Development of Loop-Mediated Isothermal Amplification (LAMP) assay for rapid detection of Fusarium oxysporum f. sp. ciceris - Wilt pathogen of chickpea

BMC Research Notes

Volumn 8, Issue 1, 2015, Pages

  Ghosh, Raju ^a   Nagavardhini, Avuthu ^a   Sengupta, Anindita ^a   Sharma, Mamta ^a  

^a INTERNATIONAL CROPS RESEARCH INSTITUTE FOR THE SEMI ARID TROPICS ICRISAT   (India)

Author keywords

Detection; Fusarium oxysporum; Hydroxynaphthol blue; Isothermal amplification; LAMP

Indexed keywords

ELONGATION FACTOR 1; FUNGAL DNA; FUNGAL PROTEIN; NAPHTHALENESULFONIC ACID DERIVATIVE; PRIMER DNA; TRISODIUM 3-HYDROXY-4-((2Z)-2-(2-OXO-4-SULFONATONAPHTHALEN-1-YLIDENE)HYDRAZINYL)NAPHTHALENE-2,7-DISULFONATE;

CHEMISTRY; CICER; CLASSIFICATION; FUSARIUM; GENETICS; GENOTYPE; ISOLATION AND PURIFICATION; LIMIT OF DETECTION; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEIC ACID AMPLIFICATION; NUCLEOTIDE SEQUENCE; PLANT DISEASE; PROCEDURES; SYNTHESIS;

BASE SEQUENCE; CICER; DNA PRIMERS; DNA, FUNGAL; FUNGAL PROTEINS; FUSARIUM; GENOTYPE; LIMIT OF DETECTION; MOLECULAR SEQUENCE DATA; NAPHTHALENESULFONATES; NUCLEIC ACID AMPLIFICATION TECHNIQUES; PEPTIDE ELONGATION FACTOR 1; PLANT DISEASES;

EID: 84924176976     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/s13104-015-0997-z     Document Type: Article

References (38)

