Real-time PCR: What relevance to plant studies?

Journal of Experimental Botany

Volumn 55, Issue 402, 2004, Pages 1445-1454

  Gachon, Claire ^a   Mingam, Annaïck ^a   Charrier, Bénédicte ^a  

^a INSTITUTE OF PLANT SCIENCES PARIS SACLAY IPS2   (France)

Author keywords

Expression; Fluorochrome; Genetically modified organism; Molecular Beacon; Pathogen; Scorpion ; SYBR green ; TaqMan ; Technique; Transgene

Indexed keywords

DNA; FOOD PRODUCTS; GENETIC ENGINEERING; HEALTH CARE; MICROORGANISMS;

GENETICALLY MODIFIED ORGANISMS (GMO); PATHOGENS;

PLANTS (BOTANY);

PLANT DNA;

GENETICALLY MODIFIED FOOD; GENETICS; METHODOLOGY; PLANT; POLYMERASE CHAIN REACTION; REVIEW; TRANSGENIC PLANT;

DNA, PLANT; FOOD, GENETICALLY MODIFIED; PLANTS; PLANTS, GENETICALLY MODIFIED; POLYMERASE CHAIN REACTION;

SCORPIONES;

EID: 3242732345     PISSN: 00220957     EISSN: None     Source Type: Journal    
DOI: 10.1093/jxb/erh181     Document Type: Review

References (94)

