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Testen AL, Puri P, Shaw RS, Domsic EC, Griffin-LaHue D, Murphy KM, Mattupalli C. A Quantitative Real-Time PCR Method to Detect the Quinoa Downy Mildew Pathogen, Peronospora variabilis. PLANT DISEASE 2024:PDIS11232308RE. [PMID: 38764340 DOI: 10.1094/pdis-11-23-2308-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2024]
Abstract
Quinoa downy mildew, caused by Peronospora variabilis, is the most devastating disease of quinoa globally. Rapid, sensitive diagnostic methods are needed to detect and quantify this pathogen in seeds and plant tissue. A hydrolysis probe-based quantitative real-time PCR (qPCR) assay including a competitive internal control was developed for P. variabilis detection. This assay could detect as low as 20 ag of DNA or approximately 25 internal transcribed spacer (ITS) copies per reaction with efficiencies ranging from 93.9 to 98.2%. No nontarget amplification was observed when tested against DNA from other downy mildew pathogens and related oomycetes. P. variabilis strains from multiple countries were detected using this assay. The assay was successfully applied to quantify the pathogen in quinoa seeds from a field trial conducted in the state of Washington. Downy mildew disease was recorded on all 14 genotypes, with the genotypes 104.88 and 106.49 recording the highest area under the disease progress curve values (mean ± SE; 3,236 ± 303 and 2,851 ± 198, respectively) and J6 and Dutchess recording the lowest (441 ± 107 and 409 ± 129, respectively). Seed washes obtained from field samples were subjected to the qPCR assay, and the pathogen was detected in all samples. The highest pathogen ITS copy number was recorded with 106.49 (194,934 ± 38,171), and the lowest was observed in Pasto (5,971 ± 1,435) and Riobamba (9,954 ± 4,243). This qPCR assay could lead to improved detection and quantification of P. variabilis as well as increased understanding of quinoa-P. variabilis interactions and epidemiology.
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Affiliation(s)
| | - Purnima Puri
- Department of Plant Pathology, Washington State University, Northwestern Washington Research and Extension Center, Mount Vernon, WA
| | - R Scott Shaw
- USDA-ARS Application Technology Research Unit, Wooster, OH
| | | | - Deirdre Griffin-LaHue
- Department of Crop and Soil Sciences, Washington State University, Northwestern Washington Research and Extension Center, Mount Vernon, WA
| | | | - Chakradhar Mattupalli
- Department of Plant Pathology, Washington State University, Northwestern Washington Research and Extension Center, Mount Vernon, WA
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Fonseca-Guerra IR, Beltrán Pineda ME, Benavides Rozo ME. Characterization of Alternaria alternata and Alternaria scrophulariae Brown Spot in Colombian quinoa ( Chenopodium quinoa). J Fungi (Basel) 2023; 9:947. [PMID: 37755055 PMCID: PMC10532934 DOI: 10.3390/jof9090947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/25/2023] [Accepted: 09/09/2023] [Indexed: 09/28/2023] Open
Abstract
Alternaria is a saprophytic and opportunistic fungus with a worldwide distribution that can affect the quality of various agricultural products, such as fruits, cereals, and pseudocereals. This research was carried out to investigate the population of this genus associated with quinoa cultivation in plots located in the Boyacá department (Colombia), the country's third-largest quinoa-producing department. The present study found 17 Alternaria isolates, of which 13 were identified as A. alternata and 4 as A. scrophulariae (formerly A. conjuncta) employed molecular markers of internal transcribed spacer (ITS) region and translation elongation factor 1α (TEF-1α). In the pathogenicity test under greenhouse conditions, all the Alternaria isolates showed some degree of pathogenicity on Piartal quinoa cultivar plants although no significant differences were found in isolates. The severity indices ranged from 2 to 5, and the percentage of affected leaves per plant ranged between 15% and 40%. This fungus affected the foliar tissue of quinoa, resulting in chlorotic and necrotic spots, symptoms that can generate a reduction in the quality and productivity of crops. This is the first time that the pathogenicity of Alternaria spp. in the Piartal variety has been described and the first report of this genera in quinoa crops of Colombia.
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Affiliation(s)
- Ingrid Rocío Fonseca-Guerra
- Enviromental Management Investigation Group, Universidad de Boyacá, Tunja 150003, Colombia; (M.E.B.P.); (M.E.B.R.)
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Tripathi A, Akhtar J, Kalaiponmani K, Dubey SC, Chalam VC. Quadruplex and q-PCR based diagnostic assay to delineate the major quarantine and other seed-borne fungal pathogens of soybean. World J Microbiol Biotechnol 2023; 39:233. [PMID: 37353610 DOI: 10.1007/s11274-023-03683-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/17/2023] [Indexed: 06/25/2023]
Abstract
Soybean is one of the most important crops grown worldwide and accounting for significant global trade including transgenic soybean. The crop is attacked by several seed-borne fungal pathogens and some of them are of quarantine concern for India. Keeping in view of the risks associated with movement of soybean seeds, sensitive and reliable molecular diagnostics have been developed for precise and simultaneous detection of three pathogens of quarantine concern for India namely, Diaporthe phaseolorum (stem blight), D. longicolla (seed decay), Peronospora manshurica (downy mildew), along with Macrophomina phaseolina causing dry root rot. The targeted pathogens after isolation from imported transgenic and non-transgenic soybean seeds were identified. Quadruplex and qPCR assays were developed targeting the sequences of different genes such as Histone-3 for detection of D. longicolla and M. phaseolina. The markers DlHisF2&R2 and MpHisF1&R1 produced 265 and 309 bp amplicons for D. longicolla and M. phaseolina, respectively. Actin gene based marker DpActF1&R2 was developed for D. phaseolorum which provided 113 bp amplicon whereas, COX2 based marker PmCoxF2&R2 was developed for P. manshurica with amplified product of 152 bp. During qPCR analysis, these markers proved highly specific and sensitive for detection of these pathogens up to 0.1 pg of template DNA. Quadruplex PCR protocol was also developed by combining these specific markers which could distinguish all the targeted pathogens simultaneously in a single reaction. The developed diagnostic protocols are extremely valuable for quarantine clearance and to ensure the safe transboundary exchange and healthy conservation of germplasm in the National Genebank.
