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Upadhaya A, Upadhaya SGC, Brueggeman R. Association mapping with a diverse population of Puccinia graminis f. sp. tritici identified avirulence loci interacting with the barley Rpg1 stem rust resistance gene. BMC Genomics 2024; 25:751. [PMID: 39090588 PMCID: PMC11295639 DOI: 10.1186/s12864-024-10670-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 07/26/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND Wheat stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is an important disease of barley and wheat. A diverse sexual Pgt population from the Pacific Northwest (PNW) region of the US contains a high proportion of individuals with virulence on the barley stem rust resistance (R) gene, Rpg1. However, the evolutionary mechanisms of this virulence on Rpg1 are mysterious considering that Rpg1 had not been deployed in the region and the gene had remained remarkably durable in the Midwestern US and prairie provinces of Canada. METHODS AND RESULTS To identify AvrRpg1 effectors, genome wide association studies (GWAS) were performed using 113 Pgt isolates collected from the PNW (n = 89 isolates) and Midwest (n = 24 isolates) regions of the US. Disease phenotype data were generated on two barley lines Morex and the Golden Promise transgenic (H228.2c) that carry the Rpg1 gene. Genotype data was generated by whole genome sequencing (WGS) of 96 isolates (PNW = 89 isolates and Midwest = 7 isolates) and RNA sequencing (RNAseq) data from 17 Midwestern isolates. Utilizing ~1.2 million SNPs generated from WGS and phenotype data (n = 96 isolates) on the transgenic line H228.2c, 53 marker trait associations (MTAs) were identified. Utilizing ~140 K common SNPs generated from combined analysis of WGS and RNAseq data, two significant MTAs were identified using the cv Morex phenotyping data. The 55 MTAs defined two distinct avirulence loci, on supercontig 2.30 and supercontig 2.11 of the Pgt reference genome of Pgt isolate CRL 75-36-700-3. The major avirulence locus designated AvrRpg1A was identified with the GWAS using both barley lines and was delimited to a 35 kb interval on supercontig 2.30 containing four candidate genes (PGTG_10878, PGTG_10884, PGTG_10885, and PGTG_10886). The minor avirulence locus designated AvrRpg1B identified with cv Morex contained a single candidate gene (PGTG_05433). AvrRpg1A haplotype analysis provided strong evidence that a dominant avirulence gene underlies the locus. CONCLUSIONS The association analysis identified strong candidate AvrRpg1 genes. Further analysis to validate the AvrRpg1 genes will fill knowledge gaps in our understanding of rust effector biology and the evolution and mechanism/s of Pgt virulence on Rpg1.
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Affiliation(s)
- Arjun Upadhaya
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
| | - Sudha G C Upadhaya
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
| | - Robert Brueggeman
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA.
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Seneviratne S, Shi G, Szabo-Hever A, Zhang Z, Peters Haugrud AR, Running KLD, Singh G, Nandety RS, Fiedler JD, McClean PE, Xu SS, Friesen TL, Faris JD. Evolution, diversity, and function of the disease susceptibility gene Snn1 in wheat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:1720-1736. [PMID: 38923651 DOI: 10.1111/tpj.16879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/29/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024]
Abstract
Septoria nodorum blotch (SNB), caused by Parastagonospora nodorum, is a disease of durum and common wheat initiated by the recognition of pathogen-produced necrotrophic effectors (NEs) by specific wheat genes. The wheat gene Snn1 was previously cloned, and it encodes a wall-associated kinase that directly interacts with the NE SnTox1 leading to programmed cell death and ultimately the development of SNB. Here, sequence analysis of Snn1 from 114 accessions including diploid, tetraploid, and hexaploid wheat species revealed that some wheat lines possess two copies of Snn1 (designated Snn1-B1 and Snn1-B2) approximately 120 kb apart. Snn1-B2 evolved relatively recently as a paralog of Snn1-B1, and both genes have undergone diversifying selection. Three point mutations associated with the formation of the first SnTox1-sensitive Snn1-B1 allele from a primitive wild wheat were identified. Four subsequent and independent SNPs, three in Snn1-B1 and one in Snn1-B2, converted the sensitive alleles to insensitive forms. Protein modeling indicated these four mutations could abolish Snn1-SnTox1 compatibility either through destabilization of the Snn1 protein or direct disruption of the protein-protein interaction. A high-throughput marker was developed for the absent allele of Snn1, and it was 100% accurate at predicting SnTox1-insensitive lines in both durum and spring wheat. Results of this study increase our understanding of the evolution, diversity, and function of Snn1-B1 and Snn1-B2 genes and will be useful for marker-assisted elimination of these genes for better host resistance.
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Affiliation(s)
- Sudeshi Seneviratne
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, 58102, USA
| | - Gongjun Shi
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, 58102, USA
| | - Agnes Szabo-Hever
- USDA-ARS Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, North Dakota, 58102, USA
| | - Zengcui Zhang
- USDA-ARS Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, North Dakota, 58102, USA
| | - Amanda R Peters Haugrud
- USDA-ARS Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, North Dakota, 58102, USA
| | - Katherine L D Running
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, 58102, USA
| | - Gurminder Singh
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, 58102, USA
| | - Raja Sekhar Nandety
- USDA-ARS Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, North Dakota, 58102, USA
| | - Jason D Fiedler
- USDA-ARS Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, North Dakota, 58102, USA
| | - Phillip E McClean
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, 58102, USA
| | - Steven S Xu
- USDA-ARS Crop Improvement and Genetics Research Unit, Western Regional Research Center, Albany, California, 94710, USA
| | - Timothy L Friesen
- USDA-ARS Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, North Dakota, 58102, USA
| | - Justin D Faris
- USDA-ARS Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, North Dakota, 58102, USA
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3
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Upadhaya A, Upadhaya SGC, Brueggeman R. Identification of Candidate Avirulence and Virulence Genes Corresponding to Stem Rust ( Puccinia graminis f. sp. tritici) Resistance Genes in Wheat. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:635-649. [PMID: 38780476 DOI: 10.1094/mpmi-05-24-0056-r] [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: 05/25/2024]
Abstract
Stem rust, caused by the biotrophic fungal pathogen Puccinia graminis f. sp. tritici (Pgt), is an important disease of wheat. However, the majority of Pgt virulence/avirulence loci and underlying genes remain uncharacterized due to the constraints of developing bi-parental populations with this obligate biotroph. Genome-wide association studies (GWAS) using a sexual Pgt population mainly collected from the Pacific Northwestern United States were used to identify candidate virulence/avirulence effector genes corresponding to the six wheat Sr genes: Sr5, Sr21, Sr8a, Sr17, Sr9a, and Sr9d. The Pgt isolates were genotyped using whole-genome shotgun sequencing that identified approximately 1.2 million single nucleotide polymorphisms (SNPs) and were phenotyped at the seedling stage on six Sr gene differential lines. Association mapping analyses identified 17 Pgt loci associated with virulence or avirulence phenotypes on six Pgt resistance genes. Among these loci, 16 interacted with a specific Sr gene, indicating Sr-gene specific interactions. However, one avirulence locus interacted with two separate Sr genes (Sr9a and Sr17), suggesting two distinct Sr genes identifying a single avirulence effector. A total of 24 unique effector gene candidates were identified, and haplotype analysis suggests that within this population, AvrSr5, AvrSr21, AvrSr8a, AvrSr17, and AvrSr9a are dominant avirulence genes, while avrSr9d is a dominant virulence gene. The putative effector genes will be fundamental for future effector gene cloning efforts, allowing for further understanding of rust effector biology and the mechanisms underlying virulence evolution in Pgt with respect to race-specific R-genes. [Formula: see text] Copyright © 2024 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)
- Arjun Upadhaya
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6420, U.S.A
| | - Sudha G C Upadhaya
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6420, U.S.A
| | - Robert Brueggeman
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6420, U.S.A
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4
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Bhunjun C, Chen Y, Phukhamsakda C, Boekhout T, Groenewald J, McKenzie E, Francisco E, Frisvad J, Groenewald M, Hurdeal VG, Luangsa-ard J, Perrone G, Visagie C, Bai F, Błaszkowski J, Braun U, de Souza F, de Queiroz M, Dutta A, Gonkhom D, Goto B, Guarnaccia V, Hagen F, Houbraken J, Lachance M, Li J, Luo K, Magurno F, Mongkolsamrit S, Robert V, Roy N, Tibpromma S, Wanasinghe D, Wang D, Wei D, Zhao C, Aiphuk W, Ajayi-Oyetunde O, Arantes T, Araujo J, Begerow D, Bakhshi M, Barbosa R, Behrens F, Bensch K, Bezerra J, Bilański P, Bradley C, Bubner B, Burgess T, Buyck B, Čadež N, Cai L, Calaça F, Campbell L, Chaverri P, Chen Y, Chethana K, Coetzee B, Costa M, Chen Q, Custódio F, Dai Y, Damm U, Santiago A, De Miccolis Angelini R, Dijksterhuis J, Dissanayake A, Doilom M, Dong W, Álvarez-Duarte E, Fischer M, Gajanayake A, Gené J, Gomdola D, Gomes A, Hausner G, He M, Hou L, Iturrieta-González I, Jami F, Jankowiak R, Jayawardena R, Kandemir H, Kiss L, Kobmoo N, Kowalski T, Landi L, Lin C, Liu J, Liu X, Loizides M, Luangharn T, Maharachchikumbura S, Mkhwanazi GM, Manawasinghe I, Marin-Felix Y, McTaggart A, Moreau P, Morozova O, Mostert L, Osiewacz H, Pem D, Phookamsak R, Pollastro S, Pordel A, Poyntner C, Phillips A, Phonemany M, Promputtha I, Rathnayaka A, Rodrigues A, Romanazzi G, Rothmann L, Salgado-Salazar C, Sandoval-Denis M, Saupe S, Scholler M, Scott P, Shivas R, Silar P, Silva-Filho A, Souza-Motta C, Spies C, Stchigel A, Sterflinger K, Summerbell R, Svetasheva T, Takamatsu S, Theelen B, Theodoro R, Thines M, Thongklang N, Torres R, Turchetti B, van den Brule T, Wang X, Wartchow F, Welti S, Wijesinghe S, Wu F, Xu R, Yang Z, Yilmaz N, Yurkov A, Zhao L, Zhao R, Zhou N, Hyde K, Crous P. What are the 100 most cited fungal genera? Stud Mycol 2024; 108:1-411. [PMID: 39100921 PMCID: PMC11293126 DOI: 10.3114/sim.2024.108.01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 03/17/2024] [Indexed: 08/06/2024] Open
Abstract
The global diversity of fungi has been estimated between 2 to 11 million species, of which only about 155 000 have been named. Most fungi are invisible to the unaided eye, but they represent a major component of biodiversity on our planet, and play essential ecological roles, supporting life as we know it. Although approximately 20 000 fungal genera are presently recognised, the ecology of most remains undetermined. Despite all this diversity, the mycological community actively researches some fungal genera more commonly than others. This poses an interesting question: why have some fungal genera impacted mycology and related fields more than others? To address this issue, we conducted a bibliometric analysis to identify the top 100 most cited fungal genera. A thorough database search of the Web of Science, Google Scholar, and PubMed was performed to establish which genera are most cited. The most cited 10 genera are Saccharomyces, Candida, Aspergillus, Fusarium, Penicillium, Trichoderma, Botrytis, Pichia, Cryptococcus and Alternaria. Case studies are presented for the 100 most cited genera with general background, notes on their ecology and economic significance and important research advances. This paper provides a historic overview of scientific research of these genera and the prospect for further research. Citation: Bhunjun CS, Chen YJ, Phukhamsakda C, Boekhout T, Groenewald JZ, McKenzie EHC, Francisco EC, Frisvad JC, Groenewald M, Hurdeal VG, Luangsa-ard J, Perrone G, Visagie CM, Bai FY, Błaszkowski J, Braun U, de Souza FA, de Queiroz MB, Dutta AK, Gonkhom D, Goto BT, Guarnaccia V, Hagen F, Houbraken J, Lachance MA, Li JJ, Luo KY, Magurno F, Mongkolsamrit S, Robert V, Roy N, Tibpromma S, Wanasinghe DN, Wang DQ, Wei DP, Zhao CL, Aiphuk W, Ajayi-Oyetunde O, Arantes TD, Araujo JC, Begerow D, Bakhshi M, Barbosa RN, Behrens FH, Bensch K, Bezerra JDP, Bilański P, Bradley CA, Bubner B, Burgess TI, Buyck B, Čadež N, Cai L, Calaça FJS, Campbell LJ, Chaverri P, Chen YY, Chethana KWT, Coetzee B, Costa MM, Chen Q, Custódio FA, Dai YC, Damm U, de Azevedo Santiago ALCM, De Miccolis Angelini RM, Dijksterhuis J, Dissanayake AJ, Doilom M, Dong W, Alvarez-Duarte E, Fischer M, Gajanayake AJ, Gené J, Gomdola D, Gomes AAM, Hausner G, He MQ, Hou L, Iturrieta-González I, Jami F, Jankowiak R, Jayawardena RS, Kandemir H, Kiss L, Kobmoo N, Kowalski T, Landi L, Lin CG, Liu JK, Liu XB, Loizides M, Luangharn T, Maharachchikumbura SSN, Makhathini Mkhwanazi GJ, Manawasinghe IS, Marin-Felix Y, McTaggart AR, Moreau PA, Morozova OV, Mostert L, Osiewacz HD, Pem D, Phookamsak R, Pollastro S, Pordel A, Poyntner C, Phillips AJL, Phonemany M, Promputtha I, Rathnayaka AR, Rodrigues AM, Romanazzi G, Rothmann L, Salgado-Salazar C, Sandoval-Denis M, Saupe SJ, Scholler M, Scott P, Shivas RG, Silar P, Souza-Motta CM, Silva-Filho AGS, Spies CFJ, Stchigel AM, Sterflinger K, Summerbell RC, Svetasheva TY, Takamatsu S, Theelen B, Theodoro RC, Thines M, Thongklang N, Torres R, Turchetti B, van den Brule T, Wang XW, Wartchow F, Welti S, Wijesinghe SN, Wu F, Xu R, Yang ZL, Yilmaz N, Yurkov A, Zhao L, Zhao RL, Zhou N, Hyde KD, Crous PW (2024). What are the 100 most cited fungal genera? Studies in Mycology 108: 1-411. doi: 10.3114/sim.2024.108.01.
