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Liu J, Liang M, Lin T, Zhao Q, Wang H, Yang S, Guo Q, Wang X, Guo H, Cui L, Yan Y, Hieno A, Kageyama K, Suga H, Li M. A LAMP-Based Toolbox Developed for Detecting the Major Pathogens Affecting the Production and Quality of the Chinese Medicinal Crop Aconitum carmichaelii. PLANT DISEASE 2023; 107:658-666. [PMID: 35852903 DOI: 10.1094/pdis-05-22-1092-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Aconitum carmichaelii Debeaux is a traditional Chinese medicinal herb that has been utilized for approximately 2,000 years. However, as cultivation has increased, there have been more reports of A. carmichaelii infections caused by four major pathogenic fungal species, Fusarium oxysporum, F. solani, Mucor circinelloides, and Sclerotium rolfsii, resulting in increased disease incidences and limited production and quality. To detect these infections, we developed a LAMP-based toolbox in this study. The cytochrome c oxidase subunit 1 (cox1) gene, translation elongation factor-1α (EF-1α), internal transcribed spacer (ITS) regions of rDNA, and alcohol dehydrogenase 1 (ADH1) gene, respectively, were used to design species-specific LAMP primer sets for F. oxysporum, F. solani, S. rolfsii, and M. circinelloides. The results showed that the LAMP-based toolbox was effective at detecting pathogens in soil and plant materials. We also used this toolbox to investigate pathogen infection in the main planting regions of A. carmichaelii. Before harvesting, F. oxysporum, M. circinelloides, and S. rolfsii were commonly found in the planting fields and in infected A. carmichaelii plants. Therefore, the toolbox we developed will be useful for tracking these infections, as well as for disease control in A. carmichaelii.
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Affiliation(s)
- Jingzhe Liu
- The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education (Shaanxi Normal University), Xi'an, Shaanxi 710119, P.R. China
| | - Mengyi Liang
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Tao Lin
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Qing Zhao
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Huiqin Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Shunyuan Yang
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Qian Guo
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Xinyi Wang
- The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education (Shaanxi Normal University), Xi'an, Shaanxi 710119, P.R. China
| | - Hua Guo
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Langjun Cui
- The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education (Shaanxi Normal University), Xi'an, Shaanxi 710119, P.R. China
| | - Yaping Yan
- The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education (Shaanxi Normal University), Xi'an, Shaanxi 710119, P.R. China
| | - Ayaka Hieno
- River Basin Research Center, Gifu University, Gifu 501-1193, Japan
| | - Koji Kageyama
- River Basin Research Center, Gifu University, Gifu 501-1193, Japan
| | - Haruhisa Suga
- Life Science Research Center, Gifu University, Gifu 501-1193, Japan
| | - Mingzhu Li
- The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education (Shaanxi Normal University), Xi'an, Shaanxi 710119, P.R. China
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
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2
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Li M, Guo Q, Liang M, Zhao Q, Lin T, Gao H, Hieno A, Kageyama K, Zhang X, Cui L, Yan Y, Qiang Y. Population Dynamics, Effective Soil Factors, and LAMP Detection Systems for Phytophthora Species Associated with Kiwifruit Diseases in China. PLANT DISEASE 2022; 106:846-853. [PMID: 34661453 DOI: 10.1094/pdis-04-21-0852-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
China has the largest area of kiwifruit production in the world. Pathogens associated with root diseases of kiwi trees have not been investigated extensively. In this research, three Phytophthora species, Phytophthora cactorum, Phytophthora cinnamomi, and Phytophthora lateralis, which are pathogenic to kiwi trees in the main planting areas of China, were studied. The population densities of these species in 128 soil samples from 32 kiwi orchards in 2017 and 2018 were measured using multiplex real-time quantitative PCR based on the ras-related protein gene Ypt1. P. cactorum was the most widely distributed of the three species in orchards of the Zhouzhi and Meixian prefectures. We used redundancy analysis to examine soil factors in the kiwi orchards to understand their effects on the population densities of the Phytophthora species. The redundancy analysis indicated that soil temperature and pH were significantly correlated with the abundance of P. cactorum and P. cinnamomi. In addition, two loop-mediated isothermal amplification detection systems for P. cactorum were developed based on the tigA gene. The color-change detection system proved to be accurate, sensitive, and faster than quantitative PCR. The results of this study, along with the loop-mediated isothermal amplification detection systems, will be of great use in the control of Phytophthora diseases for the production of kiwifruits in China.
