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Chen W, Newlands N, Hambleton S, Laroche A, Davoodi SM, Bakkeren G. Optimizing an integrated biovigilance toolbox to study the spatial distribution and dynamic changes of airborne mycobiota, with a focus on cereal rust fungi in western Canada. Mol Ecol Resour 2024; 24:e13983. [PMID: 38840549 DOI: 10.1111/1755-0998.13983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 06/07/2024]
Abstract
In the face of evolving agricultural practices and climate change, tools towards an integrated biovigilance platform to combat crop diseases, spore sampling, DNA diagnostics and predictive trajectory modelling were optimized. These tools revealed microbial dynamics and were validated by monitoring cereal rust fungal pathogens affecting wheat, oats, barley and rye across four growing seasons (2015-2018) in British Columbia and during the 2018 season in southern Alberta. ITS2 metabarcoding revealed disparity in aeromycobiota diversity and compositional structure across the Canadian Rocky Mountains, suggesting a barrier effect on air flow and pathogen dispersal. A novel bioinformatics classifier and curated cereal rust fungal ITS2 database, corroborated by real-time PCR, enhanced the precision of cereal rust fungal species identification. Random Forest modelling identified crop and land-use diversification as well as atmospheric pressure and moisture as key factors in rust distribution. As a valuable addition to explain observed differences and patterns in rust fungus distribution, trajectory HYSPLIT modelling tracked rust fungal urediniospores' northeastward dispersal from the Pacific Northwest towards southern British Columbia and Alberta, indicating multiple potential origins. Our Canadian case study exemplifies the power of an advanced biovigilance toolbox towards developing an early-warning system for farmers to detect and mitigate impending disease outbreaks.
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Affiliation(s)
- Wen Chen
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada (AAFC), Ottawa, Ontario, Canada
- Department of Biology, University of Ottawa, Marie-Curie Private, Ottawa, Ontario, Canada
| | - Nathaniel Newlands
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, British Columbia, Canada
| | - Sarah Hambleton
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada (AAFC), Ottawa, Ontario, Canada
| | - André Laroche
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
| | | | - Guus Bakkeren
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, British Columbia, Canada
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Du Z, Li Z, Liu M, Sun M, Ma X, Wang L, Kang Z, Zhao J. Virulence and Molecular Characterization Reveal Sign of Sexual Genetic Recombination of Puccinia striiformis f. sp. tritici and Puccinia striiformis f. sp. hordei in Tibet. PLANT DISEASE 2024:PDIS05230852RE. [PMID: 38268170 DOI: 10.1094/pdis-05-23-0852-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
Stripe rust of wheat and barley is caused by different formae speciales, Puccinia striiformis f. sp. tritici (Pst) and P. striiformis f. sp. hordei (Psh), respectively. To understand the relationship between the populations of the two formae speciales, a total of 260 P. striiformis isolates, including 140 from barley and 120 from wheat collected from Linzhi, Tibet, China, from 2018 to 2020, were tested on 18 barley and 13 wheat genotypes and genotyped with 26 single-nucleotide polymorphism (SNP)-based Kompetitive allele-specific PCR (KASP) markers. As a result, 260 isolates were identified as 83 virulence phenotypes (VPs), 115 of which as 9 VPs and could infect only wheat (wheat population), 111 as 54 VPs and could infect only barley (barley population), and 34 belonged to 20 VPs that could infect both wheat and barley (mixed population). Of the 149 multilocus genotypes (MLGs) that were identified, 92 were from wheat, 56 from barley, and 1 from both wheat and barley. Phenotypic and genotypic diversity was high in the populations from wheat and barley. Low linkage disequilibrium was found in most of the sampling sites of both crops, indicating strong signs of sexual reproduction (|r̄d| = 0.022 to 0.393, P = 0.004 to 0.847), whereas it was not observed in the overall population (wheat and barley sources) and the wheat, barley, and mixed populations, which may be because of the complex composition of isolates. Population structure analyses based on phenotyping and SNP-KASP genotypes supported the separation of the two formae speciales. However, MLGs and clusters containing isolates from both wheat and barley obviously indicated sexual genetic recombination between the two formae speciales. The results of the study provided an insight into evolution of Pst and Psh and showed the importance of management strategies for stripe rust of wheat and barley in regions where both crops are grown.
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Affiliation(s)
- Zhimin Du
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zejian Li
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Maxinzhi Liu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mudi Sun
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xinyao Ma
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lin Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhensheng Kang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jie Zhao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
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Mohaimin AZ, Krishnamoorthy S, Shivanand P. A critical review on bioaerosols-dispersal of crop pathogenic microorganisms and their impact on crop yield. Braz J Microbiol 2024; 55:587-628. [PMID: 38001398 PMCID: PMC10920616 DOI: 10.1007/s42770-023-01179-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Bioaerosols are potential sources of pathogenic microorganisms that can cause devastating outbreaks of global crop diseases. Various microorganisms, insects and viroids are known to cause severe crop diseases impeding global agro-economy. Such losses threaten global food security, as it is estimated that almost 821 million people are underfed due to global crisis in food production. It is estimated that global population would reach 10 billion by 2050. Hence, it is imperative to substantially increase global food production to about 60% more than the existing levels. To meet the increasing demand, it is essential to control crop diseases and increase yield. Better understanding of the dispersive nature of bioaerosols, seasonal variations, regional diversity and load would enable in formulating improved strategies to control disease severity, onset and spread. Further, insights on regional and global bioaerosol composition and dissemination would help in predicting and preventing endemic and epidemic outbreaks of crop diseases. Advanced knowledge of the factors influencing disease onset and progress, mechanism of pathogen attachment and penetration, dispersal of pathogens, life cycle and the mode of infection, aid the development and implementation of species-specific and region-specific preventive strategies to control crop diseases. Intriguingly, development of R gene-mediated resistant varieties has shown promising results in controlling crop diseases. Forthcoming studies on the development of an appropriately stacked R gene with a wide range of resistance to crop diseases would enable proper management and yield. The article reviews various aspects of pathogenic bioaerosols, pathogen invasion and infestation, crop diseases and yield.
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Affiliation(s)
- Abdul Zul'Adly Mohaimin
- Environmental and Life Sciences Programme, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Bandar Seri Begawan, BE1410, Brunei Darussalam
| | - Sarayu Krishnamoorthy
- Environmental and Life Sciences Programme, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Bandar Seri Begawan, BE1410, Brunei Darussalam
| | - Pooja Shivanand
- Environmental and Life Sciences Programme, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Bandar Seri Begawan, BE1410, Brunei Darussalam.
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Sun C, Liu YF, Liang YM, Wang L. Four new species of Puccinia from herbaceous plants in China. Mycologia 2024; 116:309-321. [PMID: 38252498 DOI: 10.1080/00275514.2023.2289697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 11/27/2023] [Indexed: 01/24/2024]
Abstract
Members of Puccinia (Pucciniaceae, Pucciniales) are known as plant pathogens worldwide, which are characterized by their morphology, host association, and molecular data of various genes. In the present study, 10 specimens of Puccinia were collected from four herbaceous plants (Anaphalis hancockii, Anthriscus sylvestris, Halenia elliptica, and Pilea pumila) in China and identified based on morphology and phylogeny. As a result, 10 samples represent four undescribed species of Puccinia, viz., P. apdensia, P. decidua, P. dermatis, and P. lianchengensis, spp. nov. P. apdensia is characterized by its smooth teliospores with thickened apex. P. decidua represents the first Puccinia species inhabiting the host Anaphalis hancockii and is distinguished from the other Puccinia species by its telia and uredinia surrounded by the epidermis. P. dermatis from Halenia elliptica differs from the other Puccinia species on the host genus Halenia by the telia that have epidermis and teliospores with sparsely irregular granulated protrusions. P. lianchengensis is characterized by its teliospore surface with fishnet ornamentation and urediniospores without prominent caps. All of the new species are described and illustrated in this study.
