Multiplex real-time quantitative pcr to detect and quantify Verticillium dahliae colonization in potato lines that differ in response to verticillium wilt

Phytopathology

Volumn 97, Issue 7, 2007, Pages 865-872

  Atallah, Z K ^a   Bae, J ^a   Jansky, S H ^a   Rouse, D I ^a   Stevenson, W R ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MONOPLEX; SOLANUM TUBEROSUM; VERTICILLIUM DAHLIAE;

EID: 34447134943     PISSN: 0031949X     EISSN: None     Source Type: Journal    
DOI: 10.1094/PHYTO-97-7-0865     Document Type: Article

References (65)

1. Atallah, Z. K., and Stevenson, W. R. 2006. A methodology to detect and quantify five pathogens causing potato tuber decay using real-time quantitative PCR. Phytopathology 96:1037-1045.
2. Bowden, R. L., and Rouse, D. I. 1987. Effects of Verticillium dahliae on photosynthesis and transpiration of potato. Phytopathology 77:1703-1703.
3. Bowden, R. L., and Rouse, D. I. 1991. Effects of Verticillium dahliae on gas exchange of potato. Phytopathology 81:293-301.
4. Bowden, R. L., Rouse, D. I., and Sharkey, T. D. 1990. Mechanism of photosynthesis decrease by Verticillium dahliae in potato. Plant Physiol. 94:1048-1055.
5. Brody, H., and Carbon, J. 1989. Electrophoretic karyotype of Aspergillus nidulans. Proc. Natl. Acad. Sci. USA 86:6260-6263.
6. Butterfield, E. J., and Devay, J. E. 1977. Reassessment of soil assays for Verticillium dahliae. Phytopathology 67:1073-1078.
7. Carbone, I., and Kohn, L. M. 1999. A method for designing primer sets for speciation studies in filamentous Ascomycetes. Mycologia 91:553-556.
8. Cochran, W. G., and Cox, G. M. 1957. Experimental Designs, 2nd ed. John Wiley and Sons, New York.
9. Collins, A., Okoli, C. A. N., Morton, A., Parry, D., Edwards, S. G., and Barbara, D. J. 2003. Isolates of Verticillium dahliae pathogenic to crucifers are of at least three distinct molecular types. Phytopathology 93:364-376.
10. Corsini, D. L., Pavek, J. J., and Davis, J. R. 1990. Verticillium wilt resistant potato germplasm - A66107-51 and A68113-4. Am. Potato J. 67:517-525.
11. Cullen, D. W., Lees, A. K., Toth, I. K., and Duncan, J. M. 2001. Conventional PCR and real-time quantitative PCR detection of Helminthosporium solani in soil and on potato tubers. Eur. J. Plant Pathol. 107:387-398.
12. Cullen, D. W., Lees, A. K., Toth, I. K., and Duncan, J. M. 2002. Detection of Colletotrichum coccodes from soil and potato tubers by conventional and quantitative real-time PCR. Plant Pathol. 51:281-292.
13. Dan, H., Ali-Khan, S. T., and Robb, J. 2001. Use of quantitative PCR diagnostics to identify tolerance and resistance to Verticillium dahliae in potato. Plant Dis. 85:700-705.
14. Davis, J. R., Pavek, J. J., and Corsini, D. L. 1983. A sensitive method for quantifying Verticillium dahliae colonization in plant tissue and evaluating resistance among potato genotypes. Phytopathology 73:1009-1014.
15. Davis, J. R., Pavek, J. J., Corsini, D. L., Sorensen, L. H., Schneider, A. T., Everson, D. O., Westermann, D. T., and Huisman, O. C. 1994. Influence of continuous cropping of several potato clones on the epidemiology of Verticillium wilt of potato. Phytopathology 84:207-214.
16. Davis, J. R., and Sorensen, L. H. 1986. Benefits and problems associated with metam-sodium treatments on potato. Am. Potato J. 63:418-419.
17. Davis, J. R., and Sorensen, L. H. 1986. Differential effects of potato genotype and metam sodium on the population dynamics of Verticillium spp. Phytopathology 76:1094-1094.
18. Davis, J. R., Sorensen, L. H., Corsini, D. L., and Hafez, S. L. 1983. Effects of continuous cropping with potato genotypes on Verticillium dahliae and Pratylenchus neglectus. Phytopathology 73:958-958.
19. Davis, J. R., Sorensen, L. H., Stark, J. C., and Westermann, D. T. 1990. Fertility and management - practices to control Verticillium wilt of the Russet Burbank potato. Am. Potato J. 67:55-65.
20. Frackman, S., Ekenberg, S., Hoffmann, K., Krenke, B., Sprecher, C., and Starts, D. 2005. Plexor technology: A new chemistry for real-time PCR. Promega Notes 90:2-4.
21. Gao, X., Jackson, T. A., Lambert, K. N., Li, S., Hartman, G. L., and Niblack, T. L. 2004. Detection and quantification of Fusarium solani f. sp. glycines in soybean roots with real-time quantitative polymerase chain reaction. Plant Dis. 88:1372-1380.
