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Kang MJ, Yu H, Kim SK, Park SR, Yang I. Quantification of trace-level DNA by real-time whole genome amplification. PLoS One 2011; 6:e28661. [PMID: 22174862 PMCID: PMC3235147 DOI: 10.1371/journal.pone.0028661] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 11/12/2011] [Indexed: 11/18/2022] Open
Abstract
Quantification of trace amounts of DNA is a challenge in analytical applications where the concentration of a target DNA is very low or only limited amounts of samples are available for analysis. PCR-based methods including real-time PCR are highly sensitive and widely used for quantification of low-level DNA samples. However, ordinary PCR methods require at least one copy of a specific gene sequence for amplification and may not work for a sub-genomic amount of DNA. We suggest a real-time whole genome amplification method adopting the degenerate oligonucleotide primed PCR (DOP-PCR) for quantification of sub-genomic amounts of DNA. This approach enabled quantification of sub-picogram amounts of DNA independently of their sequences. When the method was applied to the human placental DNA of which amount was accurately determined by inductively coupled plasma-optical emission spectroscopy (ICP-OES), an accurate and stable quantification capability for DNA samples ranging from 80 fg to 8 ng was obtained. In blind tests of laboratory-prepared DNA samples, measurement accuracies of 7.4%, -2.1%, and -13.9% with analytical precisions around 15% were achieved for 400-pg, 4-pg, and 400-fg DNA samples, respectively. A similar quantification capability was also observed for other DNA species from calf, E. coli, and lambda phage. Therefore, when provided with an appropriate standard DNA, the suggested real-time DOP-PCR method can be used as a universal method for quantification of trace amounts of DNA.
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Affiliation(s)
- Min-Jung Kang
- Center for Bio-Analysis, Korea Research Institute of Standards and Science, Daejon, Republic of Korea
| | - Hannah Yu
- Department of Bio-Analytical Science, University of Science and Technology, Daejon, Republic of Korea
| | - Sook-Kyung Kim
- Center for Bio-Analysis, Korea Research Institute of Standards and Science, Daejon, Republic of Korea
| | - Sang-Ryoul Park
- Center for Bio-Analysis, Korea Research Institute of Standards and Science, Daejon, Republic of Korea
| | - Inchul Yang
- Center for Bio-Analysis, Korea Research Institute of Standards and Science, Daejon, Republic of Korea
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Zijlstra C, Lund I, Justesen AF, Nicolaisen M, Jensen PK, Bianciotto V, Posta K, Balestrini R, Przetakiewicz A, Czembor E, van de Zande J. Combining novel monitoring tools and precision application technologies for integrated high-tech crop protection in the future (a discussion document). PEST MANAGEMENT SCIENCE 2011; 67:616-625. [PMID: 21445942 DOI: 10.1002/ps.2134] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Revised: 01/05/2011] [Accepted: 01/05/2011] [Indexed: 05/30/2023]
Abstract
The possibility of combining novel monitoring techniques and precision spraying for crop protection in the future is discussed. A generic model for an innovative crop protection system has been used as a framework. This system will be able to monitor the entire cropping system and identify the presence of relevant pests, diseases and weeds online, and will be location specific. The system will offer prevention, monitoring, interpretation and action which will be performed in a continuous way. The monitoring is divided into several parts. Planting material, seeds and soil should be monitored for prevention purposes before the growing period to avoid, for example, the introduction of disease into the field and to ensure optimal growth conditions. Data from previous growing seasons, such as the location of weeds and previous diseases, should also be included. During the growing season, the crop will be monitored at a macroscale level until a location that needs special attention is identified. If relevant, this area will be monitored more intensively at a microscale level. A decision engine will analyse the data and offer advice on how to control the detected diseases, pests and weeds, using precision spray techniques or alternative measures. The goal is to provide tools that are able to produce high-quality products with the minimal use of conventional plant protection products. This review describes the technologies that can be used or that need further development in order to achieve this goal.
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Affiliation(s)
- Carolien Zijlstra
- Wageningen UR, Plant Research International, Wageningen, The Netherlands.