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Affiliation(s)
- Chang Sun
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing 100083, China
| | - Yi-Fan Liu
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing 100083, China
| | - Ying-Mei Liang
- Museum of Beijing Forestry University, Beijing Forestry University, Beijing 100083, China
| | - Lei Wang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing 100083, China
- Beijing Museum of Natural History, Beijing 100050, China
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Long M, Hartley M, Morris RJ, Brown JKM. Classification of wheat diseases using deep learning networks with field and glasshouse images. PLANT PATHOLOGY 2023; 72:536-547. [PMID: 38516179 PMCID: PMC10953319 DOI: 10.1111/ppa.13684] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 03/23/2024]
Abstract
Crop diseases can cause major yield losses, so the ability to detect and identify them in their early stages is important for disease control. Deep learning methods have shown promise in classifying multiple diseases; however, many studies do not use datasets that represent real field conditions, necessitating either further image processing or reducing their applicability. In this paper, we present a dataset of wheat images taken in real growth situations, including both field and glasshouse conditions, with five categories: healthy plants and four foliar diseases, yellow rust, brown rust, powdery mildew and Septoria leaf blotch. This dataset was used to train a deep learning model. The resulting model, named CerealConv, reached a 97.05% classification accuracy. When tested against trained pathologists on a subset of images from the larger dataset, the model delivered an accuracy score 2% higher than the best-performing pathologist. Image masks were used to show that the model was using the correct information to drive its classifications. These results show that deep learning networks are a viable tool for disease detection and classification in the field, and disease quantification is a logical next step.
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Affiliation(s)
- Megan Long
- Department of Crop GeneticsJohn Innes CentreNorwichUK
| | - Matthew Hartley
- Department of Computational and Systems BiologyJohn Innes CentreNorwichUK
- Present address:
European Molecular Biology LaboratoryEuropean Bioinformatics InstituteHinxtonUK
| | - Richard J. Morris
- Department of Computational and Systems BiologyJohn Innes CentreNorwichUK
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Padhy AK, Sharma A, Sharma H, Srivastava P, Singh S, Kaur P, Kaur J, Kaur S, Chhuneja P, Bains NS. Combining high carotenoid, grain protein content and rust resistance in wheat for food and nutritional security. Front Genet 2023; 14:1075767. [PMID: 36741327 PMCID: PMC9893017 DOI: 10.3389/fgene.2023.1075767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 01/03/2023] [Indexed: 01/20/2023] Open
Abstract
Globally, malnutrition has given birth to an alarming predicament, especially in developing countries, and has extensively shifted consumer preferences from conventional high-energy diets to a nutritionally balanced, cost-effective, sustainable, and healthy lifestyle. In keeping with this view and the mandate for developing high-yielding, disease-resistant biofortified staple food (wheat) for catering to the demand-driven market, the current research aimed at stacking together the enhanced grain protein content, carotenoid content, and disease resistance in an elite bread wheat background. The Y gene (PsyE1) and the GpcB1 gene were used as novel sources for enhancing the grain carotenoid and protein content in the commercial elite bread wheat cultivar HD2967. The combination also led to the stacking of resistance against all three foliar rusts owing to linked resistance genes. A stepwise hybridization using Parent 1 (HD2967 + PsyE1/Lr19/Sr25) with Parent 2 (PBW550 + GpcB1/Yr36+ Yr15), coupled with a phenotypic-biochemical selection, narrowed down 2748 F2 individuals to a subset of 649 F2 plants for molecular screening. The gene-specific markers PsyE1, PsyD1, Xucw108, and Xbarc8 for the genes PsyE1, PsyD1, GpcB1, and Yr15, respectively, were employed for forward selection. Four bread wheat lines positive for all the desired genes with high carotenoid (>8ppm) and protein (>13%) content were raised to the F5 generation and will be evaluated for yield potential after bulking. These improved advanced breeding lines developed following multipronged efforts should prove a valuable and unique source for the development of cultivars with improved nutritional quality and rust resistance in wheat breeding programs.
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Affiliation(s)
| | - Achla Sharma
- *Correspondence: Achla Sharma, ; Asish Kumar Padhy,
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Zhang Y, Xin X, Matthew C, Christensen MJ, Nan Z. Pathogen Identification and Factors Influencing Infection Frequency and Severity of Fungal Rust in Four Native Grasses in Hulunber Grassland, China. PLANT DISEASE 2022; 106:3040-3049. [PMID: 35596246 DOI: 10.1094/pdis-08-21-1802-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A serious rust infection present in 2014 and 2015 on the dominant grass species (Leymus chinensis) in the Hulunber grassland of Inner Mongolia, China, and also present on three other grass species (Agropyron cristatum [wheat grass], Bromus inermis, and Festuca ovina) was investigated. Field surveys, laboratory determination of morphological characteristics, pathogenicity tests, and molecular identification methods were integrated to identify two rust-causing pathogens on L. chinensis. It was found that Puccinia elymi was the major pathogen of L. chinensis, and also infected A. cristatum and F. ovina. This is the first report of P. elymi on A. cristatum in China. P. striiformis caused stripe rust on L. chinensis and B. inermis. The incidence and severity of rust infection increased through the growing season, presumably from asexual spread by urediniospores, and was higher on grass species phylogenetically more closely related to common crop hosts of the pathogens. High host grass density and presence of a potential alternate host for P. elymi, Thalictrum squarrosum, were two further factors promoting rust incidence. These results provide insight into ecological factors linked to the rust epidemic and provide a theoretical basis for the formulation of control strategies.
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Affiliation(s)
- Yawen Zhang
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, P.R. China
- School of Pharmacy, Lanzhou University, Lanzhou 730000, P.R. China
| | - Xiaoping Xin
- National Hulunber Grassland Ecosystem Observation and Research Station, Institute of Agricultural Resources and Regional Planning; Chinese Academy of Agricultural Science, Beijing 10081, P.R. China
| | - Cory Matthew
- School of Agriculture and Environment, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand
| | - Michael J Christensen
- AgResearch, Grasslands Research Centre, Private Bag 11-008, Palmerston North 4442, New Zealand (Retired)
| | - Zhibiao Nan
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, P.R. China
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Padhy AK, Kaur P, Singh S, Kashyap L, Sharma A. Colored wheat and derived products: key to global nutritional security. Crit Rev Food Sci Nutr 2022; 64:1894-1910. [PMID: 36069286 DOI: 10.1080/10408398.2022.2119366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Ensuring food and nutritional security of fast-growing population will pose a huge challenge in future. An estimated one-half population who does not go hungry, nonetheless suffers the debilitating effects of unhealthy diets. In view of the nutritional awareness, when the major wheat breeding programs have started shifting to quality, instead of quantity in wheat, the colored wheats give a novel twist of targeting the malnutrition by enhancing the antioxidants such as anthocyanin, carotenoids, flavonoids, polyphenols etc. Moreover, changing consumer demands have picked the trend to prefer a nutritionally balanced diet over the conventional high energy diets and thus, colored wheat has opened up a hidden avenue for providing additional value to the wheat-based products. Besides providing nutrition, these pigments have the potential to replace the synthetic dyes and food colorants prevalent in the market. The review summarizes the genetics and biochemistry of the pigments of colored wheat along with their product development, nutritional status and consumer preference. The review also sheds light on the environmental effect on color accumulation and the effect of increased colorants on other quality traits of wheat.
