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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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2
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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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3
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Mao H, Jiang C, Tang C, Nie X, Du L, Liu Y, Cheng P, Wu Y, Liu H, Kang Z, Wang X. Wheat adaptation to environmental stresses under climate change: Molecular basis and genetic improvement. MOLECULAR PLANT 2023; 16:1564-1589. [PMID: 37671604 DOI: 10.1016/j.molp.2023.09.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/19/2023] [Accepted: 09/01/2023] [Indexed: 09/07/2023]
Abstract
Wheat (Triticum aestivum) is a staple food for about 40% of the world's population. As the global population has grown and living standards improved, high yield and improved nutritional quality have become the main targets for wheat breeding. However, wheat production has been compromised by global warming through the more frequent occurrence of extreme temperature events, which have increased water scarcity, aggravated soil salinization, caused plants to be more vulnerable to diseases, and directly reduced plant fertility and suppressed yield. One promising option to address these challenges is the genetic improvement of wheat for enhanced resistance to environmental stress. Several decades of progress in genomics and genetic engineering has tremendously advanced our understanding of the molecular and genetic mechanisms underlying abiotic and biotic stress responses in wheat. These advances have heralded what might be considered a "golden age" of functional genomics for the genetic improvement of wheat. Here, we summarize the current knowledge on the molecular and genetic basis of wheat resistance to abiotic and biotic stresses, including the QTLs/genes involved, their functional and regulatory mechanisms, and strategies for genetic modification of wheat for improved stress resistance. In addition, we also provide perspectives on some key challenges that need to be addressed.
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Affiliation(s)
- Hude Mao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Cong Jiang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chunlei Tang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Linying Du
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuling Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Peng Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yunfeng Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Huiquan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Xiaojie Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China.
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4
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Yu PL, Fulton JC, Hudson OH, Huguet-Tapia JC, Brawner JT. Next-generation fungal identification using target enrichment and Nanopore sequencing. BMC Genomics 2023; 24:581. [PMID: 37784013 PMCID: PMC10544392 DOI: 10.1186/s12864-023-09691-w] [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: 05/15/2023] [Accepted: 09/21/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Rapid and accurate pathogen identification is required for disease management. Compared to sequencing entire genomes, targeted sequencing may be used to direct sequencing resources to genes of interest for microbe identification and mitigate the low resolution that single-locus molecular identification provides. This work describes a broad-spectrum fungal identification tool developed to focus high-throughput Nanopore sequencing on genes commonly employed for disease diagnostics and phylogenetic inference. RESULTS Orthologs of targeted genes were extracted from 386 reference genomes of fungal species spanning six phyla to identify homologous regions that were used to design the baits used for enrichment. To reduce the cost of producing probes without diminishing the phylogenetic power, DNA sequences were first clustered, and then consensus sequences within each cluster were identified to produce 26,000 probes that targeted 114 genes. To test the efficacy of our probes, we applied the technique to three species representing Ascomycota and Basidiomycota fungi. The efficiency of enrichment, quantified as mean target coverage over the mean genome-wide coverage, ranged from 200 to 300. Furthermore, enrichment of long reads increased the depth of coverage across the targeted genes and into non-coding flanking sequence. The assemblies generated from enriched samples provided well-resolved phylogenetic trees for taxonomic assignment and molecular identification. CONCLUSIONS Our work provides data to support the utility of targeted Nanopore sequencing for fungal identification and provides a platform that may be extended for use with other phytopathogens.
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Affiliation(s)
- Pei-Ling Yu
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
| | - James C Fulton
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
- Florida Department of Agriculture and Consumer Services, Division of Plant Industry, Gainesville, FL, 32608, USA
| | - Owen H Hudson
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
| | - Jose C Huguet-Tapia
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
| | - Jeremy T Brawner
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA.
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5
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Chang CY, Yang SX, Zhang MQ, Guo YT, Li XM, Yan Y, Ding CH, Niu KX, Wang ML, Li QQ, Zhang J, Zhang X, Chen S, Xie C, Ni Z, Sun Q, Gou JY. Suppression of ZEAXANTHIN EPOXIDASE 1 restricts stripe rust growth in wheat. PLANT COMMUNICATIONS 2023; 4:100608. [PMID: 37101397 PMCID: PMC10504589 DOI: 10.1016/j.xplc.2023.100608] [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: 02/01/2023] [Revised: 02/28/2023] [Accepted: 04/23/2023] [Indexed: 05/30/2023]
Abstract
Reducing losses caused by pathogens is an effective strategy for stabilizing crop yields. Daunting challenges remain in cloning and characterizing genes that inhibit stripe rust, a devastating disease of wheat (Triticum aestivum) caused by Puccinia striiformis f. sp. tritici (Pst). We found that suppression of wheat zeaxanthin epoxidase 1 (ZEP1) increased wheat defense against Pst. We isolated the yellow rust slower 1 (yrs1) mutant of tetraploid wheat in which a premature stop mutation in ZEP1-B underpins the phenotype. Genetic analyses revealed increased H2O2 accumulation in zep1 mutants and demonstrated a correlation between ZEP1 dysfunction and slower Pst growth in wheat. Moreover, wheat kinase START 1.1 (WKS1.1, Yr36) bound, phosphorylated, and suppressed the biochemical activity of ZEP1. A rare natural allele in the hexaploid wheat ZEP1-B promoter reduced its transcription and Pst growth. Our study thus identified a novel suppressor of Pst, characterized its mechanism of action, and revealed beneficial variants for wheat disease control. This work opens the door to stacking wheat ZEP1 variants with other known Pst resistance genes in future breeding programs to enhance wheat tolerance to pathogens.
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Affiliation(s)
- Chao-Yan Chang
- Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Shu-Xian Yang
- School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Mei-Qi Zhang
- Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yue-Ting Guo
- Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiao-Ming Li
- Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yan Yan
- School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ci-Hang Ding
- Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ke-Xin Niu
- Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Meng-Lu Wang
- Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Qin-Quan Li
- Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Junli Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Jinming Road, Kaifeng 475004, China
| | - Xuebin Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Jinming Road, Kaifeng 475004, China
| | - Shisheng Chen
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China
| | - Chaojie Xie
- Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhongfu Ni
- Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Qixin Sun
- Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Jin-Ying Gou
- Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; School of Life Sciences, Fudan University, Shanghai 200438, China.
