Comparison of predictive methods and biological validation for qPCR reference genes in sunflower leaf senescence transcript analysis

Plant Cell Reports

Volumn 30, Issue 1, 2011, Pages 63-74

  Fernandez, Paula ^a,e   Rienzo, Julio A Di ^b   Moschen, Sebastián ^a,c   Dosio, Guillermo A A ^c   Aguirrezábal, Luis A N ^c   Hopp, H Esteban ^a,d   Paniego, Norma ^a   Heinz, Ruth A ^a,d  

^a INSTITUTO NACIONAL DE TECNOLOGÍA AGROPECUARIA INTA   (Argentina)

^b UNIVERSIDAD NACIONAL DE CÓRDOBA   (Argentina)

^c UNIVERSIDAD NACIONAL DE MAR DEL PLATA   (Argentina)

^d UNIVERSIDAD DE BUENOS AIRES   (Argentina)

^e UNIVERSIDAD NACIONAL DE SAN MARTÍN   (Argentina)

Author keywords

qPCR; Reference genes; Senescence; Sunflower

Indexed keywords

HELIANTHUS;

EID: 78650747259     PISSN: 07217714     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00299-010-0944-3     Document Type: Article

References (72)

1. Akaike H (1974) A new look at the statistical model identification. IEEE Trans Automat Contr 19: 716-723.
2. Altschul S, Gish W, Miller W, Myers E, Lipman D (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
3. Andersen C, Jensen J, Orntoft T (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.
4. 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 Biology 10: 49.
5. Barsalobres-Cavallari C, Severino F, Maluf M, Maia I (2009) Identification of suitable internal control genes for expression studies in Coffea arabica under different experimental conditions. BMC Molecular Biology 10(1): 1.
6. Borrás M, Madonni G, Otegui M (2003) Leaf senescence in maize hybrids: plant population, row spacing and kernel set effects. Field Crops Res 82: 13-26.
7. Brunner AM, Yakovlev IA, Strauss SH (2004) Validating internal controls for quantitative plant gene expression studies. BMC Plant Biology 4: 14.
8. Buchanan-Wollaston V, Ainsworth C (1997) Leaf senescence in Brassica napus: cloning of senescence-related genes by subtractive hybridization. J Exp Bot 52: 1117-1121.
9. Buchanan-Wollaston V, Earl S, Harrison E, Mathas E, Navabpour S, Page T, Pink D (2003) The molecular analysis of leaf senescence-a genomic approach. Plant Biotechnol J 1: 3-22.
10. Bustin S (2002) Quantification of mRNA using real-time reverse transcription PCR (RT-PCR): trends and problems. J Mol Endocrinol 29: 23-39.
11. Bustin S, Benes V, Garson J, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl M, Shipley G, Vandesompele J, Wittwer C (2009) The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 55: 611-622.
12. Chervoneva I, Li Y, Schulz S, Croker S, Wilson C, Waldman SA, Hyslop T (2010) Selection of optimal reference genes for normalization in quantitative RT-PCR. BMC Bioinformatics 11: 253.
13. Coker JS, Davies E (2003) Selection of candidate housekeeping controls in tomato plants using EST data. Biotechniques 35: 740-748.
14. Czechowski T, Bari R, Stitt M, Scheible W-R, Udvardi M (2004) Real-time RT-PCR profiling of over 1, 400 Arabidopsis transcription factors: unprecedented sensitivity reveals novel root- and shoot-specific genes. Plant J 38: 366-379.
15. Czechowski T, Stitt M, Altmann T, Udvardi M, Scheible W-R (2005) Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis. Plant Physiol 139: 5-17.
16. De Ketelaere A, Goossens K, Peelman L, Burvenich C (2006) Technical note: validation of internal control genes for gene expression analysis in bovine polymorphonuclear leukocytes. J Dairy Sci 89: 4066-4069.
17. Dombrovski JE, Martin RC (2008) Evaluation of reference genes for quantitative RT-PCR in Lolium temulentum under abiotic stress. Plant Sci 176: 390-396.
18. Duarte Silveira E, Alves-Ferreira M, Arrais Guimaraes L, Rodrigues da Silva F, de Tavares Campos Carneiro V (2009) Selection of reference genes for quantitative real-time PCR expresssion studes in the apomictic and sexual grass Brachiaria brizantha. BMC Plant Biol 9: 84.
19. Exposito-Rodriguez M, Borges A, Borges-Perez A, Perez J (2008) Selection of internal control genes for quantitative real-time RT-PCR studies during tomato development process. BMC Plant Biol 8: 31.