1. Ahmed FE. 2002. Detection of genetically modified organisms in foods. Trends in Biotechnology 20, 215-223.
2. Alary R, Serin A, Duviau MP, Joudrier P, Gautier MF. 2002. Quantification of common wheat adulteration of durum wheat pasta using real-time quantitative polymerase chain reaction (PCR). Cereal Chemistry 79, 553-558.
3. Anterola AM, Jeon JH, Davin LB, Lewis NG. 2002. Transcriptional control of monolignol biosynthesis in Pinus taeda: factors affecting monolignol ratios and carbon allocation in phenylpropanoid metabolism. Journal of Biological Chemistry 277, 18272-18280.
4. Auer CA. 2003. Tracking genes from seed to supermarket: techniques and trends. Trends in Plant Science 8, 591-597.
5. Bago B, Zipfel W, Williams RM, Jun J, Arreola R, Lammers PJ, Pfeffer PE, Shachar Hill Y. 2002. Translocation and utilization of fungal storage lipid in the arbuscular mycorrhizal symbiosis. Plant Physiology 128, 108-124.
6. Balbi V, Lomax TL. 2003. Regulation of early tomato fruit development by the Diageotropica gene. Plant Physiology 131, 186-197.
7. Berdal KG, Holst-Jensen A. 2001. Roundup Ready® soybean event-specific real-time quantitative PCR assay and estimation of the practical detection and quantification limits in GMO analyses. European Food Research and Technology 213, 432-438.
8. Berger S, Mitchell-Olds T, Stotz HU. 2002. Local and differential control of vegetative storage protein expression in response to herbivore damage in Arabidopsis thaliana. Physiologia Plantarum 114, 85-91.
9. Blanco-Portales R, Medina-Escobar N, López-Raez JA, González-Reyes JA, Villalba JM, Moyano E, Caballero JL, Muñoz-Blanco J. 2002. Cloning, expression and immunolocalization pattern of a cinnamyl alcohol dehydrogenase gene from strawberry (Fragaria x ananassa cv. Chandler). Journal of Experimental Botany 53, 1723-1734.
10. Böhm J, Hahn A, Schubert R, Bahnweg G, Adler N, Nechwatal J, Oehlmann R, Osswald W. 1999. Real-time quantitative PCR: DNA determination in isolated spores of the mycorrhizal fungus Glomus mossae and monitoring of Phytophthora infestans and Phytophthora citricola in their respective host plants. Journal of Phytopathology 147, 409-416.
11. Bovy A, de Vos R, Kemper M, et al. 2002. High-flavonol tomatoes resulting from the heterologous expression of the maize transcription factor genes LC and C1. The Plant Cell 14, 2509-2526.
12. Brodmann PD, Ilg EC, Berthoud H, Herrmann A. 2002. Real-time quantitative polymerase chain reaction methods for four genetically modified maize varieties and maize DNA content in food. Journal of AOAC International 85, 646-653.
13. Brouwer M, Lievens B, Van Hemelrijck W, Van den Ackerveken G, Cammue BP, Thomma BP. 2003. Quantification of disease progression of several microbial pathogens on Arabidopsis thaliana using real-time fluorescence PCR. FEMS Microbiological Letters 228, 241-248.
14. Brown RL, Kazan K, McGrath KC, Maclean DJ, Manners JM. 2003. A role for the GCC-box in jasmonate-mediated activation of the PDF1.2 gene of Arabidopsis. Plant Physiology 132, 1020-1032.
15. Busch M, Seuter A, Hain R. 2002. Functional analysis of the early steps of carotenoid biosynthesis in tobacco. Plant Physiology 128, 439-453.
16. Bustin SA. 2000. Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. Journal of Molecular Endocrinology 25, 169-193.
17. Bustin SA. 2002. Quantification of mRNA using real-time reverse transcription PCR (RT-PCR): trends and problems. Journal of Molecular Endocrinology 29, 23-39.
18. Chae HS, Faure F, Kieber JJ. 2003. The eto1, eto2, and eto3 mutations and cytokinin treatment increase ethylene biosynthesis in Arabidopsis by increasing the stability of ACS protein. The Plant Cell 15, 545-559.
19. Chang HS, Jones ML, Banowetz GM, Clark DG. 2003. Over-production of cytokinins in petunia flowers transformed with P-SAG12-IPT delays corolla senescence and decreases sensitivity to ethylene. Plant Physiology 132, 2174-2183.
20. Charrier B, Champion A, Henry Y, Kreis M. 2002. Expression profiling of the whole Arabidopsis Shaggy-like kinase multigene family by real-time reverse transcriptase-polymerase chain reaction. Plant Physiology 130, 577-590.
21. Choi DW, Rodriguez EM, Close TJ. 2002. Barley Cbf3 gene identification, expression pattern, and map location. Plant Physiology 129, 1781-1787.
22. Considine MJ, Daley DO, Whelan J. 2001. The expression of alternative oxidase and uncoupling protein during fruit ripening in mango. Plant Physiology 126, 1619-1629.
23. Dambrauskas G, Aves SJ, Bryant JA, Francis D, Rogers HJ. 2003. Genes encoding two essential DNA replication activation proteins, Cdc6 and Mcm3, exhibit very different patterns of expression in the tobacco BY-2 cell cycle. Journal of Experimental Botany 54, 699-706.
