traits, indicating promising coordination ability among multiple diseases resistance and other key breeding traits. To determine the genetic basis of these elite traits, GN29 was tested with 113 molecular markers for 98 genes associated with diseases resistance, stress tolerance, quality, and adaptability. The results indicated that two powdery mildew resistance (Pm) genes, Pm2 and Pm21, confirmed the outstanding resistance to powdery mildew through genetic analysis, marker detection, genomic in situ hybridization (GISH), non-denaturing fluorescence in situ hybridization (ND-FISH), and homology-based cloning; the stripe rust resistance (Yr) gene Yr26 and leaf rust resistance (Lr) genes Lr1 and Lr46 conferred the stripe rust and slow leaf rust resistance in GN29, respectively. Meanwhile, GN29 carries dwarfing genes Rht-B1b and Rht-D1a, vernalization genes vrn-A1, vrn-B1, vrn-D1, and vrn-B3, which were consistent with the phenotypic traits in dwarf characteristic and semi-winter property; carries genes Dreb1 and Ta-CRT for stress tolerance to drought, salinity, low temperature, and abscisic acid (ABA), suggesting that GN29 may also have elite stress-tolerance ability; and carries two low-molecular-weight glutenin subunit genes Glu-B3b and Glu-B3bef which contributed to high baking quality. This study not only elucidated the genetic basis of the elite traits in GN29 but also verified the capability for harmonious improvement in both multiple diseases resistance and other comprehensive traits, offering valuable information for breeding breakthrough-resistant cultivars.
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Affiliation(s)
- Bei Xiao
- Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Yanmin Qie
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences/Hebei Key Laboratory of Crop Genetic and Breeding, Shijiazhuang, 050035, China
| | - Yuli Jin
- Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Ningning Yu
- Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Nina Sun
- Institute of Grain and Oil Crops, Yantai Academy of Agricultural Sciences, Yantai, 265500, China
| | - Wei Liu
- Institute of Grain and Oil Crops, Yantai Academy of Agricultural Sciences, Yantai, 265500, China
| | - Xiaolu Wang
- Crop Research Institute, Shandong Academy of Agriculture Sciences, Jinan, 250100, China
| | - Jiaojiao Wang
- Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Zejun Qian
- Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Ya Zhao
- Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Tangyu Yuan
- Institute of Grain and Oil Crops, Yantai Academy of Agricultural Sciences, Yantai, 265500, China
| | - Linzhi Li
- Institute of Grain and Oil Crops, Yantai Academy of Agricultural Sciences, Yantai, 265500, China
| | - Fengtao Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Cheng Liu
- Crop Research Institute, Shandong Academy of Agriculture Sciences, Jinan, 250100, China.
| | - Pengtao Ma
- Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005, China.
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O'Hara T, Steed A, Goddard R, Gaurav K, Arora S, Quiroz-Chávez J, Ramírez-González R, Badgami R, Gilbert D, Sánchez-Martín J, Wingen L, Feng C, Jiang M, Cheng S, Dreisigacker S, Keller B, Wulff BBH, Uauy C, Nicholson P. The wheat powdery mildew resistance gene Pm4 also confers resistance to wheat blast. NATURE PLANTS 2024; 10:984-993. [PMID: 38898165 PMCID: PMC11208137 DOI: 10.1038/s41477-024-01718-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 05/06/2024] [Indexed: 06/21/2024]
Abstract
Wheat blast, caused by the fungus Magnaporthe oryzae, threatens global cereal production since its emergence in Brazil in 1985 and recently spread to Bangladesh and Zambia. Here we demonstrate that the AVR-Rmg8 effector, common in wheat-infecting isolates, is recognized by the gene Pm4, previously shown to confer resistance to specific races of Blumeria graminis f. sp. tritici, the cause of powdery mildew of wheat. We show that Pm4 alleles differ in their recognition of different AVR-Rmg8 alleles, and some confer resistance only in seedling leaves but not spikes, making it important to select for those alleles that function in both tissues. This study has identified a gene recognizing an important virulence factor present in wheat blast isolates in Bangladesh and Zambia and represents an important first step towards developing durably resistant wheat cultivars for these regions.