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Grants
- Programme No BT/AG/Facility/2019 Department of Biotechnology, Ministry of Science and Technology, India
- Programme No BT/AG/Facility/2019 Department of Biotechnology, Ministry of Science and Technology, India
- Programme No BT/AG/Facility/2019 Department of Biotechnology, Ministry of Science and Technology, India
- Programme No BT/AG/Facility/2019 Department of Biotechnology, Ministry of Science and Technology, India
- Programme No BT/AG/Facility/2019 Department of Biotechnology, Ministry of Science and Technology, India
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Affiliation(s)
- Aradhika Tripathi
- Division of Plant Quarantine, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India
| | - Jameel Akhtar
- Division of Plant Quarantine, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India.
| | - K Kalaiponmani
- Division of Plant Quarantine, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India
| | - Sunil C Dubey
- Division of Plant Quarantine, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India
- Indian Council of Agricultural Research, Krishi Bhawan, Dr. Rajendra Prasad Road, New Delhi, 110001, India
| | - Vasimalla Celia Chalam
- Division of Plant Quarantine, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012, India
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Fondevilla S, Arias-Giraldo LF, García-León FJ, Landa BB. Molecular Characterization of Peronospora variabilis Isolates Infecting Chenopodium quinoa and Chenopodium album in Spain. PLANT DISEASE 2023; 107:999-1004. [PMID: 36190302 DOI: 10.1094/pdis-05-22-1198-sc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Quinoa is an expanding crop in southern Spain. Downy mildew, caused by Peronospora variabilis, is the most important quinoa disease in Spain and worldwide. In Spain, this disease has also been observed on the weed Chenopodium album. The objectives of this study were to unravel the origin of the P. variabilis isolates currently infecting quinoa in southern Spain and to study their genetic diversity. We hypothesized that P. variabilis isolates infecting quinoa in Spain could have been introduced through the seeds of the quinoa varieties currently grown in the country or, alternatively, that these isolates are endemic isolates, originally infecting C. album, that jumped to quinoa. In order to test these hypotheses, we sequenced the internal transcribed spacer (ITS), cytochrome c oxidase subunit 1 (cox1), and cox2 regions of 33 P. variabilis isolates infecting C. quinoa and C. album in southern Spain and analyzed their phylogenetic relationship with isolates present in other countries infecting Chenopodium spp. cox1 gene sequences from all of the Spanish P. variabilis isolates were identical and exhibited nine single-nucleotide polymorphisms (SNPs) compared with a single P. variabilis cox1 sequence found at GenBank. Phylogenetic analyses based on the ITS ribosomal DNA region were not suitable to differentiate isolates according to their geographical origin or host. The cox2 sequences from P. variabilis Spanish isolates collected from C. quinoa and C. album were all identical and had a distinctive SNP in the last of four polymorphic sites that distinguished Spanish isolates from isolates from other countries. These results suggest that P. variabilis infecting quinoa in southern Spain could be native isolates that originally infected C. album.[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Sara Fondevilla
- Institute for Sustainable Agriculture, CSIC, Av. Menendez Pidal s/n, Córdoba 14004, Spain
| | - Luis F Arias-Giraldo
- Institute for Sustainable Agriculture, CSIC, Av. Menendez Pidal s/n, Córdoba 14004, Spain
| | | | - Blanca B Landa
- Institute for Sustainable Agriculture, CSIC, Av. Menendez Pidal s/n, Córdoba 14004, Spain
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Fusarium spp. associated with Chenopodium quinoa crops in Colombia. Sci Rep 2022; 12:20841. [PMID: 36460698 PMCID: PMC9718861 DOI: 10.1038/s41598-022-24908-w] [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: 04/18/2022] [Accepted: 11/22/2022] [Indexed: 12/03/2022] Open
Abstract
Quinoa is a plant commonly-resistance to adverse biotic and abiotic factors. However, this crop can be affected by phytopathogenic fungi. There is a lack of knowledge about the fungi associated with quinoa plants in Colombia. Through morphological and molecular identification in this study were identified four Fusarium species associated with quinoa crops: Fusarium oxysporum, Fusarium graminearum, Fusarium equiseti, and Fusarium culmorum. For this, we collected samples of panicles, leaf tissue, root tissue, and soil for isolation of different isolates of Fusarium. We performed a pathogenicity test of the fungi strains, under greenhouse conditions to evaluate the pathogenicity in seedlings of the Piartal cultivar with two inoculation methods. First inoculating the stem through a nodal wound or second inoculating the abaxial face with a brush. The results indicate the presence of four species with both molecular markers, phylogenetically distributed in these groups. The four species turned out to be pathogenic but with different degrees of virulence with significant differences between F. graminearum and F. oxysporum depending on the inoculation method. This is the first report on the presence of Fusarium species isolated from Quinoa in Colombia.
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Rollano-Peñaloza OM, Palma-Encinas V, Widell S, Mollinedo P, Rasmusson AG. The Disease Progression and Molecular Defense Response in Chenopodium Quinoa Infected with Peronospora Variabilis, the Causal Agent of Quinoa Downy Mildew. PLANTS (BASEL, SWITZERLAND) 2022; 11:2946. [PMID: 36365398 PMCID: PMC9654897 DOI: 10.3390/plants11212946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 10/05/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
Downy mildew disease, caused by the biotrophic oomycete Peronospora variabilis, is the largest threat to the cultivation of quinoa (Chenopodium quinoa Willd.) in the Andean highlands, and occurs worldwide. However, so far, no molecular study of the quinoa-Peronospora interaction has been reported. Here, we developed tools to study downy mildew disease in quinoa at the gene expression level. P. variabilis was isolated and maintained, allowing the study of downy mildew disease progression in two quinoa cultivars under controlled conditions. Quinoa gene expression changes induced by P. variabilis were analyzed by qRT-PCR, for quinoa homologues of A. thaliana pathogen-associated genes. Overall, we observed a slower disease progression and higher tolerance in the quinoa cultivar Kurmi than in the cultivar Maniqueña Real. The quinoa orthologs of putative defense genes such as the catalase CqCAT2 and the endochitinase CqEP3 showed no changes in gene expression. In contrast, quinoa orthologs of other defense response genes such as the transcription factor CqWRKY33 and the chaperone CqHSP90 were significantly induced in plants infected with P. variabilis. These genes could be used as defense response markers to select quinoa cultivars that are more tolerant to P. variabilis infection.
