Identification and validation of quantitative real-time reverse transcription PCR reference genes for gene expression analysis in teak (Tectona grandis L.f.)

BMC Research Notes

Volumn 7, Issue 1, 2014, Pages

  Galeano, Esteban ^a   Vasconcelos, Tarcísio Sales ^a   Ramiro, Daniel Alves ^a   De Martin, Valentina De Fátima ^a   Carrer, Helaine ^a  

^a UNIVERSITY OF SÃO PAULO   (Brazil)

Author keywords

Lignin; Relative expression; Transcript stability; Trees

Indexed keywords

ELONGATION FACTOR 1; PRIMER DNA; UBIQUITIN;

CHEMISTRY; ESSENTIAL GENE; FLOWER; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; LAMIACEAE; PLANT GENE; PLANT LEAF; PLANT ROOT; PLANT STEM; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEEDLING; STANDARDS;

DNA PRIMERS; FLOWERS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENES, ESSENTIAL; GENES, PLANT; LAMIACEAE; PEPTIDE ELONGATION FACTOR 1; PLANT LEAVES; PLANT ROOTS; PLANT STEMS; REAL-TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SEEDLING; UBIQUITIN;

EID: 84904525006     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/1756-0500-7-464     Document Type: Article

References (46)

1. MicroRNAs and long non-coding RNAs: prospects in diagnostics and therapy of cancer. Hauptman N, Glavac D, Radiol Oncol 2013 47 4 311 318
2. Non-coding RNAs in the development of sensory organs and related diseases. Conte I, Banfi S, Bovolenta P, Cell Mol Life Sci 2013 70 4141 4155
3. Expression profiling of genes involved in starch synthesis in sink and source organs of rice. Ohdan T, Francisco PB Jr, Sawada T, Hirose T, Terao T, Satoh H, Nakamura Y, J Exp Bot 2005 56 422 3229 3244 (Pubitemid 41746673)
4. Real-time PCR in virology. Mackay IM, Arden KE, Nitsche A, Nucleic Acids Res 2002 30 6 1292 1305 (Pubitemid 34679706)
5. Reference gene selection for quantitative real-time PCR normalization in Caragana intermedia under different abiotic stress conditions. Zhu J, Zhang L, Li W, Han S, Yang W, Qi L, PLoS One 2013 8 1 53196
6. The real-time polymerase chain reaction. Kubista M, Andrade JM, Bengtsson M, Forootan A, Jonak J, Lind K, Sindelka R, Sjoback R, Sjogreen B, Strombom L, Stahlberg A, Zoric N, Mol Asp Med 2006 27 95 125
7. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT, Clin Chem 2009 55 4 611 622
8. The implications of using an inappropriate reference gene for real-time reverse transcription PCR data normalization. Dheda K, Huggett JF, Chang JS, Kima LU, Bustin SA, Johnson MA, Rook GAW, Zumla A, Anal Biochem 2005 344 141 143 (Pubitemid 41569389)
9. Accurate normalization of real-time quantitative RT-PCR by geometric averaging of multiple internal control genes. Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F, Genome Biol 2002 3 7 34
10. Normalization of real-time quatitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Andersen CL, Jensen JL, Orntoft TF, Cancer Res 2004 64 5245 5250 (Pubitemid 39006544)
11. Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: bestkeeper-Excel-based tool using pair-wise correlations. Pfaffl MW, Tichopad A, Prgomet C, Neuvians TP, Biotechnol Lett 2004 26 509 515 (Pubitemid 38448421)
12. Selection of housekeeping genes for gene expression studies in human reticulocytes using real-time PCR. Silver N, Best S, Jiang J, Thein SL, BMC Mol Biol 2006 7 33
13. Validating internal controls for quantitative plant gene expression studies. Brunner AM, Yakovlev IA, Strauss SH, BMC Plant Biol 2004 4 14
14. Guideline to reference gene selection for quantitative real-time PCR. Radoni A, Thulke S, Mackay IM, Landt O, Siegert W, Nitsche A, Biochem Biophys Res Commun 2004 313 856 862 (Pubitemid 38050071)
15. Genome-wide identification and testing of superior reference genes for transcript normalization in arabidopsis. Czechowski T, Stitt M, Altmann T, Udvardi MK, Scheible W, Plant Physiol 2005 139 5 17 (Pubitemid 43951587)
16. Reference gene selection for quantitative real-time polymerase chain reaction in Populus. Xu M, Zhang B, Su X, Zhang S, Huang M, Anal Biochem 2011 408 337 339
17. Evaluation of the use of the Polyubiquitin Genes, Ubi4 and Ubi10 as reference genes for expression studies in Brachypodium distachyon. Chambers JP, Behpouri A, Bird A, Ng CK, PLoS One 2012 7 11 49372
18. What is the genetic origin of teak (Tectona grandis L.) introduced in Africa and in Indonesia? Verhaegen D, Fofana IJ, Logossa ZA, Ofori D, Tree Genetics Genomes 2010 6 717 733
19. Wood properties of teak (Tectona grandis) from a mature unmanaged stand in East Timor. Miranda I, Sousa V, Pereira H, J Wood Sci 2011 57 171 178
20. Variation in the natural termite resistance of teak (Tectona grandis Linn. fil.) wood as a function of tree age. Lukmandaru G, Takahashi K, Ann For Sci 2008 65 708
21. Practical first total synthesis of the potent phytotoxic (±)-naphthotectone, isolated from Tectona grandis. Guerrero-Vásquez GA, Andrade CKZ, Molinillo JMG, Macías FA, Eur J Org Chem 2013 2013 27 6175 6180