24. Dong JX, Chen CH, Chen ZX. 2003. Expression profiles of the Arabidopsis WRKY gene superfamily during plant defense response. Plant Molecular Biology 51, 21-37.
25. Dornelas MC, Wittich P, von Recklinghausen I, van Lammeren A, Kreis M. 1999. Characterization of three novel members of the Arabidopsis SHAGGY-related protein kinase (ASK) multigene family. Plant Molecular Biology 39, 137-147.
26. Filion M, St-Arnaud M, Jabaji-Hare SH. 2003. Direct quantification of fungal DNA from soil substrate using real-time PCR. Journal of Microbiological Methods 53, 67-76.
27. Freeman WM, Walker SJ, Vrana KE. 1999. Quantitative RT-PCR: pitfalls and potential. Biotechniques 26, 112-122, 124-115.
28. Ge H, Liu ZH, Church GM, Vidal M. 2001. Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nature Genetics 29, 482-486.
29. German MA, Kandel-Kfir M, Swarzberg D, Matsevitz T, Granot D. 2003. A rapid method for the analysis of zygosity in transgenic plants. Plant Science 164, 183-187.
30. Goda H, Shimada Y, Asami T, Fujioka S, Yoshida S. 2002. Microarray analysis of brassinosteroid-regulated genes in Arabidopsis. Plant Physiology 130, 1319-1334.
31. Goncçalves MC, Klerks MM, Verbeek M, Vega J, van den Heuvel JF. 2002. The use of molecular beacons combined with NASBA for the sensitive detection of Sugarcane Yellow Leaf Virus. European Journal of Plant Pathology 108, 401-407.
32. Goto DB, Naito S. 2002. AtMRD1 and AtMRU1, two novel genes with altered mRNA levels in the methionine over-accumulating mto1-1 mutant of Arabidopsis thaliana. Plant and Cell Physiology 43, 923-931.
33. Halterman DA, Wei FS, Wise RP. 2003. Powdery mildew-induced Mla mRNAs are alternatively spliced and contain multiple upstream open reading frames. Plant Physiology 131, 558-567.
34. Hammond JP, Bennett MJ, Bowen HC, Broadley MR, Eastwood DC, May ST, Rahn C, Swarup R, Woolaway KE, White PJ. 2003. Changes in gene expression in Arabidopsis shoots during phosphate starvation and the potential for developing smart plants. Plant Physiology 132, 578-596.
35. Harari-Steinberg O, Ohad I, Chamovitz DA. 2001. Dissection of the light signal transduction pathways regulating the two early light-induced protein genes in Arabidopsis. Plant Physiology 127, 986-997.
36. Heid CA, Stevens J, Livak KJ, Williams PM. 1996. Real time quantitative PCR. Genome Research 6, 986-994.
37. Hernández M, Ferrando A, Esteve T, Puigdomènech P, Prat S, Pla M. 2003a. Real-time and conventional polymerase chain reaction systems based on the metallo-carboxypeptidase inhibitor gene for specific detection and quantification of potato and tomato in processed food. Journal of Food Protection 66, 1063-1070.
38. Hernández M, Pla M, Esteve T, Prat S, Puigdomènech P, Ferrando A. 2003b. A specific real-time quantitative PCR detection system for event MON810 in maize YieldGard® based on the 3′-transgene integration sequence. Transgenic Research 12, 179-189.
39. Higuchi R, Fockler C, Dollinger G, Watson R. 1993. Kinetic PCR analysis: real-time monitoring of DNA amplification reactions. Bio/technology 11, 1026-1030.
40. Hird H, Powell J, Johnson ML, Oehlschlager S. 2003. Determination of percentage of RoundUp Ready® soya in soya flour using real-time polymerase chain reaction: Interlaboratory study. Journal of AOAC International 86, 66-71.
41. Hiriart JB, Aro EM, Lehto K. 2003. Dynamics of the VIGS-mediated chimeric silencing of the Nicotiana benthamiana ChlH gene and of the Tobacco Mosaic Virus Vector. Molecular Plant-Microbe Interactions 16, 99-106.
42. Hohne M, Santisi CR, Meyer R. 2002. Real-time multiplex PCR: an accurate method for the detection and quantification of 35S-CaMV promoter in genetically modified maize-containing food. European Food Research and Technology 215, 59-64.
43. Holmberg N, Harker M, Gibbard CL, Wallace AD, Clayton JC, Rawlins S, Hellyer A, Safford R. 2002. Sterol C-24 methyltransferase type 1 controls the flux of carbon into sterol biosynthesis in tobacco seed. Plant Physiology 130, 303-311.
44. Ingham DJ, Beer S, Money S, Hansen G. 2001. Quantitative real-time PCR assay for determining transgene copy number in transformed plants. Biotechniques 31, 132, 134, 136-140.
45. Itoh R, Fujiwara M, Nagata N, Yoshida S. 2001. A chloroplast protein homologous to the eubacterial topological specificity factor MinE plays a role in chloroplast division. Plant Physiology 127, 1644-1655.
46. Jakab G, Manrique A, Zimmerli L, Métraux JP, Mauch-Mani B. 2003. Molecular characterization of a novel lipase-like pathogen-inducible gene family of Arabidopsis. Plant Physiology 132, 2230-2239.
47. Jones L, Ratclift F, Baulcombe DC. 2001. RNA-directed transcriptional gene silencing in plants can be inherited independently of the RNA trigger and requires Met1 for maintenance. Current Biology 11, 747-757.