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6
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Chen C, Jost M, Outram MA, Friendship D, Chen J, Wang A, Periyannan S, Bartoš J, Holušová K, Doležel J, Zhang P, Bhatt D, Singh D, Lagudah E, Park RF, Dracatos PM. A pathogen-induced putative NAC transcription factor mediates leaf rust resistance in barley. Nat Commun 2023; 14:5468. [PMID: 37673864 PMCID: PMC10482968 DOI: 10.1038/s41467-023-41021-2] [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: 12/19/2022] [Accepted: 08/21/2023] [Indexed: 09/08/2023] Open
Abstract
Leaf rust, caused by Puccinia hordei, is one of the most widespread and damaging foliar diseases affecting barley. The barley leaf rust resistance locus Rph7 has been shown to have unusually high sequence and haplotype divergence. In this study, we isolate the Rph7 gene using a fine mapping and RNA-Seq approach that is confirmed by mutational analysis and transgenic complementation. Rph7 is a pathogen-induced, non-canonical resistance gene encoding a protein that is distinct from other known plant disease resistance proteins in the Triticeae. Structural analysis using an AlphaFold2 protein model suggests that Rph7 encodes a putative NAC transcription factor with a zinc-finger BED domain with structural similarity to the N-terminal DNA-binding domain of the NAC transcription factor (ANAC019) from Arabidopsis. A global gene expression analysis suggests Rph7 mediates the activation and strength of the basal defence response. The isolation of Rph7 highlights the diversification of resistance mechanisms available for engineering disease control in crops.
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Affiliation(s)
- Chunhong Chen
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Matthias Jost
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Megan A Outram
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Dorian Friendship
- The University of Sydney, Faculty of Science, Plant Breeding Institute, Cobbitty, NSW, 2570, Australia
| | - Jian Chen
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Aihua Wang
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Sambasivam Periyannan
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT, 2601, Australia
- The University of Southern Queensland, School of Agriculture and Environmental Science, Centre for Crop Health, Toowoomba, QLD, 4350, Australia
| | - Jan Bartoš
- Institute of Experimental Botany, Centre of Plant Structural and Functional Genomics, Olomouc, CZ-77900, Czech Republic
| | - Kateřina Holušová
- Institute of Experimental Botany, Centre of Plant Structural and Functional Genomics, Olomouc, CZ-77900, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of Plant Structural and Functional Genomics, Olomouc, CZ-77900, Czech Republic
| | - Peng Zhang
- The University of Sydney, Faculty of Science, Plant Breeding Institute, Cobbitty, NSW, 2570, Australia
| | - Dhara Bhatt
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Davinder Singh
- The University of Sydney, Faculty of Science, Plant Breeding Institute, Cobbitty, NSW, 2570, Australia
| | - Evans Lagudah
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, GPO Box 1700, Canberra, ACT, 2601, Australia.
| | - Robert F Park
- The University of Sydney, Faculty of Science, Plant Breeding Institute, Cobbitty, NSW, 2570, Australia.
| | - Peter M Dracatos
- The University of Sydney, Faculty of Science, Plant Breeding Institute, Cobbitty, NSW, 2570, Australia.
- La Trobe Institute for Sustainable Agriculture & Food (LISAF), Department of Animal, Plant and Soil Sciences, La Trobe University, Melbourne, VIC, 3086, Australia.
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7
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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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8
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Shamimuzzaman M, Ma G, Underwood W, Qi L. Mutation and sequencing-based cloning and functional studies of a rust resistance gene in sunflower (Helianthus annuus). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023. [PMID: 37029526 DOI: 10.1111/tpj.16238] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/16/2023] [Accepted: 03/24/2023] [Indexed: 06/19/2023]
Abstract
Rust, caused by the fungus Puccinia helianthi Schwein., is one of the most devastating diseases of sunflower (Helianthus annuus L.), affecting global production. The rust R gene R11 in sunflower line HA-R9 shows broad-spectrum resistance to P. helianthi virulent races and was previously mapped to an interval on sunflower chromosome 13 encompassing three candidate genes annotated in the XRQr1.0 reference genome assembly. In the current study, we combined ethyl methane sulfonate (EMS) mutagenesis with targeted region capture and PacBio long-read sequencing to clone the R11 gene. Sequencing of a 60-kb region spanning the R11 locus from the R11 -HA-R9 rust-resistant line and three EMS-induced susceptible mutants facilitated the identification of R11 and definition of induced mutations. The R11 gene is predicted to have a single 3996-bp open reading frame and encodes a protein of 1331 amino acids with CC-NBS-LRR domains typical of genes conferring plant resistance to biotrophic pathogens. Point mutations identified in the R11 rust-susceptible mutants resulted in premature stop codons, consistent with loss of function leading to rust susceptibility. Additional functional studies using comparative RNA sequencing of the resistant line R11 -HA-R9 and R11 -susceptible mutants revealed substantial differences in gene expression patterns associated with R11 -mediated resistance at 7 days post-inoculation with rust, and uncovered the potential roles of terpenoid biosynthesis and metabolism in sunflower rust resistance.
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Affiliation(s)
- Md Shamimuzzaman
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, 1616 Albrecht Blvd. N., Fargo, North Dakota, 58102-2765, USA
| | - Guojia Ma
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, 58108, USA
| | - William Underwood
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, 1616 Albrecht Blvd. N., Fargo, North Dakota, 58102-2765, USA
| | - Lili Qi
- USDA-Agricultural Research Service, Edward T. Schafer Agricultural Research Center, 1616 Albrecht Blvd. N., Fargo, North Dakota, 58102-2765, USA
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9
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Li G, Chen Q, Jiang W, Zhang A, Yang E, Yang Z. Molecular and Cytogenetic Identification of Wheat- Thinopyrum intermedium Double Substitution Line-Derived Progenies for Stripe Rust Resistance. PLANTS (BASEL, SWITZERLAND) 2022; 12:28. [PMID: 36616156 PMCID: PMC9823681 DOI: 10.3390/plants12010028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/23/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Thinopyrum intermedium (2n = 6x = 42, JJJSJSStSt) has been hybridized extensively with common wheat and proven to be a valuable germplasm source for improving disease resistance and yield potential of wheat. A novel disease-resistant wheat-Th. intermedium double substitution line X479, carrying 1St(1B) and 4St-4JS (4B), was identified using multi-color non-denaturing fluorescence in situ hybridization (ND-FISH). With the aim of transferring Thinopyrum-specific chromatin to wheat, a total of 573 plants from F2 and F3 progenies of X479 crossed with wheat cultivar MY11 were developed and characterized using sequential ND-FISH with multiple probes. Fifteen types of wheat-Thinopyrum translocation chromosomes were preferentially transmitted in the progenies, and the homozygous wheat-1St, and wheat-4JSL translocation lines were identified using ND-FISH, Oligo-FISH painting and CENH3 immunostaining. The wheat-4JSL translocation lines exhibited high levels of resistance to stripe rust prevalent races in field screening. The gene for stripe rust resistance was found to be physically located on FL0-0.60 of the 4JSL, using deletion lines and specific DNA markers. The new wheat-Th. intermedium translocation lines can be exploited as useful germplasms for wheat improvement.
