Selection of reliable reference genes for gene expression studies in peach using real-time PCR

Zhaoguo Tong1, Zhihong Gao1, Fei Wang1, Jun Zhou1, Zhen Zhang1
1College of Horticulture, Nanjing Agricultural University, 1 Tongwei Road, Weigang, Nanjing, 210095, PR China

Tóm tắt

Abstract Background

RT-qPCR is a preferred method for rapid and reliable quantification of gene expression studies. Appropriate application of RT-qPCR in such studies requires the use of reference gene(s) as an internal control to normalize mRNA levels between different samples for an exact comparison of gene expression level. However, recent studies have shown that no single reference gene is universal for all experiments. Thus, the identification of high quality reference gene(s) is of paramount importance for the interpretation of data generated by RT-qPCR. Only a few studies on reference genes have been done in plants and none in peach (Prunus persica L. Batsch). Therefore, the present study was conducted to identify suitable reference gene(s) for normalization of gene expression in peach.

Results

In this work, eleven reference genes were investigated in different peach samples using RT-qPCR with SYBR green. These genes are: actin 2/7 (ACT), cyclophilin (CYP2), RNA polymerase II (RP II), phospholipase A2 (PLA2), ribosomal protein L13 (RPL13), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), 18S ribosomal RNA (18S rRNA), tubblin beta (TUB), tubblin alpha (TUA), translation elongation factor 2 (TEF2) and ubiquitin 10 (UBQ10). All eleven reference genes displayed a wide range of Cq values in all samples, indicating that they expressed variably. The stability of these genes except for RPL13 was determined by three different descriptive statistics, geNorm, NormFinder and BestKeeper, which produced highly comparable results.

Conclusion

Our study demonstrates that expression stability varied greatly between genes studied in peach. Based on the results from geNorm, NormFinder and BestKeeper analyses, for all the sample pools analyzed, TEF2, UBQ10 and RP II were found to be the most suitable reference genes with a very high statistical reliability, and TEF2 and RP II for the other sample series, while 18S rRNA, RPL13 and PLA2 were unsuitable as internal controls. GAPDH and ACT also performed poorly and were less stable in our analysis. To achieve accurate comparison of levels of gene expression, two or more reference genes must be used for data normalization. The combinations of TEF2/UBQ10/RP II and TEF2/RP II were suggested for use in all samples and subsets, respectively.

Từ khóa


Tài liệu tham khảo

Ginzinger DG: Gene quantification using real-time quantitative PCR: An emerging technology hits the mainstream. Exp Hematol. 2002, 30 (6): 503-512.

Bustin SA: Quantification of mRNA using real-time reverse transcription PCR (RT-PCR): trends and problems. J Mol Endocrinol. 2002, 29 (1): 23-39.

Garson JA, Grant PR, Ayliffe U, Ferns RB, Tedder RS: Real-time PCR quantitation of hepatitis B virus DNA using automated sample preparation and murine cytomegalovirus internal control. J Virol Methods. 2005, 126 (1–2): 207-213.

Huggett J, Dheda K, Bustin S, Zumla A: Real-time RT-PCR normalisation; strategies and considerations. Genes Immun. 2005, 6 (4): 279-284.

Schmittgen TD, Zakrajsek BA: Effect of experimental treatment on housekeeping gene expression: validation by real-time, quantitative RT-PCR. J Biochem Biophys Methods. 2000, 46 (1–2): 69-81.

Thellin O, Zorzi W, Lakaye B, De Borman B, Coumans B, Hennen G, Grisar T, Igout A, Heinen E: Housekeeping genes as internal standards: use and limits. J Biotechnol. 1999, 75 (2–3): 291-295.

Cappelli K, Felicetti M, Capomaccio S, Spinsanti G, Silvestrelli M, Supplizi AV: Exercise induced stress in horses: selection of the most stable reference genes for quantitative RT-PCR normalization. BMC Mol Biol. 2008, 9: 49-

Dheda K, Huggett J, Bustin SA, Johnson MA, Rook G, Zumla A: Validation of housekeeping genes for normalizing RNA expression in real-time PCR. BioTechniques. 2004, 37: 112-119.

Suzuki T, Higgins PJ, DR C: Control selection for RNA quantitation. BioTechniques. 2000, 29: 332-337.

