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標題: 茄科細菌性斑點病菌檢測生物晶片之研發
Development of DNA Array for the Detection and Identification of Solanaceous Bacterial Spot-causing Xanthomonads
作者: Miao-Fang Ho
關鍵字: 細菌性斑點病
bacterial spot
polymerase chain reaction
DNA array
引用: 呂昀陞。2010。台灣茄科與十字花科作物 Xanthomonas 病原細菌之特性分析與檢測。中興大學植物病理學系所學位論文。 許博堯。2009。寡核?酸微陣列同時快速診斷鑑定多種重要防檢疫森林病原真菌之研發。台灣大學植物病理與微生物學研究所學位論文。 黃尚仁。2012。可同時檢測三種病毒之香蕉生物晶片系統之開發。朝陽科技大學生化科技研究所學位論文。 寧方俞。2012。鑑定及檢測茄科植物細菌性斑點病菌 Xanthomonas perforans 之聚合酵素連鎖反應技術及台灣 X. perforans 菌株之多型性分析。中興大學植物病理學系所學位論文。 Agrios, G. N. 2005. Plant diseases caused by prokaryotes. Plant pathology. 5th edition. Elsevier. Academic Press, San Diego, USA. 922pp. Albuquerque, P., Caridade, C. M., Marcal, A. R., Cruz, J., Cruz, L., Santos, C. L., Mendes, M. V., and Tavares, F. 2011. Identification of Xanthomonas fragariae, Xanthomonas axonopodis pv. phaseoli, and Xanthomonas fuscans subsp. fuscans with novel markers and using a dot blot platform coupled with automatic data analysis. Appl. Environ. Microbiol. 77: 5619-5628. Albuquerque, P., Caridade, C. M., Rodrigues, A. S., Marcal, A. R., Cruz, J., Cruz, L., Santos, C. L., and Mendes, M. V. 2012. Evolutionary and experimental assessment of novel markers for detection of Xanthomonas euvesicatoria in plant samples. PloS one 7: e37836. Ara?jo, E. R., Costa, J. R., Ferreira, M., and Quezado?Duval, A. M. 2012. Simultaneous detection and identification of the Xanthomonas species complex associated with tomato bacterial spot using species?specific primers and multiplex PCR. J. Appl. Microbiol. 113: 1479-1490. Ara?jo, E. R., Ferreira, M. A., and Quezado-Duval, A. M. 2013. Specific primers for Xanthomonas vesicatoria, a tomato bacterial spot causal agent. Eur. J. Plant Pathol. 1-5. Balogh, B., Jones, J. B., Momol, M. T., Olson, S. M., Obradovic, A., King, P., and Jackson, L. E. 2003. Improved efficacy of newly formulated bacteriophages for management of bacterial spot on tomato. Plant Dis. 87: 949-954. Bertucci, F., Bernard, K., Loriod, B., Chang, Y. C., Granjeaud, S., Birnbaum, D., Nguyen, C., Peck, K., and Jordan, B. R. 1999. Sensitivity issues in DNA array-based expression measurements and performance of nylon microarrays for small samples. Hum. Mol. Genet. 8: 1715-1722. Boonham, N., Tomlinson, J., and Mumford, R. 2007. Microarrays for rapid identification of plant viruses. Annu. Rev. Phytopathol. 45: 307-328. Bouzar, H., Jones, J. B., Stall, R. E., Hodge, N. C., Minsavage, G. V., Benedict, A. A., and Alvarez, A. M. 1994. Physiological, chemical, serological, and pathogenic analyses of a worldwide collection of Xanthomonas campestris pv. vesicatoria strains. Phytopathology 84: 663-671. Buonaurio, R., Stravato, V. M., and Cappelli, C. 1996. Occurrence of Pseudomonas syringae pv. tomato race 1 in Italy on pto gene?bearing tomato plants. J. Phytopathol. 144: 437-440. Call, D. R., Borucki, M. K., and Loge, F. J. 2003. Detection of bacterial pathogens in environmental samples using DNA microarrays. J. Microbiol. Methods 53: 235-243. Crowther, D. J. 2002. Applications of microarrays in the pharmaceutical industry. Curr. opinion Pharmacol. 2: 551-554. Davis, M. J., Gillaspie, A. G., 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. Doidge, E. M. 1921. A tomato canker. Ann. Appl. Biology 7: 407-430. Dowson, D. W. 1939. On the systematic position and generic names of the gram negative bacterial plant pathogens. Zentralbl. f. Bakt. Parasit. u. Infekt. 