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Vidal-Villarejo M, Dößelmann B, Kogler B, Hammerschmidt M, Oppliger B, Oppliger H, Schmid K. Regional diversity and leaf microbiome interactions of the fungal maize pathogen Exserohilum turcicum in Switzerland: A metagenomic analysis. Mol Ecol 2024; 33:e17482. [PMID: 39082382 DOI: 10.1111/mec.17482] [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: 04/17/2024] [Revised: 07/01/2024] [Accepted: 07/12/2024] [Indexed: 08/28/2024]
Abstract
The spread and adaptation of fungal plant pathogens in agroecosystems are facilitated by environmental homogeneity. Metagenomic sequencing of infected tissues allowed us to monitor eco-evolutionary dynamics and interactions between host, pathogen and plant microbiome. Exserohilum turcicum, the causal agent of northern corn leaf blight (NCLB) in maize, is distributed in multiple clonal lineages throughout Europe. To characterize regional pathogen diversity, we conducted metagenomic DNA sequencing on 241 infected leaf samples from the highly susceptible Swiss maize landrace Rheintaler Ribelmais, collected over 3 years (2016-2018) from an average of 14 agricultural farms within the Swiss Rhine Valley. All major European clonal lineages of E. turcicum were identified. Lineages differ by their mating types which indicates potential for sexual recombination and rapid evolution of new pathogen strains, although we found no evidence of recent recombination. The associated eukaryotic and prokaryotic leaf microbiome exhibited variation in taxonomic diversity between years and locations and is likely influenced by local weather conditions. A network analysis revealed distinct clusters of eukaryotic and prokaryotic taxa that correlates with the frequency of E. turcicum sequencing reads, suggesting causal interactions. Notably, the yeast genus Metschnikowia exhibited a strongly negative association with E. turcicum, supporting its known potential as biological control agent against fungal pathogens. Our findings show that metagenomic sequencing is a useful tool for analysing the role of environmental factors and potential pathogen-microbiome interactions in shaping pathogen dynamics and evolution, suggesting their potential for effective pathogen management strategies.
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Affiliation(s)
- Mireia Vidal-Villarejo
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
| | - Bianca Dößelmann
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
| | | | | | - Barbara Oppliger
- Rhytop GmbH, Salez, Switzerland
- Landwirtschaftliches Zentrum Sankt Gallen, Salez, Switzerland
- Verein Rheintaler Ribelmais e.V, Salez, Switzerland
| | - Hans Oppliger
- Rhytop GmbH, Salez, Switzerland
- Landwirtschaftliches Zentrum Sankt Gallen, Salez, Switzerland
- Verein Rheintaler Ribelmais e.V, Salez, Switzerland
| | - Karl Schmid
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
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Lewis CM, Morier-Gxoyiya C, Hubbard A, Nellist CF, Bebber DP, Saunders DGO. Resurgence of wheat stem rust infections in western Europe: causes and how to curtail them. THE NEW PHYTOLOGIST 2024; 243:537-542. [PMID: 38803104 DOI: 10.1111/nph.19864] [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: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 05/29/2024]
Abstract
Ten years ago, (black) stem rust - the most damaging of wheat (Triticum aestivum) rusts - re-emerged in western Europe. Disease incidences have since increased in scale and frequency. Here, we investigated the likely underlying causes and used those to propose urgently needed mitigating actions. We report that the first large-scale UK outbreak of the wheat stem rust fungus, Puccinia graminis f. sp. tritici (Pgt), in 2022 may have been caused by timely arrival of airborne urediniospores from southwest Europe. The drive towards later-maturing wheat varieties in the UK may be exacerbating Pgt incidences, which could have disastrous consequences. Indeed, infection assays showed that two UK Pgt isolates from 2022 could infect over 96% of current UK wheat varieties. We determined that the temperature response data in current disease risk simulation models are outdated. Analysis of germination rates for three current UK Pgt isolates showed substantial variation in temperature response functions, suggesting that the accuracy of disease risk simulations would be substantially enhanced by incorporating data from prevailing Pgt isolates. As Pgt incidences continue to accelerate in western Europe, we advocate for urgent action to curtail Pgt losses and help safeguard future wheat production across the region.
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Affiliation(s)
- Clare M Lewis
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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Terefe TG, Boshoff WHP, Park RF, Pretorius ZA, Visser B. Wheat Stem Rust Surveillance Reveals Two New Races of Puccinia graminis f. sp. tritici in South Africa During 2016 to 2020. PLANT DISEASE 2024; 108:20-29. [PMID: 37580885 DOI: 10.1094/pdis-06-23-1120-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
Stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is an important disease of wheat in South Africa (SA) and is primarily controlled using resistant cultivars. Understanding virulence diversity of Pgt is essential for successful breeding of resistant cultivars. Samples of infected wheat stems were collected across the major wheat-growing regions of SA from 2016 to 2020 to determine the pathogenic variability of Pgt isolates. Seven races were identified from 517 isolates pathotyped. The most frequently found races were 2SA104 (BPGSC + Sr9h,27,Kw) (35% frequency) and 2SA88 (TTKSF + Sr8b) (33%). Race 2SA42 (PTKSK + Sr8b), which was found in 2017, and 2SA5 (BFGSF + Sr9h), identified in 2017, are new races. The Ug99 variant race 2SA42 is similar in its virulence to 2SA107 (PTKST + Sr8b) except for avirulence to Sr24 and virulence to Sr8155B1. Race 2SA5 is closely related in its virulence to existing races that commonly infect triticale. Certain races showed limited geographical distribution. Races 2SA5, 2SA105, and 2SA108 were found only in the Western Cape, whereas 2SA107 and 2SA42 were detected only in the Free State province. The new and existing races were compared using microsatellite (SSR) marker analysis and their virulence on commercial cultivars was also determined. Seedling response of 113 wheat entries against the new races, using 2SA88, 2SA88+9h, 2SA106, and 2SA107 as controls, revealed 2SA107 as the most virulent (67 entries susceptible), followed by 2SA42 (64), 2SA106 (60), 2SA88+9h (59), 2SA88 (25), and 2SA5 (17). Thus, 2SA5 may not pose a significant threat to local wheat production. SSR genotyping revealed that 2SA5 is genetically distinct from all other SA Pgt races.