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Affiliation(s)
- Oscar M. Rollano-Peñaloza
- Department of Biology, Lund University, SE-223 62 Lund, Sweden
- Instituto de Investigaciones Químicas, Universidad Mayor de San Andrés, La Paz P.O. Box 12958, Bolivia
| | - Valeria Palma-Encinas
- Instituto de Investigaciones Químicas, Universidad Mayor de San Andrés, La Paz P.O. Box 12958, Bolivia
| | - Susanne Widell
- Department of Biology, Lund University, SE-223 62 Lund, Sweden
| | - Patricia Mollinedo
- Instituto de Investigaciones Químicas, Universidad Mayor de San Andrés, La Paz P.O. Box 12958, Bolivia
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Standish JR, Góngora-Castillo E, Bowman MJ, Childs KL, Tian M, Quesada-Ocampo LM. Development, Validation, and Utility of Species-Specific Diagnostic Markers for Detection of Peronospora belbahrii. PHYTOPATHOLOGY 2022; 112:1667-1675. [PMID: 35196067 DOI: 10.1094/phyto-09-21-0393-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Peronospora belbahrii is an oomycete and the cause of basil downy mildew, one of the most destructive diseases affecting basil production worldwide. Disease management is challenging due to wind-dispersed sporangia and contaminated seed; therefore, identifying P. belbahrii in seed lots before sale or planting or in the field before symptoms develop could allow for timely deployment of disease management strategies. In this study, a draft genome assembly and next-generation sequencing reads for P. belbahrii, as well as publicly available DNA-seq and RNA-seq reads of several other downy mildew pathogens, were incorporated into a bioinformatics pipeline to predict P. belbahrii-specific diagnostic markers. The specificity of each candidate marker was validated against a diverse DNA collection of P. belbahrii, host tissue, and related oomycetes using PCR. Two species-specific markers were identified and used as templates to develop a highly sensitive probe-based real-time quantitative PCR (qPCR) assay that could detect P. belbahrii in leaf tissue and seed samples. Both markers were capable of reliably detecting as low as 500 fg/µl of P. belbahrii genomic DNA and as few as 10 sporangia. The qPCR assay was then validated with seed samples collected from a basil cultivar experiment. In total, 48 seed samples were collected and tested; P. belbahrii was detected in samples of all cultivars at estimated concentrations of 600 fg/µl up to 250 pg/µl and at as few as 10 sporangia up to >1,000 sporangia. The markers and assays are valuable for diagnostics and identifying P. belbahrii-contaminated seed lots to mitigate the effects of future basil downy mildew epidemics.
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Affiliation(s)
- J R Standish
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695-7613, U.S.A
| | - E Góngora-Castillo
- Department of Biotechnology, Yucatan Center for Scientific Research, Chuburná de Hidalgo, 97205 Mérida, Yucatán, México
| | - M J Bowman
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, U.S.A
- Ball Horticultural Company, West Chicago, IL 60185, U.S.A
| | - K L Childs
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, U.S.A
| | - M Tian
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, U.S.A
| | - L M Quesada-Ocampo
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695-7613, U.S.A
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Clark KJ, Anchieta AG, da Silva MB, Kandel SL, Choi YJ, Martin FN, Correll JC, Van Denyze A, Brummer EC, Klosterman SJ. Early Detection of the Spinach Downy Mildew Pathogen in Leaves by Recombinase Polymerase Amplification. PLANT DISEASE 2022; 106:1793-1802. [PMID: 35253491 DOI: 10.1094/pdis-11-21-2398-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Downy mildew of spinach, caused by Peronospora effusa, is a major economic threat to both organic and conventional spinach production. Symptomatic spinach leaves are unmarketable and spinach with latent infections are problematic because symptoms can develop postharvest. Therefore, early detection methods for P. effusa could help producers identify infection before visible symptoms appear. Recombinase polymerase amplification (RPA) provides sensitive and specific detection of pathogen DNA and is a rapid, field-applicable method that does not require advanced technical knowledge or equipment-heavy DNA extraction. Here, we used comparative genomics to identify a unique region of the P. effusa mitochondrial genome to develop an RPA assay for the early detection of P. effusa in spinach leaves. In tandem, we established a TaqMan quantitative PCR (qPCR) assay and used this assay to validate the P. effusa specificity of the locus across Peronospora spp. and to compare assay performance. Neither the TaqMan qPCR nor the RPA showed cross reactivity with the closely related beet downy mildew pathogen, P. schachtii. TaqMan qPCR and RPA have detection thresholds of 100 and 900 fg of DNA, respectively. Both assays could detect P. effusa in presymptomatic leaves, with RPA-based detection occurring as early as 5 days before the appearance of symptoms and TaqMan qPCR-based detection occurring after 24 h of plant exposure to airborne spores. Implementation of the RPA detection method could provide real-time information for point-of-care management strategies at field sites.
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Affiliation(s)
- Kelley J Clark
- United States Department of Agriculture-Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA 93905, U.S.A
| | - Amy G Anchieta
- United States Department of Agriculture-Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA 93905, U.S.A
| | - Mychele B da Silva
- Department of Plant Sciences, University of California, Davis, CA 95616, U.S.A
| | - Shyam L Kandel
- United States Department of Agriculture-Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA 93905, U.S.A
| | - Young-Joon Choi
- Department of Biology, Kunsan National University, Gunsan, 54150, Korea
| | - Frank N Martin
- United States Department of Agriculture-Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA 93905, U.S.A
| | - James C Correll
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR 72701, U.S.A
| | - Allen Van Denyze
- Department of Plant Sciences, University of California, Davis, CA 95616, U.S.A
| | - E Charles Brummer
- Department of Plant Sciences, University of California, Davis, CA 95616, U.S.A
| | - Steven J Klosterman
- United States Department of Agriculture-Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA 93905, U.S.A
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Nolen H, Smith C, Davis TM, Poleatewich A. Evaluation of Disease Severity and Molecular Relationships Between Peronospora variabilis Isolates on Chenopodium Species in New Hampshire. PLANT DISEASE 2022; 106:564-571. [PMID: 34633235 DOI: 10.1094/pdis-06-21-1150-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: 06/13/2023]
Abstract
Quinoa is a potential new crop for New England; however, its susceptibility to downy mildew, caused by Peronospora variabilis, is a key obstacle for cultivation. The objectives of this study were to evaluate differential resistance within the Chenopodium genus, identify novel sources of resistance for use in future genetic studies or breeding programs, and investigate phylogenetic relationships of P. variabilis isolates from different Chenopodium hosts. The long-term goal of this research is to develop a resistant variety of quinoa to be grown in New England. Field trials conducted at the University of New Hampshire evaluated downy mildew disease severity on 10 Chenopodium accessions representing four species. Disease severity for each treatment was compared and significant differences in disease severity were observed between accessions. C. berlandieri var. macrocalycium ecotypes collected from Rye Beach, New Hampshire and Appledore Island, Maine exhibited the lowest disease severity over the growing season. P. variabilis was isolated from each accession, and COX2 sequences were compared. Phylogenetic analyses suggest no effect of host species on P. variabilis sequence similarity; however, isolates are shown to cluster by geographic location. This research provides the first step in identifying potential New England native sources of resistance to downy mildew within the genus Chenopodium and provides preliminary information needed to further investigate resistance at the genomic level in Chenopodium spp.