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Affiliation(s)
- Tom O'Hara
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Andrew Steed
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | - Kumar Gaurav
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Sanu Arora
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | | | | | - David Gilbert
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Javier Sánchez-Martín
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
- Department of Microbiology and Genetics, Spanish-Portuguese Agricultural Research Center (CIALE), University of Salamanca, Salamanca, Spain
| | - Luzie Wingen
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Cong Feng
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Mei Jiang
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Shifeng Cheng
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | | | - Beat Keller
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | - Brande B H Wulff
- John Innes Centre, Norwich Research Park, Norwich, UK
- 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
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5
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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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6
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Khan H, Krishnappa G, Kumar S, Devate NB, Rathan ND, Kumar S, Mishra CN, Ram S, Tiwari R, Parkash O, Ahlawat OP, Mamrutha HM, Singh GP, Singh G. Genome-wide association study identifies novel loci and candidate genes for rust resistance in wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2024; 24:411. [PMID: 38760694 PMCID: PMC11100168 DOI: 10.1186/s12870-024-05124-2] [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: 01/27/2024] [Accepted: 05/09/2024] [Indexed: 05/19/2024]
Abstract
BACKGROUND Wheat rusts are important biotic stresses, development of rust resistant cultivars through molecular approaches is both economical and sustainable. Extensive phenotyping of large mapping populations under diverse production conditions and high-density genotyping would be the ideal strategy to identify major genomic regions for rust resistance in wheat. The genome-wide association study (GWAS) population of 280 genotypes was genotyped using a 35 K Axiom single nucleotide polymorphism (SNP) array and phenotyped at eight, 10, and, 10 environments, respectively for stem/black rust (SR), stripe/yellow rust (YR), and leaf/brown rust (LR). RESULTS Forty-one Bonferroni corrected marker-trait associations (MTAs) were identified, including 17 for SR and 24 for YR. Ten stable MTAs and their best combinations were also identified. For YR, AX-94990952 on 1A + AX-95203560 on 4A + AX-94723806 on 3D + AX-95172478 on 1A showed the best combination with an average co-efficient of infection (ACI) score of 1.36. Similarly, for SR, AX-94883961 on 7B + AX-94843704 on 1B and AX-94883961 on 7B + AX-94580041 on 3D + AX-94843704 on 1B showed the best combination with an ACI score of around 9.0. The genotype PBW827 have the best MTA combinations for both YR and SR resistance. In silico study identifies key prospective candidate genes that are located within MTA regions. Further, the expression analysis revealed that 18 transcripts were upregulated to the tune of more than 1.5 folds including 19.36 folds (TraesCS3D02G519600) and 7.23 folds (TraesCS2D02G038900) under stress conditions compared to the control conditions. Furthermore, highly expressed genes in silico under stress conditions were analyzed to find out the potential links to the rust phenotype, and all four genes were found to be associated with the rust phenotype. CONCLUSION The identified novel MTAs, particularly stable and highly expressed MTAs are valuable for further validation and subsequent application in wheat rust resistance breeding. The genotypes with favorable MTA combinations can be used as prospective donors to develop elite cultivars with YR and SR resistance.
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Affiliation(s)
- Hanif Khan
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
| | - Gopalareddy Krishnappa
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India.
- ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, India.
| | - Sudheer Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
| | - Narayana Bhat Devate
- International Centre for Agriculture Research in the Dry Area - Food Legume Research Platform, Amlaha, MP, 466113, India
| | | | - Satish Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
| | | | - Sewa Ram
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
| | - Ratan Tiwari
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
| | - Om Parkash
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
| | - Om Parkash Ahlawat
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
| | | | - Gyanendra Pratap Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Gyanendra Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
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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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8
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Qiao L, Luo J, Wang H, Kong Y, Du T, Qin P, Yang B. Integrated genome-wide association and transcriptomic analysis to identify receptor kinase genes to stripe rust resistance in wheat germplasm from southwestern China. BMC PLANT BIOLOGY 2024; 24:319. [PMID: 38654176 DOI: 10.1186/s12870-024-05020-9] [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: 02/17/2024] [Accepted: 04/15/2024] [Indexed: 04/25/2024]
Abstract
Stripe rust of wheat, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important diseases of wheat worldwide. Identification of new and elite Pst-resistance loci or genes has the potential to enhance overall resistance to this pathogen. Here, we conducted an integrated genome-wide association study (GWAS) and transcriptomic analysis to screen for loci associated with resistance to stripe rust in 335 accessions from Yunnan, including 311 landraces and 24 cultivars. Based on the environmental phenotype, we identified 113 protein kinases significantly associated with Pst resistance using mixed linear model (MLM) and generalized linear model (GLM) models. Transcriptomic analysis revealed that 52 of 113 protein kinases identified by GWAS were up and down regulated in response to Pst infection. Among these genes, a total of 15 receptor kinase genes were identified associated with Pst resistance. 11 candidate genes were newly discovered in Yunnan wheat germplasm. Our results revealed that resistance alleles to stripe rust were accumulated in Yunnan wheat germplasm, implying direct or indirect selection for improving stripe rust resistance in elite wheat breeding programs.
