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Shah SAH, Andrabi SMH. A systematic review and meta-analysis of spermatozoa cryopreservation, in vitro and in vivo fertility practices in water buffalo. Vet Res Commun 2021; 45:47-74. [PMID: 33929679 DOI: 10.1007/s11259-021-09789-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 04/08/2021] [Indexed: 10/21/2022]
Abstract
We explored different aspects of buffalo spermatozoa during cryopreservation. The meta-data comprised of 285 studies, published from January 2008 to March 2020. A free web tool CADIMA as well as PRISMA 2009 Flow Diagram were used for carrying out this study. The inter-reviewer agreement among studies allocated was satisfactory for criteria A (selection bias), B (performance bias), C (detection bias) and D (attrition bias), respectively. India led the percent (%) research ladder with 34.4, followed by Pakistan (29.5), Egypt (12.3), Iran (7.7), Italy (5.6), Indonesia (3.2), China (2.1), Brazil (1.4), Thailand (1.1), Philippines and Bulgaria (0.7 each), Saudi Arabia, Turkey, Vietnam, and USA (0.4 each). Among four categories of studies, Group-1 evaluated only supplements/additives/media in the freezing semen extender (n = 191/285; 67.02%); Group-2 conducted in vivo fertilization (n = 62/285; 21.75%) and Group-3 conducted in vitro fertilization/ cleavage rate/penetration rate/ blastocyst yields (n = 28/285; 9.82%) with their specific cryodiluents/media, respectively. Group-4 conducted different experimental supplements/additives/media and carried out both in vitro and in vivo fertilization simultaneously (n = 4/285; 1.40%). Conventional spermatozoa cryopreservation was reported by 51.9% studies followed by programmable fast freezing by 20.7% studies. A few leading extender types included BioXcell (3.9%); Soyamilk-skim (3.5%); and Andromed (2.1%). The study also describes French straws for semen filling, cooling temperatures, extension time, equilibration time, cryopreservation stages, thawing temperatures, seasons, thawing time, and stains used during semen evaluation assays. The study concludes that the research on spermatozoa cryopreservation of buffalo is largely conducted at quality level and a need of applying these findings for evaluation of fertility potential (in vivo and in vitro) is indispensable for effective genetic improvement.
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Affiliation(s)
- Syed Aftab Hussain Shah
- Pakistan Scientific and Technological Information Center, Quaid-i-Azam University Campus, Islamabad, 44000, Pakistan.
| | - Syed Murtaza Hassan Andrabi
- Animal Reproduction Laboratory, Animal Sciences Institute, National Agricultural Research Center, Islamabad, 45500, Pakistan.
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2
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Riera FL, Roldán JE, Espinosa JM, Fernandez JE, Ortiz I, Hinrichs K. Application of embryo biopsy and sex determination via polymerase chain reaction in a commercial equine embryo transfer program in Argentina. Reprod Fertil Dev 2020; 31:1917-1925. [PMID: 31656221 DOI: 10.1071/rd19228] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/17/2019] [Indexed: 11/23/2022] Open
Abstract
Embryo biopsy for fetal sexing has clinical application, but few reports are available of its use within an active embryo transfer program. We evaluated results on biopsy of 459 embryos over one breeding season. There were no significant differences in pregnancy rate between biopsied and non-biopsied embryos (72% vs 73%) or for biopsied embryos recovered at the centre (73%) compared with those shipped overnight (72%). However, the pregnancy rate decreased significantly in shipped embryos biopsied ≥20h after collection. Overall, 86% of biopsies provided a sex diagnosis. The likelihood of a positive genomic (g) DNA result was significantly higher for biopsies from large blastocysts (96%) than from smaller embryos (70-85%). In total, 38% of biopsies were positive for Y chromosome DNA (Y-DNA) and were diagnosed as male. Subsequently, 95% of Y-DNA-positive embryos were confirmed as male and 78% of Y-DNA-negative embryos were confirmed as female. The accuracy of prediction of female (Y-DNA negative) was significantly higher when the biopsy sample was probed for Y-DNA only compared with probing for both gDNA and Y-DNA. We estimate that by transferring only Y-DNA-negative embryos, 3% of potential female pregnancies may have been lost, and production of male pregnancies was reduced by 72%.
