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Outram MA, Chen J, Broderick S, Li Z, Aditya S, Tasneem N, Arndell T, Blundell C, Ericsson DJ, Figueroa M, Sperschneider J, Dodds PN, Williams SJ. AvrSr27 is a zinc-bound effector with a modular structure important for immune recognition. THE NEW PHYTOLOGIST 2024; 243:314-329. [PMID: 38730532 DOI: 10.1111/nph.19801] [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: 01/02/2024] [Accepted: 04/17/2024] [Indexed: 05/13/2024]
Abstract
Effector proteins are central to the success of plant pathogens, while immunity in host plants is driven by receptor-mediated recognition of these effectors. Understanding the molecular details of effector-receptor interactions is key for the engineering of novel immune receptors. Here, we experimentally determined the crystal structure of the Puccinia graminis f. sp. tritici (Pgt) effector AvrSr27, which was not accurately predicted using AlphaFold2. We characterised the role of the conserved cysteine residues in AvrSr27 using in vitro biochemical assays and examined Sr27-mediated recognition using transient expression in Nicotiana spp. and wheat protoplasts. The AvrSr27 structure contains a novel β-strand rich modular fold consisting of two structurally similar domains that bind to Zn2+ ions. The N-terminal domain of AvrSr27 is sufficient for interaction with Sr27 and triggering cell death. We identified two Pgt proteins structurally related to AvrSr27 but with low sequence identity that can also associate with Sr27, albeit more weakly. Though only the full-length proteins, trigger Sr27-dependent cell death in transient expression systems. Collectively, our findings have important implications for utilising protein prediction platforms for effector proteins, and those embarking on bespoke engineering of immunity receptors as solutions to plant disease.
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Affiliation(s)
- Megan A Outram
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Jian Chen
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Sean Broderick
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Zhao Li
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Shouvik Aditya
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Nuren Tasneem
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Taj Arndell
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Cheryl Blundell
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Daniel J Ericsson
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
- Australian Synchrotron, Macromolecular Crystallography, Clayton, Vic., 3186, Australia
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Jana Sperschneider
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Peter N Dodds
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Simon J Williams
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
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Alafari HA, Hafez Y, Omara R, Murad R, Abdelaal K, Attia K, Khedr A. Physio-Biochemical, Anatomical, and Molecular Analysis of Resistant and Susceptible Wheat Cultivars Infected with TTKSK, TTKST, and TTTSK Novel Puccinia graminis Races. PLANTS (BASEL, SWITZERLAND) 2024; 13:1045. [PMID: 38611573 PMCID: PMC11013933 DOI: 10.3390/plants13071045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/18/2024] [Accepted: 04/01/2024] [Indexed: 04/14/2024]
Abstract
Stem rust, caused by Puccinia graminis f.sp. tritici, is one of the most dangerous rust diseases on wheat. Through physiological, biochemical, and molecular analysis, the relationship between the change in resistance of 15 wheat cultivars to stem rust disease and the response of 41 stem rust resistance genes (Sr,s) as well as TTKSK, TTKST, and TTTSK races was explained. Some cultivars and Sr genes, such as Gemmeiza-9, Gemmeiza-11, Sids-13, Sakha-94, Misr-1, Misr-2, Sr31, and Sr38, became susceptible to infection. Other new cultivars include Mir-3 and Sakha-95, and Sr genes 13, 37, 40, GT, and FR*2/SRTT3-SRTT3-SR10 remain resistant. Some resistance genes have been identified in these resistant cultivars: Sr2, Sr13, Sr24, Sr36, and Sr40. Sr31 was not detected in any cultivars. Reactive oxygen species such as hydrogen peroxide and superoxide, enzymes activities (catalase, peroxidase, and polyphenoloxidase), and electrolyte leakage were increased in the highly susceptible cultivars, while they decreased in the resistant ones. Anatomical characteristics such as the thickness of the epidermis, ground tissue, phloem tissue and vascular bundle diameter in the midrib were decreased in susceptible cultivars compared with resistant cultivars. Our results indicated that some races (TTKSK, TTKST, and TTTSK) appeared for the first time in Egypt and many other countries, which broke the resistant cultivars. The wheat rust breeding program must rely on land races and pyramiding genes in order to develop new resistance genes that will survive for a very long time.
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Affiliation(s)
- Hayat Ali Alafari
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Yaser Hafez
- EPCRS Excellence Center, Plant Pathology and Biotechnology Laboratory, Agricultural Botany Department, Faculty of Agriculture, Kafrelsheikh University, Kafr El-Sheikh 33516, Egypt (R.M.)
| | - Reda Omara
- Wheat Diseases Research Department, Plant Pathology Research Institute, Agricultural Research Center, Giza 12619, Egypt
| | - Rasha Murad
- EPCRS Excellence Center, Plant Pathology and Biotechnology Laboratory, Agricultural Botany Department, Faculty of Agriculture, Kafrelsheikh University, Kafr El-Sheikh 33516, Egypt (R.M.)
| | - Khaled Abdelaal
- EPCRS Excellence Center, Plant Pathology and Biotechnology Laboratory, Agricultural Botany Department, Faculty of Agriculture, Kafrelsheikh University, Kafr El-Sheikh 33516, Egypt (R.M.)
| | - Kotb Attia
- Center of Excellence in Biotechnology Research, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia;
| | - Amr Khedr
- EPCRS Excellence Center, Plant Pathology and Biotechnology Laboratory, Agricultural Botany Department, Faculty of Agriculture, Kafrelsheikh University, Kafr El-Sheikh 33516, Egypt (R.M.)
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3
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Arndell T, Chen J, Sperschneider J, Upadhyaya NM, Blundell C, Niesner N, Outram MA, Wang A, Swain S, Luo M, Ayliffe MA, Figueroa M, Vanhercke T, Dodds PN. Pooled effector library screening in protoplasts rapidly identifies novel Avr genes. NATURE PLANTS 2024; 10:572-580. [PMID: 38409291 PMCID: PMC11035141 DOI: 10.1038/s41477-024-01641-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 01/31/2024] [Indexed: 02/28/2024]
Abstract
Crop breeding for durable disease resistance is challenging due to the rapid evolution of pathogen virulence. While progress in resistance (R) gene cloning and stacking has accelerated in recent years1-3, the identification of corresponding avirulence (Avr) genes in many pathogens is hampered by the lack of high-throughput screening options. To address this technology gap, we developed a platform for pooled library screening in plant protoplasts to allow rapid identification of interacting R-Avr pairs. We validated this platform by isolating known and novel Avr genes from wheat stem rust (Puccinia graminis f. sp. tritici) after screening a designed library of putative effectors against individual R genes. Rapid Avr gene identification provides molecular tools to understand and track pathogen virulence evolution via genotype surveillance, which in turn will lead to optimized R gene stacking and deployment strategies. This platform should be broadly applicable to many crop pathogens and could potentially be adapted for screening genes involved in other protoplast-selectable traits.
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Affiliation(s)
- Taj Arndell
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Jian Chen
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Jana Sperschneider
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | | | - Cheryl Blundell
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Nathalie Niesner
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Megan A Outram
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Aihua Wang
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Steve Swain
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Ming Luo
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Michael A Ayliffe
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Melania Figueroa
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Thomas Vanhercke
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia.
| | - Peter N Dodds
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia.
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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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5
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Terefe TG, Boshoff WHP, Park RF, Pretorius ZA, Visser B. Wheat Stem Rust Surveillance Reveals Two New Races of Puccinia graminis f. sp. tritici in South Africa During 2016 to 2020. PLANT DISEASE 2024; 108:20-29. [PMID: 37580885 DOI: 10.1094/pdis-06-23-1120-sr] [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: 08/16/2023]
Abstract
Stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is an important disease of wheat in South Africa (SA) and is primarily controlled using resistant cultivars. Understanding virulence diversity of Pgt is essential for successful breeding of resistant cultivars. Samples of infected wheat stems were collected across the major wheat-growing regions of SA from 2016 to 2020 to determine the pathogenic variability of Pgt isolates. Seven races were identified from 517 isolates pathotyped. The most frequently found races were 2SA104 (BPGSC + Sr9h,27,Kw) (35% frequency) and 2SA88 (TTKSF + Sr8b) (33%). Race 2SA42 (PTKSK + Sr8b), which was found in 2017, and 2SA5 (BFGSF + Sr9h), identified in 2017, are new races. The Ug99 variant race 2SA42 is similar in its virulence to 2SA107 (PTKST + Sr8b) except for avirulence to Sr24 and virulence to Sr8155B1. Race 2SA5 is closely related in its virulence to existing races that commonly infect triticale. Certain races showed limited geographical distribution. Races 2SA5, 2SA105, and 2SA108 were found only in the Western Cape, whereas 2SA107 and 2SA42 were detected only in the Free State province. The new and existing races were compared using microsatellite (SSR) marker analysis and their virulence on commercial cultivars was also determined. Seedling response of 113 wheat entries against the new races, using 2SA88, 2SA88+9h, 2SA106, and 2SA107 as controls, revealed 2SA107 as the most virulent (67 entries susceptible), followed by 2SA42 (64), 2SA106 (60), 2SA88+9h (59), 2SA88 (25), and 2SA5 (17). Thus, 2SA5 may not pose a significant threat to local wheat production. SSR genotyping revealed that 2SA5 is genetically distinct from all other SA Pgt races.
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Affiliation(s)
- Tarekegn G Terefe
- Agricultural Research Council-Small Grain, Bethlehem 9700, South Africa
| | - Willem H P Boshoff
- Department of Plant Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Robert F Park
- Plant Breeding Institute Cobbitty, The University of Sydney, Narellan, NSW 2567, Australia
| | - Zacharias A Pretorius
- Department of Plant Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Botma Visser
- Department of Plant Sciences, University of the Free State, Bloemfontein 9300, South Africa
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6
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Locci F, Parker JE. Plant NLR immunity activation and execution: a biochemical perspective. Open Biol 2024; 14:230387. [PMID: 38262605 PMCID: PMC10805603 DOI: 10.1098/rsob.230387] [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: 10/23/2023] [Accepted: 12/15/2023] [Indexed: 01/25/2024] Open
Abstract
Plants deploy cell-surface and intracellular receptors to detect pathogen attack and trigger innate immune responses. Inside host cells, families of nucleotide-binding/leucine-rich repeat (NLR) proteins serve as pathogen sensors or downstream mediators of immune defence outputs and cell death, which prevent disease. Established genetic underpinnings of NLR-mediated immunity revealed various strategies plants adopt to combat rapidly evolving microbial pathogens. The molecular mechanisms of NLR activation and signal transmission to components controlling immunity execution were less clear. Here, we review recent protein structural and biochemical insights to plant NLR sensor and signalling functions. When put together, the data show how different NLR families, whether sensors or signal transducers, converge on nucleotide-based second messengers and cellular calcium to confer immunity. Although pathogen-activated NLRs in plants engage plant-specific machineries to promote defence, comparisons with mammalian NLR immune receptor counterparts highlight some shared working principles for NLR immunity across kingdoms.
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Affiliation(s)
- Federica Locci
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Jane E. Parker
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
- Cologne-Düsseldorf Cluster of Excellence on Plant Sciences (CEPLAS), 40225 Düsseldorf, Germany
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7
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Dehbi I, Achemrk O, Ezzouggari R, El Jarroudi M, Mokrini F, Legrifi I, Belabess Z, Laasli SE, Mazouz H, Lahlali R. Beneficial Microorganisms as Bioprotectants against Foliar Diseases of Cereals: A Review. PLANTS (BASEL, SWITZERLAND) 2023; 12:4162. [PMID: 38140489 PMCID: PMC10747484 DOI: 10.3390/plants12244162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023]
Abstract
Cereal production plays a major role in both animal and human diets throughout the world. However, cereal crops are vulnerable to attacks by fungal pathogens on the foliage, disrupting their biological cycle and photosynthesis, which can reduce yields by 15-20% or even 60%. Consumers are concerned about the excessive use of synthetic pesticides given their harmful effects on human health and the environment. As a result, the search for alternative solutions to protect crops has attracted the interest of scientists around the world. Among these solutions, biological control using beneficial microorganisms has taken on considerable importance, and several biological control agents (BCAs) have been studied, including species belonging to the genera Bacillus, Pseudomonas, Streptomyces, Trichoderma, Cladosporium, and Epicoccum, most of which include plants of growth-promoting rhizobacteria (PGPRs). Bacillus has proved to be a broad-spectrum agent against these leaf cereal diseases. Interaction between plant and beneficial agents occurs as direct mycoparasitism or hyperparasitism by a mixed pathway via the secretion of lytic enzymes, growth enzymes, and antibiotics, or by an indirect interaction involving competition for nutrients or space and the induction of host resistance (systemic acquired resistance (SAR) or induced systemic resistance (ISR) pathway). We mainly demonstrate the role of BCAs in the defense against fungal diseases of cereal leaves. To enhance a solution-based crop protection approach, it is also important to understand the mechanism of action of BCAs/molecules/plants. Research in the field of preventing cereal diseases is still ongoing.
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Affiliation(s)
- Ilham Dehbi
- Phytopathology Unit, Department of Plant Protection, Ecole National of Agriculture Meknes, Km10, Rte Haj Kaddour, BP S/40, Meknes 50001, Morocco; (I.D.); (O.A.); (R.E.); (I.L.); (S.-E.L.)
- Laboratory of Plant Biotechnology and Molecular Biology, Faculty of Sciences, Moulay Ismail University, BP 11201, Zitoune, Meknes 50000, Morocco;
| | - Oussama Achemrk
- Phytopathology Unit, Department of Plant Protection, Ecole National of Agriculture Meknes, Km10, Rte Haj Kaddour, BP S/40, Meknes 50001, Morocco; (I.D.); (O.A.); (R.E.); (I.L.); (S.-E.L.)
| | - Rachid Ezzouggari
- Phytopathology Unit, Department of Plant Protection, Ecole National of Agriculture Meknes, Km10, Rte Haj Kaddour, BP S/40, Meknes 50001, Morocco; (I.D.); (O.A.); (R.E.); (I.L.); (S.-E.L.)
