A real-time, quantitative PCR seed assay for Botrytis spp. that cause neck rot of onion

Plant Disease

Volumn 91, Issue 5, 2007, Pages 599-608

  Chilvers, Martin I ^a   Du Toit, Lindsey J ^a   Akamatsu, Hajime ^a   Peever, Tobin L ^a  

^a WASHINGTON STATE UNIVERSITY   (United States)

Author keywords

Kinetic PCR; Scape blight; Umbel blight

Indexed keywords

DNA; PLANTS (BOTANY); SEED;

KINETIC PCR; SCAPE BLIGHT; UMBEL BLIGHT;

BIOASSAY;

BIOLOGICAL TESTS; NUCLEIC ACIDS; PLANTS; SEEDS;

ALLIUM CEPA; BOTRYTIS; BOTRYTIS ACLADA; BOTRYTIS ALLII; BOTRYTIS BYSSOIDEA; SCLEROTINIA SCLEROTIORUM;

EID: 34247502711     PISSN: 01912917     EISSN: None     Source Type: Journal    
DOI: 10.1094/PDIS-91-5-0599     Document Type: Article

References (76)

1. Bates, J. A., and Taylor, E. J. A. 2001. Scorpion ARMS primers for SNP real-time PCR detection and quantification of Pyrenophora teres. Mol. Plant Pathol. 2:275-280.
2. Bochow, H. 1981. Studies of seed-borne transmission of Botrytis allii Munn in onion (Allium cepa L.) and possibilities of interfering by seed treatment with fungicides. Arch. Phytopathol. 8:31-38.
3. Böhm, J., Hahn, A., Schubert, R., Bahnweg, G., Adler, N., Nechwatal, J., Oehlmann, R., and Osswald, W. 1999. Real-time quantitative PCR: DNA determination in isolated spores of the mycorrhizal fungus Glomus mosseae and monitoring of Phytophthora infestans and Phytophthora citricola in their respective host plants. J. Phytopathol. 147:409-416.
4. Brewster, J. L., ed. 1994. Onions and Other Vegetable Alliums. CAB International, Wallingford, Oxon, UK.
5. Bustin, S. A., ed. 2004. A-Z of Quantitative PCR. IUL Biotechnology Series, La Jolla, CA.
6. Chilvers, M. I. 2003. Epidemiology of Botrytis spp. associated with neck rot of onion in northern Tasmania, Australia. Ph.D. diss. University of Tasmania, Burnie, Australia.
7. Chilvers, M. I., and du Toit, L. J. 2006. Detection and identification of Botrytis species associated with neck rot, scape blight, and umbel blight of onion. Plant Health Progress doi:10.1094/PHP-2006-1127-01-DG.
8. Chilvers, M. I., Hay, F. S., and Wilson, C. R. 2004. Survey for Botrytis species associated with onion in northern Tasmania, Australia. Australas. Plant Pathol. 33:419-422.
9. Chilvers, M. I., Pethybridge, S. J., Hay, F. S., and Wilson, C. R. 2004. Characterisation of Botrytis species associated with neck rot of onion in Australia. Australas. Plant Pathol. 33:29-32.
10. Cullen, D. W., and Hirsch, P. R. 1998. Simple and rapid method for direct extraction of microbial DNA from soil for PCR. Soil Biol. Biochem. 30:983-993.
11. Dennis, J. 1996. Botrytis epidemic disastrous in Tasmania. Onions Aust. 13:21-22.
12. du Toit, L. J. 2004. Management of diseases of seed crops. Pages 675-677 in: Encyclopedia of Plant and Crop Sciences. R. M. Goodman, ed. Marcel Dekker, New York.
13. du Toit, L. J., Derie, M. L., and Pelter, G. Q. 2004. Botrytis species associated with onion seed crops in Washington State. Plant Dis. 88:1061-1068.
14. du Toit, L. J., Derie, M. L., and Pelter, G. Q. 2004. Efficacy of fungicide seed treatments and foliar applications for management of Botrytis aclada in onion bulb and seed crops in Washington. Pages 185-194 in: Proc. 2004 National Allium Res. Conf., 9-10 December 2004, Grand Junction, CO.
15. 2 from contingency tables, and the calculation of P. J. R. Stat. Soc. 85:87-94.
16. Guillemette, T., Iacomi-Vasilescu, B., and Simoneau, P. 2004. Conventional and real-time PCR-based assay for detecting pathogenic Alternaria brassicae in cruciferous seed. Plant Dis. 88:490-496.