100: 177-193. Dye, D. W. 1966. Cultural and biochemical reaction of additional Xanthomonas species. New Zeal. J. Sci. 9: 913-919. Fayette, J., Roberts, P. D., Pernezny, K. L., and Jones, J. B. 2012. The role of cymoxanil and famoxadone in the management of bacterial spot on tomato and pepper and bacterial leaf spot on lettuce. Crop Protect. 31: 107-112. Gardan, L., Gouy, C., Christen, R., and Samson, R. 2003. Elevation of three subspecies of Pectobacterium carotovorum to species level: Pectobacterium atrosepticum sp. nov., Pectobacterium betavasculorum sp. nov. and Pectobacterium wasabiae sp. nov. Int. J. Syst. Evol. Microbiol. 53: 381-391. Gardner, M. W., and Kendrick, J. 1923. Bacterial spot of tomato and pepper. Phytopathology 13: 307-315. Gleason, M. L., Braun, E. J., Carlton, W. M., and Peterson, R. H. 1991. Survival and dissemination of Clavibacter michiganensis subsp. michiganensis in tomatoes. Phytopathology 81: 1519-1523. Harper, K., and Creamer, R. 1995. Hybridization detection of insect-transmitted plant viruses with digoxigenin-labeled probes. Plant Dis. 79: 563-567. Henegariu, O., Heerema, N. A., Dlouhy, S. R., Vance, G. H., and Vogt, P. H. 1997. Multiplex PCR: critical parameters and step-by-step protocol. Biotechniques 23: 504-511. Hert, A. P., Roberts, P. D., Momol, M. T., Minsavage, G. V., Tudor-Nelson, S. M., and Jones, J. B. 2005. Relative importance of bacteriocin-like genes in antagonism of Xanthomonas perforans tomato race 3 to Xanthomonas euvesicatoria tomato race 1 strains. Appl. Environ. Microbiol. 71: 3581-3588. Hert, A. P., Marutani, M., Momol, M. T., Roberts, P. D., and Jones, J. B. 2009. Analysis of pathogenicity mutants of a bacteriocin producing Xanthomonas perforans. Biol. Cont. 51: 362-369. Houseman, B. T., and Mrksich, M. 2002. Towards quantitative assays with peptide chips: a surface engineering approach. Trends Biotechnol. 20: 279-281. Huang, C. H., Vallad, G. E., Zhang, S., Wen, A., Balogh, B., Figueiredo, J. F. L., Behlau, F., Jones, J. B., Momol, M. T., and Olson, S. M. 2012. Effect of application frequency and reduced rates of acibenzolar-S-methyl on the field efficacy of induced resistance against bacterial spot on tomato. Plant Dis. 96: 221-227. Jones, J. B., Jones, J. P., Stall, R. E., and Zitter, T. A. 1991. Compendium of tomato diseases. Americal Phytopathol. Soc. Press. St. 100 pp. Jones, J. B., Minsavage, G. V., Stall, R. E., Kelly, R. 0., and Bouzar, H. 1993. Genetic analysis of a DNA region involved in expression of two epitopes associated with lipopolysaccharide in Xanthomonas campestris pv. vesicatoria. Phytopathology 83: 551-556. Jones, J. B., Stall, R. E., Scott, J., Somodi, G., Bouzar, H., and Hodge, N. 1995. A third tomato race of Xanthomonas campestris pv. vesicatoria. Plant Dis. 79: 395-398. Jones, J. B., Bouzar, H., Stall, R. E., Almira, E. C., Roberts, P. D., Bowen, B. W., Sudberry, J., Strickler, P. M., and Chun, J. 2000. Systematic analysis of xanthomonads (Xanthomonas spp.) associated with pepper and tomato lesions. Int. J. Syst. Evol. Microbiol. 50: 1211-1219. Jones, J. B., Lacy, G. H., Bouzar, H., Stall, R. E., and Schaad, N. W. 2004. Reclassification of the xanthomonads associated with bacterial spot disease of tomato and pepper. Syst. Appl. Microbiol. 