Validation of reference genes for RT-qPCR studies of gene expression in banana fruit under different experimental conditions

Planta

Volumn 234, Issue 2, 2011, Pages 377-390

  Chen, Lei ^a   Zhong, Hai ying ^a   Kuang, Jian fei ^a   Li, Jian guo ^a   Lu, Wang jin ^a   Chen, Jian ye ^a  

^a SOUTH CHINA AGRICULTURAL UNIVERSITY   (China)

Author keywords

Banana; Reference genes; RT qPCR; Validation

Indexed keywords

EID: 85027928183     PISSN: 00320935     EISSN: 14322048     Source Type: Journal    
DOI: 10.1007/s00425-011-1410-3     Document Type: Article

References (57)

1. An FY, Zhao Q, Ji YS, Li WY, Jiang ZQ, Yu XC, Zhang C, Han Y, He WR, Liu YD, Zhang SQ, Ecker JR, Guo HW (2010) Ethylene-induced stabilization of ETHYLENE INSENSITIVE3 and EIN3-LIKE1 is mediated by proteasomal degradation of EIN3 binding F-Box 1 and 2 that requires EIN2 in Arabidopsis. Plant Cell 22: 2384-2401.
2. Andersen CL, Jensen JL, Orntoft TF (2004) 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 64: 5245-5250.
3. 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.
4. 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.
5. Brunner AM, Yakovlev IA, Strauss SH (2004) Validating internal controls for quantitative plant gene expression studies. BMC Plant Biol 4: 14.
6. Bustin SA (2002) Quantification of mRNA using real-time reverse transcription PCR RT-PCR: trends and problems. Mol Endocrinol 29: 23-29.
7. Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT (2009) The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 55: 611-622.
8. Chen JY, He LH, Jiang YM, Wang Y, Joyce DC, Ji ZL, Lu WJ (2008) Role of phenylalanine ammonia-lyase in heat pretreatment-induced chilling tolerance in banana fruit. Physiol Plant 132: 318-328.
9. Chuaqui RF, Bonner RF, Best CJM, Gillespie JW, Flaig MJ, Hewitt SM, Phillips JL, Krizman DB, Tangrea MA, Ahram M, Linehan WM, Knezevic V, Emmert-Buck MR (2002) Post-analysis follow-up and validation of microarray experiments. Nat Genet 32: 509-514.
10. Cruz F, Kalaoun S, Nobile P, Colombo C, Almeida J, Barros L, Romano E, Grossi-de-Sá MF, Vaslin M, Alves-Ferreira M (2009) Evaluation of coffee reference genes for relative expression studies by quantitative real-time RT-PCR. Mol Breeding 23: 607-616.
11. Czechowski TSM, 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.
12. Derveaux S, Vandesompele J, Hellemans J (2010) How to do successful gene expression analysis using real-time PCR. Methods 50: 227-230.
13. Die JV, Román B, Nadal S, González-Verdejo CI (2010) Evaluation of candidate reference genes for expression studies in Pisum sativum under different experimental conditions. Planta 232: 145-153.
14. Dombrowski J, Martin R (2009) Evaluation of reference genes for quantitative RT-PCR in Lolium temulentum under abiotic stress. Plant Sci 176: 390-396.
15. Elitzur T, Vrebalov J, Giovannoni JJ, Goldschmidt EE, Friedman H (2010) The regulation of MADS-box gene expression during ripening of banana and their regulatory interaction with ethylene. J Exp Bot 61: 1523-1535.
16. Expósito-Rodríguez M, Borges A, Borges-Pérez A, Pérez J (2008) Selection of internal control genes for quantitative real-time RT-PCR studies during tomato development process. BMC Plant Biol 8: 131.
17. Gutierrez L, Mauriat M, Guénin S, Pelloux J, Lefebvre JF, Louvet R, Rusterucci C, Moritz T, Guerineau F, Bellini C, van Wuytswinkel O (2008) 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 6: 609-618.
18. Hellemans J, Mortier G, De Paepe A, Speleman F, Vandesompele J (2007) qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data. Genome Biol 8: R19.
