Identification and validation of reference genes for quantitative RT-PCR normalization in wheat

BMC Molecular Biology

Volumn 10, Issue , 2009, Pages

  Paolacci, Anna R ^a   Tanzarella, Oronzo A ^a   Porceddu, Enrico ^a   Ciaffi, Mario ^a  

^a UNIVERSITY OF TUSCIA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIN; ALPHA TUBULIN; COMPLEMENTARY DNA; PLANT DNA; PRIMER DNA;

ARTICLE; COMPUTER MODEL; COMPUTER PROGRAM; CONTROLLED STUDY; DEVELOPMENTAL STAGE; DNA SEQUENCE; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENETIC DATABASE; GENETIC SCREENING; GENETIC STABILITY; HOUSEKEEPING GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENE; PLANT GENETICS; PLANT TISSUE; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SYSTEM ANALYSIS; TEMPERATURE STRESS; VALIDATION PROCESS; WHEAT; EXPRESSED SEQUENCE TAG; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; METHODOLOGY; MULTIGENE FAMILY; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; STANDARD;

TRITICUM AESTIVUM;

DNA PRIMERS; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; MULTIGENE FAMILY; REFERENCE STANDARDS; REPRODUCIBILITY OF RESULTS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; TRITICUM;

EID: 64549093259     PISSN: None     EISSN: 14712199     Source Type: Journal    
DOI: 10.1186/1471-2199-10-11     Document Type: Article

References (63)

