Detection of Goss's wilt pathogen clavibacter michiganensis subsp. nebraskensis in maize by loop-mediated amplification

Phytopathology

Volumn 106, Issue 3, 2016, Pages 226-235

  Yasuhara Bell, Jarred ^a   De Silva, Asoka ^a   Heuchelin, Scott A ^b   Chaky, Jennifer L ^b   Alvarez, Anne M ^a  

^a UNIVERSITY OF HAWAII   (United States)

^b DUPONT COMPANY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; BACTERIAL PROTEIN;

ACTINOBACTERIA; GENE EXPRESSION REGULATION; GENETICS; ISOLATION AND PURIFICATION; MAIZE; METABOLISM; MICROBIOLOGY; NUCLEIC ACID AMPLIFICATION; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT DISEASE; PROCEDURES;

ACTINOBACTERIA; BACTERIAL PROTEINS; BASE SEQUENCE; DNA, BACTERIAL; GENE EXPRESSION REGULATION, BACTERIAL; NUCLEIC ACID AMPLIFICATION TECHNIQUES; PHYLOGENY; PLANT DISEASES; ZEA MAYS;

EID: 84961752039     PISSN: 0031949X     EISSN: None     Source Type: Journal    
DOI: 10.1094/PHYTO-10-15-0249-R     Document Type: Article

References (71)