22. Glass, N. L., and Donaldson, G. C. 1995. Development of primer sets designed for use with the PCR to amplify conserved genes from filamentous Ascomycetes. Appl. Environ. Microbiol. 61:1323-1330.
23. Hall, T. A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acid Symp. Ser. 41:95-98.
24. Hamm, P. B., Ingham, R. E., Jaeger, J. R., Swanson, W. H., and Volker, K. C. 2003. Soil fumigant effects on three genera of potential soilborne pathogenic fungi and their effect on potato yield in the Columbia Basin of Oregon. Plant Dis. 87:1449-1456.
25. Hoyos, G. P., Lauer, F. I., and Anderson, N. A. 1993. Early detection of Verticillium wilt resistance in a potato breeding program. Am. Potato J. 70:535-541.
26. Jansky, S., Rouse, D. I., and Kauth, P. J. 2004. Inheritance of resistance to Verticillium dahliae in diploid interspecific potato hybrids. Plant Dis. 88:1075-1078.
27. Jansky, S. H., and Rouse, D. I. 2000. Identification of potato interspecific hybrids resistant to Verticillium wilt and determination of criteria for resistance assessment. Potato Res. 43:239-251.
28. Jansky, S. H., and Rouse, D. I. 2003. Multiple disease resistance in interspecific hybrids of potato. Plant Dis. 87:266-272.
29. Jeger, M. J., Hide, G. A., VandenBoogert, P., Termorshuizen, A. J., and VanBaarlen, P. 1996. Pathology and control of soil-borne fungal pathogens of potato. Potato Res. 39:437-469.
30. Kimpinski, J., Platt, H. W., Perley, S., and Walsh, J. R. 1998. Pratylenchus spp. and Verticillium spp. in New Brunswick potato fields. Am. J. Potato Res. 75:87-91.
31. Ko, K. S., and Jung, H. S. 2002. Three nonorthologous ITS1 types are present in a polypore fungus Trichaptum abietinum. Mol. Phylogenet. Evol. 23:112-122.
32. Lees, A. K., Cullen, D. W., Sullivan, L., and Nicolson, M. J. 2002. Development of conventional and quantitative real-time PCR assays for the detection and identification of Rhizoctonia solani AG-3 in potato and soil. Plant Pathol. 51:293-302.
33. Li, K. N., Rouse, D. I., Eyestone, E. J., and German, T. L. 1999. The generation of specific DNA primers using random amplified polymorphic DNA and its application to Verticillium dahliae. Mycol. Res. 103:1361-1368.
34. Lynch, D. R., Chen, Q., Kawchuk, L. M., and Driedger, D. 2004. Verticillium wilt resistant germplasm-release of clone LRC18-21 and derivatives. Am. J. Potato Res. 81:295-297.
35. Mahuku, G. S., and Platt, H. W. 2002. Quantifying Verticillium dahliae in soils collected from potato fields using a competitive PCR assay. Am. J. Potato Res. 79:107-117.
36. Mahuku, G. S., Platt, H. W., and Maxwell, P. 1999. Comparison of polymerase chain reaction based methods with plating on media to detect and identify Verticillium wilt pathogens of potato. Can. J. Plant Pathol. 21:125-131.
37. Mercado-Blanco, J., Rodriguez-Jurado, D., Parrilla-Araujo, S., and Jimenez-Diaz, R. M. 2003. Simultaneous detection of the defoliating and nondefoliating Verticillium dahliae pathotypes in infected olive plants by duplex, nested polymerase chain reaction. Plant Dis. 87:1487-1494.
38. Mohan, S. K., Davis, J. R., Corsini, D. L., Sorensen, L. H., and Pavek, J. J. 1987. Comparison of methods for evaluation of potato genotypes for resistance to Verticillium wilt. Phytopathology 77:1702-1702.
39. Mohan, S. K., Davis, J. R., Corsini, D. L., Sorensen, L. H., and Pavek, J. J. 1990. Reaction of potato clones and accessions of Solanum spp. to Verticillium dahliae Kleb and its toxin. Potato Res. 33:449-458.
40. Morgan, G. D., Stevenson, W. R., MacGuidwin, A. E., Kelling, K. A., Binning, L. K., and Zhu, J. 2002. Plant pathogen population dynamics in potato fields. J. Nematol. 34:189-193.
41. Mpofu, S. I., and Hall, R. 2003. Accuracy and precision of population estimates of Verticillium dahliae on growth media in quantitative soil assays. Can. J. Bot. (Rev. Can. Bot.) 81:294-306.
42. Nahimana, A., Francioli, P., Blanc, D. S., Bille, J., Wakefield, A. E., and Hauser, P. M. 2000. Determination of the copy number of the nuclear rDNA and beta-tubulin genes of Pneumocystis carinii f. sp hominis using PCR multicompetitors. J. Eukaryot. Microbiol. 47:368-372.
