Simultaneous detection of Acidovorax avenae subsp. citrulli and Didymella bryoniae in cucurbit seedlots using magnetic capture hybridization and real-time polymerase chain reaction

Phytopathology

Volumn 99, Issue 6, 2009, Pages 666-678

  Ha, Y ^a   Fessehaie, A ^b   Ling, K S ^c   Wechter, W P ^c   Keinath, A P ^d   Walcott, R R ^a  

^a UNIVERSITY OF GEORGIA   (United States)

^b IOWA STATE UNIVERSITY   (United States)

^c Department of Agriculture Agricultural Research Service   (United States)

^d CLEMSON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; FUNGAL DNA;

ARTICLE; ASCOMYCETES; CHEMISTRY; COMAMONADACEAE; CUCUMBER; GENETICS; GROWTH, DEVELOPMENT AND AGING; ISOLATION AND PURIFICATION; METHODOLOGY; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEIC ACID HYBRIDIZATION; NUCLEOTIDE SEQUENCE; PLANT DISEASE; POLYMERASE CHAIN REACTION;

ASCOMYCOTA; BASE SEQUENCE; COMAMONADACEAE; CUCURBITACEAE; DNA, BACTERIAL; DNA, FUNGAL; MOLECULAR SEQUENCE DATA; NUCLEIC ACID HYBRIDIZATION; PLANT DISEASES; POLYMERASE CHAIN REACTION;

ACIDOVORAX AVENAE SUBSP. CITRULLI; BACTERIA (MICROORGANISMS); CITRULLUS LANATUS VAR. LANATUS; CUCUMIS; DIDYMELLA BRYONIAE;

EID: 67650074531     PISSN: 0031949X     EISSN: None     Source Type: Journal    
DOI: 10.1094/PHYTO-99-6-0666     Document Type: Article

References (52)