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Affiliation(s)
- F L Riera
- Centro de Reproducción Equina Doña Pilar, Ruta 188, Km 200, (6070) Lincoln (B), Argentina; and Laboratorio de Biotecnologia Reproductiva Prof. Robert M. Kenney, Sargento Cabral 748, (1669) La Lonja (B), Argentina
| | - J E Roldán
- Centro de Reproducción Equina Doña Pilar, Ruta 188, Km 200, (6070) Lincoln (B), Argentina; and Laboratorio de Biotecnologia Reproductiva Prof. Robert M. Kenney, Sargento Cabral 748, (1669) La Lonja (B), Argentina
| | - J M Espinosa
- Centro de Reproducción Equina Doña Pilar, Ruta 188, Km 200, (6070) Lincoln (B), Argentina; and Laboratorio de Biotecnologia Reproductiva Prof. Robert M. Kenney, Sargento Cabral 748, (1669) La Lonja (B), Argentina
| | - J E Fernandez
- Centro de Reproducción Equina Doña Pilar, Ruta 188, Km 200, (6070) Lincoln (B), Argentina
| | - I Ortiz
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine & Biomedical Sciences, 4466 TAMU, Texas A&M University, College Station, TX 77843-4466, USA
| | - K Hinrichs
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine & Biomedical Sciences, 4466 TAMU, Texas A&M University, College Station, TX 77843-4466, USA; and Corresponding author.
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3
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Grabicoski EMG, Jaccoud-Filho DDS, Lee D, Henneberg L, Pileggi M. Real-Time Quantitative and Ion-Metal Indicator LAMP-Based Assays for Rapid Detection of Sclerotinia sclerotiorum. PLANT DISEASE 2020; 104:1514-1526. [PMID: 32105572 DOI: 10.1094/pdis-07-19-1455-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Sclerotinia sclerotiorum is one of the most devastating and cosmopolitan plant pathogens. Rapid detection of S. sclerotiorum can provide growers an advantage in knowing what control measures should be taken to minimize crop damage and financial losses caused by it. Loop-mediated isothermal amplification (LAMP) is a fast, sensitive, and specific nucleic acid amplification method that does not require a thermal cycler. This study aimed to develop a LAMP-based assay for the specific detection of S. sclerotiorum (Ss-LAMP). A real-time quantitative LAMP reaction (Ss-qLAMP) and a calcein ion indicator-based LAMP reaction (Ss-cLAMP) were designed, optimized, and tested on fungi, plant, and soil samples. The Ss-LAMP reactions were very specific and sensitive. Applying the artificially inoculated soil samples with DNA purified by five protocols in the Ss-qLAMP reaction, it was possible to detect and quantify the pathogen DNA, regardless of the extraction protocol. Naturally infected soybean tissues had the pathogen detected by Ss-cLAMP directly in the reaction tube with no DNA extraction requirement. The assays should be applicable for many types of samples, such as soil, spore traps, and plant tissues from several crops, with no requirement for DNA extraction. The Ss-LAMP reactions took less than 1 h to complete, and they can be made directly in the field with real-time quantitative results (Ss-qLAMP) or qualitative naked-eye visual results (Ss-cLAMP). Results were obtained with 10 pg of DNA or 10 ng of crude mycelium, suggesting a detection limit close to a single DNA copy. Ss-LAMP reactions will allow rapid and accurate diagnosis of S. sclerotiorum and assist in pathogen management and control.
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Affiliation(s)
- Edilaine Mauricia Gelinski Grabicoski
- State University of Ponta Grossa, Department of Plant Science and Plant Protection, Uvaranas, 84030-900, Ponta Grossa, PR, Brazil
- State University of Maringá, Department of Agronomy, Jardim Universitário, 87020-900, Maringá, PR, Brazil
| | - David de Souza Jaccoud-Filho
- State University of Ponta Grossa, Department of Plant Science and Plant Protection, Uvaranas, 84030-900, Ponta Grossa, PR, Brazil
| | - David Lee
- National Institute of Agricultural Botany, Cambridge CB3 0LE, United Kingdom
| | - Luciane Henneberg
- State University of Ponta Grossa, Department of Plant Science and Plant Protection, Uvaranas, 84030-900, Ponta Grossa, PR, Brazil
| | - Marcos Pileggi
- State University of Ponta Grossa, Department of Structural, Molecular and Genetic Biology, Uvaranas, 84030-900, Ponta Grossa, PR, Brazil
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Panno S, Matić S, Tiberini A, Caruso AG, Bella P, Torta L, Stassi R, Davino S. Loop Mediated Isothermal Amplification: Principles and Applications in Plant Virology. PLANTS (BASEL, SWITZERLAND) 2020; 9:E461. [PMID: 32268586 PMCID: PMC7238132 DOI: 10.3390/plants9040461] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/02/2020] [Accepted: 04/02/2020] [Indexed: 01/14/2023]
Abstract
In the last decades, the evolution of molecular diagnosis methods has generated different advanced tools, like loop-mediated isothermal amplification (LAMP). Currently, it is a well-established technique, applied in different fields, such as the medicine, agriculture, and food industries, owing to its simplicity, specificity, rapidity, and low-cost efforts. LAMP is a nucleic acid amplification under isothermal conditions, which is highly compatible with point-of-care (POC) analysis and has the potential to improve the diagnosis in plant protection. The great advantages of LAMP have led to several upgrades in order to implement the technique. In this review, the authors provide an overview reporting in detail the different LAMP steps, focusing on designing and main characteristics of the primer set, different methods of result visualization, evolution and different application fields, reporting in detail LAMP application in plant virology, and the main advantages of the use of this technique.