20. Fernandez P, Di Rienzo J, Fernandez L, Hopp H, Paniego N, Heinz RA (2008) Transcriptomic identification of candidate genes involved in sunflower responses to chilling and salt stresses based on cDNA microarray analysis. BMC Plant Biol 8: 11.
21. Gan S (2003) Mitotic and postmitotic senescence in plants. Science's SAGE KE.
22. Gan S, Amasino RM (1997) Making sense of senescence. Plant Physiol 113: 313-319.
23. Gepstein S, Sabehi G, Carp M-J, Hajouj T, Nesher MFO, Yariv I, Dor C, Bassani M (2003) Large-scale identification of leaf senescence-associated genes. Plant J 36: 629-642.
24. Gonzalez-Verdejo CI, Die JV, Nadal S, Jimenez-Marín A, Moreno MT, Román B (2008) Selection of housekeeping genes for normalization by real-time RT-PCR: analysis of Or-MYB1 gene expression in Orobanche ramosa development. Anal Biochem 379: 38-43.
25. Guenin S, Mauriat M, Pelloux J, van Wuytswinkel O, Bellini C, Gutierrez L (2009) Normalization of qRT-PCR data: the necessity of adopting a systematic, experimental conditions-specific, validation of references. J Exp Bot 60: 487-493.
26. Gutierrez N, Giménez MJ, Palomino C, Avila CM (2010) Assessment of candidate reference genes for expression studies in Vicia faba L. by real-time quantitative PCR. Mol Breed. doi: 10. 1007/s11032-010-9456-7.
27. Hewezi T, Leger M, El Kayal W, Gentzbittel L (2006) Transcriptional profiling of sunflower plants growing under low temperatures reveals an extensive down-regulation of gene expression associated with chilling sensitivity. J Exp Bot 57: 3109-3122.
28. Huis R, Hawkins S, Neutelings G (2010) Selection of reference genes for quantitative gene expression normalization in flax (Linum usitatissimum L.). BMC Plant Biol 10: 7.
29. 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.
30. 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.
31. 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.
32. Kim B-R, Nam H-Y, Kim S-U, Kim S-I, Chang Y-J (2003) Normalization of reverse transcription quantitative-PCR with housekeeping genes in rice. Biotechnol Lett 25: 1869-1872.
33. Kuijk E, du Puy L, TA von Tol H, Haagsman H, Colenbrander P, Roelen B (2007) Validation of reference genes for quantitative RT-PCR studies in porcine oocytes and preimplantation embryos. BMC Dev Biol 7: 58.
34. Lechner L, Pereyra Irujo G, Granier C, Aguirrezabal L (2008) Re-watering of plants under water deficit reveals that leaf cells retain their ability to expand after the leaf has apparently reached its final size. Ann Bot 101: 1007-1015.
35. Libault M, Thibivilliers D, Bilgin D, Radwan O, Benitez M, Clough S, Stacey G (2008) Identification of four soybean reference genes for gene expression normalization. Plant Genome 1: 44-54.
36. Lim PO, Woo HR, Nam HG (2003) Molecular genetics of leaf senescence in Arabidopsis. Trends Plant Sci 8: 272-278.
37. Lim P, Kim H, Nam H (2007) Leaf senescence. Annu Rev Plant Biol 58: 115-136.
38. Lin YL, Lai ZX (2010) Reference gene selection for qPCR analysis during somatic embryogenesis in longan tree. Plant Sci 178: 359-365.
39. -{increment}{increment}Ct method. Methods 25: 402-408.
40. Lovdal 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: 238-242.
41. Luo H, Chen S, Wan H, Chen F, Gu C, Liu Z (2010) Candidate reference genes for gene expression studes in water lily. Anal Biochem. doi: 10. 1016/j. ab. 2010. 05. 002.
42. 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.
43. Maroufi A, van Bockstaele E, De Loose M (2010) Validation of reference genes for gene expression analysis in chicory (Cichorium intybus) using quantitative real-time PCR. BMC Mol Biol 11: 15.
44. Martin R, Hollenbeck V, Dombrowski J (2008) Evaluation of Reference Genes for Quantitative RT-PCR in Lolium perenne. Crop Sci 48: 1881-1887.
45. Narsai R, Ivanova A, Ng S, Whelan J (2010) Defining reference genes in Oryza sativa using organ, development, biotic and abiotic transcriptome datasets. BMC Plant Biol 10: 56.
46. National Center for Biotechnology Information (NCBI) (http://blast. ncbi. nlm. nih. gov/).
47. National Sunflower Association [http://www. sunflowernsa. com/stats/table. asp?contentID=109& htmlID=74& submit170=View& submit. x=57& submit. y=12)].