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53
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Weiland JE. Influence of Isolation Method on Recovery of Pythium Species from Forest Nursery Soils in Oregon and Washington. PLANT DISEASE 2011; 95:547-553. [PMID: 30731944 DOI: 10.1094/pdis-04-10-0242] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Pythium species are common damping-off pathogens that can cause stunting, chlorosis, and death of conifer seedlings in the Pacific Northwest (PNW) region of the United States. Despite the prevalence and importance of these pathogens in forest nurseries, relatively little is known about the identity of Pythium species associated with forest nursery soils in Washington and Oregon. A limited number of studies have reported P. aphanidermatum, P. irregulare, P. mamillatum, and P. ultimum as the predominant species in the PNW, but most studies of this genus in forest nurseries have not reported Pythium species identity. In an attempt to identify Pythium species associated with forest nursery soils, field surveys were conducted at three forest nurseries (two in Oregon and one in Washington) in 2008 using three isolation methods. Pythium species were isolated by plating soil onto a semiselective medium or by baiting soil with rhododendron leaf disks and Douglas-fir needle segments. One hundred isolates were randomly selected from each isolation method at each nursery (900 isolates total) and identified on the basis of the internal transcribed spacer (ITS) sequence. Nineteen Pythium species were identified during the survey. Species richness and abundance were strongly influenced by both nursery and isolation method. Of the 300 isolates obtained from each nursery, P. irregulare was the most commonly isolated species from nursery A in Washington (65% incidence). P. 'vipa' and P. dissotocum were the most commonly isolated species from nurseries B and C in Oregon, respectively (53 and 47% incidence, respectively).
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Affiliation(s)
- Jerry E Weiland
- United States Department of Agriculture - Agricultural Research Service, Horticultural Crops Research Laboratory, and Oregon State University, Department of Botany and Plant Pathology, Corvallis, OR 97331
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Montes-Borrego M, Muñoz-Ledesma FJ, Jiménez-Díaz RM, Landa BB. Real-Time PCR Quantification of Peronospora arborescens, the Opium Poppy Downy Mildew Pathogen, in Seed Stocks and Symptomless Infected Plants. PLANT DISEASE 2011; 95:143-152. [PMID: 30743414 DOI: 10.1094/pdis-07-10-0499] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In this study, we developed a reliable, quick, and accurate quantitative polymerase chain reaction (qPCR) assay based on the MIQE (Minimum Information for publication of Quantitative Real-Time PCR Experiments) guidelines for the quantification of Peronospora arborescens in infected downy mildew-symptomless opium poppy (Papaver somniferum) tissues and commercial seed stocks. The protocol was highly reproducible and allowed accurate quantification of pathogen DNA up to 10 fg in different plant DNA backgrounds without losing specificity and efficiency. Moreover, to further overcome difficulties conferred by the strict biotrophy of this pathogen, we developed dilution series of DNA extracted from a plasmid with the target pathogen DNA as a cloned insert. This facilitated the demonstration of the robustness of the protocol in different laboratories with different qPCR equipment and reagents, which may help in its use on a broad scale. Finally, we validated the usefulness of the qPCR protocol for quarantine purposes and downy mildew resistance screening by quantifying P. arborescens in complex, naturally infested opium poppy samples. Thus, a pathogen biomass of 0.0003 to 0.007‰ or of 0.110 to 5,557 ppm was quantified in symptomless capsules in commercial seed stocks, or in stem samples from symptomless opium poppy plants systemically infected by the pathogen, respectively.