- Laboratory of Biotechnology, Conservation, and Valorization of Natural Resources (LBCVNR), Faculty of Sciences Dhar El Mehraz, Sidi Mohamed Ben Abdallah University, Fez 30000, Morocco
| | - Moussa El Jarroudi
- Department of Environmental Sciences and Management, SPHERES Research Unit, University of Liège, 6700 Arlon, Belgium;
| | - Fouad Mokrini
- Biotechnology Unit, Regional Center of Agricultural Research, INRA–Morocco, Rabat 10080, Morocco;
| | - Ikram Legrifi
- Phytopathology Unit, Department of Plant Protection, Ecole National of Agriculture Meknes, Km10, Rte Haj Kaddour, BP S/40, Meknes 50001, Morocco; (I.D.); (O.A.); (R.E.); (I.L.); (S.-E.L.)
| | - Zineb Belabess
- Plant Protection Laboratory, Regional Center of Agricultural Research of Meknes, National Institute of Agricultural Research, Km 13, Route Haj Kaddour, BP 578, Meknes 50001, Morocco;
| | - Salah-Eddine Laasli
- Phytopathology Unit, Department of Plant Protection, Ecole National of Agriculture Meknes, Km10, Rte Haj Kaddour, BP S/40, Meknes 50001, Morocco; (I.D.); (O.A.); (R.E.); (I.L.); (S.-E.L.)
| | - Hamid Mazouz
- Laboratory of Plant Biotechnology and Molecular Biology, Faculty of Sciences, Moulay Ismail University, BP 11201, Zitoune, Meknes 50000, Morocco;
| | - Rachid Lahlali
- Phytopathology Unit, Department of Plant Protection, Ecole National of Agriculture Meknes, Km10, Rte Haj Kaddour, BP S/40, Meknes 50001, Morocco; (I.D.); (O.A.); (R.E.); (I.L.); (S.-E.L.)
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8
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Lockhart SR, Chowdhary A, Gold JAW. The rapid emergence of antifungal-resistant human-pathogenic fungi. Nat Rev Microbiol 2023; 21:818-832. [PMID: 37648790 DOI: 10.1038/s41579-023-00960-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2023] [Indexed: 09/01/2023]
Abstract
During recent decades, the emergence of pathogenic fungi has posed an increasing public health threat, particularly given the limited number of antifungal drugs available to treat invasive infections. In this Review, we discuss the global emergence and spread of three emerging antifungal-resistant fungi: Candida auris, driven by global health-care transmission and possibly facilitated by climate change; azole-resistant Aspergillus fumigatus, driven by the selection facilitated by azole fungicide use in agricultural and other settings; and Trichophyton indotineae, driven by the under-regulated use of over-the-counter high-potency corticosteroid-containing antifungal creams. The diversity of the fungi themselves and the drivers of their emergence make it clear that we cannot predict what might emerge next. Therefore, vigilance is critical to monitoring fungal emergence, as well as the rise in overall antifungal resistance.
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Affiliation(s)
- Shawn R Lockhart
- Mycotic Diseases Branch, Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Anuradha Chowdhary
- Medical Mycology Unit, Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
- National Reference Laboratory for Antimicrobial Resistance in Fungal Pathogens, Medical Mycology Unit, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Jeremy A W Gold
- Mycotic Diseases Branch, Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
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Li H, Zhang P, Luo M, Hoque M, Chakraborty S, Brooks B, Li J, Singh S, Forest K, Binney A, Zhang L, Mather D, Ayliffe M. Introgression of the bread wheat D genome encoded Lr34/Yr18/Sr57/Pm38/Ltn1 adult plant resistance gene into Triticum turgidum (durum wheat). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:226. [PMID: 37847385 PMCID: PMC10581953 DOI: 10.1007/s00122-023-04466-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: 04/04/2023] [Accepted: 09/18/2023] [Indexed: 10/18/2023]
Abstract
KEY MESSAGE Lack of function of a D-genome adult plant resistance gene upon introgression into durum wheat. The wheat Lr34/Yr18/Sr57/Pm38/Ltn1 adult plant resistance gene (Lr34), located on chromosome arm 7DS, provides broad spectrum, partial, adult plant resistance to leaf rust, stripe rust, stem rust and powdery mildew. It has been used extensively in hexaploid bread wheat (AABBDD) and conferred durable resistance for many decades. These same diseases also occur on cultivated tetraploid durum wheat and emmer wheat but transfer of D genome sequences to those subspecies is restricted due to very limited intergenomic recombination. Herein we have introgressed the Lr34 gene into chromosome 7A of durum wheat. Durum chromosome substitution line Langdon 7D(7A) was crossed to Cappelli ph1c, a mutant derivative of durum cultivar Cappelli homozygous for a deletion of the chromosome pairing locus Ph1. Screening of BC1F2 plants and their progeny by KASP and PCR markers, 90 K SNP genotyping and cytology identified 7A chromosomes containing small chromosome 7D fragments encoding Lr34. However, in contrast to previous transgenesis experiments in durum wheat, resistance to wheat stripe rust was not observed in either Cappelli/Langdon 7D(7A) or Bansi durum plants carrying this Lr34 encoding segment due to low levels of Lr34 gene expression. KEY MESSAGE
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Affiliation(s)
- Hongyu Li
- CSIRO Agriculture and Food, Clunies Ross Street, GPO Box 1700, Canberra, ACT, 2601, Australia
- Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Peng Zhang
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, 2570, Australia
| | - Ming Luo
- CSIRO Agriculture and Food, Clunies Ross Street, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Mohammad Hoque
- CSIRO Agriculture and Food, Clunies Ross Street, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Soma Chakraborty
- CSIRO Agriculture and Food, Clunies Ross Street, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Brenton Brooks
- CSIRO Agriculture and Food, Clunies Ross Street, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Jianbo Li
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, 2570, Australia
| | - Smriti Singh
- Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, NSW, 2570, Australia
| | - Kerrie Forest
- Agriculture Victoria, Department of Energy, Environment and Climate Action, AgriBio Centre for AgriBioscience, 5 Ring Rd, Bundoora, VIC, 3083, Australia
| | - Allan Binney
- School of Agriculture, Food & Wine, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
| | - Lianquan Zhang
- Triticeae Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Diane Mather
- School of Agriculture, Food & Wine, The University of Adelaide, PMB 1, Glen Osmond, SA, 5064, Australia
| | - Michael Ayliffe
- CSIRO Agriculture and Food, Clunies Ross Street, GPO Box 1700, Canberra, ACT, 2601, Australia.
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Yazdani M, Rouse MN, Steffenson BJ, Bajgain P, Patpour M, Johansson E, Rahmatov M. Developing adapted wheat lines with broad-spectrum resistance to stem rust: Introgression of Sr59 through backcrossing and selections based on genotyping-by-sequencing data. PLoS One 2023; 18:e0292724. [PMID: 37824577 PMCID: PMC10569509 DOI: 10.1371/journal.pone.0292724] [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] [Received: 07/06/2023] [Accepted: 09/26/2023] [Indexed: 10/14/2023] Open
Abstract
Control of stem rust, caused by Puccinia graminis f.sp. tritici, a highly destructive fungal disease of wheat, faces continuous challenges from emergence of new virulent races across wheat-growing continents. Using combinations of broad-spectrum resistance genes could impart durable stem rust resistance. This study attempted transfer of Sr59 resistance gene from line TA5094 (developed through CSph1bM-induced T2DS·2RL Robertsonian translocation conferring broad-spectrum resistance). Poor agronomic performance of line TA5094 necessitates Sr59 transfer to adapted genetic backgrounds and utility evaluations for wheat improvement. Based on combined stem rust seedling and molecular analyses, 2070 BC1F1 and 1230 BC2F1 plants were derived from backcrossing BAJ#1, KACHU#1, and REEDLING#1 with TA5094. Genotyping-by-sequencing (GBS) results revealed the physical positions of 15,116 SNPs on chromosome 2R. The adapted genotypes used for backcrossing were found not to possess broad-spectrum resistance to selected stem rust races, whereas Sr59-containing line TA5094 showed resistance to all races tested. Stem rust seedling assays combined with kompetitive allele-specific PCR (KASP) marker analysis successfully selected and generated the BC2F2 population, which contained the Sr59 gene, as confirmed by GBS. Early-generation data from backcrossing suggested deviations from the 3:1 segregation, suggesting that multiple genes may contribute to Sr59 resistance reactions. Using GBS marker data (40,584 SNPs in wheat chromosomes) to transfer the recurrent parent background to later-generation populations resulted in average genome recovery of 71.2% in BAJ#1*2/TA5094, 69.8% in KACHU#1*2/TA5094, and 70.5% in REEDLING#1*2/TA5094 populations. GBS data verified stable Sr59 introgression in BC2F2 populations, as evidenced by presence of the Ph1 locus and absence of the 50,936,209 bp deletion in CSph1bM. Combining phenotypic selections, stem rust seedling assays, KASP markers, and GBS data substantially accelerated transfer of broad-spectrum resistance into adapted genotypes. Thus, this study demonstrated that the Sr59 resistance gene can be introduced into elite genetic backgrounds to mitigate stem rust-related yield losses.
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Affiliation(s)
- Mahboobeh Yazdani
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Matthew N. Rouse
- United States Department of Agriculture, Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN, United States of America
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States of America
| | - Brian J. Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States of America
| | - Prabin Bajgain
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, United States of America
| | - Mehran Patpour
- Department of Agroecology, Aarhus University, Slagelse, Denmark
| | - Eva Johansson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Mahbubjon Rahmatov
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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11
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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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12
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Malchikov PN, Myasnikova MG. Development, results and prospects of the spring durum wheat breeding in Russia (post-Soviet states). Vavilovskii Zhurnal Genet Selektsii 2023; 27:591-608. [PMID: 38213466 PMCID: PMC10782032 DOI: 10.18699/vjgb-23-71] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 01/13/2024] Open
Abstract
The article outlines a brief historical background on the introduction to cultivation, distribution and breeding of spring durum wheat in the steppe and forest-steppe regions of Eurasia (the countries of the former USSR: Russia, Ukraine, and Kazakhstan). The approaches and methodology for improving durum wheat during certain scientific selection periods are given. The features of the selection program implementation and the breeding scale expansion during the creation of breeding stations at the beginning of the XX century, after the end of the Great Patriotic War, in the second half of the XX century, and at present are considered. A characteristic according to the main features and properties of varieties created in different periods is given. The achievements of the classical breeding method by comparing old and new varieties are analyzed. The efficiency and rate of wheat selection by periods in different regions of Russia is estimated. The results and methods of breeding for yield, resistance to drought, leaf diseases (Stagonospora nodorum Berk., Septoria tritici (Roeb. et Desm.), Bipolaris sorokiniana (Sacc.) Shoemaker, Pyrenophora tritici repentis (Died.) Drechs., Fusarium sp., Puccinia titicina Eriks., Puccinia graminis Pers. f. sp. tritici Eriks., Blumeria graminis (DC.) f. sp. tritici Em. Marchal), grain pathogens Ustilago tritici (Pers.) Rostr.) and pathogens causing darkening of the corcule and endosperm (Bipolaris sorokiniana (Sacc.) Shoemaker, Alternaria tenuis (Nees et Fr.), Аlternaria triticina (Prasada & Prabhu)), pests (Cephus pygmeus Lens, Osinosoma frit L., Mayetiola destructor (Say)), grain quality (protein content, amount of yellow pigments, dough rheology, sprouting resistance) and end products are presented. The prospects for the molecular marker application for a number of traits in breeding in the near future are given.
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Affiliation(s)
- P N Malchikov
- Samara Federal Research Scientific Center of the Russian Academy of Sciences, Samara Scientific Research Agriculture Institute named after N.M. Tulajkov, Bezenchuk, Samara region, Russia Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - M G Myasnikova
- Samara Federal Research Scientific Center of the Russian Academy of Sciences, Samara Scientific Research Agriculture Institute named after N.M. Tulajkov, Bezenchuk, Samara region, Russia
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13
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McCoy AG, Belanger RR, Bradley CA, Cerritos-Garcia DG, Garnica VC, Giesler LJ, Grijalba PE, Guillin E, Henriquez MA, Kim YM, Malvick DK, Matthiesen RL, Mideros SX, Noel ZA, Robertson AE, Roth MG, Schmidt CL, Smith DL, Sparks AH, Telenko DEP, Tremblay V, Wally O, Chilvers MI. A global-temporal analysis on Phytophthora sojae resistance-gene efficacy. Nat Commun 2023; 14:6043. [PMID: 37758723 PMCID: PMC10533513 DOI: 10.1038/s41467-023-41321-7] [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: 02/10/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
Plant disease resistance genes are widely used in agriculture to reduce disease outbreaks and epidemics and ensure global food security. In soybean, Rps (Resistance to Phytophthora sojae) genes are used to manage Phytophthora sojae, a major oomycete pathogen that causes Phytophthora stem and root rot (PRR) worldwide. This study aims to identify temporal changes in P. sojae pathotype complexity, diversity, and Rps gene efficacy. Pathotype data was collected from 5121 isolates of P. sojae, derived from 29 surveys conducted between 1990 and 2019 across the United States, Argentina, Canada, and China. This systematic review shows a loss of efficacy of specific Rps genes utilized for disease management and a significant increase in the pathotype diversity of isolates over time. This study finds that the most widely deployed Rps genes used to manage PRR globally, Rps1a, Rps1c and Rps1k, are no longer effective for PRR management in the United States, Argentina, and Canada. This systematic review emphasizes the need to widely introduce new sources of resistance to P. sojae, such as Rps3a, Rps6, or Rps11, into commercial cultivars to effectively manage PRR going forward.