17. Haugland, R. A., Brinkman, N., and Vesper, S. J. 2002. Evaluation of rapid DNA extraction methods for the quantitative detection of fungi using real-time PCR analysis. J. Microbial Methods 50:319-323.
18. Hayden, K. J., Rizzo, D., Tse, J., and Garbelotto, M. 2004. Detection and quantification of Phytophthora ramorum from Californian forests using a real-time polymerase chain reaction assay. Phytopathology 94:1075-1083.
19. Hennebert, G. L. 1963. Les Botrytis des Allium. Meded. LandbHoogessch. OpzoeksStns. Gent 28:851-876.
20. Hennebert, G. L. 1973. Botrytis and Botrytis like genera. Persoonia 7:183-204.
21. Kritzman, G., and Netzer, D. 1978. A selective medium for isolation and identification of Botrytis spp. from soil and onion seed. Phytoparasitica 6:3-7.
22. Kupfer, D. M., Reece, C. A., Clifton, S. W., Roe, B. A., and Prade, R. A. 1997. Multicellular ascomycetous fungal genomes contain more than 8000 genes. Fungal Genet. Biol. 21:364-372.
23. Lacy, M. L., and Lorbeer, J. W. 1995. Botrytis neck rot. Pages 18-19 in: Compendium of Onion and Garlic Diseases. H. F. Schwartz and S. K. Mohan, eds. American Phytopathological Society, St. Paul, MN.
24. Lee, H. K., Tewari, J. P., and Turkington, T. K. 2002. Quantification of seedborne infection by Rhynchosporium secalis in barley using competitive PCR. Plant Pathol. 51:217-224.
25. Lee, S. B., and Taylor, J. W. 1990. Isolation of DNA from fungal mycelia and single spores. Pages 282-287 in: PCR protocols: A Guide to Methods and Applications. M. A. Innis, D. H. Gelfand, J. J. Snisky, and T. J. White, eds. Academic Press, San Diego, CA.
26. Linfield, C. A., Kenny, S. R., and Lyons, N. F. 1995. A serological test for detecting Botrytis allii, the cause of neck rot of onion bulbs. Ann. Appl. Biol. 126:259-268.
27. Mackay, I. M., Arden, K. E., and Nitsche, A. 2002. Real-time PCR in virology. Nucleic Acids Res. 30:1292-1305.
28. Maude, R. B. 1983. The correlation between seed-borne infection by Botrytis allii and neck rot development in store. Seed Sci. Technol. 11:829-834.
29. Maude, R. B., and Presly, A. H. 1977. Neck rot (Botrytis allii) of bulb onions. I. Seed-borne infection and its relationship to the disease in the onion crop. Ann. Appl. Biol. 86:163-180.
30. Maude, R. B., and Presly, A. H. 1977. Neck rot (Botrytis allii) of bulb onions. II. Seed-borne infection in relationship to the disease in store and the effect of seed treatment. Ann. Appl. Biol. 86:181-188.
31. McNeil, M., Roberts, A. M. I., Cockerell, V., and Mulholland, V. 2004. Real-time PCR assay for quantification of Tilletia caries contamination of UK wheat seed. Plant Pathol. 53:741-750.
32. Metcalf, D. 1998. Botrytis seed testing - what the results mean? Onions Aust. 15:33-34.
33. Moller, E. M., Bahnweg, G., Sandermann, H., and Geiger, H. H. 1992. A simple and efficient protocol for isolation of high molecular weight DNA from filamentous fungi, fruit bodies, and infected plant tissue. Nucleic Acids Res. 20:6115-6116.
34. Morrison, T. M., Weis, J. J., and Wittwer, C. T. 1998. Quantification of low-copy transcripts by continuous SYBR green I monitoring during amplification. Biotechniques 24:954-962.
35. Mungari, R. J. 2001. Testing onion seed. Pages 11-12 in: Onion World, July/August 2001. Columbia Publishing, Yakima, WA.
36. Nielsen, K., Justesen, A. F., Funck Jensen, D., and Yohalem, D. S. 2001. Universally primed polymerase chain reaction alleles and internal transcribed spacer restriction fragment length polymorphisms distinguish two subgroups in Botrytis aclada distinct from B. byssoidea. Phytopathology 91:527-533.