27: 755-762. Kim, S. H., Olson, T. N., Peffer, N. D., Nikolaeva, E. V., Park, S., and Kang, S. 2010. First report of bacterial spot of tomato caused by Xanthomonas gardneri in Pennsylvania. Plant Dis. 94: 638. Kingsley, M. T., Straub, T. M., Call, D. R., Daly, D. S., Wunschel, S. C., and Chandler, D. P. 2002. Fingerprinting closely related Xanthomonas pathovars with random nonamer oligonucleotide microarrays. Appl. Environ. Microbiol. 68: 6361-6370. Kuflu, K. M., and Cuppels, D. A. 1997. Development of a diagnostic DNA probe for xanthomonads causing bacterial spot of peppers and tomatoes. Appl. Environ. Microbiol. 63: 4462-4470. Leite, Jr. R. P., Minsavage, G. V., Bonas, U., and Stall, R. E. 1994. Detection and identification of phytopathogenic Xanthomonas strains by amplification of DNA sequences related to the hrp genes of Xanthomonas campestris pv. vesicatoria. Appl. Environ. Microbiol. 60: 1068-1077. Leite, Jr. R. P., Jones, J. B., Somodi, G. C., Minsavage, G. V., and Stall, R. E. 1995. Detection of Xanthomonas campestris pv. vesicatoria associated with pepper and tomato seed by DNA amplification. Plant Dis. 79: 917-922. Lue, Y. S., Deng, W. L., Wu, Y. F., Cheng, A. S., Hsu, S. T., and Tzeng, K. C. 2010. Characterization of Xanthomonas associated with bacterial spot of tomato and pepper in Taiwan. Plant Pathol. Bull. 19: 181-190. Lueking, A., Possling, A., Huber, O., Beveridge, A., Horn, M., Eickhoff, H., Schuchardt, J., Lehrach, H., and Cahill, D. J. 2003. A nonredundant human protein chip for antibody screening and serum profiling. Mol. Cell. Proteo. 2: 1342-1349. Maughan, N. J., Lewis, F. A., and Smith, V. 2001. An introduction to arrays. J. Pathol. 195: 3-6. Mbega, E. R., Mabagala, R. B., Mortensen, C. N., and Wulff, E. G. 2012. Evaluation of essential oils as seed treatment for the control of Xanthomonas spp. associated with the bacterial leaf spot of tomato in Tanzania. J. Plant Pathol. 94: 273-281. Myung, I. S., Moon, S. Y., Jeong, I. H., Lee, Y. K., Lee, Y. H., and Ra, D. S. 2009. Bacterial spot of tomato caused by Xanthomonas perforans, a new disease in Korea. Plant Dis. 93: 1349. Obradovic, A., Jones, J. B., Balogh, B., and Momol, M. T. 2008. Integrated management of tomato bacterial spot. Integrated management of diseases caused by fungi, phytoplasma and bacteria. Springer, 211-223 pp. Obradovic, A., Mavridis, A., Rudolph, K., Janse, J. D., Arsenijevic, M., Jones, J. B., Minsavage, G. V., and Wang, J. F. 2004. Characterization and PCR-based typing of Xanthomonas campestris pv. vesicatoria from peppers and tomatoes in Serbia. Eur. J. Plant Pathol. 110: 285-292. Paret, M. L., Vallad, G. E., Averett, D. R., Jones, J. B., and Olson, S. M. 2013. Photocatalysis: effect of light-activated nanoscale formulations of TiO2 on Xanthomonas perforans and control of bacterial spot of tomato. Phytopathology 103: 228-236. Park, D. S., Shima, J. K., Kima, J. S., Limb, C. K., Shrestha, R., Hahna, J. H., and Kimd, H. G. 2009. Sensitive and specific detection of Xanthomonas campestris pv. vesicatoria by PCR using pathovar-specific primers based on rhs family gene sequences. Microbiol. Res. 164: 36-42. Sambrook, J., Maniatis, T. I., and Fritsch, E. F. 1989. Molecular cloning: A laboratory manual. 