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Affiliation(s)
- C.S. Bhunjun
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Y.J. Chen
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - C. Phukhamsakda
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - T. Boekhout
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
- The Yeasts Foundation, Amsterdam, the Netherlands
| | - J.Z. Groenewald
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - E.H.C. McKenzie
- Landcare Research Manaaki Whenua, Private Bag 92170, Auckland, New Zealand
| | - E.C. Francisco
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
- Laboratório Especial de Micologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - J.C. Frisvad
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - V. G. Hurdeal
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - J. Luangsa-ard
- BIOTEC, National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - G. Perrone
- Institute of Sciences of Food Production, National Research Council (CNR-ISPA), Via G. Amendola 122/O, 70126 Bari, Italy
| | - C.M. Visagie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - F.Y. Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - J. Błaszkowski
- Laboratory of Plant Protection, Department of Shaping of Environment, West Pomeranian University of Technology in Szczecin, Słowackiego 17, PL-71434 Szczecin, Poland
| | - U. Braun
- Martin Luther University, Institute of Biology, Department of Geobotany and Botanical Garden, Neuwerk 21, 06099 Halle (Saale), Germany
| | - F.A. de Souza
- Núcleo de Biologia Aplicada, Embrapa Milho e Sorgo, Empresa Brasileira de Pesquisa Agropecuária, Rodovia MG 424 km 45, 35701–970, Sete Lagoas, MG, Brazil
| | - M.B. de Queiroz
- Programa de Pós-graduação em Sistemática e Evolução, Universidade Federal do Rio Grande do Norte, Campus Universitário, Natal-RN, 59078-970, Brazil
| | - A.K. Dutta
- Molecular & Applied Mycology Laboratory, Department of Botany, Gauhati University, Gopinath Bordoloi Nagar, Jalukbari, Guwahati - 781014, Assam, India
| | - D. Gonkhom
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - B.T. Goto
- Programa de Pós-graduação em Sistemática e Evolução, Universidade Federal do Rio Grande do Norte, Campus Universitário, Natal-RN, 59078-970, Brazil
| | - V. Guarnaccia
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, Largo Braccini 2, 10095 Grugliasco, TO, Italy
| | - F. Hagen
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
- Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, the Netherlands
| | - J. Houbraken
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - M.A. Lachance
- Department of Biology, University of Western Ontario London, Ontario, Canada N6A 5B7
| | - J.J. Li
- College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, P.R. China
| | - K.Y. Luo
- College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, P.R. China
| | - F. Magurno
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellońska 28, 40-032 Katowice, Poland
| | - S. Mongkolsamrit
- BIOTEC, National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - V. Robert
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - N. Roy
- Molecular & Applied Mycology Laboratory, Department of Botany, Gauhati University, Gopinath Bordoloi Nagar, Jalukbari, Guwahati - 781014, Assam, India
| | - S. Tibpromma
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, Yunnan 655011, P.R. China
| | - D.N. Wanasinghe
- Center for Mountain Futures, Kunming Institute of Botany, Honghe 654400, Yunnan, China
| | - D.Q. Wang
- College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, P.R. China
| | - D.P. Wei
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, P.R. China
| | - C.L. Zhao
- College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, P.R. China
| | - W. Aiphuk
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - O. Ajayi-Oyetunde
- Syngenta Crop Protection, 410 S Swing Rd, Greensboro, NC. 27409, USA
| | - T.D. Arantes
- Laboratório de Micologia, Departamento de Biociências e Tecnologia, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, 74605-050, Goiânia, GO, Brazil
| | - J.C. Araujo
- Mykocosmos - Mycology and Science Communication, Rua JP 11 Qd. 18 Lote 13, Jd. Primavera 1ª etapa, Post Code 75.090-260, Anápolis, Goiás, Brazil
- Secretaria de Estado da Educação de Goiás (SEDUC/ GO), Quinta Avenida, Quadra 71, número 212, Setor Leste Vila Nova, Goiânia, Goiás, 74643-030, Brazil
| | - D. Begerow
- Organismic Botany and Mycology, Institute of Plant Sciences and Microbiology, Ohnhorststraße 18, 22609 Hamburg, Germany
| | - M. Bakhshi
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - R.N. Barbosa
- Micoteca URM-Department of Mycology Prof. Chaves Batista, Federal University of Pernambuco, Av. Prof. Moraes Rego, s/n, Center for Biosciences, University City, Recife, Pernambuco, Zip Code: 50670-901, Brazil
| | - F.H. Behrens
- Julius Kühn-Institute, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Geilweilerhof, D-76833 Siebeldingen, Germany
| | - K. Bensch
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - J.D.P. Bezerra
- Laboratório de Micologia, Departamento de Biociências e Tecnologia, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, 74605-050, Goiânia, GO, Brazil
| | - P. Bilański
- Department of Forest Ecosystems Protection, Faculty of Forestry, University of Agriculture in Krakow, Al. 29 Listopada 46, 31-425 Krakow, Poland
| | - C.A. Bradley
- Department of Plant Pathology, University of Kentucky, Princeton, KY 42445, USA
| | - B. Bubner
- Johan Heinrich von Thünen-Institut, Bundesforschungsinstitut für Ländliche Räume, Wald und Fischerei, Institut für Forstgenetik, Eberswalder Chaussee 3a, 15377 Waldsieversdorf, Germany
| | - T.I. Burgess
- Harry Butler Institute, Murdoch University, Murdoch, 6150, Australia
| | - B. Buyck
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 39, 75231, Paris cedex 05, France
| | - N. Čadež
- University of Ljubljana, Biotechnical Faculty, Food Science and Technology Department Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - L. Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - F.J.S. Calaça
- Mykocosmos - Mycology and Science Communication, Rua JP 11 Qd. 18 Lote 13, Jd. Primavera 1ª etapa, Post Code 75.090-260, Anápolis, Goiás, Brazil
- Secretaria de Estado da Educação de Goiás (SEDUC/ GO), Quinta Avenida, Quadra 71, número 212, Setor Leste Vila Nova, Goiânia, Goiás, 74643-030, Brazil
- Laboratório de Pesquisa em Ensino de Ciências (LabPEC), Centro de Pesquisas e Educação Científica, Universidade Estadual de Goiás, Campus Central (CEPEC/UEG), Anápolis, GO, 75132-903, Brazil
| | - L.J. Campbell
- School of Veterinary Medicine, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - P. Chaverri
- Centro de Investigaciones en Productos Naturales (CIPRONA) and Escuela de Biología, Universidad de Costa Rica, 11501-2060, San José, Costa Rica
- Department of Natural Sciences, Bowie State University, Bowie, Maryland, U.S.A
| | - Y.Y. Chen
- Guizhou Key Laboratory of Agricultural Biotechnology, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - K.W.T. Chethana
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - B. Coetzee
- Department of Plant Pathology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
- School for Data Sciences and Computational Thinking, University of Stellenbosch, South Africa
| | - M.M. Costa
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - Q. Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - F.A. Custódio
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa-MG, Brazil
| | - Y.C. Dai
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - U. Damm
- Senckenberg Museum of Natural History Görlitz, PF 300 154, 02806 Görlitz, Germany
| | - A.L.C.M.A. Santiago
- Post-graduate course in the Biology of Fungi, Department of Mycology, Federal University of Pernambuco, Av. Prof. Moraes Rego, s/n, 50740-465, Recife, PE, Brazil
| | | | - J. Dijksterhuis
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - A.J. Dissanayake
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - M. Doilom
- Innovative Institute for Plant Health/Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, Guangdong, P.R. China
| | - W. Dong
- Innovative Institute for Plant Health/Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, Guangdong, P.R. China
| | - E. Álvarez-Duarte
- Mycology Unit, Microbiology and Mycology Program, Biomedical Sciences Institute, University of Chile, Chile
| | - M. Fischer
- Julius Kühn-Institute, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Geilweilerhof, D-76833 Siebeldingen, Germany
| | - A.J. Gajanayake
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - J. Gené
- Unitat de Micologia i Microbiologia Ambiental, Facultat de Medicina i Ciències de la Salut & IURESCAT, Universitat Rovira i Virgili (URV), Reus, Catalonia Spain
| | - D. Gomdola
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Mai 50150, Thailand
| | - A.A.M. Gomes
- Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Recife-PE, Brazil
| | - G. Hausner
- Department of Microbiology, University of Manitoba, Winnipeg, MB, R3T 5N6
| | - M.Q. He
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - L. Hou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Space Nutrition and Food Engineering, China Astronaut Research and Training Center, Beijing, 100094, China
| | - I. Iturrieta-González
- Unitat de Micologia i Microbiologia Ambiental, Facultat de Medicina i Ciències de la Salut & IURESCAT, Universitat Rovira i Virgili (URV), Reus, Catalonia Spain
- Department of Preclinic Sciences, Medicine Faculty, Laboratory of Infectology and Clinical Immunology, Center of Excellence in Translational Medicine-Scientific and Technological Nucleus (CEMT-BIOREN), Universidad de La Frontera, Temuco 4810296, Chile
| | - F. Jami
- Plant Health and Protection, Agricultural Research Council, Pretoria, South Africa
| | - R. Jankowiak
- Department of Forest Ecosystems Protection, Faculty of Forestry, University of Agriculture in Krakow, Al. 29 Listopada 46, 31-425 Krakow, Poland
| | - R.S. Jayawardena
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, South Korea
| | - H. Kandemir
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - L. Kiss
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, QLD 4350 Toowoomba, Australia
- Centre for Research and Development, Eszterházy Károly Catholic University, H-3300 Eger, Hungary
| | - N. Kobmoo
- BIOTEC, National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - T. Kowalski
- Department of Forest Ecosystems Protection, Faculty of Forestry, University of Agriculture in Krakow, Al. 29 Listopada 46, 31-425 Krakow, Poland
| | - L. Landi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - C.G. Lin
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - J.K. Liu
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - X.B. Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, P.R. China
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Temesvári krt. 62, Szeged H-6726, Hungary
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
| | | | - T. Luangharn
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - S.S.N. Maharachchikumbura
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - G.J. Makhathini Mkhwanazi
- Department of Plant Pathology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
| | - I.S. Manawasinghe
- Innovative Institute for Plant Health/Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, Guangdong, P.R. China
| | - Y. Marin-Felix
- Department Microbial Drugs, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, 38106, Braunschweig, Germany
| | - A.R. McTaggart
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, Dutton Park 4102, Queensland, Australia
| | - P.A. Moreau
- Univ. Lille, ULR 4515 - LGCgE, Laboratoire de Génie Civil et géo-Environnement, F-59000 Lille, France
| | - O.V. Morozova
- Komarov Botanical Institute of the Russian Academy of Sciences, 2, Prof. Popov Str., 197376 Saint Petersburg, Russia
- Tula State Lev Tolstoy Pedagogical University, 125, Lenin av., 300026 Tula, Russia
| | - L. Mostert
- Department of Plant Pathology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
| | - H.D. Osiewacz
- Faculty for Biosciences, Institute for Molecular Biosciences, Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt/Main, Germany
| | - D. Pem
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Mai 50150, Thailand
| | - R. Phookamsak
- Center for Mountain Futures, Kunming Institute of Botany, Honghe 654400, Yunnan, China
| | - S. Pollastro
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - A. Pordel
- Plant Protection Research Department, Baluchestan Agricultural and Natural Resources Research and Education Center, AREEO, Iranshahr, Iran
| | - C. Poyntner
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - A.J.L. Phillips
- Faculdade de Ciências, Biosystems and Integrative Sciences Institute (BioISI), Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal
| | - M. Phonemany
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Mai 50150, Thailand
| | - I. Promputtha
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - A.R. Rathnayaka
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Mai 50150, Thailand
| | - A.M. Rodrigues
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo, 04023062, Brazil
| | - G. Romanazzi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - L. Rothmann
- Plant Pathology, Department of Plant Sciences, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein, 9301, South Africa
| | - C. Salgado-Salazar
- Mycology and Nematology Genetic Diversity and Biology Laboratory, U.S. Department of Agriculture, Agriculture Research Service (USDA-ARS), 10300 Baltimore Avenue, Beltsville MD, 20705, USA
| | - M. Sandoval-Denis
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - S.J. Saupe
- Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS Université de Bordeaux, 1 rue Camille Saint Saëns, 33077 Bordeaux cedex, France
| | - M. Scholler
- Staatliches Museum für Naturkunde Karlsruhe, Erbprinzenstraße 13, 76133 Karlsruhe, Germany
| | - P. Scott
- Harry Butler Institute, Murdoch University, Murdoch, 6150, Australia
- Sustainability and Biosecurity, Department of Primary Industries and Regional Development, Perth WA 6000, Australia
| | - R.G. Shivas
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, QLD 4350 Toowoomba, Australia
| | - P. Silar
- Laboratoire Interdisciplinaire des Energies de Demain, Université de Paris Cité, 75205 Paris Cedex, France
| | - A.G.S. Silva-Filho