37. Nielsen, K., Justesen, A. F., and Yohalem, D. S. 1999. PCR based detection of latent infections of Botrytis aclada Fres. in onion bulbs. Petria 9:105-108.
38. Nielsen, K., and Yohalem, D. S. 2001. Origin of a polyploid Botrytis pathogen through interspecific hybridization between Botrytis aclada and B. byssoidea. Mycologia 93:1064-1071.
39. Nielsen, K., Yohalem, D. S., and Jensen, D. F. 2002. PCR detection and RFLP differentiation of Botrytis species associated with neck rot of onion. Plant Dis. 86:682-686.
40. Okubara, P. A., Schroeder, K. L., and Paulitz, T. C. 2005. Real-time polymerase chain reaction: Applications to studies on soilborne pathogens. Can. J. Plant Pathol. 27:300-313.
41. Overduin, M. 2001. Letters to the editor. Page 13 in: Onion World, March/April 2001. Columbia Publishing, Yakima, WA.
42. Owen, J. H., Walker, J. C., and Stahmann, M. A. 1950. Variability in onion neck-rot fungi. Phytopathology 40:749-768.
43. Pantou, M. P., Mavridou, A., and Typas, M. A. 2003. IGS sequence variation, group-I introns and the complete nuclear ribosomal DNA of the entomopathogenic fungus Metarhizium: Excellent tools for isolate detection and phylogenetic analysis. Fungal Genet. Biol. 38:159-174.
44. Peever, T. L., Canihos, Y., Olsen, L., Ibanez, A., Liu, Y.-C., and Timmer, L. W. 1999. Population genetic structure and host specificity of Alternaria spp. causing brown spot of Minneola tangelo and rough lemon in Florida. Phytopathology 89:851-860.
45. Peters, I. R., Helps, C. R., Hall, E. J., and Day, M. J. 2004. Real-time RT-PCR: Considerations for efficient and sensitive assay design. J. Immunol. Methods 286:203-217.
46. Pramateftaki, P. V., Antoniou, P. P., and Typas, M. A. 2000. The complete DNA sequence of the nuclear ribosomal RNA gene complex of Verticillium dahliae: Intraspecific heterogeneity within the intergenic spacer region. Fungal Genet. Biol. 29:19-27.
47. Presly, A. H. 1985. Studies of Botrytis spp. occurring on onions (Allium cepa) and leeks (Allium porrum). Plant Pathol. 34:422-427.
48. Presly, A. H. 1985. Methods for inducing sporulation of some Botrytis species occurring on onions and leeks. Trans. Br. Mycol. Soc. 85:621-624.
49. 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.
50. Rozen, S., and Skaletsky, H. J. 2000. Primer 3 on the WWW for general users and for biologist programmers. Pages 365-386 in: Bioinformatics Methods and Protocols: Methods in Molecular Biology. S. Krawetz and S. Misener, eds. Humana Press, Totowa, NJ.
51. Sambrook, J., Fritsch, E. F., and Maniatis, T., eds. 1989. Molecular Cloning: A Laboratory Manual. 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
52. Schena, L., Nigro, F., Ippolito, A., and Gallitelli, D. 2004. Real-time quantitative PCR: A new technology to detect and study phytopathogenic and antagonistic fungi. Eur. J. Plant Pathol. 110:893-908.
53. Schreiber, A., and Ritchie, L. 1995. Washington Minor Crops. Washington State University Food and Environmental Quality Lab, Richland, WA.
54. Schroeder, K. L., Okubara, P. A., Tambong, J. T., Lévesque, C. A., and Paulitz, T. C. 2006. Identification and quantification of pathogenic Pythium spp. from soils in eastern Washington using real-time polymerase chain reaction. Phytopathology 96:637-647.
55. Schwartz, H. F., and Mohan, S. K., eds. 1995. Compendium of Onion and Garlic Diseases. American Phytopathological Society, St. Paul, MN.