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Affiliation(s)
- Haley Nolen
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH 03824
| | - Cheryl Smith
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH 03824
| | - Thomas M Davis
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH 03824
| | - Anissa Poleatewich
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH 03824
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Phytopathological Threats Associated with Quinoa ( Chenopodium quinoa Willd.) Cultivation and Seed Production in an Area of Central Italy. PLANTS 2021; 10:plants10091933. [PMID: 34579464 PMCID: PMC8467509 DOI: 10.3390/plants10091933] [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: 07/27/2021] [Revised: 09/01/2021] [Accepted: 09/14/2021] [Indexed: 11/17/2022]
Abstract
In 2017, in a new Chenopodium quinoa cultivation area (Central Italy), emergence failures of the Titicaca, Rio Bamba, and Real varieties, whose seeds were obtained the previous year (2016) in the same location, were observed. Moreover, leaf disease symptoms on the Regalona variety, whose seeds came from Chile, were detected. Visual and microscopic analyses showed the presence of browning/necrotic symptoms on the seeds of the three varieties whose emergence in the field had failed. In addition, their in vitro germination rates were strongly compromised. Fusarium spp. was isolated with high incidence from Titicaca, Rio Bamba, and Real seeds. Among the detected Fusarium species, in the phylogenetic analysis, the dominant one clustered in the sub-clade Equiseti of the Fusarium incarnatum-equiseti (FIESC) species complex. Instead, the pathogen associated with Regalona leaf symptoms was identified, by morphological and molecular features, as Peronospora variabilis, the causal agents of downy mildew. This is the first report of both P. variabilis and F. equiseti on C. quinoa in Italy. Species-specific primers also detected P. variabilis in Regalona seeds. These results underline the importance of pathogen monitoring in new quinoa distribution areas, as well as of healthy seed production and import for successful cultivation.
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Stanschewski CS, Rey E, Fiene G, Craine EB, Wellman G, Melino VJ, S. R. Patiranage D, Johansen K, Schmöckel SM, Bertero D, Oakey H, Colque-Little C, Afzal I, Raubach S, Miller N, Streich J, Amby DB, Emrani N, Warmington M, Mousa MAA, Wu D, Jacobson D, Andreasen C, Jung C, Murphy K, Bazile D, Tester M. Quinoa Phenotyping Methodologies: An International Consensus. PLANTS (BASEL, SWITZERLAND) 2021; 10:1759. [PMID: 34579292 PMCID: PMC8472428 DOI: 10.3390/plants10091759] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/09/2021] [Accepted: 08/12/2021] [Indexed: 11/30/2022]
Abstract
Quinoa is a crop originating in the Andes but grown more widely and with the genetic potential for significant further expansion. Due to the phenotypic plasticity of quinoa, varieties need to be assessed across years and multiple locations. To improve comparability among field trials across the globe and to facilitate collaborations, components of the trials need to be kept consistent, including the type and methods of data collected. Here, an internationally open-access framework for phenotyping a wide range of quinoa features is proposed to facilitate the systematic agronomic, physiological and genetic characterization of quinoa for crop adaptation and improvement. Mature plant phenotyping is a central aspect of this paper, including detailed descriptions and the provision of phenotyping cards to facilitate consistency in data collection. High-throughput methods for multi-temporal phenotyping based on remote sensing technologies are described. Tools for higher-throughput post-harvest phenotyping of seeds are presented. A guideline for approaching quinoa field trials including the collection of environmental data and designing layouts with statistical robustness is suggested. To move towards developing resources for quinoa in line with major cereal crops, a database was created. The Quinoa Germinate Platform will serve as a central repository of data for quinoa researchers globally.
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Affiliation(s)
- Clara S. Stanschewski
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia; (C.S.S.); (E.R.); (G.F.); (G.W.); (V.J.M.); (D.S.R.P.)
| | - Elodie Rey
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia; (C.S.S.); (E.R.); (G.F.); (G.W.); (V.J.M.); (D.S.R.P.)
| | - Gabriele Fiene
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia; (C.S.S.); (E.R.); (G.F.); (G.W.); (V.J.M.); (D.S.R.P.)
| | - Evan B. Craine
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA; (E.B.C.); (K.M.)
| | - Gordon Wellman
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia; (C.S.S.); (E.R.); (G.F.); (G.W.); (V.J.M.); (D.S.R.P.)
| | - Vanessa J. Melino
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia; (C.S.S.); (E.R.); (G.F.); (G.W.); (V.J.M.); (D.S.R.P.)
| | - Dilan S. R. Patiranage
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia; (C.S.S.); (E.R.); (G.F.); (G.W.); (V.J.M.); (D.S.R.P.)
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany; (N.E.); (C.J.)
| | - Kasper Johansen
- Water Desalination and Reuse Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia;
| | - Sandra M. Schmöckel
- Department Physiology of Yield Stability, Institute of Crop Science, University of Hohenheim, 70599 Stuttgart, Germany;
| | - Daniel Bertero
- Department of Plant Production, School of Agriculture, University of Buenos Aires, Buenos Aires C1417DSE, Argentina;
| | - Helena Oakey
- Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia;
| | - Carla Colque-Little
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-2630 Taastrup, Denmark; (C.C.-L.); (D.B.A.); (C.A.)
| | - Irfan Afzal
- Department of Agronomy, University of Agriculture, Faisalabad 38000, Pakistan;
| | - Sebastian Raubach
- Department of Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee AB15 8QH, UK;
| | - Nathan Miller
- Department of Botany, University of Wisconsin, 430 Lincoln Dr, Madison, WI 53706, USA;
| | - Jared Streich
- Biosciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (J.S.); (D.J.)
| | - Daniel Buchvaldt Amby
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-2630 Taastrup, Denmark; (C.C.-L.); (D.B.A.); (C.A.)
| | - Nazgol Emrani
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany; (N.E.); (C.J.)
| | - Mark Warmington
- Department of Primary Industries and Regional Development, Agriculture and Food, Kununurra, WA 6743, Australia;
| | - Magdi A. A. Mousa
- Department of Arid Land Agriculture, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
- Department of Vegetables, Faculty of Agriculture, Assiut University, Assiut 71526, Egypt
| | - David Wu
- Shanxi Jiaqi Agri-Tech Co., Ltd., Taiyuan 030006, China;
| | - Daniel Jacobson
- Biosciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (J.S.); (D.J.)
| | - Christian Andreasen
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-2630 Taastrup, Denmark; (C.C.-L.); (D.B.A.); (C.A.)
| | - Christian Jung
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany; (N.E.); (C.J.)
| | - Kevin Murphy
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA; (E.B.C.); (K.M.)
| | - Didier Bazile
- CIRAD, UMR SENS, 34398 Montpellier, France;
- SENS, CIRAD, IRD, University Paul Valery Montpellier 3, 34090 Montpellier, France
| | - Mark Tester
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia; (C.S.S.); (E.R.); (G.F.); (G.W.); (V.J.M.); (D.S.R.P.)
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12
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A Review of Chenopodium quinoa (Willd.) Diseases-An Updated Perspective. PLANTS 2021; 10:plants10061228. [PMID: 34208662 PMCID: PMC8233811 DOI: 10.3390/plants10061228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/03/2021] [Accepted: 06/07/2021] [Indexed: 12/22/2022]
Abstract
The journey of the Andean crop quinoa (Chenopodium quinoa Willd.) to unfamiliar environments and the combination of higher temperatures, sudden changes in weather, intense precipitation, and reduced water in the soil has increased the risk of observing new and emerging diseases associated with this crop. Several diseases of quinoa have been reported in the last decade. These include Ascochyta caulina, Cercospora cf. chenopodii, Colletotrichum nigrum, C. truncatum, and Pseudomonas syringae. The taxonomy of other diseases remains unclear or is characterized primarily at the genus level. Symptoms, microscopy, and pathogenicity, supported by molecular tools, constitute accurate plant disease diagnostics in the 21st century. Scientists and farmers will benefit from an update on the phytopathological research regarding a crop that has been neglected for many years. This review aims to compile the existing information and make accurate associations between specific symptoms and causal agents of disease. In addition, we place an emphasis on downy mildew and its phenotyping, as it continues to be the most economically important and studied disease affecting quinoa worldwide. The information herein will allow for the appropriate execution of breeding programs and control measures.
