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Bourgeois Y, Stritt C, Walser JC, Gordon SP, Vogel JP, Roulin AC. Genome-wide scans of selection highlight the impact of biotic and abiotic constraints in natural populations of the model grass Brachypodium distachyon. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:438-451. [PMID: 30044522 DOI: 10.1111/tpj.14042] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 06/20/2018] [Accepted: 07/17/2018] [Indexed: 06/08/2023]
Abstract
Grasses are essential plants for ecosystem functioning. Quantifying the selective pressures that act on natural variation in grass species is therefore essential regarding biodiversity maintenance. In this study, we investigate the selection pressures that act on two distinct populations of the grass model Brachypodium distachyon without prior knowledge about the traits under selection. We took advantage of whole-genome sequencing data produced for 44 natural accessions of B. distachyon and used complementary genome-wide selection scans (GWSS) methods to detect genomic regions under balancing and positive selection. We show that selection is shaping genetic diversity at multiple temporal and spatial scales in this species, and affects different genomic regions across the two populations. Gene ontology annotation of candidate genes reveals that pathogens may constitute important factors of positive and balancing selection in B. distachyon. We eventually cross-validated our results with quantitative trait locus data available for leaf-rust resistance in this species and demonstrate that, when paired with classical trait mapping, GWSS can help pinpointing candidate genes for further molecular validation. Thanks to a near base-perfect reference genome and the large collection of freely available natural accessions collected across its natural range, B. distachyon appears as a prime system for studies in ecology, population genomics and evolutionary biology.
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Affiliation(s)
- Yann Bourgeois
- New York University Abu Dhabi, PO Box 129188, Saadiyat Island, Abu Dhabi, United Arab Emirates
| | - Christoph Stritt
- Institute of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland
| | - Jean-Claude Walser
- Genetic Diversity Centre, ETH Zürich, Universitätstrasse 16, Zurich, Switzerland
| | - Sean P Gordon
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - John P Vogel
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Anne C Roulin
- Institute of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland
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52
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Xia C, Wang M, Yin C, Cornejo OE, Hulbert SH, Chen X. Genomic insights into host adaptation between the wheat stripe rust pathogen (Puccinia striiformis f. sp. tritici) and the barley stripe rust pathogen (Puccinia striiformis f. sp. hordei). BMC Genomics 2018; 19:664. [PMID: 30208837 PMCID: PMC6134786 DOI: 10.1186/s12864-018-5041-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 08/27/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Plant fungal pathogens can rapidly evolve and adapt to new environmental conditions in response to sudden changes of host populations in agro-ecosystems. However, the genomic basis of their host adaptation, especially at the forma specialis level, remains unclear. RESULTS We sequenced two isolates each representing Puccinia striiformis f. sp. tritici (Pst) and P. striiformis f. sp. hordei (Psh), different formae speciales of the stripe rust fungus P. striiformis highly adapted to wheat and barley, respectively. The divergence of Pst and Psh, estimated to start 8.12 million years ago, has been driven by high nucleotide mutation rates. The high genomic variation within dikaryotic urediniospores of P. striiformis has provided raw genetic materials for genome evolution. No specific gene families have enriched in either isolate, but extensive gene loss events have occurred in both Pst and Psh after the divergence from their most recent common ancestor. A large number of isolate-specific genes were identified, with unique genomic features compared to the conserved genes, including 1) significantly shorter in length; 2) significantly less expressed; 3) significantly closer to transposable elements; and 4) redundant in pathways. The presence of specific genes in one isolate (or forma specialis) was resulted from the loss of the homologues in the other isolate (or forma specialis) by the replacements of transposable elements or losses of genomic fragments. In addition, different patterns and numbers of telomeric repeats were observed between the isolates. CONCLUSIONS Host adaptation of P. striiformis at the forma specialis level is a complex pathogenic trait, involving not only virulence-related genes but also other genes. Gene loss, which might be adaptive and driven by transposable element activities, provides genomic basis for host adaptation of different formae speciales of P. striiformis.
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Affiliation(s)
- Chongjing Xia
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430 USA
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430 USA
| | - Chuntao Yin
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430 USA
| | - Omar E. Cornejo
- School of Biological Sciences, Washington State University, Pullman, WA 99164-7520 USA
| | - Scot H. Hulbert
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430 USA
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430 USA
- Wheat Health, Genetics, and Quality Research Unit, Agriculture Research Service, U.S. Department of Agriculture, Pullman, WA 99164-6430 USA
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53
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Bettgenhaeuser J, Gardiner M, Spanner R, Green P, Hernández-Pinzón I, Hubbard A, Ayliffe M, Moscou MJ. The genetic architecture of colonization resistance in Brachypodium distachyon to non-adapted stripe rust (Puccinia striiformis) isolates. PLoS Genet 2018; 14:e1007637. [PMID: 30265666 PMCID: PMC6161849 DOI: 10.1371/journal.pgen.1007637] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 08/15/2018] [Indexed: 12/19/2022] Open
Abstract
Multilayered defense responses ensure that plants are hosts to only a few adapted pathogens in the environment. The host range of a plant pathogen depends on its ability to fully overcome plant defense barriers, with failure at any single step sufficient to prevent life cycle completion of the pathogen. Puccinia striiformis, the causal agent of stripe rust (=yellow rust), is an agronomically important obligate biotrophic fungal pathogen of wheat and barley. It is generally unable to complete its life cycle on the non-adapted wild grass species Brachypodium distachyon, but natural variation exists for the degree of hyphal colonization by Puccinia striiformis. Using three B. distachyon mapping populations, we identified genetic loci conferring colonization resistance to wheat-adapted and barley-adapted isolates of P. striiformis. We observed a genetic architecture composed of two major effect QTLs (Yrr1 and Yrr3) restricting the colonization of P. striiformis. Isolate specificity was observed for Yrr1, whereas Yrr3 was effective against all tested P. striiformis isolates. Plant immune receptors of the nucleotide binding, leucine-rich repeat (NB-LRR) encoding gene family are present at the Yrr3 locus, whereas genes of this family were not identified at the Yrr1 locus. While it has been proposed that resistance to adapted and non-adapted pathogens are inherently different, the observation of (1) a simple genetic architecture of colonization resistance, (2) isolate specificity of major and minor effect QTLs, and (3) NB-LRR encoding genes at the Yrr3 locus suggest that factors associated with resistance to adapted pathogens are also critical for non-adapted pathogens.
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Affiliation(s)
| | | | | | - Phon Green
- The Sainsbury Laboratory, Norwich, United Kingdom
| | | | - Amelia Hubbard
- National Institute of Agricultural Botany, Cambridge, United Kingdom
| | - Michael Ayliffe
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Matthew J. Moscou
- The Sainsbury Laboratory, Norwich, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
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54
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Climate Change, Carbon Dioxide, and Pest Biology, Managing the Future: Coffee as a Case Study. AGRONOMY-BASEL 2018. [DOI: 10.3390/agronomy8080152] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The challenge of maintaining sufficient food, feed, fiber, and forests, for a projected end of century population of between 9–10 billion in the context of a climate averaging 2–4 °C warmer, is a global imperative. However, climate change is likely to alter the geographic ranges and impacts for a variety of insect pests, plant pathogens, and weeds, and the consequences for managed systems, particularly agriculture, remain uncertain. That uncertainty is related, in part, to whether pest management practices (e.g., biological, chemical, cultural, etc.) can adapt to climate/CO2 induced changes in pest biology to minimize potential loss. The ongoing and projected changes in CO2, environment, managed plant systems, and pest interactions, necessitates an assessment of current management practices and, if warranted, development of viable alternative strategies to counter damage from invasive alien species and evolving native pest populations. We provide an overview of the interactions regarding pest biology and climate/CO2; assess these interactions currently using coffee as a case study; identify the potential vulnerabilities regarding future pest impacts; and discuss possible adaptive strategies, including early detection and rapid response via EDDMapS (Early Detection & Distribution Mapping System), and integrated pest management (IPM), as adaptive means to improve monitoring pest movements and minimizing biotic losses while improving the efficacy of pest control.
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Figueroa M, Hammond‐Kosack KE, Solomon PS. A review of wheat diseases-a field perspective. MOLECULAR PLANT PATHOLOGY 2018; 19:1523-1536. [PMID: 29045052 PMCID: PMC6638159 DOI: 10.1111/mpp.12618] [Citation(s) in RCA: 186] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/10/2017] [Accepted: 09/22/2017] [Indexed: 05/19/2023]
Abstract
Wheat is one of the primary staple foods throughout the planet. Significant yield gains in wheat production over the past 40 years have resulted in a steady balance of supply versus demand. However, predicted global population growth rates and dietary changes mean that substantial yield gains over the next several decades will be needed to meet this escalating demand. A key component to meeting this challenge is better management of fungal incited diseases, which can be responsible for 15%-20% yield losses per annum. Prominent diseases of wheat that currently contribute to these losses include the rusts, blotches and head blight/scab. Other recently emerged or relatively unnoticed diseases, such as wheat blast and spot blotch, respectively, also threaten grain production. This review seeks to provide an overview of the impact, distribution and management strategies of these diseases. In addition, the biology of the pathogens and the molecular basis of their interaction with wheat are discussed.
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Affiliation(s)
- Melania Figueroa
- Department of Plant PathologyStakman‐Borlaug Center for Sustainable Plant Health, University of MinnesotaSt. PaulMN 55108USA
| | - Kim E. Hammond‐Kosack
- Department of Biointeractions and Crop ProtectionRothamsted Research, West CommonHarpendenHertfordshire AL5 2JQUK
| | - Peter S. Solomon
- Division of Plant Sciences, Research School of BiologyThe Australian National UniversityCanberraACT 2601Australia
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56
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Lan C, Randhawa MS, Huerta-Espino J, Singh RP. Genetic Analysis of Resistance to Wheat Rusts. Methods Mol Biol 2018; 1659:137-149. [PMID: 28856647 DOI: 10.1007/978-1-4939-7249-4_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Leaf rust, stripe rust, and stem rust pose a significant threat to global wheat production. Growing rust resistant cultivars is the most efficient and environment friendly method to reduce yield losses. Genetic analysis is undertaken to identify genes and study their roles in conferring rust resistance in a given wheat background. This chapter summarizes the protocol for genetic analysis of rust resistance at both seedling and adult plant stages. Additionally, it examines statistical analysis and related software to characterize quantitative trait loci (QTL) linked with rust resistance.