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Affiliation(s)
| | | | | | | | - Achla Sharma
- Punjab Agricultural University, Ludhiana, Punjab, India
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Chen W, Radford D, Hambleton S. Towards Improved Detection and Identification of Rust Fungal Pathogens in Environmental Samples Using a Metabarcoding Approach. PHYTOPATHOLOGY 2022; 112:535-548. [PMID: 34384241 DOI: 10.1094/phyto-01-21-0020-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The dispersion of fungal inocula such as the airborne spores of rust fungi (Pucciniales) can be monitored through metabarcoding of the internal transcribed spacer 2 (ITS2) of the rRNA gene in environmental DNAs. This method is largely dependent on a high-quality reference database (refDB) and primers with proper taxonomic coverage and specificity. For this study, a curated ITS2 reference database (named CR-ITS2-refDB) comprising representatives of the major cereal rust fungi and phylogenetically related species was compiled. Interspecific and intraspecific variation analyses suggested that the ITS2 region had reasonable discriminating power for the majority of the Puccinia species or species complexes in the database. In silico evaluation of nine forward and seven reverse ITS2 primers, including three newly designed, revealed marked variation in DNA amplification efficiency for the rusts. We validated the theoretical assessment of rust-enhanced (Rust2inv/ITS4var_H) and universal fungal (ITS9F/ITS4) ITS2 primer pairs by profiling the airborne rust fungal communities from environmental samples via a metabarcoding approach. Species- or subspecies-level identification of the rusts was improved by use of CR-ITS2-refDB and the Automated Oligonucleotide Design Pipeline (AODP), which identified all mutations distinguishing highly conserved DNA markers between close relatives. A generic bioinformatics pipeline was developed, including all steps used in this study from in silico evaluation of primers to accurate identification of short metabarcodes at the level of interest for defining phytopathogens. The results highlight the importance of primer selection, refDBs that are resolved to reflect phylogenetic relationships, and the use of AODP for improving the reliability of metabarcoding in phytopathogen biosurveillance.
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Affiliation(s)
- Wen Chen
- Biodiversity and Bioresources, Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, K1A 0C6, Canada
| | - Devon Radford
- Biodiversity and Bioresources, Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, K1A 0C6, Canada
| | - Sarah Hambleton
- Biodiversity and Bioresources, Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, K1A 0C6, Canada
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Tremblay ÉD, Carey J, Bilodeau GJ, Hambleton S. Four In Silico Designed and Validated qPCR Assays to Detect and Discriminate Tilletia indica and T. walkeri, Individually or as a Complex. BIOLOGY 2021; 10:biology10121295. [PMID: 34943210 PMCID: PMC8698337 DOI: 10.3390/biology10121295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 11/21/2022]
Abstract
Simple Summary Plant pathogens represent a constant threat to human and animal food, as well as the economy. International trading is constantly expanding and has been known as a means of transportation and introduction for plant pests (e.g., bacteria, viruses, fungi, and insects) in new areas. They can damage or completely ruin a harvest and there are often strict regulations for the most unwanted plant pests in order to keep their incidence confined. The fungal plant pathogen Tilletia indica causes Karnal bunt, a wheat disease that breaks or hollows grains, grows in dark powdery masses, and emits a foul fishy odor, and is therefore highly regulated by a number of country authorities, many of which respond by imposing quarantine regulations. While there are many diagnostic methods developed (microscopy, molecular assays, etc.) to identify Karnal bunt, they have limitations. This study presents four highly sensitive quantitative PCR assays with molecular probes targeting unknown genomic regions for the detection and identification of T. indica and T. walkeri—its closest relative—and the species-complex including both species. Bioinformatics analyses of DNA sequences were used to design the toolkit presented. Abstract Several fungi classified in the genus Tilletia are well-known to infect grass species including wheat (Triticum). Tilletia indica is a highly unwanted wheat pathogen causing Karnal bunt, subject to quarantine regulations in many countries. Historically, suspected Karnal bunt infections were identified by morphology, a labour-intensive process to rule out other tuberculate-spored species that may be found as contaminants in grain shipments, and the closely-related pathogen T. walkeri on ryegrass (Lolium). Molecular biology advances have brought numerous detection tools to discriminate Tilletia congeners (PCR, qPCR, etc.). While those tests may help to identify T. indica more rapidly, they share weaknesses of targeting insufficiently variable markers or lacking sensitivity in a zero-tolerance context. A recent approach used comparative genomics to identify unique regions within target species, and qPCR assays were designed in silico. This study validated four qPCR tests based on single-copy genomic regions and with highly sensitive limits of detection (~200 fg), two to detect T. indica and T. walkeri separately, and two newly designed, targeting both species as a complex. The assays were challenged with reference DNA of the targets, their close relatives, other crop pathogens, the wheat host, and environmental specimens, ensuring a high level of specificity for accurate discrimination.
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Affiliation(s)
- Émilie D. Tremblay
- Agriculture and Agri-Food Canada (AAFC), 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada;
- Correspondence: (É.D.T.); (S.H.); Tel.: +1-613-759-1728 (É.D.T.); +1-613-759-1769 (S.H.)
| | - Julie Carey
- Agriculture and Agri-Food Canada (AAFC), 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada;
| | - Guillaume J. Bilodeau
- Canadian Food Inspection Agency (CFIA), 3851 Fallowfield Road, Ottawa, ON K2H 8P9, Canada;
| | - Sarah Hambleton
- Agriculture and Agri-Food Canada (AAFC), 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada;
- Correspondence: (É.D.T.); (S.H.); Tel.: +1-613-759-1728 (É.D.T.); +1-613-759-1769 (S.H.)
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Tian X, Yao Q, Zhang Z, Cheng X, Qin J, Kang Z, Zhao J. Evidence of Occurrence of Barley Crown Rust Caused by Puccinia coronata var. hordei and Sexual Reproduction of the Pathogen Under Field Conditions in China. PLANT DISEASE 2021; 105:2990-2999. [PMID: 33728956 DOI: 10.1094/pdis-09-20-2029-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Crown rust of barley, caused by Puccinia coronata var. hordei, was first reported by Jin and Steffenson in 1992, and the fungus has been reported only in the United States and Hungary. In China, stripe, stem, and leaf rusts have been reported on barley, but not for crown rust. Recently, a sample (HZJ0004) of rust collected from barley in Qilian county in Qinghai, China, appeared different from the three rusts based on color, size, arrangements of uredinia and/or telia. Teliospores had crown-shaped appendages on the top. Based on the disease symptoms and morphology of urediniospores and teliospores, the fungus was identified as P. coronata var. hordei. Using the internal transcribed spacer sequences, the isolates HZJ0004 from barley and POR3 from buckthorn (Rhamnus sp.) were clustered in one clade with P. coronata var. hordei isolates from barley and Elymus repens but in a different clade from the isolate POC8 from wild oat and the varieties of P. coronata from oats and grasses. At the seedling stage, most of the tested cultivars of barley and rye were susceptible to P. coronata var. hordei isolates HZJ0004 and POR3, but the cultivars of oats, triticale, wheat, and most grasses of genera Aegilops, Brachypodium, Bromus, Calamagrostis, Deschampsia, Elymus, Festuca, and Phleum were resistant, indicating their host specialization on barley. To our knowledge, this is the first report of crown rust on barley in China.