48. Klok EJ, Wilson IW, Wilson D, Chapman SC, Ewing RM, Somerville SC, Peacock WJ, Dolferus R, Dennis ES. 2002. Expression profile analysis of the low-oxygen response in Arabidopsis root cultures. The Plant Cell 14, 2481-2494.
49. Kürsteiner O, Dupuis I, Kuhlemeier C. 2003. The Pyruvate decarboxylase 1 gene of Arabidopsis is required during anoxia, but not other environmental stresses. Plant Physiology 132, 968-978.
50. Lacomme C, Hrubikova K, Hein I. 2003. Enhancement of virus-induced gene silencing through viral-based production of inverted-repeats. The Plant Journal 34, 543-553.
51. Maguire TL, Grimmond S, Forrest A, Iturbe Ormaetxe I, Meksem K, Gresshoff P. 2002. Tissue-specific gene expression in soybean (Glycine max) detected by cDNA microarray analysis. Journal of Plant Physiology 159, 1361-1374.
52. Maruyama-Nakashita A, Inoue E, Watanabe-Takahashi A, Yamaya T, Takahashi H. 2003. Transcriptome profiling of sulfur-responsive genes in Arabidopsis reveals global effects of sulfur nutrition on multiple metabolic pathways. Plant Physiology 132, 597-605.
53. Mayer Z, Bagnara A, Färber P, Geisen R. 2003. Quantification of the copy number of nor-1, a gene of the aflatoxin biosynthetic pathway by real-time PCR, and its correlation to the cfu of Aspergillus flavus in foods. International Journal of Food Microbiology 82, 143-151.
54. McCartney HA, Foster SJ, Fraaije BA, Ward E. 2003. Molecular diagnostics for fungal plant pathogens. Pest Managment Science 59, 129-142.
55. Mladek C, Guger K, Hauser MT. 2003. Identification and characterization of the ARIADNE gene family in Arabidopsis. A group of putative E3 ligases. Plant Physiology 131, 21-40,
56. Montrichard F, Renard M, Alkhalfioui F, Duval FD, Macherel D. 2003. Identification and differential expression of two thioredoxin h isoforms in germinating seeds from pea. Plant Physiology 132, 1707-1715.
57. Nakazono M, Qiu F, Borsuk LA, Schnable PS. 2003. Laser-capture microdissection, a tool for the global analysis of gene expression in specific plant cell types: Identification of genes expressed differentially in epidermal cells or vascular tissues of maize. The Plant Cell 15, 583-596.
58. Nolan KE, Irwanto RR, Rose RJ. 2003. Auxin up-regulates MtSERK1 expression in both Medicago truncatula root-forming and embryogenic cultures. Plant Physiology 133, 218-230.
59. Orsel M, Krapp A, Daniel-Vedele F. 2002. Analysis of the NRT2 nitrate transporter family in Arabidopsis. Structure and gene expression. Plant Physiology 129, 886-896.
60. Panchuk II, Volkov RA, Schöffl F. 2002. Heat stress- and heat shock transcription factor-dependent expression and activity of ascorbate peroxidase in Arabidopsis. Plant Physiology 129, 838-853.
61. Petit L, Baraige F, Balois AM, Bertheau Y, Fach P. 2003. Screening of genetically modified organisms and specific detection of Bt176 maize in flours and starches by PCR-enzyme linked immunosorbent assay. European Food Research and Technology 217, 83-89.
62. Pfaffl MW. 2001. A new mathematical model for relative quantification in real-time RT- PCR. Nucleic Acids Research 29, e45.
63. 4 grass Zea mays. Journal of Biological Chemistry 278, 16973-16981.
64. Puthoff DP, Nettleton D, Rodermel SR, Baum TJ. 2003. Arabidopsis gene expression changes during cyst nematode parasitism revealed by statistical analyses of microarray expression profiles. The Plant Journal 33, 911-921.
65. + influx. Proceedings of the National Academy of Sciences, USA 99, 4079-4084.
66. Rider SD, Henderson JT, Jerome RE, Edenberg HJ, Romero-Severson J, Ogas J. 2003. Coordinate repression of regulators of embryonic identity by PICKLE during germination in Arabidopsis. The Plant Journal 35, 33-43.
67. Ronning SB, Vaitilingom M, Berdal KG, Holst-Jensen A. 2003. Event specific real-time quantitative PCR for genetically modified Bt11 maize (Zea mays). European Food Research and Technology 216, 347-354.
68. Sandberg M, Lundberg L, Ferm M, Yman IM. 2003. Real-time PCR for the detection and discrimination of cereal contamination in gluten free foods. European Food Research and Technology 217, 344-349.
69. Schaad NW, Frederick RD. 2002. Real-time PCR and its application for rapid plant disease diagnostics. Canadian Journal of Plant Pathology 24, 250-258.
70. Schaad NW, Frederick RD, Shaw J, Schneider WL, Hickson R, Petrillo MD, Luster DG. 2003. Advances in molecular-based diagnostics in meeting crop biosecurity and phytosanitary issues. Annual Review of Phytopathology 41, 305-324.
71. Schena L, Nigro F, Ippolito A. 2002. Identification and detection of Rosellinia necatrix by conventional and real-time Scorpion-PCR. European Journal of Plant Pathology 108, 355-366.