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Affiliation(s)
- Stefano Panno
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Slavica Matić
- Department of Agricultural, Forestry and Food Sciences, University of Turin, 10095 Turin, Italy;
| | - Antonio Tiberini
- Council for Agricultural Research and Economics, Research Center for Plant Protection and Certification, 00156 Rome, Italy;
| | - Andrea Giovanni Caruso
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Patrizia Bella
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Livio Torta
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Raffaele Stassi
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Salvatore Davino
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), 10135 Turin, Italy
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Bilkiss M, Shiddiky MJA, Ford R. Advanced Diagnostic Approaches for Necrotrophic Fungal Pathogens of Temperate Legumes With a Focus on Botrytis spp. Front Microbiol 2019; 10:1889. [PMID: 31474966 PMCID: PMC6702891 DOI: 10.3389/fmicb.2019.01889] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 07/30/2019] [Indexed: 01/05/2023] Open
Abstract
Plant pathogens reduce global crop productivity by up to 40% per annum, causing enormous economic loss and potential environmental effects from chemical management practices. Thus, early diagnosis and quantitation of the causal pathogen species for accurate and timely disease control is crucial. Botrytis Gray Mold (BGM), caused by Botrytis cinerea and B. fabae, can seriously impact production of temperate grain legumes separately or within a complex. Accordingly, several immunogenic and molecular probe-type protocols have been developed for their diagnosis, but these have varying levels of species-specificity, sensitivity and consequent usefulness within the paddock. To substantially improve speed, accuracy and sensitivity, advanced nanoparticle-based biosensor approaches have been developed. These novel methods have made enormous impact toward disease diagnosis in the medical sciences and offer potential for transformational change within the field of plant pathology and disease management, with early and accurate diagnosis at the point-of-care in the field. Here we review several recently developed diagnostic tools that build on traditional approaches and are available for pathogen diagnosis, specifically for Botrytis spp. diagnostic applications. We then identify the specific gaps in knowledge and current limitations to these existing tools.
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Affiliation(s)
- Marzia Bilkiss
- School of Environment and Science, Environmental Futures Research Institute, Griffith University, Nathan, QLD, Australia
| | - Muhammad J A Shiddiky
- School of Environment and Science, Environmental Futures Research Institute, Griffith University, Nathan, QLD, Australia.,Queensland Micro- and Nanotechnology Centre (QMNC), Nathan, QLD, Australia
| | - Rebecca Ford
- School of Environment and Science, Environmental Futures Research Institute, Griffith University, Nathan, QLD, Australia
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Chahar M, Anvikar A, Valecha N. Development and Evaluation of a Novel HNB Based Isothermal Amplification Assay for Fast Detection of Pyrimethamine Resistance (S108N) in Plasmodium falciparum. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16091635. [PMID: 31083343 PMCID: PMC6539687 DOI: 10.3390/ijerph16091635] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/08/2019] [Accepted: 02/11/2019] [Indexed: 11/16/2022]
Abstract
Sulphadoxine and pyrimethamine (SP) have been used as long-acting partner antimalarial drugs in artemisinin combination therapy (ACT) for falciparum malaria. The emergence and increasing spread of SP resistance in malaria-endemic areas have become a challenge for the control of malaria. Therefore, regular monitoring of the mutation status of partner drugs is important for the better management of drug policy. There are limitations with traditional molecular methods and there is an urgent need for an easy method for diagnosis of drug resistance. In this study we have introduced and developed a novel single nucleotide polymorphism loop-mediated isothermal amplification (SNP-LAMP) approach based on a hydroxynaphthol blue (HNB) indicator for the easier and quicker detection of pyrimethamine resistance in Plasmodium falciparum malaria. To implement this novel approach, many sets of LAMP primers were designed and tested. Finally, one set of forward inner primer M1 (FIPM1) of LAMP primer was selected that specifically distinguishes pyrimethamine-resistant P. falciparum malaria. The LAMP reactions were optimized at 60-66 °C for 45 min. High sensitivity (7 parasites/µL) was observed with 10-4 fold dilutions (<2 ng DNA) of genomic DNA. Moreover, this approach has the potential to be applied even in laboratories unfamiliar with PCR or other molecular methods, and in future, this can be helpful for the better management of anti-malarial policy.