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Affiliation(s)
- Xiaxia Tian
- Key State Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qiang Yao
- Institute of Plant Protection, Qinghai Academy of Agriculture and Forestry Sciences, Xining 810016, China
| | - Zedong Zhang
- Key State Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiangrui Cheng
- Key State Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jianfeng Qin
- Key State Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhensheng Kang
- Key State Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jie Zhao
- Key State 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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Genetic Diversity of Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici in Yunnan, China. PLANTS 2021; 10:plants10081735. [PMID: 34451780 PMCID: PMC8399030 DOI: 10.3390/plants10081735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 08/08/2021] [Accepted: 08/10/2021] [Indexed: 11/16/2022]
Abstract
The stripe rust of wheat is one of the devastating diseases in China, which is caused by fungus Puccinia striiformis f. sp. tritici (Pst). The Yunnan Province of China is located in the south-western part, and holds distinctive geographical and climate features, while wheat growth and epidemics of stripe rust fungus are fully dissimilar to the major wheat-growing regions of China. It is important to discover its origin and migration to control the disease. In this study, 352 isolates were sampled from 11 spots of the Yunnan Province during the wheat growing season from 2004 to 2015 and analyzed with SNPs markers of housekeeping genes. Results revealed that 220 haplotypes were inferred from the concatenating sequences; among them, 5 haplotypes (viz., 'H86', 'H18', 'H8', 'H15' and 'H23') comprised over 24.5% of the population. The haplotype diversity, nucleotide diversity, mutation rate and recombination events were 0.992, 6.04 × 10-3, 4.46 × 10-3 and 18.0 respectively, which revealed the genetic diversity of Pst populations among all locations. Four grouping methods, such as UPGMA-tree, PCA, PLS-DA and STRUCTURE, were employed for the categorization of the Pst populations conferring to their races and topographical localities. All methods were found significant and mostly had co-linear relations with each other. The analysis of molecular variance (AMOVA) conferred total variation was 9.09%, and 86.20% of variation was within the populations. The current study also exposed a comparatively high genetic multiplicity within the population, while low genetic inconsistency among the populations. Furthermore, the molecular records on the gene pole (Nm = 18.45) established that the migration of the stripe rust pathogen occurred among all locations in Yunnan province. The ancestral haplotype was detected in Yuxi. Based on the trajectories of upper airflow and genetic diversity of Pst populations in different locations, it is suggested that the locations Dehong, Dali, Lincang and Baoshan are probably a major source of Pst in Yunnan.
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Alemu SK, Huluka AB, Tesfaye K, Haileselassie T, Uauy C. Genome-wide association mapping identifies yellow rust resistance loci in Ethiopian durum wheat germplasm. PLoS One 2021; 16:e0243675. [PMID: 33999918 PMCID: PMC8128278 DOI: 10.1371/journal.pone.0243675] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 04/16/2021] [Indexed: 12/28/2022] Open
Abstract
Durum wheat is an important cereal grown in Ethiopia, a country which is also its center for genetic diversity. Yellow (stripe) rust caused by Puccinia striiformis fsp tritici is one of the most devastating diseases threatening Ethiopian wheat production. To identify sources of genetic resistance and combat this pathogen, we conducted a genome wide association study of yellow rust resistance on 300 durum wheat accessions comprising 261 landraces and 39 cultivars. The accessions were evaluated for their field resistance using a modified Cobb scale at Meraro, Kulumsa and Chefe Donsa in the 2015 and 2016 main growing seasons. Analysis of the 35K Axiom Array genotyping data of the panel resulted in a total of 8,797 polymorphic SNPs of which 7,093 were used in subsequent analyses. Population structure analysis suggested two groups in which the cultivars clearly stood out separately from the landraces. Eleven SNPs significantly associated with yellow rust resistance were identified on four chromosomes (1A, 1B, 2B, and 5A) which defined at least five genomic loci. Six of the SNPs were consistently identified on chromosome 1B singly at each and combined overall environments which explained 62.6–64.0% of the phenotypic variation (R2). Resistant allele frequency ranged from 14.0–71.0%; Zooming in to the identified resistance loci revealed the presence of disease resistance related genes involved in the plant defense system such as the ABC transporter gene family, disease resistance protein RPM1 (NBS-LRR class), Receptor kinases and Protein kinases. This study has provided SNPs for tracking the loci associated with yellow rust resistance and a diversity panel which can be used for association study of other agriculturally important traits in durum wheat.
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Affiliation(s)
- Sisay Kidane Alemu
- National Agricultural Biotechnology Research Center, Holeta, Ethiopian Institute of Agricultural Research, Addis Ababa, Ethiopia
- * E-mail:
| | - Ayele Badebo Huluka
- International Maize and Wheat Improvement Center (CIMMYT), Addis Ababa, Ethiopia
| | - Kassahun Tesfaye
- Institute of Biotechnology and DMCMB, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
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Alternate Hosts of Puccinia striiformis f. sp. tritici and Their Role. Pathogens 2020; 9:pathogens9060434. [PMID: 32498285 PMCID: PMC7350320 DOI: 10.3390/pathogens9060434] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/24/2020] [Accepted: 05/27/2020] [Indexed: 01/06/2023] Open
Abstract
Understanding the interactions between the host and the pathogen is important in developing resistant cultivars and strategies for controlling the disease. Since the discovery of Berberis and Mahonia spp. as alternate hosts of the wheat stripe rust pathogen, Puccinia striiformis Westend. f. sp. tritici Erikss. (Pst), their possible role in generating new races of Pst through sexual reproduction has become a hot topic. To date, all the investigations about the role of alternate hosts in the occurrence of the wheat stripe rust epidemics revealed that it depends on alternate host species and environmental conditions. In this review, we summarized the current status of alternate hosts of Pst, their interactions with the pathogen, their importance in genetic diversity and disease epidemics. Most importantly, the recent research progress in understanding the role of alternate hosts of Pst is provided.
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Mehmood S, Sajid M, Husnain SK, Zhao J, Huang L, Kang Z. Study of Inheritance and Linkage of Virulence Genes in a Selfing Population of a Pakistani Dominant Race of Puccinia striiformis f. sp. tritici. Int J Mol Sci 2020; 21:ijms21051685. [PMID: 32121459 PMCID: PMC7084513 DOI: 10.3390/ijms21051685] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 11/16/2022] Open
Abstract
Wheat stripe rust is a severe threat of almost all wheat-growing regions in the world. Being an obligate biotrophic fungus, Puccinia striiformis f. sp. tritici (PST) produces new virulent races that break the resistance of wheat varieties. In this study, 115 progeny isolates were generated through sexual reproduction on susceptible Himalayan Berberis pseudumbellata using a dominant Pakistani race (574232) of PST. The parental isolate and progeny isolates were characterized using 24 wheat Yr single-gene lines and ten simple sequence repeat (SSR) markers. From the one-hundred-and-fifteen progeny isolates, 25 virulence phenotypes (VPs) and 60 multilocus genotypes were identified. The parental and all progeny isolates were avirulent to Yr5, Yr10, Yr15, Yr24, Yr32, Yr43, YrSp, YrTr1, YrExp2, Yr26, and YrTye and virulent to Yr1, Yr2, Yr6, Yr7, Yr8, Yr9, Yr17, Yr25, Yr27, Yr28, YrA, Yr44, and Yr3. Based on the avirulence/virulence phenotypes, we found that VPs virulent to Yr1, Yr2, Yr9, Yr17, Yr47, and YrA were controlled by one dominant gene; those to YrSp, YrTr1, and Yr10 by two dominant genes; and those to YrExp2 by two complementary dominant genes. The results are useful in breeding stripe rust-resistant wheat varieties and understanding virulence diversity.