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Affiliation(s)
- Tarekegn G Terefe
- Agricultural Research Council-Small Grain, Bethlehem 9700, South Africa
| | - Willem H P Boshoff
- Department of Plant Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Robert F Park
- Plant Breeding Institute Cobbitty, The University of Sydney, Narellan, NSW 2567, Australia
| | - Zacharias A Pretorius
- Department of Plant Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Botma Visser
- Department of Plant Sciences, University of the Free State, Bloemfontein 9300, South Africa
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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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Patpour M, Hovmøller MS, Rodriguez-Algaba J, Randazzo B, Villegas D, Shamanin VP, Berlin A, Flath K, Czembor P, Hanzalova A, Sliková S, Skolotneva ES, Jin Y, Szabo L, Meyer KJG, Valade R, Thach T, Hansen JG, Justesen AF. Wheat Stem Rust Back in Europe: Diversity, Prevalence and Impact on Host Resistance. FRONTIERS IN PLANT SCIENCE 2022; 13:882440. [PMID: 35720526 PMCID: PMC9202592 DOI: 10.3389/fpls.2022.882440] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 05/03/2022] [Indexed: 05/13/2023]
Abstract
The objective of this study was to investigate the re-emergence of a previously important crop pathogen in Europe, Puccinia graminis f.sp. tritici, causing wheat stem rust. The pathogen has been insignificant in Europe for more than 60 years, but since 2016 it has caused epidemics on both durum wheat and bread wheat in local areas in southern Europe, and additional outbreaks in Central- and West Europe. The prevalence of three distinct genotypes/races in many areas, Clade III-B (TTRTF), Clade IV-B (TKTTF) and Clade IV-F (TKKTF), suggested clonal reproduction and evolution by mutation within these. None of these genetic groups and races, which likely originated from exotic incursions, were detected in Europe prior to 2016. A fourth genetic group, Clade VIII, detected in Germany (2013), was observed in several years in Central- and East Europe. Tests of representative European wheat varieties with prevalent races revealed high level of susceptibility. In contrast, high diversity with respect to virulence and Simple Sequence Repeat (SSR) markers were detected in local populations on cereals and grasses in proximity to Berberis species in Spain and Sweden, indicating that the alternate host may return as functional component of the epidemiology of wheat stem rust in Europe. A geographically distant population from Omsk and Novosibirsk in western Siberia (Russia) also revealed high genetic diversity, but clearly different from current European populations. The presence of Sr31-virulence in multiple and highly diverse races in local populations in Spain and Siberia stress that virulence may emerge independently when large geographical areas and time spans are considered and that Sr31-virulence is not unique to Ug99. All isolates of the Spanish populations, collected from wheat, rye and grass species, were succesfully recovered on wheat, which underline the plasticity of host barriers within P. graminis. The study demonstrated successful alignment of two genotyping approaches and race phenotyping methodologies employed by different laboratories, which also allowed us to line up with previous European and international studies of wheat stem rust. Our results suggest new initiatives within disease surveillance, epidemiological research and resistance breeding to meet current and future challenges by wheat stem rust in Europe and beyond.
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Affiliation(s)
- Mehran Patpour
- Department of Agroecology, Aarhus University, Slagelse, Denmark
| | | | | | - Biagio Randazzo
- Società Semplice Agricola Randazzo (AS.A.R.), Palermo, Italy
| | - Dolors Villegas
- Institute for Food and Agricultural Research and Technology (IRTA), Lleida, Spain
| | | | - Anna Berlin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Science, Uppsala, Sweden
| | - Kerstin Flath
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Field Crops and Grassland, Quedlinburg, Germany
| | - Pawel Czembor
- Plant Breeding & Acclimatization Institute – National Research Institute, Radzików, Poland
| | - Alena Hanzalova
- Department of Genetics and Plant Breeding Methods, Crop Research Institute, Prague, Czechia
| | | | | | - Yue Jin
- USDA-ARS Cereal Disease Laboratory, University of Minnesota, Minneapolis, MN, United States
| | - Les Szabo
- USDA-ARS Cereal Disease Laboratory, University of Minnesota, Minneapolis, MN, United States
| | | | | | - Tine Thach
- Department of Agroecology, Aarhus University, Slagelse, Denmark
| | - Jens G. Hansen
- Department of Agroecology, Aarhus University, Slagelse, Denmark
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