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Affiliation(s)
- Madhvi Chahar
- Division of Epidemiology and Clinical Research, National Institute of Malaria Research, Sector-8 Dwarka, New Delhi 110077, India.
| | - Anup Anvikar
- Division of Epidemiology and Clinical Research, National Institute of Malaria Research, Sector-8 Dwarka, New Delhi 110077, India.
| | - Neena Valecha
- Division of Epidemiology and Clinical Research, National Institute of Malaria Research, Sector-8 Dwarka, New Delhi 110077, India.
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7
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Dobhal S, Larrea-Sarmiento A, Alvarez AM, Arif M. Development of a loop-mediated isothermal amplification assay for specific detection of all known subspecies of Clavibacter michiganensis. J Appl Microbiol 2018; 126:388-401. [PMID: 30307676 DOI: 10.1111/jam.14128] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/03/2018] [Accepted: 10/05/2018] [Indexed: 01/02/2023]
Abstract
AIMS Clavibacter michiganensis is an important bacterial plant pathogen that causes vast destruction to agriculturally important crops worldwide. Early detection is critical to evaluate disease progression and to implement efficient control measures to avoid serious epidemics. In this study, we developed a sensitive, specific and robust loop-mediated isothermal amplification (LAMP) assay for detection of all known subspecies of C. michiganensis. METHODS AND RESULTS Whole genome comparative genomics approach was taken to identify a unique and conserved region within all known subspecies of C. michiganensis. Primer specificity was evaluated in silico and with 64 bacterial strains included in inclusivity and exclusivity panels; no false positives or false negatives were detected. Both the sensitivity and spiked assay of the developed LAMP assay was 1 fg of the pathogen DNA per reaction. A 100% accuracy was observed when tested with infected plant samples. CONCLUSIONS The developed LAMP assay is simple, sensitive, robust and easy to perform using different detection platforms and chemistries. SIGNIFICANCE AND IMPACT OF THE STUDY The developed LAMP assay can detect all known subspecies of C. michiganensis. The LAMP process can be performed isothermally at 65°C and results can be visually assessed, which makes this technology a promising tool for monitoring the disease progression and for accurate pathogen detection at point-of-care.
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Affiliation(s)
- S Dobhal
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - A Larrea-Sarmiento
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - A M Alvarez
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - M Arif
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
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8
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Duan YB, Yang Y, Wang JX, Chen CJ, Steinberg G, Fraaije BA, Zhou MG. Simultaneous Detection of Multiple Benzimidazole-Resistant β-Tubulin Variants of Botrytis cinerea using Loop-Mediated Isothermal Amplification. PLANT DISEASE 2018; 102:2016-2024. [PMID: 30133354 DOI: 10.1094/pdis-03-18-0542-re] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Optimal disease management depends on the ability to monitor the development of fungicide resistance in plant pathogen populations. Benzimidazole resistance is caused by the point mutations of the β-tubulin gene in Botrytis cinerea, and three mutations (E198A, E198K, and E198V) at codon 198 account for more than 98% of all resistant strains. Although traditional methods remain a cornerstone in monitoring fungicide resistance, molecular methods that do not require the isolation of pathogens can detect resistance alleles present at low frequencies, and require less time and labor than traditional methods. In this study, we present an efficient, rapid, and highly specific method for detecting highly benzimidazole-resistant B. cinerea isolates based on loop-mediated isothermal amplification (LAMP). By using specific primers, we could simultaneously detect all three resistance-conferring mutations at codon 198. The LAMP reaction components and conditions were optimized, and the best reaction temperatures and times were 60 to 62°C and 45 min, respectively. When B. cinerea field isolates were assessed for benzimidazole resistance, similar results were obtained with LAMP, minimal inhibition concentration, and sequencing. The LAMP assay developed in the current study was highly suitable for detection of highly benzimidazole-resistant field isolates of B. cinerea.
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Affiliation(s)
- Ya Bing Duan
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Ying Yang
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Jian Xin Wang
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Chang Jun Chen
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, Jiangsu Province, 210095, China
| | - Gero Steinberg
- Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Bart A Fraaije
- Biointeractions & Crop Protection Department, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Ming Guo Zhou
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University
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Fan F, Yin WX, Li GQ, Lin Y, Luo CX. Development of a LAMP Method for Detecting SDHI Fungicide Resistance in Botrytis cinerea. PLANT DISEASE 2018; 102:1612-1618. [PMID: 30673416 DOI: 10.1094/pdis-12-17-1933-re] [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
Resistance to succinate dehydrogenase inhibitors (SDHI) in Botrytis cinerea is associated with point mutations in the target gene succinate dehydrogenase subunit B (SdhB). The substitution from histidine to arginine at codon 272 (H272R) is currently the predominant mutation in SDHI-resistant populations in B. cinerea worldwide. In order to monitor the development of resistance to SDHI, a rapid, simple, and efficient method with high specificity to the H272R point mutation was developed based on loop-mediated isothermal amplification (LAMP). To specifically detect the H272R mutation, a set of four primers was designed based on the sequence of SdhB, and the LAMP reaction was optimized. When SYBR Green I was added after reaction, only samples with the H272R mutation showed the color change (from brown to fluorescent yellow), indicating that this set of primers could successfully discriminate the H272R genotype from other genotypes. Specificity and accuracy tests showed that this LAMP assay had high specificity and accuracy. Moreover, the LAMP method was further simplified with fungal mycelia and conidia as the amplification template which could be prepared within 5 min. Due to the low cost, simplicity, high efficiency, and specificity, the developed LAMP assay may contribute to the monitoring of resistance development to SDHI in B. cinerea, especially in field and high-throughput experiments.