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Affiliation(s)
- Sajid Mehmood
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, China; (S.M.); (Z.K.)
| | - Marina Sajid
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China;
| | - Syed Kamil Husnain
- Plant Pathology Section, Barani Agricultural Research Institute, Chakwal 48800, Punjab, Pakistan;
| | - Jie Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, China; (S.M.); (Z.K.)
- Correspondence: (J.Z.); (L.H.); Tel.: +86-29-870-18-1317 (J.Z.); +86-29-8709-1312 (L.H.)
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, China; (S.M.); (Z.K.)
- Correspondence: (J.Z.); (L.H.); Tel.: +86-29-870-18-1317 (J.Z.); +86-29-8709-1312 (L.H.)
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, China; (S.M.); (Z.K.)
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He MQ, Zhao RL, Hyde KD, Begerow D, Kemler M, Yurkov A, McKenzie EHC, Raspé O, Kakishima M, Sánchez-Ramírez S, Vellinga EC, Halling R, Papp V, Zmitrovich IV, Buyck B, Ertz D, Wijayawardene NN, Cui BK, Schoutteten N, Liu XZ, Li TH, Yao YJ, Zhu XY, Liu AQ, Li GJ, Zhang MZ, Ling ZL, Cao B, Antonín V, Boekhout T, da Silva BDB, De Crop E, Decock C, Dima B, Dutta AK, Fell JW, Geml J, Ghobad-Nejhad M, Giachini AJ, Gibertoni TB, Gorjón SP, Haelewaters D, He SH, Hodkinson BP, Horak E, Hoshino T, Justo A, Lim YW, Menolli N, Mešić A, Moncalvo JM, Mueller GM, Nagy LG, Nilsson RH, Noordeloos M, Nuytinck J, Orihara T, Ratchadawan C, Rajchenberg M, Silva-Filho AGS, Sulzbacher MA, Tkalčec Z, Valenzuela R, Verbeken A, Vizzini A, Wartchow F, Wei TZ, Weiß M, Zhao CL, Kirk PM. Notes, outline and divergence times of Basidiomycota. FUNGAL DIVERS 2019. [DOI: 10.1007/s13225-019-00435-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
AbstractThe Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the Ascomycota. The present work provides an overview of all validly published, currently used basidiomycete genera to date in a single document. An outline of all genera of Basidiomycota is provided, which includes 1928 currently used genera names, with 1263 synonyms, which are distributed in 241 families, 68 orders, 18 classes and four subphyla. We provide brief notes for each accepted genus including information on classification, number of accepted species, type species, life mode, habitat, distribution, and sequence information. Furthermore, three phylogenetic analyses with combined LSU, SSU, 5.8s, rpb1, rpb2, and ef1 datasets for the subphyla Agaricomycotina, Pucciniomycotina and Ustilaginomycotina are conducted, respectively. Divergence time estimates are provided to the family level with 632 species from 62 orders, 168 families and 605 genera. Our study indicates that the divergence times of the subphyla in Basidiomycota are 406–430 Mya, classes are 211–383 Mya, and orders are 99–323 Mya, which are largely consistent with previous studies. In this study, all phylogenetically supported families were dated, with the families of Agaricomycotina diverging from 27–178 Mya, Pucciniomycotina from 85–222 Mya, and Ustilaginomycotina from 79–177 Mya. Divergence times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system, and also provide a better understanding of their phylogeny and evolution.
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Mehmood S, Sajid M, Zhao J, Khan T, Zhan G, Huang L, Kang Z. Identification of Berberis Species Collected from the Himalayan Region of Pakistan Susceptible to Puccinia striiformis f. sp. tritici. PLANT DISEASE 2019; 103:461-467. [PMID: 30657429 DOI: 10.1094/pdis-01-18-0154-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Puccinia striiformis f. sp. tritici (Pst), the stripe rust pathogen infecting cereal crops and grasses, was believed to have a hemicyclic life cycle consisting of uredinial and telial stages before the recent discovery of barberry (Berberis spp.) as an alternate (aecial) host for the fungus. This discovery has improved the understanding of the biology of the stripe rust pathogen. The Himalayan and near-Himalayan regions of Pakistan, China, and Nepal are considered as the center of diversity for Pst pathogen. High genetic diversity has been reported in these areas, probably resulting from the sexual reproduction of the stripe rust fungus. To determine if Berberis species growing in Pakistan are susceptible to Pst, we collected seeds of five species and two subspecies from the Himalayan region in 2016 and inoculated the seedlings with germinated teliospores of a Pakistani Pst isolate under controlled conditions. Pycnia and aecia were produced on all inoculated plants of these species and subspecies, and were demonstrated as Pst by successful infection of wheat plants with aeciospores. This study showed that the tested Pakistani Berberis species and subspecies are susceptible to Pst under controlled conditions.
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Affiliation(s)
- Sajid Mehmood
- 1 State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Marina Sajid
- 2 College of Food Science and Engineering, Northwest A&F University, Yangling 712100, Shaanxi, China; and
| | - Jie Zhao
- 1 State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Tika Khan
- 3 Integrated Mountain Area Research Center, Department of Biological Sciences, Karakoram International University, Gilgit 15100, Gilgit-Baltistan, Pakistan
| | - Gangming Zhan
- 1 State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Lili Huang
- 1 State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Zhensheng Kang
- 1 State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
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Kenaley SC, Quan M, Aime MC, Bergstrom GC. New insight into the species diversity and life cycles of rust fungi (Pucciniales) affecting bioenergy switchgrass (Panicum virgatum) in the Eastern and Central United States. Mycol Prog 2018. [DOI: 10.1007/s11557-018-1434-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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21
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Kuzdraliński A, Kot A, Szczerba H, Ostrowska A, Nowak M, Muszyńska M, Lechowski M, Muzyka P. Novel PCR Assays for the Detection of Biological Agents Responsible for Wheat Rust Diseases: Puccinia triticina and Puccinia striiformis f. sp. tritici. J Mol Microbiol Biotechnol 2017; 27:299-305. [PMID: 29183031 DOI: 10.1159/000481799] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 09/27/2017] [Indexed: 11/19/2022] Open
Abstract
The species Puccinia triticina (Pt) and Puccinia striiformis f. sp. tritici (Pst) are devastating cereal pathogens that cause leaf and stripe rust diseases. We developed PCR assays for the species-specific detection of Pt and Pst, 2 biological agents that cause wheat rust disease. For each pathogen, we validated 3 primer sets that target the second largest subunits of the RNA polymerase II (rpb2) and β-tubulin 1 (tub1) genes. The specificities of the primers were verified using naturally infected plant materials with visual symptoms of disease. All primer sets amplified a single DNA fragment of the expected length. The primer sets LidPr15/16, LidPr1/2, and LidPs13/14 were able to detect small amounts of pure fungal DNA with sensitivities of 0.1, 1, and 10 pg/μL, respectively. A sufficient detection limit (1 pg/μL to 5 ng/μL) was observed for all assays when the sensitivity test was performed with host plant DNA. The study also evaluated the simultaneous detection of both rust pathogens, and the multiplex PCR assay generated amplicons of 240 and 144 bp in length for Pts (LidPs9/10) and Pt (LidPr1/2), respectively.
