Selection of reference genes for quantitative gene expression studies in Platycladus orientalis (cupressaceae) using real-time PCR

PLoS ONE

Volumn 7, Issue 3, 2012, Pages

  Chang, Ermei ^a   Shi, Shengqing ^a   Liu, Jianfeng ^a   Cheng, Tielong ^a   Xue, Liang ^a   Yang, Xiuyan ^a   Yang, Wenjuan ^a   Lan, Qian ^a   Jiang, Zeping ^a  

^a RESEARCH INSTITUTE OF FORESTRY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ABSCISIC ACID; MACROGOL; SODIUM CHLORIDE; TRANSCRIPTOME; MACROGOL DERIVATIVE; PHYTOHORMONE;

ACCURACY; ALPHA TUBULIN GENE; ARTICLE; COLD; COMPUTER PROGRAM; CONTROLLED STUDY; CUPRESSACEAE; DEVELOPMENTAL STAGE; GENE EXPRESSION; GENE EXPRESSION PROFILING; HEAT; NAC DOMAIN PROTEIN GENE; NONHUMAN; PLANT DEVELOPMENT; PLANT GENE; PLANT STRESS; PLANT TISSUE; PLATYCLADUS ORIENTALIS; QUANTITATIVE REAL TIME POLYMERASE CHAIN REACTION; REAL TIME POLYMERASE CHAIN REACTION; RELIABILITY; SALINITY; SENESCENCE; SENSITIVITY AND SPECIFICITY; UBIQUITIN CONJUGATING ENZYME E2 GENE; DRUG EFFECT; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; STANDARD; TIME;

CUPRESSACEAE; PLATYCLADUS ORIENTALIS;

ABSCISIC ACID; BASE SEQUENCE; COLD TEMPERATURE; CUPRESSACEAE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; HOT TEMPERATURE; MOLECULAR SEQUENCE DATA; PLANT GROWTH REGULATORS; POLYETHYLENE GLYCOLS; REFERENCE STANDARDS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SODIUM CHLORIDE; TIME FACTORS;

EID: 84859123346     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0033278     Document Type: Article

References (60)