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13
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Fujiwara K, Inoue H, Sonoda R, Iwamoto Y, Kusaba M, Tashiro N, Miyasaka A. Real-Time PCR Detection of the Onion Downy Mildew Pathogen Peronospora destructor From Symptomless Onion Seedlings and Soils. PLANT DISEASE 2021; 105:643-649. [PMID: 33467897 DOI: 10.1094/pdis-05-20-1095-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
An outbreak of downy mildew disease of onion, caused by Peronospora destructor, in Japan in 2016 necessitated a reevaluation of the primary inoculum sources to optimize disease management. Detection of the P. destructor pathogen in plants with asymptomatic infection and in soil would guide the application of fungicides according to the extent of infection before disease development. Here, we detected P. destructor in both plants and soil using newly developed primer sets (Pd ITS and Pd ITS 614) by both conventional and real-time PCR. Validation by real-time PCR with Pd ITS 614 showed that P. destructor DNA was amplified from symptomless seedlings at 3.7 × 102 to 1.0 × 100 conidium cells/50 mg leaf tissue, suggesting the detection of asymptomatic infection. Real-time PCR with Pd ITS amplified pathogen DNA from field soils at 1.6 × 103 to 8.3 × 101 oospore cells/g of soil. This real-time PCR assay provides a useful tool for identifying and quantifying inoculum sources, which may be the foundation of the design of integrated disease management strategies.
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Affiliation(s)
- Kazuki Fujiwara
- Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Koshi, Kumamoto 861-1192, Japan
| | - Hiroyoshi Inoue
- Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Koshi, Kumamoto 861-1192, Japan
| | - Ryoichi Sonoda
- Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Koshi, Kumamoto 861-1192, Japan
| | - Yutaka Iwamoto
- Hyogo Prefectural Technology Center for Agriculture, Forestry and Fisheries, Kasai, Hyogo 679-0198, Japan
| | - Motoaki Kusaba
- Faculty of Agriculture, Saga University, Saga City, Saga 840-8502, Japan
| | - Nobuya Tashiro
- Saga Prefectural Upland Farming Research and Extension Center, Karatsu, Saga 847-0326, Japan
| | - Atsushi Miyasaka
- Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Koshi, Kumamoto 861-1192, Japan
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Hinojosa L, Leguizamo A, Carpio C, Muñoz D, Mestanza C, Ochoa J, Castillo C, Murillo A, Villacréz E, Monar C, Pichazaca N, Murphy K. Quinoa in Ecuador: Recent Advances under Global Expansion. PLANTS 2021; 10:plants10020298. [PMID: 33557315 PMCID: PMC7915685 DOI: 10.3390/plants10020298] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 01/20/2021] [Accepted: 02/01/2021] [Indexed: 12/27/2022]
Abstract
Quinoa is a highly diverse crop domesticated in the Andean region of South America with broad adaptation to a wide range of marginal environments. Quinoa has garnered interest worldwide due to its nutritional and health benefits. Over the last decade, quinoa production has expanded outside of the Andean region, prompting multiple studies investigating the potential for quinoa cultivation in novel environments. Currently, quinoa is grown in countries spanning five continents, including North America, Europe, Asia, Africa, and Oceania. Here, we update the advances of quinoa research in Ecuador across different topics, including (a) current quinoa production situation with a focus on breeding progress, (b) traditional seed production, and (c) the impact of the work of the nongovernment organization “European Committee for Training and Agriculture” with quinoa farmers in Chimborazo province. Additionally, we discuss genetic diversity, primary pests and diseases, actions for adapting quinoa to tropical areas, and recent innovations in quinoa processing in Ecuador. Finally, we report a case study describing a participatory breeding project between Washington State University and the Association of Andean Seed and Nutritional Food Producers Mushuk Yuyay in the province of Cañar.
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Affiliation(s)
- Leonardo Hinojosa
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, 1098XH Amsterdam, The Netherlands
- Correspondence:
| | - Alex Leguizamo
- Comité Europeo Para la Formación y la Agricultura (CEFA), Guayas 22-46 y Venezuela, Lago Agrio EC210105, Ecuador;
| | - Carlos Carpio
- Facultad de Recursos Naturales, Escuela Superior Politécnica de Chimborazo, Panamericana Sur km 1 1/2, Riobamba EC060155, Ecuador;
| | - Diego Muñoz
- Grupo de Desarrollo de Tecnologías para la Reducción y Racionalización de Agroquímicos, Riobamba EC060155, Ecuador;
| | - Camilo Mestanza
- Facultad de Ciencias Pecuarias, Carrera de Ingeniería Agropecuaria, Universidad Técnica Estatal de Quevedo-(UTEQ), km 7 ½ vía Quevedo–El Empalme, Mocache, Los Ríos EC120509, Ecuador;
| | - José Ochoa
- Instituto Nacional de Investigaciones Agropecuarias Estación Experimental Santa Catalina, Panamericana Sur Km 1, Quito EC171107, Ecuador or (J.O.); (C.C.); (A.M.); (E.V.)
- Facultad de Ciencias Agrícolas, Universidad Central del Ecuador, Jerónimo Leiton s/n y Av. La Gasca, Quito EC170521, Ecuador
| | - Carmen Castillo
- Instituto Nacional de Investigaciones Agropecuarias Estación Experimental Santa Catalina, Panamericana Sur Km 1, Quito EC171107, Ecuador or (J.O.); (C.C.); (A.M.); (E.V.)
| | - Angel Murillo
- Instituto Nacional de Investigaciones Agropecuarias Estación Experimental Santa Catalina, Panamericana Sur Km 1, Quito EC171107, Ecuador or (J.O.); (C.C.); (A.M.); (E.V.)
| | - Elena Villacréz
- Instituto Nacional de Investigaciones Agropecuarias Estación Experimental Santa Catalina, Panamericana Sur Km 1, Quito EC171107, Ecuador or (J.O.); (C.C.); (A.M.); (E.V.)