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Affiliation(s)
- Mingzhu Li
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, Shaanxi Normal University, Xi'an 710119, China
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Qian Guo
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Mengyi Liang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Qing Zhao
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Tao Lin
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Han Gao
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Ayaka Hieno
- River Basin Research Center, Gifu University, Gifu 501-1193, Japan
| | - Koji Kageyama
- River Basin Research Center, Gifu University, Gifu 501-1193, Japan
| | - Xin Zhang
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, Shaanxi Normal University, Xi'an 710119, China
| | - Langjun Cui
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, Shaanxi Normal University, Xi'an 710119, China
| | - Yaping Yan
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, Shaanxi Normal University, Xi'an 710119, China
| | - Yi Qiang
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, Shaanxi Normal University, Xi'an 710119, China
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3
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Li M, Hieno A, Motohashi K, Suga H, Kageyama K. Pythium intermedium, a species complex consisting of three phylogenetic species found in cool-temperate forest ecosystems. Fungal Biol 2021; 125:1017-1025. [PMID: 34776229 DOI: 10.1016/j.funbio.2021.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 06/07/2021] [Accepted: 07/15/2021] [Indexed: 10/20/2022]
Abstract
Pythium intermedium plays a vital role in the carbon cycle of cool-temperate forests and is widely distributed in Japan's forest soils. In this study, we performed a phylogenetic analysis of the P. intermedium species complex using DNA sequences from multiple loci. The study included 35 isolates from cool-temperate forest soils, seven known P. intermedium isolates, and six known Pythium attrantheridium isolates. We also performed morphological observations and mating tests. Our results showed that all the isolates formed one large clade but were divided into three subclades. Furthermore, we observed many mating reactions between isolates from different subclades, including between P. attrantheridium and P. intermedium. Therefore, we suggest that P. intermedium, P. attrantheridium, and another phylogenetic species belong to one species complex. This is the first report of a species complex within P. intermedium and will be helpful in understanding the evolution of Pythium species in natural ecosystems.
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Affiliation(s)
- Mingzhu Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China; River Basin Research Center, Gifu University, Gifu, 501-1193, Japan.
| | - Ayaka Hieno
- River Basin Research Center, Gifu University, Gifu, 501-1193, Japan
| | - Keiichi Motohashi
- Faculty of Regional Environment Science, Tokyo University of Agriculture, Tokyo, 156-8502, Japan
| | - Haruhisa Suga
- Life Science Research Center, Gifu University, Gifu, 501-1193, Japan
| | - Koji Kageyama
- River Basin Research Center, Gifu University, Gifu, 501-1193, Japan
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Arora H, Sharma A, Sharma S, Haron FF, Gafur A, Sayyed RZ, Datta R. Pythium Damping-Off and Root Rot of Capsicum annuum L.: Impacts, Diagnosis, and Management. Microorganisms 2021; 9:microorganisms9040823. [PMID: 33924471 PMCID: PMC8069622 DOI: 10.3390/microorganisms9040823] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 04/07/2021] [Accepted: 04/09/2021] [Indexed: 11/16/2022] Open
Abstract
Capsicum annuum L. is a significant horticulture crop known for its pungent varieties and used as a spice. The pungent character in the plant, known as capsaicinoid, has been discovered to have various health benefits. However, its production has been affected due to various exogenous stresses, including diseases caused by a soil-borne pathogen, Pythium spp. predominantly affecting the Capsicum plant in younger stages and causing damping-off, this pathogen can incite root rot in later plant growth stages. Due to the involvement of multiple Pythium spp. and their capability to disperse through various routes, their detection and diagnosis have become crucial. However, the quest for a point-of-care technology is still far from over. The use of an integrated approach with cultural and biological techniques for the management of Pythium spp. can be the best and most sustainable alternative to the traditionally used and hazardous chemical approach. The lack of race-specific resistance genes against Pythium spp. can be compensated with the candidate quantitative trait loci (QTL) genes in C. annuum L. This review will focus on the epidemiological factors playing a major role in disease spread, the currently available diagnostics in species identification, and the management strategies with a special emphasis on Pythium spp. causing damping-off and root rot in different cultivars of C. annuum L.