- IFungiLab, Departamento de Ciências e Matemática (DCM), Instituto Federal de Educação, Ciência e Tecnologia de São Paulo (IFSP), São Paulo, BraziI
| | - C.M. Souza-Motta
- Micoteca URM-Department of Mycology Prof. Chaves Batista, Federal University of Pernambuco, Av. Prof. Moraes Rego, s/n, Center for Biosciences, University City, Recife, Pernambuco, Zip Code: 50670-901, Brazil
| | - C.F.J. Spies
- Agricultural Research Council - Plant Health and Protection, Private Bag X5017, Stellenbosch, 7599, South Africa
| | - A.M. Stchigel
- Unitat de Micologia i Microbiologia Ambiental, Facultat de Medicina i Ciències de la Salut & IURESCAT, Universitat Rovira i Virgili (URV), Reus, Catalonia Spain
| | - K. Sterflinger
- Institute of Natural Sciences and Technology in the Arts (INTK), Academy of Fine Arts Vienna, Augasse 2–6, 1090, Vienna, Austria
| | - R.C. Summerbell
- Sporometrics, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - T.Y. Svetasheva
- Tula State Lev Tolstoy Pedagogical University, 125, Lenin av., 300026 Tula, Russia
| | - S. Takamatsu
- Mie University, Graduate School, Department of Bioresources, 1577 Kurima-Machiya, Tsu 514-8507, Japan
| | - B. Theelen
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - R.C. Theodoro
- Laboratório de Micologia Médica, Instituto de Medicina Tropical do RN, Universidade Federal do Rio Grande do Norte, 59078-900, Natal, RN, Brazil
| | - M. Thines
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt Am Main, Germany
| | - N. Thongklang
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - R. Torres
- IRTA, Postharvest Programme, Edifici Fruitcentre, Parc Agrobiotech de Lleida, Parc de Gardeny, 25003, Lleida, Catalonia, Spain
| | - B. Turchetti
- Department of Agricultural, Food and Environmental Sciences and DBVPG Industrial Yeasts Collection, University of Perugia, Italy
| | - T. van den Brule
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
- TIFN, P.O. Box 557, 6700 AN Wageningen, the Netherlands
| | - X.W. Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - F. Wartchow
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, Paraiba, João Pessoa, Brazil
| | - S. Welti
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, 38106, Braunschweig, Germany
| | - S.N. Wijesinghe
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Mai 50150, Thailand
| | - F. Wu
- State Key Laboratory of Efficient Production of Forest Resources, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - R. Xu
- School of Food Science and Engineering, Yangzhou University, Yangzhou 225127, China
- Internationally Cooperative Research Center of China for New Germplasm Breeding of Edible Mushroom, Jilin Agricultural University, Changchun 130118, China
| | - Z.L. Yang
- Syngenta Crop Protection, 410 S Swing Rd, Greensboro, NC. 27409, USA
- Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
| | - N. Yilmaz
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - A. Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - L. Zhao
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - R.L. Zhao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - N. Zhou
- Department of Biological Sciences and Biotechnology, Botswana University of Science and Technology, Private Bag, 16, Palapye, Botswana
| | - K.D. Hyde
- School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
- Innovative Institute for Plant Health/Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, Guangdong, P.R. China
- Key Laboratory of Economic Plants and Biotechnology and the Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - P.W. Crous
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht
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Chen JR, Aguirre-Carvajal K, Xue DY, Chang HC, Arone-Maxwell L, Lin YP, Armijos-Jaramillo V, Oliva R. Exploring the genetic makeup of Xanthomonas species causing bacterial spot in Taiwan: evidence of population shift and local adaptation. Front Microbiol 2024; 15:1408885. [PMID: 38846563 PMCID: PMC11153759 DOI: 10.3389/fmicb.2024.1408885] [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: 03/29/2024] [Accepted: 05/13/2024] [Indexed: 06/09/2024] Open
Abstract
The introduction of plant pathogens can quickly reshape disease dynamics in island agro-ecologies, representing a continuous challenge for local crop management strategies. Xanthomonas pathogens causing tomato bacterial spot were probably introduced in Taiwan several decades ago, creating a unique opportunity to study the genetic makeup and adaptive response of this alien population. We examined the phenotypic and genotypic identity of 669 pathogen entries collected across different regions of Taiwan in the last three decades. The analysis detected a major population shift, where X. euvesicatoria and X. vesicatoria races T1 and T2 were replaced by new races of X. perforans. After its introduction, race T4 quickly became dominant in all tomato-growing areas of the island. The genomic analysis of 317 global genomes indicates that the Xanthomonas population in Taiwan has a narrow genetic background, most likely resulting from a small number of colonization events. However, despite the apparent genetic uniformity, X. perforans race T4 shows multiple phenotypic responses in tomato lines. Additionally, an in-depth analysis of effector composition suggests diversification in response to local adaptation. These include unique mutations on avrXv3 which might allow the pathogen to overcome Xv3/Rx4 resistance gene. The findings underscore the dynamic evolution of a pathogen when introduced in a semi-isolated environment and provide insights into the potential management strategies for this important disease of tomato.
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Affiliation(s)
- Jaw-Rong Chen
- Safe and Sustainable Value Chain, World Vegetable Center, Shanhua, Taiwan
| | - Kevin Aguirre-Carvajal
- Research Center of Information and Communication Technologies, University of A Coruña, A Coruña, Spain
- Bio-Cheminformatics Research Group, Universidad de Las Américas, Quito, Ecuador
| | - Dao-Yuan Xue
- Seed and Seedling Management Section, Taiwan Seed Improvement and Propagation Station, Ministry of Agriculture, Taichung, Taiwan
| | - Hung-Chia Chang
- Safe and Sustainable Value Chain, World Vegetable Center, Shanhua, Taiwan
| | | | - Ya-Ping Lin
- Safe and Sustainable Value Chain, World Vegetable Center, Shanhua, Taiwan
| | - Vinicio Armijos-Jaramillo
- Bio-Cheminformatics Research Group, Universidad de Las Américas, Quito, Ecuador
- Facultad de Ingeniería y Ciencias Aplicadas, Universidad de Las Américas, Quito, Ecuador
| | - Ricardo Oliva
- Safe and Sustainable Value Chain, World Vegetable Center, Shanhua, Taiwan
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Kaur N, Mehl HL, Langston D, Haak DC. Evaluation of Stagonospora Nodorum Blotch Severity and Parastagonospora nodorum Population Structure and Genetic Diversity Across Multiple Locations and Wheat Varieties in Virginia. PHYTOPATHOLOGY 2024; 114:258-268. [PMID: 37316953 DOI: 10.1094/phyto-10-22-0392-r] [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: 06/16/2023]
Abstract
Parastagonospora nodorum is a necrotrophic pathogen that causes Stagonospora nodorum blotch (SNB) in wheat. Wheat varieties grown in Virginia vary in susceptibility to SNB, and the severity of SNB varies across locations and years. However, the impacts of wheat genetic backgrounds and environments on SNB severity and the structure of P. nodorum populations in the region have not been well studied. Thus, a population genetic study was conducted utilizing P. nodorum isolates collected from different wheat varieties and locations in Virginia. A total of 320 isolates were collected at seven locations over 2 years from five wheat varieties. Isolates were genotyped using multilocus simple sequence repeat markers, and necrotrophic effector (NE) and mating type genes were amplified using gene-specific primers. Wheat varieties varied in susceptibility to SNB, but site-specific environmental conditions were the primary drivers of disease severity. Fungal populations were genetically diverse, but no genetic subdivision was observed among locations or varieties. The ratio of the two mating type idiomorphs was not significantly different from 1:1, consistent with the P. nodorum population undergoing sexual reproduction. Three major NE genes were detected within the P. nodorum population, but not with equal frequency. However, NE gene profiles were similar for groups of isolates originating from different varieties, suggesting that wheat genetic backgrounds do not differentially select for NEs. There was no evidence of population structure among P. nodorum populations in Virginia and, thus, no support for wheat genetic backgrounds shaping these populations. Finally, although varieties only exhibited moderate resistance to SNB, current levels of resistance are likely to be durable over time and remain a useful tool for integrated management of SNB in the region. [Formula: see text] Copyright © 2024 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)
- Navjot Kaur
- School of Plant and Environmental Sciences, VA Tech, Blacksburg, VA 24061
- Virginia Tech Tidewater Agricultural Research and Extension Center, Suffolk, VA 23437
| | - Hillary L Mehl
- School of Plant and Environmental Sciences, VA Tech, Blacksburg, VA 24061
- Virginia Tech Tidewater Agricultural Research and Extension Center, Suffolk, VA 23437
| | - David Langston
- School of Plant and Environmental Sciences, VA Tech, Blacksburg, VA 24061
- Virginia Tech Tidewater Agricultural Research and Extension Center, Suffolk, VA 23437
| | - David C Haak
- School of Plant and Environmental Sciences, VA Tech, Blacksburg, VA 24061
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Kariyawasam GK, Nelson AC, Williams SJ, Solomon PS, Faris JD, Friesen TL. The Necrotrophic Pathogen Parastagonospora nodorum Is a Master Manipulator of Wheat Defense. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:764-773. [PMID: 37581456 DOI: 10.1094/mpmi-05-23-0067-irw] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
Parastagonospora nodorum is a necrotrophic pathogen of wheat that is particularly destructive in major wheat-growing regions of the United States, northern Europe, Australia, and South America. P. nodorum secretes necrotrophic effectors that target wheat susceptibility genes to induce programmed cell death (PCD), resulting in increased colonization of host tissue and, ultimately, sporulation to complete its pathogenic life cycle. Intensive research over the last two decades has led to the functional characterization of five proteinaceous necrotrophic effectors, SnTox1, SnToxA, SnTox267, SnTox3, and SnTox5, and three wheat susceptibility genes, Tsn1, Snn1, and Snn3D-1. Functional characterization has revealed that these effectors, in addition to inducing PCD, have additional roles in pathogenesis, including chitin binding that results in protection from wheat chitinases, blocking defense response signaling, and facilitating plant colonization. There are still large gaps in our understanding of how this necrotrophic pathogen is successfully manipulating wheat defense to complete its life cycle. This review summarizes our current knowledge, identifies knowledge gaps, and provides a summary of well-developed tools and resources currently available to study the P. nodorum-wheat interaction, which has become a model for necrotrophic specialist interactions. Further functional characterization of the effectors involved in this interaction and work toward a complete understanding of how P. nodorum manipulates wheat defense will provide fundamental knowledge about this and other necrotrophic interactions. Additionally, a broader understanding of this interaction will contribute to the successful management of Septoria nodorum blotch disease on wheat. [Formula: see text] Copyright © 2023 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)
- Gayan K Kariyawasam
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102, U.S.A
| | - Ashley C Nelson
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102, U.S.A
| | - Simon J Williams
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Peter S Solomon
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Justin D Faris
- Cereal Crops Research Unit, USDA-ARS, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102, U.S.A
| | - Timothy L Friesen
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102, U.S.A
- Cereal Crops Research Unit, USDA-ARS, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102, U.S.A
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8
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Adhikari U, Brown J, Ojiambo PS, Cowger C. Effects of Host and Weather Factors on the Growth Rate of Septoria nodorum Blotch Lesions on Winter Wheat. PHYTOPATHOLOGY 2023; 113:1898-1907. [PMID: 37147578 DOI: 10.1094/phyto-12-22-0476-r] [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: 05/07/2023]
Abstract
Septoria nodorum blotch (SNB), caused by Parastagonospora nodorum, is a major disease of winter wheat that occurs frequently in the central and southeastern United States. Quantitative resistance to SNB in wheat is determined by various disease resistance components and their interaction with environmental factors. A study was conducted in North Carolina from 2018 to 2020 to characterize SNB lesion size and growth rate and to quantify the effects of temperature and relative humidity on lesion expansion in winter wheat cultivars with different levels of resistance. Disease was initiated in the field by spreading P. nodorum-infected wheat straw in experimental plots. Cohorts (groups of foliar lesions arbitrarily selected and tagged as an observational unit) were sequentially selected and monitored throughout each season. Lesion area was measured at regular intervals, and weather data were collected using in-field data loggers and the nearest weather stations. Final mean lesion area was approximately seven times greater on susceptible than on moderately resistant cultivars, and lesion growth rate was approximately four times higher on susceptible than on moderately resistant cultivars. Across trials and cultivars, temperature had a strong effect of increasing lesion growth rates (P < 0.001), while relative humidity had no significant effect (P = 0.34). Lesion growth rate declined slightly and steadily over the duration of cohort assessment. Our results demonstrate that restricting lesion growth is an important component of SNB resistance in the field and suggest that the ability to limit lesion size may be a useful breeding goal.
