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Gupta PK, Vasistha NK, Singh S, Joshi AK. Genetics and breeding for resistance against four leaf spot diseases in wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1023824. [PMID: 37063191 PMCID: PMC10096043 DOI: 10.3389/fpls.2023.1023824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 02/28/2023] [Indexed: 06/19/2023]
Abstract
In wheat, major yield losses are caused by a variety of diseases including rusts, spike diseases, leaf spot and root diseases. The genetics of resistance against all these diseases have been studied in great detail and utilized for breeding resistant cultivars. The resistance against leaf spot diseases caused by each individual necrotroph/hemi-biotroph involves a complex system involving resistance (R) genes, sensitivity (S) genes, small secreted protein (SSP) genes and quantitative resistance loci (QRLs). This review deals with resistance for the following four-leaf spot diseases: (i) Septoria nodorum blotch (SNB) caused by Parastagonospora nodorum; (ii) Tan spot (TS) caused by Pyrenophora tritici-repentis; (iii) Spot blotch (SB) caused by Bipolaris sorokiniana and (iv) Septoria tritici blotch (STB) caused by Zymoseptoria tritici.
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Affiliation(s)
- Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
- Murdoch’s Centre for Crop and Food Innovation, Murdoch University, Murdoch, WA, Australia
- Borlaug Institute for South Asia (BISA), National Agricultural Science Complex (NASC), Dev Prakash Shastri (DPS) Marg, New Delhi, India
| | - Neeraj Kumar Vasistha
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
- Department of Genetics-Plant Breeding and Biotechnology, Dr Khem Singh Gill, Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour, India
| | - Sahadev Singh
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
| | - Arun Kumar Joshi
- Borlaug Institute for South Asia (BISA), National Agricultural Science Complex (NASC), Dev Prakash Shastri (DPS) Marg, New Delhi, India
- The International Maize and Wheat Improvement Center (CIMMYT), National Agricultural Science Complex (NASC), Dev Prakash Shastri (DPS) Marg, New Delhi, India
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Peters Haugrud AR, Zhang Z, Friesen TL, Faris JD. Genetics of resistance to septoria nodorum blotch in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3685-3707. [PMID: 35050394 DOI: 10.1007/s00122-022-04036-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/23/2021] [Indexed: 05/12/2023]
Abstract
Septoria nodorum blotch (SNB) is a foliar disease of wheat caused by the necrotrophic fungal pathogen Parastagonospora nodorum. Research over the last two decades has shown that the wheat-P. nodorum pathosystem mostly follows an inverse gene-for-gene model. The fungus produces necrotrophic effectors (NEs) that interact with specific host gene products encoded by dominant sensitivity (S) genes. When a compatible interaction occurs, a 'defense response' in the host leads to programmed cell death thereby provided dead/dying cells from which the pathogen, being a necrotroph, can acquire nutrients allowing it to grow and sporulate. To date, nine S gene-NE interactions have been characterized in this pathosystem. Five NE-encoding genes, SnTox1, SnTox3, SnToxA, SnTox5, and SnTox267, have been cloned along with three host S genes, Tsn1, Snn1, and Snn3-D1. Studies have shown that P. nodorum hijacks multiple and diverse host targets to cause disease. SNB resistance is often quantitative in nature because multiple compatible interactions usually occur concomitantly. NE gene expression plays a key role in disease severity, and the effect of each compatible interaction can vary depending on the other existing compatible interactions. Numerous SNB-resistance QTL have been identified in addition to the known S genes, and more research is needed to understand the nature of these resistance loci. Marker-assisted elimination of S genes through conventional breeding practices and disruption of S genes using gene editing techniques are both effective strategies for the development of SNB-resistant wheat cultivars, which will become necessary as the global demand for sustenance grows.
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Affiliation(s)
| | - Zengcui Zhang
- USDA-ARS Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND, 58102, USA
| | - Timothy L Friesen
- USDA-ARS Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND, 58102, USA
| | - Justin D Faris
- USDA-ARS Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND, 58102, USA.
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Accounting for heading date gene effects allows detection of small-effect QTL associated with resistance to Septoria nodorum blotch in wheat. PLoS One 2022; 17:e0268546. [PMID: 35588401 PMCID: PMC9119491 DOI: 10.1371/journal.pone.0268546] [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: 11/02/2021] [Accepted: 05/03/2022] [Indexed: 11/19/2022] Open
Abstract
In humid and temperate areas, Septoria nodorum blotch (SNB) is a major fungal disease of common wheat (Triticum aestivum L.) in which grain yield is reduced when the pathogen, Parastagonospora nodorum, infects leaves and glumes during grain filling. Foliar SNB susceptibility may be associated with sensitivity to P. nodorum necrotrophic effectors (NEs). Both foliar and glume susceptibility are quantitative, and the underlying genetics are not understood in detail. We genetically mapped resistance quantitative trait loci (QTL) to leaf and glume blotch using a double haploid (DH) population derived from the cross between the moderately susceptible cultivar AGS2033 and the resistant breeding line GA03185-12LE29. The population was evaluated for SNB resistance in the field in four successive years (2018–2021). We identified major heading date (HD) and plant height (PH) variants on chromosomes 2A and 2D, co-located with SNB escape mechanisms. Five QTL with small effects associated with adult plant resistance to SNB leaf and glume blotch were detected on 1A, 1B, and 6B linkage groups. These QTL explained a relatively small proportion of the total phenotypic variation, ranging from 5.6 to 11.8%. The small-effect QTL detected in this study did not overlap with QTL associated with morphological and developmental traits, and thus are sources of resistance to SNB.