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Affiliation(s)
- Guangrong Li
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Qiheng Chen
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Wenxi Jiang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Ahui Zhang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Ennian Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Zujun Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
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10
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Mapuranga J, Chang J, Yang W. Combating powdery mildew: Advances in molecular interactions between Blumeria graminis f. sp. tritici and wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:1102908. [PMID: 36589137 PMCID: PMC9800938 DOI: 10.3389/fpls.2022.1102908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
Wheat powdery mildew caused by a biotrophic fungus Blumeria graminis f. sp. tritici (Bgt), is a widespread airborne disease which continues to threaten global wheat production. One of the most chemical-free and cost-effective approaches for the management of wheat powdery mildew is the exploitation of resistant cultivars. Accumulating evidence has reported that more than 100 powdery mildew resistance genes or alleles mapping to 63 different loci (Pm1-Pm68) have been identified from common wheat and its wild relatives, and only a few of them have been cloned so far. However, continuous emergence of new pathogen races with novel degrees of virulence renders wheat resistance genes ineffective. An essential breeding strategy for achieving more durable resistance is the pyramiding of resistance genes into a single genotype. The genetics of host-pathogen interactions integrated with temperature conditions and the interaction between resistance genes and their corresponding pathogen a virulence genes or other resistance genes within the wheat genome determine the expression of resistance genes. Considerable progress has been made in revealing Bgt pathogenesis mechanisms, identification of resistance genes and breeding of wheat powdery mildew resistant cultivars. A detailed understanding of the molecular interactions between wheat and Bgt will facilitate the development of novel and effective approaches for controlling powdery mildew. This review gives a succinct overview of the molecular basis of interactions between wheat and Bgt, and wheat defense mechanisms against Bgt infection. It will also unleash the unsung roles of epigenetic processes, autophagy and silicon in wheat resistance to Bgt.
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11
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Park RF, Boshoff WHP, Cabral AL, Chong J, Martinelli JA, McMullen MS, Fetch JWM, Paczos-Grzęda E, Prats E, Roake J, Sowa S, Ziems L, Singh D. Breeding oat for resistance to the crown rust pathogen Puccinia coronata f. sp. avenae: achievements and prospects. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3709-3734. [PMID: 35665827 PMCID: PMC9729147 DOI: 10.1007/s00122-022-04121-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 05/01/2022] [Indexed: 05/05/2023]
Abstract
Crown rust, caused by Puccinia coronata f. sp. avenae (Pca), is a significant impediment to global oat production. Some 98 alleles at 92 loci conferring resistance to Pca in Avena have been designated; however, allelic relationships and chromosomal locations of many of these are unknown. Long-term monitoring of Pca in Australia, North America and elsewhere has shown that it is highly variable even in the absence of sexual recombination, likely due to large pathogen populations that cycle between wild oat communities and oat crops. Efforts to develop cultivars with genetic resistance to Pca began in the 1950s. Based almost solely on all all-stage resistance, this has had temporary benefits but very limited success. The inability to eradicate wild oats, and their common occurrence in many oat growing regions, means that future strategies to control Pca must be based on the assumption of a large and variable prevailing pathogen population with high evolutionary potential, even if cultivars with durable resistance are deployed and grown widely. The presence of minor gene, additive APR to Pca in hexaploid oat germplasm opens the possibility of pyramiding several such genes to give high levels of resistance. The recent availability of reference genomes for diploid and hexaploid oat will undoubtedly accelerate efforts to discover, characterise and develop high throughput diagnostic markers to introgress and pyramid resistance to Pca in high yielding adapted oat germplasm.
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Affiliation(s)
- R F Park
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia.
| | - W H P Boshoff
- Department of Plant Sciences, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - A L Cabral
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, Canada
| | - J Chong
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, Canada
| | - J A Martinelli
- Department of Crop Science, Agronomy School, Federal University of Rio Grande Do Sul (UFRGS), Av. Bento Gonçalves, 7712, Porto Alegre, RS, 91501-970, Brazil
| | - M S McMullen
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58105-5051, USA
| | - J W Mitchell Fetch
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, Canada
| | - E Paczos-Grzęda
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, 20-950, Lublin, Poland
| | - E Prats
- CSIC-Institute for Sustainable Agriculture, Avda. Menéndez Pidal s/n. , 14004, Córdoba, Spain
| | - J Roake
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
| | - S Sowa
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, 20-950, Lublin, Poland
| | - L Ziems
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
| | - D Singh
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
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12
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Yang N, Ovenden B, Baxter B, McDonald MC, Solomon PS, Milgate A. Multi-stage resistance to Zymoseptoria tritici revealed by GWAS in an Australian bread wheat diversity panel. FRONTIERS IN PLANT SCIENCE 2022; 13:990915. [PMID: 36352863 PMCID: PMC9637935 DOI: 10.3389/fpls.2022.990915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Septoria tritici blotch (STB) has been ranked the third most important wheat disease in the world, threatening a large area of wheat production. Although major genes play an important role in the protection against Zymoseptoria tritici infection, the lifespan of their resistance unfortunately is very short in modern wheat production systems. Combinations of quantitative resistance with minor effects, therefore, are believed to have prolonged and more durable resistance to Z. tritici. In this study, new quantitative trait loci (QTLs) were identified that are responsible for seedling-stage resistance and adult-plant stage resistance (APR). More importantly was the characterisation of a previously unidentified QTL that can provide resistance during different stages of plant growth or multi-stage resistance (MSR). At the seedling stage, we discovered a new isolate-specific QTL, QSt.wai.1A.1. At the adult-plant stage, the new QTL QStb.wai.6A.2 provided stable and consistent APR in multiple sites and years, while the QTL QStb.wai.7A.2 was highlighted to have MSR. The stacking of multiple favourable MSR alleles was found to improve resistance to Z. tritici by up to 40%.
