1
|
Paineau M, Minio A, Mestre P, Fabre F, Mazet ID, Couture C, Legeai F, Dumartinet T, Cantu D, Delmotte F. Multiple deletions of candidate effector genes lead to the breakdown of partial grapevine resistance to downy mildew. THE NEW PHYTOLOGIST 2024; 243:1490-1505. [PMID: 39021210 DOI: 10.1111/nph.19861] [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: 10/17/2023] [Accepted: 03/21/2024] [Indexed: 07/20/2024]
Abstract
Grapevine downy mildew, caused by the oomycete Plasmopara viticola (P. viticola, Berk. & M. A. Curtis; Berl. & De Toni), is a global threat to Eurasian wine grapes Vitis vinifera. Although resistant grapevine varieties are becoming more accessible, P. viticola populations are rapidly evolving to overcome these resistances. We aimed to uncover avirulence genes related to Rpv3.1-mediated grapevine resistance. We sequenced the genomes and characterized the development of 136 P. viticola strains on resistant and sensitive grapevine cultivars. A genome-wide association study was conducted to identify genomic variations associated with resistant-breaking phenotypes. We identified a genomic region associated with the breakdown of Rpv3.1 grapevine resistance (avrRpv3.1 locus). A diploid-aware reassembly of the P. viticola INRA-Pv221 genome revealed structural variations in this locus, including a 30 kbp deletion. Virulent P. viticola strains displayed multiple deletions on both haplotypes at the avrRpv3.1 locus. These deletions involve two paralog genes coding for proteins with 800-900 amino acids and signal peptides. These proteins exhibited a structure featuring LWY-fold structural modules, common among oomycete effectors. When transiently expressed, these proteins induced cell death in grapevines carrying Rpv3.1 resistance, confirming their avirulence nature. This discovery sheds light on the genetic mechanisms enabling P. viticola to adapt to grapevine resistance, laying a foundation for developing strategies to manage this destructive crop pathogen.
Collapse
Affiliation(s)
- Manon Paineau
- INRAE, Bordeaux Sciences Agro, SAVE, ISVV, F-33340, Villenave d'Ornon, France
- Department of Viticulture and Enology, University of California Davis, Davis, 95616, CA, USA
| | - Andrea Minio
- Department of Viticulture and Enology, University of California Davis, Davis, 95616, CA, USA
| | - Pere Mestre
- INRAE, Université de Strasbourg, SVQV, F-68125, Colmar, France
| | - Frédéric Fabre
- INRAE, Bordeaux Sciences Agro, SAVE, ISVV, F-33340, Villenave d'Ornon, France
| | - Isabelle D Mazet
- INRAE, Bordeaux Sciences Agro, SAVE, ISVV, F-33340, Villenave d'Ornon, France
| | - Carole Couture
- INRAE, Bordeaux Sciences Agro, SAVE, ISVV, F-33340, Villenave d'Ornon, France
| | - Fabrice Legeai
- INRAE, IGEPP, F-35650, Le-Rheu, France
- INRIA, IRISA, GenOuest Core Facility, F-35000, Rennes, France
| | | | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, Davis, 95616, CA, USA
- Genome Center, University of California Davis, Davis, 95616, CA, USA
| | - François Delmotte
- INRAE, Bordeaux Sciences Agro, SAVE, ISVV, F-33340, Villenave d'Ornon, France
| |
Collapse
|
2
|
Peters Haugrud AR, Shi G, Seneviratne S, Running KLD, Zhang Z, Singh G, Szabo-Hever A, Acharya K, Friesen TL, Liu Z, Faris JD. Genome-wide association mapping of resistance to the foliar diseases septoria nodorum blotch and tan spot in a global winter wheat collection. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:54. [PMID: 37337566 PMCID: PMC10276793 DOI: 10.1007/s11032-023-01400-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 06/02/2023] [Indexed: 06/21/2023]
Abstract
Septoria nodorum blotch (SNB) and tan spot, caused by the necrotrophic fungal pathogens Parastagonospora nodorum and Pyrenophora tritici-repentis, respectively, often occur together as a leaf spotting disease complex on wheat (Triticum aestivum L.). Both pathogens produce necrotrophic effectors (NEs) that contribute to the development of disease. Here, genome-wide association analysis of a diverse panel of 264 winter wheat lines revealed novel loci on chromosomes 5A and 5B associated with sensitivity to the NEs SnTox3 and SnTox5 in addition to the known sensitivity genes for NEs Ptr/SnToxA, SnTox1, SnTox3, and SnTox5. Sensitivity loci for SnTox267 and Ptr ToxB were not detected. Evaluation of the panel with five P. nodorum isolates for SNB development indicated the Snn3-SnTox3 and Tsn1-SnToxA interactions played significant roles in disease development along with additional QTL on chromosomes 2A and 2D, which may correspond to the Snn7-SnTox267 interaction. For tan spot, the Tsc1-Ptr ToxC interaction was associated with disease caused by two isolates, and a novel QTL on chromosome 7D was associated with a third isolate. The Tsn1-ToxA interaction was associated with SNB but not tan spot. Therefore some, but not all, of the previously characterized host gene-NE interactions in these pathosystems play significant roles in disease development in winter wheat. Based on these results, breeders should prioritize the selection of resistance alleles at the Tsc1, Tsn1, Snn3, and Snn7 loci as well as the 2A and 7D QTL to obtain good levels of resistance to SNB and tan spot in winter wheat. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01400-5.