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Affiliation(s)
- Caixia Lan
- CIMMYT, Km. 45 Carretera Mex-Veracruz, El Batan, Texcoco, Mexico DF, Mexico.
| | | | - Julio Huerta-Espino
- Campo Experimental Valle de México INIFAP, Apdo., Postal 10, 56230, Chapingo, Edo. de México, Mexico
| | - Ravi P Singh
- CIMMYT, Km. 45 Carretera Mex-Veracruz, El Batan, Texcoco, Mexico DF, Mexico
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57
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Schwessinger B, Sperschneider J, Cuddy WS, Garnica DP, Miller ME, Taylor JM, Dodds PN, Figueroa M, Park RF, Rathjen JP. A Near-Complete Haplotype-Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici Reveals High Interhaplotype Diversity. mBio 2018; 9:e02275-17. [PMID: 29463659 PMCID: PMC5821087 DOI: 10.1128/mbio.02275-17] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 01/09/2018] [Indexed: 01/01/2023] Open
Abstract
A long-standing biological question is how evolution has shaped the genomic architecture of dikaryotic fungi. To answer this, high-quality genomic resources that enable haplotype comparisons are essential. Short-read genome assemblies for dikaryotic fungi are highly fragmented and lack haplotype-specific information due to the high heterozygosity and repeat content of these genomes. Here, we present a diploid-aware assembly of the wheat stripe rust fungus Puccinia striiformis f. sp. tritici based on long reads using the FALCON-Unzip assembler. Transcriptome sequencing data sets were used to infer high-quality gene models and identify virulence genes involved in plant infection referred to as effectors. This represents the most complete Puccinia striiformis f. sp. tritici genome assembly to date (83 Mb, 156 contigs, N50 of 1.5 Mb) and provides phased haplotype information for over 92% of the genome. Comparisons of the phase blocks revealed high interhaplotype diversity of over 6%. More than 25% of all genes lack a clear allelic counterpart. When we investigated genome features that potentially promote the rapid evolution of virulence, we found that candidate effector genes are spatially associated with conserved genes commonly found in basidiomycetes. Yet, candidate effectors that lack an allelic counterpart are more distant from conserved genes than allelic candidate effectors and are less likely to be evolutionarily conserved within the P. striiformis species complex and Pucciniales In summary, this haplotype-phased assembly enabled us to discover novel genome features of a dikaryotic plant-pathogenic fungus previously hidden in collapsed and fragmented genome assemblies.IMPORTANCE Current representations of eukaryotic microbial genomes are haploid, hiding the genomic diversity intrinsic to diploid and polyploid life forms. This hidden diversity contributes to the organism's evolutionary potential and ability to adapt to stress conditions. Yet, it is challenging to provide haplotype-specific information at a whole-genome level. Here, we take advantage of long-read DNA sequencing technology and a tailored-assembly algorithm to disentangle the two haploid genomes of a dikaryotic pathogenic wheat rust fungus. The two genomes display high levels of nucleotide and structural variations, which lead to allelic variation and the presence of genes lacking allelic counterparts. Nonallelic candidate effector genes, which likely encode important pathogenicity factors, display distinct genome localization patterns and are less likely to be evolutionary conserved than those which are present as allelic pairs. This genomic diversity may promote rapid host adaptation and/or be related to the age of the sequenced isolate since last meiosis.
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Affiliation(s)
- Benjamin Schwessinger
- Research School of Biology, the Australian National University, Acton, ACT, Australia
| | - Jana Sperschneider
- Centre for Environment and Life Sciences, CSIRO Agriculture and Food, Perth, WA, Australia
| | - William S Cuddy
- Plant Breeding Institute, Faculty of Agriculture and Environment, the University of Sydney, Narellan, NSW, Australia
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia
| | - Diana P Garnica
- Research School of Biology, the Australian National University, Acton, ACT, Australia
| | - Marisa E Miller
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Jennifer M Taylor
- Black Mountain Laboratories, CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Peter N Dodds
- Black Mountain Laboratories, CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Melania Figueroa
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
- Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, Minnesota, USA
| | - Robert F Park
- Plant Breeding Institute, Faculty of Agriculture and Environment, the University of Sydney, Narellan, NSW, Australia
| | - John P Rathjen
- Research School of Biology, the Australian National University, Acton, ACT, Australia
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58
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Ali S, Rodriguez-Algaba J, Thach T, Sørensen CK, Hansen JG, Lassen P, Nazari K, Hodson DP, Justesen AF, Hovmøller MS. Yellow Rust Epidemics Worldwide Were Caused by Pathogen Races from Divergent Genetic Lineages. FRONTIERS IN PLANT SCIENCE 2017; 8:1057. [PMID: 28676811 PMCID: PMC5477562 DOI: 10.3389/fpls.2017.01057] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 05/31/2017] [Indexed: 05/21/2023]
Abstract
We investigated whether the recent worldwide epidemics of wheat yellow rust were driven by races of few clonal lineage(s) or populations of divergent races. Race phenotyping of 887 genetically diverse Puccinia striiformis isolates sampled in 35 countries during 2009-2015 revealed that these epidemics were often driven by races from few but highly divergent genetic lineages. PstS1 was predominant in North America; PstS2 in West Asia and North Africa; and both PstS1 and PstS2 in East Africa. PstS4 was prevalent in Northern Europe on triticale; PstS5 and PstS9 were prevalent in Central Asia; whereas PstS6 was prevalent in epidemics in East Africa. PstS7, PstS8 and PstS10 represented three genetic lineages prevalent in Europe. Races from other lineages were in low frequencies. Virulence to Yr9 and Yr27 was common in epidemics in Africa and Asia, while virulence to Yr17 and Yr32 were prevalent in Europe, corresponding to widely deployed resistance genes. The highest diversity was observed in South Asian populations, where frequent recombination has been reported, and no particular race was predominant in this area. The results are discussed in light of the role of invasions in shaping pathogen population across geographical regions. The results emphasized the lack of predictability of emergence of new races with high epidemic potential, which stresses the need for additional investments in population biology and surveillance activities of pathogens on global food crops, and assessments of disease vulnerability of host varieties prior to their deployment at larger scales.
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Affiliation(s)
- Sajid Ali
- Department of Agroecology, Global Rust Reference Centre, Aarhus UniversitySlagelse, Denmark
| | | | - Tine Thach
- Department of Agroecology, Global Rust Reference Centre, Aarhus UniversitySlagelse, Denmark
| | - Chris K. Sørensen
- Department of Agroecology, Global Rust Reference Centre, Aarhus UniversitySlagelse, Denmark
| | - Jens G. Hansen
- Department of Agroecology, Global Rust Reference Centre, Aarhus UniversitySlagelse, Denmark
| | - Poul Lassen
- Department of Agroecology, Global Rust Reference Centre, Aarhus UniversitySlagelse, Denmark
| | - Kumarse Nazari
- International Center for Agricultural Research in the Dry Areas, Regional Cereal Rust Research Centre, Aegean Agricultural Research Instituteİzmir, Turkey
| | - David P. Hodson
- International Maize and Wheat Improvement Center, CIMMYTAddis Ababa, Ethiopia
| | - Annemarie F. Justesen
- Department of Agroecology, Global Rust Reference Centre, Aarhus UniversitySlagelse, Denmark
| | - Mogens S. Hovmøller
- Department of Agroecology, Global Rust Reference Centre, Aarhus UniversitySlagelse, Denmark
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Muleta KT, Bulli P, Rynearson S, Chen X, Pumphrey M. Loci associated with resistance to stripe rust (Puccinia striiformis f. sp. tritici) in a core collection of spring wheat (Triticum aestivum). PLoS One 2017; 12:e0179087. [PMID: 28591221 PMCID: PMC5462451 DOI: 10.1371/journal.pone.0179087] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 05/23/2017] [Indexed: 11/21/2022] Open
Abstract
Stripe rust, caused by Puccinia striiformis Westend. f. sp. tritici Erikss. (Pst) remains one of the most significant diseases of wheat worldwide. We investigated stripe rust resistance by genome-wide association analysis (GWAS) in 959 spring wheat accessions from the United States Department of Agriculture-Agricultural Research Service National Small Grains Collection, representing major global production environments. The panel was characterized for field resistance in multi-environment field trials and seedling resistance under greenhouse conditions. A genome-wide set of 5,619 informative SNP markers were used to examine the population structure, linkage disequilibrium and marker-trait associations in the germplasm panel. Based on model-based analysis of population structure and hierarchical Ward clustering algorithm, the accessions were clustered into two major subgroups. These subgroups were largely separated according to geographic origin and improvement status of the accessions. A significant correlation was observed between the population sub-clusters and response to stripe rust infection. We identified 11 and 7 genomic regions with significant associations with stripe rust resistance at adult plant and seedling stages, respectively, based on a false discovery rate multiple correction method. The regions harboring all, except three, of the QTL identified from the field and greenhouse studies overlap with positions of previously reported QTL. Further work should aim at validating the identified QTL using proper germplasm and populations to enhance their utility in marker assisted breeding.
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Affiliation(s)
- Kebede T. Muleta
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
| | - Peter Bulli
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
| | - Sheri Rynearson
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
| | - Xianming Chen
- USDA-ARS, Wheat Health, Genetics, and Quality Research Unit, and Department of Plant Pathology, Washington State University, Pullman, Washington, United States of America
| | - Michael Pumphrey
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
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Kolmer JA, Mirza JI, Imtiaz M, Shah SJA. Genetic Differentiation of the Wheat Leaf Rust Fungus Puccinia triticina in Pakistan and Genetic Relationship to Other Worldwide Populations. PHYTOPATHOLOGY 2017; 107:786-790. [PMID: 28398164 DOI: 10.1094/phyto-10-16-0388-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Collections of Puccinia triticina, the wheat leaf rust pathogen, were obtained from Pakistan in 2008, 2010, 2011, 2013, and 2014. Collections were also obtained from Bhutan in 2013. Single uredinial isolates were derived and tested for virulence phenotype to 20 lines of Thatcher wheat that differ for single leaf rust resistance genes, and for molecular genotype with 23 simple-sequence repeat (SSR) primers. Twenty-four virulence phenotypes were described among the 89 isolates tested for virulence. None of the isolates had virulence to Thatcher lines with Lr9, Lr24, or Lr18. Virulence to most of the other Thatcher lines was over 50%. The two most common virulence phenotypes, FHPSQ and KHPQQ, had virulence to Lr16, Lr17, and Lr26. Twenty-seven SSR genotypes were found among the 38 isolates tested for molecular variation. The SSR genotypes had high levels of observed heterozygosity and significant correlation with virulence phenotype, which indicated clonal reproduction. Cluster analysis and principal component plots indicated three groups of SSR genotypes that also varied significantly for virulence. Isolates with MBDSS and MCDSS virulence phenotypes from Pakistan and Bhutan were highly related for SSR genotype and virulence to isolates from Turkey, Europe, Central Asia, the Middle East, North America and South America, indicating the possible migration of the rust fungus between continental regions.
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Affiliation(s)
- J A Kolmer
- First author: United States Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN 55108; second author: Pakistan Agricultural Research Council, Crop Disease Institute, Sunny Bank Muree, Pakistan; third author: International Maize and Wheat Improvement Center, CSI Building, NARC, Park Road, Islamabad 44000, Pakistan; and fourth author: Nuclear Institute for Food and Agriculture, Plant Protection Division, G. T. Road, Peshawar, Pakistan
| | - J I Mirza
- First author: United States Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN 55108; second author: Pakistan Agricultural Research Council, Crop Disease Institute, Sunny Bank Muree, Pakistan; third author: International Maize and Wheat Improvement Center, CSI Building, NARC, Park Road, Islamabad 44000, Pakistan; and fourth author: Nuclear Institute for Food and Agriculture, Plant Protection Division, G. T. Road, Peshawar, Pakistan
| | - M Imtiaz
- First author: United States Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN 55108; second author: Pakistan Agricultural Research Council, Crop Disease Institute, Sunny Bank Muree, Pakistan; third author: International Maize and Wheat Improvement Center, CSI Building, NARC, Park Road, Islamabad 44000, Pakistan; and fourth author: Nuclear Institute for Food and Agriculture, Plant Protection Division, G. T. Road, Peshawar, Pakistan
| | - S J A Shah
- First author: United States Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN 55108; second author: Pakistan Agricultural Research Council, Crop Disease Institute, Sunny Bank Muree, Pakistan; third author: International Maize and Wheat Improvement Center, CSI Building, NARC, Park Road, Islamabad 44000, Pakistan; and fourth author: Nuclear Institute for Food and Agriculture, Plant Protection Division, G. T. Road, Peshawar, Pakistan
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El Jarroudi M, Kouadio L, Bock CH, El Jarroudi M, Junk J, Pasquali M, Maraite H, Delfosse P. A Threshold-Based Weather Model for Predicting Stripe Rust Infection in Winter Wheat. PLANT DISEASE 2017; 101:693-703. [PMID: 30678577 DOI: 10.1094/pdis-12-16-1766-re] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Wheat stripe rust (caused by Puccinia striiformis f. sp. tritici) is a major threat in most wheat growing regions worldwide, which potentially causes substantial yield losses when environmental conditions are favorable. Data from 1999 to 2015 for three representative wheat-growing sites in Luxembourg were used to develop a threshold-based weather model for predicting wheat stripe rust. First, the range of favorable weather conditions using a Monte Carlo simulation method based on the Dennis model were characterized. Then, the optimum combined favorable weather variables (air temperature, relative humidity, and rainfall) during the most critical infection period (May-June) was identified and was used to develop the model. Uninterrupted hours with such favorable weather conditions over each dekad (i.e., 10-day period) during May-June were also considered when building the model. Results showed that a combination of relative humidity >92% and 4°C < temperature < 16°C for a minimum of 4 continuous hours, associated with rainfall ≤0.1 mm (with the dekad having these conditions for 5 to 20% of the time), were optimum to the development of a wheat stripe rust epidemic. The model accurately predicted infection events: probabilities of detection were ≥0.90 and false alarm ratios were ≤0.38 on average, and critical success indexes ranged from 0.63 to 1. The method is potentially applicable to studies of other economically important fungal diseases of other crops or in different geographical locations. If weather forecasts are available, the threshold-based weather model can be integrated into an operational warning system to guide fungicide applications.