| | - Carlos Monar
- Facultad de Ciencias Agropecuarias, Recursos Naturales y del Ambiente, Campus Laguacoto II, Universidad Estatal de Bolívar, Vía Guaranda a San Simón, Guaranda EC020150, Ecuador;
| | - Nicolas Pichazaca
- Asociación de Productores de Semilla y Alimentos Nutricionales Andinos-Mushuk Yuyay (APROSANAMY), Cañar EC030304, Ecuador;
| | - Kevin Murphy
- Sustainable Seed Systems Lab, Department of Crop and Soil Sciences, College of Agricultural, Human, and Natural Resource Sciences, Washington State University, Pullman, WA 99164-6420, USA;
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15
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Colque-Little C, Abondano MC, Lund OS, Amby DB, Piepho HP, Andreasen C, Schmöckel S, Schmid K. Genetic variation for tolerance to the downy mildew pathogen Peronospora variabilis in genetic resources of quinoa (Chenopodium quinoa). BMC PLANT BIOLOGY 2021; 21:41. [PMID: 33446098 PMCID: PMC7809748 DOI: 10.1186/s12870-020-02804-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 12/16/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND Quinoa (Chenopodium quinoa Willd.) is an ancient grain crop that is tolerant to abiotic stress and has favorable nutritional properties. Downy mildew is the main disease of quinoa and is caused by infections of the biotrophic oomycete Peronospora variabilis Gaüm. Since the disease causes major yield losses, identifying sources of downy mildew tolerance in genetic resources and understanding its genetic basis are important goals in quinoa breeding. RESULTS We infected 132 South American genotypes, three Danish cultivars and the weedy relative C. album with a single isolate of P. variabilis under greenhouse conditions and observed a large variation in disease traits like severity of infection, which ranged from 5 to 83%. Linear mixed models revealed a significant effect of genotypes on disease traits with high heritabilities (0.72 to 0.81). Factors like altitude at site of origin or seed saponin content did not correlate with mildew tolerance, but stomatal width was weakly correlated with severity of infection. Despite the strong genotypic effects on mildew tolerance, genome-wide association mapping with 88 genotypes failed to identify significant marker-trait associations indicating a polygenic architecture of mildew tolerance. CONCLUSIONS The strong genetic effects on mildew tolerance allow to identify genetic resources, which are valuable sources of resistance in future quinoa breeding.
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Affiliation(s)
- Carla Colque-Little
- Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegaard Allé 13, DK-2630, Taastrup, Denmark
| | - Miguel Correa Abondano
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Fruwirthstrasse 21, D-70599, Stuttgart, Germany
| | - Ole Søgaard Lund
- Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegaard Allé 13, DK-2630, Taastrup, Denmark
| | - Daniel Buchvaldt Amby
- Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegaard Allé 13, DK-2630, Taastrup, Denmark
| | - Hans-Peter Piepho
- Institute of Crop Science, University of Hohenheim, Fruwirthstrasse 21, D-70599, Stuttgart, Germany
| | - Christian Andreasen
- Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegaard Allé 13, DK-2630, Taastrup, Denmark
| | - Sandra Schmöckel
- Institute of Crop Science, University of Hohenheim, Fruwirthstrasse 21, D-70599, Stuttgart, Germany
| | - Karl Schmid
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Fruwirthstrasse 21, D-70599, Stuttgart, Germany.
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16
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Thangavel T, Jones S, Scott JB, Livermore M, Wilson CR. Detection of Two Peronospora spp., Responsible for Downy Mildew, in Opium Poppy Seed. PLANT DISEASE 2018; 102:2277-2284. [PMID: 30211657 DOI: 10.1094/pdis-03-18-0503-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Downy mildew is a serious threat to opium poppy production globally. In recent years, two pathogen species, Peronospora somniferi and Peronospora meconopsidis, which induce distinct symptoms, have been confirmed in Australia. In order to manage the spread of these pathogens, identifying the sources of inoculum is essential. In this study, we assessed pathogen presence associated with poppy seed. We developed PCR and qPCR assays targeting the coxI and coxII gene regions, for the detection, differentiation, and quantification of P. somniferi and P. meconopsidis in poppy seed. These results were complemented and compared with direct seed histological examination and a seed washing combined with viability staining for oospore detection. The majority of seed lots from all harvest years contained detectable P. meconopsidis, the earliest (1987) predating the first official record of the disease in Tasmania (1996). In contrast, only seed lots harvested in 2012 or later contained P. somniferi, evidence of its more recent introduction. P. meconopsidis contamination was estimated to be as high as 33.04 pg DNA/g of seed and P. somniferi as high as 35.17 pg DNA/g of seed. Incidence of pathogen contamination of seeds, estimated via a group testing protocol, ranged from 0 to 9% (P. meconopsidis) or 0 to 11% (P. somniferi). Mycelia were predominately found external to the seed coat. Seed washing and viability staining demonstrated that putatively viable oospores were present in the majority of seed lots. Transmission testing confirmed both pathogens can be successfully transmitted from infested seed to infected seedling. PCR and qPCR pathogen assays were found to be reliable and offer a routine test for determining pathogen inoculum in poppy seeds.
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Affiliation(s)
- Tamilarasan Thangavel
- Tasmanian Institute of Agriculture (TIA), University of Tasmania, New Town, Tasmania 7008, Australia
| | - Suzanne Jones
- TIA, University of Tasmania, Burnie TAS 7320, Australia
| | - Jason B Scott
- TIA, University of Tasmania, Burnie TAS 7320, Australia
| | - Mark Livermore
- Tasmanian Alkaloids Pty Ltd, P.O. Box 130, Westbury, TAS 7303, Australia
| | - Calum R Wilson
- TIA, University of Tasmania, New Town, Tasmania 7008, Australia
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17
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Crandall SG, Rahman A, Quesada-Ocampo LM, Martin FN, Bilodeau GJ, Miles TD. Advances in Diagnostics of Downy Mildews: Lessons Learned from Other Oomycetes and Future Challenges. PLANT DISEASE 2018; 102:265-275. [PMID: 30673522 DOI: 10.1094/pdis-09-17-1455-fe] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Downy mildews are plant pathogens that damage crop quality and yield worldwide. Among the most severe and notorious crop epidemics of downy mildew occurred on grapes in the mid-1880s, which almost destroyed the wine industry in France. Since then, there have been multiple outbreaks on sorghum and millet in Africa, tobacco in Europe, and recent widespread epidemics on lettuce, basil, cucurbits, and spinach throughout North America. In the mid-1970s, loss of corn to downy mildew in the Philippines was estimated at US$23 million. Today, crops that are susceptible to downy mildews are worth at least $7.5 billion of the United States' economy. Although downy mildews cause devastating economic losses in the United States and globally, this pathogen group remains understudied because they are difficult to culture and accurately identify. Early detection of downy mildews in the environment is critical to establish pathogen presence and identity, determine fungicide resistance, and understand how pathogen populations disperse. Knowing when and where pathogens emerge is also important for identifying critical control points to restrict movement and to contain populations. Reducing the spread of pathogens also decreases the likelihood of sexual recombination events and discourages the emergence of novel virulent strains. A major challenge in detecting downy mildews is that they are obligate pathogens and thus cannot be cultured in artificial media to identify and maintain specimens. However, advances in molecular detection techniques hold promise for rapid and in some cases, relatively inexpensive diagnosis. In this article, we discuss recent advances in diagnostic tools that can be used to detect downy mildews. First, we briefly describe downy mildew taxonomy and genetic loci used for detection. Next, we review issues encountered when identifying loci and compare various traditional and novel platforms for diagnostics. We discuss diagnosis of downy mildew traits and issues to consider when detecting this group of organisms in different environments. We conclude with challenges and future directions for successful downy mildew detection.