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John E, Jacques S, Phan HTT, Liu L, Pereira D, Croll D, Singh KB, Oliver RP, Tan KC. Variability in an effector gene promoter of a necrotrophic fungal pathogen dictates epistasis and effector-triggered susceptibility in wheat. PLoS Pathog 2022; 18:e1010149. [PMID: 34990464 PMCID: PMC8735624 DOI: 10.1371/journal.ppat.1010149] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 11/26/2021] [Indexed: 12/31/2022] Open
Abstract
The fungus Parastagonospora nodorum uses proteinaceous necrotrophic effectors (NEs) to induce tissue necrosis on wheat leaves during infection, leading to the symptoms of septoria nodorum blotch (SNB). The NEs Tox1 and Tox3 induce necrosis on wheat possessing the dominant susceptibility genes Snn1 and Snn3B1/Snn3D1, respectively. We previously observed that Tox1 is epistatic to the expression of Tox3 and a quantitative trait locus (QTL) on chromosome 2A that contributes to SNB resistance/susceptibility. The expression of Tox1 is significantly higher in the Australian strain SN15 compared to the American strain SN4. Inspection of the Tox1 promoter region revealed a 401 bp promoter genetic element in SN4 positioned 267 bp upstream of the start codon that is absent in SN15, called PE401. Analysis of the world-wide P. nodorum population revealed that a high proportion of Northern Hemisphere isolates possess PE401 whereas the opposite was observed in representative P. nodorum isolates from Australia and South Africa. The presence of PE401 removed the epistatic effect of Tox1 on the contribution of the SNB 2A QTL but not Tox3. PE401 was introduced into the Tox1 promoter regulatory region in SN15 to test for direct regulatory roles. Tox1 expression was markedly reduced in the presence of PE401. This suggests a repressor molecule(s) binds PE401 and inhibits Tox1 transcription. Infection assays also demonstrated that P. nodorum which lacks PE401 is more pathogenic on Snn1 wheat varieties than P. nodorum carrying PE401. An infection competition assay between P. nodorum isogenic strains with and without PE401 indicated that the higher Tox1-expressing strain rescued the reduced virulence of the lower Tox1-expressing strain on Snn1 wheat. Our study demonstrated that Tox1 exhibits both 'selfish' and 'altruistic' characteristics. This offers an insight into a complex NE-NE interaction that is occurring within the P. nodorum population. The importance of PE401 in breeding for SNB resistance in wheat is discussed.
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Affiliation(s)
- Evan John
- Centre for Crop and Disease Management, Curtin University, Bentley, Perth, Western Australia, Australia
- Curtin University, Bentley, Perth, Western Australia, Australia
| | - Silke Jacques
- Centre for Crop and Disease Management, Curtin University, Bentley, Perth, Western Australia, Australia
- Curtin University, Bentley, Perth, Western Australia, Australia
| | - Huyen T. T. Phan
- Centre for Crop and Disease Management, Curtin University, Bentley, Perth, Western Australia, Australia
- Curtin University, Bentley, Perth, Western Australia, Australia
| | - Lifang Liu
- Centre for Crop and Disease Management, Curtin University, Bentley, Perth, Western Australia, Australia
- Curtin University, Bentley, Perth, Western Australia, Australia
| | - Danilo Pereira
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Karam B. Singh
- Centre for Crop and Disease Management, Curtin University, Bentley, Perth, Western Australia, Australia
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Floreat, Western Australia, Australia
| | | | - Kar-Chun Tan
- Centre for Crop and Disease Management, Curtin University, Bentley, Perth, Western Australia, Australia
- Curtin University, Bentley, Perth, Western Australia, Australia
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Francki MG, Walker E, McMullan CJ, Morris WG. Evaluation of Septoria Nodorum Blotch (SNB) Resistance in Glumes of Wheat ( Triticum aestivum L.) and the Genetic Relationship With Foliar Disease Response. Front Genet 2021; 12:681768. [PMID: 34267781 PMCID: PMC8276050 DOI: 10.3389/fgene.2021.681768] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/07/2021] [Indexed: 11/13/2022] Open
Abstract
Septoria nodorum blotch (SNB) is a necrotrophic disease of wheat prominent in some parts of the world, including Western Australia (WA) causing significant losses in grain yield. The genetic mechanisms for resistance are complex involving multiple quantitative trait loci. In order to decipher comparable or independent regulation, this study identified the genetic control for glume compared to foliar resistance across four environments in WA against 37 different isolates. High proportion of the phenotypic variation across environments was contributed by genotype (84.0% for glume response and 82.7% for foliar response) with genotype-by-environment interactions accounting for a proportion of the variation for both glume and foliar response (14.7 and 16.2%, respectively). Despite high phenotypic correlation across environments, most of the eight and 14 QTL detected for glume and foliar resistance using genome wide association analysis (GWAS), respectively, were identified as environment-specific. QTL for glume and foliar resistance neither co-located nor were in LD in any particular environment indicating autonomous genetic mechanisms control SNB response in adult plants, regulated by independent biological mechanisms and influenced by significant genotype-by- environment interactions. Known Snn and Tsn loci and QTL were compared with 22 environment-specific QTL. None of the eight QTL for glume or the 14 for foliar response were co-located or in linkage disequilibrium with Snn and only one foliar QTL was in LD with Tsn loci on the physical map. Therefore, glume and foliar response to SNB in wheat is regulated by multiple environment-specific loci which function independently, with limited influence of known NE-Snn interactions for disease progression in Western Australian environments. Breeding for stable resistance would consequently rely on recurrent phenotypic selection to capture and retain favorable alleles for both glume and foliar resistance relevant to a particular environment.