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Affiliation(s)
| | | | | | | | | | | | | | - Eduardo Guillin
- Instituto Nacional de Tecnologia Agropecuaria, Buenos Aires, Argentina
| | | | - Yong Min Kim
- Agriculture and Agri-Food Canada, Brandon, Manitoba, Canada
| | | | | | | | | | | | | | | | | | - Adam H Sparks
- Department of Primary Industries and Regional Development, Perth, WA, Australia
- University of Southern Queensland, Toowoomba, Qld, Australia
| | | | | | - Owen Wally
- Agriculture and Agri-Food Canada, Harrow, ON, Canada
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14
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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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15
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Prasad P, Thakur R, Bhardwaj SC, Savadi S, Gangwar OP, Lata C, Adhikari S, Kumar S, Kundu S, Manjul AS, Prakasha TL, Navathe S, Hegde GM, Game BC, Mishra KK, Khan H, Gupta V, Mishra CN, Kumar S, Kumar S, Singh G. Virulence and genetic analysis of Puccinia graminis tritici in the Indian sub-continent from 2016 to 2022 and evaluation of wheat varieties for stem rust resistance. FRONTIERS IN PLANT SCIENCE 2023; 14:1196808. [PMID: 37521927 PMCID: PMC10376725 DOI: 10.3389/fpls.2023.1196808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/20/2023] [Indexed: 08/01/2023]
Abstract
Wheat stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), has re-emerged as one of the major concerns for global wheat production since the evolution of Ug99 and other virulent pathotypes of Pgt from East Africa, Europe, Central Asia, and other regions. Host resistance is the most effective, economic, and eco-friendly approach for managing stem rust. Understanding the virulence nature, genetic diversity, origin, distribution, and evolutionary pattern of Pgt pathotypes over time and space is a prerequisite for effectively managing newly emerging Pgt isolates through host resistance. In the present study, we monitored the occurrence of stem rust of wheat in India and neighboring countries from 2016 to 2022, collected 620 single-pustule isolates of Pgt from six states of India and Nepal, analyzed them on Indian stem rust differentials, and determined their virulence phenotypes and molecular genotypes. The Ug99 type of pathotypes did not occur in India. Pathotypes 11 and 40A were most predominant during these years. Virulence phenotyping of these isolates identified 14 Pgt pathotypes, which were genotyped using 37 Puccinia spp.-specific polymorphic microsatellites, followed by additional phylogenetic analyses using DARwin. These analyses identified three major molecular groups, demonstrating fewer lineages, clonality, and long-distance migration of Pgt isolates in India. Fourteen of the 40 recently released Indian wheat varieties exhibited complete resistance to all 23 Pgt pathotypes at the seedling stage. Twelve Sr genes were postulated in 39 varieties based on their seedling response to Pgt pathotypes. The values of slow rusting parameters i.e. coefficient of infection, area under disease progress curve, and infection rates, assessed at adult plant stage at five geographically different locations during two crop seasons, indicated the slow rusting behavior of several varieties. Six Sr genes (Sr2, Sr57, Sr58, Sr24, Sr31, and Sr38) were identified in 24 wheat varieties using molecular markers closely linked to these genes. These findings will guide future breeding programs toward more effective management of wheat stem rust.
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Affiliation(s)
- Pramod Prasad
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, India
| | - Rajnikant Thakur
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, India
| | - S. C. Bhardwaj
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, India
| | - Siddanna Savadi
- Division of Crop Improvement, ICAR-Directorate of Cashew Research, Puttur, Karnataka, India
| | - O. P. Gangwar
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, India
| | - Charu Lata
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, India
| | - Sneha Adhikari
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, India
| | - Subodh Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, India
| | - Sonu Kundu
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, India
| | - A. S. Manjul
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, India
| | - T. L. Prakasha
- ICAR-Indian Agricultural Research Institute, Indore, Regional Station, Madhya Pradesh, India
| | - Sudhir Navathe
- Genetics and Plant Breeding Group, Agharkar Research Institute, Pune, India
| | - G. M. Hegde
- All India Coordinated Research Project on Wheat & Barley, University of Agricultural Sciences, Dharwad, Karnataka, India
| | - B. C. Game
- Mahatma Phule Krishi Vidyapeeth, Rahuri, Agricultural Research Station, Niphad, Maharashtra, India
| | - K. K. Mishra
- JNKVV, Zonal Agricultural Research Station, Powarkheda, Narmadapuram, Madhya Pradesh, India
| | - Hanif Khan
- Crop Improvement Division, ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| | - Vikas Gupta
- Crop Improvement Division, ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| | - C. N. Mishra
- Crop Improvement Division, ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| | - Satish Kumar
- Crop Improvement Division, ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| | - Sudheer Kumar
- Crop Improvement Division, ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| | - Gyanendra Singh
- Crop Improvement Division, ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
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16
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Maserumule M, Rauwane M, Madala NE, Ncube E, Figlan S. Defence-related metabolic changes in wheat ( Triticum aestivum L.) seedlings in response to infection by Puccinia graminis f. sp. tritici. FRONTIERS IN PLANT SCIENCE 2023; 14:1166813. [PMID: 37377801 PMCID: PMC10292758 DOI: 10.3389/fpls.2023.1166813] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/16/2023] [Indexed: 06/29/2023]
Abstract
Stem rust caused by the pathogen Puccinia graminis f. sp. tritici is a destructive fungal disease-causing major grain yield losses in wheat. Therefore, understanding the plant defence regulation and function in response to the pathogen attack is required. As such, an untargeted LC-MS-based metabolomics approach was employed as a tool to dissect and understand the biochemical responses of Koonap (resistant) and Morocco (susceptible) wheat varieties infected with two different races of P. graminis (2SA88 [TTKSF] and 2SA107 [PTKST]). Data was generated from the infected and non-infected control plants harvested at 14- and 21- days post-inoculation (dpi), with 3 biological replicates per sample under a controlled environment. Chemo-metric tools such as principal component analysis (PCA), orthogonal projection to latent structures-discriminant analysis (OPLS-DA) were used to highlight the metabolic changes using LC-MS data of the methanolic extracts generated from the two wheat varieties. Molecular networking in Global Natural Product Social (GNPS) was further used to analyse biological networks between the perturbed metabolites. PCA and OPLS-DA analysis showed cluster separations between the varieties, infection races and the time-points. Distinct biochemical changes were also observed between the races and time-points. Metabolites were identified and classified using base peak intensities (BPI) and single ion extracted chromatograms from samples, and the most affected metabolites included flavonoids, carboxylic acids and alkaloids. Network analysis also showed high expression of metabolites from thiamine and glyoxylate, such as flavonoid glycosides, suggesting multi-faceted defence response strategy by understudied wheat varieties towards P. graminis pathogen infection. Overall, the study provided the insights of the biochemical changes in the expression of wheat metabolites in response to stem rust infection.
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Affiliation(s)
- Mercy Maserumule
- Department of Agriculture and Animal Health, School of Agriculture and Life Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Roodepoort, South Africa
| | - Molemi Rauwane
- Department of Agriculture and Animal Health, School of Agriculture and Life Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Roodepoort, South Africa
- Department of Botany, Nelson Mandela University, South Campus, Port Elizabeth, South Africa
| | - Ntakadzeni E. Madala
- Department of Biochemistry and Microbiology, Faculty of Sciences, Agriculture and Engineering, University of Venda, Thohoyandou, Limpopo, South Africa
| | - Efficient Ncube
- Department of Agriculture and Animal Health, School of Agriculture and Life Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Roodepoort, South Africa
| | - Sandiswa Figlan
- Department of Agriculture and Animal Health, School of Agriculture and Life Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Roodepoort, South Africa
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17
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Li H, Luo J, Zhang W, Hua L, Li K, Wang J, Xu B, Yang C, Wang G, Rouse MN, Dubcovsky J, Chen S. High-resolution mapping of SrTm4, a recessive resistance gene to wheat stem rust. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:120. [PMID: 37103626 PMCID: PMC10140103 DOI: 10.1007/s00122-023-04369-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/17/2023] [Indexed: 05/13/2023]
Abstract
KEY MESSAGE The diploid wheat recessive stem rust resistance gene SrTm4 was fine-mapped to a 754-kb region on chromosome arm 2AmL and potential candidate genes were identified. Race Ug99 of Puccinia graminis f. sp. tritici (Pgt), the causal agent of wheat stem (or black) rust is one of the most serious threats to global wheat production. The identification, mapping, and deployment of effective stem rust resistance (Sr) genes are critical to reduce this threat. In this study, we generated SrTm4 monogenic lines and found that this gene confers resistance to North American and Chinese Pgt races. Using a large mapping population (9522 gametes), we mapped SrTm4 within a 0.06 cM interval flanked by marker loci CS4211 and 130K1519, which corresponds to a 1.0-Mb region in the Chinese Spring reference genome v2.1. A physical map of the SrTm4 region was constructed with 11 overlapping BACs from the resistant Triticum monococcum PI 306540. Comparison of the 754-kb physical map with the genomic sequence of Chinese Spring and a discontinuous BAC sequence of DV92 revealed a 593-kb chromosomal inversion in PI 306540. Within the candidate region, we identified an L-type lectin-domain containing receptor kinase (LLK1), which was disrupted by the proximal inversion breakpoint, as a potential candidate gene. Two diagnostic dominant markers were developed to detect the inversion breakpoints. In a survey of T. monococcum accessions, we identified 10 domesticated T. monococcum subsp. monococcum genotypes, mainly from the Balkans, carrying the inversion and showing similar mesothetic resistant infection types against Pgt races. The high-density map and tightly linked molecular markers developed in this study are useful tools to accelerate the deployment of SrTm4-mediated resistance in wheat breeding programs.
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Affiliation(s)
- Hongna Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China
| | - Jing Luo
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China
| | - Wenjun Zhang
- Department of Plant Sciences, University of California, Davis, CA95616, USA
| | - Lei Hua
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China
| | - Kun Li
- Department of Plant Sciences, University of California, Davis, CA95616, USA
| | - Jian Wang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Binyang Xu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chen Yang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guiping Wang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China
| | - Matthew N Rouse
- US Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory and Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA.
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA95616, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
| | - Shisheng Chen
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China.
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18
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Norman M, Bariana H, Bansal U, Periyannan S. The Keys to Controlling Wheat Rusts: Identification and Deployment of Genetic Resistance. PHYTOPATHOLOGY 2023; 113:667-677. [PMID: 36897760 DOI: 10.1094/phyto-02-23-0041-ia] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Rust diseases are among the major constraints for wheat production worldwide due to the emergence and spread of highly destructive races of Puccinia. The most common approach to minimize yield losses due to rust is to use cultivars that are genetically resistant. Modern wheat cultivars, landraces, and wild relatives can contain undiscovered resistance genes, which typically encode kinase or nucleotide-binding site leucine rich repeat (NLR) domain containing receptor proteins. Recent research has shown that these genes can provide either resistance in all growth stages (all-stage resistance; ASR) or specially in later growth stages (adult-plant resistance; APR). ASR genes are pathogen and race-specific, meaning can function against selected races of the Puccinia fungus due to the necessity to recognize specific avirulence molecules in the pathogen. APR genes are either pathogen-specific or multipathogen resistant but often race-nonspecific. Prediction of resistance genes through rust infection screening alone remains complex when more than one resistance gene is present. However, breakthroughs during the past half century such as the single-nucleotide polymorphism-based genotyping techniques and resistance gene isolation strategies like mutagenesis, resistance gene enrichment, and sequencing (MutRenSeq), mutagenesis and chromosome sequencing (MutChromSeq), and association genetics combined with RenSeq (AgRenSeq) enables rapid transfer of resistance from source to modern cultivars. There is a strong need for combining multiple genes for better efficacy and longer-lasting resistance. Hence, techniques like gene cassette creation speeds up the gene combination process, but their widespread adoption and commercial use is limited due to their transgenic nature.
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Affiliation(s)
- Michael Norman
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, NSW 2570, Australia
- Commonwealth Scientific and Industrial Research Organization Agriculture and Food, Canberra, ACT 2601, Australia
| | - Harbans Bariana
- School of Science, Western Sydney University, Bourke Road, Richmond, NSW 2753, Australia
| | - Urmil Bansal
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, NSW 2570, Australia
| | - Sambasivam Periyannan
- School of Agriculture and Environmental Science & Centre for Crop Health, University of Southern Queensland, Toowoomba, Qld 4350, Australia
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19
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Sun H, Wang Z, Wang R, Chen S, Ni X, Gao F, Zhang Y, Xu Y, Wu X, Li T. Identification of wheat stem rust resistance genes in wheat cultivars from Hebei province, China. FRONTIERS IN PLANT SCIENCE 2023; 14:1156936. [PMID: 37063217 PMCID: PMC10098322 DOI: 10.3389/fpls.2023.1156936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/13/2023] [Indexed: 06/19/2023]
Abstract
Wheat stem rust is caused by Puccinia graminis f. sp. tritici. This major disease has been effectively controlled via resistance genes since the 1970s. The appearance and spread of new races of P. graminis f. sp. tritici (eg., Ug99, TKTTF, and TTRTF) have renewed the interest in identifying the resistance gene and breeding cultivars resistant to wheat stem rust. In this study, gene postulation, pedigree analysis, and molecular detection were used to determine the presence of stem rust resistance genes in 65 commercial wheat cultivars from Hebei Province. In addition, two predominant races 21C3CTHTM and 34MRGQM were used to evaluate the resistance of these cultivars at the adult-plant stage in 2021-2022. The results revealed that 6 Sr genes (namely, Sr5, Sr17, Sr24, Sr31, Sr32, Sr38, and SrTmp), either singly or in combination, were identified in 46 wheat cultivars. Overall, 37 wheat cultivars contained Sr31. Sr5 and Sr17 were present in 3 and 3 cultivars, respectively. Gao 5218 strong gluten, Jie 13-Ji 7369, and Kenong 1006 contained Sr24, Sr32, and Sr38, respectively. No wheat cultivar contained Sr25 and Sr26. In total, 50 (76.9%) wheat cultivars were resistant to all tested races of P. graminis f. sp. tritici in field test in 2021-2022. This study is important for breeding wheat cultivars with resistance to stem rust.