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Affiliation(s)
- Adam Kuzdraliński
- Department of Biotechnology, Human Nutrition and Science of Food Commodities, University of Life Sciences, Lublin, Poland
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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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Kiran K, Rawal HC, Dubey H, Jaswal R, Bhardwaj SC, Prasad P, Pal D, Devanna BN, Sharma TR. Dissection of genomic features and variations of three pathotypes of Puccinia striiformis through whole genome sequencing. Sci Rep 2017; 7:42419. [PMID: 28211474 PMCID: PMC5314344 DOI: 10.1038/srep42419] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 01/10/2017] [Indexed: 01/28/2023] Open
Abstract
Stripe rust of wheat, caused by Puccinia striiformis f. sp. tritici, is one of the important diseases of wheat. We used NGS technologies to generate a draft genome sequence of two highly virulent (46S 119 and 31) and a least virulent (K) pathotypes of P. striiformis from the Indian subcontinent. We generated ~24,000-32,000 sequence contigs (N50;7.4-9.2 kb), which accounted for ~86X-105X sequence depth coverage with an estimated genome size of these pathotypes ranging from 66.2-70.2 Mb. A genome-wide analysis revealed that pathotype 46S 119 might be highly evolved among the three pathotypes in terms of year of detection and prevalence. SNP analysis revealed that ~47% of the gene sets are affected by nonsynonymous mutations. The extracellular secreted (ES) proteins presumably are well conserved among the three pathotypes, and perhaps purifying selection has an important role in differentiating pathotype 46S 119 from pathotypes K and 31. In the present study, we decoded the genomes of three pathotypes, with 81% of the total annotated genes being successfully assigned functional roles. Besides the identification of secretory genes, genes essential for pathogen-host interactions shall prove this study as a huge genomic resource for the management of this disease using host resistance.
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Affiliation(s)
- Kanti Kiran
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Hukam C Rawal
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Himanshu Dubey
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - R Jaswal
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Subhash C Bhardwaj
- Indian Institute of Wheat and Barley Research, Regional Station Flowerdale, Shimla, H.P., India
| | - P Prasad
- Indian Institute of Wheat and Barley Research, Regional Station Flowerdale, Shimla, H.P., India
| | - Dharam Pal
- Indian Agricultural Research Institute, Regional Station, Shimla, H.P., India
| | - B N Devanna
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Tilak R Sharma
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
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Phylogenetics and Phylogenomics of Rust Fungi. FUNGAL PHYLOGENETICS AND PHYLOGENOMICS 2017; 100:267-307. [DOI: 10.1016/bs.adgen.2017.09.011] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Kenaley SC, Hudler GW, Bergstrom GC. Detection and phylogenetic relationships of Puccinia emaculata and Uromyces graminicola (Pucciniales) on switchgrass in New York State using rDNA sequence information. Fungal Biol 2016; 120:791-806. [PMID: 27109375 DOI: 10.1016/j.funbio.2016.01.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 01/25/2016] [Accepted: 01/27/2016] [Indexed: 10/22/2022]
Abstract
The species of rust fungi (Pucciniales) inciting disease on switchgrass (Panicum virgatum) grown in bioenergy feedstock systems across the north-central and eastern United States remain unclear. In the present study, the species number and phylogenetic relationships of rust species affecting switchgrass were examined in 2011-2013 at two sites in New York State as well as selected sites in Alabama, Iowa, Nebraska, Pennsylvania, South Dakota, and West Virginia using ribosomal RNA gene data (partial internal transcribed spacer [ITS] 1, complete 5.8 subunit [S] and ITS2, and partial 28S). Uredinial group and teliospore morphology were also utilized to delimit taxa in collection years 2012 and 2013. Maximum likelihood, maximum parsimony, and Bayesian analyses demonstrated two monophyletic clades. Clade I consisted of Puccinia emaculata and included the majority of single-sorus samples across sites, whereas, Clade II included multiple samples from Iowa, Nebraska, and South Dakota. Single-telial samples for Clade I possessed only two-celled teliospores while Clade II samples possessed only one-celled teliospores, and hence, were readily diagnosed morphologically to P. emaculata and Uromyces graminicola, respectively. No U. graminicola sequences exist in GenBank to compare with our Clade II samples; however, based on teliospore morphology, the identity of Clade II taxa is U. graminicola.
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Affiliation(s)
- Shawn C Kenaley
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY 14853-5904, USA.
| | - George W Hudler
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY 14853-5904, USA
| | - Gary C Bergstrom
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY 14853-5904, USA
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Li K, Hegarty J, Zhang C, Wan A, Wu J, Guedira GB, Chen X, Muñoz-Amatriaín M, Fu D, Dubcovsky J. Fine mapping of barley locus Rps6 conferring resistance to wheat stripe rust. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:845-859. [PMID: 26875072 PMCID: PMC4799263 DOI: 10.1007/s00122-015-2663-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 12/22/2015] [Indexed: 05/22/2023]
Abstract
KEY MESSAGE Barley resistance to wheat stripe rust has remained effective for a long time and, therefore, the genes underlying this resistance can be a valuable tool to engineer durable resistance in wheat. Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a major disease of wheat that is causing large economic losses in many wheat-growing regions of the world. Deployment of Pst resistance genes has been an effective strategy for controlling this pathogen, but many of these genes have been defeated by new Pst races. In contrast, genes providing resistance to this wheat pathogen in other grass species (nonhost resistance) have been more durable. Barley varieties (Hordeum vulgare ssp. vulgare) are predominately immune to wheat Pst, but we identified three accessions of wild barley (Hordeum vulgare ssp. spontaneum) that are susceptible to Pst. Using these accessions, we mapped a barley locus conferring resistance to Pst on the distal region of chromosome arm 7HL and designated it as Rps6. The detection of the same locus in the cultivated barley 'Tamalpais' and in the Chinese barley 'Y12' by an allelism test suggests that Rps6 may be a frequent component of barley intermediate host resistance to Pst. Using a high-density mapping population (>10,000 gametes) we precisely mapped Rps6 within a 0.14 cM region (~500 kb contig) that is colinear to regions in Brachypodium (<94 kb) and rice (<9 kb). Since no strong candidate gene was identified in these colinear regions, a dedicated positional cloning effort in barley will be required to identify Rps6. The identification of this and other barley genes conferring resistance to Pst can contribute to our understanding of the mechanisms for durable resistance against this devastating wheat pathogen.