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Affiliation(s)
- Michael G Francki
- Department of Primary Industries and Regional Development, South Perth, WA, Australia.,State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, Australia
| | - Esther Walker
- Department of Primary Industries and Regional Development, South Perth, WA, Australia.,State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, Australia
| | | | - W George Morris
- Department of Primary Industries and Regional Development, South Perth, WA, Australia
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Downie RC, Lin M, Corsi B, Ficke A, Lillemo M, Oliver RP, Phan HTT, Tan KC, Cockram J. Septoria Nodorum Blotch of Wheat: Disease Management and Resistance Breeding in the Face of Shifting Disease Dynamics and a Changing Environment. PHYTOPATHOLOGY 2021; 111:906-920. [PMID: 33245254 DOI: 10.1094/phyto-07-20-0280-rvw] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The fungus Parastagonospora nodorum is a narrow host range necrotrophic fungal pathogen that causes Septoria nodorum blotch (SNB) of cereals, most notably wheat (Triticum aestivum). Although commonly observed on wheat seedlings, P. nodorum infection has the greatest effect on the adult crop. It results in leaf blotch, which limits photosynthesis and thus crop growth and yield. It can also affect the wheat ear, resulting in glume blotch, which directly affects grain quality. Reports of P. nodorum fungicide resistance, the increasing use of reduced tillage agronomic practices, and high evolutionary potential of the pathogen, combined with changes in climate and agricultural environments, mean that genetic resistance to SNB remains a high priority in many regions of wheat cultivation. In this review, we summarize current information on P. nodorum population structure and its implication for improved SNB management. We then review recent advances in the genetics of host resistance to P. nodorum and the necrotrophic effectors it secretes during infection, integrating the genomic positions of these genetic loci by using the recently released wheat reference genome assembly. Finally, we discuss the genetic and genomic tools now available for SNB resistance breeding and consider future opportunities and challenges in crop health management by using the wheat-P. nodorum interaction as a model.
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Affiliation(s)
- Rowena C Downie
- John Bingham Laboratory, NIAB, Cambridge, CB3 0LE, United Kingdom
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Min Lin
- Norwegian University of Life Sciences, Ås NO-1432, Norway
| | - Beatrice Corsi
- John Bingham Laboratory, NIAB, Cambridge, CB3 0LE, United Kingdom
| | - Andrea Ficke
- Norwegian Institute for Bioeconomy Research, Ås NO-1432, Norway
| | - Morten Lillemo
- Norwegian University of Life Sciences, Ås NO-1432, Norway
| | | | - Huyen T T Phan
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley 6102, Perth, WA, Australia
| | - Kar-Chun Tan
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley 6102, Perth, WA, Australia
| | - James Cockram
- John Bingham Laboratory, NIAB, Cambridge, CB3 0LE, United Kingdom
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Li D, Walker E, Francki M. Genes Associated with Foliar Resistance to Septoria Nodorum Blotch of Hexaploid Wheat ( Triticum aestivum L.). Int J Mol Sci 2021; 22:ijms22115580. [PMID: 34070394 PMCID: PMC8197541 DOI: 10.3390/ijms22115580] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/14/2021] [Accepted: 05/22/2021] [Indexed: 11/25/2022] Open
Abstract
The genetic control of host response to the fungal necrotrophic disease Septoria nodorum blotch (SNB) in bread wheat is complex, involving many minor genes. Quantitative trait loci (QTL) controlling SNB response were previously identified on chromosomes 1BS and 5BL. The aim of this study, therefore, was to align and compare the genetic map representing QTL interval on 1BS and 5BS with the reference sequence of wheat and identify resistance genes (R-genes) associated with SNB response. Alignment of QTL intervals identified significant genome rearrangements on 1BS between parents of the DH population EGA Blanco, Millewa and the reference sequence of Chinese Spring with subtle rearrangements on 5BL. Nevertheless, annotation of genomic intervals in the reference sequence were able to identify and map 13 and 12 R-genes on 1BS and 5BL, respectively. R-genes discriminated co-located QTL on 1BS into two distinct but linked loci. NRC1a and TFIID mapped in one QTL on 1BS whereas RGA and Snn1 mapped in the linked locus and all were associated with SNB resistance but in one environment only. Similarly, Tsn1 and WK35 were mapped in one QTL on 5BL with NETWORKED 1A and RGA genes mapped in the linked QTL interval. This study provided new insights on possible biochemical, cellular and molecular mechanisms responding to SNB infection in different environments and also addressed limitations of using the reference sequence to identify the full complement of functional R-genes in modern varieties.