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Affiliation(s)
- Huiyan Sun
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Ziye Wang
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Rui Wang
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Si Chen
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Xinyu Ni
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Fu Gao
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Yazhao Zhang
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Yiwei Xu
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Xianxin Wu
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Tianya Li
- College of Plant Protection, Shenyang Agricultural University, Shenyang, Liaoning, China
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20
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Michel S, Löschenberger F, Ametz C, Bürstmayr H. Toward combining qualitative race-specific and quantitative race-nonspecific disease resistance by genomic selection. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:79. [PMID: 36952008 PMCID: PMC10036288 DOI: 10.1007/s00122-023-04312-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 01/27/2023] [Indexed: 06/17/2023]
Abstract
A novel genomic selection strategy offers the unique opportunity to develop qualitative race-specific resistant varieties that possess high levels of the more durable quantitative race-nonspecific resistance in their genetic background. Race-specific qualitative resistance genes (R-genes) are conferring complete resistance in many pathosystems, but are frequently overcome by new virulent pathogen races. Once the deployed R-genes are overcome, a wide variation of quantitative disease resistance (QDR) can be observed in a set of previously race-specific, i.e., completely resistant genotypes-a phenomenon known as "vertifolia effect." This race-nonspecific QDR is considered to be more durable in the long term, but provides merely a partial protection against pathogens. This simulation study aimed to detangle race-specific R-gene-mediated resistance of pending selection candidates and the QDR in their genetic background by employing different genomic selection strategies. True breeding values that reflected performance data for rust resistance in wheat were simulated, and used in a recurrent genomic selection based on several prediction models and training population designs. Using training populations that were devoid of race-specific R-genes was thereby pivotal for an efficient improvement of QDR in the long term. Marker-assisted preselection for the presence of R-genes followed by a genomic prediction for accumulating the many small to medium effect loci underlying QDR in the genetic background of race-specific resistant genotypes appeared furthermore to be a promising approach to select simultaneously for both types of resistance. The practical application of such a knowledge-driven genomic breeding strategy offers the opportunity to develop varieties with multiple layers of resistance, which have the potential to prevent intolerable crop losses under epidemic situations by displaying a high level of QDR even when race-specific R-genes have been overcome by evolving pathogen populations.
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Affiliation(s)
- Sebastian Michel
- Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences Vienna, Konrad-Lorenz-Str. 20, 3430, Tulln, Austria.
| | | | - Christian Ametz
- Saatzucht Donau GesmbH & CoKG, Saatzuchtstrasse 11, 2301, Probstdorf, Austria
| | - Hermann Bürstmayr
- Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences Vienna, Konrad-Lorenz-Str. 20, 3430, Tulln, Austria
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21
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Bellah H, Gazeau G, Gélisse S, Amezrou R, Marcel TC, Croll D. A highly multiplexed assay to monitor pathogenicity, fungicide resistance and gene flow in the fungal wheat pathogen Zymoseptoria tritici. PLoS One 2023; 18:e0281181. [PMID: 36745583 PMCID: PMC9901794 DOI: 10.1371/journal.pone.0281181] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 01/17/2023] [Indexed: 02/07/2023] Open
Abstract
Crop pathogens pose severe risks to global food production due to the rapid rise of resistance to pesticides and host resistance breakdowns. Predicting future risks requires monitoring tools to identify changes in the genetic composition of pathogen populations. Here we report the design of a microfluidics-based amplicon sequencing assay to multiplex 798 loci targeting virulence and fungicide resistance genes, and randomly selected genome-wide markers for the fungal pathogen Zymoseptoria tritici. The fungus causes one of the most devastating diseases on wheat showing rapid adaptation to fungicides and host resistance. We optimized the primer design by integrating polymorphism data from 632 genomes of the same species. To test the performance of the assay, we genotyped 192 samples in two replicates. Analysis of the short-read sequence data generated by the assay showed a fairly stable success rate across samples to amplify a large number of loci. The performance was consistent between samples originating from pure genomic DNA as well as material extracted directly from infected wheat leaves. In samples with mixed genotypes, we found that the assay recovers variations in allele frequencies. We also explored the potential of the amplicon assay to recover transposable element insertion polymorphism relevant for fungicide resistance. As a proof-of-concept, we show that the assay recovers the pathogen population structure across French wheat fields. Genomic monitoring of crop pathogens contributes to more sustainable crop protection and yields.
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Affiliation(s)
- Hadjer Bellah
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Gwilherm Gazeau
- INRAE, UR BIOGER, Université Paris-Saclay, Thiverval-Grignon, France
| | - Sandrine Gélisse
- INRAE, UR BIOGER, Université Paris-Saclay, Thiverval-Grignon, France
| | - Reda Amezrou
- INRAE, UR BIOGER, Université Paris-Saclay, Thiverval-Grignon, France
| | - Thierry C. Marcel
- INRAE, UR BIOGER, Université Paris-Saclay, Thiverval-Grignon, France
- * E-mail: (TCM); (DC)
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
- * E-mail: (TCM); (DC)
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22
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Hovmøller MS, Thach T, Justesen AF. Global dispersal and diversity of rust fungi in the context of plant health. Curr Opin Microbiol 2023; 71:102243. [PMID: 36462410 DOI: 10.1016/j.mib.2022.102243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 10/26/2022] [Accepted: 11/03/2022] [Indexed: 12/02/2022]
Abstract
Long-distance dispersal of plant pathogens at the continental scale may have strong implications on plant health, in particular when incursions result in spread of disease to new territories where the disease was previously absent or insignificant. These dispersions may be caused by airborne transmission of spores or accidental spread via human travel and trade. Recent surveillance efforts of cereal rust fungi have demonstrated that incursion of new strains with superior fitness into areas where the disease is already established may have similar implications on plant health. Since dispersal events are highly stochastic, irrespective of transmission mechanism, critical mitigation efforts include preparedness by coordinated pathogen surveillance activities, host crop diversification, and breeding for disease resistance with low vulnerability to sudden changes in the pathogen population.
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Affiliation(s)
- Mogens S Hovmøller
- Aarhus University, Department of Agroecology, Global Rust Reference Center, Forsøgsvej 1, DK-4200 Slagelse, Denmark.
| | - Tine Thach
- Aarhus University, Department of Agroecology, Global Rust Reference Center, Forsøgsvej 1, DK-4200 Slagelse, Denmark
| | - Annemarie F Justesen
- Aarhus University, Department of Agroecology, Global Rust Reference Center, Forsøgsvej 1, DK-4200 Slagelse, Denmark
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23
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Abdedayem W, Patpour M, Laribi M, Justesen AF, Kouki H, Fakhfakh M, Hovmøller MS, Yahyaoui AH, Hamza S, Ben M’Barek S. Wheat Stem Rust Detection and Race Characterization in Tunisia. PLANTS (BASEL, SWITZERLAND) 2023; 12:552. [PMID: 36771636 PMCID: PMC9919909 DOI: 10.3390/plants12030552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/12/2023] [Accepted: 01/14/2023] [Indexed: 06/18/2023]
Abstract
Climate changes over the past 25 years have led to conducive conditions for invasive and transboundary fungal disease occurrence, including the re-emergence of wheat stem rust disease, caused by Puccinia graminis f.sp. tritici (Pgt) in East Africa, Europe, and the Mediterranean basin. Since 2018, sporadic infections have been observed in Tunisia. In this study, we investigated Pgt occurrence at major Tunisian wheat growing areas. Pgt monitoring, assessment, and sampling from planted trap nurseries at five different locations over two years (2021 and 2022) revealed the predominance of three races, namely TTRTF (Clade III-B), TKKTF (Clade IV-F), and TKTTF (Clade IV-B). Clade III-B was the most prevalent in 2021 as it was detected at all locations, while in 2022 Pgt was only reported at Beja and Jendouba, with the prevalence of Clade IV-B. The low levels of disease incidence during these two years and Pgt population diversity suggest that this fungus most likely originated from exotic incursions and that climate factors could have caused disease establishment in Tunisia. Further evaluation under the artificial disease pressure of Tunisian wheat varieties and weather-based modeling for early disease detection in the Mediterranean area could be helpful in monitoring and predicting wheat stem rust emergence and epidemics.
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Affiliation(s)
- Wided Abdedayem
- National Agronomic Institute of Tunisia (INAT), 43 Avenue Charles Nicolle, Tunis 1002, Tunisia
- CRP Wheat Septoria Precision Phenotyping Platform, Tunis 1082, Tunisia
| | - Mehran Patpour
- Department of Agroecology, Aarhus University, 4200 Slagelse, Denmark
| | - Marwa Laribi
- CRP Wheat Septoria Precision Phenotyping Platform, Tunis 1082, Tunisia
| | | | - Hajer Kouki
- CRP Wheat Septoria Precision Phenotyping Platform, Tunis 1082, Tunisia
| | - Moez Fakhfakh
- Comptoir Multiservices Agricoles, 82, Avenue Louis Brailles, Tunis 1002, Tunisia
| | | | - Amor H. Yahyaoui
- CRP Wheat Septoria Precision Phenotyping Platform, Tunis 1082, Tunisia
- Borlaug Training Foundation, Colorado State University, Fort Collins, CO 80523-1170, USA
| | - Sonia Hamza
- National Agronomic Institute of Tunisia (INAT), 43 Avenue Charles Nicolle, Tunis 1002, Tunisia
| | - Sarrah Ben M’Barek
- CRP Wheat Septoria Precision Phenotyping Platform, Tunis 1082, Tunisia
- Laboratory of ‘Appui à la Durabilité des Systèmes de Production Agricole Dans la Région du Nord-Ouest’, Higher School of Agriculture of Kef (ESAK), Regional Field Crops Research Center of Beja (CRRGC) BP 350, Beja 9000, Tunisia
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24
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Sehgal D, Dhakate P, Ambreen H, Shaik KHB, Rathan ND, Anusha NM, Deshmukh R, Vikram P. Wheat Omics: Advancements and Opportunities. PLANTS (BASEL, SWITZERLAND) 2023; 12:426. [PMID: 36771512 PMCID: PMC9919419 DOI: 10.3390/plants12030426] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/07/2022] [Accepted: 12/14/2022] [Indexed: 06/18/2023]
Abstract
Plant omics, which includes genomics, transcriptomics, metabolomics and proteomics, has played a remarkable role in the discovery of new genes and biomolecules that can be deployed for crop improvement. In wheat, great insights have been gleaned from the utilization of diverse omics approaches for both qualitative and quantitative traits. Especially, a combination of omics approaches has led to significant advances in gene discovery and pathway investigations and in deciphering the essential components of stress responses and yields. Recently, a Wheat Omics database has been developed for wheat which could be used by scientists for further accelerating functional genomics studies. In this review, we have discussed various omics technologies and platforms that have been used in wheat to enhance the understanding of the stress biology of the crop and the molecular mechanisms underlying stress tolerance.
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Affiliation(s)
- Deepmala Sehgal
- International Maize and Wheat Improvement Center (CIMMYT), El Batán, Texcoco 56237, Mexico
- Syngenta, Jealott’s Hill International Research Centre, Bracknell, Berkshire RG42 6EY, UK
| | - Priyanka Dhakate
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110076, India
| | - Heena Ambreen
- School of Life Sciences, University of Sussex, Brighton BN1 9RH, UK
| | - Khasim Hussain Baji Shaik
- Faculty of Agriculture Sciences, Georg-August-Universität, Wilhelmsplatz 1, 37073 Göttingen, Germany
| | - Nagenahalli Dharmegowda Rathan
- Indian Agricultural Research Institute (ICAR-IARI), New Delhi 110012, India
- Corteva Agriscience, Hyderabad 502336, Telangana, India
| | | | - Rupesh Deshmukh
- Department of Biotechnology, Central University of Haryana, Mahendragarh 123031, Haryana, India
| | - Prashant Vikram
- Bioseed Research India Ltd., Hyderabad 5023324, Telangana, India
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25
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Kwiatek MT, Noweiska A, Bobrowska R, Czapiewska A, Aygün M, Munyamahoro FD, Mikołajczyk S, Tomkowiak A, Kurasiak-Popowska D, Poślednik P. Novel Tetraploid Triticale (Einkorn Wheat × Rye)-A Source of Stem Rust Resistance. PLANTS (BASEL, SWITZERLAND) 2023; 12:278. [PMID: 36678992 PMCID: PMC9865463 DOI: 10.3390/plants12020278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/15/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
Among cereals, triticale (×Trititcoseale Wittmack ex A. Camus) represents a number of advantages such as high grain yield even in marginal environments, tolerance to drought, cold and acid soils, as well as lower production costs. Together with high biomass of grain and straw, triticale is also considered as an industrial energy crop. As an artificial hybrid, it has not evolved naturally, which is reflected in narrow genetic diversity causing a resistance collapse in recent years. Here, we describe a novel, synthetic tetraploid triticale, which was developed by the crossing of rye (Secale cereale L.) with einkorn wheat (Triticum monococcum spp. monococcum), which possess Sr35 stem rust resistance gene. Three subsequent generations of alloploids were obtained by chromosome doubling followed by self-pollination. The cytogenetic analyses revealed that the amphiploids possess a set of 28 chromosomes (14 of Am-genome and 14 of R-genome). The values of the most important yield-shaping traits for these tetraploid triticale form, including thousand-grain weight, plant height and stem length were higher compared to parental genotypes, as well as standard hexaploid triticale cultivars. This study shows that this tetraploid triticale genetic stock can be an interesting pre-breeding germplasm for triticale improvement or can be developed as a new alternative crop.