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Affiliation(s)
- Urmila Adhikari
- Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, U.S.A
| | - James Brown
- John Innes Centre, Norwich Research Park, Colney, Norwich, U.K
| | - Peter S Ojiambo
- Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, U.S.A
| | - Christina Cowger
- Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, U.S.A
- U.S. Department of Agriculture-Agricultural Research Service, Raleigh, NC, U.S.A
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9
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Ndinga-Muniania C, Wornson N, Fulcher MR, Borer ET, Seabloom EW, Kinkel L, May G. Cryptic functional diversity within a grass mycobiome. PLoS One 2023; 18:e0287990. [PMID: 37471328 PMCID: PMC10358963 DOI: 10.1371/journal.pone.0287990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/17/2023] [Indexed: 07/22/2023] Open
Abstract
Eukaryotic hosts harbor tremendously diverse microbiomes that affect host fitness and response to environmental challenges. Fungal endophytes are prominent members of plant microbiomes, but we lack information on the diversity in functional traits affecting their interactions with their host and environment. We used two culturing approaches to isolate fungal endophytes associated with the widespread, dominant prairie grass Andropogon gerardii and characterized their taxonomic diversity using rDNA barcode sequencing. A randomly chosen subset of fungi representing the diversity of each leaf was then evaluated for their use of different carbon compound resources and growth on those resources. Applying community phylogenetic analyses, we discovered that these fungal endophyte communities are comprised of phylogenetically distinct assemblages of slow- and fast-growing fungi that differ in their use and growth on differing carbon substrates. Our results demonstrate previously undescribed and cryptic functional diversity in carbon resource use and growth in fungal endophyte communities of A. gerardii.
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Affiliation(s)
- Cedric Ndinga-Muniania
- Plant and Microbial Biology Graduate Program, University of Minnesota, St. Paul, Minnesota, United States of America
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Nicholas Wornson
- School of Statistics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Plant Pathology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Michael R Fulcher
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture, Frederick, Maryland, United States of America
| | - Elizabeth T Borer
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Eric W Seabloom
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Linda Kinkel
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
- Department of Plant Pathology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Georgiana May
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
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10
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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.
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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
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11
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Aboukhaddour R, Hafez M, McDonald M, Moffat CS, Navathe S, Friesen TL, Strelkov SE, Oliver RP, Tan KC, Liu Z, Moolhuijzen PM, Phan H, See PT, Solomon PS. A Revised Nomenclature for ToxA Haplotypes Across Multiple Fungal Species. PHYTOPATHOLOGY 2023; 113:1180-1184. [PMID: 36809076 DOI: 10.1094/phyto-01-23-0017-sc] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
ToxA is one of the most studied proteinaceous necrotrophic effectors produced by plant pathogens. It has been identified in four pathogens (Pyrenophora tritici-repentis, Parastagonospora nodorum, Parastagonospora pseudonodorum [formerly Parastagonospora avenaria f. sp. tritici], and Bipolaris sorokiniana) causing leaf spot diseases on cereals worldwide. To date, 24 different ToxA haplotypes have been identified. Some P. tritici-repentis and related species also express ToxB, another small protein necrotrophic effector. We present here a revised and standardized nomenclature for these effectors, which could be extended to other poly-haplotypic genes found across multiple species.
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Affiliation(s)
- Reem Aboukhaddour
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Center, Lethbridge, Alberta, Canada
| | - Mohamed Hafez
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Center, Lethbridge, Alberta, Canada
| | - Megan McDonald
- School of Biosciences, University of Birmingham, Institute of Microbiology and Infection, Edgbaston, Birmingham, U.K
| | - Caroline S Moffat
- Centre for Crop Disease and Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Sudhir Navathe
- Agharkar Research Institute, Department Science and Technology, Govt. of India, Pune, 411004, India
| | - Timothy L Friesen
- USDA-ARS, Edward T. Schafer Agricultural Research Center, Cereal Crops Research Unit, Fargo, ND 58102-2765, U.S.A
- Department of Plant Pathology, North Dakota State University, Fargo, ND, U.S.A
| | - Stephen E Strelkov
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | | | - Kar-Chun Tan
- Centre for Crop Disease and Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, ND, U.S.A
| | - Paula M Moolhuijzen
- Centre for Crop Disease and Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Huyen Phan
- Centre for Crop Disease and Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Pao Theen See
- Centre for Crop Disease and Management, School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Peter S Solomon
- Division of Plant Sciences, Research School of Biology, The Australian National University ACT, Australia
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12
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Lovelace AH, Dorhmi S, Hulin MT, Li Y, Mansfield JW, Ma W. Effector Identification in Plant Pathogens. PHYTOPATHOLOGY 2023; 113:637-650. [PMID: 37126080 DOI: 10.1094/phyto-09-22-0337-kd] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Effectors play a central role in determining the outcome of plant-pathogen interactions. As key virulence proteins, effectors are collectively indispensable for disease development. By understanding the virulence mechanisms of effectors, fundamental knowledge of microbial pathogenesis and disease resistance have been revealed. Effectors are also considered double-edged swords because some of them activate immunity in disease resistant plants after being recognized by specific immune receptors, which evolved to monitor pathogen presence or activity. Characterization of effector recognition by their cognate immune receptors and the downstream immune signaling pathways is instrumental in implementing resistance. Over the past decades, substantial research effort has focused on effector biology, especially concerning their interactions with virulence targets or immune receptors in plant cells. A foundation of this research is robust identification of the effector repertoire from a given pathogen, which depends heavily on bioinformatic prediction. In this review, we summarize methodologies that have been used for effector mining in various microbial pathogens which use different effector delivery mechanisms. We also discuss current limitations and provide perspectives on how recently developed analytic tools and technologies may facilitate effector identification and hence generation of a more complete vision of host-pathogen interactions. [Formula: see text] Copyright © 2023 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)
| | - Sara Dorhmi
- The Sainsbury Laboratory, Norwich, NR4 7UH, U.K
- Department of Microbiology and Plant Pathology, University of California Riverside, CA 92521, U.S.A
| | | | - Yufei Li
- The Sainsbury Laboratory, Norwich, NR4 7UH, U.K
| | - John W Mansfield
- Faculty of Natural Sciences, Imperial College London, London, SW7 2BX, U.K
| | - Wenbo Ma
- The Sainsbury Laboratory, Norwich, NR4 7UH, U.K
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13
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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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14
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The use of evolutionary analyses to predict functionally relevant traits in filamentous plant pathogens. Curr Opin Microbiol 2023; 73:102244. [PMID: 36889024 DOI: 10.1016/j.mib.2022.102244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 10/27/2022] [Accepted: 11/03/2022] [Indexed: 03/08/2023]
Abstract
Identifying traits involved in plant-pathogen interactions is one of the major objectives in molecular plant pathology. Evolutionary analyses may assist in the identification of genes encoding traits that are involved in virulence and local adaptation, including adaptation to agricultural intervention strategies. In the past decades, the number of available genome sequences of fungal plant pathogens has rapidly increased, providing a rich source for the discovery of functionally important genes as well as inference of species histories. Positive selection in the form of diversifying or directional selection leaves particular signatures in genome alignments and can be identified with statistical genetics methods. This review summarises the concepts and approaches used in evolutionary genomics and lists major discoveries related to plant-pathogen adaptative evolution. We underline the significant contribution of evolutionary genomics in discovering virulence-related traits and the study of plant-pathogen ecology and adaptive evolution.
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15
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Guo Y, Betzen B, Salcedo A, He F, Bowden RL, Fellers JP, Jordan KW, Akhunova A, Rouse MN, Szabo LJ, Akhunov E. Population genomics of Puccinia graminis f.sp. tritici highlights the role of admixture in the origin of virulent wheat rust races. Nat Commun 2022; 13:6287. [PMID: 36271077 PMCID: PMC9587050 DOI: 10.1038/s41467-022-34050-w] [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: 03/31/2022] [Accepted: 10/12/2022] [Indexed: 12/25/2022] Open
Abstract
Puccinia graminis f.sp. tritici (Pgt) causes stem rust disease in wheat that can result in severe yield losses. The factors driving the evolution of its virulence and adaptation remain poorly characterized. We utilize long-read sequencing to develop a haplotype-resolved genome assembly of a U.S. isolate of Pgt. Using Pgt haplotypes as a reference, we characterize the structural variants (SVs) and single nucleotide polymorphisms in a diverse panel of isolates. SVs impact the repertoire of predicted effectors, secreted proteins involved in host-pathogen interaction, and show evidence of purifying selection. By analyzing global and local genomic ancestry we demonstrate that the origin of 8 out of 12 Pgt clades is linked with either somatic hybridization or sexual recombination between the diverged donor populations. Our study shows that SVs and admixture events appear to play an important role in broadening Pgt virulence and the origin of highly virulent races, creating a resource for studying the evolution of Pgt virulence and preventing future epidemic outbreaks.
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Affiliation(s)
- Yuanwen Guo
- grid.36567.310000 0001 0737 1259Department of Plant Pathology, Kansas State University, Manhattan, KS USA
| | - Bliss Betzen
- grid.36567.310000 0001 0737 1259Department of Plant Pathology, Kansas State University, Manhattan, KS USA ,grid.36567.310000 0001 0737 1259Present Address: USDA-APHIS-PPQ Field Operations, Kansas State University, Manhattan, KS USA
| | - Andres Salcedo
- grid.36567.310000 0001 0737 1259Department of Plant Pathology, Kansas State University, Manhattan, KS USA ,grid.40803.3f0000 0001 2173 6074Present Address: Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC USA
| | - Fei He
- grid.36567.310000 0001 0737 1259Department of Plant Pathology, Kansas State University, Manhattan, KS USA ,grid.9227.e0000000119573309Present Address: State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Robert L. Bowden
- grid.512831.cUSDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS USA
| | - John P. Fellers
- grid.512831.cUSDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS USA
| | - Katherine W. Jordan
- grid.36567.310000 0001 0737 1259Department of Plant Pathology, Kansas State University, Manhattan, KS USA ,grid.512831.cUSDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS USA
| | - Alina Akhunova
- grid.36567.310000 0001 0737 1259Department of Plant Pathology, Kansas State University, Manhattan, KS USA ,grid.36567.310000 0001 0737 1259Integrated Genomics Facility, Kansas State University, Manhattan, KS USA
| | - Mathew N. Rouse
- grid.512864.c0000 0000 8881 3436Department of Plant Pathology, University of Minnesota & USDA-ARS, Cereal Disease Lab, St. Paul, MN USA
| | - Les J. Szabo
- grid.512864.c0000 0000 8881 3436Department of Plant Pathology, University of Minnesota & USDA-ARS, Cereal Disease Lab, St. Paul, MN USA
| | - Eduard Akhunov
- grid.36567.310000 0001 0737 1259Department of Plant Pathology, Kansas State University, Manhattan, KS USA ,grid.36567.310000 0001 0737 1259Wheat Genetics Resource Center, Kansas State University, Manhattan, KS USA
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16
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Mapuranga J, Zhang N, Zhang L, Chang J, Yang W. Infection Strategies and Pathogenicity of Biotrophic Plant Fungal Pathogens. Front Microbiol 2022; 13:799396. [PMID: 35722337 PMCID: PMC9201565 DOI: 10.3389/fmicb.2022.799396] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 04/19/2022] [Indexed: 01/01/2023] Open
Abstract
Biotrophic plant pathogenic fungi are widely distributed and are among the most damaging pathogenic organisms of agriculturally important crops responsible for significant losses in quality and yield. However, the pathogenesis of obligate parasitic pathogenic microorganisms is still under investigation because they cannot reproduce and complete their life cycle on an artificial medium. The successful lifestyle of biotrophic fungal pathogens depends on their ability to secrete effector proteins to manipulate or evade plant defense response. By integrating genomics, transcriptomics, and effectoromics, insights into how the adaptation of biotrophic plant fungal pathogens adapt to their host populations can be gained. Efficient tools to decipher the precise molecular mechanisms of rust–plant interactions, and standardized routines in genomics and functional pipelines have been established and will pave the way for comparative studies. Deciphering fungal pathogenesis not only allows us to better understand how fungal pathogens infect host plants but also provides valuable information for plant diseases control, including new strategies to prevent, delay, or inhibit fungal development. Our review provides a comprehensive overview of the efforts that have been made to decipher the effector proteins of biotrophic fungal pathogens and demonstrates how rapidly research in the field of obligate biotrophy has progressed.