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Affiliation(s)
- Kun Li
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, Shandong, China
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Joshua Hegarty
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Chaozhong Zhang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Anmin Wan
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164, USA
| | - Jiajie Wu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Gina Brown Guedira
- USDA-ARS, Plant Science Research Unit, Department of Crop Science, North Carolina State University, Raleigh, NC, 27695, USA
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164, USA
- USDA-ARS, Wheat Genetics, Quality, Physiology, and Disease Research Unit, Pullman, WA, 99164, USA
| | - María Muñoz-Amatriaín
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Daolin Fu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
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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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Wang MN, Chen XM. Barberry Does Not Function as an Alternate Host for Puccinia striiformis f. sp. tritici in the U. S. Pacific Northwest Due to Teliospore Degradation and Barberry Phenology. PLANT DISEASE 2015; 99:1500-1506. [PMID: 30695954 DOI: 10.1094/pdis-12-14-1280-re] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Sexual reproduction of the stem rust pathogen, Puccinia graminis f. sp. tritici (Pgt), on barberry (Berberis vulgaris) has been shown to provide initial inoculum for the development of the disease on wheat and barley and also generate diverse races of the pathogen. However, in our previous study, the stripe rust pathogen, P. striiformis f. sp. tritici (Pst), was not found on barberry in the U. S. Pacific Northwest. To determine why Pgt is able to infect the alternate host, while Pst cannot under the natural conditions, the viabilities of teliospores of both Pgt and Pst were investigated from 2011 to 2014 by determining the germination rates using telial samples collected periodically from wheat fields. Teliospores of Pst usually produced in July were physically degraded during winter, and their germination rate decreased from 50 to 90% in August to less than 1% in the following March and no germination after May. In contrast, Pgt teliospores usually produced in July and August remained physically intact and physiologically dormant, and could not germinate until February. Germination of Pgt teliospores gradually increased to 90% in May, at which time young leaves of barberry were susceptible to infection. In addition, a time-series experiment was conducted for inoculation of barberry plants with Pst teliospores. The results showed that Pst teliospores need a minimum of 32 h continual dew-forming conditions to infect barberry, and infection reaches a peak after incubation of inoculated plants for 88 h. The lack of a prolonged period of leaf wetness conditions during the season of telial maturity effectively negates Pst infection of barberry plants in the Pacific Northwest.
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Affiliation(s)
- M N Wang
- Department of Plant Pathology, Washington State University, Pullman 99164-6430
| | - X M Chen
- USDA-ARS, Wheat Genetics, Quality, Physiology, and Disease Research Unit, and Department of Plant Pathology, Washington State University, Pullman 99164-6430
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Rioux S, Mimee B, Gagnon AÈ, Hambleton S. First report of stripe rust (Puccinia striiformis f. sp. tritici) on wheat in Quebec, Canada. ACTA ACUST UNITED AC 2015. [DOI: 10.7202/1028400ar] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Stripe rust, Puccinia striiformis f. sp. tritici, is one of the world’s most important diseases of wheat. In Canada, stripe rust is found mainly in the western provinces (British Columbia, Alberta and Saskatchewan) and, more recently, in the provinces of Manitoba and Ontario. Here, we report the first detection of stripe rust on wheat in the province of Quebec, Canada. Leaves showing yellowish sporulation arranged in narrow stripes were found in wheat performance trials at the research station of Université Laval, in Saint-Augustin-de-Desmaures. Morphological identification was confirmed by several PCR assays targeting specific genomic sequences and a rDNA gene segment (ITS2/28S).
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Affiliation(s)
- Sylvie Rioux
- Centre de recherche sur les grains, 2700 rue Einstein, Québec (Québec), Canada G1P 3W8
| | - Benjamin Mimee
- Horticulture Research and Development Centre, Agriculture and Agri-Food Canada, 430 boul. Gouin, Saint-Jean-sur-Richelieu (Québec), Canada J3B 3E6
| | - Annie-Ève Gagnon
- Centre de recherche sur les grains, 740 chemin Trudeau, Saint-Mathieu-de-Beloeil (Québec), Canada J3G 0E2
| | - Sarah Hambleton
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, K.W. Neatby Building, 960 Carling Avenue, Ottawa (Ontario), Canada K1A 0C6
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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: 31] [Impact Index Per Article: 3.1] [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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Rodriguez-Algaba J, Walter S, Sørensen CK, Hovmøller MS, Justesen AF. Sexual structures and recombination of the wheat rust fungus Puccinia striiformis on Berberis vulgaris. Fungal Genet Biol 2014; 70:77-85. [DOI: 10.1016/j.fgb.2014.07.005] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Revised: 05/07/2014] [Accepted: 07/09/2014] [Indexed: 12/01/2022]
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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: 187] [Impact Index Per Article: 18.7] [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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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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Liu M, Szabo LJ, Hambleton S, Anikster Y, Kolmer JA. Molecular Phylogenetic Relationships of the Brown Leaf Rust Fungi on Wheat, Rye, and Other Grasses. PLANT DISEASE 2013; 97:1408-1417. [PMID: 30708475 DOI: 10.1094/pdis-02-13-0152-re] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The classification of brown leaf rust fungi (Puccinia recondita complex and allied species) on wheat (Triticum aestivum), rye (Secale cereale), and other grasses in the family Poaceae has experienced a long history of controversy and uncertainty due to the reduced morphological characteristics available for taxonomy and difficulty of conducting interfertility experiments. However, because these are pathogens on important crops, it is important to clarify the species delimitations reflecting the natural lineages. In this study, phylogenetic analyses were conducted with DNA sequence data from the ribosomal DNA internal transcribed spacer region and elongation factor 1-α to elucidate this species complex. Three phylogenetic lineages were recovered within the complex of rye leaf rust fungi, P. recondita sensu stricto, which is congruent with existing classifications based on DNA content, sexual compatibility, and morphological studies. The brown leaf rust fungus on wheat (P. triticina) grouped with the related species P. persistens on Elymus repens and E. intermedia as a strongly supported clade. Collections on other Elymus spp. were separated into six clades. Based on the phylogenetic affinities of nine type specimens and aecial host associations, potential taxonomic names were evaluated for selected lineages.
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Affiliation(s)
- Miao Liu
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS) Cereal Disease Laboratory, St. Paul, MN 55108
| | - Les J Szabo
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS) Cereal Disease Laboratory, St. Paul, MN 55108
| | - Sarah Hambleton
- Biodiversity (Mycology and Botany), Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, ONT K1A 0C6, Canada
| | - Yehoshua Anikster
- Institute for Cereal Crops Improvement, George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv 69978, Israel
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Berlin A, Kyaschenko J, Justesen AF, Yuen J. Rust Fungi Forming Aecia on Berberis spp. in Sweden. PLANT DISEASE 2013; 97:1281-1287. [PMID: 30722146 DOI: 10.1094/pdis-10-12-0989-re] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Barberry (Berberis spp.) hosts the aecial stage of several rust species, including Puccinia graminis, which causes stem rust on grasses and cereals. The aecial stage of this pathogen has received less attention because it is not as economically important compared with the uredinial and telial stages. The main objective of this study was to identify and describe the rust species that were found on Berberis spp. collected in different parts of Sweden. A morphological study, including spore measurements and aecia descriptions, was conducted, as well as DNA sequence analyses (using the internal transcribed spacer region and the EF1-α gene). Based on spore and aecia morphology as well as the genetic analyses, three different taxa could be distinguished on barberry: P. graminis f. sp. avenae, P. graminis f. sp. tritci/secalis, and P. arrhenatheri. The genetic analysis revealed little or no differentiation between P. graminis f. sp. tritici and P. graminis f. sp. secalis and, thus, this group of samples was denominated P. graminis f. sp. tritici/secalis. Aecial morphology may be used to differentiate between different taxa. In particular, examination of aecial cross-sections may be used to distinguish between P. graminis f. sp. avenae and P. graminis f. sp. tritici/secalis. A clear differentiation in the mode of growth on barberry was also found; P. arrhenatheri always appeared systemic whereas P. graminis always appeared localized.