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Affiliation(s)
- F Fan
- Key Lab of Horticultural Plant Biology, Ministry of Education, and College of Plant Science and Technology
| | - W X Yin
- College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring & Safety Control in Hubei Province
| | - G Q Li
- College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring & Safety Control in Hubei Province
| | - Y Lin
- Key Lab of Horticultural Plant Biology, Ministry of Education, and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - C X Luo
- Key Lab of Horticultural Plant Biology, Ministry of Education, and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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10
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Duan Y, Yang Y, Wang Y, Pan X, Wu J, Cai Y, Li T, Zhao D, Wang J, Zhou M. Loop-Mediated Isothermal Amplification for the Rapid Detection of the F200Y Mutant Genotype of Carbendazim-Resistant Isolates of Sclerotinia sclerotiorum. PLANT DISEASE 2016; 100:976-983. [PMID: 30686158 DOI: 10.1094/pdis-10-15-1185-re] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The point mutation at codon 200 (TTC→TAC, F200Y) confers moderate resistance to carbendazim in Sclerotinia sclerotiorum. This mutant genotype (F200Y) has been detected mainly by determining the minimum inhibitory concentration (MIC), which requires 3 to 5 days. Here, we developed a loop-mediated isothermal amplification (LAMP) assay for the rapid detection of the F200Y mutant genotype of carbendazim-resistant isolates of S. sclerotiorum. Specific LAMP primers were designed and concentrations of LAMP components were optimized. The optimal reaction conditions were 62 to 63°C for 45 min. The new LAMP assay requires no special equipment and is highly sensitive and specific (the i.e., it generated positive results with F200Y mutant genotype but generated negative results with other carbendazim-resistant mutants and with a variety of carbendazim-resistant mutants of Botrytis cinerea and Fusarium graminearum). Inclusion of the loop backward (LB) primer reduced the reaction time to 15 min. Results were identical with LAMP and MIC determinations. The advantages of the LB-accelerated LAMP assay for detection of the F200Y mutant genotype were demonstrated by assaying sclerotia produced on rape stems that were artificially inoculated in the field. The results indicated that the new LAMP assay represents an improved way to detect the F200Y mutant genotype of carbendazim-resistant isolates of S. sclerotiorum.
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Affiliation(s)
- Yabing Duan
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ying Yang
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yong Wang
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiayan Pan
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jian Wu
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yiqiang Cai
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tao Li
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Donglei Zhao
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jianxin Wang
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mingguo Zhou
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
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11
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Duan YB, Yang Y, Wang JX, Liu CC, He LL, Zhou MG. Development and application of loop-mediated isothermal amplification for detecting the highly benzimidazole-resistant isolates in Sclerotinia sclerotiorum. Sci Rep 2015; 5:17278. [PMID: 26606972 PMCID: PMC4660316 DOI: 10.1038/srep17278] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 10/28/2015] [Indexed: 01/22/2023] Open
Abstract
Resistance of benzimidazole fungicides is related to the point mutation of the β-tubulin gene in Sclerotinia sclerotiorum. The point mutation at codon 198 (GAG → GCG, E198A) occurs in more than 90% of field resistant populations in China. Traditional detection methods of benzimidazole-resistant mutants of S. sclerotiorum are time-consuming, tedious and inefficient. To establish a suitable and rapid detection of benzimidazole-resistant mutants of S. sclerotiorum, an efficient and simple method with high specificity was developed based on loop-mediated isothermal amplification (LAMP). Eight sets of LAMP primers were designed and four sets were optimized to specially distinguish benzimidazole-resistant mutants of S. sclerotiorum. With the optimal LAMP primers, the concentration of LAMP components was optimized and the reaction conditions were set as 60-64 °C for 60 min. This method had a good specificity, sensitivity, stability and repeatability. In the 1491 sclerotia, 614 (41.18%) were positive by LAMP, and 629 (42.19%) positive by MIC. Therefore, the LAMP assay is more feasible to detect benzimidazole-resistant mutants of S. sclerotiorum than traditional detection methods.