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Affiliation(s)
- Sharifa G Crandall
- California State University Monterey Bay, School of Natural Sciences, Seaside, CA, 93955
| | - Alamgir Rahman
- North Carolina State University, Department of Plant Pathology, Raleigh, NC, 27695
| | | | - Frank N Martin
- USDA-ARS, Crop Improvement and Protection Research Unit, Salinas, CA, 93905
| | | | - Timothy D Miles
- California State University Monterey Bay, School of Natural Sciences, Seaside, CA, 93955
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18
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Withers S, Gongora-Castillo E, Gent D, Thomas A, Ojiambo PS, Quesada-Ocampo LM. Using Next-Generation Sequencing to Develop Molecular Diagnostics for Pseudoperonospora cubensis, the Cucurbit Downy Mildew Pathogen. PHYTOPATHOLOGY 2016; 106:1105-1116. [PMID: 27314624 DOI: 10.1094/phyto-10-15-0260-fi] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Advances in next-generation sequencing (NGS) allow for rapid development of genomics resources needed to generate molecular diagnostics assays for infectious agents. NGS approaches are particularly helpful for organisms that cannot be cultured, such as the downy mildew pathogens, a group of biotrophic obligate oomycetes that infect crops of economic importance. Unlike most downy mildew pathogens that are highly host-specific, Pseudoperonospora cubensis causes disease on a broad range of crops belonging to the family Cucurbitaceae. In this study, we identified candidate diagnostic markers for P. cubensis by comparing NGS data from a diverse panel of P. cubensis and P. humuli isolates, two very closely related oomycete species. P. cubensis isolates from diverse hosts and geographical regions in the United States were selected for sequencing to ensure that candidates were conserved in P. cubensis isolates infecting different cucurbit hosts. Genomic regions unique to and conserved in P. cubensis isolates were identified through bioinformatics. These candidate regions were then validated using PCR against a larger collection of isolates from P. cubensis, P. humuli, and other oomycetes. Overall seven diagnostic markers were found to be specific to P. cubensis. These markers could be used for pathogen diagnostics on infected tissue, or adapted for monitoring airborne inoculum with real-time PCR and spore traps.
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Affiliation(s)
- S Withers
- First, second, fourth, fifth, and sixth authors: Department of Plant Pathology, North Carolina State University, Raleigh 27695-7616; third author: U.S. Department of Agriculture-Agricultural Research Service, Forage Seed and Cereal Research Unit, and Oregon State University, Corvallis 97331; and fourth and fifth authors: Center for Integrated Fungal Research, North Carolina State University, Raleigh 27695-7567
| | - E Gongora-Castillo
- First, second, fourth, fifth, and sixth authors: Department of Plant Pathology, North Carolina State University, Raleigh 27695-7616; third author: U.S. Department of Agriculture-Agricultural Research Service, Forage Seed and Cereal Research Unit, and Oregon State University, Corvallis 97331; and fourth and fifth authors: Center for Integrated Fungal Research, North Carolina State University, Raleigh 27695-7567
| | - D Gent
- First, second, fourth, fifth, and sixth authors: Department of Plant Pathology, North Carolina State University, Raleigh 27695-7616; third author: U.S. Department of Agriculture-Agricultural Research Service, Forage Seed and Cereal Research Unit, and Oregon State University, Corvallis 97331; and fourth and fifth authors: Center for Integrated Fungal Research, North Carolina State University, Raleigh 27695-7567
| | - A Thomas
- First, second, fourth, fifth, and sixth authors: Department of Plant Pathology, North Carolina State University, Raleigh 27695-7616; third author: U.S. Department of Agriculture-Agricultural Research Service, Forage Seed and Cereal Research Unit, and Oregon State University, Corvallis 97331; and fourth and fifth authors: Center for Integrated Fungal Research, North Carolina State University, Raleigh 27695-7567
| | - P S Ojiambo
- First, second, fourth, fifth, and sixth authors: Department of Plant Pathology, North Carolina State University, Raleigh 27695-7616; third author: U.S. Department of Agriculture-Agricultural Research Service, Forage Seed and Cereal Research Unit, and Oregon State University, Corvallis 97331; and fourth and fifth authors: Center for Integrated Fungal Research, North Carolina State University, Raleigh 27695-7567
| | - L M Quesada-Ocampo
- First, second, fourth, fifth, and sixth authors: Department of Plant Pathology, North Carolina State University, Raleigh 27695-7616; third author: U.S. Department of Agriculture-Agricultural Research Service, Forage Seed and Cereal Research Unit, and Oregon State University, Corvallis 97331; and fourth and fifth authors: Center for Integrated Fungal Research, North Carolina State University, Raleigh 27695-7567
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19
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Herrera Paredes S, Lebeis SL. Giving back to the community: microbial mechanisms of plant–soil interactions. Funct Ecol 2016. [DOI: 10.1111/1365-2435.12684] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sur Herrera Paredes
- Department of Biology Howard Hughes Medical Institute, Curriculum in Bioinformatics and Computational Biology University of North Carolina Chapel Hill North Carolina 27599‐3280 USA
| | - Sarah L. Lebeis
- Department of Microbiology University of Tennessee Knoxville Tennessee 37996‐0845 USA
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20
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Choi YJ, Beakes G, Glockling S, Kruse J, Nam B, Nigrelli L, Ploch S, Shin HD, Shivas RG, Telle S, Voglmayr H, Thines M. Towards a universal barcode of oomycetes--a comparison of the cox1 and cox2 loci. Mol Ecol Resour 2015; 15:1275-88. [PMID: 25728598 PMCID: PMC5736100 DOI: 10.1111/1755-0998.12398] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 01/28/2015] [Accepted: 02/02/2015] [Indexed: 11/30/2022]
Abstract
Oomycetes are a diverse group of eukaryotes in terrestrial, limnic and marine habitats worldwide and include several devastating plant pathogens, for example Phytophthora infestans (potato late blight). The cytochrome c oxidase subunit 2 gene (cox2) has been widely used for identification, taxonomy and phylogeny of various oomycete groups. However, recently the cox1 gene was proposed as a DNA barcode marker instead, together with ITS rDNA. The cox1 locus has been used in some studies of Pythium and Phytophthora, but has rarely been used for other oomycetes, as amplification success of cox1 varies with different lineages and sample ages. To determine which out of cox1 or cox2 is best suited as a universal oomycete barcode, we compared these two genes in terms of (i) PCR efficiency for 31 representative genera, as well as for historic herbarium specimens, and (ii) sequence polymorphism, intra- and interspecific divergence. The primer sets for cox2 successfully amplified all oomycete genera tested, while cox1 failed to amplify three genera. In addition, cox2 exhibited higher PCR efficiency for historic herbarium specimens, providing easier access to barcoding-type material. Sequence data for several historic type specimens exist for cox2, but there are none for cox1. In addition, cox2 yielded higher species identification success, with higher interspecific and lower intraspecific divergences than cox1. Therefore, cox2 is suggested as a partner DNA barcode along with ITS rDNA instead of cox1. The cox2-1 spacer could be a useful marker below species level. Improved protocols and universal primers are presented for all genes to facilitate future barcoding efforts.