Collapse
Affiliation(s)
- Amanda R. Peters Haugrud
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, , Fargo, ND 58102 USA
| | - Gongjun Shi
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102 USA
| | - Sudeshi Seneviratne
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58102 USA
| | | | - Zengcui Zhang
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, , Fargo, ND 58102 USA
| | - Gurminder Singh
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58102 USA
| | - Agnes Szabo-Hever
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, , Fargo, ND 58102 USA
| | - Krishna Acharya
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58102 USA
| | - Timothy L. Friesen
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, , Fargo, ND 58102 USA
| | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102 USA
| | - Justin D. Faris
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, , Fargo, ND 58102 USA
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
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.
Collapse
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.
| |
Collapse
|
5
|
Veselova S, Nuzhnaya T, Burkhanova G, Rumyantsev S, Maksimov I. Reactive Oxygen Species in Host Plant Are Required for an Early Defense Response against Attack of Stagonospora nodorum Berk. Necrotrophic Effectors SnTox. PLANTS 2021; 10:plants10081586. [PMID: 34451631 PMCID: PMC8398409 DOI: 10.3390/plants10081586] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/24/2021] [Accepted: 07/28/2021] [Indexed: 02/03/2023]
Abstract
Reactive oxygen species (ROS) play a central role in plant immune responses. The most important virulence factors of the Stagonospora nodorum Berk. are multiple fungal necrotrophic effectors (NEs) (SnTox) that affect the redox-status and cause necrosis and/or chlorosis in wheat lines possessing dominant susceptibility genes (Snn). However, the effect of NEs on ROS generation at the early stages of infection has not been studied. We studied the early stage of infection of various wheat genotypes with S nodorum isolates -Sn4VD, SnB, and Sn9MN, carrying a different set of NE genes. Our results indicate that all three NEs of SnToxA, SnTox1, SnTox3 significantly contributed to cause disease, and the virulence of the isolates depended on their differential expression in plants (Triticum aestivum L.). The Tsn1–SnToxA, Snn1–SnTox1and Snn3–SnTox3 interactions played an important role in inhibition ROS production at the initial stage of infection. The Snn3–SnTox3 inhibited ROS production in wheat by affecting NADPH-oxidases, peroxidases, superoxide dismutase and catalase. The Tsn1–SnToxA inhibited ROS production in wheat by affecting peroxidases and catalase. The Snn1–SnTox1 inhibited the production of ROS in wheat by mainly affecting a peroxidase. Collectively, these results show that the inverse gene-for gene interactions between effector of pathogen and product of host sensitivity gene suppress the host’s own PAMP-triggered immunity pathway, resulting in NE-triggered susceptibility (NETS). These results are fundamentally changing our understanding of the development of this economical important wheat disease.
Collapse
Affiliation(s)
- Svetlana Veselova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre, Russian Academy of Sciences, Prospekt Oktyabrya, 71, 450054 Ufa, Russia; (T.N.); (G.B.); (S.R.); (I.M.)
- Correspondence:
| | - Tatyana Nuzhnaya
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre, Russian Academy of Sciences, Prospekt Oktyabrya, 71, 450054 Ufa, Russia; (T.N.); (G.B.); (S.R.); (I.M.)
- Ufa Institute of Biology, Ufa Federal Research Centre, Russian Academy of Sciences, Prospekt Oktyabrya, 69, 450054 Ufa, Russia
| | - Guzel Burkhanova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre, Russian Academy of Sciences, Prospekt Oktyabrya, 71, 450054 Ufa, Russia; (T.N.); (G.B.); (S.R.); (I.M.)
| | - Sergey Rumyantsev
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre, Russian Academy of Sciences, Prospekt Oktyabrya, 71, 450054 Ufa, Russia; (T.N.); (G.B.); (S.R.); (I.M.)
| | - Igor Maksimov
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre, Russian Academy of Sciences, Prospekt Oktyabrya, 71, 450054 Ufa, Russia; (T.N.); (G.B.); (S.R.); (I.M.)
| |
Collapse
|