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Affiliation(s)
- Ya Bing Duan
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ying Yang
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jian Xin Wang
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Cong Chao Liu
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ling Ling He
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ming Guo Zhou
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
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Su CW, Li CY, Lee JCI, Ji DD, Li SY, Daniel B, Syndercombe-Court D, Linacre A, Hsieh HM. A novel application of real-time RT-LAMP for body fluid identification: using HBB detection as the model. Forensic Sci Med Pathol 2015; 11:208-15. [DOI: 10.1007/s12024-015-9668-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/06/2015] [Indexed: 11/28/2022]
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Ghosh R, Nagavardhini A, Sengupta A, Sharma M. Development of Loop-Mediated Isothermal Amplification (LAMP) assay for rapid detection of Fusarium oxysporum f. sp. ciceris - wilt pathogen of chickpea. BMC Res Notes 2015; 8:40. [PMID: 25886622 PMCID: PMC4332723 DOI: 10.1186/s13104-015-0997-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 01/26/2015] [Indexed: 11/29/2022] Open
Abstract
Background Fusarium oxysporum f. sp. ciceris (Foc), the causal agent of Fusarium wilt is a devastating pathogen of chickpea. In chickpea, various soil borne pathogens produce (s) similar symptoms, therefore cannot be distinguished easily at field level. There is real need for a rapid, inexpensive, and easy to operate and maintain genotyping tool to facilitate accurate disease diagnosis and surveillance for better management of Fusarium wilt outbreaks. Results In this study, we developed a loop-mediated isothermal amplification (LAMP) assay targeting the elongation factor 1 alpha gene sequence for visual detection of Foc. The LAMP reaction was optimal at 63°C for 60 min. When hydroxynaphthol blue (HNB) was added before amplification, samples with Foc DNA developed a characteristic sky blue colour but those without DNA or with the DNA of six other plant pathogenic fungi did not. Results obtained with LAMP and HNB were confirmed when LAMP products were subjected to gel electrophoresis. The detection limit of this LAMP assay for Foc was 10 fg of genomic DNA per reaction, while that of conventional PCR was 100 pg. Conclusions In conclusion, it was found that a LAMP assay combined with HNB is simple, rapid, sensitive, and specific. The LAMP assay does not require specialized equipment, hence can be used in the field for the rapid detection of Foc. This is the first report of the use of LAMP assay for the detection of Foc. The presented LAMP method provides a specific, sensitive and rapid diagnostic tool for the distinction of Foc, with the potential to be standardized as a detection method for Foc in endemic areas and will be very useful for monitoring the disease complex in the field further suggesting the management strategies. Electronic supplementary material The online version of this article (doi:10.1186/s13104-015-0997-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Raju Ghosh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, PO 502324, Andhra Pradesh, India.
| | - Avuthu Nagavardhini
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, PO 502324, Andhra Pradesh, India.
| | - Anindita Sengupta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, PO 502324, Andhra Pradesh, India.
| | - Mamta Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, PO 502324, Andhra Pradesh, India.
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Pan L, Li J, Zhang WN, Dong L. Detection of the I1781L mutation in fenoxaprop-p-ethyl-resistant American sloughgrass (Beckmannia syzigachne Steud.), based on the loop-mediated isothermal amplification method. PEST MANAGEMENT SCIENCE 2015; 71:123-30. [PMID: 24644047 DOI: 10.1002/ps.3777] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 03/11/2014] [Accepted: 03/12/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND The increasing use of fenoxaprop-p-ethyl has resulted in evolved resistance in American sloughgrass (Beckmannia syzigachne Steud.). Target-site-based resistance to acetyl-CoA carboxylase (ACCase) inhibitors in B. syzigachne occurs owing to an isoleucine-to-leucine substitution at residue 1781 (I1781L) of the ACCase enzyme. A rapid detection method is needed to identify the resistance-conferring substitution. RESULTS Four populations of B. syzigachne that were resistant to fenoxaprop-p-ethyl and contained the I1781L substitution were identified. Conventional PCR and derived cleaved amplified polymorphic sequence (dCAPS) methods were used to detect the mutation. Additionally, a rapid nucleic acid detection method, loop-mediated isothermal amplification (LAMP), was successfully developed and used to detect the genetic mutation underlying the I1781L substitution in the B. syzigachne ACCase enzyme. CONCLUSION This report is the first to describe the application of a LAMP assay for mutation detection in herbicide-resistant weeds. The assay does not require specialised equipment: only a standard laboratory bath is needed. This technique could be employed for detecting the I1781L substitution in B. syzigachne plants and seeds.