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Affiliation(s)
- Nannan Yang
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Ben Ovenden
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Brad Baxter
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
| | - Megan C. McDonald
- University of Birmingham, School of Biosciences, Birmingham, West Midlands, United Kingdom
| | - Peter S. Solomon
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Andrew Milgate
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
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13
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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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14
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Li G, Li J, Zhang Y, Ma Q, Yang E, Zhang P, Dundas I, Yang Z. Molecular and cytogenetic dissection of stripe rust resistance gene Yr83 from rye 6R and generation of resistant germplasm in wheat breeding. FRONTIERS IN PLANT SCIENCE 2022; 13:1035784. [PMID: 36299784 PMCID: PMC9589168 DOI: 10.3389/fpls.2022.1035784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Rye 6R-derived stripe rust resistance gene Yr83 in wheat background was physically mapped to fraction length (FL) 0.87-1.00 on the long arm by non-denaturing-fluorescence in situ hybridization (ND-FISH), Oligo-FISH painting and 6R-specific PCR markers.Stripe rust resistance gene Yr83 derived from chromosome 6R of rye (Secale cereale) "Merced" has displayed high resistance to both Australian and Chinese wheat stripe rust isolates. With the aim to physically map Yr83 to a more precise region, new wheat- 6R deletion and translocation lines were produced from derived progenies of the 6R(6D) substitution line. The non-denaturing fluorescence in situ hybridization (ND-FISH) patterns of 6R were established to precisely characterize the variations of 6R in different wheat backgrounds. Comparative ND-FISH analysis localized the breakpoints of 6RL chromosomes relative to Oligo-pSc200 and Oligo-pSc119.2 rich sites in deletion lines. Molecular marker and resistance analyses confirmed that Yr83 is physically located at the fraction length (FL) 0.87-1.00 of 6RL and covers the corresponding region of 806-881 Mb in the reference genome of Lo7. Oligo-FISH painting demonstrated that the region carrying Yr83 is syntenic to the distal end of long arm of homoeologous group 7 of the Triticeae genome. The developed wheat-6R lines carrying the Yr83 gene will be useful for breeding for rust resistance.
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Affiliation(s)
- Guangrong Li
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Jianbo Li
- School of Life and Environmental Sciences, Plant Breeding Institute, The University of Sydney, Cobbitty, NSW, Australia
| | - Yao Zhang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Qiang Ma
- Characteristic Crops Research Institute, Chongqing Academy of Agricultural Sciences, Yongchuan, China
| | - Ennian Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Peng Zhang
- School of Life and Environmental Sciences, Plant Breeding Institute, The University of Sydney, Cobbitty, NSW, Australia
| | - Ian Dundas
- School of Agriculture, Food and Wine, The University of Adelaide, Waite, Glen Osmond, SA, Australia
| | - Zujun Yang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
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15
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Hussain B, Akpınar BA, Alaux M, Algharib AM, Sehgal D, Ali Z, Aradottir GI, Batley J, Bellec A, Bentley AR, Cagirici HB, Cattivelli L, Choulet F, Cockram J, Desiderio F, Devaux P, Dogramaci M, Dorado G, Dreisigacker S, Edwards D, El-Hassouni K, Eversole K, Fahima T, Figueroa M, Gálvez S, Gill KS, Govta L, Gul A, Hensel G, Hernandez P, Crespo-Herrera LA, Ibrahim A, Kilian B, Korzun V, Krugman T, Li Y, Liu S, Mahmoud AF, Morgounov A, Muslu T, Naseer F, Ordon F, Paux E, Perovic D, Reddy GVP, Reif JC, Reynolds M, Roychowdhury R, Rudd J, Sen TZ, Sukumaran S, Ozdemir BS, Tiwari VK, Ullah N, Unver T, Yazar S, Appels R, Budak H. Capturing Wheat Phenotypes at the Genome Level. FRONTIERS IN PLANT SCIENCE 2022; 13:851079. [PMID: 35860541 PMCID: PMC9289626 DOI: 10.3389/fpls.2022.851079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Recent technological advances in next-generation sequencing (NGS) technologies have dramatically reduced the cost of DNA sequencing, allowing species with large and complex genomes to be sequenced. Although bread wheat (Triticum aestivum L.) is one of the world's most important food crops, efficient exploitation of molecular marker-assisted breeding approaches has lagged behind that achieved in other crop species, due to its large polyploid genome. However, an international public-private effort spanning 9 years reported over 65% draft genome of bread wheat in 2014, and finally, after more than a decade culminated in the release of a gold-standard, fully annotated reference wheat-genome assembly in 2018. Shortly thereafter, in 2020, the genome of assemblies of additional 15 global wheat accessions was released. As a result, wheat has now entered into the pan-genomic era, where basic resources can be efficiently exploited. Wheat genotyping with a few hundred markers has been replaced by genotyping arrays, capable of characterizing hundreds of wheat lines, using thousands of markers, providing fast, relatively inexpensive, and reliable data for exploitation in wheat breeding. These advances have opened up new opportunities for marker-assisted selection (MAS) and genomic selection (GS) in wheat. Herein, we review the advances and perspectives in wheat genetics and genomics, with a focus on key traits, including grain yield, yield-related traits, end-use quality, and resistance to biotic and abiotic stresses. We also focus on reported candidate genes cloned and linked to traits of interest. Furthermore, we report on the improvement in the aforementioned quantitative traits, through the use of (i) clustered regularly interspaced short-palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated gene-editing and (ii) positional cloning methods, and of genomic selection. Finally, we examine the utilization of genomics for the next-generation wheat breeding, providing a practical example of using in silico bioinformatics tools that are based on the wheat reference-genome sequence.