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Affiliation(s)
- Moussa El Jarroudi
- Department of Environmental Sciences and Management, Université de Liège, Arlon, B-6700 Belgium
| | - Louis Kouadio
- International Centre for Applied Climate Sciences, University of Southern Queensland, Toowoomba, QLD 4350 Australia
| | - Clive H Bock
- United States Department of Agriculture-Agricultural Research Service SEFTNRL, Byron, GA 31008
| | - Mustapha El Jarroudi
- Laboratory of Mathematics and Applications, Department of Mathematics, Université Abdelmalek Essaâdi, Tangier, Morocco
| | - Jürgen Junk
- Environmental Research and Innovation, Luxembourg Institute of Science and Technology, Belvaux, L-4422 Grand-Duché de Luxembourg
| | - Matias Pasquali
- Department of Food, Environmental and Nutritional Sciences, University of Milano, Milan 20233, Italy
| | - Henri Maraite
- Earth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, 1348 Belgium
| | - Philippe Delfosse
- Environmental Research and Innovation, Luxembourg Institute of Science and Technology, Belvaux, L-4422 Grand-Duché de Luxembourg
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Rodriguez-Algaba J, Sørensen CK, Labouriau R, Justesen AF, Hovmøller MS. Genetic diversity within and among aecia of the wheat rust fungus Puccinia striiformis on the alternate host Berberis vulgaris. Fungal Biol 2017; 121:541-549. [PMID: 28606349 DOI: 10.1016/j.funbio.2017.03.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 03/10/2017] [Indexed: 10/19/2022]
Abstract
An isolate of the fungus Puccinia striiformis, causing yellow (stripe) rust on cereals and grasses, was selfed on the alternate (sexual) host, Berberis vulgaris. This enabled us to investigate genetic variability of progeny isolates within and among aecia. Nine aecial clusters each consisting of an aecium (single aecial cup) and nine clusters containing multiple aecial cups were selected from 18 B. vulgaris leaves. Aeciospores from each cluster were inoculated on susceptible wheat seedlings and 64 progeny isolates were recovered. Molecular genotyping using 37 simple sequence repeat markers confirmed the parental origin of all progeny isolates. Thirteen molecular markers, which were heterozygous in the parental isolate, were used to analyse genetic diversity within and among aecial cups. The 64 progeny isolates resulted in 22 unique recombinant multilocus genotypes and none of them were resampled in different aecial clusters. Isolates derived from a single cup were always of the same genotype whereas isolates originating from clusters containing up to nine aecial cups revealed one to three genotypes per cluster. These results implied that each aecium was the result of a successful fertilization in a corresponding pycnium and that an aecium consisted of genetically identical aeciospores probably multiplied via repetitive mitotic divisions. Furthermore, the results suggested that aecia within a cluster were the result of independent fertilization events often involving genetically different pycniospores. The application of molecular markers represented a major advance in comparison to previous studies depending on phenotypic responses on host plants. The study allowed significant conclusions about fundamental aspects of the biology and genetics of an important cereal rust fungus.
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Affiliation(s)
- Julian Rodriguez-Algaba
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Forsøgsvej 1, 4200 Slagelse, Denmark.
| | - Chris K Sørensen
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Forsøgsvej 1, 4200 Slagelse, Denmark
| | - Rodrigo Labouriau
- Department of Mathematics, Faculty of Science and Technology, Aarhus University, Ny Munkegade 118, 8000 Aarhus, Denmark
| | - Annemarie F Justesen
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Forsøgsvej 1, 4200 Slagelse, Denmark
| | - Mogens S Hovmøller
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Forsøgsvej 1, 4200 Slagelse, Denmark
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63
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Liu W, Maccaferri M, Bulli P, Rynearson S, Tuberosa R, Chen X, Pumphrey M. Genome-wide association mapping for seedling and field resistance to Puccinia striiformis f. sp. tritici in elite durum wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:649-667. [PMID: 28039515 DOI: 10.1007/s00122-016-2841-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 12/13/2016] [Indexed: 05/06/2023]
Abstract
Genome-wide association analysis in tetraploid wheat revealed novel and diverse loci for seedling and field resistance to stripe rust in elite spring durum wheat accessions from worldwide. Improving resistance to stripe rust, caused by Puccinia striiformis f. sp. tritici, is a major objective for wheat breeding. To identify effective stripe rust resistance loci, a genome-wide association study (GWAS) was conducted using 232 elite durum wheat (Triticum turgidum ssp. durum) lines from worldwide breeding programs. Genotyping with the 90 K iSelect wheat single nucleotide polymorphism (SNP) array resulted in 11,635 markers distributed across the genome. Response to stripe rust infection at the seedling stage revealed resistant and susceptible accessions present in rather balanced frequencies for the six tested races, with a higher frequency of susceptible responses to United States races as compared to Italian races (61.1 vs. 43.1% of susceptible accessions). Resistance at the seedling stage only partially explained adult plant resistance, which was found to be more frequent with 67.7% of accessions resistant across six nurseries in the United States. GWAS identified 82 loci associated with seedling stripe rust resistance, five of which were significant at the false discovery rate adjusted P value <0.1 and 11 loci were detected for the field response at the adult plant stages in at least two environments. Notably, Yrdurum-1BS.1 showed the largest effect for both seedling and field resistance, and is therefore considered as a major locus for resistance in tetraploid wheat. Our GWAS study is the first of its kind for stripe rust resistance in tetraploid wheat and provides an overview of resistance in elite germplasm and reports new loci that can be used in breeding resistant cultivars.
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Affiliation(s)
- Weizhen Liu
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA.
| | - Marco Maccaferri
- Department of Agricultural Sciences, University of Bologna, 40127, Bologna, Italy
| | - Peter Bulli
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
| | - Sheri Rynearson
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
| | - Roberto Tuberosa
- Department of Agricultural Sciences, University of Bologna, 40127, Bologna, Italy
| | - Xianming Chen
- Wheat Health, Genetics, and Quality Research Unit, USDA-ARS, Pullman, WA, 99164-6430, USA
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA
| | - Michael Pumphrey
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA.
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64
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Schwessinger B. Fundamental wheat stripe rust research in the 21 st century. THE NEW PHYTOLOGIST 2017; 213:1625-1631. [PMID: 27575735 DOI: 10.1111/nph.14159] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 07/05/2016] [Indexed: 05/27/2023]
Abstract
Contents 1625 I. 1625 II. 1626 III. 1626 IV. 1626 V. 1628 VI. 1629 VII. 1629 1630 References 1630 SUMMARY: In the 21st century, the wheat stripe rust fungus has evolved to be the largest biotic limitation to global wheat production. New pathogen genotypes are more aggressive and able to infect previously resistant wheat varieties, leading to rapid pathogen migration across and between continents. We now know the full life cycle, microevolutionary relationships and past migration routes on a global scale. Current sequencing technologies have provided the first fungal draft genomes and simplified plant resistance gene cloning. Yet, we know nothing about the molecular and microevolutionary mechanisms that facilitate the infection process and cause new devastating pathogen races. These are the questions that need to be addressed by exploiting the synergies between novel 21st century biology tools and decades of dedicated pathology work.
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Affiliation(s)
- Benjamin Schwessinger
- The Australian National University, Research School Biology, 134 Linnaeus Way, Acton, ACT, 2601, Australia
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65
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Hu X, Ma L, Liu T, Wang C, Peng Y, Pu Q, Xu X. Population Genetic Analysis of Puccinia striiformis f. sp. tritici Suggests Two Distinct Populations in Tibet and the Other Regions of China. PLANT DISEASE 2017; 101:288-296. [PMID: 30681929 DOI: 10.1094/pdis-02-16-0190-re] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is an important disease on wheat, seriously threatening wheat production worldwide. China is one of the largest stripe rust epidemic regions in the world. The pathogen sexual reproduction and migration routes between Tibet and the other regions in China are still unknown. In this study, we obtained 961 Pst isolates from 1,391 wheat leaf samples from Gansu (277), Shaanxi (253), Sichuan (172), and Tibet (259), comprising 13 natural populations, and genotyped them with simple sequence repeat (SSR) markers. The isolates can be divided into two distinct clusters based on DAPC and STRUCTURE analyses. The genetic diversity of Longnan (in Gansu) and Yibin (in Sichuan) populations was the highest and lowest among the 13 populations, respectively. The hypothesis of multilocus linkage disequilibrium was rejected for the populations from Linzhi in the Himalayan, Longnan, Hanzhong, Guangyuan, Mianyang, Liangshan, and Chendu in the south Qinling Mountains at the level of P = 0.01, which indicated significant linkage among markers in these populations. Populations in the other regions had extensive gene exchange (Nm > 4); little gene exchange was found between Tibet and the other regions (Nm < 1). The results suggest that the Tibet epidemic region of Pst is highly differentiated from the other epidemic regions in China.
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Affiliation(s)
- Xiaoping Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lijie Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Taiguo Liu
- State Key Laboratory for the Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing 100193, China
| | - Conghao Wang
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuelin Peng
- Tibet Agricultural and Animal Husbandry College, Linzhi 860000, China
| | - Qiong Pu
- Tibet Autonomous Region Agricultural Technology Extension and Service Center, Lhasa 850000, Tibet
| | - Xiangming Xu
- NIAB East Malling Research, New Road, East Malling, ME19 6BJ, Kent, U.K
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Zheng L, Zhao J, Liang X, Zhan G, Jiang S, Kang Z. Identification of a Novel Alternaria alternata Strain Able to Hyperparasitize Puccinia striiformis f. sp. tritici, the Causal Agent of Wheat Stripe Rust. Front Microbiol 2017; 8:71. [PMID: 28197134 PMCID: PMC5281574 DOI: 10.3389/fmicb.2017.00071] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 01/11/2017] [Indexed: 11/13/2022] Open
Abstract
The obligate bitrophic fungus Puccinia striiformis f. sp. tritici (Pst) causes stripe (yellow) rust on wheat worldwide. Here, we report a novel fungal strain able to hyperparasitize Pst. The strain was isolated from gray-colored rust pustules, and was identified as Alternaria alternata (Fr.: Fr.) keissler based on a combination of morphological characteristics and multi-locus (ITS, GAPDH, and RPB2) phylogeny. Upon artificial inoculation, the hyperparasite reduced the production and viability of urediniospores, and produced a typical gray-colored rust pustule symptom. Scanning electron microscopy demonstrated that the strain could efficiently penetrate and colonize Pst urediniospores. This study first demonstrates that A. alternata could parasitize Pst and indicates its potential application in the biological control of wheat stripe rust disease.