72. Schenk PM, Kazan K, Manners JM, Anderson JP, Simpson RS, Wilson IW, Somerville SC, Maclean DJ. 2003. Systemic gene expression in Arabidopsis during an incompatible interaction with Alternaria brassicicola. Plant Physiology 132, 999-1010.
73. Schnerr H, Niessen L, Vogel RF. 2001. Real time detection of the tri5 gene in Fusarium species by LightCycler™-PCR using SYBR®-Green 1 for continuous fluorescence monitoring. International Journal of Food Microbiology 71, 53-61.
74. Shen GA, Pang YZ, Lin CF, Wei C, Qian XY, Jiang LZ, Du XL, Li KG, Attia K, Yang JS. 2003. Cloning and characterization of a novel Hsp100/C1p gene (OsC1pD) from Oryza sativa. DNA Sequence 14, 285-293.
75. Shimada Y, Goda H, Nakamura A, Takatsuto S, Fujioka S, Yoshida S. 2003. Organ-specific expression of brassinosteroid-biosynthetic genes and distribution of endogenous brassinosteroids in Arabidopsis. Plant Physiology 131, 287-297.
76. Suzuki H, Nakayama T, Yonekura-Sakakibara K, Fukui Y, Nakamura N, Yamaguchi M, Tanaka Y, Kusumi T, Nishino T. 2002. cDNA cloning, heterologous expressions, and functional characterization of malonyl-coenzyme Aranthocyanidin 3-0-glucoside-6″-O-malonyltransferase from dahlia flowers. Plant Physiology 130, 2142-2151.
77. Tan BC, Joseph LM, Deng WT, Liu LJ, Li QB, Cline K, McCarty DR. 2003. Molecular characterization of the Arabidopsis 9-cis epoxycarotenoid dioxygenase gene family. The Plant Journal 35, 44-56.
78. Taverniers I, Windels P, Van Bockstaele E, De Loose M. 2001. Use of cloned DNA fragments for event-specific quantification of genetically modified organisms in pure and mixed food products. European Food Research and Technology 213, 417-424.
79. Teramoto H, Nakamori A, Minagawa J, Ono T. 2002. Light-intensity- dependent expression of Lhc gene family encoding light-harvesting chlorophyll-a/b proteins of photosystem II in Chlamydomonas reinhardtii. Plant Physiology 130, 325-333.
80. Terzi V, Malnati M, Barbanera M, Stanca AM, Faccioli P. 2003. Development of analytical systems based on real-time PCR for Triticum species-specific detection and quantitation of bread wheat contamination in semolina and pasta. Journal of Cereal Science 38, 87-94.
81. The Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796-815.
82. Thomas C, Meyer D, Wolff M, Himber C, Alioua M, Steinmetz A. 2003. Molecular characterization and spatial expression of the sunflower ABP1 gene. Plant Molecular Biology 52, 1025-1036.
83. Vaïtilingom M, Pijnenburg H, Gendre F, Brignon P. 1999. Real-time quantitative PCR detection of genetically modified Maximizer maize and RoundUp Ready soybean in some representative foods. Journal of Agricultural and Food Chemistry 47, 5261-5266.
84. van Wees SCM, Chang HS, Zhu T, Glazebrook J. 2003. Characterization of the early response of Arabidopsis to Alternaria brassicicola infection using expression profiling. Plant Physiology 132, 606-617.
85. Wang RC, Okamoto M, Xing XJ, Crawford NM. 2003. Microarray analysis of the nitrate response in Arabidopsis roots and shoots reveals over 1000 rapidly responding genes and new linkages to glucose, trehalose-6-phosphate, iron, and sulfate metabolism. Plant Physiology 132, 556-567.
86. Weller SA, Elphinstone JG, Smith NC, Boonham N, Stead DE. 2000. Detection of Ralstonia solanacearum strains with a quantitative, multiplex, real-time, fluorogenic PCR (TaqMan®) assay. Applied and Environmental Microbiology 66, 2853-2858.
87. Windels P, Bertrand S, Depicker A, Moens W, Van Bockstaele E, Loose M. 2003. Qualitative and event-specific PCR real-time detection methods for StarLink maize. European Food Research and Technology 216, 259-263.
88. Winton LM, Manter DK, Stone JK, Hansen EM. 2003. Comparison of biochemical, molecular, and visual methods to quantify Phaeocryptopus gaeumannii in Douglas-Fir foliage. Phytopathology 93, 121-126.
89. Wittwer CT, Herrmann MG, Moss AA, Rasmussen RP. 1997a. Continuous fluorescence monitoring of rapid cycle DNA amplification. Biotechniques 22, 130-131, 134-138.
90. Wittwer CT, Ririe KM, Andrew RV, David DA, Gundry RA, Balis UJ. 1997b. The LightCycler: a microvolume multisample fluorimeter with rapid temperature control. Biotechniques 22, 176-181.
91. Wurmbach E, Yuen T, Sealfon SC. 2003. Focused microarray analysis. Methods 31, 306-316.
92. 450 gene superfamily of Arabidopsis thaliana. Gene 272, 61-74.
93. Yokoyama R, Nishitani K. 2001. A comprehensive expression analysis of all members of a gene family encoding cell-wall enzymes allowed us to predict cis-regulatory regions involved in cell-wall construction in specific organs of Arabidopsis. Plant and Cell Physiology 42, 1025-1033.
94. Zeitler R, Pietsch K, Waiblinger HU. 2002. Validation of real-time PCR methods for the quantification of transgenic contaminations in rape seed. European Food Research and Technology 214, 346-351.