56. Schweigkofler, W., O'Donnell, K., and Garbelotto, M. 2004. Detection and quantification of airborne conidia of Fusarium circinatum, the causal agent of pine pitch canker, from two California sites by using a real-time PCR approach combined with a simple spore trapping method. Appl. Environ. Microbiol. 70:3512-3520.
57. Shah, C. A., Böni, J., Bisset, L. R., Seebach, J. D., and Schüpbach, J. 2003. Ultra-sensitive and specific detection of porcine endogenous retrovirus (PERV) using a sequence-captured real-time PCR approach. J. Virol. Methods 109:209-216.
58. Shirane, N., Masuko, M., and Hayashi, Y. 1989. Light microscopic observation of nuclei and mitotic chromosomes of Botrytis species. Phytopathology 79:728-730.
59. Silvar, C., Díaz, J., and Merino, F. 2005. Real-time polymerase chain reaction quantification of Phytophthora capsici in different pepper genotypes. Phytopathology 95:1423-1429.
60. Staats, M., van Baarlen, P., and van Kan, J. A. L. 2005. Molecular phylogeny of the plant pathogenic genus Botrytis and the evolution of host specificity. Mol. Biol. Evol. 22:333-346.
61. Stewart, A., and Franicevic, S. C. 1994. Infected seed as a source of inoculum for Botrytis infection of onion bulbs in store. Australas. Plant Pathol. 23:36-40.
62. Suarez, M. B., Walsh, K., Boonham, N., O'Neill, T., Pearson, S., and Barker, I. 2005. Development of real-time PCR (TaqMan®) assays for the detection and quantification of Botrytis cinerea in planta. Plant Physiol. Biochem. 43:890-899.
63. Taylor, E., Bates, J., Kenyon, D., Maccaferri, M., and Thomas, J. 2001. Modern molecular methods for characterisation and diagnosis of seed-borne fungal pathogens. J. Plant Pathol. 83:75-81.
64. Taylor, E. J. A., Stevens, E. A., Morreale, G., Lee, D., Kenyon, D. M., and Thomas, J. E. 2001. Rapid-cycle PCR detection of Pyrenophora graminea from barley seed. Plant Pathol. 50:347-355.
65. Thomas, J., Schreiber, A., Pelter, G. Q., and Havens, D. 1997. Washington's small-seeded vegetable seed industry. Washington State Univ. Ext. Bull. No. 1829, Pullman, WA.
66. Thompson, J. D., Higgins, D. G., and Gibson, T. J. 1994. Clustal W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
67. Tichelaar, G. M. 1967. Studies on the biology of Botrytis allii on Allium cepa. Neth. J. Plant Pathol. 73:157-160.
68. Tylkowska, K., and Dorna, H. 2001. Onion (Allium cepa) seed and plant health with special reference to Botrytis allii. Phytopathol. Pol. 21:55-68.
69. van der Heide, J. 2001. Trade talk. Page 11 in: Onion World, May/June. Columbia Publishing, Yakima, WA.
70. Vandermark, G. J., and Barker, B. M. 2003. Quantifying Phytophthora medicaginis in susceptible and resistant alfalfa with a real-time fluorescent PCR assay. J. Phytopathol. 151:577-583.
71. Walcott, R. R. 2003. Detection of seedborne pathogens. HortTechnology 13:40-47.
72. Walcott, R. R., Gitaitis, R. D., and Langston, D. B. J. 2004. Detection of Botrytis aclada in onion seed using magnetic capture hybridization and the polymerase chain reaction. Seed Sci. Technol. 32:425-438.
73. Walker, J. C. 1925. Two undescribed species of Botrytis associated with the neck rot diseases of onion bulbs. Phytopathology 15:708-713.
74. Winton, L. M., Stone, J. K., Watrud, L. S., and Hansen, E. M. 2002. Simultaneous one-tube quantification of host and pathogen DNA with real-time polymerase chain reaction. Phytopathology 92:112-116.
75. Wong, M. L., and Medrano, J. F. 2005. Real-time PCR for mRNA quantification. BioTechniques 39:75-85.
76. Yohalem, D. S., Nielsen, K., and Nicholaisen, M. 2003. Taxonomic and nomenclatural clarification of the onion neck rotting Botrytis species. Mycotaxon 85:175-182.