1. Czechowski T Bari RP Stitt M Scheible W-R Udvardi MK Real-time RT-PCR profiling of over 1400 Arabidopsis transcription factors: Unprecedented sensitivity reveals novel root- and shoot-specific genes Plant J 2004, 38:366-379 10.1111/j.1365-313X.2004.02051.x 15078338
2. Gachon C Mingam A Charrier B Real-time PCR: What relevance to plant studies? J Exp Bot 2004, 55:1445-1454 10.1093/jxb/erh181 15208338
3. Caldana C Scheible W-R Mueller-Roeber Ruzicic S A quantitative RT-PCR platform for high-throughput expression profiling of 2500 rice transcription factors Plant Methods 2007, 3:7 1914063 17559651 10.1186/ 1746-4811-3-7
4. Bustin SA Quantification of mRNA using real-time reverse transcription PCR RT-PCR: Trends and problems J Mol Endocrinol 2002, 29:23-29 10.1677/ jme.0.0290023 12200227
5. Ginzinger DG Gene quantification using real-time quantitative PCR: An emerging technology hits the mainstream Exp Hematol 2002, 30(6):503-512 10.1016/S0301-472X(02)00806-8 12063017
6. Huggett J Dheda K Bustin S Zumla A Real-time RT-PCR normalisation; strategies and considerations Genes Immun 2005, 6(4):279-284 10.1038/ sj.gene.6364190 15815687
7. Thellin O Zorzi W Lakaye B De Borman B Coumans B Henne G Grisar T Igout A Heinen E Housekeeping genes as internal standards: Use and limits J Biotechnol 1999, 75(2-3):191-195 10617337 10.1016/S0168-1656(99)00163-7
8. Suzuki T Higgins PJ Crawford DR Control selection for RNA quantitation Biotechniques 2000, 29:332-337 10948434
9. Selvey S Thompson EW Matthaei K Lea RA Irving MG Griffiths LR Beta-actin an unsuitable internal control for RT-PCR Mol Cell Probes 2001, 15(5):307-311 10.1006/mcpr.2001.0376 11735303
10. Lee PD Sladek R Greenwood CMT Hudson TJ Control genes and variability: absence of ubiquitous reference transcripts in diverse mammalian expression studies Genome Res 2001, 12:292-297 10.1101/gr.217802
11. Ohl F Jung M Xu C Stephan C Rabien A Burkhardt M Nitsche A Kristiansen G Loening SA Radonic A Jung K Gene expression studies in prostate cancer tissue: Which reference gene should be selected for normalization? J Mol Med 2005, 83(12):1014-1024 10.1007/s00109-005-0703-z 16211407
12. Czechowski T Stitt M Altman 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 1203353 16166256 10.1104/pp.105.063743
13. 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 126239 12184808 10.1186/gb-2002-3-7-research0034
14. 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 10.1023/B:BILE.0000019559.84305.47 15127793
15. 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 10.1158/ 0008-5472.CAN-04-0496 15289330
16. Brunner AM Yakovlev IA Strauss SH Validating internal controls for quantitative plant gene expression studies BMC Plant Biol 2004, 4:14 515301 15317655 10.1186/1471-2229-4-14
17. Goncalves S Cairney J Maroco J Oliveira MM Miguel C Evaluation of control transcripts in real-time RT-PCR expression analysis during maritime pine embryogenesis Planta 2005, 222:556-563 10.1007/ s00425-005-1562-0 16034587
18. 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, 56:2907-2914 10.1093/jxb/eri285 16188960
19. 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 Com 2006, 345:646-651 10.1016/ j.bbrc.2006.04.140 16690022
20. 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, 6:27 1654153 17105665 10.1186/1471-2229-6-27
21. Faccioli P Ciceri GP Provero P Stanca AM Morcia C Terzi V 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 2007, 63:679-688 10.1007/s11103-006-9116-9 17143578
22. Gutierrez L Mauriat M Pelloux J Bellini C Van Wuytswinkel O Towards a systematic validation of references in Real-Time RT-PCR Plant Cell 2008, 20:1734-1735 10.1105/tpc.108.059774 18664615
23. Gutierrez L Mauriat M Guenin S Pelloux J Lefevre 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 Biotechnology J 2008, 6:609-618 10.1111/ j.1467-7652.2008.00346.x
24. Feuillet C Keller B Comparative genomics in the grass family: Molecular characterization of grass genome structure and evolution Ann Bot 2002, 89:3-10 10.1093/aob/mcf008 12096816
25. La Rota M Sorrells ME Comparative DNA sequence analysis of mapped wheat ESTs reveals the complexity of genome relationships between rice and wheat Funct Integr Genomics 2004, 4:34-46 10.1007/s10142-003-0098-2 14740255
26. Singh NK Dalal V Batra K Singh BK Chitra G et al Single-copy genes define a conserved order between rice and wheat for understanding differences caused by duplication, deletion, and transposition of genes Funct Integr Genomics 2007, 7:17-35 10.1007/s10142-006-0033-4 16865332
27. Crismani W Baumann U Sutton T Shirley N Webster T Spangenberg G Langridge P Able JA Microarray expression analysis of meiosis and microsporogenesis in hexaploid bread wheat BMC Genomics 2006, 7:267 1647286 17052357 10.1186/1471-2164-7-267
28. Wan Y Poole RL Huttly AK Toscano-Underwood C Feeney K Welhan S et al Transcriptome analysis of grain development in hexaploid wheat BMC genomics 2008, 9:121 2292175 18325108 10.1186/1471-2164-9-121
29. Xue GP McIntyre CL Jenkins CLD Glassop D van Herwaarden AF Shorter R Molecular dissection of variation in carbohydrate metabolism related to water-soluble carboydrate accumulation in stems of wheat Plant Physiol 2008, 146:441-454 2245852 18083795 10.1104/pp.107.113076
30. Clarke B Rahman S A microarray analysis of wheat grain hardness Theor Appl Genet 2005, 110:1259-1267 10.1007/s00122-005-1962-3 15806348
31. Kawaura K Mochida K Yamazaki Y Ogihara Y Transcriptome analysis of salinity stress responses in common wheat using a 22k oligo-DNA microarray Funct Integr Genomics 2006, 6:132-142 10.1007/ s10142-005-0010-3 16328439
32. Gregersen PL Holm PB Transcriptome analysis of senescence in the flag leaf of wheat (Triticum aestivum L.) Plant Biotechnol J 2007, 5:192-206 10.1111/j.1467-7652.2006.00232.x 17207268
33. Bustin SA Benes V Nolan T Pfaffl MW Quantitative real-time RT-PCR - a perspective J Mol Endocrinol 2005, 34:597-601 10.1677/jme.1.01755 15956331