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Affiliation(s)
- Miguel Montes-Borrego
- Department of Crop Protection, Institute of Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), P.O. Box 4084, 14080 Córdoba, Spain, and College of Agriculture and Forestry (ETSIAM), University of Córdoba (UCO), Campus de Rabanales, Ctra. Madrid-Cádiz, km 396, 14071 Córdoba, Spain
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55
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Ryuk JA, Choi GY, Kim YH, Lee HW, Lee MY, Choi JE, Ko BS. Application of genetic marker and real-time polymerase chain reaction for discrimination between Forsythia viridissima and Forsythia suspensa. Biol Pharm Bull 2010; 33:1133-7. [PMID: 20606302 DOI: 10.1248/bpb.33.1133] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Forsythiae Fructus has been used as a herbal medicine for a fruit of Forsythia viridissima LINDLEY or Forsythia suspensa VAHL (Oleaceae). In Korea, the fruit of Forsythia viridissima is used and in China, the fruit of Forsythia suspensa is used generally. There are differences in the amount and distribution of constituents between Forsythia viridissima (FV) and Forsythia suspensa (FS). Accordingly, a discrimination of these two herbal drugs is needed. In this study, we designed FV genetic marker based on the internal transcribed spacer (ITS) sequence of nuclear ribosomal DNA that can discriminate Forsythia viridissima and Forsythia suspensa and species-specific amplification product 252 bp was confirmed. Using the real-time polymerase chain reaction (PCR) (allelic discrimination) analysis, an accurate discrimination between Forsythia viridissima and Forsythia suspensa was accomplished. Accordingly, with the use of PCR analysis based on ITS region sequence of ribosomal DNA and the real-time PCR analysis which can efficiently discriminate between Forsythia viridissima and Forsythia suspensa was developed.
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Affiliation(s)
- Jin Ah Ryuk
- Korea Institute of Oriental Medicine 483 Exporo, Yuseong-gu, Daejeon 305-811, Korea
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56
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Reinhart KO, Royo AA, Kageyama SA, Clay K. Canopy gaps decrease microbial densities and disease risk for a shade-intolerant tree species. ACTA OECOLOGICA-INTERNATIONAL JOURNAL OF ECOLOGY 2010. [DOI: 10.1016/j.actao.2010.07.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Li M, Senda M, Komatsu T, Suga H, Kageyama K. Development of real-time PCR technique for the estimation of population density of Pythium intermedium in forest soils. Microbiol Res 2010; 165:695-705. [PMID: 20116230 DOI: 10.1016/j.micres.2009.11.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Revised: 11/14/2009] [Accepted: 11/21/2009] [Indexed: 10/19/2022]
Abstract
Pythium intermedium is known to play an important role in the carbon cycling of cool-temperate forest soils. In this study, a fast, precise and effective real-time PCR technique for estimating the population densities of P. intermedium from soils was developed using species-specific primers. Specificity was confirmed both with conventional PCR and real-time PCR. The detection limit (sensitivity) was determined and amplification standard curves were generated using SYBR Green II fluorescent dye. A rapid and accurate assay for quantification of P. intermedium in Takayama forest soils of Japan was developed using a combination of a new DNA extraction method and PCR primers were developed for real-time PCR. And the distribution of P. intermedium in forest soil was investigated with both soil plating method and the developed real-time PCR technique. This new technique will be a useful tool and can be applied to practical use for studying the role of Pythium species in forest and agricultural ecosystems.
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Affiliation(s)
- Mingzhu Li
- The United Graduate School of Agriculture Science, Gifu University, Gifu 501-1193, Japan.
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58
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Wielgoss A, Nechwatal J, Bogs C, Mendgen K. Host plant development, water level and water parameters shape Phragmites australis-associated oomycete communities and determine reed pathogen dynamics in a large lake. FEMS Microbiol Ecol 2009; 69:255-65. [DOI: 10.1111/j.1574-6941.2009.00701.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Yan G, Smiley RW, Okubara PA, Skantar A, Easley SA, Sheedy JG, Thompson AL. Detection and Discrimination of Pratylenchus neglectus and P. thornei in DNA Extracts from Soil. PLANT DISEASE 2008; 92:1480-1487. [PMID: 30764446 DOI: 10.1094/pdis-92-11-1480] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A species-specific polymerase chain reaction (PCR) method was developed to detect and identify the root-lesion nematodes Pratylenchus neglectus and P. thornei from soil. A primer set was designed from Pratylenchus 28S rRNA gene sequences of the D3 expansion domain. Primer specificity was confirmed with 23 isolates of 15 nematode species and other plant-parasitic and non-plant-parasitic nematodes typically present in the soil communities, and with six fungal species commonly associated with wheat root rot. DNA obtained using a commercially available kit and a method developed in our laboratory gave comparable amplification. PCR conditions were optimized and the two species were differentiated by PCR products of 144 bp for P. neglectus and 288 bp for P. thornei. With this assay, we detected a single juvenile in 1 g of sterile, inoculated soil. Examination of 30 field soil samples revealed that this method was applicable to a range of soils naturally infested with these two pathogens in Oregon. This PCR-based method is rapid, efficient, and reliable, does not require expertise in nematode taxonomy and morphology, and could be used as a rapid diagnostic tool for commercial and research applications for disease forecasting and management.