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Affiliation(s)
- Babar Hussain
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
- Department of Biotechnology, Faculty of Life Sciences, University of Central Punjab, Lahore, Pakistan
| | | | - Michael Alaux
- Université Paris-Saclay, INRAE, URGI, Versailles, France
| | - Ahmed M. Algharib
- Department of Environment and Bio-Agriculture, Faculty of Agriculture, Al-Azhar University, Cairo, Egypt
| | - Deepmala Sehgal
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Zulfiqar Ali
- Institute of Plant Breeding and Biotechnology, MNS University of Agriculture, Multan, Pakistan
| | - Gudbjorg I. Aradottir
- Department of Pathology, The National Institute of Agricultural Botany, Cambridge, United Kingdom
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Arnaud Bellec
- French Plant Genomic Resource Center, INRAE-CNRGV, Castanet Tolosan, France
| | - Alison R. Bentley
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Halise B. Cagirici
- Crop Improvement and Genetics Research, USDA, Agricultural Research Service, Albany, CA, United States
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Fred Choulet
- French National Research Institute for Agriculture, Food and the Environment, INRAE, GDEC, Clermont-Ferrand, France
| | - James Cockram
- The John Bingham Laboratory, The National Institute of Agricultural Botany, Cambridge, United Kingdom
| | - Francesca Desiderio
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Pierre Devaux
- Research & Innovation, Florimond Desprez Group, Cappelle-en-Pévèle, France
| | - Munevver Dogramaci
- USDA, Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
| | - Gabriel Dorado
- Department of Bioquímica y Biología Molecular, Campus Rabanales C6-1-E17, Campus de Excelencia Internacional Agroalimentario (ceiA3), Universidad de Córdoba, Córdoba, Spain
| | | | - David Edwards
- University of Western Australia, Perth, WA, Australia
| | - Khaoula El-Hassouni
- State Plant Breeding Institute, The University of Hohenheim, Stuttgart, Germany
| | - Kellye Eversole
- International Wheat Genome Sequencing Consortium (IWGSC), Bethesda, MD, United States
| | - Tzion Fahima
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Haifa, Israel
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, ACT, Australia
| | - Sergio Gálvez
- Department of Languages and Computer Science, ETSI Informática, Campus de Teatinos, Universidad de Málaga, Andalucía Tech, Málaga, Spain
| | - Kulvinder S. Gill
- Department of Crop Science, Washington State University, Pullman, WA, United States
| | - Liubov Govta
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Haifa, Israel
| | - Alvina Gul
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Goetz Hensel
- Center of Plant Genome Engineering, Heinrich-Heine-Universität, Düsseldorf, Germany
- Division of Molecular Biology, Centre of Region Haná for Biotechnological and Agriculture Research, Czech Advanced Technology and Research Institute, Palacký University, Olomouc, Czechia
| | - Pilar Hernandez
- Institute for Sustainable Agriculture (IAS-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Córdoba, Spain
| | | | - Amir Ibrahim
- Crop and Soil Science, Texas A&M University, College Station, TX, United States
| | | | | | - Tamar Krugman
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Haifa, Israel
| | - Yinghui Li
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Haifa, Israel
| | - Shuyu Liu
- Crop and Soil Science, Texas A&M University, College Station, TX, United States
| | - Amer F. Mahmoud
- Department of Plant Pathology, Faculty of Agriculture, Assiut University, Assiut, Egypt
| | - Alexey Morgounov
- Food and Agriculture Organization of the United Nations, Riyadh, Saudi Arabia
| | - Tugdem Muslu
- Molecular Biology, Genetics and Bioengineering, Sabanci University, Istanbul, Turkey
| | - Faiza Naseer
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, Quedlinburg, Germany
| | - Etienne Paux
- French National Research Institute for Agriculture, Food and the Environment, INRAE, GDEC, Clermont-Ferrand, France
| | - Dragan Perovic
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, Quedlinburg, Germany
| | - Gadi V. P. Reddy
- USDA-Agricultural Research Service, Southern Insect Management Research Unit, Stoneville, MS, United States
| | - Jochen Christoph Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Matthew Reynolds
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Rajib Roychowdhury
- Institute of Evolution and Department of Environmental and Evolutionary Biology, University of Haifa, Haifa, Israel
| | - Jackie Rudd
- Crop and Soil Science, Texas A&M University, College Station, TX, United States
| | - Taner Z. Sen
- Crop Improvement and Genetics Research, USDA, Agricultural Research Service, Albany, CA, United States
| | | | | | | | - Naimat Ullah
- Institute of Biological Sciences (IBS), Gomal University, D. I. Khan, Pakistan
| | - Turgay Unver
- Ficus Biotechnology, Ostim Teknopark, Ankara, Turkey
| | - Selami Yazar
- General Directorate of Research, Ministry of Agriculture, Ankara, Turkey
| | | | - Hikmet Budak
- Montana BioAgriculture, Inc., Missoula, MT, United States
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16
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Pal N, Jan I, Saini DK, Kumar K, Kumar A, Sharma PK, Kumar S, Balyan HS, Gupta PK. Meta-QTLs for multiple disease resistance involving three rusts in common wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2385-2405. [PMID: 35699741 DOI: 10.1007/s00122-022-04119-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/28/2022] [Indexed: 05/20/2023]
Abstract
In wheat, multiple disease resistance meta-QTLs (MDR-MQTLs) and underlying candidate genes for the three rusts were identified which may prove useful for development of resistant cultivars. Rust diseases in wheat are a major threat to global food security. Therefore, development of multiple disease-resistant cultivars (resistant to all three rusts) is a major goal in all wheat breeding programs worldwide. In the present study, meta-QTLs and candidate genes for multiple disease resistance (MDR) involving all three rusts were identified using 152 individual QTL mapping studies for resistance to leaf rust (LR), stem rust (SR), and yellow rust (YR). From these 152 studies, a total of 1,146 QTLs for resistance to three rusts were retrieved, which included 368 QTLs for LR, 291 QTLs for SR, and 487 QTLs for YR. Of these 1,146 QTLs, only 718 QTLs could be projected onto the consensus map saturated with 2, 34,619 markers. Meta-analysis of the projected QTLs resulted in the identification of 86 MQTLs, which included 71 MDR-MQTLs. Ten of these MDR-MQTLs were referred to as the 'Breeders' MQTLs'. Seventy-eight of the 86 MQTLs could also be anchored to the physical map of the wheat genome, and 54 MQTLs were validated by marker-trait associations identified during earlier genome-wide association studies. Twenty MQTLs (including 17 MDR-MQTLs) identified in the present study were co-localized with 44 known R genes. In silico expression analysis allowed identification of several differentially expressed candidate genes (DECGs) encoding proteins carrying different domains including the following: NBS-LRR, WRKY domains, F-box domains, sugar transporters, transferases, etc. The introgression of these MDR loci into high-yielding cultivars should prove useful for developing high yielding cultivars with resistance to all the three rusts.
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Affiliation(s)
- Neeraj Pal
- Department of Molecular Biology and Genetic Engineering, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttrakhand, 263145, India
| | - Irfat Jan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Kuldeep Kumar
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - Anuj Kumar
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - P K Sharma
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - Sundip Kumar
- Department of Molecular Biology and Genetic Engineering, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttrakhand, 263145, India
| | - H S Balyan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India
| | - P K Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India.
- Murdoch's Centre for Crop & Food Innovation, Murdoch University, Murdoch, Perth, WA 6150, Australia.