1. FAOSTAT. Agriculture. http://faostat.fao.org.
2. AGRISTAT. Statistics at a glance 2011. http://agricoop. nic.in/agristatics.htm.
3. Haware MP, Nene YL. Races of Fusarium oxysporum. Plant Dis. 1982;66:809-10.
4. Halila MH, Strange RN. Identification of the causal agent of wilt of chickpea in Tunisia as Fusarium oxysporum f. sp. ciceri race. Phytopathol Mediterr. 1996;35:67-74.
5. Navas-Cortes JA, Hau B, Jimeiez-Diaz RM. Yield loss in chickpeas in relation to development of Fusarium wilt epidemics. Phytopathology. 2000;90:1269-78.
6. Jimeez-Gasco MM, Navas-Cortes JA, Jimeez-Diaz RM. The Foc/Cicer a pathosystem: a case study of the evolution of plant-pathogenic fungi into races and pathotypes. Internat Microbiol. 2004;7:95-104.
7. Sharma M, Nagavardhini A, Thudi M, Ghosh R, Pande S, Varshney RK. Development of DArT markers and assessment of diversity in Fusarium oxysporum f. sp. ciceris, wilt pathogen of chickpea (Cicer arietinum L.). BMC Genomics. 2014;15:454.
8. Faburay B, Geysen D, Munstermann S, Bell-Sakyi L, Jongejan F. Longitudinal monitoring of Ehrlichia ruminantium infection in Gambian lambs and kids by pCS20 PCR and MAP1-B ELISA. BMC Infect Dis. 2007;7:85.
9. Martinez D, Vachiery N, Stachurski F, Kandassamy Y, Raliniaina M, Aprelon R, et al. Nested PCR for detection and genotyping of Ehrlichia ruminantium: use in genetic diversity analysis. Ann N Y Acad Sci. 2004;1026:106-13.
10. Peixoto CC, Marcelino I, Vachiery N, Bensaid A, Martinez D, Carrondo MJ, et al. Quantification of Ehrlichia ruminantium by real time PCR. Vet Microbiol. 2005;107:273-8.
11. Steyn HC, Pretorius A, McCrindle CM, Steinmann CM, Van Kleef M. A quantitative real-time PCR assay for Ehrlichia ruminantium using pCS20. Vet Microbiol. 2008;131:258-65.
12. Pan L, Zhang L, Wang G, Liu Q, Yu Y, Wang S, et al. Rapid, simple, and sensitive detection of Anaplasma phagocytophilum by loop-mediated isothermal amplification of the msp2 Gene. Mol Biol Rep. 2011;38(6):4063-70.
13. Opel KL, Chung D, McCord BR. A study of PCR inhibition mechanisms using real time PCR. J Forensic Sci. 2010;55:25-33.
14. Notomi T, Okayama H, Masubuchi H, Yonekawa T, Watanabe K, et al. Loop-mediated isothermal amplification of DNA. Nucleic Acids Res. 2000;28:E63.
15. Mori Y, Notomi T, Loop-mediated isothermal amplification (LAMP). A rapid, accurate, and cost-effective diagnostic method for infectious diseases. J Infect Chemother. 2009;15:62-9.
16. Caipang CM, Haraguchi I, Ohira T, Hirono I, Aoki T. Rapid detection of a fish iridovirus using loop-mediated isothermal amplification (LAMP). J Virol Methods. 2004;121:155-61.
17. Tomita N, Mori Y, Kanda H, Notomi T. Loop-mediated isothermal amplification (LAMP) of gene sequences and simple visual detection of products. Nat Protoc. 2008;3:877-82.
18. Kaneko H, Kawana T, Fukushima E, Suzutani T. Tolerance of loop-mediated isothermal amplification to a culture medium and biological substances. J Biochem Biophys Methods. 2007;70:499-501.
19. Nagamine K, Hase T, Notomi T. Accelerated reaction by loop-mediated isothermal amplification using loop primers. Mol Cell Probes. 2002;16:223-9.
20. Goto M, Honda E, Ogura A, Nomoto A, Hanaki K. Colorimetric detection of loop-mediated isothermal amplification reaction by using hydroxy naphthol blue. Biotechniques. 2009;46:167-72.
21. Zoheir KM, Allam AA. A rapid improved method for sexing embryo of water buffalo. Theriogenology. 2011;76:83-7.
22. Bekele B, Hodgetts J, Tomlinson J, Boonham N, Nikoli, P, Swarbrick P, et al. Use of a real-time LAMP isothermal assay for detecting 16SrII and 16SrXII phytoplasmas in fruit and weeds of the Ethiopian Rift Valley. Plant Pathol. 2011;60:345-55.
23. Pan W, Wang JY, Shen HY, Zhao MQ, Ju CM, Dong XY, et al. Development and application of the novel visual loopmediated isothermal amplification of Omp25 sequence for rapid detection of Brucella sp. J Anim Vet Adv. 2011;10:2120-6.
24. Parida M, Posadas G, Inoue S, Hasebe F, Morita K. Realtime reverse transcription loop-mediated isothermal amplification for rapid detection of West Nile virus. J Clin Microbiol. 2004;42:257-63.
25. Niessen L, Vogel RF. Detection of Fusarium graminearum DNA using a loopmediated isothermal amplification (LAMP) assay. Int J Food Microbiol. 2010;140:183-91.
26. Mori Y, Nagamine K, Tomita N, Notomi T. Detection of loop-mediated isothermal amplification reaction by turbidity derived from magnesium pyrophosphate formation. Biochem Biophys Res Commun. 2001;289:150-4.
27. Bista BR, Ishwad C, Wadowsky RM, Manna P, Randhawa PS, Gupta G, et al. Development of a loop-mediated isothermal amplification assay for rapid detection of BK virus. J Clin Microbiol. 2007;45:1581-7.
28. Iwamoto T, Sonobe T, Hayashi K. Loop-mediated isothermal amplification for direct detection of Mycobacterium tuberculosis complex, M. avium, and M. intracellulare in sputum samples. J Clin Microbiol. 2003;41:2616-22.
29. Yoshida A, Nagashima S, Ansai T, Tachibana M, Kato H, Watari H, et al. Loopmediated isothermal amplification method for rapid detection of the periodontopathic bacteria Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola. J Clin Microbiol. 2005;43:2418-24.
30. Qiao YM, Guo YC, Zhang XE, Zhou YF, Zhang ZP, Wei HP, et al. Loopmediated isothermal amplification for rapid detection of Bacillus anthracis spores. Biotechnol Lett. 2007;29:1939-46.
31. Tomlinson JA, Barker I, Boonham N. Faster, simpler, more-specific methods for improved molecular detection of Phytophthora ramorum in the field. Appl Environ Microbiol. 2007;73:4040-7.
32. Nowotny N, Mostl K, Maderbacher R, Odorfer G, Schuh M. Serological studies in Austrian fattening pigs with respiratory disorders. Acta Vet Hung. 1994;42:377-9.
33. Curtis KA, Rudolph DL, Owen SM. Rapid detection of HIV-1 by reversetranscription, loop-mediated isothermal amplification (RT-LAMP). J Virol Methods. 2008;151:264-70.
34. Hill J, Beriwal S, Chandra I, Paul VK, Kapil A, et al. Loop-mediated isothermal amplification assay for rapid detection of common strains of Escherichia coli. J Clin Microbiol. 2008;46:2800-4.
35. Parida M, Horioke K, Ishida H, Dash PK, Saxena P, Jana AM, et al. Rapid detection and differentiation of dengue virus serotypes by a real-time reverse transcription-loop-mediated isothermal amplification assay. J Clin Microbiol. 2005;43:2895-903.
36. Wastling SL, Picozzi K, Kakembo AS, Welburn SC. LAMP for human African trypanosomiasis: a comparative study of detection formats. PLOS Neglect Trop D. 2010;4:e865.
37. Pande S, Rao NJ, Sharma M. Establishment of chickpea wilt pathogen Fusarium oxysporum f. sp. ciceris in the soil through seed transmission. Plant Pathol J. 2007;23(1):3-6.
38. Murray MG, Thompson WF. Rapid isolation of high molecular weight DNA. Nucleic Acids Res. 1980;8:4321-5.