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Affiliation(s)
- Himanshu Arora
- Centre for Rural Development and Technology, Indian Institute of Technology, New Delhi 110016, India; (H.A.); (S.S.)
| | - Abhishek Sharma
- Amity Food and Agriculture Foundation, Amity University, Noida 201313, Uttar Pradesh, India
- Correspondence: (A.S.); (R.Z.S.); (R.D.)
| | - Satyawati Sharma
- Amity Food and Agriculture Foundation, Amity University, Noida 201313, Uttar Pradesh, India
| | - Farah Farhanah Haron
- Pest and Disease Management Program, Horticulture Research Center, Malaysian Agriculture Research and Development Institute (MARDI), Persiaran MARDI-UPM, Serdang 43400, Selangor, Malaysia;
| | - Abdul Gafur
- Sinarmas Forestry Corporate Research and Development, Perawang 28772, Indonesia;
| | - R. Z. Sayyed
- Department of Microbiology, PSGVP Mandal’s Arts, Science, Commerce College, Shahada 425409, Maharashtra, India
- Correspondence: (A.S.); (R.Z.S.); (R.D.)
| | - Rahul Datta
- Department of Geology and Pedology, Mendel University in Brno, 613 00 Brno-sever-Černá Pole, Czech Republic
- Correspondence: (A.S.); (R.Z.S.); (R.D.)
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5
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Xu M, Samworth RJ. High-dimensional nonparametric density estimation via symmetry and shape constraints. Ann Stat 2021. [DOI: 10.1214/20-aos1972] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Min Xu
- Department of Statistics, Rutgers University
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6
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Van der Heyden H, Bilodeau GJ, Carisse O, Charron JB. Monitoring of Peronospora destructor Primary and Secondary Inoculum by Real-Time qPCR. PLANT DISEASE 2020; 104:3183-3191. [PMID: 33044917 DOI: 10.1094/pdis-03-20-0687-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Onion downy mildew (ODM), caused by Peronospora destructor, is a serious threat for onion growers worldwide. In southwestern Québec, Canada, a steady increase in occurrence of ODM has been observed since the mid-2000s. On onion, P. destructor can develop local and systemic infections producing numerous sporangia which act as initial inoculum locally and also for neighboring areas. It also produces oospores capable of surviving in soils and tissues for a prolonged period of time. A recent study showed that ODM epidemics are strongly associated with weather conditions related to production and survival of overwintering inoculum, stressing the need to understand the role of primary (initial) and secondary inoculum. However, P. destructor is an obligate biotrophic pathogen, which complicates the study of inoculum sources. This study aimed at developing a molecular assay specific to P. destructor, allowing its quantification in environmental samples. In this study, a reliable and sensitive hydrolysis probe-based assay multiplexed with an internal control was developed on the internal transcribed spacer (ITS) region to quantify soil- and airborne inoculum of P. destructor. The assay specificity was tested against 17 isolates of P. destructor obtained from different locations worldwide, other members of the order Peronosporales, and various onion pathogens. Validation with artificially inoculated soil and air samples suggested a sensitivity of less than 10 sporangia g-1 of dry soil and 1 sporangium m-3 of air. Validation with environmental air samples shows a linear relationship between microscopic and real-time quantitative PCR counts. In naturally infested soils, inoculum ranged from 0 to 162 sporangia equivalent g-1 of dry soil, which supported the hypothesis of overwintering under northern climates. This assay will be useful for primary and secondary inoculum monitoring to help characterize ODM epidemiology and could be used for daily tactical and short-term strategic decision-making.