2nd ed. Cold spring harbor laboratory, cold spring harbor USA 267: 9289-9293. Samson, R., Legendre, J. B., Christen, R., Fischer-Le Saux, M., Achouak, W., and Gardan, L., 2005. Transfer of Pectobacterium chrysanthemi (Burkholder et al. 1953) Brenner et al. 1973 and Brenneria paradisiaca to the genus Dickeya gen. nov. as Dickeya chrysanthemi comb. nov. and Dickeya paradisiaca comb. nov. and delineation of four novel species, Dickeya dadantii sp. nov., Dickeya dianthicola sp. nov., Dickeya dieffenbachiae sp. nov. and Dickeya zeae sp. nov. Int. J. Syst. Evol. Microbiol. 55: 1415-1427. Schena, M., Shalon, D., Davis, R. W., and Brown, P. O. 1995. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467-470. Sijam, K., Chang, C. J., and Gitaitis, R. D. 1991. An agar medium for the isolation and identification of Xanthomonas campestris pv. vesicatoria from seed. Phytopathology 81: 831-834. Southern, E. M., Maskos, U., and Elder, J. K. 1992. Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: evaluation using experimental models. Genomics 13: 1008-1017. Stall, R. E., Beaulieu, C., Egel, D., Hodge, N. C., Leite, R. P., Minsavage, G. V., Bouzar, H., Jones, J. B., Alvarez, M. A., and Benedict, A. A. 1994. Two genetically diverse groups of strains are included in Xanthomonas campestris pv. vesicatoria. Int. J. Syst. Bacteriol. 44: 47-53. ?utic, D. 1957. Bakterioze crvenog patlidzana (tomato bacteriosis). Rev. Appl. Mycol. 36: 734-735. Tudor-Nelson, S. M., Minsavage, G. V., Stall, R. E., and Jones, J. B. 2003. Bacteriocin-like substances from tomato race 3 strains of Xanthomonas campestris pv. vesicatoria. Phytopathology 93: 1415-1421. Van Ettekoven, K. 2000. Seed health testing methods reference manual. ISHI-Vegetable. Vauterin, L., Hoste, B., Kersters, K., and Swings, J. 1995. Reclassification of Xanthomonas. Int. J. Syst. Bacteriol. 45: 472-489. Vauterin, L., Swings, J., Kersters, K., Gillis, M., Mew, T. W., Schroth, M. N., Palleroni, N. J., Hildebrand, D. C., Stead, D. E., Civerolo, E. L., Hayward, A. C., Mara?te, H., Stall, R. E., Vidaver, A. K., and Bradbury, J. F. 1990. Towards an improved taxonomy of Xanthomonas. Int. J. Syst. Bacteriol. 40: 312-316. 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. Weisburg, W. G., Barns, S. M., Pelletier, D. A., and Lane, D. J. 1991. 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 173: 697-703. Xin, Z., Velten, J. P., Oliver, M. J., and Burke, J. J. 2003. High-throughput DNA extraction method suitable for PCR. Biotechniques 34: 820-827. Yabuuchi, E., Kosako, Y., Yano, I., Hotta, H., and Nishiuchi, Y., 1995. Transfer of two Burkholderia and an Alcaligenes species to Ralstonia Gen. Nov.: proposal of Ralstonia pickettii (Ralston, Palleroni and Doudoroff 1973) Comb. Nov., Ralstonia solanacearum (Smith 1896) Comb. Nov. and Ralstonia eutropha (Davis 1969) Comb. Nov. Microbiol. Immunol. 39: 897-904. Young, J. M., Dye, D. W., Bradbury, J. F., Panagopoulos, C. G., and Robbs, C. F. 1978. A proposed nomenclature and classification for plant pathogenic bacteria. New Zeal. J. Agric. Res. 21: 153-177. Zhu, H., Klemic, J. F., Chang, S., Bertone, P., Casamayor, A., Klemic, K. G., Smith, D., Gerstein, M., Reed, M. A., and Snyder, M. 2000. Analysis of yeast protein kinases using protein chips. Nat. Genet. 26: 283-289.