34. 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 Com 2004, 313:856-862 10.1016/j.bbrc.2003.11.177 14706621
35. McDowell JM Huang S McKinney EC An Y-Q Meagher RB Structure and evolution of the actin gene family in Arabidopsis thaliana Genetics 1996, 142:587-602 1206991 8852856
36. Farajalla MR Gulick PJ The α-tubulin gene family in wheat (Triticum aestivum L.) and differential gene expression during cold acclimation Genome 50, 502-510 10.1139/G07-027 17612619
37. Wheeler DL Barrett T Benson DA Bryant SH Canese K Chetvernin V Church DM DiCuccio M Edgar R Federhen S Feolo M Database resources of the National Center for Biotechnology Information Nucleic Acids Res 2007, 36:13-21 10.1093/nar/gkm1000
38. Quackenbush J Cho J Lee D Liang F Holt I Karamycheva S Parvizi V Pertea G Sultana R White J The TIGR Gene Indices: Analysis of gene transcript sequences in higly sampled eukaryotic species Nucleic Acids Res 29, 159-164 29813 11125077 10.1093/nar/29.1.159
39. Ciaffi M Paolacci AR Dominici L Tanzarella OA Porceddu E Molecular characterization of gene sequences coding for protein disulfide isomerase (PDI) in durum wheat (Triticum turgidum ssp durum) Gene 2001, 265:147-156 10.1016/S0378-1119(01)00348-1 11255017
40. Ciaffi M Paolacci AR D'Aloisio E Tanzarella OA Porceddu E Cloning and characterization of wheat PDI (protein disulfide isomerase) homoeologous genes and promoter sequences Gene 2006, 366:209-218 10.1016/ j.gene.2005.07.032 16289628
41. Tsvetanov S Ohno R Tsuda K Takumi S Mori N Atanassov A Nakamura C A cold-responsive wheat (Triticum aestivum L.) gene wcor14 identified in a winter-hardy cultivar "Mironovska 808" Genes Genet Syst 2000, 75:49-57 10.1266/ggs.75.49 10846621
42. Ndong C Danyluk J Wilson KE Pocok T Huner NPA Sarhan F Cold-regulated cereal chloroplast late embryogenesis abundant-like proteins. Molecular characterization and functional analyses Plant Physiol 2002, 129:1368-1381 166530 12114590 10.1104/pp.001925
43. Campbell JL Klueva NY Zheng HG Nieto-Sotelo J Ho THD Nguyen HT Cloning of new members of heat shock protein HSP101 gene family in wheat (Triticum aestivum L. Moench) inducible by heat, dehydration, and ABA Biochimica et Biophysica Acta 2001, 1517:270-277 11342108
44. Gulli M Corradi M Rampino P Marmiroli N Perrotta C Four members of the HSP101 gene family are differentially regulated in Triticum durum Desf FEBS Letters 2007, 581:4841-4849 10.1016/j.febslet.2007.09.010 17888913
45. Katiyar-Agarwal S Agarwal M Gallie DR Grover A Search for cellular functions of plant Hsp100/Clp family proteins Crit Rev Plant Sci 2001, 20:277-295 10.1016/S0735-2689(01)80043-5
46. Wells DR Tanguay RL Le H Gallie DR HSP101 functions as a specific translational regulatory protein whose activity is regulated by nutrient status Genes Dev 1998, 20:3236-3251 10.1101/gad.12.20.3236
47. geNorm manual http://medgen.ugent.be/~jvdesomp/genorm/geNorm_manual.pdf
48. Hsiao L-L Dangond F Yosida T Hong R Jensen RV Misra J Dillon W Lee KF Clark KE et al A compendium of gene expression in normal human tissues Physiol Genomics 2001, 7:97-104 11773596
49. Eisenberg E Levanon EY Human housekeeping genes are compact Trends in Genetics 2003, 7:362-365 10.1016/S0168-9525(03)00140-9
50. Zhu J He F Song S Wang J Yu J How many human genes can be defined as housekeeping with current expression data? BMC genomics 2008, 9:172 2396180 18416810 10.1186/1471-2164-9-172
51. Wong ML Medrano JF Real-time PCR for mRNA quantification Biotechniques 2005, 39:75-85 10.2144/05391RV01 16060372
52. Charrier B Champion A Henry Y Kreis M Expression profiling of the whole Arabidopsis shaggy-like kinase multigene family by real-time reverse transcriptase-polymerase chain reaction Plant Physiol 2002, 130:577-590 166588 12376626 10.1104/pp.009175
53. 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 Molecular Biology 2008, 9:59 2443375 18573215 10.1186/1471-2199-9-59
54. Lyng MB Laenkholm A-V Pallisgaard N Ditzel HJ Identification of genes for normalization of real-time RT-PCR data in breast carcinomas BMC Cancer 2008, 8:20 2248196 18211679 10.1186/1471-2407-8-20
55. Szabo A Perou CM Karaca M Perreard L Quackenbush JF Bernard PS Statistical modelling for selecting housekeeper genes Genome Biol 2004, 5:R59 507884 15287981 10.1186/gb-2004-5-8-r59
56. Haller F Kulle B Schwager S Gunawan B Von HA Sultmann H Fuzesi L Equivalence test in quantitative reverse transcription polymerase chain reaction: Confirmation of reference genes suitable for normalization Anal Biochem 2004, 335:1-9 10.1016/j.ab.2004.08.024 15519565
57. Maccoux LJ Clements DN Salway F Day PJR Identification of new reference genes for the normalization of canine osteoarthritic tissue transcripts from microarray data BMC Molecular Biology 2007, 8:62 1976117 17651481 10.1186/1471-2199-8-62
58. Hibbeler S Scharsack JP Becker S Housekeeping genes for quantitative expression studies in the three-spined stickleback Gasterosteus aculeatus BMC Molecular Biology 2008, 9:18 2254436 18230138 10.1186/ 1471-2199-9-18
59. Bonefeld BE Elfving B Wegener G Reference genes for normalization: A study of rat brain tissue SYNAPSE 2008, 63:302-309 10.1002/syn.20496
60. Yu H Luscombe NM Qian J Gerstein M Genomic analysis of gene expression relationships in transcriptional regulatory networks Trends Genet 2003, 19:422-427 10.1016/S0168-9525(03)00175-6 12902159
61. Ransbotin V Reusch TBH Housekeeping gene selection for quantitative real-time PCR assays in the seagrass Zostera marina subjected to heat stress Limnology and Oceanography-Methods 2006, 4:367-373
62. Schmid H Cohen CD Henger A Irrgang S Schlondoff D Kretzler M Validation of endogenous controls for gene expression analysis in microdissected human renal biopsies Kidney Int 2003, 64:356-360 10.1046/ j.1523-1755.2003.00074.x 12787429
63. Hoerndli FJ Toigo M Schild A Gotz J Day PJ Reference genes identified in SH-SY5Y cells using custom-made gene array with validation by quantitative polymerase chain reaction Anal Biochem 2004, 335:30-41 10.1016/j.ab.2004.08.028 15519568