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Affiliation(s)
- Guiping Yan
- Oregon State University, Columbia Basin Agricultural Research Center, Pendleton 97801
| | - Richard W Smiley
- Oregon State University, Columbia Basin Agricultural Research Center, Pendleton 97801
| | - Patricia A Okubara
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Root Disease and Biological Control Research Unit, Pullman, WA 99164
| | | | - Sandra A Easley
- Oregon State University, Columbia Basin Agricultural Research Center, Pendleton
| | - Jason G Sheedy
- Oregon State University, Columbia Basin Agricultural Research Center, Pendleton
| | - Alison L Thompson
- Oregon State University, Columbia Basin Agricultural Research Center, Pendleton
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Okubara PA, Schroeder KL, Paulitz TC. Identification and quantification of Rhizoctonia solani and R. oryzae using real-time polymerase chain reaction. PHYTOPATHOLOGY 2008; 98:837-47. [PMID: 18943261 DOI: 10.1094/phyto-98-7-0837] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Rhizoctonia solani and R. oryzae are the principal causal agents of Rhizoctonia root rot in dryland cereal production systems of the Pacific Northwest. To facilitate the identification and quantification of these pathogens in agricultural samples, we developed SYBR Green I-based real-time quantitative-polymerase chain reaction (Q-PCR) assays specific to internal transcribed spacers ITS1 and ITS2 of the nuclear ribosomal DNA of R. solani and R. oryzae. The assays were diagnostic for R. solani AG-2-1, AG-8, and AG-10, three genotypes of R. oryzae, and an AG-I-like binucleate Rhizoctonia species. Quantification was reproducible at or below a cycle threshold (Ct) of 33, or 2 to 10 fg of mycelial DNA from cultured fungi, 200 to 500 fg of pathogen DNA from root extracts, and 20 to 50 fg of pathogen DNA from soil extracts. However, pathogen DNA could be specifically detected in all types of extracts at about 100-fold below the quantification levels. Soils from Ritzville, WA, showing acute Rhizoctonia bare patch harbored 9.4 to 780 pg of R. solani AG-8 DNA per gram of soil.. Blastn, primer-template duplex stability, and phylogenetic analyses predicted that the Q-PCR assays will be diagnostic for isolates from Australia, Israel, Japan, and other countries.
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Affiliation(s)
- P A Okubara
- U.S. Department of Agriculture-Agriculture Research Service, Root Disease and Biological Control Research Unit, Pullman, Washington 99164-6430, USA.
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Le Floch G, Tambong J, Vallance J, Tirilly Y, Lévesque A, Rey P. Rhizosphere persistence of three Pythium oligandrum strains in tomato soilless culture assessed by DNA macroarray and real-time PCR. FEMS Microbiol Ecol 2007; 61:317-26. [PMID: 17627780 DOI: 10.1111/j.1574-6941.2007.00348.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
In tomato soilless culture, plant-disease optimal control and growth promotion are achieved when the rhizosphere is heavily colonized by the biocontrol agent Pythium oligandrum. Discrepancies in performance are generally attributed to the poor persistence of P. oligandrum on roots. In this study, three selected strains of P. oligandrum were introduced into the rhizosphere of greenhouse-grown tomato plants, and their persistence was assessed by DNA macroarray hybridization and real-time PCR. The experimental data from DNA detection and plate counting were compared. PCR-based methods detected P. oligandrum throughout the 6-month growing season, whereas plate counting indicated its presence only over the first 3 months. Moreover, the DNA array method provided information about the various Pythium species present in the rhizosphere: P. dissotocum was frequently detected on roots of plants, without distinction between plants inoculated or not inoculated with the antagonist. The detection of other Pythium species was noticed sporadically (P. ultimum, P. sylvaticum and P. intermedium), independent of the treatment. Even though the yield enhancement is not significant throughout the entire growing season, data obtained from epidemiological studies demonstrate an enhancement of P. oligandrum persistence on the rhizosphere of plants and less use of mycoparasitism.