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17
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Luo J, Rouse MN, Hua L, Li H, Li B, Li T, Zhang W, Gao C, Wang Y, Dubcovsky J, Chen S. Identification and characterization of Sr22b, a new allele of the wheat stem rust resistance gene Sr22 effective against the Ug99 race group. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:554-563. [PMID: 34695276 PMCID: PMC8882774 DOI: 10.1111/pbi.13737] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/09/2021] [Accepted: 10/19/2021] [Indexed: 05/09/2023]
Abstract
Wheat stem (or black) rust, caused by Puccinia graminis f. sp. tritici (Pgt), has been historically among the most devastating global fungal diseases of wheat. The recent occurrence and spread of new virulent races such as Ug99 have prompted global efforts to identify and isolate more effective stem rust resistance (Sr) genes. Here, we report the map‐based cloning of the Ug99‐effective SrTm5 gene from diploid wheat Triticum monococcum accession PI 306540 that encodes a typical coiled‐coil nucleotide‐binding leucine‐rich repeat protein. This gene, designated as Sr22b, is a new allele of Sr22 with a rare insertion of a large (13.8‐kb) retrotransposon into its second intron. Biolistic transformation of an ~112‐kb circular bacterial artificial chromosome plasmid carrying Sr22b into the susceptible wheat variety Fielder was sufficient to confer resistance to stem rust. In a survey of 168 wheat genotypes, Sr22b was present only in cultivated T. monococcum subsp. monococcum accessions but absent in all tested tetraploid and hexaploid wheat lines. We developed a diagnostic molecular marker for Sr22b and successfully introgressed a T. monococcum chromosome segment containing this gene into hexaploid wheat to accelerate its deployment and pyramiding with other Sr genes in wheat breeding programmes. Sr22b can be a valuable component of gene pyramids or transgenic cassettes combining different resistance genes to control this devastating disease.
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Affiliation(s)
- Jing Luo
- Peking University Institute of Advanced Agricultural SciencesWeifangShandong261000China
| | - Matthew N. Rouse
- USDA‐ARS Cereal Disease Laboratory and Department of Plant PathologyUniversity of MinnesotaSt. PaulMN55108USA
| | - Lei Hua
- Peking University Institute of Advanced Agricultural SciencesWeifangShandong261000China
| | - Hongna Li
- Peking University Institute of Advanced Agricultural SciencesWeifangShandong261000China
| | - Boshu Li
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Genome EditingInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
| | - Tianya Li
- College of Plant ProtectionShenyang Agricultural UniversityShenyangLiaoning110000China
| | - Wenjun Zhang
- Department of Plant SciencesUniversity of CaliforniaDavisCA95616USA
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Genome EditingInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
| | - Yanpeng Wang
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Genome EditingInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
| | - Jorge Dubcovsky
- Department of Plant SciencesUniversity of CaliforniaDavisCA95616USA
- Howard Hughes Medical InstituteChevy ChaseMD20815USA
| | - Shisheng Chen
- Peking University Institute of Advanced Agricultural SciencesWeifangShandong261000China
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18
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Singh R, Kumar K, Bharadwaj C, Verma PK. Broadening the horizon of crop research: a decade of advancements in plant molecular genetics to divulge phenotype governing genes. PLANTA 2022; 255:46. [PMID: 35076815 DOI: 10.1007/s00425-022-03827-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 01/08/2022] [Indexed: 06/14/2023]
Abstract
Advancements in sequencing, genotyping, and computational technologies during the last decade (2011-2020) enabled new forward-genetic approaches, which subdue the impediments of precise gene mapping in varied crops. The modern crop improvement programs rely heavily on two major steps-trait-associated QTL/gene/marker's identification and molecular breeding. Thus, it is vital for basic and translational crop research to identify genomic regions that govern the phenotype of interest. Until the advent of next-generation sequencing, the forward-genetic techniques were laborious and time-consuming. Over the last 10 years, advancements in the area of genome assembly, genotyping, large-scale data analysis, and statistical algorithms have led faster identification of genomic variations regulating the complex agronomic traits and pathogen resistance. In this review, we describe the latest developments in genome sequencing and genotyping along with a comprehensive evaluation of the last 10-year headways in forward-genetic techniques that have shifted the focus of plant research from model plants to diverse crops. We have classified the available molecular genetic methods under bulk-segregant analysis-based (QTL-seq, GradedPool-Seq, QTG-Seq, Exome QTL-seq, and RapMap), target sequence enrichment-based (RenSeq, AgRenSeq, and TACCA), and mutation-based groups (MutMap, NIKS algorithm, MutRenSeq, MutChromSeq), alongside improvements in classical mapping and genome-wide association analyses. Newer methods for outcrossing, heterozygous, and polyploid plant genetics have also been discussed. The use of k-mers has enriched the nature of genetic variants which can be utilized to identify the phenotype-causing genes, independent of reference genomes. We envisage that the recent methods discussed herein will expand the repertoire of useful alleles and help in developing high-yielding and climate-resilient crops.
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Affiliation(s)
- Ritu Singh
- Plant Immunity Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Kamal Kumar
- Plant Immunity Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Chellapilla Bharadwaj
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110020, India
| | - Praveen Kumar Verma
- Plant Immunity Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
- Plant Immunity Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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19
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Kushwaha SK, Åhman I, Bengtsson T. ResCap: plant resistance gene prediction and probe generation pipeline for resistance gene sequence capture. BIOINFORMATICS ADVANCES 2021; 1:vbab033. [PMID: 36700100 PMCID: PMC9710708 DOI: 10.1093/bioadv/vbab033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/15/2021] [Accepted: 11/07/2021] [Indexed: 01/28/2023]
Abstract
Summary The discovery of novel resistance genes (R-genes) is an important component in disease resistance breeding. Nevertheless, R-gene identification from wild species and close relatives of plants is not only a difficult but also a cumbersome process. In this study, ResCap, a support vector machine-based high-throughput R-gene prediction and probe generation pipeline has been developed to generate probes from genomic datasets. ResCap contains two integral modules. The first module identifies the R-genes and R-gene like sequences under four categories containing different domains such as TIR-NBS-LRR (TNL), CC-NBS-LRR (CNL), Receptor-like kinase (RLK) and Receptor-like proteins (RLPs). The second module generates probes from extracted nucleotide sequences of resistance genes to conduct sequence capture (SeqCap) experiments. For the validation of ResCap pipeline, ResCap generated probes were synthesized and a sequence capture experiment was performed to capture expressed resistance genes among six spring barley genotypes. The developed ResCap pipeline in combination with the performed sequence capture experiment has shown to increase precision of R-gene identification while simultaneously allowing rapid gene validation including non-sequenced plants. Availability and implementation The ResCap pipeline is available at http://rescap.ltj.slu.se/ResCap/. Contact sandeep.kushwaha@slu.se or sandeep@niab.org.in. Supplementary information Supplementary materials are available at Bioinformatics Advances online.