1. Amagliani, G., Omiccioli, E., del Campo, A., Bruce, I. J., Brandi, G., and Magnani, M. 2006. Development of a magnetic capture hybridization PCR assay for Listeria monocytogenes direct detection in milk samples. J. Appl. Microbiol. 100:375-383.
2. Anonymous. 2004. National Seed Health System, Seed Health Methods, Vegetable Crop Methods. Published online by the NSHS-USDA-APHIS. http://www.seedhealth.org.
3. Arezi, B., Xing, W., Sorge, J. A., and Hogrefe, H. H. 2003. Amplification efficiency of thermostable DNA polymerases. Anal. Biochem. 321:226-235.
4. Chen, J., and Griffiths, M. W. 2001. Detection of Salmonella and simultaneous detection of Salmonella and Shiga-like toxin-producing Escherichia coli using the magnetic capture hybridization polymerase chain reaction. Lett. Appl. Microbiol. 32:7-11.
5. Chen, J. R., Johnson, R., and Griffiths, M. 1998. Detection of vero-toxigenic Escherichia coli by magnetic capture hybridization PCR. Appl. Environ. Microbiol. 64:147-152.
6. Chilvers, M. I., du Toit, L. J., Akamatsu, H., and Peever, T. L. 2007. A real-time, quantitative PCR seed assay for Botrytis spp. that cause neck rot of onion. Plant Dis. 91:599-608.
7. Chiu, W. F., and Walker, J. C. 1949. Physiology and pathogenicity of the cucurbit black rot fungus. J. Agric. Res. 78:589-615.
8. DeBoer, S. H., Ward, L. J., Li, X., and Chittaranjan, S. 1995. Attenuation of PCR inhibition in the presence of plant compounds by addition of Blotto. Nucleic Acids Res. 23:2567-2568.
9. de Moraes, R. R., Maruniak, J. E., and Funderburk, J. E. 1999. Methods for detection of Anticarsia gemmatalis nucleopolyhedrovirus DNA in soil. Appl. Environ. Microbiol. 65:2307-2311.
10. Dupont, K., Vogensen, F. K., and Josephsen, J. 2005. Detection of lactococcal 936-species bacteriophages in whey by magnetic capture hybridization PCR targeting a variable region of receptor-binding protein genes. J. Appl. Microbiol. 98:1001-1009.
11. Enroth, H., and Engstrand, L. 1995. Immunomagnetic separation and PCR for detection of Helicobacter pylori in water and stool specimens. J. Clin. Microbiol. 33:2162-2165.
12. Gitaitis, R., and Walcott, R. R. 2007. The epidemiology and management of seedborne bacterial diseases. Annu. Rev. Phytopathol. 45:371-397.
13. Guillemette, T., Iacomi-Vasilescu, B., and Simoneau, P. 2004. Con-ventional and real-time PCR-based assay for detecting pathogenic Alternaria brassicae in cruciferous seed. Plant Dis. 88:490-496.
14. Hayward, C. 1996. Molecular biology in systematics and diagnosis of phytopathogenic prokaryotes. Phytoparasitica 24:271-275.
15. Jacobsen, C. S. 1995. Microscale detection of specific bacterial DNA in soil with a magnetic capture hybridization and PCR amplification assay. Appl. Environ. Microbiol. 61:3347-3352.
16. Keinath, A. P. 2000. Effect of protectant fungicide application schedules on gummy stem blight epidemics and marketable yield of watermelon. Plant Dis. 84:254-260.
17. Keinath, A. P. 2002. Survival of Didymella bryoniae in buried watermelon vines in South Carolina. Plant Dis. 86:32-38.
18. Keinath, A. P., Farnham, M. W., and Zitter, T. A. 1995. Morphological, pathological, and genetic differentiation of Didymella bryoniae and Phoma spp. isolated from cucurbits. Phytopathology 85:364-369.
19. Keinath, A. P., Somai, B. M., and Dean, R. A. 2001. Method of diag-nosing gummy stem blight in plants using a polymerase chain reaction assay. U. S. Patent 6, 258, 537 B1.
20. King, E. O., Ward, M. K., and Raney, D. E. 1954. Two simple media for the demonstration of pyocyanin and fluorescin. J. Lab. Clin. Med. 44:301-307.
21. Koch, C. A., Li, P. C. H., and Utkhede, R. S. 2005. Evaluation of thin films of agarose on glass for hybridization of DNA to identify plant pathogens with microarray technology. Anal. Biochem. 342:93-102.
22. Koch, C. A., and Utkhede, R. S. 2002. Diagnosis and identification of Didymella bryoniae, causal agent of gummy stem blight of greenhouse cucumbers, using a dot blot technique. J. Hortic. Sci. Biotechnol. 77:62-66.
23. Koch, C. A., and Utkhede, R. S. 2004. Development of a multiplex classical polymerase chain reaction technique for detection of Didymella bryoniae in infected cucumber tissues and greenhouse air samples. Can. J. Plant Pathol. 26:291-298.
24. Koike, S. T. 1997. First report of gummy stem blight, caused by Didymella bryoniae, on watermelon transplants in California. Plant Dis. 81:1331.
25. Kontanis, E. J., and Reed, F. A. 2006. Evaluation of real-time PCR amplification efficiencies to detect PCR inhibitors. J. Forensic Sci. 51 (4) :795-804.
26. Kothera, R. T., Keinath, A. P., Dean, R. A., and Farnham, M. W. 2003. AFLP analysis of a worldwide collection of Didymella bryoniae. Mycol. Res. 107:297-304.
27. Krasilnikova, M. M., and Veselkov, A. G. 1996. Enhancing the specificity of peptide nucleic acid binding with DNA. Mol. Biol. 30:226-230.