1. Agarkova, I. V., Lambrecht, P. A., and Vidaver, A. K. 2011. Genetic diversity and population structure of Clavibacter michiganensis subsp. nebraskensis. Can. J. Microbiol. 57:366-374.
2. Altschul, S. F., Gish, W., Miller, W., Ew, M., and Lipman, D. J. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
3. Alvarez, A. M., Derie, M., Benedict, A., and Gabrielson, R. 1993. Characteristics of a monoclonal antibody to Clavibacter michiganensis subsp. michiganensis. Phytopathology 83:1405.
4. Alvarez, A. M., and Kaneshiro, W. S. 1999:Pages 93-97 in: Detection and identification of Clavibacter michiganensis subsp. michiganensis in tomato seed. Intl. Seed Testing Assn., Zurich, Switzerland.
5. Alvarez, A. M., Kaneshiro, W. S., and Vine, B. G. 2005. Diversity of Clavibacter michiganensis subsp. michiganensis populations in tomato seed: What is the significance? Acta Hortic. 695:205-213.
6. Bach, H.-J., Jessen, I., Schloter, M., and Munch, J. C. 2003. A Taqman-PCR protocol for quantification and differentiation of the phytopathogenic Clavibacter michiganensis subspecies. J. Microbiol. Methods 52:85-91.
7. Biddle, J. A., Braun, E. J., and McGee, D. C. 1985. Epidemiology and seed transmission of Goss's wilt in corn. Proc. Iowa Acad. Sci. 92:Abstract 19.
8. Biddle, J. A., McGee, D. C., and Braun, E. J. 1990. Seed transmission of Clavibacter michiganense subsp. michiganense in corn. Plant Dis. 74:908-911.
9. Calub, A. G., Schuster, M. L., Compton, W. A., and Gardner, C. O. 1974a. Effect of plant age and inoculum concentration on leaf freckles and wilt of corn. Crop Sci. 14:398-401.
10. Calub, A. G., Schuster, M. L., Compton, W. A., and Gardner, C. O. 1974b. Improved technique for evaluating resistance of corn to Corynebacterium nebraskense. Crop Sci. 14:716-718.
11. Carlson, M. L., and Wicks, Z. W. III. 1991. Relationship between leaf freckles and wilt severity and yield losses in closely related maize hybrids. Phytopathology 81:95-98.
12. Craw, P., and Balachandran, W. 2012. Isothermal nucleic amplification technologies for point-of-care diagnostics: A critical review. Lab Chip 12: 2469-2486.
13. Davis, M. J., Gillespie, A. G. J., Vidaver, A. K., and Harris, R. W. 1984. Clavibacter: A new genus containing some phytopathogenic coryneform bacteria, including Clavibacter xyli subsp. xyli sp. nov, subsp. nov. and Clavibacter xyli subsp. cynodontis subsp. nov., pathogens that cause ratoon stunting disease of sugarcane and bermudagrass stunting disease. Int. J. Syst. Bacteriol. 34:107-117.
14. Doupnik, J. R., and Wysong, D. S. 1977. Page 22 in: Nebraska Corn Variety Tests for Reactions to Goss's Wilt and Blight. University of Nebraska, Lincoln.
15. Eichenlaub, R., and Gartemann, K. H. 2011. The Clavibacter michiganensis subspecies: Molecular investigation of gram-positive bacterial plant pathogens. Annu. Rev. Phytopathol. 49:71-720.
16. Eichenlaub, R., Gartemann, K. H., and Burger, A. 2006. Clavibacter michiganensis, a group of Gram-positive phytopathogenic bacteria. Pages 385-422 in: Plant-Associated Bacteria. S. S. Ganamanikam, ed. Springer, Dordrecht, the Netherlands.
17. FAOSTAT. 2012. Food and agricultural commodities production. In: Food and Agricultural Organization of the United Nations, FAOSTAT.
18. Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.
19. Fujino, M., Yoshida, N., Yamaguchi, S., Hosaka, N., Ota, Y., Notomi, T., and Nakayama, T. 2005. A simple method for the detection of measles virus genome by loop-mediated isothermal amplification (LAMP). J. Med. Virol. 76:406-413.
20. Gitaitis, R. D., Beaver, R. W., and Voloudakis, A. E. 1991. Detection of Clavibacter michiganensis subsp. michiganensis in symptomless tomato transplants. Plant Dis. 75:834-838.
21. González, A. J., and Trapiello, E. 2014. Clavibacter michiganensis subsp. phaseoli subsp. nov., pathogenic in bean. Int. J. Syst. Evol. Microbiol. 64: 1752-1755.
22. Gross, D. C., and Vidaver, A. K. 1979. A selective medium for isolation of Corynebacterium nebraskense from soil and plant parts. Phytopathology 69:82-87.
23. Harris-Baldwin, A., and Gudmestad, N. C. 1996. Identification of phytopathogenic coryneform bacteria using the Biolog automated microbial identification system. Plant Dis. 80:874-878.
24. Jenkins, D. M., Kubota, R., Dong, J., Li, Y., and Higashiguchi, D. 2011. Handheld device for real-time, quantitative, LAMP-based detection of Salmonella enterica using assimilating probes. Biosens. Bioelectron. 30: 255-260.
25. Jukes, T. H., and Cantor, C. R. 1969. Evolution of protein molecules. Pages 21-132 in: Mammalian Protein Metabolism. H. N. Munro, ed. Academic Press, New York.