22. The effect of a teak (Tectona grandis) plantation on the establishment of native species in an abandoned pasture in Costa Rica. Healey SP, Gara RI, For Ecol Manag 2003 176 497 507 (Pubitemid 36224714)
23. Teak plantations: economic bonanza or environmental disaster? Hallett JT, Diaz-Calvo J, Villa-Castillo J, Wagner MR, J For 2011 109 5 288 292
24. Selection of reference genes for quantitative gene expression studies in Platycladus orientalis (Cupressaceae) using real-time PCR. Chang E, Shi S, Liu J, Cheng T, Xue L, Yang X, Yang W, Lan Q, Jiang Z, PLoS One 2012 7 3 33278
25. Selection of reliable reference genes for gene expression studies using real-time PCR in tung tree during seed development. Han X, Lu M, Chen Y, Zhan Z, Cui Q, Wang Y, PLoS One 2012 7 8 43084
26. Reference gene selection for quantitative real-time PCR normalization in Quercus suber. Marum L, Miguel A, Ricardo CP, Miguel C, PLoS One 2012 7 4 35113
27. Identification and validation of reference genes for Populus euphratica gene expression analysis during abiotic stresses by quantitative real-time PCR. Wang HL, Chen J, Tian Q, Wang S, Xia X, Yin W, Physiol Plant 2014 in press
28. Evaluation of reference genes for accurate normalization of gene expression for real time-quantitative PCR in Pyrus pyrifolia using different tissue samples and seasonal conditions. Imai T, Ubi BE, Saito T, Moriguchi T, PLoS One 2014 9 1 86492
29. Basic local alignment search tool. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, J Mol Biol 1990 215 403 410
30. Quantification Strategies in Real-Time PCR. Pfaffl MW, The Real-Time PCR Encyclopedia, A-Z of Quantitative PCR La Jolla: International University Line, Bustin SA, 2004 87 120
31. -ΔΔCT method. Livak KJ, Schmittgen TD, Methods 2001 25 402 408 (Pubitemid 34164012)
32. An improved RNA isolation method for plant tissues containing high levels of phenolic compounds or carbohydrates. Salzman RA, Fujita T, Zhu-Salzman K, Hasegawa PM, Bressan RA, Plant Mol Biol reports/ISPMB 1999 17 11 17 (Pubitemid 129640666)
33. Reference gene selection for qPCR analysis during somatic embryogenesis in longan tree. Lin YL, Lai ZX, Plant Sci 2010 178 359 365
34. Stable internal reference genes for normalization of real-time RT-PCR in tobacco (Nicotiana tabacum) during development and abiotic stress. Schmidt GW, Delaney SK, Mol Genet Genomics 2010 283 233 241
35. Validation of reference genes for quantitative RT-PCR studies of gene expression in perennial ryegrass (Lolium perenne L.). Lee JM, Roche JR, Donaghy DJ, Thrush A, Sathish P, BMC Mol Biol 2010 11 8
36. Evaluation of appropriate reference genes for gene expression studies in pepper by quantitative real-time PCR. Bin WS, Wei LK, Ping DW, Li Z, Wei G, Bing LJ, Gui PB, Jian WH, Feng CJ, Mol Breed 2012 30 1393 1400
37. Exploring valid reference genes for gene expression studies in Brachypodium distachyon by real-time PCR. Hong S, Seo PJ, Yang M, Xiang F, Park C, BMC Plant Biol 2008 8 112
38. Selection of internal control genes for quantitative real-time RT-PCR studies during tomato development process. Expósito-Rodríguez M, Borges AA, Borges-Pérez A, Pérez JA, BMC Plant Biol 2008 8 131
39. Selection and validation of endogenous reference genes for qRT-PCR analysis in leafy spurge (euphorbia esula). Chao WS, Doǧramaci M, Foley ME, Horvath DP, Anderson JV, PLoS One 2012 7 8 42839
40. Validation of reference genes for gene expression studies in virus-infected Nicotiana benthamiana using quantitative real-time PCR. Liu D, Shi L, Han C, Yu J, Li D, Zhang Y, PLoS One 2012 7 9 46451
41. Identification of four soybean reference genes for gene expression normalization. Libault M, Thibivilliers S, Bilgin DD, Radwan O, Benitez M, Clough SJ, Stacey G, Plant Genome 2008 1 1 44 54
42. Identification of suitable internal control genes for expression studies in Coffea Arabica under different experimental conditions. Barsalobres-Cavallari CF, Severino FE, Maluf MP, Maia IG, BMC Mol Biol 2009 10 1
43. Functional characterization of Cinnamyl alcohol dehydrogenase and caffeic acid O-methyltransferase in Brachypodium distachyon. Trabucco GM, Matos DA, Lee SJ, Saathoff AJ, Priest HD, Mockler TC, Sarath G, Hazen SP, BMC Biotechnol 2013 13 61
44. Phylogeny and expression profiling of CAD and CAD-like genes in hybrid Populus (P. Deltoides × P. Nigra): evidence from herbivore damage for subfunctionalization and functional divergence. Barakat A, Bagniewska-Zadworna A, Frost CJ, Carlson JE, BMC Plant Biol 2010 10 100
45. Gene expression profiling and silencing reveal that monolignol biosynthesis plays a critical role in penetration defense in wheat against powdery mildew invasion. Bhuiyan NH, Selvaraj G, Wei Y, King J, J Exp Bot 2009 60 2 509 521
46. Involvement of a cinnamyl alcohol dehydrogenase of Quercus suber in the defence response to infection by Phyutophthora cinnamomi. Coelho AC, Horta M, Neves D, Cravador A, Physiol Mol Plant Pathol 2006 69 62 72 (Pubitemid 46766690)