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Affiliation(s)
- Dora Li
- State Agricultural Biotechnology Centre, Murdoch University, South St, Murdoch, WA 6150, Australia; (D.L.); (E.W.)
| | - Esther Walker
- State Agricultural Biotechnology Centre, Murdoch University, South St, Murdoch, WA 6150, Australia; (D.L.); (E.W.)
- Department of Primary Industries and Regional Development, 3 Baron Hay Ct, South Perth, WA 6151, Australia
| | - Michael Francki
- State Agricultural Biotechnology Centre, Murdoch University, South St, Murdoch, WA 6150, Australia; (D.L.); (E.W.)
- Department of Primary Industries and Regional Development, 3 Baron Hay Ct, South Perth, WA 6151, Australia
- Correspondence:
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Francki MG, Walker E, McMullan CJ, Morris WG. Multi-Location Evaluation of Global Wheat Lines Reveal Multiple QTL for Adult Plant Resistance to Septoria Nodorum Blotch (SNB) Detected in Specific Environments and in Response to Different Isolates. FRONTIERS IN PLANT SCIENCE 2020; 11:771. [PMID: 32655592 PMCID: PMC7325896 DOI: 10.3389/fpls.2020.00771] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 05/15/2020] [Indexed: 05/26/2023]
Abstract
The slow rate of genetic gain for improving resistance to Septoria nodorum blotch (SNB) is due to the inherent complex interactions between host, isolates, and environments. Breeding for improved SNB resistance requires evaluation and selection of wheat genotypes consistently expressing low SNB response in different target production environments. The study focused on evaluating 232 genotypes from global origins for resistance to SNB in the flag leaf expressed in different Western Australian environments. The aim was to identify resistant donor germplasm against historical and contemporary pathogen isolates and enhance our knowledge of the genetic basis of genotype-by-environment interactions for SNB response. Australian wheat varieties, inbred lines from Centro Internacional de Mejoramiento de Maiz y Trigo (CIMMYT), and International Center for Agricultural Research in the Dry Areas (ICARDA), and landraces from discrete regions of the world showed low to moderate phenotypic correlation for disease response amongst genotypes when evaluated with historical and contemporary isolates at two locations across 3 years in Western Australia (WA). Significant (P < 0.001) genotype-by-environment interactions were detected regardless of same or different isolates used as an inoculum source. Joint regression analysis identified 19 genotypes that consistently expressed low disease severity under infection with different isolates in multi-locations. The CIMMYT inbred lines, 30ZJN09 and ZJN12 Qno25, were particularly pertinent as they had low SNB response and highest trait stability at two locations across 3 years. Genome wide association studies detected 20 QTL associated with SNB resistance on chromosomes 1A, 1B, 4B, 5A, 5B, 6A, 7A, 7B, and 7D. QTL on chromosomes 1B and 5B were previously reported in similar genomic regions. Multiple QTL were identified on 1B, 5B, 6A, and 5A and detected in response to SNB infection against different isolates and specific environments. Known SnTox-Snn interactions were either not evident or variable across WA environments and SNB response may involve other multiple complex biological mechanisms.