Bas A, Forsberg G, Hammarstrom S, Hammarstrom ML: Utility of the housekeeping genes 18S rRNA, beta-actin and glyceraldehyde-3-phosphate-dehydrogenase for normalization in real-time quantitative reverse transcriptase-polymerase chain reaction analysis of gene expression in human T lymphocytes. Scand J Immunol. 2004, 59 (6): 566-573.

Yperman J, De Visscher G, Holvoet P, Flameng W: Beta-actin cannot be used as a control for gene expression in ovine interstitial cells derived from heart valves. J Heart Valve Dis. 2004, 13 (5): 848-853.

Barber RD, Harmer DW, Coleman RA, Clark BJ: GAPDH as a housekeeping gene: analysis of GAPDH mRNA expression in a panel of 72 human tissues. Physiol Genomics. 2005, 21 (3): 389-395.

Nicot N, Hausman JF, Hoffmann L, Evers D: Housekeeping gene selection for real-time RT-PCR normalization in potato during biotic and abiotic stress. J Exp Bot. 2005, 56 (421): 2907-2914.

Ishitani R, Sunaga K, Hirano A, Saunders P, Katsube N, Chuang DM: Evidence that glyceraldehyde-3-phosphate dehydrogenase is involved in age-induced apoptosis in mature cerebellar neurons in culture. J Neurochem. 1996, 66 (3): 928-935.

Singh R, Green M: Sequence-specific binding of transfer RNA by glyceraldehyde-3-phosphate dehydrogenase. Science. 1993, 259 (5093): 365-368.

Dheda K, Huggett JF, Chang JS, Kim LU, Bustin SA, Johnson MA, Rook GAW, Zumla A: The implications of using an inappropriate reference gene for real-time reverse transcription PCR data normalization. Anal Biochem. 2005, 344 (1): 141-143.

Tatsumi K, Ohashi K, Taminishi S, Okano T, Yoshioka A, Shima M: Reference gene selection for real-time RT-PCR in regenerating mouse livers. Biochem Biophys Res Commun. 2008, 374 (1): 106-110.

Paolacci A, Tanzarella O, Porceddu E, Ciaffi M: Identification and validation of reference genes for quantitative RT-PCR normalization in wheat. BMC molecular biology. 2009, 10 (1): 11-

Burton RA, Shirley NJ, King BJ, Harvey AJ, Fincher GB: The CesA Gene Family of Barley. Quantitative Analysis of Transcripts Reveals Two Groups of Co-Expressed Genes. Plant Physiol. 2004, 134 (1): 224-236.

Ding J, Jia J, Yang L, Wen H, Zhang C, Liu W, Zhang D: Validation of a rice specific gene, sucrose phosphate synthase, used as the endogenous reference gene for qualitative and real-time quantitative PCR detection of transgenes. J Agric Food Chem. 2004, 52 (11): 3372-3377.

Jain M, Nijhawan A, Tyagi AK, Khurana JP: Validation of housekeeping genes as internal control for studying gene expression in rice by quantitative real-time PCR. Biochem Biophys Res Commun. 2006, 345 (2): 646-651.

Kim BR, Nam HY, Kim SU, Kim SI, Chang YJ: Normalization of reverse transcription quantitative-PCR with housekeeping genes in rice. Biotechnol Lett. 2003, 25 (21): 1869-1872.

Jian B, Liu B, Bi Y, Hou W, Wu C, Han T: Validation of internal control for gene expression study in soybean by quantitative real-time PCR. BMC Mol Biol. 2008, 9 (1): 59-

Reid KE, Olsson N, Schlosser J, Peng F, Lund ST: An optimized grapevine RNA isolation procedure and statistical determination of reference genes for real-time RT-PCR during berry development. BMC Plant Biol. 2006, 6 (1): 27-

Brunner AM, Yakovlev IA, Strauss SH: Validating internal controls for quantitative plant gene expression studies. BMC Plant Biol. 2004, 4 (1): 14-

Coker JS, Davies E: Selection of candidate housekeeping controls in tomato plants using EST data. BioTechniques. 2003, 35: 740-748.