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Affiliation(s)
- Sandeep K Kushwaha
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma 234 22, Sweden,Bioinformatics, National Institute of Animal Biotechnology, Hyderabad 500 032, India,To whom correspondence should be addressed.
| | - Inger Åhman
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma 234 22, Sweden
| | - Therése Bengtsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma 234 22, Sweden
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20
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Klymiuk V, Coaker G, Fahima T, Pozniak CJ. Tandem Protein Kinases Emerge as New Regulators of Plant Immunity. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1094-1102. [PMID: 34096764 PMCID: PMC8761531 DOI: 10.1094/mpmi-03-21-0073-cr] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Plant-pathogen interactions result in disease development in a susceptible host. Plants actively resist pathogens via a complex immune system comprising both surface-localized receptors that sense the extracellular space as well as intracellular receptors recognizing pathogen effectors. To date, the majority of cloned resistance genes encode intracellular nucleotide-binding leucine-rich repeat receptor proteins. Recent discoveries have revealed tandem kinase proteins (TKPs) as another important family of intracellular proteins involved in plant immune responses. Five TKP genes-barley Rpg1 and wheat WTK1 (Yr15), WTK2 (Sr60), WTK3 (Pm24), and WTK4-protect against devastating fungal diseases. Moreover, a large diversity and numerous putative TKPs exist across the plant kingdom. This review explores our current knowledge of TKPs and serves as a basis for future studies that aim to develop and exploit a deeper understanding of innate plant immunity receptor proteins.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Valentyna Klymiuk
- Crop Development Centre and Department of Plant Sciences,
University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Gitta Coaker
- Department of Plant Pathology, University of California,
Davis, CA, U.S.A
| | - Tzion Fahima
- Institute of Evolution, University of Haifa, 199 Abba-Hushi
Avenue, Mt. Carmel, 3498838 Haifa, Israel
- Department of Evolutionary and Environmental Biology,
University of Haifa, 199 Abba-Hushi Avenue, Mt. Carmel, 3498838 Haifa, Israel
| | - Curtis J. Pozniak
- Crop Development Centre and Department of Plant Sciences,
University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
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21
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Martini JWR, Molnar TL, Crossa J, Hearne SJ, Pixley KV. Opportunities and Challenges of Predictive Approaches for Harnessing the Potential of Genetic Resources. FRONTIERS IN PLANT SCIENCE 2021; 12:674036. [PMID: 34276731 PMCID: PMC8281018 DOI: 10.3389/fpls.2021.674036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 05/17/2021] [Indexed: 06/13/2023]
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22
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Zhang J, Hewitt TC, Boshoff WHP, Dundas I, Upadhyaya N, Li J, Patpour M, Chandramohan S, Pretorius ZA, Hovmøller M, Schnippenkoetter W, Park RF, Mago R, Periyannan S, Bhatt D, Hoxha S, Chakraborty S, Luo M, Dodds P, Steuernagel B, Wulff BBH, Ayliffe M, McIntosh RA, Zhang P, Lagudah ES. A recombined Sr26 and Sr61 disease resistance gene stack in wheat encodes unrelated NLR genes. Nat Commun 2021; 12:3378. [PMID: 34099713 PMCID: PMC8184838 DOI: 10.1038/s41467-021-23738-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 05/10/2021] [Indexed: 12/25/2022] Open
Abstract
The re-emergence of stem rust on wheat in Europe and Africa is reinforcing the ongoing need for durable resistance gene deployment. Here, we isolate from wheat, Sr26 and Sr61, with both genes independently introduced as alien chromosome introgressions from tall wheat grass (Thinopyrum ponticum). Mutational genomics and targeted exome capture identify Sr26 and Sr61 as separate single genes that encode unrelated (34.8%) nucleotide binding site leucine rich repeat proteins. Sr26 and Sr61 are each validated by transgenic complementation using endogenous and/or heterologous promoter sequences. Sr61 orthologs are absent from current Thinopyrum elongatum and wheat pan genome sequences, contrasting with Sr26 where homologues are present. Using gene-specific markers, we validate the presence of both genes on a single recombinant alien segment developed in wheat. The co-location of these genes on a small non-recombinogenic segment simplifies their deployment as a gene stack and potentially enhances their resistance durability. The tall wheat grass-derived stem rust resistance genes Sr26 and Sr61 are among a few ones that are effective to all current dominant races of stem rust, including Ug99. Here, the authors show that the two genes are present in a small non-recombinogenic segment but encode two unrelated NLR proteins.
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Affiliation(s)
- Jianping Zhang
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, Australia.,CSIRO Agriculture & Food, Canberra, ACT, Australia
| | - Timothy C Hewitt
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, Australia.,CSIRO Agriculture & Food, Canberra, ACT, Australia
| | - Willem H P Boshoff
- Department of Plant Sciences, University of the Free State, Bloemfontein, South Africa
| | - Ian Dundas
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | | | - Jianbo Li
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, Australia
| | - Mehran Patpour
- Department of Agroecology, Aarhus University, Slagelse, Denmark
| | | | - Zacharias A Pretorius
- Department of Plant Sciences, University of the Free State, Bloemfontein, South Africa
| | | | | | - Robert F Park
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, Australia
| | - Rohit Mago
- CSIRO Agriculture & Food, Canberra, ACT, Australia
| | | | - Dhara Bhatt
- CSIRO Agriculture & Food, Canberra, ACT, Australia
| | - Sami Hoxha
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, Australia
| | | | - Ming Luo
- CSIRO Agriculture & Food, Canberra, ACT, Australia
| | - Peter Dodds
- CSIRO Agriculture & Food, Canberra, ACT, Australia
| | | | | | | | - Robert A McIntosh
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, Australia
| | - Peng Zhang
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, Australia.
| | - Evans S Lagudah
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, Australia. .,CSIRO Agriculture & Food, Canberra, ACT, Australia.
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23
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Zwyrtková J, Šimková H, Doležel J. Chromosome genomics uncovers plant genome organization and function. Biotechnol Adv 2020; 46:107659. [PMID: 33259907 DOI: 10.1016/j.biotechadv.2020.107659] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 10/10/2020] [Accepted: 11/13/2020] [Indexed: 02/07/2023]
Abstract
The identification of causal genomic loci and their interactions underlying various traits in plants has been greatly aided by progress in understanding the organization of the nuclear genome. This provides clues to the responses of plants to environmental stimuli at the molecular level. Apart from other uses, these insights are needed to fully explore the potential of new breeding techniques that rely on genome editing. However, genome analysis and sequencing is not straightforward in the many agricultural crops and their wild relatives that possess large and complex genomes. Chromosome genomics streamlines this task by dissecting the genome to single chromosomes whose DNA is then used instead of nuclear DNA. This results in a massive and lossless reduction in DNA sample complexity, reduces the time and cost of the experiment, and simplifies data interpretation. Flow cytometric sorting of condensed mitotic chromosomes makes it possible to purify single chromosomes in large quantities, and as the DNA remains intact this process can be coupled successfully with many techniques in molecular biology and genomics. Since the first experiments with flow cytometric sorting in the late 1980s, numerous applications have been developed, and chromosome genomics has been having a significant impact in many areas of research, including the sequencing of complex genomes of important crops and gene cloning. This review discusses these applications, describes their contribution to advancements in plant genome analysis and gene cloning, and outlines future directions.