43. Nicot, P. C., and Rouse, D. I. 1987. Relationship between soil inoculum density of Verticillium dahliae and systemic colonization of potato stems in commercial fields over time. Phytopathology 77:1346-1355.
44. Paris, R., and Lamattina, L. 2002. Increased ratio of mitochondrial rDNA to cytoplasmic rDNA during zoosporic and germinating cyst stages of the life cycle of Phytophthora infestans (Mont.) de Bary. Can. J. Microbiol. 48:268-274.
45. Pegg, G. F., and Street, P. F. S. 1984. Measurement of Verticillium alboatrum in high and low resistance hop cultivars. Trans. Br. Mycol. Soc. 82:99-106.
46. Powelson, M. L., and Rowe, R. C. 1993. Biology and management of early dying of potatoes. Annu. Rev. Phytopathol. 31:111-126.
47. Ristaino, J. B., Madritch, M., Trout, C. L., and Parra, G. 1998. PCR amplification of ribosomal DNA for species identification in the plant pathogen genus Phytophthora. Appl. Environ. Microbiol. 64:948-954.
48. Rowe, R. C., Davis, J. R., Powelson, M. L., and Rouse, D. I. 1987. Potato early dying - causal agents and management strategies. Plant Dis. 71:482-489.
49. Rowe, R. C., and Powelson, M. L. 2002. Potato early dying: management challenges in a changing production environment. Plant Dis. 86:1184-1193.
50. Rozen, S., and Skaletsky, H. 2000. Primer3 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. Sadras, V. O., Quiroz, F. Echarte, L., Escande, A., and Pereyra, V. R. 2000. Effect of Verticillium dahliae on photosynthesis, leaf expansion and senescence of field-grown sunflower. Ann. Bot. 86:1007-1015.
52. Saeed, I. A. M., MacGuidwin, A. E., Rouse, D. I., and Sharkey, T. D. 1999. Limitation to photosynthesis in Pratylenchus penetrans- and Verticillium dahliae-infected potato. Crop Sci. 39:1340-1346.
53. 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.
54. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F., and Higgins, D. G. 1997. The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876-4882.
55. 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.
56. Tooley, P. W., Bunyard, B. A., Carras, M. M., and Hatziloukas, E. 1997. Development of PCR primers from internal transcribed spacer region 2 for detection of Phytophthora species infecting potatoes. Appl. Environ. Microbiol. 63:1467:1475.
57. Tooley, P. W., Carras, M. M., and Lambert, D. H. 1998. Application of a PCR-based test for detection of potato late blight and pink pot in tubers. Am. J. Potato Res. 75:187-194.
58. Trout, C. L., Ristaino, J. B., Madritch, M., and Wangsomboondee, T. 1997. Rapid detection of Phytophthora infestans in late blight-infected potato and tomato using PCR. Plant Dis. 81:1042-1048.
59. Valsesia, G., Gobbin, D., Patocchi, A., Vecchione, A., Pertot, I., and Gessler, C. 2005. Development of a high-throughput method for quantification of Plasmopara viticola DNA in grapevine leaves by means of quantitative real-time polymerase chain reaction. Phytopathology 95:672-678.
60. Wen, K., Seguin, P., St-Arnaud, M., and Jabaji-Hare, S. 2005. Real-time quantitative RT-PCR of defense-associated gene transcripts of Rhizoctonia solani-infected bean seedlings in response to inoculation with a nonpathogenic binucleate Rhizoctonia isolate. Phytopathology 95:345-353.
61. Wheeler, T. A., Madden, L. V., Rowe, R. C., and Riedel, R. M. 2000. Effects of quadrat size and time of year for sampling of Verticillium dahliae and lesion nematodes in potato fields. Plant Dis. 84:961-966.
62. Wheeler, T. A., Rowe, R. C., Riedel, R. M., and Madden, L. V. 1994. Influence of cultivar resistance to Verticillium spp. on potato early dying. Am. Potato J. 71:39-57.
63. Winton, L. M., Manter, D. K., Stone, J. K., and Hansen, E. A. 2003. Comparison of biochemical, molecular, and visual methods to quantify Phaeocryptopus gaeumannii in Douglas-Fir foliage. Phytopathology 93:121-126.
64. 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.
65. Zuker, M., Mathews, D. H., and Turner, D. H. 1999. Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide in RNA Biochemistry and biotechnology. J. Barciszewski and B. F. C. Clark, eds. Kluwer Academic Publishers, Dordrecht, the Netherlands.