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Affiliation(s)
| | | | | | | | | | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F UniversityYangling, China
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67
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Hovmøller MS, Rodriguez-Algaba J, Thach T, Sørensen CK. Race Typing of Puccinia striiformis on Wheat. Methods Mol Biol 2017; 1659:29-40. [PMID: 28856638 DOI: 10.1007/978-1-4939-7249-4_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A procedure for virulence phenotyping of isolates of yellow (stripe) rust using spray inoculation of wheat seedlings by spores suspended in an engineered fluid, Novec™ 7100, is presented. Differential sets consisting of near-isogenic Avocet lines, selected lines from the "World" and "European" sets, and additional varieties showing race-specificity facilitate a robust assessment of race, irrespectively of geographical and evolutionary origin of isolates. A simple procedure for purification of samples consisting of multiple races is also presented.
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Affiliation(s)
- Mogens S Hovmøller
- Department of Agroecology, Aarhus University, Forsogsvej 1, 4200, Slagelse, Denmark.
| | | | - Tine Thach
- Department of Agroecology, Aarhus University, Forsogsvej 1, 4200, Slagelse, Denmark
| | - Chris K Sørensen
- Department of Agroecology, Aarhus University, Forsogsvej 1, 4200, Slagelse, Denmark
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68
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McDonald BA, Stukenbrock EH. Rapid emergence of pathogens in agro-ecosystems: global threats to agricultural sustainability and food security. Philos Trans R Soc Lond B Biol Sci 2016; 371:20160026. [PMID: 28080995 PMCID: PMC5095548 DOI: 10.1098/rstb.2016.0026] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/14/2016] [Indexed: 01/06/2023] Open
Abstract
Agricultural ecosystems are composed of genetically depauperate populations of crop plants grown at a high density and over large spatial scales, with the regional composition of crop species changing little from year to year. These environments are highly conducive for the emergence and dissemination of pathogens. The uniform host populations facilitate the specialization of pathogens to particular crop cultivars and allow the build-up of large population sizes. Population genetic and genomic studies have shed light on the evolutionary mechanisms underlying speciation processes, adaptive evolution and long-distance dispersal of highly damaging pathogens in agro-ecosystems. These studies document the speed with which pathogens evolve to overcome crop resistance genes and pesticides. They also show that crop pathogens can be disseminated very quickly across and among continents through human activities. In this review, we discuss how the peculiar architecture of agro-ecosystems facilitates pathogen emergence, evolution and dispersal. We present four example pathosystems that illustrate both pathogen specialization and pathogen speciation, including different time frames for emergence and different mechanisms underlying the emergence process. Lastly, we argue for a re-design of agro-ecosystems that embraces the concept of dynamic diversity to improve their resilience to pathogens. This article is part of the themed issue 'Tackling emerging fungal threats to animal health, food security and ecosystem resilience'.
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Affiliation(s)
- Bruce A McDonald
- Plant Pathology Group, ETH Zurich, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - Eva H Stukenbrock
- Environmental Genomics Group, Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306 Plön, Germany
- Christian-Albrechts University of Kiel, Am Botanischen Garten 1-9, 24118 Kiel, Germany
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69
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Quantitative Proteomics Reveals the Defense Response of Wheat against Puccinia striiformis f. sp. tritici. Sci Rep 2016; 6:34261. [PMID: 27678307 PMCID: PMC5039691 DOI: 10.1038/srep34261] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 09/12/2016] [Indexed: 01/09/2023] Open
Abstract
Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is considered one of the most aggressive diseases to wheat production. In this study, we used an iTRAQ-based approach for the quantitative proteomic comparison of the incompatible Pst race CYR23 in infected and non-infected leaves of the wheat cultivar Suwon11. A total of 3,475 unique proteins were identified from three key stages of interaction (12, 24, and 48 h post-inoculation) and control groups. Quantitative analysis showed that 530 proteins were differentially accumulated by Pst infection (fold changes >1.5, p < 0.05). Among these proteins, 10.54% was classified as involved in the immune system process and stimulus response. Intriguingly, bioinformatics analysis revealed that a set of reactive oxygen species metabolism-related proteins, peptidyl–prolyl cis–trans isomerases (PPIases), RNA-binding proteins (RBPs), and chaperonins was involved in the response to Pst infection. Our results were the first to show that PPIases, RBPs, and chaperonins participated in the regulation of the immune response in wheat and even in plants. This study aimed to provide novel routes to reveal wheat gene functionality and better understand the early events in wheat–Pst incompatible interactions.
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70
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Huang L, Raats D, Sela H, Klymiuk V, Lidzbarsky G, Feng L, Krugman T, Fahima T. Evolution and Adaptation of Wild Emmer Wheat Populations to Biotic and Abiotic Stresses. ANNUAL REVIEW OF PHYTOPATHOLOGY 2016; 54:279-301. [PMID: 27296141 DOI: 10.1146/annurev-phyto-080614-120254] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The genetic bottlenecks associated with plant domestication and subsequent selection in man-made agroecosystems have limited the genetic diversity of modern crops and increased their vulnerability to environmental stresses. Wild emmer wheat, the tetraploid progenitor of domesticated wheat, distributed along a wide range of ecogeographical conditions in the Fertile Crescent, has valuable "left behind" adaptive diversity to multiple diseases and environmental stresses. The biotic and abiotic stress responses are conferred by series of genes and quantitative trait loci (QTLs) that control complex resistance pathways. The study of genetic diversity, genomic organization, expression profiles, protein structure and function of biotic and abiotic stress-resistance genes, and QTLs could shed light on the evolutionary history and adaptation mechanisms of wild emmer populations for their natural habitats. The continuous evolution and adaptation of wild emmer to the changing environment provide novel solutions that can contribute to safeguarding food for the rapidly growing human population.
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Affiliation(s)
- Lin Huang
- Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa, Haifa 3498838, Israel;
| | - Dina Raats
- Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa, Haifa 3498838, Israel;
| | - Hanan Sela
- The Institute for Cereal Crops Improvement, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Valentina Klymiuk
- Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa, Haifa 3498838, Israel;
| | - Gabriel Lidzbarsky
- Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa, Haifa 3498838, Israel;
| | - Lihua Feng
- Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa, Haifa 3498838, Israel;
| | - Tamar Krugman
- Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa, Haifa 3498838, Israel;
| | - Tzion Fahima
- Department of Evolutionary and Environmental Biology and The Institute of Evolution, University of Haifa, Haifa 3498838, Israel;
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71
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Liu C, Pedersen C, Schultz-Larsen T, Aguilar GB, Madriz-Ordeñana K, Hovmøller MS, Thordal-Christensen H. The stripe rust fungal effector PEC6 suppresses pattern-triggered immunity in a host species-independent manner and interacts with adenosine kinases. THE NEW PHYTOLOGIST 2016. [PMID: 27252028 DOI: 10.1111/nph.14034] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 04/25/2016] [Indexed: 05/20/2023]
Abstract
We identified a wheat stripe rust (Puccinia striiformis) effector candidate (PEC6) with pattern-triggered immunity (PTI) suppression function and its corresponding host target. PEC6 compromised PTI host species-independently. In Nicotiana benthamiana, it hampers reactive oxygen species (ROS) accumulation and callose deposition induced by Pseudomonas fluorescens. In Arabidopsis, plants expressing PEC6 were more susceptible to Pseudomonas syringae pv. tomato (Pto) DC3000 ΔAvrPto/ΔAvrPtoB. In wheat, PEC6-suppression of P. fluorescens-elicited PTI was revealed by the fact that it allowed activation of effector-triggered immunity by Pto DC3000. Knocking down of PEC6 expression by virus-mediated host-induced gene silencing decreased the number of rust pustules, uncovering PEC6 as an important pathogenicity factor. PEC6, overexpressed in plant cells without its signal peptide, was localized to the nucleus and cytoplasm. A yeast two-hybrid assay showed that PEC6 interacts with both wheat and Arabidopsis adenosine kinases (ADKs). Knocking down wheat ADK expression by virus-induced gene silencing reduced leaf growth and enhanced the number of rust pustules, indicating that ADK is important in plant development and defence. ADK plays essential roles in regulating metabolism, cytokinin interconversion and methyl transfer reactions, and our data propose a model where PEC6 may affect one of these processes by targeting ADK to favour fungal growth.
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Affiliation(s)
- Changhai Liu
- Section for Plant and Soil Science, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg C, DK-1871, Denmark
| | - Carsten Pedersen
- Section for Plant and Soil Science, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg C, DK-1871, Denmark
| | - Torsten Schultz-Larsen
- Section for Plant and Soil Science, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg C, DK-1871, Denmark
| | - Geziel B Aguilar
- Section for Plant and Soil Science, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg C, DK-1871, Denmark
| | - Kenneth Madriz-Ordeñana
- Section for Plant and Soil Science, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg C, DK-1871, Denmark
| | - Mogens S Hovmøller
- Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse, DK-4200, Denmark
| | - Hans Thordal-Christensen
- Section for Plant and Soil Science, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg C, DK-1871, Denmark
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72
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Sørensen CK, Thach T, Hovmøller MS. Evaluation of Spray and Point Inoculation Methods for the Phenotyping of Puccinia striiformis on Wheat. PLANT DISEASE 2016; 100:1064-1070. [PMID: 30682276 DOI: 10.1094/pdis-12-15-1477-re] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The fungus Puccinia striiformis causes yellow (stripe) rust on wheat worldwide. In the present article, new methods utilizing an engineered fluid (Novec 7100) as a carrier of urediniospores were compared with commonly used inoculation methods. In general, Novec 7100 facilitated a faster and more flexible application procedure for spray inoculation and it gave highly reproducible results for virulence phenotyping. Six point inoculation methods were compared to find the most suitable for assessment of pathogen aggressiveness. The use of Novec 7100 and dry dilution with Lycopodium spores gave an inoculation success rate of 100% in two independent trials, which was significantly higher and more consistent than for spore suspension in Soltrol 170, water, water + Tween 20, and Noble agar + Tween 20. Both Soltrol 170 and Novec 7100 allowed precise quantification of inoculum, which is important for the assessment of quantitative epidemiological parameters. New protocols for spray and point inoculation of P. striiformis on wheat are presented, along with the prospect for applying these in rust research and resistance breeding activities.