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17
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Rafiqi M, Jelonek L, Diouf AM, Mbaye A, Rep M, Diarra A. Profile of the in silico secretome of the palm dieback pathogen, Fusarium oxysporum f. sp. albedinis, a fungus that puts natural oases at risk. PLoS One 2022; 17:e0260830. [PMID: 35617325 PMCID: PMC9135196 DOI: 10.1371/journal.pone.0260830] [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: 11/15/2021] [Accepted: 04/28/2022] [Indexed: 11/18/2022] Open
Abstract
Understanding biotic changes that occur alongside climate change constitute a research priority of global significance. Here, we address a plant pathogen that poses a serious threat to life on natural oases, where climate change is already taking a toll and severely impacting human subsistence. Fusarium oxysporum f. sp. albedinis is a pathogen that causes dieback disease on date palms, a tree that provides several critical ecosystem services in natural oases; and consequently, of major importance in this vulnerable habitat. Here, we assess the current state of global pathogen spread, we annotate the genome of a sequenced pathogen strain isolated from the native range and we analyse its in silico secretome. The palm dieback pathogen secretes a large arsenal of effector candidates including a variety of toxins, a distinguished profile of secreted in xylem proteins (SIX) as well as an expanded protein family with an N-terminal conserved motif [SG]PC[KR]P that could be involved in interactions with host membranes. Using agrobiodiversity as a strategy to decrease pathogen infectivity, while providing short term resilient solutions, seems to be widely overcome by the pathogen. Hence, the urgent need for future mechanistic research on the palm dieback disease and a better understanding of pathogen genetic diversity.
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Affiliation(s)
- Maryam Rafiqi
- Plant Pathology Program, Agrobiosciences, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
| | - Lukas Jelonek
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Aliou Moussa Diouf
- Plant Pathology Program, Agrobiosciences, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
| | - AbdouLahat Mbaye
- Plant Pathology Program, Agrobiosciences, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
| | - Martijn Rep
- Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Alhousseine Diarra
- Digital 4 Research Labs, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
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18
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Yuan Z, Wu Q, Xu L, Druzhinina IS, Stukenbrock EH, Nieuwenhuis BPS, Zhong Z, Liu ZJ, Wang X, Cai F, Kubicek CP, Shan X, Wang J, Shi G, Peng L, Martin FM. Genomic landscape of a relict fir-associated fungus reveals rapid convergent adaptation towards endophytism. THE ISME JOURNAL 2022; 16:1294-1305. [PMID: 34916613 PMCID: PMC9038928 DOI: 10.1038/s41396-021-01176-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 12/02/2021] [Accepted: 12/08/2021] [Indexed: 12/24/2022]
Abstract
Comparative and pan-genomic analyses of the endophytic fungus Pezicula neosporulosa (Helotiales, Ascomycota) from needles of the relict fir, Abies beshanzuensis, showed expansions of carbohydrate metabolism and secondary metabolite biosynthetic genes characteristic for unrelated plant-beneficial helotialean, such as dark septate endophytes and ericoid mycorrhizal fungi. The current species within the relatively young Pliocene genus Pezicula are predominantly saprotrophic, while P. neosporulosa lacks such features. To understand the genomic background of this putatively convergent evolution, we performed population analyses of 77 P. neosporulosa isolates. This revealed a mosaic structure of a dozen non-recombining and highly genetically polymorphic subpopulations with a unique mating system structure. We found that one idiomorph of a probably duplicated mat1-2 gene was found in putatively heterothallic isolates, while the other co-occurred with mat1-1 locus suggesting homothallic reproduction for these strains. Moreover, 24 and 81 genes implicated in plant cell-wall degradation and secondary metabolite biosynthesis, respectively, showed signatures of the balancing selection. These findings highlight the evolutionary pattern of the two gene families for allowing the fungus a rapid adaptation towards endophytism and facilitating diverse symbiotic interactions.
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Affiliation(s)
- Zhilin Yuan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, 100091, Beijing, China. .,Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China.
| | - Qi Wu
- grid.458488.d0000 0004 0627 1442State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Liangxiong Xu
- grid.411411.00000 0004 0644 5457School of Life Sciences, Huizhou University, Huizhou, 516007 China
| | - Irina S. Druzhinina
- grid.27871.3b0000 0000 9750 7019Key Laboratory of Plant Immunity, Fungal Genomics Laboratory (FungiG), College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095 China ,grid.5329.d0000 0001 2348 4034Institute of Chemical, Environmental & Bioscience Engineering (ICEBE), TU Wien, Vienna, A1060 Austria
| | - Eva H. Stukenbrock
- grid.9764.c0000 0001 2153 9986Botanical Institute, Christian-Albrechts Universität zu Kiel, 24118 Kiel, Germany ,grid.419520.b0000 0001 2222 4708Environmental Genomics Research Group, Max-Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - Bart P. S. Nieuwenhuis
- grid.5252.00000 0004 1936 973XDivision of Evolutionary Biology, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Zhenhui Zhong
- grid.256111.00000 0004 1760 2876State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China ,grid.19006.3e0000 0000 9632 6718Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095 USA
| | - Zhong-Jian Liu
- grid.256111.00000 0004 1760 2876Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xinyu Wang
- grid.509676.bResearch Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400 China
| | - Feng Cai
- grid.27871.3b0000 0000 9750 7019Key Laboratory of Plant Immunity, Fungal Genomics Laboratory (FungiG), College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095 China
| | - Christian P. Kubicek
- grid.5329.d0000 0001 2348 4034Institute of Chemical, Environmental & Bioscience Engineering (ICEBE), TU Wien, Vienna, A1060 Austria
| | - Xiaoliang Shan
- grid.216566.00000 0001 2104 9346State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, 100091 Beijing, China ,grid.509676.bResearch Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400 China
| | - Jieyu Wang
- grid.458495.10000 0001 1014 7864Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
| | - Guohui Shi
- grid.458488.d0000 0004 0627 1442State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Long Peng
- grid.216566.00000 0001 2104 9346State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, 100091 Beijing, China ,grid.509676.bResearch Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400 China
| | - Francis M. Martin
- grid.29172.3f0000 0001 2194 6418Université de Lorraine, INRAe, UMR 1136 Interactions Arbres/Microorganismes, INRAe-Grand Est-Nancy, 54280 Champenoux, France
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19
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Wang J, Zhan G, Tian Y, Zhang Y, Xu Y, Kang Z, Zhao J. Role of Sexual Reproduction in the Evolution of the Wheat Stripe Rust Fungus Races in China. PHYTOPATHOLOGY 2022; 112:1063-1071. [PMID: 34784735 DOI: 10.1094/phyto-08-21-0331-r] [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: 06/13/2023]
Abstract
Experimental and population genetic approaches have reshaped our view of how fungal pathogens reproduce, with consequences for our understanding of fungal invasions. Puccinia striiformis f. sp. tritici, the causal agent of stripe rust, poses a severe threat to wheat production worldwide. The sexual stage of P. striiformis f. sp. tritici was discovered >10 years ago, but how it affects the evolution of the pathogen, especially the emergence of the new virulent races, remains largely unknown. Here, using population genetic analyses, we demonstrate that sexual reproduction plays an important role in the evolution of P. striiformis f. sp. tritici races in China, specifically the newly emerged and devastating race virulent to resistance gene Yr26, which is widely used in China and exerts strong selective pressure on the pathogen population. Association analysis identified six genes encoding secreted proteins as candidates for virulence on wheat cultivars carrying the Yr26 resistance gene. Our results highlight the important role of sexual reproduction and selection exerted by hosts in the emergence of new virulent races in China.
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Affiliation(s)
- Jierong Wang
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Gangming Zhan
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuan Tian
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ying Zhang
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yiwen Xu
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhensheng Kang
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jing Zhao
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China
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20
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Kariyawasam GK, Richards JK, Wyatt NA, Running KLD, Xu SS, Liu Z, Borowicz P, Faris JD, Friesen TL. The Parastagonospora nodorum necrotrophic effector SnTox5 targets the wheat gene Snn5 and facilitates entry into the leaf mesophyll. THE NEW PHYTOLOGIST 2022; 233:409-426. [PMID: 34231227 PMCID: PMC9291777 DOI: 10.1111/nph.17602] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/27/2021] [Indexed: 05/11/2023]
Abstract
Parastagonospora nodorum is an economically important necrotrophic fungal pathogen of wheat. Parastagonospora nodorum secretes necrotrophic effectors that target wheat susceptibility genes to induce programmed cell death (PCD). In this study, we cloned and functionally validated SnTox5 and characterized its role in pathogenesis. We used whole genome sequencing, genome-wide association study (GWAS) mapping, CRISPR-Cas9-based gene disruption, gain-of-function transformation, quantitative trait locus (QTL) analysis, haplotype and isoform analysis, protein modeling, quantitative PCR, and laser confocal microscopy to validate SnTox5 and functionally characterize SnTox5. SnTox5 is a mature 16.26 kDa protein with high structural similarity to SnTox3. Wild-type and mutant P. nodorum strains and wheat genotypes of SnTox5 and Snn5, respectively, were used to show that SnTox5 not only targets Snn5 to induce PCD but also facilitates the colonization of the mesophyll layer even in the absence of Snn5. Here we show that SnTox5 facilitates the efficient colonization of the mesophyll tissue and elicits PCD specific to host lines carrying Snn5. The homology to SnTox3 and the ability of SnTox5 to facilitate the colonizing of the mesophyll also suggest a role in the suppression of host defense before PCD induction.
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Affiliation(s)
| | - Jonathan K. Richards
- Department of Plant Pathology and Crop PhysiologyLouisiana State University – Agricultural CenterBaton RougeLA70803USA
| | - Nathan A. Wyatt
- Cereal Crops Research UnitUnited States Department of Agriculture‐Agricultural Research ServiceEdward T. Schafer Agricultural Research CenterFargoND58102USA
| | | | - Steven S. Xu
- Cereal Crops Research UnitUnited States Department of Agriculture‐Agricultural Research ServiceEdward T. Schafer Agricultural Research CenterFargoND58102USA
| | - Zhaohui Liu
- Department of Plant PathologyNorth Dakota State UniversityFargoND58102USA
| | - Pawel Borowicz
- Department of Animal SciencesNorth Dakota State UniversityFargoND58102USA
| | - Justin D. Faris
- Cereal Crops Research UnitUnited States Department of Agriculture‐Agricultural Research ServiceEdward T. Schafer Agricultural Research CenterFargoND58102USA
- Department of Plant ScienceNorth Dakota State UniversityFargoND58102USA
| | - Timothy L. Friesen
- Department of Plant PathologyNorth Dakota State UniversityFargoND58102USA
- Cereal Crops Research UnitUnited States Department of Agriculture‐Agricultural Research ServiceEdward T. Schafer Agricultural Research CenterFargoND58102USA
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21
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Richards JK, Kariyawasam GK, Seneviratne S, Wyatt NA, Xu SS, Liu Z, Faris JD, Friesen TL. A triple threat: the Parastagonospora nodorum SnTox267 effector exploits three distinct host genetic factors to cause disease in wheat. THE NEW PHYTOLOGIST 2022; 233:427-442. [PMID: 34227112 PMCID: PMC9292537 DOI: 10.1111/nph.17601] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/27/2021] [Indexed: 05/21/2023]
Abstract
Parastagonospora nodorum is a fungal pathogen of wheat. As a necrotrophic specialist, it deploys effector proteins that target dominant host susceptibility genes to elicit programmed cell death (PCD). Here we identify and functionally validate the effector targeting the host susceptibility genes Snn2, Snn6 and Snn7. We utilized whole-genome sequencing, association mapping, gene-disrupted mutants, gain-of-function transformants, virulence assays, bioinformatics and quantitative PCR to characterize these interactions. A single proteinaceous effector, SnTox267, targeted Snn2, Snn6 and Snn7 to trigger PCD. Snn2 and Snn6 functioned cooperatively to trigger PCD in a light-dependent pathway, whereas Snn7-mediated PCD functioned in a light-independent pathway. Isolates harboring 20 SnTox267 protein isoforms quantitatively varied in virulence. The diversity and distribution of isoforms varied between populations, indicating adaptation to local selection pressures. SnTox267 deletion resulted in the upregulation of effector genes SnToxA, SnTox1 and SnTox3. We validated a novel effector operating in an inverse-gene-for-gene manner to target three genetically distinct host susceptibility genes and elicit PCD. The discovery of the complementary gene action of Snn2 and Snn6 indicates their potential function in a guard or decoy model. Additionally, differences in light dependency in the elicited pathways and upregulation of unlinked effectors sheds new light onto a complex fungal necrotroph-host interaction.