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Affiliation(s)
- Hervé Van der Heyden
- Cie de Recherche Phytodata, 291 rue de la coopérative, Sherrington, QC, Canada
- Department of Plant Science, McGill University, Macdonald Campus, 21,111 Lakeshore Road, Ste-Anne-de-Bellevue, QC, Canada
| | | | - Odile Carisse
- Agriculture and Agri-Food Canada, 430 Boulevard Gouin, St-Jean-sur-Richelieu, QC, Canada
| | - Jean-Benoit Charron
- Department of Plant Science, McGill University, Macdonald Campus, 21,111 Lakeshore Road, Ste-Anne-de-Bellevue, QC, Canada
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7
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Si Ammour M, Bove F, Toffolatti SL, Rossi V. A Real-Time PCR Assay for the Quantification of Plasmopara viticola Oospores in Grapevine Leaves. FRONTIERS IN PLANT SCIENCE 2020; 11:1202. [PMID: 32849746 PMCID: PMC7426466 DOI: 10.3389/fpls.2020.01202] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 07/24/2020] [Indexed: 05/28/2023]
Abstract
Grapevine downy mildew caused by Plasmopara viticola is one of the most important diseases in vineyards. Oospores that overwinter in the leaf litter above the soil are the sole source of inoculum for primary infections of P. viticola; in addition to triggering the first infections in the season, the oospores in leaf litter also contribute to disease development during the season. In the current study, a quantitative polymerase chain reaction (qPCR) method that was previously developed to detect P. viticola DNA in fresh grapevine leaves was assessed for its ability to quantify P. viticola oospores in diseased, senescent grapevine leaves. The qPCR assay was specific to P. viticola and sensitive to decreasing amounts of both genomic DNA and numbers of P. viticola oospores used to generate qPCR standard curves. When the qPCR assay was compared to microscope counts of oospores in leaves with different levels of P. viticola infestation, a strong linear relationship (R2 = 0.70) was obtained between the numbers of P. viticola oospores per gram of leaves as determined by qPCR vs. microscopic observation. Unlike microscopic observation, the qPCR assay was able to detect significant differences between leaf samples with a low level of oospore infestation (25% infested leaves and 75% non-infested leaves) vs. samples without infestation, and this ability was not influenced by the weight of the leaf sample. The results indicate that the qPCR method is sensitive and provides reliable estimates of the number of P. viticola oospores in grapevine leaves. Additional research is needed to determine whether the qPCR method is useful for quantifying P. viticola oospores in grapevine leaf litter.
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Affiliation(s)
- Melissa Si Ammour
- Department of Sustainable Crop Production, DI.PRO.VE.S., Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Federica Bove
- Department of Sustainable Crop Production, DI.PRO.VE.S., Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Silvia Laura Toffolatti
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio e Agroenergia (DiSAA), Università degli Studi di Milano, Milano, Italy
| | - Vittorio Rossi
- Department of Sustainable Crop Production, DI.PRO.VE.S., Università Cattolica del Sacro Cuore, Piacenza, Italy
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Ray M, Dash S, Achary KG, Nayak S, Singh S. Development and evaluation of polyclonal antibodies for detection of Pythium aphanidermatum and Fusarium oxysporum in ginger. FOOD AGR IMMUNOL 2017. [DOI: 10.1080/09540105.2017.1365820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Monalisa Ray
- Centre for Biotechnology, Siksha “O” Anusandhan University, Bhubaneswar, India
| | - Swagatika Dash
- Centre for Biotechnology, Siksha “O” Anusandhan University, Bhubaneswar, India
| | | | - Sanghamitra Nayak
- Centre for Biotechnology, Siksha “O” Anusandhan University, Bhubaneswar, India
| | - Shikha Singh
- Centre for Biotechnology, Siksha “O” Anusandhan University, Bhubaneswar, India
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Saravanakumar K, Fan L, Fu K, Yu C, Wang M, Xia H, Sun J, Li Y, Chen J. Cellulase from Trichoderma harzianum interacts with roots and triggers induced systemic resistance to foliar disease in maize. Sci Rep 2016; 6:35543. [PMID: 27830829 PMCID: PMC5103226 DOI: 10.1038/srep35543] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 09/29/2016] [Indexed: 01/06/2023] Open
Abstract
Trichoderma harzianum is well known to exhibit induced systemic resistance (ISR) to Curvularia leaf spot. We previously reported that a C6 zinc finger protein (Thc6) is responsible for a major contribution to the ISR to the leaf disease, but the types of effectors and the signals mediated by Thc6 from Trichoderma are unclear. In this work, we demonstrated that two hydrolases, Thph1 and Thph2, from T. harzianum were regulated by Thc6. Furthermore, an electrophoretic mobility shift assay (EMSA) study revealed that Thc6 regulated mRNA expression by binding to GGCTAA and GGCTAAA in the promoters of the Thph1 and Thph2 genes, respectively. Moreover, the Thph1 and Thph2 proteins triggered the transient production of reactive oxygen species (ROS) and elevated the free cytosolic calcium levels in maize leaf. Furthermore, the genes related to the jasmonate/ethylene signaling pathway were up-regulated in the wild-type maize strain. However, the ΔThph1- or ΔThph2-deletion mutants could not activate the immune defense-related genes in maize to protect against leaf disease. Therefore, we conclude that functional Thph1 and Thph2 may be required in T. harzianum to activate ISR in maize.