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Affiliation(s)
- Chris K Sørensen
- Department of Agroecology, Aarhus University, Flakkebjerg, Forsøgsvej 1, DK-4200 Slagelse, Denmark
| | - Tine Thach
- Department of Agroecology, Aarhus University, Flakkebjerg, Forsøgsvej 1, DK-4200 Slagelse, Denmark
| | - Mogens S Hovmøller
- Department of Agroecology, Aarhus University, Flakkebjerg, Forsøgsvej 1, DK-4200 Slagelse, Denmark
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73
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Dobon A, Bunting DCE, Cabrera-Quio LE, Uauy C, Saunders DGO. The host-pathogen interaction between wheat and yellow rust induces temporally coordinated waves of gene expression. BMC Genomics 2016; 17:380. [PMID: 27207100 PMCID: PMC4875698 DOI: 10.1186/s12864-016-2684-4] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 04/29/2016] [Indexed: 11/16/2022] Open
Abstract
Background Understanding how plants and pathogens modulate gene expression during the host-pathogen interaction is key to uncovering the molecular mechanisms that regulate disease progression. Recent advances in sequencing technologies have provided new opportunities to decode the complexity of such interactions. In this study, we used an RNA-based sequencing approach (RNA-seq) to assess the global expression profiles of the wheat yellow rust pathogen Puccinia striiformis f. sp. tritici (PST) and its host during infection. Results We performed a detailed RNA-seq time-course for a susceptible and a resistant wheat host infected with PST. This study (i) defined the global gene expression profiles for PST and its wheat host, (ii) substantially improved the gene models for PST, (iii) evaluated the utility of several programmes for quantification of global gene expression for PST and wheat, and (iv) identified clusters of differentially expressed genes in the host and pathogen. By focusing on components of the defence response in susceptible and resistant hosts, we were able to visualise the effect of PST infection on the expression of various defence components and host immune receptors. Conclusions Our data showed sequential, temporally coordinated activation and suppression of expression of a suite of immune-response regulators that varied between compatible and incompatible interactions. These findings provide the framework for a better understanding of how PST causes disease and support the idea that PST can suppress the expression of defence components in wheat to successfully colonize a susceptible host. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2684-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Albor Dobon
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | - Luis Enrique Cabrera-Quio
- The Genome Analysis Centre, Norwich Research Park, Norwich, UK.,The Sainsbury Laboratory, Norwich Research Park, Norwich, UK
| | | | - Diane G O Saunders
- John Innes Centre, Norwich Research Park, Norwich, UK. .,The Genome Analysis Centre, Norwich Research Park, Norwich, UK.
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74
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Walter S, Ali S, Kemen E, Nazari K, Bahri BA, Enjalbert J, Hansen JG, Brown JK, Sicheritz‐Pontén T, Jones J, de Vallavieille‐Pope C, Hovmøller MS, Justesen AF. Molecular markers for tracking the origin and worldwide distribution of invasive strains of Puccinia striiformis. Ecol Evol 2016; 6:2790-804. [PMID: 27066253 PMCID: PMC4800029 DOI: 10.1002/ece3.2069] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 02/15/2016] [Accepted: 02/22/2016] [Indexed: 01/07/2023] Open
Abstract
Investigating the origin and dispersal pathways is instrumental to mitigate threats and economic and environmental consequences of invasive crop pathogens. In the case of Puccinia striiformis causing yellow rust on wheat, a number of economically important invasions have been reported, e.g., the spreading of two aggressive and high temperature adapted strains to three continents since 2000. The combination of sequence-characterized amplified region (SCAR) markers, which were developed from two specific AFLP fragments, differentiated the two invasive strains, PstS1 and PstS2 from all other P. striiformis strains investigated at a worldwide level. The application of the SCAR markers on 566 isolates showed that PstS1 was present in East Africa in the early 1980s and then detected in the Americas in 2000 and in Australia in 2002. PstS2 which evolved from PstS1 became widespread in the Middle East and Central Asia. In 2000, PstS2 was detected in Europe, where it never became prevalent. Additional SSR genotyping and virulence phenotyping revealed 10 and six variants, respectively, within PstS1 and PstS2, demonstrating the evolutionary potential of the pathogen. Overall, the results suggested East Africa as the most plausible origin of the two invasive strains. The SCAR markers developed in the present study provide a rapid, inexpensive, and efficient tool to track the distribution of P. striiformis invasive strains, PstS1 and PstS2.
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Affiliation(s)
- Stephanie Walter
- Department of AgroecologyAarhus UniversityFlakkebjergDK‐4200SlagelseDenmark
| | - Sajid Ali
- Department of AgroecologyAarhus UniversityFlakkebjergDK‐4200SlagelseDenmark
- Institute of Biotechnology & Genetic EngineeringThe University of Agriculture, Peshawar25000PeshawarPakistan
| | - Eric Kemen
- The Sainsbury LaboratoryNorwich Research ParkNorwichNR4 7UHUK
- Present address: Eric Kemen Max Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 1050829CologneGermany
| | - Kumarse Nazari
- ICARDARegional Cereal Rust Research CentreAegean Agricultural Research Institute P.K. 9Menemen/İZMİRTurkey
| | - Bochra A. Bahri
- National Institute of Agronomy of Tunisia (INAT)Avenue Charles Nicolle43 TN‐1082 El MahrajèneTunisia
| | - Jérôme Enjalbert
- INRA UMR 320 Génétique VégétaleFerme du MoulonF‐91190Gif sur YvetteFrance
| | - Jens G. Hansen
- Department of AgroecologyAarhus UniversityFlakkebjergDK‐4200SlagelseDenmark
| | | | - Thomas Sicheritz‐Pontén
- Center for Biological Sequence AnalysisDepartment of Systems BiologyTechnical University of DenmarkBuilding 208DK‐2800Kongens LyngbyDenmark
| | - Jonathan Jones
- The Sainsbury LaboratoryNorwich Research ParkNorwichNR4 7UHUK
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Cheng P, Chen XM, See DR. Grass Hosts Harbor More Diverse Isolates of Puccinia striiformis Than Cereal Crops. PHYTOPATHOLOGY 2016; 106:362-371. [PMID: 26667189 DOI: 10.1094/phyto-07-15-0155-r] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Puccinia striiformis causes stripe rust on cereal crops and many grass species. However, it is not clear whether the stripe rust populations on grasses are able to infect cereal crops and how closely they are related to each other. In this study, 103 isolates collected from wheat, barley, triticale, rye, and grasses in the United States were characterized by virulence tests and simple sequence repeat (SSR) markers. Of 69 pathotypes identified, 41 were virulent on some differentials of wheat only, 10 were virulent on some differentials of barley only, and 18 were virulent on some differentials of both wheat and barley. These pathotypes were clustered into three groups: group one containing isolates from wheat, triticale, rye, and grasses; group two isolates were from barley and grasses; and group three isolates were from grasses and wheat. SSR markers identified 44 multilocus genotypes (MLGs) and clustered them into three major molecular groups (MG) with MLGs in MG3 further classified into three subgroups. Isolates from cereal crops were present in one or more of the major or subgroups, but not all, whereas grass isolates were present in all of the major and subgroups. The results indicate that grasses harbor more diverse isolates of P. striiformis than the cereals.
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Affiliation(s)
- P Cheng
- First, second, and third authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; and second and third authors: U.S. Department of Agriculture-Agriculture Research Service, Wheat Genetics, Quality, Physiology and Disease Research Unit, Pullman, WA 99164-6430
| | - X M Chen
- First, second, and third authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; and second and third authors: U.S. Department of Agriculture-Agriculture Research Service, Wheat Genetics, Quality, Physiology and Disease Research Unit, Pullman, WA 99164-6430
| | - D R See
- First, second, and third authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; and second and third authors: U.S. Department of Agriculture-Agriculture Research Service, Wheat Genetics, Quality, Physiology and Disease Research Unit, Pullman, WA 99164-6430
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76
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Secreted protein gene derived-single nucleotide polymorphisms (SP-SNPs) reveal population diversity and differentiation of Puccinia striiformis f. sp. tritici in the United States. Fungal Biol 2016; 120:729-44. [PMID: 27109369 DOI: 10.1016/j.funbio.2016.02.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Revised: 02/18/2016] [Accepted: 02/23/2016] [Indexed: 11/21/2022]
Abstract
Single nucleotide polymorphism (SNP) is a powerful molecular marker technique that has been widely used in population genetics and molecular mapping studies for various organisms. However, the technique has not been used for studying Puccinia striiformis f. sp. tritici (Pst), the wheat stripe rust pathogen. In this study, we developed over a hundred secreted protein gene-derived SNP (SP-SNP) markers and used 92 markers to study the population structure of Pst. From 352 isolates collected in the United States, we identified 242 multi-locus genotypes. The SP-SNP genotypes had a moderate, but significant correlation with the virulence phenotype data. Clustering of the multi-locus genotypes was consistent by various analyses, revealing distinct genetic groups. Analysis of molecular variance detected significant differences between the eastern and western US Pst populations. High heterozygosity was found in the US population with significant differences identified among epidemiological regions. Analysis of population differentiation revealed that populations between the eastern and western US were highly differentiated while moderate differentiation was found in populations within the western or eastern US. Isolates from the western US were more diverse than isolates from the eastern US. The information is useful for guiding the disease management in different epidemiological regions.
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77
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Friskop AJ, Gulya TJ, Harveson RM, Humann RM, Acevedo M, Markell SG. Phenotypic Diversity of Puccinia helianthi (Sunflower Rust) in the United States from 2011 and 2012. PLANT DISEASE 2015; 99:1604-1609. [PMID: 30695963 DOI: 10.1094/pdis-11-14-1127-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Puccinia helianthi, causal agent of sunflower rust, is a macrocyclic and autoecious pathogen. Widespread sexual reproduction of P. helianthi was documented in North Dakota and Nebraska for the first time in 2008 and has since frequently occurred. Concurrently, an increase in sunflower rust incidence, severity, and subsequent yield loss on sunflower has occurred since 2008. Rust can be managed with resistance genes but determination of virulence phenotypes is important for effective gene deployment and hybrid selection. However, the only P. helianthi virulence data available in the United States was generated prior to 2009 and consisted of aggregate virulence phenotypes determined on bulk field collections. The objective of this study was to determine the phenotypic diversity of P. helianthi in the United States. P. helianthi collections were made from cultivated, volunteer, and wild Helianthus spp. at 104 locations across seven U.S. states and one Canadian province in 2011 and 2012. Virulence phenotypes of 238 single-pustule isolates were determined on the internationally accepted differential set. In total, 29 races were identified, with races 300 and 304 occurring most frequently in 2011 and races 304 and 324 occurring most frequently in 2012. Differences in race prevalence occurred between survey years and across geography but were similar among host types. Four isolates virulent to all genes in the differential set (race 777) were identified. The resistance genes found in differential lines HA-R3 (R4b), MC29 (R2 and R10), and HA-R2 (R5) conferred resistance to 96.6, 83.6, and 78.6% of the isolates tested, respectively.
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Affiliation(s)
- Andrew J Friskop
- Department of Plant Pathology, North Dakota State University, Fargo 58102
| | - Thomas J Gulya
- United States Department of Agriculture-Agricultural Research Service Northern Crop Science Laboratory, Fargo, ND 58108
| | | | - Ryan M Humann
- Department of Plant Pathology, North Dakota State University, Fargo
| | | | - Samuel G Markell
- Department of Plant Pathology, North Dakota State University, Fargo
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78
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Dawson AM, Bettgenhaeuser J, Gardiner M, Green P, Hernández-Pinzón I, Hubbard A, Moscou MJ. The development of quick, robust, quantitative phenotypic assays for describing the host-nonhost landscape to stripe rust. FRONTIERS IN PLANT SCIENCE 2015; 6:876. [PMID: 26579142 PMCID: PMC4621417 DOI: 10.3389/fpls.2015.00876] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 10/02/2015] [Indexed: 05/24/2023]
Abstract
Nonhost resistance is often conceptualized as a qualitative separation from host resistance. Classification into these two states is generally facile, as they fail to fully describe the range of states that exist in the transition from host to nonhost. This poses a problem when studying pathosystems that cannot be classified as either host or nonhost due to their intermediate status relative to these two extremes. In this study, we investigate the efficacy of the Poaceae-stripe rust (Puccinia striiformis Westend.) interaction for describing the host-nonhost landscape. First, using barley (Hordeum vulgare L.) and Brachypodium distachyon (L.) P. Beauv. We observed that macroscopic symptoms of chlorosis and leaf browning were associated with hyphal colonization by P. striiformis f. sp. tritici, respectively. This prompted us to adapt a protocol for visualizing fungal structures into a phenotypic assay that estimates the percent of leaf colonized. Use of this assay in intermediate host and intermediate nonhost systems found the frequency of infection decreases with evolutionary divergence from the host species. Similarly, we observed that the pathogen's ability to complete its life cycle decreased faster than its ability to colonize leaf tissue, with no incidence of pustules observed in the intermediate nonhost system and significantly reduced pustule formation in the intermediate host system as compared to the host system, barley-P. striiformis f. sp. hordei. By leveraging the stripe rust pathosystem in conjunction with macroscopic and microscopic phenotypic assays, we now hope to dissect the genetic architecture of intermediate host and intermediate nonhost resistance using structured populations in barley and B. distachyon.