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Affiliation(s)
- A Berlin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden
| | - J Kyaschenko
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden
| | - A F Justesen
- Department of Agroecology, Plant Pathology and Entomology, Aarhus University, 4200, Slagelse, Denmark
| | - J Yuen
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences
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Zhao J, Wang L, Wang Z, Chen X, Zhang H, Yao J, Zhan G, Chen W, Huang L, Kang Z. Identification of eighteen Berberis species as alternate hosts of Puccinia striiformis f. sp. tritici and virulence variation in the pathogen isolates from natural infection of barberry plants in China. PHYTOPATHOLOGY 2013; 103:927-34. [PMID: 23514262 DOI: 10.1094/phyto-09-12-0249-r] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
ABSTRACT The wheat stripe rust pathogen (Puccinia striiformis f. sp. tritici) population in China has been reported to be a distinct genetic group with higher diversity than those in many other countries. Genetic recombination in the P. striiformis f. sp. tritici population has been identified with molecular markers but whether sexual reproduction occurs in China is unknown. In this study, we surveyed barberry plants for infection by rust fungi in the stripe rust "hotspot" regions in Gansu, Sichuan, and Shaanxi provinces; collected barberry plants and inoculated plants of 20 Berberis spp. with germinated teliospores under controlled greenhouse conditions for susceptibility to P. striiformis f. sp. tritici; and tested P. striiformis f. sp. tritici isolates obtained from aecia on naturally infected barberry plants on the wheat genotypes used to differentiate Chinese P. striiformis f. sp. tritici races to determine virulence variations. Different Berberis spp. were widely distributed and most surveyed plants had pycnia and aecia of rust fungi throughout the surveyed regions. In total, 28 Berberis spp. were identified during our study. From 20 Berberis spp. tested with teliospores of P. striiformis f. sp. tritici from wheat plants, 18 species were susceptible under greenhouse conditions. Among 3,703 aecia sampled from barberry plants of three species (Berberis shensiana, B. brachypoda, and B. soulieana) under natural infections in Gansu and Shaanxi provinces, four produced P. striiformis f. sp. tritici uredinia on susceptible wheat 'Mingxian 169'. Sequence of the internal transcribed spacer (ITS) regions of the four isolates from barberry shared 99% identity with the P. striiformis f. sp. tritici sequences in the National Center for Biotechnology Information database. The four isolates had virulence patterns different from all previously reported races collected from wheat plants. Furthermore, 82 single-uredinium isolates obtained from the four barberry isolates had high virulence diversity rates of 9.0 to 28.1%, indicating that the diverse isolates were produced through sexual reproduction on barberry plants under natural conditions. In addition to P. striiformis f. sp. tritici, sequence analysis of polymerase chain reaction products of the ITS regions and inoculation tests on wheat identified P. graminis (the stem rust pathogen). Our results indicated that P. striiformis f. sp. tritici can infect some Berberis spp. under natural conditions, and the sexual cycle of the fungus may contribute to the diversity of P. striiformis f. sp. tritici in China.
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Affiliation(s)
- Jie Zhao
- Key State 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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Liu M, Hambleton S. Laying the foundation for a taxonomic review of Puccinia coronata s.l. in a phylogenetic context. Mycol Prog 2012. [DOI: 10.1007/s11557-012-0814-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Beirn LA, Moy M, Meyer WA, Clarke BB, Crouch JA. Molecular Analysis of Turfgrass Rusts Reveals the Widespread Distribution of Puccinia coronata as a Pathogen of Kentucky Bluegrass in the United States. PLANT DISEASE 2011; 95:1547-1557. [PMID: 30732017 DOI: 10.1094/pdis-01-11-0073] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Over the past 10 years, rust diseases have become increasingly prevalent on certain cultivars of Kentucky bluegrass. This pattern suggests that new races or new species of rust fungi may have emerged. To test this hypothesis, 66 samples of turfgrass rust fungi collected from across the United States were evaluated based on sequences of the internal transcribed spacer (ITS)-5.8S rDNA region. Phylogenetic analysis revealed three species: Puccinia coronata, P. graminis, and P. striiformis, comprising 67, 28, and 5% of the samples, respectively. P. coronata was frequently found in association with Kentucky bluegrass, a host-pathogen relationship that has not been previously reported. Comparison of molecular analyses with the use of standard field identification techniques-host association and pustule pigmentation-showed that 58% of the Kentucky bluegrass samples would have been incorrectly diagnosed using nonmolecular criteria. To avoid such misidentifications, a real-time polymerase chain reaction diagnostic protocol was developed for turfgrass-associated P. graminis, P. coronata, and P. striiformis using ITS sequences. Accurate, reproducible, species-specific identifications were made using as few as 50 to 150 urediniospores, even in mixed infections. This study represents the first DNA-based evaluation of turfgrass rust fungi and provides a quick and reliable sequence-based protocol as an alternative to less reliable field-based identification techniques.
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Affiliation(s)
- Lisa A Beirn
- Rutgers University, Department of Plant Biology and Pathology, New Brunswick, NJ 08901
| | - Melinda Moy
- Rutgers University, Department of Plant Biology and Pathology, New Brunswick, NJ 08901
| | - William A Meyer
- Rutgers University, Department of Plant Biology and Pathology, New Brunswick, NJ 08901
| | - Bruce B Clarke
- Rutgers University, Department of Plant Biology and Pathology, New Brunswick, NJ 08901
| | - Jo Anne Crouch
- United States Department of Agriculture-Agricultural Research Service, Systematic Mycology and Microbiology Laboratory, Beltsville, MD 20705
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Hovmøller MS, Sørensen CK, Walter S, Justesen AF. Diversity of Puccinia striiformis on cereals and grasses. ANNUAL REVIEW OF PHYTOPATHOLOGY 2011; 49:197-217. [PMID: 21599494 DOI: 10.1146/annurev-phyto-072910-095230] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Yellow (stripe) rust is a common fungal disease on cereals and grasses. It is caused by Puccinia striiformis sensu lato, which is biotrophic and heteroecious. The pathogen is specialized on the primary host at both species and cultivar levels, whereas several Berberis spp. may serve as alternate hosts. One lineage infects mainly cereals and at least two lineages are restricted to grasses. P. striiformis on cereals has a typical clonal population structure in many areas, resulting from asexual reproduction, but high diversity, suggesting frequent recombination, has been observed in certain areas in Asia. Yellow rust is spreading by airborne spores potentially across long distances, which may contribute to sudden disease epidemics in new areas. This has been the case since 2000, where large-scale epidemics in warmer wheat-growing areas have been ascribed to the emergence of two closely related yellow rust strains with increased aggressiveness and tolerance to warm temperatures.
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Affiliation(s)
- Mogens S Hovmøller
- Department of Integrated Pest Management, Faculty of Agricultural Sciences, Aarhus University, Denmark.
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