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Affiliation(s)
- Michael G. Francki
- Department of Primary Industries and Regional Development, South Perth, WA, Australia
- State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, Australia
| | - Esther Walker
- Department of Primary Industries and Regional Development, South Perth, WA, Australia
- State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, Australia
| | | | - W. George Morris
- Department of Primary Industries and Regional Development, South Perth, WA, Australia
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Phan HTT, Rybak K, Bertazzoni S, Furuki E, Dinglasan E, Hickey LT, Oliver RP, Tan KC. Novel sources of resistance to Septoria nodorum blotch in the Vavilov wheat collection identified by genome-wide association studies. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:1223-1238. [PMID: 29470621 PMCID: PMC5945755 DOI: 10.1007/s00122-018-3073-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 02/16/2018] [Indexed: 05/02/2023]
Abstract
KEY MESSAGE The fungus Parastagonospora nodorum causes Septoria nodorum blotch (SNB) of wheat. A genetically diverse wheat panel was used to dissect the complexity of SNB and identify novel sources of resistance. The fungus Parastagonospora nodorum is the causal agent of Septoria nodorum blotch (SNB) of wheat. The pathosystem is mediated by multiple fungal necrotrophic effector-host sensitivity gene interactions that include SnToxA-Tsn1, SnTox1-Snn1, and SnTox3-Snn3. A P. nodorum strain lacking SnToxA, SnTox1, and SnTox3 (toxa13) retained wild-type-like ability to infect some modern wheat cultivars, suggesting evidence of other effector-mediated susceptibility gene interactions or the lack of host resistance genes. To identify genomic regions harbouring such loci, we examined a panel of 295 historic wheat accessions from the N. I. Vavilov Institute of Plant Genetic Resources in Russia, which is comprised of genetically diverse landraces and breeding lines registered from 1920 to 1990. The wheat panel was subjected to effector bioassays, infection with P. nodorum wild type (SN15) and toxa13. In general, SN15 was more virulent than toxa13. Insensitivity to all three effectors contributed significantly to resistance against SN15, but not toxa13. Genome-wide association studies using phenotypes from SN15 infection detected quantitative trait loci (QTL) on chromosomes 1BS (Snn1), 2DS, 5AS, 5BS (Snn3), 3AL, 4AL, 4BS, and 7AS. For toxa13 infection, a QTL was detected on 5AS (similar to SN15), plus two additional QTL on 2DL and 7DL. Analysis of resistance phenotypes indicated that plant breeders may have inadvertently selected for effector insensitivity from 1940 onwards. We identify accessions that can be used to develop bi-parental mapping populations to characterise resistance-associated alleles for subsequent introgression into modern bread wheat to minimise the impact of SNB.
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Affiliation(s)
- Huyen T T Phan
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Kasia Rybak
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Stefania Bertazzoni
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Eiko Furuki
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Eric Dinglasan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Lee T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Richard P Oliver
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Kar-Chun Tan
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.
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Francki MG, Walker E, Li DA, Forrest K. High-density SNP mapping reveals closely linked QTL for resistance to Stagonospora nodorum blotch (SNB) in flag leaf and glume of hexaploid wheat. Genome 2017; 61:145-149. [PMID: 29237140 DOI: 10.1139/gen-2017-0203] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The genetic control of adult plant resistance to Stagonospora nodorum blotch (SNB) is complex, consisting of genes with minor effects interacting in an additive manner. Earlier studies detected quantitative trait loci (QTL) for flag leaf resistance in successive years on chromosomes 1B, 2A, 2D, and 5B using SSR- and DArT-based genetic maps of progeny from the crosses EGA Blanco/Millewa, 6HRWSN125/WAWHT2074, and P92201D5/P91193D1. Similarly, QTL for glume resistance detected in successive years and multiple environments were identified on chromosomes 2D and 4B from genetic maps of P92201D5/P91193D1 and 6HRWSN125/WAWHT2074, respectively. The SSR- and DArT-based genetic maps had an average distance of 6.5, 7.8, and 9.7 cM between marker loci for populations EGA/Millewa, P92201D5/P91193D1, and 6HRWSN125/WAWHT2074, respectively. This study used single nucleotide polymorphism (SNP) markers from the iSelect Infinium 90K genotyping array to fine-map genomic regions harbouring QTL for flag leaf and glume SNB resistance, reducing the average distance between markers to 2.9, 3.3, and 3.4 cM for populations P92201D5/P91193D1, EGA/Millewa, and 6HRWSN125/WAWHT2074, respectively. Increasing the marker density of the genetic maps with SNPs did not identify any new QTL for SNB resistance but discriminated previously identified co-located QTL into separate but closely linked QTL.