28. Langrell, S. R. H., and Barbara, D. J. 2001. Magnetic capture hybridi-zation for improved PCR detection of Nectria galligena from lignified apple extracts. Plant Mol. Biol. Rep. 19:5-11.
29. Latin, R. X., and Hopkins, D. L. 1995. Bacterial fruit blotch of water-melon-the hypothetical exam question becomes reality. Plant Dis. 79:761-765.
30. National Agricultural Statistics Service. 2008. Vegetables 2007 Summary. NASS, USDA, Vg 1-2 (08) :7-35
31. Nielsen, P. E., and Christensen, L. 1996. Strand displacement binding of a duplex forming homopurine PNA to a homopyrimidine duplex DNA target. J. Am. Chem. Soc. 118:2287-2288.
32. O'Sullivan, C. E., Kasai, M., Francesconi, A., Petraitis, V., Petraitiene, R., Kelaher, A. M., Sarafandi, A. A., and Walsh, T. J. 2003. Development and validation of a quantitative real-time PCR assay using fluorescence resonance energy transfer technology for detection of Aspergillus fumigatus in experimental invasive pulmonary aspergillosis. J. Clin. Microbiol. 41:5676-5682.
33. Pruvost, M., and Geigl, E.-M. 2004. Real-time quantitative PCR to assess the authenticity of ancient DNA amplification. J. Arch. Sci. 31:1191-1197.
34. Pryor, B. M., and Gilbertson, R. L. 2001. A PCR-based assay for detection of Alternaria radicina on carrot seed. Plant Dis. 85:18-23.
35. Punithalingam, E., and Holliday, P. 1972. Didymella bryoniae. CMI Description of Pathogenic Fungi and Bacteria. No. 332. Commonwealth Mycol. Inst., Kew, England.
36. Rane, K. K., and Latin, R. X. 1992. Bacterial fruit blotch of water-melon-association of the pathogen with seed. Plant Dis. 76:509-512.
37. Saiki, R. K., Gelfand, D. H., Stoffel, S., Scharf, S. J., Higuchi, R., Horn, G. T., Mullis, K. B., and Erlich, H. A. 1988. Primer directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487-491.
38. Sambrook, J., and Russell, D. W., eds. 2001. Molecular Cloning: A Labora-tory Manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
39. Schaad, N. W., Sowell, G., Goth, R. W., Colwell, R. R., and Webb, R. E. 1978. Pseudomonas pseudoalcaligenes subsp. citrulli subsp. nov. Int. J. Syst. Bacteriol. 28:117-125.
40. Shin, G. Y., Manuel, R. J., Ghori, S., Brecker, S., and Breathnach, A. S. 2005. Molecular technique identifies the pathogen responsible for culture negative infective endocarditis. Heart 91:47-48.
41. Somai, B. M., Dean, R. A., Farnham, M. W., Zitter, T. A., and Keinath, A. P. 2002. Internal transcribed spacer regions 1 and 2 and random amplified polymorphic DNA analysis of Didymella bryoniae and related Phoma species isolated from cucurbits. Phytopathology 92:997-1004.
42. Somai, B. M., Keinath, A. P., and Dean, R. A. 2002. Development of PCR-ELISA for detection and differentiation of Didymella bryoniae from related Phoma species. Plant Dis. 86:710-716.
43. Song, W. Y., Kim, H. M., Hwang, C. Y., and Schaad, N. W. 2004. Detection of Acidovorax avenae ssp. avenae in rice seeds using BIO-PCR. J. Phytopathol. 152:667-676.
44. Straub, T. M., Dockendorff, B. P., Quinonez-Diaz, M. D., Valdez, C. O., Shutthanandan, J. I., Tarasevich, B. J., Grate, J. W., and Bruckner-Lea, C. J. 2005. Automated methods for multiplexed pathogen detection. J. Microbiol. Methods 62:303-316.
45. Walcott, R. R., Castro, A. C., Fessehaie, A., and Ling, K. 2006. Progress towards a commercial PCR-based seed assay for Acidovorax avenae subsp. citrulli. Seed Sci. Technol. 34:101-116.
46. Walcott, R. R., Fessehaie, A., and Castro, A. C. 2004. Differences in pathogenicity between two genetically distinct groups of Acidovorax avenae subsp. citrulli on cucurbit hosts. J. Phytopathol. 152:277-285.
47. Walcott, R. R., and Gitaitis, R. D. 2000. Detection of Acidovorax avenae subsp. citrulli in watermelon seed using immunomagnetic separation and the polymerase chain reaction. Plant Dis. 84:470-474.
48. Walcott, R. R., Gitaitis, R. D., and Langston, D. B. 2004. Detection of Botrytis aclad a in onion seed using magnetic capture hybridization and the polymerase chain reaction. Seed Sci. Technol. 32:425-438.
49. Weiland, J. J. 1997. Rapid DNA preparation from fungal spores and mycelia. Fungal Genet. Newsl. 44:60-63.
50. Willems, A., Goor, M., Thielemans, S., Gillis, M., Kersters, K., and Deley, J. 1992. Transfer of several phytopathogenic Pseudomonas species to Acidovorax as Acidovorax avenae subsp. avenae subsp. Nov. Comb. Nov. Acidovorax avenae subsp. citrulli, Acidovorax avenae subsp. cattleyae, and Acidovorax konjaci. Int. J. Syst. Bacteriol. 42:107-119.
51. Zhang, T., Herbert, H., and Fang, P. 2006. Applications of real-time polymerase chain reaction for quantification of microorganisms in environmental samples. Appl. Microbiol. Biotechnol. 70:281-289.
52. Zitter, T. A., Hopkins, D. L., and Thomas, C. E., eds. 1996. Compendium of Cucurbit Diseases. The American Phytopathological Society, St. Paul, MN.