Exposito-Rodriguez M, Borges A, Borges-Perez A, Perez J: Selection of internal control genes for quantitative real-time RT-PCR studies during tomato development process. BMC Plant Biology. 2008, 8 (1): 131-

Barsalobres-Cavallari C, Severino F, Maluf M, Maia I: Identification of suitable internal control genes for expression studies in Coffea arabica under different experimental conditions. BMC molecular biology. 2009, 10 (1): 1-

Czechowski T, Stitt M, Altmann T, Udvardi MK, Scheible W-R: Genome-wide identification and testing of superior reference genes for transcript normalization in arabidopsis. Plant Physiol. 2005, 139 (1): 5-17.

Remans T, Smeets K, Opdenakker K, Mathijsen D, Vangronsveld J, Cuypers A: Normalisation of real-time RT-PCR gene expression measurements in arabidopsis thaliana exposed to increased metal concentrations. Planta. 2008, 227 (6): 1343-1349.

Fischer RL, Bennett AB: Role of cell wall hydrolases in fruit ripening. Plant Mol Biol. 1991, 42: 675-703.

Fonseca S, Hackler L, Zvara Á, Ferreira S, Bald A, Dudits D, Pais MS, Puskás LG: Monitoring gene expression along pear fruit development, ripening and senescence using cDNA microarrays. Plant Sci. 2004, 167 (3): 457-469.

Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F: Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 2002, 3 (7): RESEARCH0034-

Pfaffl MW, Tichopad A, Prgomet C, Neuvians TP: Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper – Excel-based tool using pair-wise correlations. Biotechnol Lett. 2004, 26 (6): 509-515.

Andersen CL, Jensen JL, Orntoft TF: Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer Res. 2004, 64 (15): 5245-5250.

Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT: The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem. 2009, 55 (4): 611-622.

geNorm Software. http://medgen.ugent.be/~jvdesomp/genorm/

Tricarico C, Pinzani P, Bianchi S, Paglierani M, Distante V, Pazzagli M, Bustin SA, Orlando C: Quantitative real-time reverse transcription polymerase chain reaction: normalization to rRNA or single housekeeping genes is inappropriate for human tissue biopsies. Anal Biochem. 2002, 309 (2): 293-300.

Hellemans J, Mortier G, De Paepe A, Speleman F, Vandesompele J: qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data. Genome Biol. 2007, 8: R19-

García-Vallejo JJ, Van het Hof B, Robben J, Van Wijk JAE, Van Die I, Joziasse DH, Van Dijk W: Approach for defining endogenous reference genes in gene expression experiments. Anal Biochem. 2004, 329 (2): 293-299.

Haller F, Kulle B, Schwager S, Gunawan B, Heydebreck Av, Sültmannd H, Füzesi L: Equivalence test in quantitative reverse transcription polymerase chain reaction: confirmation of reference genes suitable for normalization. Anal Biochem. 2004, 335 (1): 1-9.

Brunner AM, Yakovlev IA, Strauss SH: Validating internal controls for quantitative plant gene expression studies. BMC Plant Biology. 2004, 4 (1): 14-

Radonic A, Thulke S, Mackay IM, Landt O, Siegert W, Nitsche A: Guideline to reference gene selection for quantitative real-time PCR. Biochem Biophys Res Commun. 2004, 313 (4): 856-862.

de Kok JB, Roelofs RW, Giesendorf BA, Pennings JL, Waas ET, Feuth T, Swinkels DW, Span PN: Normalization of gene expression measurements in tumor tissues: comparison of 13 endogenous control genes. Lab Invest. 2005, 85 (1): 154-159.

Szabo A, Perou CM, Karaca M, Perreard L, Palais R, Quackenbush JF, Bernard PS: Statistical modeling for selecting housekeeper genes. Genome Biol. 2004, 5 (8): R59-

Ayers D, Clements D, Salway F, Day P: Expression stability of commonly used reference genes in canine articular connective tissues. BMC Veterinary Research. 2007, 3: 7-

Proud CG: Peptide-chain elongation in eukaryotes. Mol Biol Rep. 1994, 19 (3): 161-170.

Løvdal T, Lillo C: Reference gene selection for quantitative real-time PCR normalization in tomato subjected to nitrogen, cold, and light stress. Analytical Biochemistry. 2009, 387 (2): 238-242.