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Affiliation(s)
| | | | | | - Phon Green
- The Sainsbury Laboratory, Norwich Research ParkNorwich, UK
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79
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Luo H, Wang X, Zhan G, Wei G, Zhou X, Zhao J, Huang L, Kang Z. Genome-Wide Analysis of Simple Sequence Repeats and Efficient Development of Polymorphic SSR Markers Based on Whole Genome Re-Sequencing of Multiple Isolates of the Wheat Stripe Rust Fungus. PLoS One 2015; 10:e0130362. [PMID: 26068192 PMCID: PMC4467034 DOI: 10.1371/journal.pone.0130362] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 05/18/2015] [Indexed: 12/30/2022] Open
Abstract
The biotrophic parasitic fungus Puccinia striiformis f. sp. tritici (Pst) causes stripe rust, a devastating disease of wheat, endangering global food security. Because the Pst population is highly dynamic, it is difficult to develop wheat cultivars with durable and highly effective resistance. Simple sequence repeats (SSRs) are widely used as molecular markers in genetic studies to determine population structure in many organisms. However, only a small number of SSR markers have been developed for Pst. In this study, a total of 4,792 SSR loci were identified using the whole genome sequences of six isolates from different regions of the world, with a marker density of one SSR per 22.95 kb. The majority of the SSRs were di- and tri-nucleotide repeats. A database containing 1,113 SSR markers were established. Through in silico comparison, the previously reported SSR markers were found mainly in exons, whereas the SSR markers in the database were mostly in intergenic regions. Furthermore, 105 polymorphic SSR markers were confirmed in silico by their identical positions and nucleotide variations with INDELs identified among the six isolates. When 104 in silico polymorphic SSR markers were used to genotype 21 Pst isolates, 84 produced the target bands, and 82 of them were polymorphic and revealed the genetic relationships among the isolates. The results show that whole genome re-sequencing of multiple isolates provides an ideal resource for developing SSR markers, and the newly developed SSR markers are useful for genetic and population studies of the wheat stripe rust fungus.
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Affiliation(s)
- Huaiyong Luo
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, People's Republic of China
| | - Xiaojie Wang
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, People's Republic of China
| | - Gangming Zhan
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, People's Republic of China
| | - Guorong Wei
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, People's Republic of China
| | - Xinli Zhou
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, People's Republic of China
| | - Jing Zhao
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, People's Republic of China
| | - Lili Huang
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, People's Republic of China
| | - Zhensheng Kang
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, People's Republic of China
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80
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Wheat rusts never sleep but neither do sequencers: will pathogenomics transform the way plant diseases are managed? Genome Biol 2015; 16:44. [PMID: 25853180 PMCID: PMC4346120 DOI: 10.1186/s13059-015-0615-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Field pathogenomics adds highly informative data to surveillance surveys by enabling rapid evaluation of pathogen variability, population structure and host genotype.
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81
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Cheng Y, Wang X, Yao J, Voegele RT, Zhang Y, Wang W, Huang L, Kang Z. Characterization of protein kinase PsSRPKL, a novel pathogenicity factor in the wheat stripe rust fungus. Environ Microbiol 2015; 17:2601-17. [PMID: 25407954 DOI: 10.1111/1462-2920.12719] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 11/09/2014] [Accepted: 11/10/2014] [Indexed: 12/31/2022]
Abstract
As in other eukaryotes, protein kinases (PKs) are generally evolutionarily conserved and play major regulatory roles in plant pathogenic fungi. Many PKs have been proven to be important for pathogenesis in model fungal plant pathogens, but little is currently known about their roles in the pathogenesis of cereal rust fungi, devastating pathogens in agriculture worldwide. Here, we report on an in planta highly induced PK gene PsSRPKL from the wheat stripe rust fungus Puccinia striiformis f. sp. tritici (Pst), one of the most important cereal rust fungi. PsSRPKL belongs to a group of PKs that are evolutionarily specific to cereal rust fungi. It shows a high level of intraspecies polymorphism in the kinase domains and directed green fluorescent protein chimers to plant nuclei. Overexpression of PsSRPKL in fission yeast induces aberrant cell morphology and a decreased resistance to environmental stresses. Most importantly, PsSRPKL is proven to be an important pathogenicity factor responsible for fungal growth and responses to environmental stresses, therefore contributing significantly to Pst virulence in wheat. We hypothesize that cereal rust fungi have developed specific PKs as pathogenicity factors for adaptation to their host species during evolution. Thus, our findings provide significant insights into pathogenicity and virulence evolution in cereal rust fungi.
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Affiliation(s)
- Yulin Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaojie Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Juanni Yao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ralf T Voegele
- Fachgebiet Phytopathologie, Fakultät Agrarwissenschaften, Institut für Phytomedizin, Universität Hohenheim, Stuttgart, Germany
| | - Yanru Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Wumei Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
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82
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Luo H, Wang X, Zhan G, Wei G, Zhou X, Zhao J, Huang L, Kang Z. Genome-Wide Analysis of Simple Sequence Repeats and Efficient Development of Polymorphic SSR Markers Based on Whole Genome Re-Sequencing of Multiple Isolates of the Wheat Stripe Rust Fungus. PLoS One 2015. [PMID: 26448643 DOI: 10.1145/2818302] [Citation(s) in RCA: 1207] [Impact Index Per Article: 134.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023] Open
Abstract
The biotrophic parasitic fungus Puccinia striiformis f. sp. tritici (Pst) causes stripe rust, a devastating disease of wheat, endangering global food security. Because the Pst population is highly dynamic, it is difficult to develop wheat cultivars with durable and highly effective resistance. Simple sequence repeats (SSRs) are widely used as molecular markers in genetic studies to determine population structure in many organisms. However, only a small number of SSR markers have been developed for Pst. In this study, a total of 4,792 SSR loci were identified using the whole genome sequences of six isolates from different regions of the world, with a marker density of one SSR per 22.95 kb. The majority of the SSRs were di- and tri-nucleotide repeats. A database containing 1,113 SSR markers were established. Through in silico comparison, the previously reported SSR markers were found mainly in exons, whereas the SSR markers in the database were mostly in intergenic regions. Furthermore, 105 polymorphic SSR markers were confirmed in silico by their identical positions and nucleotide variations with INDELs identified among the six isolates. When 104 in silico polymorphic SSR markers were used to genotype 21 Pst isolates, 84 produced the target bands, and 82 of them were polymorphic and revealed the genetic relationships among the isolates. The results show that whole genome re-sequencing of multiple isolates provides an ideal resource for developing SSR markers, and the newly developed SSR markers are useful for genetic and population studies of the wheat stripe rust fungus.
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Affiliation(s)
- Huaiyong Luo
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, People's Republic of China; State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, People's Republic of China
| | - Xiaojie Wang
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, People's Republic of China; State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, People's Republic of China
| | - Gangming Zhan
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, People's Republic of China; State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, People's Republic of China
| | - Guorong Wei
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, People's Republic of China; State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, People's Republic of China
| | - Xinli Zhou
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, People's Republic of China; State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, People's Republic of China
| | - Jing Zhao
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, People's Republic of China; State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, People's Republic of China
| | - Lili Huang
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, People's Republic of China; State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, People's Republic of China
| | - Zhensheng Kang
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, People's Republic of China; State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, People's Republic of China
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83
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Barzman M, Lamichhane JR, Booij K, Boonekamp P, Desneux N, Huber L, Kudsk P, Langrell SRH, Ratnadass A, Ricci P, Sarah JL, Messean A. Research and Development Priorities in the Face of Climate Change and Rapidly Evolving Pests. SUSTAINABLE AGRICULTURE REVIEWS 2015. [DOI: 10.1007/978-3-319-16742-8_1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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84
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Bettgenhaeuser J, Gilbert B, Ayliffe M, Moscou MJ. Nonhost resistance to rust pathogens - a continuation of continua. FRONTIERS IN PLANT SCIENCE 2014; 5:664. [PMID: 25566270 PMCID: PMC4263244 DOI: 10.3389/fpls.2014.00664] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 11/07/2014] [Indexed: 05/25/2023]
Abstract
The rust fungi (order: Pucciniales) are a group of widely distributed fungal plant pathogens, which can infect representatives of all vascular plant groups. Rust diseases significantly impact several crop species and considerable research focuses on understanding the basis of host specificity and nonhost resistance. Like many pathogens, rust fungi vary considerably in the number of hosts they can infect, such as wheat leaf rust (Puccinia triticina), which can only infect species in the genera Triticum and Aegilops, whereas Asian soybean rust (Phakopsora pachyrhizi) is known to infect over 95 species from over 42 genera. A greater understanding of the genetic basis determining host range has the potential to identify sources of durable resistance for agronomically important crops. Delimiting the boundary between host and nonhost has been complicated by the quantitative nature of phenotypes in the transition between these two states. Plant-pathogen interactions in this intermediate state are characterized either by (1) the majority of accessions of a species being resistant to the rust or (2) the rust only being able to partially complete key components of its life cycle. This leads to a continuum of disease phenotypes in the interaction with different plant species, observed as a range from compatibility (host) to complete immunity within a species (nonhost). In this review we will highlight how the quantitative nature of disease resistance in these intermediate interactions is caused by a continuum of defense barriers, which a pathogen needs to overcome for successfully establishing itself in the host. To illustrate continua as this underlying principle, we will discuss the advances that have been made in studying nonhost resistance towards rust pathogens, particularly cereal rust pathogens.
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Affiliation(s)
| | - Brian Gilbert
- Commonwealth Scientific and Industrial Research Organisation, Agriculture FlagshipCanberra, ACT, Australia
| | - Michael Ayliffe
- Commonwealth Scientific and Industrial Research Organisation, Agriculture FlagshipCanberra, ACT, Australia
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85
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Sparks AH, Forbes GA, Hijmans RJ, Garrett KA. Climate change may have limited effect on global risk of potato late blight. GLOBAL CHANGE BIOLOGY 2014; 20:3621-31. [PMID: 24687916 DOI: 10.1111/gcb.12587] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 03/12/2014] [Indexed: 05/20/2023]
Abstract
Weather affects the severity of many plant diseases, and climate change is likely to alter the patterns of crop disease severity. Evaluating possible future patterns can help focus crop breeding and disease management research. We examined the global effect of climate change on potato late blight, the disease that caused the Irish potato famine and still is a common potato disease around the world. We used a metamodel and considered three global climate models for the A2 greenhouse gas emission scenario for three 20-year time-slices: 2000-2019, 2040-2059 and 2080-2099. In addition to global analyses, five regions were evaluated where potato is an important crop: the Andean Highlands, Indo-Gangetic Plain and Himalayan Highlands, Southeast Asian Highlands, Ethiopian Highlands, and Lake Kivu Highlands in Sub-Saharan Africa. We found that the average global risk of potato late blight increases initially, when compared with historic climate data, and then declines as planting dates shift to cooler seasons. Risk in the agro-ecosystems analyzed, varied from a large increase in risk in the Lake Kivu Highlands in Rwanda to decreases in the Southeast Asian Highlands of Indonesia.