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Affiliation(s)
- Michael G Francki
- a Department of Agriculture and Food Western Australia, South Perth WA 6151, Australia.,b State Agricultural Biotechnology Centre, Murdoch University, Murdoch WA, 6150, Australia
| | - Esther Walker
- a Department of Agriculture and Food Western Australia, South Perth WA 6151, Australia.,b State Agricultural Biotechnology Centre, Murdoch University, Murdoch WA, 6150, Australia
| | - Dora A Li
- b State Agricultural Biotechnology Centre, Murdoch University, Murdoch WA, 6150, Australia
| | - Kerrie Forrest
- c Department of Economic Development, Jobs, Transport and Resources, Agriculture Victoria Research, Agribio, Bundoora, VIC, Australia
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Ruud AK, Windju S, Belova T, Friesen TL, Lillemo M. Mapping of SnTox3-Snn3 as a major determinant of field susceptibility to Septoria nodorum leaf blotch in the SHA3/CBRD × Naxos population. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1361-1374. [PMID: 28365817 DOI: 10.1007/s00122-017-2893-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 03/18/2017] [Indexed: 05/03/2023]
Abstract
The effect of the SnTox3-Snn3 interaction was documented for the first time under natural infection at the adult plant stage in the field. Co-segregating SNP markers were identified. Parastagonospora nodorum is a necrotrophic pathogen of wheat, causing Septoria nodorum blotch (SNB) affecting both the leaf and glume. P. nodorum is the major leaf blotch pathogen on spring wheat in Norway. Resistance to the disease is quantitative, but several host-specific interactions between necrotrophic effectors (NEs) and host sensitivity (Snn) genes have been identified, playing a major role at the seedling stage. However, the effect of these interactions in the field under natural infection has not been investigated. In the present study, we saturated the genetic map of the recombinant inbred (RI) population SHA3/CBRD × Naxos using the Illumina 90 K SNP chip. The population had previously been evaluated for segregation of SNB susceptibility in field trials. Here, we infiltrated the population with the purified NEs SnToxA, SnTox1 and SnTox3, and mapped the Snn3 locus on 5BS based on sensitivity segregation and SNP marker data. We also conducted inoculation and culture filtrate (CF) infiltration experiments on the population with four selected P. nodorum isolates from Norway and North America. Remapping of quantitative trait loci (QTL) for field resistance showed that the SnTox3-Snn3 interaction could explain 24% of the phenotypic variation in the field, and more than 51% of the variation in seedling inoculations. To our knowledge, this is the first time the effect of this interaction has been documented at the adult plant stage under natural infection in the field.
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Affiliation(s)
- Anja Karine Ruud
- Department of Plant Sciences, Norwegian University of Life Sciences, Post Box 5003, 1432, Ås, Norway
| | - Susanne Windju
- Department of Plant Sciences, Norwegian University of Life Sciences, Post Box 5003, 1432, Ås, Norway
- Graminor AS, Bjørke Gård, Hommelstadvegen 60, 2322, Ridabu, Norway
| | - Tatiana Belova
- Department of Plant Sciences, Norwegian University of Life Sciences, Post Box 5003, 1432, Ås, Norway
| | - Timothy L Friesen
- Northern Crop Science Laboratory, USDA-ARS, 1307 North 18th Street, Fargo, ND, 58102, USA
- Department of Plant Pathology, North Dakota State University, Walster Hall, Fargo, ND, 58102, USA
| | - Morten Lillemo
- Department of Plant Sciences, Norwegian University of Life Sciences, Post Box 5003, 1432, Ås, Norway.
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12
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Wang X, Luo G, Yang W, Li Y, Sun J, Zhan K, Liu D, Zhang A. Genetic diversity, population structure and marker-trait associations for agronomic and grain traits in wild diploid wheat Triticum urartu. BMC PLANT BIOLOGY 2017; 17:112. [PMID: 28668082 PMCID: PMC5494140 DOI: 10.1186/s12870-017-1058-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 06/14/2017] [Indexed: 12/19/2022]
Abstract
BACKGROUND Wild diploid wheat, Triticum urartu (T. urartu) is the progenitor of bread wheat, and understanding its genetic diversity and genome function will provide considerable reference for dissecting genomic information of common wheat. RESULTS In this study, we investigated the morphological and genetic diversity and population structure of 238 T. urartu accessions collected from different geographic regions. This collection had 19.37 alleles per SSR locus and its polymorphic information content (PIC) value was 0.76, and the PIC and Nei's gene diversity (GD) of high-molecular-weight glutenin subunits (HMW-GSs) were 0.86 and 0.88, respectively. UPGMA clustering analysis indicated that the 238 T. urartu accessions could be classified into two subpopulations, of which Cluster I contained accessions from Eastern Mediterranean coast and those from Mesopotamia and Transcaucasia belonged to Cluster II. The wide range of genetic diversity along with the manageable number of accessions makes it one of the best collections for mining valuable genes based on marker-trait association. Significant associations were observed between simple sequence repeats (SSR) or HMW-GSs and six morphological traits: heading date (HD), plant height (PH), spike length (SPL), spikelet number per spike (SPLN), tiller angle (TA) and grain length (GL). CONCLUSIONS Our data demonstrated that SSRs and HMW-GSs were useful markers for identification of beneficial genes controlling important traits in T. urartu, and subsequently for their conservation and future utilization, which may be useful for genetic improvement of the cultivated hexaploid wheat.