48. Nicot N, Hausman J-F, Hoffman L, Evers D (2005) Housekeeping gene selection for real-time PCR normalization in potato during biotic and abiotic stress. J Exp Bot 56: 2907-2914.
49. Olbrich M, Gerstner E, Welzl G, Fleischmann F, Obwald W, Bahnweg G, Ernst D (2008) Quantification of mRNAs and housekeeping gene selection for quantitative real-time RT-PCR normalization in European Beech (Fagus sylvatica L.) during abiotic and biotic stress. Z Naturforsch C 63: 574-582.
50. Pabinger S, Thallinger G, Snajder R, Eichjorn H, Rader R, Trajanoski Z (2009) QPCR: application for real-time PCR data management and analysis. BMC Bioinformatics 10: 268.
51. Paolacci A, Tanzarella O, Porceddu E, Ciaffi M (2009) Identification and validation of reference genes for quantitative RT-PCR normalization in wheat. BMC Mol Biol 10: 11.
52. Pfaffl MW (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acid Res 29: e45.
53. Pfaffl M, Tichopád A, Prgomet C, Neuvians T (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.
54. Pic E, Teyssandier de la Serve B, Tardieu F, Turc O (2002) Leaf senescence induced by mild water deficit follows the same sequence of macroscopic, biochemical, and molecular events as monocarpic senescence in pea. Plant Physiol 128: 236-246.
55. Pommel B, Gallais A, Coque M, Quelleré I, Hirel B, Prioul J, Andrieu B, Floriot M (2006) Carbon and nitrogen allocation and grain filling in three maize hybrids differing in leaf senescence. Eur J Agron 24: 203-211.
56. Quackenbush J (2002) Microarray data normalization and transformation. Nat Genet 32: 496-501.
57. 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 313: 856-862.
58. 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.
59. Remans T, Smeets K, Opdenakker K, Mathijsen D, Vangronsveld J, Cuypers A (2008) Normalisation of real-time PCR gene expression measurements in Arabidopsis thaliana exposed to increased metal concentrations. Planta 227(6): 1343-1349. doi: 10. 1007/s00425-008-0706-4.
60. Sadras V, Echarte L, Andrade F (2000) Profiles of leaf senescence during reproductive growth of sunflower and maize. Ann Bot 85: 187-195.
61. 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.
62. Scholdberg TA, Norden TD, Nelson DD, Ronald Jenkins G (2009) Evaluating precision and accuracy when quantifying different endogenous control reference genes in maize using real-time PCR. J Agric Food Chem 57: 2903-2911.
63. Spanakis E (1993) Problems related to the interpretation of autoradiographic data on gene expression using common constitutive transcripts as controls. Nucleic Acids Res 21: 3809-3819.
64. Suzuki T, Higgins PJ, Crawford DR (2000) Control selection for RNA quantitation. Biotechniques 29: 332-337.
65. Szabo A, Perou CM, Karaca M, Perreard L, Quackenbush JF, Bernard PS (2004) Statistical modeling for selecting housekeeper genes. Genome Biology 5: R59.
66. The Dana Farber Cancer Institute Sunflower Gene Index Project (http://compbio. dfci. harvard. edu/tgi/cgi-bin/tgi/gimain. pl?gudb=sunflower).
67. Thorrez L, van Deun K, Tranchevent LC, van Lommel L, Engelen K, Marchal K, Moreau Y, van Mechelen I, Schuit F (2008) Using ribosomal protein genes as reference: a tale of caution. PLoS One 3: e1854.
68. Tong Z, Gao Z, 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.
69. Vandesompele J, De Preter K, Pattyn F, Poppe B, van Roy N, De Paepe A, Speleman F (2002) Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biology 3(7): RESEARCH0034.
70. Wan H, Zhao Z, Qian C, Sui Y, Malik A, Chen J (2009) Selection of appropriate reference genes for gene expression studies by quantitative real-time polymerase chain reaction in cucumber. Anal Biochem. doi: 10. 1016/j. ab. 2009. 12. 008.
71. Weaver M, Amasino R (2001) Senescence is induced in individually darkened Arabidopsis leaves, but inhibited in whole darkened plants. Plant Physiol 127: 876-886.
72. Yang Y, Hou S, Cui G, Chen S, Wei J, Huang L (2010) Characterization of reference genes for quantitative real-time PCR analysis in various tissues of Salvia miltiorrhiza. Mol Biol Rep 37: 507-513.