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Affiliation(s)
- Jonathan K. Richards
- Department of Plant Pathology and Crop PhysiologyLouisiana State University Agricultural CenterBaton RougeLA70803USA
| | | | | | - Nathan A. Wyatt
- Cereal Crops Research UnitEdward T. Schaffer Agricultural Research CenterUSDA‐ARSFargoND58102USA
| | - Steven S. Xu
- Department of Plant SciencesNorth Dakota State UniversityFargoND58102USA
- Cereal Crops Research UnitEdward T. Schaffer Agricultural Research CenterUSDA‐ARSFargoND58102USA
| | - Zhaohui Liu
- Department of Plant PathologyNorth Dakota State UniversityFargoND58102USA
| | - Justin D. Faris
- Department of Plant SciencesNorth Dakota State UniversityFargoND58102USA
- Cereal Crops Research UnitEdward T. Schaffer Agricultural Research CenterUSDA‐ARSFargoND58102USA
| | - Timothy L. Friesen
- Department of Plant PathologyNorth Dakota State UniversityFargoND58102USA
- Cereal Crops Research UnitEdward T. Schaffer Agricultural Research CenterUSDA‐ARSFargoND58102USA
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22
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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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23
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An automated and combinative method for the predictive ranking of candidate effector proteins of fungal plant pathogens. Sci Rep 2021; 11:19731. [PMID: 34611252 PMCID: PMC8492765 DOI: 10.1038/s41598-021-99363-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 09/16/2021] [Indexed: 01/29/2023] Open
Abstract
Fungal plant-pathogens promote infection of their hosts through the release of 'effectors'-a broad class of cytotoxic or virulence-promoting molecules. Effectors may be recognised by resistance or sensitivity receptors in the host, which can determine disease outcomes. Accurate prediction of effectors remains a major challenge in plant pathology, but if achieved will facilitate rapid improvements to host disease resistance. This study presents a novel tool and pipeline for the ranking of predicted effector candidates-Predector-which interfaces with multiple software tools and methods, aggregates disparate features that are relevant to fungal effector proteins, and applies a pairwise learning to rank approach. Predector outperformed a typical combination of secretion and effector prediction methods in terms of ranking performance when applied to a curated set of confirmed effectors derived from multiple species. We present Predector ( https://github.com/ccdmb/predector ) as a useful tool for the ranking of predicted effector candidates, which also aggregates and reports additional supporting information relevant to effector and secretome prediction in a simple, efficient, and reproducible manner.
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24
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Spanner R, Taliadoros D, Richards J, Rivera-Varas V, Neubauer J, Natwick M, Hamilton O, Vaghefi N, Pethybridge S, Secor GA, Friesen TL, Stukenbrock EH, Bolton MD. Genome-Wide Association and Selective Sweep Studies Reveal the Complex Genetic Architecture of DMI Fungicide Resistance in Cercospora beticola. Genome Biol Evol 2021; 13:6367780. [PMID: 34499119 DOI: 10.1093/gbe/evab209] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2021] [Indexed: 12/21/2022] Open
Abstract
The rapid and widespread evolution of fungicide resistance remains a challenge for crop disease management. The demethylation inhibitor (DMI) class of fungicides is a widely used chemistry for managing disease, but there has been a gradual decline in efficacy in many crop pathosystems. Reliance on DMI fungicides has increased resistance in populations of the plant pathogenic fungus Cercospora beticola worldwide. To better understand the genetic and evolutionary basis for DMI resistance in C. beticola, a genome-wide association study (GWAS) and selective sweep analysis were conducted for the first time in this species. We performed whole-genome resequencing of 190 C. beticola isolates infecting sugar beet (Beta vulgaris ssp. vulgaris). All isolates were phenotyped for sensitivity to the DMI tetraconazole. Intragenic markers on chromosomes 1, 4, and 9 were significantly associated with DMI fungicide resistance, including a polyketide synthase gene and the gene encoding the DMI target CbCYP51. Haplotype analysis of CbCYP51 identified a synonymous mutation (E170) and nonsynonymous mutations (L144F, I387M, and Y464S) associated with DMI resistance. Genome-wide scans of selection showed that several of the GWAS mutations for fungicide resistance resided in regions that have recently undergone a selective sweep. Using radial plate growth on selected media as a fitness proxy, we did not find a trade-off associated with DMI fungicide resistance. Taken together, we show that population genomic data from a crop pathogen can allow the identification of mutations conferring fungicide resistance and inform about their origins in the pathogen population.
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Affiliation(s)
- Rebecca Spanner
- Northern Crop Science Laboratory, United States Department of Agriculture, Fargo, North Dakota, USA.,Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, USA
| | - Demetris Taliadoros
- Environmental Genomics Group, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Christian-Albrechts University of Kiel, Germany
| | - Jonathan Richards
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - Viviana Rivera-Varas
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, USA
| | - Jonathan Neubauer
- Northern Crop Science Laboratory, United States Department of Agriculture, Fargo, North Dakota, USA
| | - Mari Natwick
- Northern Crop Science Laboratory, United States Department of Agriculture, Fargo, North Dakota, USA
| | - Olivia Hamilton
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, USA
| | - Niloofar Vaghefi
- Centre for Crop Health, University of Southern Queensland, Toowoomba, Queensland, Australia
| | - Sarah Pethybridge
- School of Integrative Plant Science, Cornell University, Geneva, New York, USA
| | - Gary A Secor
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, USA
| | - Timothy L Friesen
- Northern Crop Science Laboratory, United States Department of Agriculture, Fargo, North Dakota, USA.,Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, USA
| | - Eva H Stukenbrock
- Botanical Institute, Christian-Albrechts University of Kiel, Kiel, Germany.,Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Melvin D Bolton
- Northern Crop Science Laboratory, United States Department of Agriculture, Fargo, North Dakota, USA.,Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, USA
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25
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Friesen TL, Faris JD. Characterization of Effector-Target Interactions in Necrotrophic Pathosystems Reveals Trends and Variation in Host Manipulation. ANNUAL REVIEW OF PHYTOPATHOLOGY 2021; 59:77-98. [PMID: 33909478 DOI: 10.1146/annurev-phyto-120320-012807] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Great strides have been made in defining the details of the plant defense response involving biotrophic fungal and bacterial pathogens. The groundwork for the current model was laid by H.H. Flor and others who defined the gene-for-gene hypothesis, which is now known to involve effector-triggered immunity (ETI). PAMP-triggered immunity (PTI) is also a highly effective response to most pathogens because of the recognition of common pathogen molecules by pattern recognition receptors. In this article, we consider the three pathogens that make up the foliar disease complex of wheat, Zymoseptoria tritici, Pyrenophora tritici-repentis, and Parastagonospora nodorum, to review the means by which necrotrophic pathogens circumvent, or outright hijack, the ETI and PTI pathways to cause disease.
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Affiliation(s)
- Timothy L Friesen
- Edward T. Schafer Agricultural Research Center, USDA-ARS, Fargo, North Dakota 58102, USA; ,
| | - Justin D Faris
- Edward T. Schafer Agricultural Research Center, USDA-ARS, Fargo, North Dakota 58102, USA; ,
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26
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Pereira D, Oggenfuss U, McDonald BA, Croll D. Population genomics of transposable element activation in the highly repressive genome of an agricultural pathogen. Microb Genom 2021; 7:000540. [PMID: 34424154 PMCID: PMC8549362 DOI: 10.1099/mgen.0.000540] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/03/2021] [Indexed: 12/13/2022] Open
Abstract
The activity of transposable elements (TEs) can be an important driver of genetic diversity with TE-mediated mutations having a wide range of fitness consequences. To avoid deleterious effects of TE activity, some fungi have evolved highly sophisticated genomic defences to reduce TE proliferation across the genome. Repeat-induced point mutation (RIP) is a fungal-specific TE defence mechanism efficiently targeting duplicated sequences. The rapid accumulation of RIPs is expected to deactivate TEs over the course of a few generations. The evolutionary dynamics of TEs at the population level in a species with highly repressive genome defences is poorly understood. Here, we analyse 366 whole-genome sequences of Parastagonospora nodorum, a fungal pathogen of wheat with efficient RIP. A global population genomics analysis revealed high levels of genetic diversity and signs of frequent sexual recombination. Contrary to expectations for a species with RIP, we identified recent TE activity in multiple populations. The TE composition and copy numbers showed little divergence among global populations regardless of the demographic history. Miniature inverted-repeat transposable elements (MITEs) and terminal repeat retrotransposons in miniature (TRIMs) were largely underlying recent intra-species TE expansions. We inferred RIP footprints in individual TE families and found that recently active, high-copy TEs have possibly evaded genomic defences. We find no evidence that recent positive selection acted on TE-mediated mutations rather that purifying selection maintained new TE insertions at low insertion frequencies in populations. Our findings highlight the complex evolutionary equilibria established by the joint action of TE activity, selection and genomic repression.
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Affiliation(s)
- Danilo Pereira
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
- Present address: Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, D-24306 Plön, Germany
| | - Ursula Oggenfuss
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Bruce A. McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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27
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Derbyshire MC, Harper LA, Lopez-Ruiz FJ. Positive Selection of Transcription Factors Is a Prominent Feature of the Evolution of a Plant Pathogenic Genus Originating in the Miocene. Genome Biol Evol 2021; 13:6325025. [PMID: 34289036 PMCID: PMC8379374 DOI: 10.1093/gbe/evab167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2021] [Indexed: 01/18/2023] Open
Abstract
Tests based on the dN/dS statistic are used to identify positive selection of nonsynonymous polymorphisms. Using these tests on alignments of all orthologs from related species can provide insights into which gene categories have been most frequently positively selected. However, longer alignments have more power to detect positive selection, creating a detection bias that could create misleading results from functional enrichment tests. Most studies of positive selection in plant pathogens focus on genes with specific virulence functions, with little emphasis on broader molecular processes. Furthermore, no studies in plant pathogens have accounted for detection bias due to alignment length when performing functional enrichment tests. To address these research gaps, we analyze 12 genomes of the phytopathogenic fungal genus Botrytis, including two sequenced in this study. To establish a temporal context, we estimated fossil-calibrated divergence times for the genus. We find that Botrytis likely originated 16–18 Ma in the Miocene and underwent continuous radiation ending in the Pliocene. An untargeted scan of Botrytis single-copy orthologs for positive selection with three different statistical tests uncovered evidence for positive selection among proteases, signaling proteins, CAZymes, and secreted proteins. There was also a strong overrepresentation of transcription factors among positively selected genes. This overrepresentation was still apparent after two complementary controls for detection bias due to sequence length. Positively selected sites were depleted within DNA-binding domains, suggesting changes in transcriptional responses to internal and external cues or protein–protein interactions have undergone positive selection more frequently than changes in promoter fidelity.
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Affiliation(s)
- Mark C Derbyshire
- Centre for Crop and Disease Management, Curtin University, Perth, Western Australia, Australia
| | - Lincoln A Harper
- Centre for Crop and Disease Management, Curtin University, Perth, Western Australia, Australia
| | - Francisco J Lopez-Ruiz
- Centre for Crop and Disease Management, Curtin University, Perth, Western Australia, Australia
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28
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Chen JY, Zhang DD, Huang JQ, Li R, Wang D, Song J, Puri KD, Yang L, Kong ZQ, Tong BZ, Li JJ, Huang YS, Simko I, Klosterman SJ, Dai XF, Subbarao KV. Dynamics of Verticillium dahliae race 1 population under managed agricultural ecosystems. BMC Biol 2021; 19:131. [PMID: 34172070 PMCID: PMC8235872 DOI: 10.1186/s12915-021-01061-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/01/2021] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Plant pathogens and their hosts undergo adaptive changes in managed agricultural ecosystems, by overcoming host resistance, but the underlying genetic adaptations are difficult to determine in natural settings. Verticillium dahliae is a fungal pathogen that causes Verticillium wilt on many economically important crops including lettuce. We assessed the dynamics of changes in the V. dahliae genome under selection in a long-term field experiment. RESULTS In this study, a field was fumigated before the Verticillium dahliae race 1 strain (VdLs.16) was introduced. A derivative 145-strain population was collected over a 6-year period from this field in which a seggregating population of lettuce derived from Vr1/vr1 parents were evaluated. We de novo sequenced the parental genome of VdLs.16 strain and resequenced the derivative strains to analyze the genetic variations that accumulate over time in the field cropped with lettuce. Population genomics analyses identified 2769 single-nucleotide polymorphisms (SNPs) and 750 insertion/deletions (In-Dels) in the 145 isolates compared with the parental genome. Sequence divergence was identified in the coding sequence regions of 378 genes and in the putative promoter regions of 604 genes. Five-hundred and nine SNPs/In-Dels were identified as fixed. The SNPs and In-Dels were significantly enriched in the transposon-rich, gene-sparse regions, and in those genes with functional roles in signaling and transcriptional regulation. CONCLUSIONS Under the managed ecosystem continuously cropped to lettuce, the local adaptation of V. dahliae evolves at a whole genome scale to accumulate SNPs/In-Dels nonrandomly in hypervariable regions that encode components of signal transduction and transcriptional regulation.