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Affiliation(s)
- Xin Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Guangbin Luo
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Wenlong Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101 China
| | - Yiwen Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101 China
| | - Jiazhu Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101 China
| | - Kehui Zhan
- College of Agronomy/The Collaborative Innovation Center of Grain Crops in Henan, Henan Agricultural University, No. 95 Wenhua Road, Zhengzhou, 450002 China
| | - Dongcheng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101 China
| | - Aimin Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101 China
- College of Agronomy/The Collaborative Innovation Center of Grain Crops in Henan, Henan Agricultural University, No. 95 Wenhua Road, Zhengzhou, 450002 China
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13
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Thapa R, Brown-Guedira G, Ohm HW, Mateos-Hernandez M, Wise KA, Goodwin SB. Determining the order of resistance genes against Stagonospora nodorum blotch, Fusarium head blight and stem rust on wheat chromosome arm 3BS. BMC Res Notes 2016; 9:58. [PMID: 26833226 PMCID: PMC4736272 DOI: 10.1186/s13104-016-1859-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 01/14/2016] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Stagonospora nodorum blotch (SNB), Fusarium head blight (FHB) and stem rust (SR), caused by the fungi Parastagonospora (synonym Stagonospora) nodorum, Fusarium graminearum and Puccinia graminis, respectively, significantly reduce yield and quality of wheat. Three resistance factors, QSng.sfr-3BS, Fhb1 and Sr2, conferring resistance, respectively, to SNB, FHB and SR, each from a unique donor line, were mapped previously to the short arm of wheat chromosome 3B. Based on published reports, our hypothesis was that Sr2 is the most distal, Fhb1 the most proximal and QSng.sfr-3BS is in between Sr2 and Fhb1 on wheat chromosome arm 3BS. RESULTS To test this hypothesis, 1600 F2 plants from crosses between parental lines Arina, Alsen and Ocoroni86, conferring resistance genes QSng.sfr-3BS, Fhb1 and Sr2, respectively, were genotyped and phenotyped for SNB along with the parental lines. Five closely linked single-nucleotide polymorphism (SNP) markers were used to make the genetic map and determine the gene order. CONCLUSIONS The results indicate that QSng.sfr-3BS is located between the other two resistance genes on chromosome 3BS. Knowing the positional order of these resistance genes will aid in developing a wheat line with all three genes in coupling, which has the potential to provide broad-spectrum resistance preventing grain yield and quality losses.
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Affiliation(s)
- Rima Thapa
- Department of Agronomy, Purdue University, 915 W. State Street, West Lafayette, IN, 47907-2054, USA.
| | - Gina Brown-Guedira
- USDA-ARS Plant Science Research, North Carolina State University, Raleigh, NC, 27695-7620, USA.
| | - Herbert W Ohm
- Department of Agronomy, Purdue University, 915 W. State Street, West Lafayette, IN, 47907-2054, USA.
| | | | - Kiersten A Wise
- Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN, 47907-2054, USA.
| | - Stephen B Goodwin
- USDA-ARS, Department of Botany and Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN, 47907-2054, USA.
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14
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Lu Q, Lillemo M. Molecular mapping of adult plant resistance to Parastagonospora nodorum leaf blotch in bread wheat lines 'Shanghai-3/Catbird' and 'Naxos'. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:2635-44. [PMID: 25277822 DOI: 10.1007/s00122-014-2404-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 09/20/2014] [Indexed: 05/03/2023]
Abstract
The field resistance to Parastagonospora nodorum leaf blotch in SHA3/CBRD is based on many genes with minor effects. Parastagonospora nodorum leaf blotch is a severe wheat disease in Norway and other regions with humid and rainy climate. It causes grain shriveling and reduced yield in years of epidemics. Shanghai-3/Catbird (SHA3/CBRD), a CIMMYT breeding line, was observed to be resistant to P. nodorum leaf blotch in the field. The objective of the current study was to map the genetic factors related to its resistance. A recombinant inbred line population from a cross between SHA3/CBRD and the susceptible German spring cv. Naxos was tested in field trials over 4 years (2010, 2011, 2012 and 2013) with natural infection supplied with mist irrigation. Leaf blotch severity was scored together with plant height, heading date and maturity date in these trials. A testing data set was also available from other field trials with the same population. Totally, two major and six minor QTL were detected for leaf blotch resistance. The major QTL on chromosome 3BL with resistance contributed by Naxos was consistent across all environments and explained up to 12 % of the phenotypic variation. Another major QTL on 3B with resistance from SHA3/CBRD was significant in 2010, 2013 and the testing data set and explained up to 12 % of the phenotypic variation. Minor QTL were detected on 1B, 3AS, 5BS, 5BL, 7A and 7B. The 5BS QTL was likely caused by Snn3-B1, with sensitivity contributed by Naxos. The 5BL QTL mapped to the Tsn1 region, but was likely caused by other mechanisms since both parents were insensitive to ToxA.