26. Kaneshiro, W. S. 2003. Detection and characterization of virulent, hypovirulent, and nonvirulent Clavibacter michiganensis subsp. michiganensis. University of Hawaii at Manoa, Honolulu.
27. Kaneshiro, W. S., and Alvarez, A. M. 2001. Specificity of PCR and ELISA assays for hypovirulent and avirulent Clavibacter michiganensis subsp. michiganensis. (Abstr.) Phytopathology 91(suppl.):S46.
28. Kaneshiro, W. S., Mizumoto, C. Y., and Alvarez, A. M. 2006. Differentiation of Clavibacter michiganensis subsp. michiganensis from seed-borne saprophytes using ELISA, Biolog and 16S DNA sequencing. Eur. J. Plant Pathol. 116:45-56.
29. Kokošková, B., Miŕaz, I., and Fousek, J. 2010. Comparison of specificity and sensitivity of immunochemical and molecular techniques for determination of Clavibacter michiganensis subsp. michiganensis. Folia Microbiol. (Praha) 55:239-244.
30. Korus, K. A. 2011. Evaluating commercially available diagnostic tests for the detection of Clavibacter michiganensis subsp. nebraskensis, cause of Goss's bacterial wilt and leaf blight in corn. University of Nebraska, Lincoln, NE.
31. Korus, K. A., Timmerman, A. D., French-Monar, R. D., and Jackson, T. A. 2011. First report of Goss's bacterial wilt and leaf blight (Clavibacter michiganensis subsp. nebraskensis) of corn in Texas. Plant Dis. 95:73.
32. Krämer, I., and Griesbach, E. 2005. Use of ELISA for detection of Clavibacter michiganensis subsp. michiganensis in tomato. OEPP/EPPO Bull. 25:185- 193.
33. Kubota, R., Alvarez, A. M., Su, W. W., and Jenkins, D. M. 2011. FRET-based assimilating probe for sequence-specific real-time monitoring of loopmediated isothermal amplification (LAMP). Biol. Eng. Trans. 4:81-100.
34. Labarre, P., Gerlach, J. L., Wilmoth, J., Beddoe, A., Singleton, J., and Weigl, B. H. 2010. Non-instrumented nucleic acid amplification (NINA): Instrument-free molecular malaria diagnostics for low-resource settings. Conf. Proc. IEEE Eng. Med. Biol. Soc. 2010:1097-1099.
35. Louws, F. J., Bell, J., Medina-Mora, C. M., Smart, C. D., Opgenorth, D., Ishimaru, C. A., Hausbeck, M. K., de Bruijn, F. J., and Fulbright, D. W. 1998. rep-PCR-mediated genomic fingerprinting: A rapid and effective method to identify Clavibacter michiganensis. Phytopathology 88:862-868.
36. Miller, T. E., and Schroth, M. N. 1972. Monitoring the epiphytic population of Erwinia amylovora on pear with a selective medium. Phytopathology 62: 1175-1182.
37. Mori, Y., Hirano, T., and Notomi, T. 2006. Sequence specific visual detection of LAMP reactions by addition of cationic polymers. BMC Biotechnol. 6:3.
38. Mori, Y., Kitao, M., Tomita, N., and Notomi, T. 2004. Real-time turbidimetry of LAMP reaction for quantifying template DNA. J. Biochem. Biophys. Methods 59:145-157.
39. Mori, Y., Nagamine, K., Tomita, N., and Notomi, T. 2001. Detection of loopmediated isothermal amplification by turbidity derived from magnesium pyrophosphate formation. Biochem. Biophys. Res. Commun. 289:150-154.
40. Nei, M., and Kumar, S. 2000. Molecular Evolution and Phylogenetics. Oxford University Press, New York.
41. Ngong-Nassah, E. N., Carson, M. L., and Wicks, Z. W. 1992. Inheritance of resistance to leaf freckles and wilt caused by Clavibacter michiganense subsp. nebraskense in early maturing maize inbred lines. Phytopathology 82:142-146.
42. Pataky, J. K. 1985. Relationships among reactions of sweet corn hybrids to Goss's wilt, Stewart's bacterial wilt, and northern corn leaf blight. Plant Dis. 69:845-848.
43. Pataky, J. K. 1989. Influence of host resistance and growth stage at the time of inoculation on Stewart's wilt and Goss's wilt development and sweet corn hybrid yield. Plant Dis. 73:339-345.
44. Pataky, J. K., and Headrick, J. M. 1988. Classification of sweet corn hybrid reactions to common rust, northern leaf blight, Stewart's wilt, and Goss's wilt and associated yield reductions. Phytopathology 78:172-178.
45. Rocheford, T. R., Vidaver, A. K., Gardner, C. O., and Arbrust, D. L. 1985. Effect of wind-generated sand abrasion on infection of corn (Zea mays L.) by Corynebacterium michiganense spp. nebraskense. Phytopathology 75:1378.
46. Ruhl, G., Wise, K., Creswell, T., Leonberger, A., and Speers, C. 2009. First report of Goss's bacterial wilt and leaf blight on corn caused by Clavibacter michiganensis subsp. nebraskensis in Indiana. Plant Dis. 93:841.
47. Saitou, N., and Nei, M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