1. Yoo WG, Kim TI, Li S, Kwon OS, Cho PY, et al. (2009) Reference genes for quantitative analysis on Clonorchis sinensis gene expression by real-time PCR. Parasitol Res 104 (2): 321-328.
2. Ohdan T, Francisco PB, Sawada T, Hirose T, Terao T, et al. (2005) Expression profiling of genes involved in starch synthesis in sink and source organs of rice. J Exp Bot 56: 3329-3244.
3. Ishimaru T, Hirose T, Matsuda T, Goto A, Takahashi K, et al. (2005) Expression patterns of genes encoding carbohydrate-metabolizing enzymes and their relationship to grain filling in rice (Oryza sativa L.): comparsion of caryopses located at different positions in a panicle. Plant Cell Physiol 46: 620-628.
4. Kanegae H, Miyoshi K, Hirose T, Tsuchimoto S, Mori M, et al. (2005) Expressions of rice sucrose non- fermenting-1 related protein kinase 1 genes are differently regulated during the caryopsis development. Plant Physiol Biochem 43: 669-679.
5. Narayanan NN, Vasconcelos MW, Grusak MA, (2007) Expression profiling of Oryza sativa metal homeostasis genes in different rice cultivars using a cDNA macroarray. Plant Physiol Biochem 45: 277-286.
6. Mahoney DJ, Carey K, Fu MH, Snow R, Cameron-Smith D, et al. (2004) Real-time RT-PCR analysis of housekeeping genes in human skeletal muscle following acute exercise. Physiol Genomics 18: 226-231.
7. Demidenko NV, Logacheva MD, Penin AA, (2011) Selection and validation of reference genes for quantitative real-time PCR in Buckwheat (Fagopyrum esculentum) based on transcriptome sequence data. PLoS ONE 6 (5): e19434.
8. Tong ZG, Gao ZH, Wang F, Zhou J, Zhang Z, (2009) Selection of reliable reference genes for gene expression studies in peach using real-time PCR. BMC Mol Biol 10: 71.
9. Kwon MJ, Oh E, Lee S, Roh MR, Kim SE, et al. (2009) Identification of novel reference genes using multiplatform expression data and their validation for quantitative gene expression analysis. PLoS ONE 4 (7): e6162.
10. Løvdal T, Lillo C, (2009) Reference gene selection for quantitative real-time PCR normalization in tomato subjected to nitrogen, cold, and light stress. Anal Biochem 387 (2): 238-242.
11. Hoenemann C, Hohe A, (2011) Selection of reference genes for normalization of quantitative real-time PCR in cell cultures of Cyclamen persicum. Electron J Biotechnol 14 (1): 12-13.
12. Everaert BR, Boulet GA, Timmermans JP, Vrints CJ, (2011) Importance of suitable reference gene selection for quantitative real-time PCR: special reference to mouse myocardial infarction studies. PLoS ONE 6 (8): e23793.
13. Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, et al. (2002) Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 3 (7): 0034-0040.
14. Tricarico C, Pinzani P, Bianchi S, Paglierani M, Distante V, et al. (2002) Quantitative real-time reverse transcription polymerase chain reaction: normalization to rRNA or single housekeeping genes is inappropriate for human tissue biopsies. Anal Biochem 309 (2): 293-300.
15. Radonic A, Thulke S, Mackay IM, Landt O, Siegert W, et al. (2004) Guideline to reference gene selection for quantitative real-time PCR. Biochem Biophys Res Commun 313 (4): 856-862.
16. Czechowski T, Stitt M, Altmann T, Udvardi MK, Scheible WR, (2005) Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis. Plant Physiol 139: 5-17.
17. Yang LT, Pan AH, Jia JW, Ding JY, Chen JX, et al. (2005) Validation of a tomato-specific gene, LAT52, used as an endogenous reference gene in qualitative and real-time quantitative PCR detection of transgenic tomatoes. J Agric Food Chem 53 (2): 183-190.
18. Chen X, Truksa M, Shah S, Weselake RJ, (2010) A survey of quantitative real-time polymerase chain reaction internal reference genes for expression studies in Brassica napus. Anal Biochem 405 (1): 138-140.
19. Artico S, Nardeli SM, Brilhante O, Grossi-de-Sa MF, Alves-Ferreira M, (2010) Identification and evaluation of new reference genes in Gossypium hirsutum for accurate normalization of real-time quantitative RT-PCR data. BMC Plant Biol 10: 49.
20. Barsalobres-Cavallari CF, Severino FE, Maluf MP, Maia IG, (2009) Identification of suitable internal control genes for expression studies in Coffea arabica under different experimental conditions. BMC Mol Biol 10: 1.
21. Die JV, Román B, Nadal S, González-Verdejo CI, (2010) Evaluation of candidate reference genes for expression studies in Pisumsativum under different experimental conditions. Planta 232 (1): 145-153.
22. Luo HL, Chen SM, Wan HJ, Chen FD, Gu CS, et al. (2010) Candidate reference genes for gene expression studies in water lily. Anal Biochem 404 (1): 100-102.
23. Remans T, Smeets K, Opdenakker K, Mathijsen D, Vangronsveld J, et al. (2008) Normalisation of real-time RT-PCR gene expression measurements in Arabidopsis thaliana exposed to increased metal concentrations. Planta 227 (6): 1343-1349.
24. Jain M, Nijhawan A, Tyagi AK, Khurana JP, (2006) Validation of housekeeping genes as internal control for studying gene expression in rice by quantitative real-time PCR. Biochem Biophys Res Commun 345 (2): 646-651.
25. Kim BR, Nam HY, Kim SU, Kim SI, Chang YJ, (2003) Normalization of reverse transcription quantitative-PCR with housekeeping genes in rice. Biotechnol Lett 25 (21): 1869-1872.
26. Hong SY, Seo PJ, Yang MS, Xiang F, Park CM, (2008) Exploring valid reference genes for gene expression studies in Brachypodium distachyon by real-time PCR. BMC Plant Biol 8: 112.
27. Paolacci AR, Tanzarella OA, Porceddu E, Ciaffi M, (2009) Identification and validation of reference genes for quantitative RT-PCR normalization in wheat. BMC Mol Biol 10: 11.
28. Faccioli P, Ciceri GP, Provero P, Stanca AM, Morcia C, et al. (2007) A combined strategy of "in silico" transcriptome analysis and web search engine optimization allows an agile identification of reference genes suitable for normalization in gene expression studies. Plant Mol Biol 63 (5): 679-688.