19. Hong SY, Seo PJ, Yang MS, Xiang F, Park CM (2008) Exploring valid reference genes for gene expression studies in Brachypodium distacyon by real-time PCR. BMC Plant Biol 8: 112.
20. Hu R, Fan C, Li H, Zhang Q, Fu Y-F (2009) Evaluation of putative reference genes for gene expression normalization in soybean by quantitative real-time RT-PCR. BMC Mol Biol 10: 93.
21. Huggett J, Dheda K, Bustin S, Zumla A (2005) Real-time RT-PCR normalization, strategies and considerations. Genes Immun 6: 279-284.
22. Inaba A, Liu X, Yokotani N, Yamane M, Lu WJ, Nakano R, Kubo Y (2007) Differential feedback regulation of ethylene biosynthesis in pulp and peel tissues of banana fruit. J Exp Bot 58: 1047-1057.
23. Iskandar HM, Simpson RS, Casu RE, Bonnet GD, Maclean DJ, Manners JM (2004) Comparison of reference genes for quantitative real-time polymerase chain reaction analysis of gene in sugarcane. Plant Mol Biol Rep 22: 325-337.
24. Jain M (2009) Genome-wide identification of novel internal control genes for normalization of gene expression during various stages of development in rice. Plant Sci 176: 702-706.
25. 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: 646-651.
26. Jian B, Liu B, Bi Y, Hou W, Wu C, Han T (2008) Validation of internal control for gene expression study in soybean by quantitative real-time PCR. BMC Mol Biol 9: 59.
27. Kim B, Nam H, Kim S, Chang YJ (2003) Normalization of reverse transcription quantitative-PCR with housekeeping genes in rice. Biotechnol Lett 25: 1869-1872.
28. Le Bail A, Dittami S, de Franco PO, Rousvoal S, Cock M, Tonon T, Charrier B (2008) Normalisation genes for expression analyses in the brown alga model Ectocarpus siliculosus. BMC Mol Biol 9: 75.
29. Lee JM, Roche JR, Donaghy DJ, Thrush A, Sathish P (2010) Validation of reference genes for quantitative RT-PCR studies of gene expression in perennial ryegrass (Lolium perenne L.). BMC Mol Biol 11: 8.
30. Libault M, Thibivilliers S, Bilgin DD, Radwan O, Benitez M, Clough SJ, Stacey G (2008) Identification of four soybean reference genes for gene expression normalization. Plant Genome 1: 44-54.
31. Lin YL, Lai ZX (2010) Reference gene selection for qPCR analysis during somatic embryogenesis in longan tree. Plant Sci 178: 359-365.
32. Ma BC, Tang WL, Ma LY, Li LL, Zhang LB, Zhu SJ (2009) The role of chitinase gene expression in the defense of harvested banana against anthracnose disease. J Amer Soc Hort Sci 134: 379-386.
33. Mallona I, Lischewski S, Weiss J, Hause B, Egea-Cortines M (2010) Validation of reference genes for quantitative real-time PCR during leaf and flower development in Petunia hybrida. BMC Plant Biol 10: 4.
34. Maroufi A, Bockstaele EV, Loose MD (2010) Validation of reference genes for gene expression analysis in chicory (Cichorium intybus) using quantitative real-time PCR. BMC Mol Biol 11: 15.
35. Martin RC, Hollenbeck VG, Dombrowski JE (2008) Evaluation of reference genes for quantitative RT-PCR in Lolium perenne. Crop Sci 48: 1881-1887.
36. Mbéguié-A-Mbéguié D, Hubert O, Fils-Lycaon B, Chillet M, Baurens FC (2008) EIN3-like gene expression during fruit ripening of Cavendish banana (Musa acuminata cv. Grande naine). Physiol Plant 133: 435-448.
37. Mbéguié-A-Mbéguié D, Hubert O, Baurens FC, Matsumoto T, Chillet M, Fils-Lycaon B, Sidibé-Bocs S (2009) Expression patterns of cell wall-modifying genes from banana during fruit ripening and in relationship with finger drop. J Exp Bot 60: 2021-2034.