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Affiliation(s)
- Liang Qiao
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Jianfei Luo
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Huiyutang Wang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Yixi Kong
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Tingting Du
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Peng Qin
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Baoju Yang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China.
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9
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Zhao Y, Han G, Qie Y, Song J, Zi Y, Xiao B, Wang J, Qian Z, Huang X, Liu R, Zhang J, Song L, Jin Y, Ma P. Characterization of the powdery mildew resistance locus in wheat breeding line Jimai 809 and its breeding application. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:28. [PMID: 38545461 PMCID: PMC10963687 DOI: 10.1007/s11032-024-01467-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 03/15/2024] [Indexed: 04/24/2024]
Abstract
Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a severe disease that affects the yield and quality of wheat. Popularization of resistant cultivars in production is the preferred strategy to control this disease. In the present study, the Chinese wheat breeding line Jimai 809 showed excellent agronomic performance and high resistance to powdery mildew at the whole growth stage. To dissect the genetic basis for this resistance, Jimai 809 was crossed with the susceptible wheat cultivar Junda 159 to produce segregation populations. Genetic analysis showed that a single dominant gene, temporarily designated PmJM809, conferred the resistance to different Bgt isolates. PmJM809 was then mapped on the chromosome arm 2BL and flanked by the markers CISSR02g-1 and CIT02g-13 with genetic distances 0.4 and 0.8 cM, respectively, corresponding to a physical interval of 704.12-708.24 Mb. PmJM809 differed from the reported Pm genes on chromosome arm 2BL in origin, resistance spectrum, physical position and/or genetic diversity of the mapping interval, also suggesting PmJM809 was located on a complex interval with multiple resistance genes. To analyze and screen the candidate gene(s) of PmJM809, six genes related to disease resistance in the candidate interval were evaluated their expression patterns using an additional set of wheat samples and time-course analysis post-inoculation of the Bgt isolate E09. As a result, four genes were speculated as the key candidate or regulatory genes. Considering its comprehensive agronomic traits and resistance findings, PmJM809 was expected to be a valuable gene resource in wheat disease resistance breeding. To efficiently transfer PmJM809 into different genetic backgrounds, 13 of 19 closely linked markers were confirmed to be suitable for marker-assisted selection. Using these markers, a series of wheat breeding lines with harmonious disease resistance and agronomic performance were selected from the crosses of Jimai 809 and several susceptible cultivars. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01467-8.