Hochstrasser M: Evolution and function of ubiquitin-like protein-conjugation systems. Nat Cell Biol. 2000, 2 (8): E153-157.

Marivet J, Frendo P, Burkard G: Effects of antibiotic stresses on cyclophilin in maize and bean and sequence analysis of bean cyclophilin cDNA. Plant Sci. 1992, 84: 171-178.

Iskandar H, Simpson R, Casu R, Bonnett G, Maclean D, Manners J: Comparison of reference genes for quantitative real-time polymerase chain reaction analysis of gene expression in sugarcane. Plant Mol Biol Rep. 2004, 22 (4): 325-337.

Gonzalez-Verdejo CI, Die JV, Nadal S, Jimenez-Marin A, Moreno MT, Roman B: Selection of housekeeping genes for normalization by real-time RT-PCR: analysis of Or-MYB1 gene expression in orobanche ramosa development. Anal Biochem. 2008, 379 (2): 176-181.

RT-PCR: The basic. http://www.ambion.com/techlib/basics/rtpcr/index.html

Takle GW, K TI, Brurberg MB: Evaluation of reference genes for real-time RT-PCR expression studies in the plant pathogen pectobacterium atrosepticum. BMC Plant Biol. 2007, 7: 50-

Vera MI, Norambuena L, Alvarez M, Figueroa J, Molina A, Leon G, Krauskopf M: Reprogramming of nucleolar gene expression during the acclimatization of the carp. Cell Mol Biol Res. 1993, 39 (7): 665-674.

Stürzenbaum SR, Kille P: Control genes in quantitative molecular biological techniques: the variability of invariance. Comp Biochem Phys B: Biochem Mol Biol. 2001, 130 (3): 281-289.

Gutierrez L, Mauriat M, Guenin S, Pelloux J, Lefebvre JF, Louvet R, Rusterucci C, Moritz T, Guerineau F, Bellini C, Van Wuytswinkel O: The lack of a systematic validation of reference genes: a serious pitfall undervalued in reverse transcription-polymerase chain reaction (RT-PCR) analysis in plants. Plant Biotechnol J. 2008, 609-618. 6

Begheldo M, Ziliotto F, Rasori A, Bonghi C: The use of μPEACH 1.0 to investigate the role of ethylene in the initiation of peach fruit ripening. Advances in Plant Ethylene Research. 2007, 265-267.

Ziosi V, Bonghi C, Bregoli AM, Trainotti L, Biondi S, Sutthiwal S, Kondo S, Costa G, Torrigiani P: Jasmonate-induced transcriptional changes suggest a negative interference with the ripening syndrome in peach fruit. J Exp Bot. 2008, 59 (3): 563-573.

Liguori G, Weksler A, Zutahi Y, Lurie S, Kosto I: Effect of 1-methylcyclopropene on ripening of melting flesh peaches and nectarines. Postharvest Biol Tec. 2004, 31 (3): 263-268.

Trainotti L, Pavanello A, Zanin D: PpEG4 is a peach endo-beta-1, 4-glucanase gene whose expression in climacteric peaches does not follow a climacteric pattern. J Exp Bot. 2006, 57 (3): 589-598.

Meisel L, Fonseca B, González S, Baezayates R, Cambiazo V, Campos R, Gonzalez M, Orellana A, Retamales J, Silva H: A rapid and efficient method for purifying high quality total RNA from peaches (Prunus persica) for functional genomics analyses. Biol Res. 2005, 38: 83-88.

Peach EST database. http://compbio.dfci.harvard.edu/tgi/cgi-bin/tgi/gimain.pl?gudb=peach

TAIR BLAST. http://www.arabidopsis.org/Blast/index.jsp

Fleige S, MW P: RNA integrity and the effect on the realtime qRT-PCR performance. Mol Aspects Med. 2006, 27: 126-139.

Zuker M: Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003, 31 (13): 3406-3415.

Ramakers C, Ruijter JM, Deprez RH, Moorman AF: Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data. Neurosci Lett. 2003, 339 (1): 62-66.

Livak KJ, Schmittgen TD: Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCT method. Methods. 2001, 25 (4): 402-408.

NormFinder Software. http://www.mdl.dk/publicationsnormfinder.htm

BestKeeper Software. http://www.gene-quantification.de/bestkeeper.html