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Affiliation(s)
- Michał T. Kwiatek
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland
| | - Aleksandra Noweiska
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland
| | - Roksana Bobrowska
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland
| | - Adrianna Czapiewska
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland
| | - Mert Aygün
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland
| | | | - Sylwia Mikołajczyk
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland
| | - Agnieszka Tomkowiak
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland
| | - Danuta Kurasiak-Popowska
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland
| | - Paweł Poślednik
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland
- Agricultural Research Station, Poznań University of Life Sciences, Dłoń 4, 63-912 Miejska Górka, Poland
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26
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Evdokimov MG, Yusov VS, Kiryakova MN, Meshkova LV, Pakhotina IV, Glushakov DA. Promising genetic sources for the creation of varieties of durum spring wheat in Western Siberia. Vavilovskii Zhurnal Genet Selektsii 2022; 26:609-621. [PMID: 36532626 PMCID: PMC9727540 DOI: 10.18699/vjgb-22-75] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 07/13/2022] [Accepted: 07/29/2022] [Indexed: 03/14/2024] Open
Abstract
The study, expansion and preservation of the genetic diversity of the source material, and its purposeful use in hybridization is the basis for the creation of adaptive varieties of durum spring wheat that are resistant to biotic and abiotic factors of the environment of Western Siberia. The objects of research were samples of durum spring wheat. Over the years of research (2000-2020), about 3 thousand samples were worked out from the world gene pool of various countries and regions: from the collection of the VIR, the gene pool from Mexico (CIMMYT) within the framework of the agreement and cooperation program (2000-2007), from 2000 to the present time under the program of the Kazakh-Siberian Spring Wheat Breeding Network (KASIB), from other scientif ic institutions of Russia in exchange activities. Using generally accepted techniques, the obtained material was studied for a complex of traits: yield, adaptability, grain quality, resistance to diseases. In the cycle of studying the gene pool from CIMMYT, 50 genotypes were identif ied in terms of yield at the level of the Omskaja jantarnaja standard, 276 grains by test weight, 131 samples by pasta color, 131 samples by resistance to hard smut, and 112 by resistance to powdery mildew. Almost all samples were not affected by leaf rust. The study set showed high sensitivity to extreme conditions and most forms of interest in quality and disease resistance were low-productive in our environment. In KASIB nurseries, 29 samples were identif ied in terms of yield and adaptability, 29 samples in terms of grain quality, 21 in terms of resistance to diseases, including 8 resistant to stem rust. In the set of varieties received from the VIR, 15 genotypes were adaptive, 16 had high grain quality, 11 were resistant to stem rust. In the breeding material, 17 samples of the local population resistant to stem rust (6 of them were comprehensively resistant) and 25 race-resistant to Ug99 were identif ied. The genotypes identif ied as a result of research are of interest as sources of valuable traits.
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Affiliation(s)
| | - V S Yusov
- Omsk Agrarian Scientific Center, Omsk, Russia
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27
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Olivera PD, Szabo LJ, Kokhmetova A, Morgounov A, Luster DG, Jin Y. Puccinia graminis f. sp. tritici Population Causing Recent Wheat Stem Rust Epidemics in Kazakhstan Is Highly Diverse and Includes Novel Virulence Pathotypes. PHYTOPATHOLOGY 2022; 112:2403-2415. [PMID: 35671480 DOI: 10.1094/phyto-08-21-0320-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Wheat stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is a reemerging disease that caused severe epidemics in northern Kazakhstan and western Siberia in the period of 2015 to 2019. We analyzed 51 stem rust samples collected between 2015 and 2017 in five provinces in Kazakhstan. A total of 112 Pgt races were identified from 208 single-pustule isolates. These races are phenotypically and genotypically diverse, and most of them are likely of sexual origin. No differentiation of phenotypes and single-nucleotide polymorphism genotypes was observed between isolates from Akmola and North Kazakhstan provinces, supporting the idea of a wide dispersal of inoculum in the northern regions of the country. Similarities in virulence profiles with Pgt races previously reported in Siberia, Russia, suggest that northern Kazakhstan and western Siberia constitute a single stem rust epidemiological region. In addition to the races of sexual origin, six races reported in Europe, the Caucasus, and East Africa were detected in Kazakhstan, indicating that this epidemiological region is not isolated, and spore inflow from the west occurs. Virulence alone or in combination to several genes effective against the Ug99 race group was detected, including novel virulence on Sr32 + Sr40 and Sr47. The occurrence of a highly diverse Pgt population with virulence to an important group of Sr genes demonstrated the importance of the pathogen's sexual cycle in generating new and potentially damaging virulence combinations.
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Affiliation(s)
- P D Olivera
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - L J Szabo
- USDA-ARS Cereal Disease Laboratory, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - A Kokhmetova
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
| | - A Morgounov
- International Maize and Wheat Improvement Center (CIMMYT), Ankara, Turkey
| | - D G Luster
- USDA-ARS Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD 21702, U.S.A
| | - Y Jin
- USDA-ARS Cereal Disease Laboratory, University of Minnesota, St. Paul, MN 55108, U.S.A
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28
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Sharma JS, McCartney CA, McCallum BD, Hiebert CW. Fine mapping and marker development for the wheat leaf rust resistance gene Lr32. G3 (BETHESDA, MD.) 2022; 13:6762863. [PMID: 36255270 PMCID: PMC9911047 DOI: 10.1093/g3journal/jkac274] [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: 11/06/2022]
Abstract
Wheat leaf rust is caused by the fungal pathogen Puccinia triticina and is one of the wheat diseases of concern globally. Among the known leaf rust resistance genes (Lr) genes, Lr32 is a broadly effective gene derived from the diploid species Aegilops tauschii coss. accession RL5497-1 and has been genetically mapped to chromosome arm 3DS. However, Lr32 resistance has not been utilized in current cultivars in part due to the lack of modern, predictive DNA markers. The goals of this study were to fine map the Lr32 region and develop SNP-based kompetitive allele-specific polymerase chain reaction markers. The genomic analysis was conducted by using doubled haploid and F2-derived mapping populations. For marker development, a 90K wheat chip array, 35K and 820K Axiom R SNPs, A. tauschii pseudomolecules v4.0 and International Wheat Genome Sequencing Consortium ReqSeq v2.1 reference genomes were used. Total 28 kompetitive allele-specific polymerase chain reaction and 2 simple sequence repeat markers were developed. The Lr32 region was fine mapped between kompetitive allele-specific polymerase chain reaction markers Kwh142 and Kwh355 that flanked 34-35 Mb of the diploid and hexaploid reference genomes. Leaf rust resistance mapped as a Mendelian trait that cosegregated with 20 markers, recombination restriction limited the further resolution of the Lr32 region. A total of 10-11 candidate genes associated with disease resistance were identified between the flanking regions on both reference genomes, with the majority belonging to the nucleotide-binding domain and leucine-rich repeat gene family. The validation analysis selected 2 kompetitive allele-specific polymerase chain reaction markers, Kwh147 and Kwh722, for marker-assisted selection. The presence of Lr32 along with other Lr genes such as Lr67 and Lr34 would increase the resistance in future wheat breeding lines and have a high impact on controlling wheat leaf rust.
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Affiliation(s)
- Jyoti Saini Sharma
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, Morden, MB R6M 1Y5, Canada
| | - Curt A McCartney
- Department of Plant Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Brent D McCallum
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, Morden, MB R6M 1Y5, Canada
| | - Colin W Hiebert
- Corresponding author: Agriculture and Agri-Food Canada, Morden Research and Development Centre, 101 Route 100, Morden, MB R6M 1Y5, Canada.
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29
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Karelov A, Kozub N, Sozinova O, Pirko Y, Sozinov I, Yemets A, Blume Y. Wheat Genes Associated with Different Types of Resistance against Stem Rust ( Puccinia graminis Pers.). Pathogens 2022; 11:pathogens11101157. [PMID: 36297214 PMCID: PMC9608978 DOI: 10.3390/pathogens11101157] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/25/2022] [Accepted: 10/05/2022] [Indexed: 11/13/2022] Open
Abstract
Stem rust is one wheat's most dangerous fungal diseases. Yield losses caused by stem rust have been significant enough to cause famine in the past. Some races of stem rust are considered to be a threat to food security even nowadays. Resistance genes are considered to be the most rational environment-friendly and widely used way to control the spread of stem rust and prevent yield losses. More than 60 genes conferring resistance against stem rust have been discovered so far (so-called Sr genes). The majority of the Sr genes discovered have lost their effectiveness due to the emergence of new races of stem rust. There are some known resistance genes that have been used for over 50 years and are still effective against most known races of stem rust. The goal of this article is to outline the different types of resistance against stem rust as well as the effective and noneffective genes, conferring each type of resistance with a brief overview of their origin and usage.
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Affiliation(s)
- Anatolii Karelov
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 04123 Kyiv, Ukraine
- Institute of Plant Protection, National Academy of Agrarian Sciences of Ukraine, 03022 Kyiv, Ukraine
- Correspondence: (A.K.); (Y.B.)
| | - Natalia Kozub
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 04123 Kyiv, Ukraine
- Institute of Plant Protection, National Academy of Agrarian Sciences of Ukraine, 03022 Kyiv, Ukraine
| | - Oksana Sozinova
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 04123 Kyiv, Ukraine
- Institute of Plant Protection, National Academy of Agrarian Sciences of Ukraine, 03022 Kyiv, Ukraine
| | - Yaroslav Pirko
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 04123 Kyiv, Ukraine
| | - Igor Sozinov
- Institute of Plant Protection, National Academy of Agrarian Sciences of Ukraine, 03022 Kyiv, Ukraine
| | - Alla Yemets
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 04123 Kyiv, Ukraine
| | - Yaroslav Blume
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 04123 Kyiv, Ukraine
- Correspondence: (A.K.); (Y.B.)
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Megerssa SH, Ammar K, Acevedo M, Bergstrom GC, Dreisigacker S, Randhawa M, Brown-Guedira G, Ward B, Sorrells ME. QTL mapping of seedling and field resistance to stem rust in DAKIYE/Reichenbachii durum wheat population. PLoS One 2022; 17:e0273993. [PMID: 36201474 PMCID: PMC9536579 DOI: 10.1371/journal.pone.0273993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 08/19/2022] [Indexed: 11/18/2022] Open
Abstract
Stem rust caused by the fungus Puccinia graminis f.sp. tritici Eriks. & E. Henn. (Pgt) threatens the global production of both durum wheat (Triticum turgidum L. ssp. durum (Desf.) Husnot) and common wheat (Triticum aestivum L.). The objective of this study was to evaluate a durum wheat recombinant inbred line (RIL) population from a cross between a susceptible parent 'DAKIYE' and a resistant parent 'Reichenbachii' developed by the International Center for the Improvement of Maize and Wheat (CIMMYT) 1) for seedling response to races JRCQC and TTRTF and 2) for field response to a bulk of the current Pgt races prevalent in Ethiopia and Kenya and 3) to map loci associated with seedling and field resistances in this population. A total of 224 RILs along with their parents were evaluated at the seedling stage in the Ethiopian Institute for Agricultural Research greenhouse at Debre Zeit, Ethiopia and in the EIAR and KALRO fields in Ethiopia and Kenya, for two seasons from 2019 to 2020. The lines were genotyped using the genotyping-by-sequencing approach. A total of 843 single nucleotide polymorphism markers for 175 lines were used for quantitative trait locus (QTL) analyses. Composite interval mapping (CIM) identified three QTL on chromosomes 3B, 4B and 7B contributed by the resistant parent. The QTL on chromosome 3B was identified at all growth stages and it explained 11.8%, 6.5%, 6.4% and 15.3% of the phenotypic variation for responses to races JRCQC, TTRTF and in the field trials ETMS19 and KNMS19, respectively. The power to identify additional QTL in this population was limited by the number of high-quality markers, since several markers with segregation distortion were eliminated. A cytological study is needed to understand the presence of chromosomal rearrangements. Future evaluations of additional durum lines and RIL families identification of durable adult plant resistance sources is crucial for breeding stem rust resistance in durum wheat in the future.
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Affiliation(s)
- Shitaye Homma Megerssa
- Ethiopian Institute of Agricultural (EIAR), Addis Ababa, Ethiopia
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States of America
- * E-mail:
| | - Karim Ammar
- International Maize and Wheat Improvement Center (CIMMYT), Mexico D. F., Mexico
| | - Maricelis Acevedo
- Department of Global Development, Cornell University, Ithaca, NY, United States of America
| | - Gary Carlton Bergstrom
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY, United States of America
| | | | - Mandeep Randhawa
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | | | - Brian Ward
- USDA-ARS Plant Science Unit, Raleigh, NC, United States of America
| | - Mark Earl Sorrells
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States of America
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31
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Kozub NO, Sozinov IO, Bidnyk HY, Demianova NO, Sozinova OI, Karelov AV, Borzykh OI, Blume YB. Identification of Genotypes with Recombinant Arm 1RS In Bread Wheat Segregating F5 Populations from Crosses Between Carriers of 1BL.1RS and 1AL.1RS. CYTOL GENET+ 2022. [DOI: 10.3103/s0095452722050061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Geographical Correlation and Genetic Diversity of Newly Emerged Races within the Ug99 Lineage of Stem Rust Pathogen, Puccinia graminis f. sp. tritici, in Different Wheat-Producing Areas. J Fungi (Basel) 2022; 8:jof8101041. [PMID: 36294606 PMCID: PMC9605546 DOI: 10.3390/jof8101041] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/02/2022] [Accepted: 09/26/2022] [Indexed: 11/17/2022] Open
Abstract
Wheat stem rust caused by Puccinia graminis f. sp. tritici is one of the most destructive wheat diseases worldwide. Identifying stem rust races in general, Ug99 lineage particularly, and determining resistance genes are critical goals for disease assessment. Thirty wheat varieties and monogenic lines with major stem rust resistance genes (Sr) were examined here over the course of three succeeding seasons from 2020 to 2022. Fourteen stem rust races have been identified in ten African countries, as well as Central and West Asia and North Africa (CWANA) and ten European countries. The Ug99 group (Clade I) included four races (TTKSK, TTKST, TTKTK, and TTKTT) and was reported in five African countries (Egypt, Kenya, Rwanda, Tanzania, and Uganda) and Iran, but none of the European countries. On the other hand, none of the races in Clade III-B (TTRTF) and Clade IV-B (TKTTF and TTTTF) were found in Egypt. Furthermore, Egyptian races were clustered separately from races identified from other countries, and six races were found only in Egypt, including PKSTC, RKTTH, TKTTC, TTTSK, TCKTC, and TKTTH. Races from Kenya, Tanzania, Uganda, Rwanda, and Iran were all closely associated with one another, according to correlation analysis. However, most races identified from other investigated regions, including Eritrea, Spain, Ethiopia, Morocco, Italy, Poland, Kenya, Tanzania, and Uganda, were adversely linked with Egyptian races. The diagnostic 350 bp long PCR fragment linked with virulence to Sr31, Clement (Sr31), and Brigardier (Sr31) was used to identify the TTKSK (Ug99) race. The identification of the regional associations and genetic diversity of newly emerged races within the Ug99 lineage of P. graminis tritici in Africa, Asia, and Europe is one of the key goals of this study. It will help plant breeders to develop new resistant lines against the virulent races, especially TTKSK (Ug99) and TTTSK. This helps in ensuring global food security in the context of climate change.