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Affiliation(s)
- Jie-Yin Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dan-Dan Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | | | - Ran Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dan Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jian Song
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Krishna D Puri
- Department of Plant Pathology, University of California, Davis, c/o U.S. Agricultural Research Station, Salinas, CA, USA
| | - Lin Yang
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Zhi-Qiang Kong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | | | - Jun-Jiao Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | | | - Ivan Simko
- United States Department of Agriculture, Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA, USA
| | - Steven J Klosterman
- United States Department of Agriculture, Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA, USA.
| | - Xiao-Feng Dai
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Krishna V Subbarao
- Department of Plant Pathology, University of California, Davis, c/o U.S. Agricultural Research Station, Salinas, CA, USA.
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29
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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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Croll D, Crous P, Pereira D, Mordecai E, McDonald B, Brunner P. Genome-scale phylogenies reveal relationships among Parastagonospora species infecting domesticated and wild grasses. PERSOONIA 2021; 46:116-128. [PMID: 35935891 PMCID: PMC9311395 DOI: 10.3767/persoonia.2021.46.04] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/19/2021] [Indexed: 02/02/2023]
Abstract
Several plant pathogenic Parastagonospora species have been identified infecting wheat and other cereals over the past 50 years. As new lineages were discovered, naming conventions grew unwieldy and the relationships with previously recognized species remained unclear. We used genome sequencing to clarify relationships among these species and provided new names for most of these species. Six of the nine described Parastagonospora species were recovered from wheat, with five of these species coming from Iran. Genome sequences revealed that three strains thought to be hybrids between P. nodorum and P. pseudonodorum were not actually hybrids, but rather represented rare gene introgressions between those species. Our data are consistent with the hypothesis that P. nodorum originated as a pathogen of wild grasses in the Fertile Crescent, then emerged as a wheat pathogen via host-tracking during the domestication of wheat in the same region. The discovery of a diverse array of Parastagonospora species infecting wheat in Iran suggests that new wheat pathogens could emerge from this region in the future. Citation: Croll D, Crous PW, Pereira D, et al. 2021. Genome-scale phylogenies reveal relationships among Parastagonospora species infecting domesticated and wild grasses. Persoonia 46: 116-128. https://doi.org/10.3767/persoonia.2021.46.04.
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Affiliation(s)
- D. Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland
| | - P.W. Crous
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - D. Pereira
- Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, CH-8092 Zurich, Switzerland
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany
- Environmental Genomics, Christian-Albrechts University of Kiel, 24118, Kiel, Germany
| | - E.A. Mordecai
- Biology Department, Stanford University, 327 Campus Drive, Stanford, California, 94305 USA
| | - B.A. McDonald
- Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, CH-8092 Zurich, Switzerland
| | - P.C. Brunner
- Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, CH-8092 Zurich, Switzerland
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Bertazzoni S, Jones DAB, Phan HT, Tan KC, Hane JK. Chromosome-level genome assembly and manually-curated proteome of model necrotroph Parastagonospora nodorum Sn15 reveals a genome-wide trove of candidate effector homologs, and redundancy of virulence-related functions within an accessory chromosome. BMC Genomics 2021; 22:382. [PMID: 34034667 PMCID: PMC8146201 DOI: 10.1186/s12864-021-07699-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 05/11/2021] [Indexed: 11/19/2022] Open
Abstract
Background The fungus Parastagonospora nodorum causes septoria nodorum blotch (SNB) of wheat (Triticum aestivum) and is a model species for necrotrophic plant pathogens. The genome assembly of reference isolate Sn15 was first reported in 2007. P. nodorum infection is promoted by its production of proteinaceous necrotrophic effectors, three of which are characterised – ToxA, Tox1 and Tox3. Results A chromosome-scale genome assembly of P. nodorum Australian reference isolate Sn15, which combined long read sequencing, optical mapping and manual curation, produced 23 chromosomes with 21 chromosomes possessing both telomeres. New transcriptome data were combined with fungal-specific gene prediction techniques and manual curation to produce a high-quality predicted gene annotation dataset, which comprises 13,869 high confidence genes, and an additional 2534 lower confidence genes retained to assist pathogenicity effector discovery. Comparison to a panel of 31 internationally-sourced isolates identified multiple hotspots within the Sn15 genome for mutation or presence-absence variation, which was used to enhance subsequent effector prediction. Effector prediction resulted in 257 candidates, of which 98 higher-ranked candidates were selected for in-depth analysis and revealed a wealth of functions related to pathogenicity. Additionally, 11 out of the 98 candidates also exhibited orthology conservation patterns that suggested lateral gene transfer with other cereal-pathogenic fungal species. Analysis of the pan-genome indicated the smallest chromosome of 0.4 Mbp length to be an accessory chromosome (AC23). AC23 was notably absent from an avirulent isolate and is predominated by mutation hotspots with an increase in non-synonymous mutations relative to other chromosomes. Surprisingly, AC23 was deficient in effector candidates, but contained several predicted genes with redundant pathogenicity-related functions. Conclusions We present an updated series of genomic resources for P. nodorum Sn15 – an important reference isolate and model necrotroph – with a comprehensive survey of its predicted pathogenicity content. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07699-8.
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Affiliation(s)
| | - Darcy A B Jones
- Centre for Crop & Disease Management, Curtin University, Perth, Australia
| | - Huyen T Phan
- Centre for Crop & Disease Management, Curtin University, Perth, Australia.
| | - Kar-Chun Tan
- Centre for Crop & Disease Management, Curtin University, Perth, Australia.
| | - James K Hane
- Centre for Crop & Disease Management, Curtin University, Perth, Australia. .,Curtin Institute for Computation, Curtin University, Perth, Australia.
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GWAS analysis reveals distinct pathogenicity profiles of Australian Parastagonospora nodorum isolates and identification of marker-trait-associations to septoria nodorum blotch. Sci Rep 2021; 11:10085. [PMID: 33980869 PMCID: PMC8115087 DOI: 10.1038/s41598-021-87829-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 04/05/2021] [Indexed: 12/25/2022] Open
Abstract
The fungus Parastagonospora nodorum is the causal agent of septoria nodorum leaf blotch (SNB) and glume blotch which are common in many wheat growing regions in the world. The disease is complex and could be explained by multiple interactions between necrotrophic effectors secreted by the pathogen and matching susceptibility genes in wheat. An Australian P. nodorum population was clustered into five groups with contrasting properties. This study was set to identify their pathogenicity profiles using a diverse wheat panel of 134 accessions which are insensitive to SnToxA and SnTox1 in both in vitro and in vivo conditions. SNB seedling resistance/susceptibility to five representative isolates from the five clusters, responses to crude culture-filtrates (CFs) of three isolates and sensitivity to SnTox3 semi-purified effector together with 11,455 SNP markers have been used for linkage disequilibrium (LD) and association analyses. While quantitative trait loci (QTL) on 1D, 2A, 2B, 4B, 5B, 6A, 6B, 7A, 7D chromosomes were consistently detected across isolates and conditions, distinct patterns and isolate specific QTL were also observed among these isolates. In this study, SnTox3–Snn3-B1 interaction for the first time in Australia and SnTox3–Snn3-D1 interaction for the first time in bread wheat were found active using wild-type isolates. These findings could be due to new SnTox3 haplotype/isoform and exotic CIMMYT/ICARDA and Vavilov germplasm used, respectively. This study could provide useful information for dissecting novel and different SNB disease components, helping to prioritise research targets and contributing valuable information on genetic loci/markers for marker-assisted selection in SNB resistance wheat breeding programme.
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Monroe JG, McKay JK, Weigel D, Flood PJ. The population genomics of adaptive loss of function. Heredity (Edinb) 2021; 126:383-395. [PMID: 33574599 PMCID: PMC7878030 DOI: 10.1038/s41437-021-00403-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/28/2020] [Accepted: 01/01/2021] [Indexed: 12/23/2022] Open
Abstract
Discoveries of adaptive gene knockouts and widespread losses of complete genes have in recent years led to a major rethink of the early view that loss-of-function alleles are almost always deleterious. Today, surveys of population genomic diversity are revealing extensive loss-of-function and gene content variation, yet the adaptive significance of much of this variation remains unknown. Here we examine the evolutionary dynamics of adaptive loss of function through the lens of population genomics and consider the challenges and opportunities of studying adaptive loss-of-function alleles using population genetics models. We discuss how the theoretically expected existence of allelic heterogeneity, defined as multiple functionally analogous mutations at the same locus, has proven consistent with empirical evidence and why this impedes both the detection of selection and causal relationships with phenotypes. We then review technical progress towards new functionally explicit population genomic tools and genotype-phenotype methods to overcome these limitations. More broadly, we discuss how the challenges of studying adaptive loss of function highlight the value of classifying genomic variation in a way consistent with the functional concept of an allele from classical population genetics.
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Affiliation(s)
- J Grey Monroe
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany.
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616, USA.
| | - John K McKay
- College of Agriculture, Colorado State University, Fort Collins, CO, 80523, USA
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Pádraic J Flood
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Department of Plant Breeding, Wageningen University, Wageningen, The Netherlands
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Abstract
Plant pathogens can adapt to quantitative resistance, eroding its effectiveness. The aim of this work was to reveal the genomic basis of adaptation to such a resistance in populations of the fungus Pseudocercospora fijiensis, a major devastating pathogen of banana, by studying convergent adaptation on different cultivars. Samples from P. fijiensis populations showing a local adaptation pattern on new banana hybrids with quantitative resistance were compared, based on a genome scan approach, with samples from traditional and more susceptible cultivars in Cuba and the Dominican Republic. Whole-genome sequencing of pools of P. fijiensis isolates (pool-seq) sampled from three locations per country was conducted according to a paired population design. The findings of different combined analyses highly supported the existence of convergent adaptation on the study cultivars between locations within but not between countries. Five to six genomic regions involved in this adaptation were detected in each country. An annotation analysis and available biological data supported the hypothesis that some genes within the detected genomic regions may play a role in quantitative pathogenicity, including gene regulation. The results suggested that the genetic basis of fungal adaptation to quantitative plant resistance is at least oligogenic, while highlighting the existence of specific host-pathogen interactions for this kind of resistance.IMPORTANCE Understanding the genetic basis of pathogen adaptation to quantitative resistance in plants has a key role to play in establishing durable strategies for resistance deployment. In this context, a population genomic approach was developed for a major plant pathogen (the fungus Pseudocercospora fijiensis causing black leaf streak disease of banana) whereby samples from new resistant banana hybrids were compared with samples from more susceptible conventional cultivars in two countries. A total of 11 genomic regions for which there was strong evidence of selection by quantitative resistance were detected. An annotation analysis and available biological data supported the hypothesis that some of the genes within these regions may play a role in quantitative pathogenicity. These results suggested a polygenic basis of quantitative pathogenicity in this fungal pathogen and complex molecular plant-pathogen interactions in quantitative disease development involving several genes on both sides.
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Singh NK, Dutta A, Puccetti G, Croll D. Tackling microbial threats in agriculture with integrative imaging and computational approaches. Comput Struct Biotechnol J 2020; 19:372-383. [PMID: 33489007 PMCID: PMC7787954 DOI: 10.1016/j.csbj.2020.12.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/08/2020] [Accepted: 12/13/2020] [Indexed: 11/29/2022] Open
Abstract
Pathogens and pests are one of the major threats to agricultural productivity worldwide. For decades, targeted resistance breeding was used to create crop cultivars that resist pathogens and environmental stress while retaining yields. The often decade-long process of crossing, selection, and field trials to create a new cultivar is challenged by the rapid rise of pathogens overcoming resistance. Similarly, antimicrobial compounds can rapidly lose efficacy due to resistance evolution. Here, we review three major areas where computational, imaging and experimental approaches are revolutionizing the management of pathogen damage on crops. Recognizing and scoring plant diseases have dramatically improved through high-throughput imaging techniques applicable both under well-controlled greenhouse conditions and directly in the field. However, computer vision of complex disease phenotypes will require significant improvements. In parallel, experimental setups similar to high-throughput drug discovery screens make it possible to screen thousands of pathogen strains for variation in resistance and other relevant phenotypic traits. Confocal microscopy and fluorescence can capture rich phenotypic information across pathogen genotypes. Through genome-wide association mapping approaches, phenotypic data helps to unravel the genetic architecture of stress- and virulence-related traits accelerating resistance breeding. Finally, joint, large-scale screenings of trait variation in crops and pathogens can yield fundamental insights into how pathogens face trade-offs in the adaptation to resistant crop varieties. We discuss how future implementations of such innovative approaches in breeding and pathogen screening can lead to more durable disease control.