48. Schneider, K. L., Marrero, G., Alvarez, A. M., and Presting, G. G. 2011. Classification of plant associated bacteria using RIF, a computationally derived DNA marker. PLoS One 6:e18496.
49. Schuster, M. L. 1970. Robert W. Goss 1891-1970. Obituary. Phytopathology 60:1156.
50. Schuster, M. L. 1972. Leaf freckles and wilt, a new corn disease. Proc. Annu. Corn Sorghum Res. Conf. 27:176-191.
51. Schuster, M. L., Compton, W. A., and Hoff, B. 1972. Reaction of corn inbred lines to the new Nebraska leaf freckles and wilt bacterium. Plant Dis. Rep. 56:863-865.
52. Schuster, M. L., and Coyne, D. P. 1974. Survival mechanisms of phytopathogenic bacteria. Annu. Rev. Phytopathol. 12:199-221.
53. Schuster, M. L., Hoff, B., and Compton, W. A. 1975. Variation, maintenance, loss, and failure to recover virulence in Corynebacterium nebraskense. Plant Dis. Rep. 59:101-105.
54. Smidt, M., and Vidaver, A. K. 1986. Population dynamics of Clavibacter michiganense subsp. nebraskense in field-grown dent corn and popcorn. Plant Dis. 70:1031-1036.
55. Smith, N. C., Hennessy, J., and Stead, D. E. 2001. Repetitive sequence-derived PCR profiling using the BOX-A1R primer for rapid identification of the plant pathogen Clavibacter michiganensis subsp. sepedonicus. Eur. J. Plant Pathol. 107:739-748.
56. Sudarshana, P., May, M., Kurowski, C., and Thomas, S. 2012. Characterization of saprophytic bacteria that react with Clavibacter michiganensis subsp. michiganensis in seed health testing. Phytopathology 102(Suppl. 4):115.
57. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., and Kumar, S. 2011. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28:2731-2739.
58. Tomita, N., Mori, Y., Kanda, H., and Notomi, T. 2008. Loop-mediated isothermal amplification (LAMP) of gene sequences and simple visual detection products. Nat. Protoc. 3:877-882.
59. Vidaver, A. K., Gross, D. C., Wysong, D. S., and Doupnik, J. R. 1981. Diversity of Corynebacterium nebraskense strains causing Goss's bacterial wilt and blight of corn. Plant Dis. 65:480-483.
60. Vidaver, A. K., and Mandel, M. 1974. Corynebacterium nebraskense, a new, orange-pigmented phytopathogenic species. Int. J. Syst. Bacteriol. 24: 482-485.
61. Waleron, M., Waleron, K., Kamasa, J., Przewodowski, W., and Lojkowaska, E. 2011. Polymorphism analysis of housekeeping genes for identification and differentiation of Clavibacter michiganensis subspecies. Eur. J. Plant Pathol. 131:341-354.
62. Weisburg, W. G., Barns, S. M., Pelleteir, D. A., and Lane, D. J. 1991. 16S ribosomal amplification for phylogenetic study. J. Bacteriol. 173:697- 703.
63. Wysong, D. S., Doupnik, J. R., and Lane, L. 1981. Goss's wilt and corn lethal necrosis - Can they become a major problem? Pages 104-130 in: Proc. Annu. Corn Sorghum Res. Conf. American Seed Trade Association, Washington, D.C.
64. Wysong, D. S., Vidaver, A. K., Stevens, H., and Stenberg, D. 1973. Occurrence and spread of an undescribed species of Corynebacterium, pathogenic on corn in the western corn belt. Plant Dis. Rep. 57:291-294.
65. Yasuhara-Bell, J. 2014. Establishment and validation of loop-mediated amplification for specific detection of tomato bacterial pathogen Clavibacter michiganensis subsp. michiganensis. University of Hawaii, Honolulu, HI.
66. Yasuhara-Bell, J., and Alvarez, A. M. 2015. Seed-associated Clavibacter spp. are clearly distinguishable from Clavibacter michiganensis subsp. michiganensis. Int. J. Syst. Evol. Microbiol. 65:811-826.
67. Yasuhara-Bell, J., Ayin, C. M., Hatada, A., Yoo, Y., Schlub, R. L., and Alvarez, A. M. 2015a. Detection of Klebsiella variicola and K. oxytoca by loopmediated amplification. J. Plant Pathol. Microbiol. 6:271.
68. Yasuhara-Bell, J., Baysal-Gurel, F., Miller, S. A., and Alvarez, A. M. 2015b. Utility of a loop-mediated amplification assay for detection of Clavibacter michiganensis subsp. michiganensis in seeds and plant tissues. Can. J. Plant Pathol. 37:260-266.
69. Yasuhara-Bell, J., Kubota, R., Jenkins, D. M., and Alvarez, A. M. 2013. Loopmediated amplification of the Clavibacter michiganensis subsp. michiganensis micA gene is highly specific. Phytopathology 103:1220-1226.
70. Yasuhara-Bell, J., Marrero, G., and Alvarez, A. M. 2014. Genes clvA, clvF and clvG are unique to Clavibacter michiganensis subsp. michiganensis and highly conserved. Eur. J. Plant Pathol. 140:655-664.
71. Zaluga, J., Heylen, K., Van Hoorde, K., Hoste, B., Van Vaerenbergh, J., Maes, M., and De Vos, P. 2011. GyrB sequence analysis and MALDI-TOF MS as identification tools for plant pathogenic Clavibacter. Syst. Appl. Microbiol. 34:400-407.