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Wheat genomic study for genetic improvement of traits in China. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1718-1775. [PMID: 36018491 DOI: 10.1007/s11427-022-2178-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/10/2022] [Indexed: 01/17/2023]
Abstract
Bread wheat (Triticum aestivum L.) is a major crop that feeds 40% of the world's population. Over the past several decades, advances in genomics have led to tremendous achievements in understanding the origin and domestication of wheat, and the genetic basis of agronomically important traits, which promote the breeding of elite varieties. In this review, we focus on progress that has been made in genomic research and genetic improvement of traits such as grain yield, end-use traits, flowering regulation, nutrient use efficiency, and biotic and abiotic stress responses, and various breeding strategies that contributed mainly by Chinese scientists. Functional genomic research in wheat is entering a new era with the availability of multiple reference wheat genome assemblies and the development of cutting-edge technologies such as precise genome editing tools, high-throughput phenotyping platforms, sequencing-based cloning strategies, high-efficiency genetic transformation systems, and speed-breeding facilities. These insights will further extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process, ultimately contributing to more sustainable agriculture in China and throughout the world.
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Szabo LJ, Olivera PD, Wanyera R, Visser B, Jin Y. Development of a Diagnostic Assay for Differentiation Between Genetic Groups in Clades I, II, III, and IV of Puccinia graminis f. sp. tritici. PLANT DISEASE 2022; 106:2211-2220. [PMID: 35072510 DOI: 10.1094/pdis-10-21-2161-re] [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] [Indexed: 05/26/2023]
Abstract
Wheat stem rust has reemerged as a serious disease caused by new variants of Puccinia graminis f. sp. tritici. Variants with significant virulence and broad geographic distribution (Africa, Central Asia, and Europe) include the Ug99 race group, race TTRTF, and TKTTF race group. Genetic analysis has placed isolates representing these critical new virulent races into 12 genetic groups that make up clades I to IV. Development of molecular diagnostic assays for these 12 genetic groups will be an important component of global surveillance efforts. A single-nucleotide polymorphism database was mined for candidate markers that would differentiate between these 12 genetic groups. Thirty-five candidate markers were screened, and a core set of 17 markers was tested against a set of 94 isolates representing a broad range of genotypes and race phenotypes. These core markers were 100% accurate in identifying the 12 genetic groups for 52 isolates in clades I to IV, and no false positives were observed with nontarget isolates. The assay has built-in redundancy so that minor genetic changes or errors in genotyping calling will not affect the accuracy of the results. This assay is also effective in identifying the genetic groups in clade V from Germany and Georgia, the three main subgroups in North American clade VI, and clade VII consisting of race TTTTF found in North and South America. This assay provides a rapid diagnostic tool for both living and nonliving samples to detect these critical new races or race groups of P. graminis f. sp. tritici.[Formula: see text] Copyright © 2022 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)
- Les J Szabo
- USDA ARS Cereal Disease Laboratory, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Pablo D Olivera
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Ruth Wanyera
- Kenya Agricultural and Livestock Research Organization, Njoro 20107, Kenya
| | - Botma Visser
- Department of Plant Sciences, University of Free State, Bloemfontein 9300, South Africa
| | - Yue Jin
- USDA ARS Cereal Disease Laboratory, University of Minnesota, St. Paul, MN 55108, U.S.A
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Genievskaya Y, Pecchioni N, Laidò G, Anuarbek S, Rsaliyev A, Chudinov V, Zatybekov A, Turuspekov Y, Abugalieva S. Genome-Wide Association Study of Leaf Rust and Stem Rust Seedling and Adult Resistances in Tetraploid Wheat Accessions Harvested in Kazakhstan. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11151904. [PMID: 35893608 PMCID: PMC9329756 DOI: 10.3390/plants11151904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/13/2022] [Accepted: 07/20/2022] [Indexed: 05/05/2023]
Abstract
Leaf rust (LR) and stem rust (SR) are diseases increasingly impacting wheat production worldwide. Fungal pathogens producing rust diseases in wheat may cause yield losses of up to 50−60%. One of the most effective methods for preventing such losses is the development of resistant cultivars with high yield potential. This goal can be achieved through complex breeding studies, including the identification of key genetic factors controlling rust disease resistance. The objective of this study was to identify sources of tetraploid wheat resistance to LR and SR races, both at the seedling growth stage in the greenhouse and at the adult plant stage in field experiments, under the conditions of the North Kazakhstan region. A panel consisting of 193 tetraploid wheat accessions was used in a genome-wide association study (GWAS) for the identification of quantitative trait loci (QTLs) associated with LR and SR resistance, using 16,425 polymorphic single-nucleotide polymorphism (SNP) markers in the seedling and adult stages of plant development. The investigated panel consisted of seven tetraploid subspecies (Triticum turgidum ssp. durum, ssp. turanicum, ssp. turgidum, ssp. polonicum, ssp. carthlicum, ssp. dicoccum, and ssp. dicoccoides). The GWAS, based on the phenotypic evaluation of the tetraploid collection’s reaction to the two rust species at the seedling (in the greenhouse) and adult (in the field) stages, revealed 38 QTLs (p < 0.001), comprising 17 for LR resistance and 21 for SR resistance. Ten QTLs were associated with the reaction to LR at the seedling stage, while six QTLs were at the adult plant stage and one QTL was at both the seedling and adult stages. Eleven QTLs were associated with SR response at the seedling stage, while nine QTLs were at the adult plant stage and one QTL was at both the seedling and adult stages. A comparison of these results with previous LR and SR studies indicated that 11 of the 38 QTLs are presumably novel loci. The QTLs identified in this work can potentially be used for marker-assisted selection of tetraploid and hexaploid wheat for the breeding of new LR- and SR-resistant cultivars.
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Affiliation(s)
- Yuliya Genievskaya
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (Y.G.); (S.A.); (A.Z.); (Y.T.)
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Nicola Pecchioni
- Research Centre for Cereal and Industrial Crops, 71122 Foggia, Italy; (N.P.); (G.L.)
| | - Giovanni Laidò
- Research Centre for Cereal and Industrial Crops, 71122 Foggia, Italy; (N.P.); (G.L.)
| | - Shynar Anuarbek
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (Y.G.); (S.A.); (A.Z.); (Y.T.)
| | - Aralbek Rsaliyev
- Laboratory of Phytosanitary Safety, Research Institute of Biological Safety Problems, Gvardeisky 080409, Kazakhstan;
| | - Vladimir Chudinov
- Breeding Department, Karabalyk Agricultural Experimental Station, Nauchnoe 110908, Kazakhstan;
| | - Alibek Zatybekov
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (Y.G.); (S.A.); (A.Z.); (Y.T.)
| | - Yerlan Turuspekov
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (Y.G.); (S.A.); (A.Z.); (Y.T.)
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Saule Abugalieva
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (Y.G.); (S.A.); (A.Z.); (Y.T.)
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
- Correspondence: ; Tel.: +7-727-394-8006
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Kumar S, Jacob SR, Mir RR, Vikas VK, Kulwal P, Chandra T, Kaur S, Kumar U, Kumar S, Sharma S, Singh R, Prasad S, Singh AM, Singh AK, Kumari J, Saharan MS, Bhardwaj SC, Prasad M, Kalia S, Singh K. Indian Wheat Genomics Initiative for Harnessing the Potential of Wheat Germplasm Resources for Breeding Disease-Resistant, Nutrient-Dense, and Climate-Resilient Cultivars. Front Genet 2022; 13:834366. [PMID: 35846116 PMCID: PMC9277310 DOI: 10.3389/fgene.2022.834366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 05/09/2022] [Indexed: 11/13/2022] Open
Abstract
Wheat is one of the major staple cereal food crops in India. However, most of the wheat-growing areas experience several biotic and abiotic stresses, resulting in poor quality grains and reduced yield. To ensure food security for the growing population in India, there is a compelling need to explore the untapped genetic diversity available in gene banks for the development of stress-resistant/tolerant cultivars. The improvement of any crop lies in exploring and harnessing the genetic diversity available in its genetic resources in the form of cultivated varieties, landraces, wild relatives, and related genera. A huge collection of wheat genetic resources is conserved in various gene banks across the globe. Molecular and phenotypic characterization followed by documentation of conserved genetic resources is a prerequisite for germplasm utilization in crop improvement. The National Genebank of India has an extensive and diverse collection of wheat germplasm, comprising Indian wheat landraces, primitive cultivars, breeding lines, and collection from other countries. The conserved germplasm can contribute immensely to the development of wheat cultivars with high levels of biotic and abiotic stress tolerance. Breeding wheat varieties that can give high yields under different stress environments has not made much headway due to high genotypes and environmental interaction, non-availability of truly resistant/tolerant germplasm, and non-availability of reliable markers linked with the QTL having a significant impact on resistance/tolerance. The development of new breeding technologies like genomic selection (GS), which takes into account the G × E interaction, will facilitate crop improvement through enhanced climate resilience, by combining biotic and abiotic stress resistance/tolerance and maximizing yield potential. In this review article, we have summarized different constraints being faced by Indian wheat-breeding programs, challenges in addressing biotic and abiotic stresses, and improving quality and nutrition. Efforts have been made to highlight the wealth of Indian wheat genetic resources available in our National Genebank and their evaluation for the identification of trait-specific germplasm. Promising genotypes to develop varieties of important targeted traits and the development of different genomics resources have also been highlighted.
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Affiliation(s)
- Sundeep Kumar
- Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
- *Correspondence: Sundeep Kumar,
| | - Sherry R. Jacob
- Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-Kashmir), Jammu and Kashmir, India
| | - V. K. Vikas
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Pawan Kulwal
- State Level Biotechnology Centre, Mahatma Phule Krishi Vidyapeeth, Rahuri, India
| | - Tilak Chandra
- Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Satinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Uttam Kumar
- Borlaug Institute for South Asia, Ludhiana, India
| | - Suneel Kumar
- Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Shailendra Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, Uttar Pradesh
| | - Ravinder Singh
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu (SKUAST-Jammu), Jammu and Kashmir, India
| | - Sai Prasad
- Indian Agriculture Research Institute Regional Research Station, Indore, India
| | - Anju Mahendru Singh
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
| | - Amit Kumar Singh
- Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Jyoti Kumari
- Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - M. S. Saharan
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | | | - Manoj Prasad
- Laboratory of Plant Virology, National Institute of Plant Genome Research, New Delhi, India
| | - Sanjay Kalia
- Department of Biotechnology, Ministry of Science and Technology, New Delhi, India
| | - Kuldeep Singh
- Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
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Salotti I, Bove F, Rossi V. Development and Validation of a Mechanistic, Weather-Based Model for Predicting Puccinia graminis f. sp. tritici Infections and Stem Rust Progress in Wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:897680. [PMID: 35693159 PMCID: PMC9184802 DOI: 10.3389/fpls.2022.897680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/09/2022] [Indexed: 05/09/2023]
Abstract
Stem rust (or black rust) of wheat, caused by Puccinia graminis f. sp. tritici (Pgt), is a re-emerging, major threat to wheat production worldwide. Here, we retrieved, analyzed, and synthetized the available information about Pgt to develop a mechanistic, weather-driven model for predicting stem rust epidemics caused by uredospores. The ability of the model to predict the first infections in a season was evaluated using field data collected in three wheat-growing areas of Italy (Emilia-Romagna, Apulia, and Sardinia) from 2016 to 2021. The model showed good accuracy, with a posterior probability to correctly predict infections of 0.78 and a probability that there was no infection when not predicted of 0.96. The model's ability to predict disease progress during the growing season was also evaluated by using published data obtained from trials in Minnesota, United States, in 1968, 1978, and 1979, and in Pennsylvania, United States, in 1986. Comparison of observed versus predicted data generated a concordance correlation coefficient of 0.96 and an average distance between real data and the fitted line of 0.09. The model could therefore be considered accurate and reliable for predicting epidemics of wheat stem rust and could be tested for its ability to support risk-based control of the disease.
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Affiliation(s)
- Irene Salotti
- Department of Sustainable Crop Production (DI.PRO.VES.), Università Cattolica del Sacro Cuore, Piacenza, Italy
| | | | - Vittorio Rossi
- Department of Sustainable Crop Production (DI.PRO.VES.), Università Cattolica del Sacro Cuore, Piacenza, Italy
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Mago R, Chen C, Xia X, Whan A, Forrest K, Basnet BR, Perera G, Chandramohan S, Randhawa M, Hayden M, Bansal U, Huerta-Espino J, Singh RP, Bariana H, Lagudah E. Adult plant stem rust resistance in durum wheat Glossy Huguenot: mapping, marker development and validation. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1541-1550. [PMID: 35199199 DOI: 10.1007/s00122-022-04052-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 01/28/2022] [Indexed: 05/12/2023]
Abstract
Adult plant stem rust resistance locus, QSrGH.cs-2AL, was identified in durum wheat Glossy Huguenot and mendelised as Sr63. Markers closely linked with Sr63 were developed. An F3 population from a Glossy Huguenot (GH)/Bansi cross used in a previous Australian study was advanced to F6 for molecular mapping of adult plant stem rust resistance. Maturity differences among F6 lines confounded assessments of stem rust response. GH was crossed with a stem rust susceptible F6 recombinant inbred line (RIL), GHB14 (M14), with similar maturity and an F6:7 population was developed through single seed descent method. F7 and F8 RILs were tested along with the parents at different locations. The F6 individual plants and both parents were genotyped using the 90 K single nucleotide polymorphism (SNP) wheat array. Stem rust resistance QTL on the long arms of chromosomes 1B (QSrGH.cs-1BL) and 2A (QSrGH.cs-2AL) were detected. QSrGH.cs-1BL and QSrGH.cs-2AL were both contributed by GH and explained 22% and 18% adult plant stem rust response variation, respectively, among GH/M14 RIL population. RILs carrying combinations of these QTL reduced more than 14% stem rust severity compared to those that possessed QSrGH.cs-1BL and QSrGH.cs-2AL individually. QSrGH.cs1BL was demonstrated to be the same as Sr58/Lr46/Yr29/Pm39 through marker genotyping. Lines lacking QSrGH.cs-1BL were used to Mendelise QSrGH.cs-2AL. Based on genomic locations of previously catalogued stem rust resistance genes and the QSrGH.cs-2AL map, it appeared to represent a new APR locus and was permanently named Sr63. SNP markers associated with Sr63 were converted to kompetetive allele-specific PCR (KASP) assays and were validated on a set of durum cultivars.