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Affiliation(s)
- Nikhil Kumar Singh
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland
| | - Anik Dutta
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, CH-8092 Zurich, Switzerland
| | - Guido Puccetti
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland
- Syngenta Crop Protection AG, CH-4332 Stein, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland
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Hafez M, Gourlie R, Despins T, Turkington TK, Friesen TL, Aboukhaddour R. Parastagonospora nodorum and Related Species in Western Canada: Genetic Variability and Effector Genes. PHYTOPATHOLOGY 2020; 110:1946-1958. [PMID: 32689900 DOI: 10.1094/phyto-05-20-0207-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Parastagonospora nodorum is an important fungal pathogen that causes Septoria nodorum blotch (SNB) in wheat. This pathogen produces several necrotrophic effectors that act as virulence factors; three have been cloned, SnToxA, SnTox1, and SnTox3. In this study, P. nodorum and its sister species P. avenaria f. tritici (Pat1) were isolated from wheat node and grain samples collected from distanced sites in western Canada during 2018. The presence of effector genes and associated haplotypes were determined by PCR and sequence analysis. An internal transcribed spacer-restriction fragment length polymorphism test was developed to distinguish between leaf spotting pathogens (P. nodorum, Pat1, Pyrenophora tritici-repentis, and Bipolaris sorokiniana). P. nodorum was mainly recovered from wheat nodes and to a lesser extent from the grains, while Pat1 was exclusively isolated from grain samples. The effector genes were present in almost all P. nodorum isolates, with the ToxA haplotype 5 (H5) being most prevalent, while a novel ToxA haplotype (denoted here H21) is reported for the first time. In Pat1, only combinations of SnTox1 and SnTox3 genes were present. A ToxA haplotype network was also constructed to assess the evolutionary relationship among globally found haplotypes to date. Finally, cultivars representing wheat development in Canada for the last century were tested for sensitivity to Sn-effectors and to the presence of Tsn1, the ToxA sensitivity gene. Of tested cultivars, 32.9 and 56.9% were sensitive to SnTox1 and SnTox3, respectively, and Tsn1 was present in 59% of the cultivars. In conclusion, P. nodorum and Pat1 were prevalent wheat pathogens in Canada with a potential tissue-specific colonization capacity, while producing necrotrophic effectors to which wheat is sensitive.
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Affiliation(s)
- Mohamed Hafez
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Center, Lethbridge, Alberta, Canada (working address)
- Department of Botany and Microbiology, Faculty of Science, Suez University, Suez, Egypt (permanent address)
| | - Ryan Gourlie
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Center, Lethbridge, Alberta, Canada (working address)
| | - Therese Despins
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Center, Lethbridge, Alberta, Canada (working address)
| | - Thomas K Turkington
- Agriculture and Agri-Food Canada, Lacombe Research and Development Center, Lacombe, Alberta, Canada
| | - Timothy L Friesen
- U.S. Department of Agriculture, Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, U.S.A
| | - Reem Aboukhaddour
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Center, Lethbridge, Alberta, Canada (working address)
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Pereira D, McDonald BA, Croll D. The Genetic Architecture of Emerging Fungicide Resistance in Populations of a Global Wheat Pathogen. Genome Biol Evol 2020; 12:2231-2244. [PMID: 32986802 PMCID: PMC7846115 DOI: 10.1093/gbe/evaa203] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/22/2020] [Indexed: 12/22/2022] Open
Abstract
Containing fungal diseases often depends on the application of fungicidal compounds. Fungicides can rapidly lose effectiveness due to the rise of resistant individuals in populations. However, the lack of knowledge about resistance mutations beyond known target genes challenges investigations into pathways to resistance. We used whole-genome sequencing data and association mapping to reveal the multilocus genetic architecture of fungicide resistance in a global panel of 159 isolates of Parastagonospora nodorum, an important fungal pathogen of wheat. We found significant differences in azole resistance among global field populations. The populations evolved distinctive combinations of resistance alleles which can interact when co-occurring in the same genetic background. We identified 34 significantly associated single nucleotide polymorphisms located in close proximity to genes associated with fungicide resistance in other fungi, including a major facilitator superfamily transporter. Using fungal colony growth rates and melanin production at different temperatures as fitness proxies, we found no evidence that resistance was constrained by genetic trade-offs. Our study demonstrates how genome-wide association studies of a global collection of pathogen strains can recapitulate the emergence of fungicide resistance. The distinct complement of resistance mutations found among populations illustrates how the evolutionary trajectory of fungicide adaptation can be complex and challenging to predict.
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Affiliation(s)
- Danilo Pereira
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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Faris JD, Friesen TL. Plant genes hijacked by necrotrophic fungal pathogens. CURRENT OPINION IN PLANT BIOLOGY 2020; 56:74-80. [PMID: 32492572 DOI: 10.1016/j.pbi.2020.04.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 03/30/2020] [Accepted: 04/07/2020] [Indexed: 05/22/2023]
Abstract
Plant fungal pathogens can be classified according to their lifestyles. Biotrophs feed on living tissue and constitute an economically significant group of pathogens historically. Necrotrophs, which feed on dead tissue, have become economically significant over recent decades, especially those of the Dothideomycetes, which produce necrotrophic effectors (NEs) to modulate the host response. Some of these pathogens interact with their hosts in an inverse gene-for-gene manner, where NEs are recognized by specific dominant genes in the host leading to host-mediated programmed cell death allowing the pathogen to cause disease. Whereas the NE genes tend to be unique, several of the plant 'susceptibility' genes belong to the nucleotide-binding leucine-rich repeat class of disease 'resistance' genes, and one is a wall-associated kinase. These susceptible interactions exhibit hallmarks of defense responses to biotrophic pathogens. Therefore, there is now accumulating evidence that many necrotrophic specialists hijack the resistance mechanisms that are effective against biotrophic pathogens.
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Affiliation(s)
- Justin D Faris
- USDA-Agricultural Research Service, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102, United States.
| | - Timothy L Friesen
- USDA-Agricultural Research Service, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102, United States
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Lin M, Ficke A, Cockram J, Lillemo M. Genetic Structure of the Norwegian Parastagonospora nodorum Population. Front Microbiol 2020; 11:1280. [PMID: 32612592 PMCID: PMC7309014 DOI: 10.3389/fmicb.2020.01280] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 05/19/2020] [Indexed: 01/27/2023] Open
Abstract
The necrotrophic fungal pathogen Parastagonospora nodorum causes Septoria nodorum blotch (SNB), which is one of the dominating leaf blotch diseases of wheat in Norway. A total of 165 P. nodorum isolates were collected from three wheat growing regions in Norway from 2015 to 2017. These isolates, as well as nine isolates from other countries, were analyzed for genetic variation using 20 simple sequence repeat (SSR) markers. Genetic analysis of the isolate collection indicated that the P. nodorum pathogen population infecting Norwegian spring and winter wheat underwent regular sexual reproduction and exhibited a high level of genetic diversity, with no genetic subdivisions between sampled locations, years or host cultivars. A high frequency of the presence of necrotrophic effector (NE) gene SnToxA was found in Norwegian P. nodorum isolates compared to other parts of Europe, and we hypothesize that the SnToxA gene is the major virulence factor among the three known P. nodorum NE genes (SnToxA, SnTox1, and SnTox3) in the Norwegian pathogen population. While the importance of SNB has declined in much of Europe, Norway has remained as a P. nodorum hotspot, likely due at least in part to local adaptation of the pathogen population to ToxA sensitive Norwegian spring wheat cultivars.
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Affiliation(s)
- Min Lin
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Andrea Ficke
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
| | - James Cockram
- John Bingham Laboratory, NIAB, Cambridge, United Kingdom
| | - Morten Lillemo
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences (NMBU), Ås, Norway
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Phan HTT, Jones DAB, Rybak K, Dodhia KN, Lopez-Ruiz FJ, Valade R, Gout L, Lebrun MH, Brunner PC, Oliver RP, Tan KC. Low Amplitude Boom-and-Bust Cycles Define the Septoria Nodorum Blotch Interaction. FRONTIERS IN PLANT SCIENCE 2020; 10:1785. [PMID: 32082346 PMCID: PMC7005668 DOI: 10.3389/fpls.2019.01785] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 12/20/2019] [Indexed: 05/30/2023]
Abstract
INTRODUCTION Septoria nodorum blotch (SNB) is a complex fungal disease of wheat caused by the Dothideomycete fungal pathogen Parastagonospora nodorum. The fungus infects through the use of necrotrophic effectors (NEs) that cause necrosis on hosts carrying matching dominant susceptibility genes. The Western Australia (WA) wheatbelt is a SNB "hot spot" and experiences significant under favorable conditions. Consequently, SNB has been a major target for breeders in WA for many years. MATERIALS AND METHODS In this study, we assembled a panel of 155 WA P. nodorum isolates collected over a 44-year period and compared them to 23 isolates from France and the USA using 28 SSR loci. RESULTS The WA P. nodorum population was clustered into five groups with contrasting properties. 80% of the studied isolates were assigned to two core groups found throughout the collection location and time. The other three non-core groups that encompassed transient and emergent populations were found in restricted locations and time. Changes in group genotypes occurred during periods that coincided with the mass adoption of a single or a small group of widely planted wheat cultivars. When introduced, these cultivars had high scores for SNB resistance. However, the field resistance of these new cultivars often declined over subsequent seasons prompting their replacement with new, more resistant varieties. Pathogenicity assays showed that newly emerged isolates non-core are more pathogenic than old isolates. It is likely that the non-core groups were repeatedly selected for increased virulence on the contemporary popular cultivars. DISCUSSION The low level of genetic diversity within the non-core groups, difference in virulence, low abundance, and restriction to limited locations suggest that these populations more vulnerable to a population crash when the cultivar was replaced by one that was genetically different and more resistant. We characterize the observed pattern as a low-amplitude boom-and-bust cycle in contrast with the classical high amplitude boom-and-bust cycles seen for biotrophic pathogens where the contrast between resistance and susceptibility is typically much greater. Implications of the results are discussed relating to breeding strategies for more sustainable SNB resistance and more generally for pathogens with NEs.
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Affiliation(s)
- Huyen T. T. Phan
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Darcy A. B. Jones
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Kasia Rybak
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Kejal N. Dodhia
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Francisco J. Lopez-Ruiz
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Romain Valade
- ARVALIS Institut du Végétal Avenue Lucien Brétignières, Bâtiment INRA Bioger, Thiverval-Grignon, France
| | - Lilian Gout
- UMR INRA Bioger Agro-ParisTech, Thiverval-Grignon, France
| | | | - Patrick C. Brunner
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Richard P. Oliver
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Kar-Chun Tan
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
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Cowger C, Ward B, Brown-Guedira G, Brown JKM. Role of Effector-Sensitivity Gene Interactions and Durability of Quantitative Resistance to Septoria Nodorum Blotch in Eastern U.S. Wheat. FRONTIERS IN PLANT SCIENCE 2020; 11:155. [PMID: 32210986 PMCID: PMC7067980 DOI: 10.3389/fpls.2020.00155] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/31/2020] [Indexed: 05/02/2023]
Abstract
Important advances have been made in understanding the relationship of necrotrophic effectors (NE) and host sensitivity (Snn) genes in the Parastagonospora nodorum-wheat pathosystem. Yet much remains to be learned about the role of these interactions in determining wheat resistance levels in the field, and there is mixed evidence on whether breeding programs have selected against Snn genes due to their role in conferring susceptibility. SNB occurs ubiquitously in the U.S. Atlantic seaboard, and the environment is especially well suited to field studies of resistance to natural P. nodorum populations, as there are no other important wheat leaf blights. Insights into the nature of SNB resistance have been gleaned from multi-year data on phenotypes and markers in cultivars representative of the region's germplasm. In this perspective article, we review the evidence that in this eastern region of the U.S., wheat cultivars have durable quantitative SNB resistance and Snn-NE interactions are of limited importance. This conclusion is discussed in light of the relevant available information from other parts of the world.
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Affiliation(s)
- Christina Cowger
- U.S. Department of Agriculture – Agricultural Research Service, North Carolina State University, Raleigh, NC, United States
- *Correspondence: Christina Cowger,
| | - Brian Ward
- U.S. Department of Agriculture – Agricultural Research Service, North Carolina State University, Raleigh, NC, United States
| | - Gina Brown-Guedira
- U.S. Department of Agriculture – Agricultural Research Service, North Carolina State University, Raleigh, NC, United States
| | - James K. M. Brown
- Department of Crop Genetics, John Innes Centre, Norwich, United Kingdom
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