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Affiliation(s)
- Lang Pan
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China; Key Laboratory of Integrated Management of Crop Diseases and Pests (Nanjing Agricultural University), Ministry of Education, Nanjing, China
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Duan Y, Zhang X, Ge C, Wang Y, Cao J, Jia X, Wang J, Zhou M. Development and application of loop-mediated isothermal amplification for detection of the F167Y mutation of carbendazim-resistant isolates in Fusarium graminearum. Sci Rep 2014; 4:7094. [PMID: 25403277 PMCID: PMC4235284 DOI: 10.1038/srep07094] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 10/29/2014] [Indexed: 11/24/2022] Open
Abstract
Resistance of Fusarium graminearum to carbendazim is caused by point mutations in the β2-tubulin gene. The point mutation at codon 167 (TTT → TAT, F167Y) occurs in more than 90% of field resistant isolates in China. To establish a suitable method for rapid detection of the F167Y mutation in F. graminearum, an efficient and simple method with high specificity was developed based on loop-mediated isothermal amplification (LAMP). A set of four primers was designed and optimized to specially distinguish the F167Y mutation genotype. The LAMP reaction was optimal at 63 °C for 60 min. When hydroxynaphthol blue dye (HNB) was added prior to amplification, samples with DNA of the F167Y mutation developed a characteristic sky blue color after the reaction but those without DNA or with different DNA did not. Results of HNB staining method were reconfirmed by gel electrophoresis. The developed LAMP had good specificity, stability and repeatability and was suitable for monitoring carbendazim-resistance populations of F. graminearum in agricultural production.
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Affiliation(s)
- Yabing Duan
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoke Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Changyan Ge
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yong Wang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Junhong Cao
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaojing Jia
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jianxin Wang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mingguo Zhou
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
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Duan YB, Ge CY, Zhang XK, Wang JX, Zhou MG. Development and evaluation of a novel and rapid detection assay for Botrytis cinerea based on loop-mediated isothermal amplification. PLoS One 2014; 9:e111094. [PMID: 25329402 PMCID: PMC4203854 DOI: 10.1371/journal.pone.0111094] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 09/22/2014] [Indexed: 11/19/2022] Open
Abstract
Botrytis cinerea is a devastating plant pathogen that causes grey mould disease. In this study, we developed a visual detection method of B. cinerea based on the Bcos5 sequence using loop-mediated isothermal amplification (LAMP) with hydroxynaphthol blue dye (HNB). The LAMP reaction was optimal at 63 °C for 45 min. When HNB was added prior to amplification, samples with B. cinerea DNA developed a characteristic sky blue color after the reaction but those without DNA or with DNA of other plant pathogenic fungi did not. Results of HNB staining method were reconfirmed when LAMP products were subjected to gel electrophoresis. The detection limit of this LAMP assay for B. cinerea was 10(-3) ng µL(-1) of genomic DNA per reaction, which was 10-fold more sensitive than conventional PCR (10(-2) ng µL(-1)). Detection of the LAMP assay for inoculum of B. cinerea was possible in the inoculated tomato and strawberry petals. In the 191 diseased samples, 180 (94.2%) were confirmed as positive by LAMP, 172 (90.1%) positive by the tissue separation, while 147 (77.0%) positive by PCR. Because the LAMP assay performed well in aspects of sensitivity, specificity, repeatability, reliability, and visibility, it is suitable for rapid detection of B. cinerea in infected plant materials prior to storage and during transportation, such as cut flowers, fruits and vegetables.
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Affiliation(s)
- Ya-Bing Duan
- College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Chang-Yan Ge
- College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Xiao-Ke Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Jian-Xin Wang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
| | - Ming-Guo Zhou
- College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu Province, China
- * E-mail:
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Zhang X, Zhang H, Pu J, Qi Y, Yu Q, Xie Y, Peng J. Development of a real-time fluorescence loop-mediated isothermal amplification assay for rapid and quantitative detection of Fusarium oxysporum f. sp. cubense tropical race 4 in soil. PLoS One 2013; 8:e82841. [PMID: 24376590 PMCID: PMC3869718 DOI: 10.1371/journal.pone.0082841] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 11/07/2013] [Indexed: 12/02/2022] Open
Abstract
Fusarium oxysporum f. sp. cubense (Foc), the causal agent of Fusarium wilt (Panama disease), is one of the most devastating diseases of banana (Musa spp.). The Foc tropical race 4 (TR4) is currently known as a major concern in global banana production. No effective resistance is known in Musa to Foc, and no effective measures for controlling Foc once banana plants have been infected in place. Early and accurate detection of Foc TR4 is essential to protect banana industry and guide banana planting. A real-time fluorescence loop-mediated isothermal amplification assay (RealAmp) was developed for the rapid and quantitative detection of Foc TR4 in soil. The detection limit of the RealAmp assay was approximately 0.4 pg/µl plasmid DNA when mixed with extracted soil DNA or 10(3) spores/g of artificial infested soil, and no cross-reaction with other relative pathogens were observed. The RealAmp assay for quantifying genomic DNA of TR4 was confirmed by testing both artificially and naturally infested samples. Quantification of the soil-borne pathogen DNA of Foc TR4 in naturally infested samples was no significant difference compared to classic real-time PCR (P>0.05). Additionally, RealAmp assay was visual with an improved closed-tube visual detection system by adding SYBR Green I fluorescent dye to the inside of the lid prior to amplification, which avoided the inhibitory effects of the stain on DNA amplification and makes the assay more convenient in the field and could thus become a simple, rapid and effective technique that has potential as an alternative tool for the detection and monitoring of Foc TR4 in field, which would be a routine DNA-based testing service for the soil-borne pathogen in South China.