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Affiliation(s)
- Kandasamy Saravanakumar
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P.R. China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, P.R. China
- Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Shanghai, P.R. China
| | - Lili Fan
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P.R. China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, P.R. China
- Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Shanghai, P.R. China
| | - Kehe Fu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P.R. China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, P.R. China
- Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Shanghai, P.R. China
| | - Chuanjin Yu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P.R. China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, P.R. China
- Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Shanghai, P.R. China
| | - Meng Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P.R. China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, P.R. China
- Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Shanghai, P.R. China
| | - Hai Xia
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P.R. China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, P.R. China
- Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Shanghai, P.R. China
| | - Jianan Sun
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P.R. China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, P.R. China
- Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Shanghai, P.R. China
| | - Yaqian Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P.R. China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, P.R. China
- Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Shanghai, P.R. China
| | - Jie Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, P.R. China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, P.R. China
- Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, Shanghai, P.R. China
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10
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Alcala AVC, Paulitz TC, Schroeder KL, Porter LD, Derie ML, du Toit LJ. Pythium Species Associated with Damping-off of Pea in Certified Organic Fields in the Columbia Basin of Central Washington. PLANT DISEASE 2016; 100:916-925. [PMID: 30686151 DOI: 10.1094/pdis-07-15-0774-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Organic vegetable production accounted for 19% of the total organic acreage in Washington State in 2013, with 1,700 ha of certified organic vegetable pea. However, production is challenged constantly with the threat of poor emergence after planting due to damping-off caused by Pythium spp. A survey of Pythium spp. in organic vegetable production areas of the semiarid Columbia Basin of central Washington was carried out in fall 2009 to identify species associated with damping-off during early spring planting. Of 305 isolates baited from soil sampled from 37 certified organic fields, 264 were identified to 16 Pythium spp. by sequencing the internal transcribed spacer region of ribosomal DNA. A soil DNA-CFU regression curve was developed using real-time quantitative polymerase chain reaction assays for each of the three predominant pathogenic species (Pythium abappressorium, the P. irregulare complex, and P. ultimum var. ultimum) found in soil sampled from the 37 fields. The P. irregulare complex, P. abappressorium, and P. ultimum var. ultimum were detected in 57, 78, and 100% of the fields sampled, respectively. A regression analysis was used to determine that P. ultimum var. ultimum ranged from 14 to 332 CFU/g of soil in the 37 fields, the P. irregulare complex ranged from 25 to 228 CFU/g of soil, and P. abappressorium DNA was below the quantifiable limit. In summary, P. ultimum var. ultimum was the most prevalent pathogenic Pythium sp. detected in certified organic fields in the semiarid Columbia Basin of central Washington but multiple Pythium spp. may be associated with damping-off in cool and wet, early spring planting conditions.