38. Mukesh J, Aashima N, Akhilesh KT, Jitendra PK (2006) Validation of housekeeping genes as internal control for studying gene expression in rice by quantitative real-time PCR. Biochem Biophys Res Commun 345: 646-651.
39. 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: 2907-2914.
40. Nolan T, Hands RE, Bustin SA (2006) Quantification of mRNA using real-time RTPCR. Nat Protocols 1: 1559-1582.
41. Paolacci AR, Tanzarella OA, Porceddu EP, Ciaffi M (2009) Identification and validation of reference genes for quantitative RT-PCR normalization in wheat. BMC Mol Biol 10: 11.
42. Pfaffl MWTA, 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: 509-515.
43. Radonic A, Thulke S, Mackay IM, Landt O, Siegert W, Nitsche A (2004) Guideline to reference gene selection for quantitative real-time PCR. Biochem Biophys Res Commun 23: 856-862.
44. 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.
45. Remans T, Smeets K, Opdenakker K, Mathijsen D, Vangronsveld J, Cuypers A (2008) Normalisation of real-time RT-PCR gene expression measurements in Arabidopsis thaliana exposed to increased metal concentrations. Planta 227: 1343-1349.
46. Roy CS, Roy S, Singh SK, Sengupta DN (2010) Molecular characterization and differential expression of beta-1, 3-glucanase during ripening in banana fruit in response to ethylene, auxin, ABA, wounding, cold and light-dark cycles. Plant Cell Rep 29: 813-828.
47. Schmidt GW, Delaney SK (2010) Stable internal reference genes for normalization of real-time RT-PCR in tobacco (Nicotiana tabacum) during development and abiotic stress. Mol Genet Genomics 283: 233-241.
48. Silveira ED, Alves-Ferreira M, Guimarães LA, Rodrigues da Silva F, Carneiro V (2009) Selection of reference genes for quantitative real-time PCR expression studies in the apomictic and sexual grass Brachiaria brizantha. BMC Plant Biol 9: 84.
49. Tang WL, Zhu SJ, Li LL, Liu DJ, Irving DE (2010) Differential expressions of PR1 and chitinase genes in harvested bananas during ripening, and in response to ethephon, benzothiadizole and methyl jasmonate. Postharvest Biol Technol 57: 86-91.
50. Tong Z, Gao Z, Wang F, Zhou J, Zhang Z (2009) Selection of reliable reference genes for gene expression studies in peach using realtime PCR. BMC Mol Biol 10: 71.
51. Tu L, Zhang X, Liu D, Jin S, Cao J, Zhu L, Deng F, Tan J, Zhang C (2007) Suitable internal control genes for qRT-PCR normalization in cotton fiber development and somatic embryogenesis. Chin Sci Bull 52: 3110-3117.
52. Vandesompele J, De Preter K, Pattyn F, Poppe B, van Roy N, De Paepe A, Speleman F (2002) Accurate normalisation of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 3: 1-11.
53. Wan CY, Wilkins TA (1994) A modified hot borate method significantly enhances the yield of high-quality RNA from cotton (Gossypiumhirsutum L.). Anal Biochem 223: 7-12.
54. Wan HJ, Zhao ZG, Qian CT, Sui YH, Malik AA, Chen JF (2010) Selection of appropriate reference genes for gene expression studies by quantitative real-time polymerase chain reaction in cucumber. Anal Biochem 399: 257-261.
55. Wang Y, Wu J, Xu BY, Liu JH, Zhang JB, Jia CH, Jin ZQ (2010) Cloning of an ADP-ribosylation factor gene from banana (Musa acuminata) and its expression patterns in postharvest ripening fruit. J Plant Physiol 167: 989-995.
56. Wong ML, Medrano JF (2005) Real-time PCR for mRNA quantitation. BioTechniques 39: 75-85.
57. Yang YG, Wu Y, Pirrello J, Regad F, Bouzayen M, Deng W, Li ZG (2009) Silencing Sl-EBF1 and Sl-EBF2 expression causes constitutive ethylene response phenotype, accelerated plant senescence, and fruit ripening in tomato. J Exp Bot 61: 697-708.