29. Jian B, Liu B, Bi YR, Hou WS, Wu CX, et al. (2008) Validation of internal control for gene expression study in soybean by quantitative real-time PCR. BMC Mol Biol 9: 59.
30. Libault M, Thibivilliers S, Bilgin D, Radwan O, Benitez M, et al. (2008) Identification of four soybean reference genes for gene expression normalization. Plant Genome 1 (1): 44-54.
31. Expósito-Rodríguez M, Borges AA, Borges-Pérez A, Pérez JA, (2008) Selection of internal control genes for quantitative real-time RT-PCR studies during tomato development process. BMC Plant Biol 8: 131.
32. Nicot N, Hausman JF, Hoffmann L, Evers D, (2005) Housekeeping gene selection for real-time RT-PCR normalization in potato during biotic and abiotic stress. J Exp Bot 56 (421): 2907-2914.
33. Iskandar HM, Simpson RS, Casu RE, Bonnett GD, Maclean DJ, (2004) Comparison of reference genes for quantitative real-time polymerase chain reaction analysis of gene expression in sugarcane. Plant Mol Biol 22 (4): 325-337.
34. Brunner AM, Yakovlev IA, Strauss SH, (2004) Validating internal controls for quantitative plant gene expression studies. BMC Plant Biol 4: 14.
35. Li XP, He YP, Wu XJ, Ren QF, (2011) Water stress experiments of Platycladus orientalis and Pinus tablaeformis young trees. Forest Res 24(1) 91-96 (in Chinese with English abstract).
36. Jiang P, Shi J, Niu PX, Lu Y, (2009) Effect on activities of defensive enzymes and MDA content in leaves of Platycladus orientalis under naturally decreasing temperature. J Shihezi Univ (Natural Science) 27 30-33 (in Chinese with English abstract).
37. Zhang YJ, Cong RC, Zhao Q, Zhang GH, Li YH, et al. (2010) Physiological indexes applied to characterize aging old trees. Sci Silv Sin 46(3) 134-138 (in Chinese with English abstract).
38. Lanner RM, (2002) Why do trees live so long? Ageing Res Rev 1 (4): 653-671.
39. Peñuelas J, (2005) A big issue for trees. Nature 437: 965-966.
40. Thellin O, Zorzi W, Lakaye B, De Borman B, Coumans B, et al. (1999) Housekeeping genes as internal standards: use and limits. J Biotechnol 75 (2-3): 291-295.
41. Suzuki T, Higgins PJ, Crawford DR, (2000) Control selection for RNA quantitation. Biotechniques 29 (2): 332-337.
42. Glare EM, Divjak M, Bailey MJ, Walters EH, (2002) β-Actin and GAPDH housekeeping gene expression in asthmatic airways is variable and not suitable for normalising mRNA levels. Thorax 57: 765-770.
43. He XJ, Mu RL, Cao WH, Zhang ZG, Zhang JS, et al. (2005) AtNAC2, a transcription factor downstream of ethylene and auxin signaling pathways, is involved in salt stress response and lateral root development. Plant J 44 (6): 903-916.
44. Kim JH, Woo HR, Kim J, Lim PO, Lee IC, et al. (2009) Trifurcate feed-forward regulation of age-dependent cell death involving miR164 in Arabidopsis. Science 323 (5917): 1053-1057.
45. Balazadeh S, Siddiqui H, Allu AD, Matallana-Ramirez LP, Caldana C, et al. (2010) A gene regulatory network controlled by NAC transcription factor ANAC092/AtNAC2/ORE1 during salt-promoted senescence. Plant J 62 (2): 250-264.
46. Breeze E, Harrison E, McHattie S, Hughes L, Hickman R, et al. (2011) High-resolution temporal profiling of transcripts during Arabidopsis leaf senescence reveals a distinct chronology of processes and regulation. Plant Cell 23 (3): 873-894.
47. McCurley AT, Callard GV, (2008) Characterization of housekeeping genes in zebrafish: male-female differences and effects of tissue type, developmental stage and chemical treatment. BMC Mol Biol 9: 102.
48. Bustin SA, (2000) Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J Mol Endocrinol 25 (2): 169-193.
49. Scharlaken B, de Graaf DC, Goossens K, Brunain M, Peelman LJ, et al. (2008) Reference gene selection for insect expression studies using quantitative real-time PCR: The head of the honeybee, Apis mellifera, after a bacterial challenge. J Insect Sci 8 (33): 1-10.
50. Zhao WJ, Li Y, Gao PF, Sun ZH, Sun TS, et al. (2011) Validation of reference genes for real-time quantitative PCR studies in gene expression levels of Lactobacillus casei Zhang. J Ind Microbiol Biotechnol 38 (9): 1279-1286.
51. Pfaffl MW, Tichopad A, Prgomet C, Neuvians TP, (2004) Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper-Excel-based tool using pair-wise correlations. Biotechnol Lett 26 (6): 509-515.
52. Migocka M, Papierniak A, (2010) Identification of suitable reference genes for studying gene expression in cucumber plants subjected to abiotic stress and growth regulators. Mol Breeding 28 (3): 343-357.
53. Xu M, Zhang B, Su XH, Zhang SG, Huang MR, (2011) Reference gene selection for quantitative real-time polymerase chain reaction in Populus. Anal Biochem 408 (2): 337-339.
54. Marten M, Stefanie S, Stefan L, (2010) Selection of reliable reference genes during THP-1 monocyte differentiation into macrophages. BMC Mol Biol 11: 90.
55. Coker JS, Davis E, (2003) Selection of candidate housekeeping controls in tomato plants using EST data. Biotechniques 35 (4): 740-748.
56. Reid KE, Olsson N, Schlosser J, Peng F, Lund ST, (2006) An optimized grapevine RNA isolation procedure and statistical determination of reference genes for real-time RT-PCR during berry development. BMC Plant Biol 6: 27.
57. Yan HZ, Liou RF, (2006) Selection of internal control genes for real-time quantitative RT-PCR assays in the oomycete plant pathogen Phytophthora parasitica. Fungal Genet Biol 43 (6): 430-438.
58. geNorm software website. 9 Available: [Http://medgen.ugent.be/~jvdesomp/geNorm]. Accessed 2011 Sept.
59. NormFinder software website. 9 Available: [http://www.mdl.dk/publicationsnormfinder.htm]. Accessed 2011 Sept.
60. BestKeeper software website. 9 Available: [Http://www.gene-quantification.de/bestkeeper.html]. Accessed 2011 Sept.