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Affiliation(s)
- Rohit Mago
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT, 2601, Australia.
| | - Chunhong Chen
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT, 2601, Australia
| | - Xiaodi Xia
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT, 2601, Australia
| | - Alex Whan
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT, 2601, Australia
| | - Kerrie Forrest
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, Agribio, 5 Ring Rd, Bundoora, VIC, 3083, Australia
| | - Bhoja R Basnet
- CIMMYT, Carretera Mexico-Veracruz Km 18, El Batan, Texcoco, Estado de México, Mexico
| | - Geetha Perera
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT, 2601, Australia
| | - Sutha Chandramohan
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT, 2601, Australia
| | - Mandeep Randhawa
- ICRAF House, CIMMYT Kenya, United Nations Avenue, Gigiri, Village Market, P.O. Box 1041, 00621, Nairobi, Kenya
| | - Matthew Hayden
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, Agribio, 5 Ring Rd, Bundoora, VIC, 3083, Australia
| | - Urmil Bansal
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia
| | - Julio Huerta-Espino
- Campo Experimental Valle de México, INIFAP, Chapingo, Estado de México, Mexico
| | - Ravi P Singh
- CIMMYT, Carretera Mexico-Veracruz Km 18, El Batan, Texcoco, Estado de México, Mexico
| | - Harbans Bariana
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney Plant Breeding Institute, 107 Cobbitty Road, Cobbitty, NSW, 2570, Australia.
| | - Evans Lagudah
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT, 2601, Australia.
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Reynolds MP, Slafer GA, Foulkes JM, Griffiths S, Murchie EH, Carmo-Silva E, Asseng S, Chapman SC, Sawkins M, Gwyn J, Flavell RB. A wiring diagram to integrate physiological traits of wheat yield potential. NATURE FOOD 2022; 3:318-324. [PMID: 37117579 DOI: 10.1038/s43016-022-00512-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 04/08/2022] [Indexed: 04/30/2023]
Abstract
As crop yields are pushed closer to biophysical limits, achieving yield gains becomes increasingly challenging and will require more insight into deterministic pathways to yields. Here, we propose a wiring diagram as a platform to illustrate the interrelationships of the physiological traits that impact wheat yield potential and to serve as a decision support tool for crop scientists. The wiring diagram is based on the premise that crop yield is a function of photosynthesis (source), the investment of assimilates into reproductive organs (sinks) and the underlying processes that enable expression of both. By illustrating these linkages as coded wires, the wiring diagram can show connections among traits that may not have been apparent, and can inform new research hypotheses and guide crosses designed to accumulate beneficial traits and alleles in breeding. The wiring diagram can also serve to create an ever-richer common point of reference for refining crop models in the future.
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Affiliation(s)
| | - Gustavo Ariel Slafer
- Catalonian Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
- Center for Research in Agrotechnology (AGROTECNIO), Lleida, Spain.
- University of Lleida, Lleida, Spain.
| | | | | | | | | | | | | | - Mark Sawkins
- International Wheat Yield Partnership (IWYP), College Station, TX, USA
- Texas A&M AgriLife Research, Weslaco, TX, USA
| | - Jeff Gwyn
- International Wheat Yield Partnership (IWYP), College Station, TX, USA
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Tassi AD, Ramos-González PL, Sinico TE, Kitajima EW, Freitas-Astúa J. Circulative Transmission of Cileviruses in Brevipalpus Mites May Involve the Paracellular Movement of Virions. Front Microbiol 2022; 13:836743. [PMID: 35464977 PMCID: PMC9019602 DOI: 10.3389/fmicb.2022.836743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
Plant viruses transmitted by mites of the genus Brevipalpus are members of the genera Cilevirus, family Kitaviridae, or Dichorhavirus, family Rhabdoviridae. They produce non-systemic infections that typically display necrotic and/or chlorotic lesions around the inoculation loci. The cilevirus citrus leprosis virus C (CiLV-C) causes citrus leprosis, rated as one of the most destructive diseases affecting this crop in the Americas. CiLV-C is vectored in a persistent manner by the flat mite Brevipalpus yothersi. Upon the ingestion of viral particles with the content of the infected plant cell, virions must pass through the midgut epithelium and the anterior podocephalic gland of the mites. Following the duct from this gland, virions reach the salivary canal before their inoculation into a new plant cell through the stylet canal. It is still unclear whether CiLV-C multiplies in mite cells and what mechanisms contribute to its movement through mite tissues. In this study, based on direct observation of histological sections from viruliferous mites using the transmission electron microscope, we posit the hypothesis of the paracellular movement of CiLV-C in mites which may involve the manipulation of septate junctions. We detail the presence of viral particles aligned in the intercellular spaces between cells and the gastrovascular system of Brevipalpus mites. Accordingly, we propose putative genes that could control either active or passive paracellular circulation of viral particles inside the mites.
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Affiliation(s)
- Aline Daniele Tassi
- Laboratório de Biologia Molecular Aplicada, Instituto Biológico, São Paulo, Brazil.,Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo, Piracicaba, Brazil
| | | | - Thais Elise Sinico
- Laboratório de Biologia Molecular Aplicada, Instituto Biológico, São Paulo, Brazil.,Centro de Citricultura Sylvio Moreira, Cordeirópolis, Brazil
| | - Elliot Watanabe Kitajima
- Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo, Piracicaba, Brazil
| | - Juliana Freitas-Astúa
- Laboratório de Biologia Molecular Aplicada, Instituto Biológico, São Paulo, Brazil.,Embrapa Mandioca e Fruticultura, Cruz das Almas, Brazil
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Mallick N, Jha SK, Agarwal P, Mall A, M. N, Kumar S, Choudhary MK, Bansal S, Saharan MS, Sharma JB. Marker-Assisted Improvement of Bread Wheat Variety HD2967 for Leaf and Stripe Rust Resistance. PLANTS (BASEL, SWITZERLAND) 2022; 11:1152. [PMID: 35567153 PMCID: PMC9103291 DOI: 10.3390/plants11091152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/07/2022] [Accepted: 03/11/2022] [Indexed: 06/15/2023]
Abstract
The mega wheat variety HD2967 was improved for leaf and stripe rust resistance by marker-assisted backcross breeding. After its release in 2011, HD2967 became susceptible to stripe rust and moderately susceptible to leaf rust. The leaf rust resistance gene LrTrk was transferred into HD2967 from the durum wheat genotype Trinakria. Then, HD2967 was crossed with Trinakria to produce F1 plant foreground selection for LrTrk and background selection for the recurrent parent genotype was carried out in BC1F1, BC2F1 and BC2F2 generations. Foreground selection was carried out with the linked marker Xgwm234, while polymorphic SSR markers between parents were used for background selection. Background selection resulted in the rapid recovery of the recurrent parent genome. A morphological evaluation of 6 near isogenic lines (NILs)-2 resistant to leaf and stripe rust, and 4 resistant to leaf rust only-showed no significant differences in yields among NILs and the recurrent parent HD2967. All of the 6 NILs showed the presence of 2NS/2AS translocation, carrying the linked genes Lr37/Sr38/Yr17 present in HD2967 and the targeted leaf rust resistance gene LrTrk. Two NILs also showed additional resistance to stripe rust. Therefore, these NILs with rust resistance and an at par yielding ability of H2967 can replace the susceptible cultivar HD2967 to reduce yield losses due to disease.
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Affiliation(s)
- Niharika Mallick
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; (S.K.J.); (P.A.); (A.M.); (N.M.); (S.K.); (M.K.C.); (S.B.); (J.B.S.)
| | - Shailendra K. Jha
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; (S.K.J.); (P.A.); (A.M.); (N.M.); (S.K.); (M.K.C.); (S.B.); (J.B.S.)
| | - Priyanka Agarwal
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; (S.K.J.); (P.A.); (A.M.); (N.M.); (S.K.); (M.K.C.); (S.B.); (J.B.S.)
| | - Anchal Mall
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; (S.K.J.); (P.A.); (A.M.); (N.M.); (S.K.); (M.K.C.); (S.B.); (J.B.S.)
- Department of Genetics & Tree Propagation, Forest Research Institute, Dehradun 248006, India
| | - Niranjana M.
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; (S.K.J.); (P.A.); (A.M.); (N.M.); (S.K.); (M.K.C.); (S.B.); (J.B.S.)
| | - Sachin Kumar
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; (S.K.J.); (P.A.); (A.M.); (N.M.); (S.K.); (M.K.C.); (S.B.); (J.B.S.)
| | - Manish K. Choudhary
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; (S.K.J.); (P.A.); (A.M.); (N.M.); (S.K.); (M.K.C.); (S.B.); (J.B.S.)
| | - Shreshtha Bansal
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; (S.K.J.); (P.A.); (A.M.); (N.M.); (S.K.); (M.K.C.); (S.B.); (J.B.S.)
| | - M. S. Saharan
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India;
| | - J. B. Sharma
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; (S.K.J.); (P.A.); (A.M.); (N.M.); (S.K.); (M.K.C.); (S.B.); (J.B.S.)
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Prasad P, Thakur RK, Savadi S, Bhardwaj SC, Gangwar OP, Lata C, Adhikari S, Kumar S. Genetic Diversity and Population Structure Reveal Cryptic Genetic Variation and Long Distance Migration of Puccinia graminis f. sp. tritici in the Indian Subcontinent. Front Microbiol 2022; 13:842106. [PMID: 35495673 PMCID: PMC9044083 DOI: 10.3389/fmicb.2022.842106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/16/2022] [Indexed: 11/29/2022] Open
Abstract
Stem rust caused by Puccinia graminis f. sp. tritici (Pgt) is a devastating disease of wheat worldwide since time immemorial. Several wheat stem rust outbreaks have been reported worldwide including India. Approximately 7 mha wheat area in central and peninsular India is highly vulnerable to stem rust epidemics. In this study, a repository of 29 single genotype uredospore pathotypes, representing five geographical regions, was characterized by investigating their virulence phenotype and simple sequence repeat (SSR) genotypes using 37 reproducible polymorphic SSR markers, 32 of which had ≥ 0.50 polymorphic information content (PIC) value. Virulence phenotypes were used to evaluate the virulence frequency (VF) and construct a hypothetical evolutionary hierarchy of these pathotypes. We projected seven lineages to explain the evolutionary pattern of the Pgt population. The VF of these pathotypes ranged between 0% and 100%. The virulence-based neighbor-joining (NJ) cluster analysis grouped Pgt pathotypes into five virulence groups. Likewise, five molecular groups were categorized using molecular genotypes. The molecular grouping was supported by principal coordinate analysis (PCoA), which revealed 25% of the cumulative variance contributed by the first two axes. Analysis of molecular variance (AMOVA) revealed 8 and 92% of the variation among and within the populations, respectively. The Mantel test confirmed a positive but weak correlation (R 2 = 0.15) between virulence phenotypes and SSR genotypes. The highest and lowest values of different genetic diversity parameters (Na, Ne, I, He, uHe, and %P) revealed maximum and minimum variability in the Pgt population from Maharashtra and Uttar Pradesh, respectively. The population structure analysis clustered 29 Pgt pathotypes into two subpopulations and an admixture. Our results demonstrated that there was significant genetic diversity among Pgt pathotypes resulting from their long-distance dispersal ability complemented by gene flow. These findings provide insights into the virulence patterns, genetic variations, and possible evolution of Pgt pathotypes, which would support strategic stem rust resistance breeding.
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Affiliation(s)
- Pramod Prasad
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | - Rajni Kant Thakur
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | | | | | - Om Prakash Gangwar
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | - Charu Lata
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | - Sneha Adhikari
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | - Subodh Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
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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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Phenotyping Mediterranean Durum Wheat Landraces for Resistance to Zymoseptoria tritici in Tunisia. Genes (Basel) 2022; 13:genes13020355. [PMID: 35205399 PMCID: PMC8872163 DOI: 10.3390/genes13020355] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/21/2022] [Accepted: 02/09/2022] [Indexed: 02/01/2023] Open
Abstract
Durum wheat landraces have huge potential for the identification of genetic factors valuable for improving resistance to biotic stresses. Tunisia is known as a hot spot for Septoria tritici blotch disease (STB), caused by the fungus Zymoseptoria tritici (Z. tritici). In this context, a collection of 3166 Mediterranean durum wheat landraces were evaluated at the seedling and adult stages for STB resistance in the 2016–2017 cropping season under field conditions in Kodia (Tunisia). Unadapted/susceptible accessions were eliminated to reach the final set of 1059 accessions; this was termed the Med-collection, which comprised accessions from 13 countries and was also screened in the 2018–2019 cropping season. The Med-collection showed high frequency of resistance reactions, among which over 50% showed an immune reaction (HR) at both seedling and adult growth stages. Interestingly, 92% of HR and R accessions maintained their resistance levels across the two years, confirming the highly significant correlation found between seedling- and adult-stage reactions. Plant Height was found to have a negative significant effect on adult-stage resistance, suggesting that either this trait can influence disease severity, or that it can be due to environmental/epidemiological factors. Accessions from Italy showed the highest variability, while those from Portugal, Spain and Tunisia showed the highest levels of resistance at both growth stages, suggesting that the latter accessions may harbor novel QTLs effective for STB resistance.