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Affiliation(s)
- Gaetan Le Floch
- Laboratoire de Biodiversité et d'Ecologie Microbienne, Université de Bretagne Occidentale, Plouzané, France.
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Malvick DK, Impullitti AE. Detection and Quantification of Phialophora gregata in Soybean and Soil Samples with a Quantitative, Real-Time PCR Assay. PLANT DISEASE 2007; 91:736-742. [PMID: 30780483 DOI: 10.1094/pdis-91-6-0736] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Brown stem rot of soybean, caused by the soilborne fungus Phialophora gregata, is a common and widespread disease of soybean (Glycine max) in the midwestern United States. This pathogen is challenging to study due to a long latent period and slow growth. A TaqMan probe-based quantitative, real-time polymerase chain reaction (qPCR) assay was developed for sensitive and specific detection and quantification of genotypes A and B of P. gregata in plant and soil samples. It is sensitive with detection limits of 50 fg of pure genomic DNA, 100 copies of the target DNA sequence, and approximately 400 conidia. The qPCR assay is approximately 1,000 times more sensitive in detecting DNA and conidia of P. gregata, and is more rapid and less sensitive to PCR inhibitors from soybean stems than a standard PCR (sPCR) assay. Using this single-step qPCR assay, low levels of infection were detected in soybean stems at least 1 to 2 weeks prior to symptom development and before P. gregata was detected with sPCR. This assay also was used to detect the pathogen in field-grown plants and in naturally infested field soils. This new qPCR assay is a powerful tool for rapid, specific, and sensitive detection, diagnosis, and quantification of P. gregata in plants and soil, and for advancing studies of the ecology of P. gregata and its interactions with host plants.
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Affiliation(s)
- D K Malvick
- Department of Plant Pathology, University of Minnesota, St. Paul 55108
| | - A E Impullitti
- Department of Plant Pathology, University of Minnesota, St. Paul 55108
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Chilvers MI, du Toit LJ, Akamatsu H, Peever TL. A Real-Time, Quantitative PCR Seed Assay for Botrytis spp. that Cause Neck Rot of Onion. PLANT DISEASE 2007; 91:599-608. [PMID: 30780707 DOI: 10.1094/pdis-91-5-0599] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A real-time fluorescent polymerase chain reaction (PCR) assay was developed using SYBR Green chemistry to quantify the Botrytis spp. associated with onion (Allium cepa) seed that are also able to induce neck rot of onion bulbs, i.e., B. aclada, B. allii, and B. byssoidea. The nuclear ribosomal intergenic spacer (IGS) regions of target and nontarget Botrytis spp. were sequenced, aligned, and used to design a primer pair specific to B. aclada, B. allii, and B. byssoidea. Primers and amplification parameters were optimized to avoid amplifying the related species B. cinerea, B. porri, and B. squamosa, as well as Sclerotinia sclerotiorum and isolates of 15 other fungal species commonly found associated with onion seed. The primers reliably detected 10 fg of genomic DNA per PCR reaction extracted from pure cultures of B. aclada and B. allii. Conventional assays of surface-disinfested and nondisinfested seed on an agar medium were used to determine the incidence of neck rot Botrytis spp. associated with each of 23 commercial onion seed lots, and the real-time PCR assay was used to determine the quantity of DNA of neck rot Botrytis spp. in each seed lot. A linear relationship could not be found between the incidence of seed infected with the neck rot Botrytis spp. using the conventional agar seed assays and the quantity of DNA of the neck rot Botrytis spp. detected by the real-time PCR assay. However, the real-time PCR assay appeared to be more sensitive than the conventional agar assay, allowing detection of neck rot Botrytis spp. in 5 of the 23 seed lots that tested negative using the conventional agar seed assay.
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Affiliation(s)
| | | | | | - Tobin L Peever
- Associate Professor, Washington State University, Department of Plant Pathology, Pullman 99164-6430
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