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Affiliation(s)
- Xin Zhang
- Ministry of Agriculture Key Laboratory of Integrated Pest Management on Tropical Crops, Environmental and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - He Zhang
- Ministry of Agriculture Key Laboratory of Integrated Pest Management on Tropical Crops, Environmental and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jinji Pu
- Ministry of Agriculture Key Laboratory of Integrated Pest Management on Tropical Crops, Environmental and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yanxiang Qi
- Ministry of Agriculture Key Laboratory of Integrated Pest Management on Tropical Crops, Environmental and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Qunfang Yu
- Ministry of Agriculture Key Laboratory of Integrated Pest Management on Tropical Crops, Environmental and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yixian Xie
- Ministry of Agriculture Key Laboratory of Integrated Pest Management on Tropical Crops, Environmental and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jun Peng
- Ministry of Agriculture Key Laboratory of Integrated Pest Management on Tropical Crops, Environmental and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- State Key Laboratory of Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, China
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Peng J, Zhan Y, Zeng F, Long H, Pei Y, Guo J. Development of a real-time fluorescence loop-mediated isothermal amplification assay for rapid and quantitative detection of Fusarium oxysporum f. sp. niveum in soil. FEMS Microbiol Lett 2013; 349:127-34. [PMID: 24256412 DOI: 10.1111/1574-6968.12305] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 10/13/2013] [Accepted: 10/15/2013] [Indexed: 11/30/2022] Open
Abstract
Fusarium wilt caused by Fusarium oxysporum f. sp. niveum (Fon) is one of the major limiting factors for watermelon production worldwide. Rapid and accurate detection of the causal pathogen is the cornerstone of integrated disease management. In this paper, a real-time fluorescence loop-mediated isothermal amplification (RealAmp) assay was developed for the rapid and quantitative detection of Fon in soil. Positive products were amplified only from Fon isolates and not from any other species or formae speciales of F. oxysporum tested, showing a high specificity of the primer sets. The detection limit of the RealAmp assay was 1.2 pg μL(-1) genomic DNA or 10(3) spores g(-1) of artificially inoculated soil, whereas real-time PCR could detect as low as 12 fg μL(-1) or 10(2) spores g(-1). The RealAmp assay was further applied to detect eight artificially inoculated and 85 field soil samples. No significant differences were found between the results tested by the RealAmp and real-time PCR assays. The RealAmp assay is a simple, rapid and effective technique for the quantitative detection and monitoring of Fon in soil under natural conditions.
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Affiliation(s)
- Jun Peng
- Key Laboratory of the Ministry of Agriculture for Integrated Pest Management on Tropical Crops, Institute of Environmental and Plant Protection, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
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Abstract
Embryo biotechnology has become one of the prominent high businesses worldwide. This technology has evolved through three major changes, that is, traditional embryo transfer (in vivo embryo production by donor superovulation), in vitro embryo production by ovum pick up with in vitro fertilization and notably current cloning technique by somatic cell nuclear transfer and transgenic animal production. Embryo biotechnology has widely been used in dairy and beef cattle industry and commercial bovine embryo transfer has become a large international business. Currently, many developed biotechnologies during the period from early oocyte stage to pre-implantation embryos can be used to create new animal breeds and accelerate genetic progression. Based on recent advances in embryo biotechnologies and authors current studies, this review will focus on a description of the application of this technology to beef cattle improvement and discuss how to use this technology to accelerate beef cattle breeding and production. The main topics of this presentation include the following: (i) how to increase calf production numbers from gametes including sperm and oocyte; (ii) multiple ovulation and embryo transfer breeding schemes; (iii) in vitro fertilization and intracytoplasm sperm injection in bovine; (iv) pronuclear development and transgenic animals; (v) sex selection from sperm and embryos; (vi) cloning and androgenesis; (vii) blastocyst development and embryonic stem cells; (viii) preservation of beef cattle genetic resources; and (ix) conclusions.
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Affiliation(s)
- B Wu
- Arizona Center for Reproductive Endocrinology and Infertility, Tucson, AZ 85712, USA.
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