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Shewabez E, Bekele E, Alemu A, Mugnai L, Tadesse W. Genetic characterization and genome-wide association mapping for stem rust resistance in spring bread wheat. BMC Genom Data 2022; 23:11. [PMID: 35164670 PMCID: PMC8845374 DOI: 10.1186/s12863-022-01030-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 01/31/2022] [Indexed: 12/11/2022] Open
Abstract
Background Emerging wheat stem rust races have become a major threat to global wheat production. Finding additional loci responsible for resistance to these races and incorporating them into currently cultivated varieties is the most economic and environmentally sound strategy to combat this problem. Thus, this study was aimed at characterizing the genetic diversity and identifying the genetic loci conferring resistance to the stem rust of wheat. To accomplish this, 245 elite lines introduced from the International Center for Agricultural Research in the Dry Areas (ICARDA) were evaluated under natural stem rust pressure in the field at the Debre Zeit Agricultural Research Center, Ethiopia. The single nucleotide polymorphisms (SNP) marker data was retrieved from a 15 K SNP wheat array. A mixed linear model was used to investigate the association between SNP markers and the best linear unbiased prediction (BLUP) values of the stem rust coefficient of infection (CI). Results Phenotypic analysis revealed that 46% of the lines had a coefficient of infection (CI) in a range of 0 to 19. Genome-wide average values of 0.38, 0.20, and 0.71 were recorded for Nei’s gene diversity, polymorphism information content, and major allele frequency, respectively. A total of 46 marker-trait associations (MTAs) encompassed within eleven quantitative trait loci (QTL) were detected on chromosomes 1B, 3A, 3B, 4A, 4B, and 5A for CI. Two major QTLs with –log10 (p) ≥ 4 (EWYP1B.1 and EWYP1B.2) were discovered on chromosome 1B. Conclusions This study identified several novel markers associated with stem rust resistance in wheat with the potential to facilitate durable rust resistance development through marker-assisted selection. It is recommended that the resistant wheat genotypes identified in this study be used in the national wheat breeding programs to improve stem rust resistance. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-022-01030-4.
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Rauf Y, Bajgain P, Rouse MN, Khanzada KA, Bhavani S, Huerta-Espino J, Singh RP, Imtiaz M, Anderson JA. Molecular Characterization of Genomic Regions for Adult Plant Resistance to Stem Rust in a Spring Wheat Mapping Population. PLANT DISEASE 2022; 106:439-450. [PMID: 34353123 DOI: 10.1094/pdis-03-21-0672-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: 06/13/2023]
Abstract
Adult plant resistance (APR) to wheat stem rust has been one of the approaches for resistance breeding since the evolution of the Ug99 race group and other races. This study was conducted to dissect and understand the genetic basis of APR to stem rust in spring wheat line 'Copio'. A total of 176 recombinant inbred lines (RILs) from the cross of susceptible parent 'Apav' with Copio were phenotyped for stem rust resistance in six environments. Composite interval mapping using 762 genotyping-by-sequencing markers identified 16 genomic regions conferring stem rust resistance. Assays with gene-linked molecular markers revealed that Copio carried known APR genes Sr2 and Lr46/Yr29/Sr58 in addition to the 2NS/2AS translocation that harbors race-specific genes Sr38, Lr37, and Yr17. Three quantitative trait loci (QTLs) were mapped on chromosomes 2B, two QTLs on chromosomes 3A, 3B, and 6A each, and one QTL on each of chromosomes 2A, 1B, 2D, 4B, 5D, 6D, and 7A. The QTL QSr.umn.5D is potentially a new resistance gene and contributed to quantitative resistance in Copio. The RILs with allelic combinations of Sr2, Sr38, and Sr58 had 27 to 39% less stem rust coefficient of infection in all field environments compared with RILs with none of these genes, and this gene combination was most effective in the U.S. environments. We conclude that Copio carries several genes that provide both race-specific and non-race-specific resistance to diverse races of stem rust fungus and can be used by breeding programs in pyramiding other effective genes to develop durable resistance in wheat.
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Affiliation(s)
- Yahya Rauf
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Prabin Bajgain
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Matthew N Rouse
- Cereal Disease Lab, United States Department of Agriculture, St. Paul, MN 55108, U.S.A
| | - Khalil A Khanzada
- Cereal Disease Research Institute, Pakistan Agricultural Research Council, University of Karachi 75270, Pakistan
| | - Sridhar Bhavani
- Global Wheat Program, International Maize and Wheat Improvement Center, Mexico City, 06600, Mexico
| | - Julio Huerta-Espino
- Global Wheat Program, International Maize and Wheat Improvement Center, Mexico City, 06600, Mexico
| | - Ravi P Singh
- Global Wheat Program, International Maize and Wheat Improvement Center, Mexico City, 06600, Mexico
| | - Muhammad Imtiaz
- Global Wheat Program, International Maize and Wheat Improvement Center, National Agricultural Research Center, Islamabad 44000, Pakistan
| | - James A Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, U.S.A
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Upadhaya A, Upadhaya SG, Brueggeman R. The Wheat Stem Rust ( Puccinia graminis f. sp. tritici) Population from Washington Contains the Most Virulent Isolates Reported on Barley. PLANT DISEASE 2022; 106:223-230. [PMID: 34546770 DOI: 10.1094/pdis-06-21-1195-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: 06/13/2023]
Abstract
A diverse sexual population of wheat stem rust, Puccinia graminis f. sp. tritici, exists in the Pacific Northwest region of the United States because of the natural presence of Mahonia spp. that serves as alternate hosts to complete its sexual life cycle. The region appears to be a center of stem rust diversity in North America where novel virulence gene combinations can emerge that could overcome deployed barley and wheat stem rust resistances. A total of 100 single pustule isolates derived from stem rust samples collected from barley in Eastern Washington during the 2019 growing season were assayed for virulence on the two known effective barley stem rust resistance genes/loci, Rpg1 and the rpg4/5-mediated resistance locus (RMRL) at the seedling stage. Interestingly, 99% of the P. graminis f. sp. tritici isolates assayed were virulent on barley variety Morex carrying the Rpg1 gene, and 62% of the isolates were virulent on the variety Golden Promise transformant (H228.2c) that carries a single-copy insertion of the Rpg1 gene from Morex and is more resistant than Morex to many Rpg1 avirulent isolates. Also, 16% of the isolates were virulent on the near isogenic line HQ-1, which carries the RMRL introgression from the barley line Q21861 in the susceptible Harrington background. Alarmingly, 10% of the isolates were virulent on barley line Q21861, which contains both Rpg1 and RMRL. Thus, we report on the first P. graminis f. sp. tritici isolates worldwide with virulence on both Rpg1 and RMRL when stacked together, representing the most virulent P. graminis f. sp. tritici isolates reported on barley.
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Affiliation(s)
- Arjun Upadhaya
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164
| | - Sudha Gc Upadhaya
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164
| | - Robert Brueggeman
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164
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Patpour M, Hovmøller MS, Rodriguez-Algaba J, Randazzo B, Villegas D, Shamanin VP, Berlin A, Flath K, Czembor P, Hanzalova A, Sliková S, Skolotneva ES, Jin Y, Szabo L, Meyer KJG, Valade R, Thach T, Hansen JG, Justesen AF. Wheat Stem Rust Back in Europe: Diversity, Prevalence and Impact on Host Resistance. FRONTIERS IN PLANT SCIENCE 2022; 13:882440. [PMID: 35720526 PMCID: PMC9202592 DOI: 10.3389/fpls.2022.882440] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 05/03/2022] [Indexed: 05/13/2023]
Abstract
The objective of this study was to investigate the re-emergence of a previously important crop pathogen in Europe, Puccinia graminis f.sp. tritici, causing wheat stem rust. The pathogen has been insignificant in Europe for more than 60 years, but since 2016 it has caused epidemics on both durum wheat and bread wheat in local areas in southern Europe, and additional outbreaks in Central- and West Europe. The prevalence of three distinct genotypes/races in many areas, Clade III-B (TTRTF), Clade IV-B (TKTTF) and Clade IV-F (TKKTF), suggested clonal reproduction and evolution by mutation within these. None of these genetic groups and races, which likely originated from exotic incursions, were detected in Europe prior to 2016. A fourth genetic group, Clade VIII, detected in Germany (2013), was observed in several years in Central- and East Europe. Tests of representative European wheat varieties with prevalent races revealed high level of susceptibility. In contrast, high diversity with respect to virulence and Simple Sequence Repeat (SSR) markers were detected in local populations on cereals and grasses in proximity to Berberis species in Spain and Sweden, indicating that the alternate host may return as functional component of the epidemiology of wheat stem rust in Europe. A geographically distant population from Omsk and Novosibirsk in western Siberia (Russia) also revealed high genetic diversity, but clearly different from current European populations. The presence of Sr31-virulence in multiple and highly diverse races in local populations in Spain and Siberia stress that virulence may emerge independently when large geographical areas and time spans are considered and that Sr31-virulence is not unique to Ug99. All isolates of the Spanish populations, collected from wheat, rye and grass species, were succesfully recovered on wheat, which underline the plasticity of host barriers within P. graminis. The study demonstrated successful alignment of two genotyping approaches and race phenotyping methodologies employed by different laboratories, which also allowed us to line up with previous European and international studies of wheat stem rust. Our results suggest new initiatives within disease surveillance, epidemiological research and resistance breeding to meet current and future challenges by wheat stem rust in Europe and beyond.
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Affiliation(s)
- Mehran Patpour
- Department of Agroecology, Aarhus University, Slagelse, Denmark
| | - Mogens S. Hovmøller
- Department of Agroecology, Aarhus University, Slagelse, Denmark
- *Correspondence: Mogens S. Hovmøller,
| | | | - Biagio Randazzo
- Società Semplice Agricola Randazzo (AS.A.R.), Palermo, Italy
| | - Dolors Villegas
- Institute for Food and Agricultural Research and Technology (IRTA), Lleida, Spain
| | | | - Anna Berlin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Science, Uppsala, Sweden
| | - Kerstin Flath
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Field Crops and Grassland, Quedlinburg, Germany
| | - Pawel Czembor
- Plant Breeding & Acclimatization Institute – National Research Institute, Radzików, Poland
| | - Alena Hanzalova
- Department of Genetics and Plant Breeding Methods, Crop Research Institute, Prague, Czechia
| | | | | | - Yue Jin
- USDA-ARS Cereal Disease Laboratory, University of Minnesota, Minneapolis, MN, United States
| | - Les Szabo
- USDA-ARS Cereal Disease Laboratory, University of Minnesota, Minneapolis, MN, United States
| | | | | | - Tine Thach
- Department of Agroecology, Aarhus University, Slagelse, Denmark
| | - Jens G. Hansen
- Department of Agroecology, Aarhus University, Slagelse, Denmark
| | - Annemarie F. Justesen
- Department of Agroecology, Aarhus University, Slagelse, Denmark
- Annemarie F. Justesen,
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50
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Zatybekov A, Genievskaya Y, Rsaliyev A, Maulenbay A, Yskakova G, Savin T, Turuspekov Y, Abugalieva S. Identification of Quantitative Trait Loci for Leaf Rust and Stem Rust Seedling Resistance in Bread Wheat Using a Genome-Wide Association Study. PLANTS (BASEL, SWITZERLAND) 2021; 11:plants11010074. [PMID: 35009078 PMCID: PMC8747073 DOI: 10.3390/plants11010074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/22/2021] [Accepted: 12/22/2021] [Indexed: 05/22/2023]
Abstract
In recent years, leaf rust (LR) and stem rust (SR) have become a serious threat to bread wheat production in Kazakhstan. Most local cultivars are susceptible to these rusts, which has affected their yield and quality. The development of new cultivars with high productivity and LR and SR disease resistance, including using marker-assisted selection, is becoming an important priority in local breeding projects. Therefore, the search for key genetic factors controlling resistance in all plant stages, including the seedling stage, is of great significance. In this work, we applied a genome-wide association study (GWAS) approach using 212 local bread wheat accessions that were phenotyped for resistance to specific races of Puccinia triticina Eriks. (Pt) and Puccinia graminis f. sp. tritici (Pgt) at the seedling stages. The collection was genotyped using a 20 K Illumina iSelect SNP assay, and 11,150 polymorphic SNP markers were selected for the association mapping. Using a mixed linear model, we identified 11 quantitative trait loci (QTLs) for five out of six specific races of Pt and Pgt. The comparison of the results from this GWAS with those from previously published work showed that nine out of eleven QTLs for LR and SR resistance had been previously reported in a GWAS study at the adult plant stages of wheat growth. Therefore, it was assumed that these nine common identified QTLs were effective for all-stage resistance to LR and SR, and the two other QTLs appear to be novel QTLs. In addition, five out of these nine QTLs that had been identified earlier were found to be associated with yield components, suggesting that they may directly influence the field performance of bread wheat. The identified QTLs, including novel QTLs found in this study, may play an essential role in the breeding process for improving wheat resistance to LR and SR.
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Affiliation(s)
- Alibek Zatybekov
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.Z.); (Y.G.); (Y.T.)
| | - Yuliya Genievskaya
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.Z.); (Y.G.); (Y.T.)
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050038, Kazakhstan
| | - Aralbek Rsaliyev
- Laboratory of Phytosanitary Safety, Research Institute of Biological Safety Problems, Gvardeisky 080409, Kazakhstan; (A.R.); (A.M.); (G.Y.)
| | - Akerke Maulenbay
- Laboratory of Phytosanitary Safety, Research Institute of Biological Safety Problems, Gvardeisky 080409, Kazakhstan; (A.R.); (A.M.); (G.Y.)
| | - Gulbahar Yskakova
- Laboratory of Phytosanitary Safety, Research Institute of Biological Safety Problems, Gvardeisky 080409, Kazakhstan; (A.R.); (A.M.); (G.Y.)
| | - Timur Savin
- Department of Science, S. Seifullin Kazakh Agro Technical University, Nur-Sultan 010011, Kazakhstan;
| | - Yerlan Turuspekov
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.Z.); (Y.G.); (Y.T.)
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050038, Kazakhstan
| | - Saule Abugalieva
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.Z.); (Y.G.); (Y.T.)
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050038, Kazakhstan
- Correspondence:
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