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Affiliation(s)
- Adam H Sparks
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton Plant Sciences Center, Manhattan, KS, 66506, USA; International Rice Research Institute (IRRI), Los Baños, Laguna, 4031, Philippines
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86
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Cheng P, Chen XM. Virulence and Molecular Analyses Support Asexual Reproduction of Puccinia striiformis f. sp. tritici in the U.S. Pacific Northwest. PHYTOPATHOLOGY 2014; 104:1208-20. [PMID: 24779354 DOI: 10.1094/phyto-11-13-0314-r] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici, occurs every year and causes significant yield losses in the U.S. Pacific Northwest (PNW). A large number of P. striiformis f. tritici races are identified every year and predominant races have changed rapidly. Barberry and mahonia plants, which have been identified under controlled conditions as alternate hosts for the fungus, are found in the region. However, whether sexual reproduction occurs in the P. striiformis f. sp. tritici population under natural conditions is not clear. To determine the reproduction mode of the P. striiformis f. sp. tritici population using virulence and molecular markers, a systematic collection of leaf samples with a single stripe of uredia was made in 26 fields in the PNW in 2010. In total, 270 isolates obtained from the PNW collection, together with 66 isolates from 20 other states collected in the same year, were characterized by virulence tests and simple sequence repeat (SSR) markers. In total, 21 races and 66 multilocus genotypes (MLGs) were detected, of which 15 races and 32 MLGs were found in the PNW. Cluster analysis with the SSR marker data revealed two genetic groups, which were significantly correlated to the two virulence groups. The analyses of genotype/individual ratio, multilocus linkage disequilibrium, and heterozygosity strongly supported asexual reproduction for the pathogen population in the PNW, as well as other regions of the United States.
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87
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Chen W, Wellings C, Chen X, Kang Z, Liu T. Wheat stripe (yellow) rust caused by Puccinia striiformis f. sp. tritici. MOLECULAR PLANT PATHOLOGY 2014; 15:433-46. [PMID: 24373199 PMCID: PMC6638732 DOI: 10.1111/mpp.12116] [Citation(s) in RCA: 175] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
UNLABELLED Stripe (yellow) rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a serious disease of wheat occurring in most wheat areas with cool and moist weather conditions during the growing season. The basidiomycete fungus is an obligate biotrophic parasite that is difficult to culture on artificial media. Pst is a macrocyclic, heteroecious fungus that requires both primary (wheat or grasses) and alternate (Berberis or Mahonia spp.) host plants to complete its life cycle. Urediniospores have the capacity for wind dispersal over long distances, which may, under high inoculum pressure, extend to thousands of kilometres from the initial infection sites. Stripe rust, which is considered to be the current major rust disease affecting winter cereal production across the world, has been studied intensively for over a century. This review summarizes the current knowledge of the Pst-wheat pathosystem, with emphasis on the life cycle, uredinial infection process, population biology of the pathogen, genes for stripe rust resistance in wheat and molecular perspectives of wheat-Pst interactions. TAXONOMY The stripe rust pathogen, Puccinia striiformis Westend. (Ps), is classified in kingdom Fungi, phylum Basidiomycota, class Urediniomycetes, order Uredinales, family Pucciniaceae, genus Puccinia. Ps is separated below the species level by host specialization on various grass genera, comprising up to nine formae speciales, of which P. striiformis f. sp. tritici Erikss. (Pst) causes stripe (or yellow) rust on wheat. HOST RANGE Uredinial/telial hosts: Pst mainly infects common wheat (Triticum aestivum L.), durum wheat (T. turgidum var. durum L.), cultivated emmer wheat (T. dicoccum Schrank), wild emmer wheat (T. dicoccoides Korn) and triticale (Triticosecale). Pst can infect certain cultivated barleys (Hordeum vulgare L.) and rye (Secale cereale L.), but generally does not cause severe epidemics. In addition, Pst may infect naturalized and improved pasture grass species, such as Elymus canadensis L., Leymus secalinus Hochst, Agropyron spp. Garetn, Hordeum spp. L., Phalaris spp. L and Bromus unioloides Kunth. Pycnial/aecial (alternative) hosts: Barberry (Berberis chinensis, B. koreana, B. holstii, B. vulgaris, B. shensiana, B. potaninii, B. dolichobotrys, B. heteropoda, etc.) and Oregon grape (Mahonia aquifolium). DISEASE SYMPTOMS Stripe rust appears as a mass of yellow to orange urediniospores erupting from pustules arranged in long, narrow stripes on leaves (usually between veins), leaf sheaths, glumes and awns on susceptible plants. Resistant wheat cultivars are characterized by various infection types from no visual symptoms to small hypersensitive flecks to uredinia surrounded by chlorosis or necrosis with restricted urediniospore production. On seedlings, uredinia produced by the infection of a single urediniospore are not confined by leaf veins, but progressively emerge from the infection site in all directions, potentially covering the entire leaf surface. Individual uredinial pustules are oblong, 0.4-0.7 mm in length and 0.1 mm in width. Urediniospores are broadly ellipsoidal to broadly obovoid, (16-)18-30(-32) × (15-)17-27(-28) μm, with a mean of 24.5 × 21.6 μm, yellow to orange in colour, echinulate, and with 6-18 scattered germ pores. Urediniospores can germinate rapidly when free moisture (rain or dew) occurs on leaf surfaces and when the temperatures range is between 7 and 12 °C. At higher temperatures or during the later growing stages of the host, black telia are often produced, which are pulvinate to oblong, 0.2-0.7 mm in length and 0.1 mm in width. The teliospores are predominantly two-celled, dark brown with thick walls, mostly oblong-clavate, (24-)31-56(-65) × (11-)14-25(-29) μm in length and width, and rounded or flattened at the apex.
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Affiliation(s)
- Wanquan Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, West Yuan Ming Yuan Road, Beijing, 100193, China
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Tellier A, Lemaire C. Coalescence 2.0: a multiple branching of recent theoretical developments and their applications. Mol Ecol 2014; 23:2637-52. [DOI: 10.1111/mec.12755] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 04/08/2014] [Accepted: 04/13/2014] [Indexed: 02/01/2023]
Affiliation(s)
- Aurélien Tellier
- Section of Population Genetics; Center of Life and Food Sciences Weihenstephan; Technische Universität München; 85354 Freising Germany
| | - Christophe Lemaire
- LUNAM; UMR1345 Institut de Recherche en Horticulture et Semences; Université d'Angers; SFR 4207 QUASAV 49045 Angers France
- INRA; UMR1345 Institut de Recherche en Horticulture et Semences; 49071 Beaucouzé France
- AgroCampus-Ouest; UMR1345 Institut de Recherche en Horticulture et Semences; 49045 Angers France
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Yang Y, Zhao J, Xing H, Wang J, Zhou K, Zhan G, Zhang H, Kang Z. Different non-host resistance responses of two rice subspecies, japonica and indica, to Puccinia striiformis f. sp. tritici. PLANT CELL REPORTS 2014; 33:423-33. [PMID: 24306352 DOI: 10.1007/s00299-013-1542-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2013] [Revised: 10/25/2013] [Accepted: 11/12/2013] [Indexed: 05/26/2023]
Abstract
KEY MESSAGE Japonica and indica have different non-host resistance (NHR) abilities to Puccinia striiformis f. sp. tritici ( Pst ), and hydrogen peroxide (H 2 O 2 ) has a positive function in NHR to japonica against Pst. ABSTRACT Non-host interactions between Puccinia striiformis f. sp. tritici (Pst) and two rice subspecies were characterized using 23 rice varieties, including 11 japonica and 12 indica. Results showed that the infected fungal structures were easily produced in the leaves of indica, whereas only several substomatal vesicles and primary infection hyphae were observed in the leaves of japonica. This result indicated that indica is less resistant or more susceptible to Pst than japonica. Hydrogen peroxide accumulated in the initial phase of japonica-Pst interaction but not in indica-Pst interaction. A set of reactive oxygen species (ROS)-related genes was also induced in response to Pst infection, suggesting that ROS activation is one of the major mechanisms of non-host resistance of rice to Pst.
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Affiliation(s)
- Yuheng Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
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91
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Ali S, Gladieux P, Rahman H, Saqib MS, Fiaz M, Ahmad H, Leconte M, Gautier A, Justesen AF, Hovmøller MS, Enjalbert J, de Vallavieille-Pope C. Inferring the contribution of sexual reproduction, migration and off-season survival to the temporal maintenance of microbial populations: a case study on the wheat fungal pathogenPuccinia striiformisf.sp.tritici. Mol Ecol 2014; 23:603-17. [DOI: 10.1111/mec.12629] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 11/30/2013] [Accepted: 12/04/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Sajid Ali
- INRA UR 1290 BIOGER-CPP; BP01 78850 Thiverval-Grignon France
- Institute of Biotechnology and Genetic Engineering; The University of Agriculture; Peshawar 25000 Pakistan
- Department of Agroecology; Aarhus University; Flakkebjerg; DK-4200 Slagelse Denmark
| | - Pierre Gladieux
- Department of Plant and Microbial Biology; University of California; Berkeley CA 94720-3102 USA
- Ecologie, Systématique et Evolution; UMR8079; Univ Paris-Sud; 91405 Orsay France
- Ecologie, Systématique et Evolution; UMR8079; CNRS; 91405 Orsay France
| | - Hidayatur Rahman
- Department of Plant Breeding and Genetics; The University of Agriculture; Peshawar 25000 Pakistan
| | - Muhammad S. Saqib
- Department of Plant Breeding and Genetics; The University of Agriculture; Peshawar 25000 Pakistan
| | | | | | - Marc Leconte
- INRA UR 1290 BIOGER-CPP; BP01 78850 Thiverval-Grignon France
| | | | | | - Mogens S. Hovmøller
- Department of Agroecology; Aarhus University; Flakkebjerg; DK-4200 Slagelse Denmark
| | - Jérôme Enjalbert
- INRA UMR 320 Génétique Végétale; Ferme du Moulon; 91190 Gif sur Yvette France
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92
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Ali S, Gladieux P, Leconte M, Gautier A, Justesen AF, Hovmøller MS, Enjalbert J, de Vallavieille-Pope C. Origin, migration routes and worldwide population genetic structure of the wheat yellow rust pathogen Puccinia striiformis f.sp. tritici. PLoS Pathog 2014; 10:e1003903. [PMID: 24465211 PMCID: PMC3900651 DOI: 10.1371/journal.ppat.1003903] [Citation(s) in RCA: 188] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Accepted: 12/12/2013] [Indexed: 11/24/2022] Open
Abstract
Analyses of large-scale population structure of pathogens enable the identification of migration patterns, diversity reservoirs or longevity of populations, the understanding of current evolutionary trajectories and the anticipation of future ones. This is particularly important for long-distance migrating fungal pathogens such as Puccinia striiformis f.sp. tritici (PST), capable of rapid spread to new regions and crop varieties. Although a range of recent PST invasions at continental scales are well documented, the worldwide population structure and the center of origin of the pathogen were still unknown. In this study, we used multilocus microsatellite genotyping to infer worldwide population structure of PST and the origin of new invasions based on 409 isolates representative of distribution of the fungus on six continents. Bayesian and multivariate clustering methods partitioned the set of multilocus genotypes into six distinct genetic groups associated with their geographical origin. Analyses of linkage disequilibrium and genotypic diversity indicated a strong regional heterogeneity in levels of recombination, with clear signatures of recombination in the Himalayan (Nepal and Pakistan) and near-Himalayan regions (China) and a predominant clonal population structure in other regions. The higher genotypic diversity, recombinant population structure and high sexual reproduction ability in the Himalayan and neighboring regions suggests this area as the putative center of origin of PST. We used clustering methods and approximate Bayesian computation (ABC) to compare different competing scenarios describing ancestral relationship among ancestral populations and more recently founded populations. Our analyses confirmed the Middle East-East Africa as the most likely source of newly spreading, high-temperature-adapted strains; Europe as the source of South American, North American and Australian populations; and Mediterranean-Central Asian populations as the origin of South African populations. Although most geographic populations are not markedly affected by recent dispersal events, this study emphasizes the influence of human activities on recent long-distance spread of the pathogen.