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Affiliation(s)
- Qiongxian Lu
- Department of Plant Sciences, Norwegian University of Life Sciences, P.O. Box 5003, 1432, Ås, Norway
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15
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Gurung S, Mamidi S, Bonman JM, Xiong M, Brown-Guedira G, Adhikari TB. Genome-wide association study reveals novel quantitative trait Loci associated with resistance to multiple leaf spot diseases of spring wheat. PLoS One 2014; 9:e108179. [PMID: 25268502 PMCID: PMC4182470 DOI: 10.1371/journal.pone.0108179] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 08/23/2014] [Indexed: 11/18/2022] Open
Abstract
Accelerated wheat development and deployment of high-yielding, climate resilient, and disease resistant cultivars can contribute to enhanced food security and sustainable intensification. To facilitate gene discovery, we assembled an association mapping panel of 528 spring wheat landraces of diverse geographic origin for a genome-wide association study (GWAS). All accessions were genotyped using an Illumina Infinium 9K wheat single nucleotide polymorphism (SNP) chip and 4781 polymorphic SNPs were used for analysis. To identify loci underlying resistance to the major leaf spot diseases and to better understand the genomic patterns, we quantified population structure, allelic diversity, and linkage disequilibrium. Our results showed 32 loci were significantly associated with resistance to the major leaf spot diseases. Further analysis identified QTL effective against major leaf spot diseases of wheat which appeared to be novel and others that were previously identified by association analysis using Diversity Arrays Technology (DArT) and bi-parental mapping. In addition, several identified SNPs co-localized with genes that have been implicated in plant disease resistance. Future work could aim to select the putative novel loci and pyramid them in locally adapted wheat cultivars to develop broad-spectrum resistance to multiple leaf spot diseases of wheat via marker-assisted selection (MAS).
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Affiliation(s)
- Suraj Gurung
- Department of Plant Pathology, University of California Davis, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Salinas, California, United States of America
| | - Sujan Mamidi
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, United States of America
| | - J. Michael Bonman
- USDA-ARS, Small Grains and Potato Germplasm Research Unit, Aberdeen, Idaho, United States of America
| | - Mai Xiong
- USDA-ARS, Plant Science Research Unit, Department of Crop Science, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Gina Brown-Guedira
- USDA-ARS, Plant Science Research Unit, Department of Crop Science, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Tika B. Adhikari
- Center for Integrated Pest Management and Department of Plant Pathology, North Carolina State University, Raleigh, North Carolina, United States of America
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16
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Chooi YH, Muria-Gonzalez MJ, Solomon PS. A genome-wide survey of the secondary metabolite biosynthesis genes in the wheat pathogen Parastagonospora nodorum.. Mycology 2014; 5:192-206. [PMID: 25379341 PMCID: PMC4205913 DOI: 10.1080/21501203.2014.928386] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 05/22/2014] [Indexed: 12/02/2022] Open
Abstract
The model pathogen Parastagonospora nodorum is a necrotroph and the causal agent of the wheat disease Septoria nodorum blotch (SNB). The sequenced P. nodorum genome has revealed that the fungus harbours a large number of secondary metabolite genes. Secondary metabolites are known to play important roles in the virulence of plant pathogens, but limited knowledge is available about the SM repertoire of this wheat pathogen. Here, we review the secondary metabolites that have been isolated from P. nodorum and related species of the same genus and provide an in-depth genome-wide overview of the secondary metabolite gene clusters encoded in the P. nodorum genome. The secondary metabolite gene survey reveals that P. nodorum is capable of producing a diverse range of small molecules and exciting prospects exist for discovery of novel virulence factors and bioactive molecules.
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Affiliation(s)
- Yit-Heng Chooi
- Plant Sciences Division, Research School of Biology, The Australian National University , Canberra , 0200 , Australia
| | - Mariano Jordi Muria-Gonzalez
- Plant Sciences Division, Research School of Biology, The Australian National University , Canberra , 0200 , Australia
| | - Peter S Solomon
- Plant Sciences Division, Research School of Biology, The Australian National University , Canberra , 0200 , Australia
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17
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Adhikari TB, Jackson EW, Gurung S, Hansen JM, Bonman JM. Association mapping of quantitative resistance to Phaeosphaeria nodorum in spring wheat landraces from the USDA National Small Grains Collection. PHYTOPATHOLOGY 2011; 101:1301-10. [PMID: 21692647 DOI: 10.1094/phyto-03-11-0076] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Stagonospora nodorum blotch (SNB), caused by Phaeosphaeria nodorum, is a destructive disease of wheat (Triticum aestivum) found throughout the United States. Host resistance is the only economically feasible option for managing the disease; however, few SNB-resistant wheat cultivars are known to exist. In this study, we report findings from an association mapping (AM) of resistance to P. nodorum in 567 spring wheat landraces of diverse geographic origin. The accessions were evaluated for seedling resistance to P. nodorum in a greenhouse. Phenotypic data and 625 polymorphic diversity array technology (DArT) markers have been used for linkage disequilibrium (LD) and association analyses. The results showed that seven DArT markers on five chromosomes (2D, 3B, 5B, 6A, and 7A) were significantly associated with resistance to P. nodorum. Genetic regions on 2D, 3B, and 5B correspond to previously mapped quantitative trait loci (QTL) conferring resistance to P. nodorum whereas the remaining QTL appeared to be novel. These results demonstrate that the use of AM is an effective method for identifying new genomic regions associated with resistance to P. nodorum in spring wheat landraces. Additionally, the novel resistance found in this study could be useful in wheat breeding aimed at controlling SNB.
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Affiliation(s)
- Tika B Adhikari
- Department of Plant Pathology, North Dakota State University, Frago, ND, USA.
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