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Affiliation(s)
- Ana Vida C Alcala
- Washington State University Mount Vernon NWREC, Mount Vernon 98273-4768
| | - Timothy C Paulitz
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Pullman, WA 99164-6430
| | - Kurtis L Schroeder
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Pullman, WA 99164-6430
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11
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Li M, Ishiguro Y, Kageyama K, Zhu Z. A simple method for normalization of DNA extraction to improve the quantitative detection of soil-borne plant pathogenic oomycetes by real-time PCR. Lett Appl Microbiol 2015; 61:179-85. [PMID: 25970140 DOI: 10.1111/lam.12441] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 05/04/2015] [Accepted: 05/06/2015] [Indexed: 11/28/2022]
Abstract
UNLABELLED Most of the current research into the quantification of soil-borne pathogenic oomycetes lacks determination of DNA extraction efficiency, probably leading to an incorrect estimation of DNA quantity. In this study, we developed a convenient method by using a 100 bp artificially synthesized DNA sequence derived from the mitochondrion NADH dehydrogenase subunit 2 gene of Thunnus thynnus as a control to determine the DNA extraction efficiency. The control DNA was added to soils and then co-extracted along with soil genomic DNA. DNA extraction efficiency was determined by the control DNA. Two different DNA extraction methods were compared and evaluated using different types of soils, and the commercial kit was proved to give more consistent results. We used the control DNA combined with real-time PCR to quantify the oomycete DNAs from 12 naturally infested soils. Detectable target DNA concentrations were three to five times higher after normalization. Our tests also showed that the extraction efficiencies varied on a sample-to-sample basis and were <50%. Therefore, the method introduced here is simple and useful for the accurate quantification of soil-borne pathogenic oomycetes. SIGNIFICANCE AND IMPACT OF THE STUDY Oomycetes include many important plant pathogens. Accurate quantification of these pathogens is essential in the management of diseases. This study reports an easy method utilizing an external DNA control for the normalization of DNA extraction by real-time PCR. By combining two different efficient soil DNA extraction methods, the developed quantification method dramatically improved the results. This study also proves that the developed normalization method is necessary and useful for the accurate quantification of soil-borne plant pathogenic oomycetes.
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Affiliation(s)
- M Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Y Ishiguro
- River Basin Research Center, Gifu University, Gifu, Japan
| | - K Kageyama
- River Basin Research Center, Gifu University, Gifu, Japan
| | - Z Zhu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
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Biasi A, Martin F, Schena L. Identification and validation of polymorphic microsatellite loci for the analysis of Phytophthora nicotianae populations. J Microbiol Methods 2015; 110:61-7. [PMID: 25601792 DOI: 10.1016/j.mimet.2015.01.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 01/13/2015] [Accepted: 01/14/2015] [Indexed: 11/25/2022]
Abstract
A large number of SSR loci were screened in the genomic assemblies of 14 different isolates of Phytophthora nicotianae and primers were developed for amplification of 17 markers distributed among different contigs. These loci were highly polymorphic and amplified from genetically distant isolates of the pathogen. Among these, nine were further validated using a multiplexed genotyping assay with differentially labeled primers (FAM or HEX) to allow for duplex PCR amplification. The use of reverse primers with a 5' PIG tail was important to increase the quality and reliability of the analyses. A total of 46 alleles were detected in 5 tester isolates of P. nicotianae representing the breadth of diversity in the species. Furthermore, a high incidence of heterozygosity was determined with two alleles detected in 67% of the primer/isolate combinations. Three different alleles where detected for a single locus/isolate combination, indicating variation in ploidy. These markers represent a valuable new tool for the characterization of populations of P. nicotianae.
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Affiliation(s)
- Antonio Biasi
- Dipartimento di Agraria, Università degli Studi Mediterranea, Località Feo di Vito, 89122 Reggio Calabria, Italy
| | - Frank Martin
- United States Department of Agriculture-Agricultural Research Service, 1636 East Alisal Street, 93905 Salinas, CA, United States
| | - Leonardo Schena
- Dipartimento di Agraria, Università degli Studi Mediterranea, Località Feo di Vito, 89122 Reggio Calabria, Italy.
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Schroeder KL, Martin FN, de Cock AWAM, Lévesque CA, Spies CFJ, Okubara PA, Paulitz TC. Molecular Detection and Quantification of Pythium Species: Evolving Taxonomy, New Tools, and Challenges. PLANT DISEASE 2013; 97:4-20. [PMID: 30722255 DOI: 10.1094/pdis-03-12-0243-fe] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The genus Pythium is one of the most important groups of soilborne plant pathogens, present in almost every agricultural soil and attacking the roots of thousands of hosts, reducing crop yield and quality. Most species are generalists, necrotrophic pathogens that infect young juvenile tissue. In fact, Cook and Veseth have called Pythium the "common cold" of wheat, because of its chronic nature and ubiquitous distribution. Where Pythium spp. are the cause of seedling damping-off or emergence reduction, the causal agent can easily be identified based on symptoms and culturing. In more mature plants, however, infection by Pythium spp. is more difficult to diagnose, because of the nonspecific symptoms that could have abiotic causes such as nutrient deficiencies or be due to other root rotting pathogens. Molecular methods that can accurately identify and quantify this important group are needed for disease diagnosis and management recommendations and to better understand the epidemiology and ecology of this important group. The purpose of this article is to outline the current state-of-the-art in the detection and quantification of this important genus. In addition, we will introduce the reader to new changes in the taxonomy of this group.