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Affiliation(s)
- Sajid Ali
- INRA UR 1290 BIOGER-CPP, Thiverval-Grignon, France
- Institute of Biotechnology and Genetic Engineering, the University of Agriculture, Peshawar, Pakistan
- Department of Agroecology, Aarhus University, Slagelse, Denmark
| | - Pierre Gladieux
- UMR 8079 Ecologie Systematique Evolution, Univ. Paris-Sud., CNRS-F, Orsay, France
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Marc Leconte
- INRA UR 1290 BIOGER-CPP, Thiverval-Grignon, France
| | | | | | | | - Jérôme Enjalbert
- INRA UMR 320 Génétique Végétale, Ferme du Moulon, Gif sur Yvette, France
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93
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Cantu D, Segovia V, MacLean D, Bayles R, Chen X, Kamoun S, Dubcovsky J, Saunders DGO, Uauy C. Genome analyses of the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici reveal polymorphic and haustorial expressed secreted proteins as candidate effectors. BMC Genomics 2013; 14:270. [PMID: 23607900 PMCID: PMC3640902 DOI: 10.1186/1471-2164-14-270] [Citation(s) in RCA: 171] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 04/11/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Wheat yellow (stripe) rust caused by Puccinia striiformis f. sp. tritici (PST) is one of the most devastating diseases of wheat worldwide. To design effective breeding strategies that maximize the potential for durable disease resistance it is important to understand the molecular basis of PST pathogenicity. In particular, the characterisation of the structure, function and evolutionary dynamics of secreted effector proteins that are detected by host immune receptors can help guide and prioritize breeding efforts. However, to date, our knowledge of the effector repertoire of cereal rust pathogens is limited. RESULTS We re-sequenced genomes of four PST isolates from the US and UK to identify effector candidates and relate them to their distinct virulence profiles. First, we assessed SNP frequencies between all isolates, with heterokaryotic SNPs being over tenfold more frequent (5.29 ± 2.23 SNPs/kb) than homokaryotic SNPs (0.41 ± 0.28 SNPs/kb). Next, we implemented a bioinformatics pipeline to integrate genomics, transcriptomics, and effector-focused annotations to identify and classify effector candidates in PST. RNAseq analysis highlighted transcripts encoding secreted proteins that were significantly enriched in haustoria compared to infected tissue. The expression of 22 candidate effector genes was characterised using qRT-PCR, revealing distinct temporal expression patterns during infection in wheat. Lastly, we identified proteins that displayed non-synonymous substitutions specifically between the two UK isolates PST-87/7 and PST-08/21, which differ in virulence to two wheat varieties. By focusing on polymorphic variants enriched in haustoria, we identified five polymorphic effector candidates between PST-87/7 and PST-08/21 among 2,999 secreted proteins. These allelic variants are now a priority for functional validation as virulence/avirulence effectors in the corresponding wheat varieties. CONCLUSIONS Integration of genomics, transcriptomics, and effector-directed annotation of PST isolates has enabled us to move beyond the single isolate-directed catalogues of effector proteins and develop a framework for mining effector proteins in closely related isolates and relate these back to their defined virulence profiles. This should ultimately lead to more comprehensive understanding of the PST pathogenesis system, an important first step towards developing more effective surveillance and management strategies for one of the most devastating pathogens of wheat.
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Affiliation(s)
- Dario Cantu
- Department of Viticulture & Enology, University of California Davis, Davis, USA
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94
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Zhan J, McDonald BA. Experimental measures of pathogen competition and relative fitness. ANNUAL REVIEW OF PHYTOPATHOLOGY 2013; 51:131-53. [PMID: 23767846 DOI: 10.1146/annurev-phyto-082712-102302] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Competition among pathogen strains for limited host resources can have a profound effect on pathogen evolution. A better understanding of the principles and consequences of competition can be useful in designing more sustainable disease management strategies. The competitive ability and relative fitness of a pathogen strain are determined by its intrinsic biological properties, the resistance and heterogeneity of the corresponding host population, the population density and genetic relatedness of the competing strains, and the physical environment. Competitive ability can be inferred indirectly from fitness components, such as basic reproduction rate or transmission rate. However, pathogen strains that exhibit higher fitness components when they infect a host alone may not exhibit a competitive advantage when they co-infect the same host. The most comprehensive measures of competitive ability and relative fitness come from calculating selection coefficients in a mixed infection in a field setting. Mark-release-recapture experiments can be used to estimate fitness costs associated with unnecessary virulence and fungicide resistance.
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Affiliation(s)
- Jiasui Zhan
- Key Lab for Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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95
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Fighting Plant Diseases Through the Application of Bacillus and Pseudomonas Strains. SOIL BIOLOGY 2013. [DOI: 10.1007/978-3-642-39317-4_9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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96
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Zheng W, Huang L, Huang J, Wang X, Chen X, Zhao J, Guo J, Zhuang H, Qiu C, Liu J, Liu H, Huang X, Pei G, Zhan G, Tang C, Cheng Y, Liu M, Zhang J, Zhao Z, Zhang S, Han Q, Han D, Zhang H, Zhao J, Gao X, Wang J, Ni P, Dong W, Yang L, Yang H, Xu JR, Zhang G, Kang Z. High genome heterozygosity and endemic genetic recombination in the wheat stripe rust fungus. Nat Commun 2013; 4:2673. [PMID: 24150273 PMCID: PMC3826619 DOI: 10.1038/ncomms3673] [Citation(s) in RCA: 160] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 09/26/2013] [Indexed: 11/08/2022] Open
Abstract
Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive diseases of wheat. Here we report a 110-Mb draft sequence of Pst isolate CY32, obtained using a 'fosmid-to-fosmid' strategy, to better understand its race evolution and pathogenesis. The Pst genome is highly heterozygous and contains 25,288 protein-coding genes. Compared with non-obligate fungal pathogens, Pst has a more diverse gene composition and more genes encoding secreted proteins. Re-sequencing analysis indicates significant genetic variation among six isolates collected from different continents. Approximately 35% of SNPs are in the coding sequence regions, and half of them are non-synonymous. High genetic diversity in Pst suggests that sexual reproduction has an important role in the origin of different regional races. Our results show the effectiveness of the 'fosmid-to-fosmid' strategy for sequencing dikaryotic genomes and the feasibility of genome analysis to understand race evolution in Pst and other obligate pathogens.
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Affiliation(s)
- Wenming Zheng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Physiology, Ecology and Genetic Improvement of Food Crop in Henan Province and College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan Province 450002, China
- These authors contributed equally to this work
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
- These authors contributed equally to this work
| | - Jinqun Huang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
- These authors contributed equally to this work
| | - Xiaojie Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xianming Chen
- USDA-ARS and Department of Plant Pathology, Washington State University, Pullman, Washington 99164-6430, USA
| | - Jie Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jun Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hua Zhuang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chuangzhao Qiu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Jie Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Huiquan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xueling Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Guoliang Pei
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Gangming Zhan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chunlei Tang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yulin Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Minjie Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jinshan Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhongtao Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shijie Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qingmei Han
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hongchang Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jing Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaoning Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jianfeng Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Peixiang Ni
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Wei Dong
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Linfeng Yang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Huanming Yang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Jin-Rong Xu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | - Gengyun Zhang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
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Characterization and inheritance of resistance to stripe rust in the wheat line Guinong775. YI CHUAN = HEREDITAS 2012; 34:1607-13. [DOI: 10.3724/sp.j.1005.2012.01607] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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98
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Dean R, Van Kan JAL, Pretorius ZA, Hammond-Kosack KE, Di Pietro A, Spanu PD, Rudd JJ, Dickman M, Kahmann R, Ellis J, Foster GD. The Top 10 fungal pathogens in molecular plant pathology. MOLECULAR PLANT PATHOLOGY 2012. [PMID: 22471698 DOI: 10.1111/j.1364-3703.2012.2011.00783.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The aim of this review was to survey all fungal pathologists with an association with the journal Molecular Plant Pathology and ask them to nominate which fungal pathogens they would place in a 'Top 10' based on scientific/economic importance. The survey generated 495 votes from the international community, and resulted in the generation of a Top 10 fungal plant pathogen list for Molecular Plant Pathology. The Top 10 list includes, in rank order, (1) Magnaporthe oryzae; (2) Botrytis cinerea; (3) Puccinia spp.; (4) Fusarium graminearum; (5) Fusarium oxysporum; (6) Blumeria graminis; (7) Mycosphaerella graminicola; (8) Colletotrichum spp.; (9) Ustilago maydis; (10) Melampsora lini, with honourable mentions for fungi just missing out on the Top 10, including Phakopsora pachyrhizi and Rhizoctonia solani. This article presents a short resumé of each fungus in the Top 10 list and its importance, with the intent of initiating discussion and debate amongst the plant mycology community, as well as laying down a bench-mark. It will be interesting to see in future years how perceptions change and what fungi will comprise any future Top 10.
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Affiliation(s)
- Ralph Dean
- Department of Plant Pathology, Fungal Genomics Laboratory, North Carolina State University, Raleigh, NC 27695, USA
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99
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Dean R, Van Kan JAL, Pretorius ZA, Hammond-Kosack KE, Di Pietro A, Spanu PD, Rudd JJ, Dickman M, Kahmann R, Ellis J, Foster GD. The Top 10 fungal pathogens in molecular plant pathology. MOLECULAR PLANT PATHOLOGY 2012; 13:414-30. [PMID: 22471698 PMCID: PMC6638784 DOI: 10.1111/j.1364-3703.2011.00783.x] [Citation(s) in RCA: 2081] [Impact Index Per Article: 173.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The aim of this review was to survey all fungal pathologists with an association with the journal Molecular Plant Pathology and ask them to nominate which fungal pathogens they would place in a 'Top 10' based on scientific/economic importance. The survey generated 495 votes from the international community, and resulted in the generation of a Top 10 fungal plant pathogen list for Molecular Plant Pathology. The Top 10 list includes, in rank order, (1) Magnaporthe oryzae; (2) Botrytis cinerea; (3) Puccinia spp.; (4) Fusarium graminearum; (5) Fusarium oxysporum; (6) Blumeria graminis; (7) Mycosphaerella graminicola; (8) Colletotrichum spp.; (9) Ustilago maydis; (10) Melampsora lini, with honourable mentions for fungi just missing out on the Top 10, including Phakopsora pachyrhizi and Rhizoctonia solani. This article presents a short resumé of each fungus in the Top 10 list and its importance, with the intent of initiating discussion and debate amongst the plant mycology community, as well as laying down a bench-mark. It will be interesting to see in future years how perceptions change and what fungi will comprise any future Top 10.
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Affiliation(s)
- Ralph Dean
- Department of Plant Pathology, Fungal Genomics Laboratory, North Carolina State University, Raleigh, NC 27695, USA
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100
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Abstract
Comparing to natural ecosystems, the evolution of plant pathogens in agricultural ecosystems is generally faster due to high-density monocultures, large-scale application of agrochemicals, and international trade in agricultural products. Knowledge of the population genetics and evolutionary biology of plant pathogens is necessary to understand disease epidemiology, effectively breed and use resistant cultivars, and control plant diseases. In this article, we outlined the aims of population genetic studies in plant pathogens, discuss contributions of five evolutionary forces (i.e., mutation, gene flow, recombination, random genetic drift, and natural selection) to origin, maintenance, and distribution of genetic variation in time and space, and gave an overview of current research status in this field.
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Affiliation(s)
- Wen Zhu
- Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China.
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