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Affiliation(s)
- Jana Zwyrtková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900 Olomouc, Czech Republic.
| | - Hana Šimková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-77900 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, CZ-77900 Olomouc, Czech Republic.
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24
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Md Hatta MA, Ghosh S, Athiyannan N, Richardson T, Steuernagel B, Yu G, Rouse MN, Ayliffe M, Lagudah ES, Radhakrishnan GV, Periyannan SK, Wulff BBH. Extensive Genetic Variation at the Sr22 Wheat Stem Rust Resistance Gene Locus in the Grasses Revealed Through Evolutionary Genomics and Functional Analyses. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:1286-1298. [PMID: 32779520 DOI: 10.1094/mpmi-01-20-0018-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
In the last 20 years, severe wheat stem rust outbreaks have been recorded in Africa, Europe, and Central Asia. This previously well controlled disease, caused by the fungus Puccinia graminis f. sp. tritici, has reemerged as a major threat to wheat cultivation. The stem rust (Sr) resistance gene Sr22 encodes a nucleotide-binding and leucine-rich repeat receptor which confers resistance to the highly virulent African stem rust isolate Ug99. Here, we show that the Sr22 gene is conserved among grasses in the Triticeae and Poeae lineages. Triticeae species contain syntenic loci with single-copy orthologs of Sr22 on chromosome 7, except Hordeum vulgare, which has experienced major expansions and rearrangements at the locus. We also describe 14 Sr22 sequence variants obtained from both Triticum boeoticum and the domesticated form of this species, T. monococcum, which have been postulated to encode both functional and nonfunctional Sr22 alleles. The nucleotide sequence analysis of these alleles identified historical sequence exchange resulting from recombination or gene conversion, including breakpoints within codons, which expanded the coding potential at these positions by introduction of nonsynonymous substitutions. Three Sr22 alleles were transformed into wheat cultivar Fielder and two postulated resistant alleles from Schomburgk (hexaploid wheat introgressed with T. boeoticum segment carrying Sr22) and T. monococcum accession PI190945, respectively, conferred resistance to P. graminis f. sp. tritici race TTKSK, thereby unequivocally confirming Sr22 effectiveness against Ug99. The third allele from accession PI573523, previously believed to confer susceptibility, was confirmed as nonfunctional against Australian P. graminis f. sp. tritici race 98-1,2,3,5,6.[Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- M Asyraf Md Hatta
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Malaysia
| | - Sreya Ghosh
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Naveenkumar Athiyannan
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food, General Post Office Box 1700, Canberra, ACT 2601, Australia
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
| | - Terese Richardson
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food, General Post Office Box 1700, Canberra, ACT 2601, Australia
| | | | - Guotai Yu
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Matthew N Rouse
- United States Department of Agriculture-Agricultural Research Service Cereal Disease Laboratory, St. Paul, MN 55108, U.S.A
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Michael Ayliffe
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food, General Post Office Box 1700, Canberra, ACT 2601, Australia
| | - Evans S Lagudah
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food, General Post Office Box 1700, Canberra, ACT 2601, Australia
| | | | - Sambasivam K Periyannan
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food, General Post Office Box 1700, Canberra, ACT 2601, Australia
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
| | - Brande B H Wulff
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
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25
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Babu P, Baranwal DK, Harikrishna, Pal D, Bharti H, Joshi P, Thiyagarajan B, Gaikwad KB, Bhardwaj SC, Singh GP, Singh A. Application of Genomics Tools in Wheat Breeding to Attain Durable Rust Resistance. FRONTIERS IN PLANT SCIENCE 2020; 11:567147. [PMID: 33013989 PMCID: PMC7516254 DOI: 10.3389/fpls.2020.567147] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/12/2020] [Indexed: 11/13/2023]
Abstract
Wheat is an important source of dietary protein and calories for the majority of the world's population. It is one of the largest grown cereal in the world occupying over 215 M ha. Wheat production globally is challenged by biotic stresses such as pests and diseases. Of the 50 diseases of wheat that are of economic importance, the three rust diseases are the most ubiquitous causing significant yield losses in the majority of wheat production environments. Under severe epidemics they can lead to food insecurity threats amid the continuous evolution of new races of the pathogens, shifts in population dynamics and their virulence patterns, thereby rendering several effective resistance genes deployed in wheat breeding programs vulnerable. This emphasizes the need to identify, characterize, and deploy effective rust-resistant genes from diverse sources into pre-breeding lines and future wheat varieties. The use of genetic resistance has been marked as eco-friendly and to curb the further evolution of rust pathogens. Deployment of multiple rust resistance genes including major and minor genes in wheat lines could enhance the durability of resistance thereby reducing pathogen evolution. Advances in next-generation sequencing (NGS) platforms and associated bioinformatics tools have revolutionized wheat genomics. The sequence alignment of the wheat genome is the most important landmark which will enable genomics to identify marker-trait associations, candidate genes and enhanced breeding values in genomic selection (GS) studies. High throughput genotyping platforms have demonstrated their role in the estimation of genetic diversity, construction of the high-density genetic maps, dissecting polygenic traits, and better understanding their interactions through GWAS (genome-wide association studies) and QTL mapping, and isolation of R genes. Application of breeder's friendly KASP assays in the wheat breeding program has expedited the identification and pyramiding of rust resistance alleles/genes in elite lines. The present review covers the evolutionary trends of the rust pathogen and contemporary wheat varieties, and how these research strategies galvanized to control the wheat killer genus Puccinia. It will also highlight the outcome and research impact of cost-effective NGS technologies and cloning of rust resistance genes amid the public availability of common and tetraploid wheat reference genomes.
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Affiliation(s)
- Prashanth Babu
- Indian Agricultural Research Institute (ICAR), New Delhi, India
| | | | - Harikrishna
- Indian Agricultural Research Institute (ICAR), New Delhi, India
| | - Dharam Pal
- Indian Agricultural Research Institute (ICAR), New Delhi, India
| | - Hemlata Bharti
- Directorate of Medicinal and Aromatic Plants Research (ICAR), Anand, India
| | - Priyanka Joshi
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | | | | | | | | | - Anupam Singh
- DCM SHRIRAM-Bioseed Research India, ICRISAT, Hyderabad, India
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