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Affiliation(s)
| | | | | | - C André Lévesque
- Agriculture and Agri-Food Canada, Central Experimental Farm, Ottawa, ON
| | | | - Patricia A Okubara
- USDA-ARS, Root Disease and Biological Control Research Unit, Pullman, WA
| | - Timothy C Paulitz
- USDA-ARS, Root Disease and Biological Control Research Unit, Pullman, WA
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Martin FN, Abad ZG, Balci Y, Ivors K. Identification and Detection of Phytophthora: Reviewing Our Progress, Identifying Our Needs. PLANT DISEASE 2012; 96:1080-1103. [PMID: 30727075 DOI: 10.1094/pdis-12-11-1036-fe] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
With the increased attention given to the genus Phytophthora in the last decade in response to the ecological and economic impact of several invasive species (such as P. ramorum, P. kernoviae, and P. alni), there has been a significant increase in the number of described species. In part, this is due to the extensive surveys in historically underexplored ecosystems (e.g., forest and stream ecosystems) undertaken to determine the spread of invasive species and the involvement of Phytophthora species in forest decline worldwide (e.g., oak decline). The past decade has seen an approximate doubling in the number of described species within the genus Phytophthora, and the number will likely continue to increase as more surveys are completed and greater attention is devoted to clarifying phylogenetic relationships and delineating boundaries in species complexes. The development of molecular resources, the availability of credible sequence databases to simplify identification of new species, and the sequencing of several genomes have provided a solid framework to gain a better understanding of the biology, diversity, and taxonomic relationships within the genus. This information is much needed considering the impact invasive or exotic Phytophthora species have had on natural ecosystems and the regulatory issues associated with their management. While this work is improving our ability to identify species based on phylogenetic grouping, it has also revealed that the genus has a much greater diversity than previously appreciated.
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Affiliation(s)
- Frank N Martin
- USDA, ARS, Crop Improvement and Protection Research Unit, Salinas, CA
| | - Z Gloria Abad
- USDA, APHIS, PPQ, Center for Plant Health Science and Technology (CPHST), Beltsville Laboratory, MD
| | - Yilmaz Balci
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD
| | - Kelly Ivors
- Department of Plant Pathology, NC State University, Mountain Hort. Crops Research & Extension Center, Mills River, NC
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Li M, Asano T, Suga H, Kageyama K. A Multiplex PCR for the Detection of Phytophthora nicotianae and P. cactorum, and a Survey of Their Occurrence in Strawberry Production Areas of Japan. PLANT DISEASE 2011; 95:1270-1278. [PMID: 30731689 DOI: 10.1094/pdis-01-11-0076] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We aimed to simultaneously detect two pathogens causing strawberry diseases, Phytophthora nicotianae and P. cactorum, by multiplex polymerase chain reaction (PCR), and to survey their occurrence in the main strawberry production areas of Japan. Due to the need to combine different primer pairs for multiplex PCR and the low specificity of published specific primers for P. nicotianae and P. cactorum, new species-specific primers for P. nicotianae and P. cactorum were designed based on the internal transcribed spacer regions of ribosomal DNA and the ras-related protein gene Ypt1, respectively. Specificity of the designed primers was demonstrated using 68 isolates, including Phytophthora spp., Pythium spp., and other soilborne pathogens. Multiplex PCR discriminated between P. nicotianae and P. cactorum in DNA mixtures of mycelia of the two species. Moreover, both species were detected in artificially and naturally infested soils, indicating that these markers can be used in diagnosis of strawberry diseases. For investigation of the geographic distribution of the two pathogens in Japan, soil samples were collected in 89 strawberry fields from eight prefectures (Gifu, Saga, Nara, Tochigi, Chiba, Shizuoka, Yamanashi, and Hokkaido) of Japan. The method that was developed was successfully applied to survey P. nicotianae and P. cactorum, and distribution of the two pathogens in strawberry plantings in Japan was determined.
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Affiliation(s)
- Mingzhu Li
- The United Graduate School of Agriculture Science
| | | | | | - Koji Kageyama
- River Basin Research Center, Gifu University, Gifu 501-1193, Japan
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