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Affiliation(s)
- Young-Joon Choi
- Institute of Ecology, Evolution and Diversity, Faculty of Biosciences, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - Gordon Beakes
- Division of Biology, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | | | - Julia Kruse
- Institute of Ecology, Evolution and Diversity, Faculty of Biosciences, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - Bora Nam
- Institute of Ecology, Evolution and Diversity, Faculty of Biosciences, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - Lisa Nigrelli
- Institute of Ecology, Evolution and Diversity, Faculty of Biosciences, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - Sebastian Ploch
- Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Institute of Population Genetics,University of Duesseldorf, Universtitätsstr. 1, D-40225 Duesseldorf, Germany
| | - Hyeon-Dong Shin
- Division of Environmental Science and Ecological Engineering, Korea University, 136-701 Seoul, South Korea
| | - Roger G. Shivas
- Plant Pathology Herbarium, Biosecurity Queensland, Ecosciences Precinct, GPO Box 267, Brisbane, 4001 Queensland, Australia
| | - Sabine Telle
- Institute of Ecology, Evolution and Diversity, Faculty of Biosciences, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - Hermann Voglmayr
- Division of Systematic and Evolutionary Botany, Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Wien, Austria
- Department of Forest and Soil Sciences, Institute of Forest Entomology, Forest Pathology and Forest Protection, BOKU-University of Natural Resources and Life Sciences, Peter Jordan-Straße 82, 1190 Wien, Austria
| | - Marco Thines
- Institute of Ecology, Evolution and Diversity, Faculty of Biosciences, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
- Integrative Fungal Research Cluster (IPF), Georg-Voigt-Str. 14-16, D-60325 Frankfurt am Main, Germany
- Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
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Rioux RA, Shultz J, Garcia M, Willis DK, Casler M, Bonos S, Smith D, Kerns J. Sclerotinia homoeocarpa overwinters in turfgrass and is present in commercial seed. PLoS One 2014; 9:e110897. [PMID: 25333928 PMCID: PMC4204931 DOI: 10.1371/journal.pone.0110897] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Accepted: 09/25/2014] [Indexed: 11/18/2022] Open
Abstract
Dollar spot is the most economically important disease of amenity turfgrasses in the United States, yet little is known about the source of primary inoculum for this disease. With the exception of a few isolates from the United Kingdom, Sclerotinia homoeocarpa, the causal agent of dollar spot, does not produce spores. Consequently, it was assumed that overwintering of this organism in soil, thatch, and plant debris provides primary inoculum for dollar spot epidemics. Overwintering of S. homoeocarpa in roots and shoots of symptomatic and asymptomatic creeping bentgrass turfgrass was quantified over the course of a three-year field experiment. Roots did not consistently harbor S. homoeocarpa, whereas S. homoeocarpa was isolated from 30% of symptomatic shoots and 10% of asymptomatic shoots in the spring of two out of three years. The presence of stroma-like pathogen material on leaf blades was associated with an increase in S. homoeocarpa isolation and colony diameter at 48 hpi. Commercial seed has also been hypothesized to be a potential source of initial inoculum for S. homoeocarpa. Two or more commercial seed lots of six creeping bentgrass cultivars were tested for contamination with S. homoeocarpa using culture-based and molecular detection methods. A viable, pathogenic isolate of S. homoeocarpa was isolated from one commercial seed lot and contamination of this lot was confirmed with nested PCR using S. homoeocarpa specific primers. A sensitive nested PCR assay detected S. homoeocarpa contamination in eight of twelve (75%) commercial seed lots. Seed source, but not cultivar or resistance to dollar spot, influenced contamination by S. homoeocarpa. Overall, this research suggests that seeds are a potential source of initial inoculum for dollar spot epidemics and presents the need for further research in this area.
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Affiliation(s)
- Renée A. Rioux
- Department of Plant of Plant Path Pathology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- NewLeaf Symbiotics, BRDG Park, St. Louis, Missouri, United States of America
| | - Jeanette Shultz
- Department of Plant of Plant Path Pathology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Neuroscience, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Michelle Garcia
- Department of Plant of Plant Path Pathology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Biological Sciences, University of Texas El-Paso, El Paso, Texas, United States of America
| | - David Kyle Willis
- Department of Plant of Plant Path Pathology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Michael Casler
- USDA-ARS, U.S. Dairy Forage Research Center, Madison, Wisconsin, United States of America
| | - Stacy Bonos
- Department of Plant Science, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Damon Smith
- Department of Plant of Plant Path Pathology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - James Kerns
- Department of Plant of Plant Path Pathology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Plant Pathology, North Carolina State University, Raleigh, North Carolina, United States of America
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22
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Cohen Y, Rubin AE, Galperin M, Ploch S, Runge F, Thines M. Seed transmission of Pseudoperonospora cubensis. PLoS One 2014; 9:e109766. [PMID: 25329308 PMCID: PMC4201460 DOI: 10.1371/journal.pone.0109766] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 09/05/2014] [Indexed: 11/28/2022] Open
Abstract
Pseudoperonospora cubensis, an obligate biotrophic oomycete causing devastating foliar disease in species of the Cucurbitaceae family, was never reported in seeds or transmitted by seeds. We now show that P. cubensis occurs in fruits and seeds of downy mildew-infected plants but not in fruits or seeds of healthy plants. About 6.7% of the fruits collected during 2012-2014 have developed downy mildew when homogenized and inoculated onto detached leaves and 0.9% of the seeds collected developed downy mildew when grown to the seedling stage. This is the first report showing that P. cubensis has become seed-transmitted in cucurbits. Species-specific PCR assays showed that P. cubensis occurs in ovaries, fruit seed cavity and seed embryos of cucurbits. We propose that international trade of fruits or seeds of cucurbits might be associated with the recent global change in the population structure of P. cubensis.
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Affiliation(s)
- Yigal Cohen
- Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Avia E. Rubin
- Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Mariana Galperin
- Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Sebastian Ploch
- Biodiversity and Climate Research Centre, Frankfurt, Germany
| | - Fabian Runge
- Institute of Botany (210), University of Hohenheim, Stuttgart, Germany
| | - Marco Thines
- Biodiversity and Climate Research Centre, Frankfurt, Germany
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