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Affiliation(s)
- Ya Zhao
- Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005 China
| | - Guohao Han
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050021 China
| | - Yanmin Qie
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Hebei Laboratory of Crop Genetic and Breeding, Shijiazhuang, 050035 China
| | - Jianmin Song
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 China
| | - Yan Zi
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 China
| | - Bei Xiao
- Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005 China
| | - Jiaojiao Wang
- Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005 China
| | - Zejun Qian
- Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005 China
| | - Xiaomei Huang
- Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005 China
| | - Ruishan Liu
- Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005 China
| | - Jiadong Zhang
- Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005 China
| | - Lihong Song
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036 China
| | - Yuli Jin
- Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005 China
| | - Pengtao Ma
- Yantai Key Laboratory of Characteristic Agricultural Biological Resources Conservation and Germplasm Innovative Utilization, College of Life Sciences, Yantai University, Yantai, 264005 China
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10
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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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11
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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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12
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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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13
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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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14
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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: 17] [Impact Index Per Article: 17.0] [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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15
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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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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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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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18
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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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19
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Xu S, Lyu Z, Zhang N, Li M, Wei X, Gao Y, Cheng X, Ge W, Li X, Bao Y, Yang Z, Ma X, Wang H, Kong L. Genetic mapping of the wheat leaf rust resistance gene Lr19 and development of translocation lines to break its linkage with yellow pigment. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:200. [PMID: 37639002 DOI: 10.1007/s00122-023-04425-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 07/24/2023] [Indexed: 08/29/2023]
Abstract
KEY MESSAGE The leaf rust resistance gene Lr19, which is present on the long arm of chromosome 7E1 in Thinopyrum ponticum, was mapped within a 0.3-cM genetic interval, and translocation lines were developed to break its linkage with yellow pigmentation The leaf rust resistance locus Lr19, which was transferred to wheat (Triticum aestivum) from its relative Thinopyrum ponticum in 1966, still confers broad resistance to most known races of the leaf rust pathogen Puccinia triticina (Pt) worldwide. However, this gene has not previously been fine-mapped, and its tight linkage with a gene causing yellow pigmentation has limited its application in bread wheat breeding. In this study, we genetically mapped Lr19 using a bi-parental population from a cross of two wheat-Th. ponticum substitution lines, the Lr19-carrying line 7E1(7D) and the leaf rust-susceptible line 7E2(7D). Genetic analysis of the F2 population and the F2:3 families showed that Lr19 was a single dominant gene. Genetic markers allowed the gene to be mapped within a 0.3-cM interval on the long arm of Th. ponticum chromosome 7E1, flanked by markers XsdauK3734 and XsdauK2839. To reduce the size of the Th. ponticum chromosome segment carrying Lr19, the Chinese Spring Ph1b mutant was employed to promote recombination between the homoeologous chromosomes of the wheat chromosome 7D and the Th. ponticum chromosome 7E1. Two translocation lines with short Th. ponticum chromosome fragments carrying Lr19 were identified using the genetic markers closely linked to Lr19. Both translocation lines were resistant to 16 Pt races collected throughout China. Importantly, the linkage between Lr19 and yellow pigment content was broken in one of the lines. Thus, the Lr19 linked markers and translocation lines developed in this study are valuable resources in marker-assisted selection as part of common wheat breeding programs.
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Affiliation(s)
- Shoushen Xu
- National Key Laboratory of Wheat Improvement, Shandong Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Zhongfan Lyu
- National Key Laboratory of Wheat Improvement, Shandong Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Na Zhang
- College of Plant Protection, Technological Innovation Center for Biological Control Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, 071001, Hebei, People's Republic of China
| | - Mingzhu Li
- National Key Laboratory of Wheat Improvement, Shandong Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Xinyi Wei
- National Key Laboratory of Wheat Improvement, Shandong Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Yuhang Gao
- National Key Laboratory of Wheat Improvement, Shandong Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Xinxin Cheng
- National Key Laboratory of Wheat Improvement, Shandong Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Wenyang Ge
- National Key Laboratory of Wheat Improvement, Shandong Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Xuefeng Li
- National Key Laboratory of Wheat Improvement, Shandong Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Yinguang Bao
- National Key Laboratory of Wheat Improvement, Shandong Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Zujun Yang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 611731, Sichun, People's Republic of China
| | - Xin Ma
- National Key Laboratory of Wheat Improvement, Shandong Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China
| | - Hongwei Wang
- National Key Laboratory of Wheat Improvement, Shandong Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China.
| | - Lingrang Kong
- National Key Laboratory of Wheat Improvement, Shandong Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, People's Republic of China.
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20
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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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21
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Fahima T, Coaker G. Pathogen perception and deception in plant immunity by kinase fusion proteins. Nat Genet 2023; 55:908-909. [PMID: 37217715 PMCID: PMC10754050 DOI: 10.1038/s41588-023-01396-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Two studies describe kinase fusion proteins (KFPs) that regulate the perception and deception of wheat pathogens. These highlight the emergence of KFPs as plant immune regulators and emphasize the importance of crop wild relatives as a reservoir for resistance breeding and global food security.
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Affiliation(s)
- Tzion Fahima
- Institute of Evolution, University of Haifa, Haifa, Israel.
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel.
| | - Gitta Coaker
- Department of Plant Pathology, University of California, Davis, CA, USA.
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22
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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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