摘要: 茄科細菌性斑點病菌 (bacterial spot-causing xanthomonads, BSX)為國際重要之植物檢疫病原,於茄科作物上可造成嚴重的經濟損失。在台灣已被報導之BSX有Xanthomonas euvesicatoria、X. perforans及X. vesicatoria。應用X. euvesicatoria、X. perforans及X. vesicatoria之專一性引子對RST13/RST14、HpaF-f/HpaF-r及Xv1f/Xv1r進行多重引子聚合酵素連鎖反應 (multiplex polymerase chain reaction, multiplex PCR),可將台灣現有之BSX進行鑑別。由於BSX可藉由種子傳播,開發快速準確之檢測技術更顯得重要。DNA生物晶片檢測技術具有高靈敏度及專一性,近年來已被應用於多種植物病原之檢測,然目前尚未有可供檢測BSX之生物晶片,因此本研究擬進行BSX檢測生物晶片之研發。本研究分別利用專一性引子對RST13/RST14、HpaF-f/HpaF-r及Xv1f/Xv1r對三種BSX菌株進行PCR,以獲得專一性DNA片段,利用此些DNA片段進行DNA生物晶片之製作,經雜合反應測試後,顯示此生物晶片具有專一性。進一步測試DNA生物晶片之雜合反應時間及呈色反應時間與靈敏度關聯,結果顯示,於雜合1小時呈色30分鐘之條件下,其檢測靈敏度可達10 ρg。此外,應用multiplex PCR技術,配合BSX生物晶片測試,結果顯示可同時檢測鑑定此三種BSX菌株。進行最適化之測試結果顯示,以1 μM毛地黃素配合multiplex PCR,所獲得之探針專一性最佳。此BSX生物晶片實際應用於人工帶菌種子及人工接種之罹病番茄植株檢測上,可有效將此三種BSX檢測並鑑定。本研究研發出可同時檢測並鑑定之BSX生物晶片,未來可提供防檢疫人員進行BSX之檢測,並擬訂防治策略。
Bacterial spot is an important disease of tomato and pepper in Taiwan. This disease was caused by the solanaceous bacterial spot-causing xanthomonads (BSX) that including Xanthomonas euvesicatoria, X. vesicatoria, X. perforans and X.gardneri. BSX are considered as important quarantine phytopathogenic bacteria because of they can be transmitted by seeds and seedlings. In Taiwan, three BSX, X.euvesicatoria, X. perforans and X. vesicatoria were occurred, and they were detected and distinguished by multiplex polymerase chain reaction (multiplex PCR). In this study, the highly specific and efficient DNA array technique was used to developed the detection technique for BSX. The BSX DNA array was made by a nylon membrane and fixed the specific DNA fragments amplified by PCR with primer pairs HpaF-f/r, RST13/14 and Xv1f/1r, respectively. The result of specificity test of the DNA array showed that the specific signals were emerged on the BSX strains. The detection limit of the DNA array developed in this study was 10 ρg with 1 hr hybridization and 30 min colorization. The probe labeled with 1 μM digoxigenin in multiplex PCR could detect and distinguish BSX by hybridized with BSX DNA array. The BSX DNA array could detection and distinguish BSX from artificially infested tomato seeds and artificially infested tomato tissue. The BSX DNA array developed in this study will be used for plant quarantine to detect and distinguish BSX from plant samples and developing control strategies of BSX.
文章公開時間: 2016-08-31
Appears in Collections:植物病理學系



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