Assessing reference genes for accurate transcript normalization using quantitative real-time PCR in Pearl Millet [Pennisetum glaucum (L.) R. Br.]

PLoS ONE

Volumn 9, Issue 8, 2014, Pages

  Saha, Prasenjit ^a   Blumwald, Eduardo ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABIOTIC STRESS; ACT GENE; ARTICLE; GENE EXPRESSION; GENE IDENTIFICATION; GENOTYPE; HORMONAL THERAPY; NONHUMAN; PEARL MILLET; PLANT DEVELOPMENT; PLANT GENE; PLANT TISSUE; PP2A GENE; QUALITY CONTROL PROCEDURES; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; REFERENCE GENE; REFERENCE VALUE; TIP41 GENE; TRANSCRIPT NORMALIZATION; TRANSGENE; UBC2 GENE; UBQ5 GENE; VALIDATION PROCESS; BIOSYNTHESIS; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PENNISETUM; PHYSIOLOGY; PROCEDURES; SOFTWARE; STANDARD; STANDARDS;

PLANT PROTEIN;

GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; PENNISETUM; PLANT PROTEINS; REAL-TIME POLYMERASE CHAIN REACTION; REFERENCE STANDARDS; SOFTWARE;

EID: 84920120365     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0106308     Document Type: Article

References (53)

1. Ejeta G, Hassen MM, Mertz ET (1987) In vitro digestibility and amino acid composition of pearl millet (Pennisetum typhoides) and other cereals. Proc Natl Acad Sci U S A 84: 6016-6019.
2. Hill GM, Hanna WW (1990) Nutritive characteristics of pearl millet grain in beef cattle diets. J Anim Sci 68: 2061-2066.
3. Li P, Brutnell TP (2011) Setaria viridis and Setaria italica, model genetic systems for the Panicoid grasses. J Exp Bot 62: 3031-3037.
4. Upadhyaya HD, Reddy KN, Gowda CLL (2007) Pearl millet germplasm at ICRISAT genebank-status and impact. SAT eJournal 3: 1-5.
5. Yadav RS, Sehgal D, Vadez V (2011) Using genetic mapping and genomics approaches in understanding and improving drought tolerance in pearl millet. J Exp Bot 62: 397-408.
6. O'Kennedy MM, Stark HC, Dube N (2011) Biolistic-mediated transformation protocols for maize and pearl millet using pre-cultured immature zygotic embryos and embryogenic tissue. Methods Mol Biol 710: 343-354.
7. Mishra RN, Reddy PS, Nair S, Markandeya G, Reddy AR, et al. (2007) Isolation and characterization of expressed sequence tags (ESTs) from subtracted cDNA libraries of Pennisetum glaucum seedlings. Plant Mol Biol 64: 713-732. (Pubitemid 47036787)
8. Wong ML, Medrano JF (2005) Real-time PCR for mRNA quantitation. Biotechniques 39: 75-85.
9. Guenin S, Mauriat M, Pelloux J, Van Wuytswinkel O, Bellini C, et al. (2009) Normalization of qRT-PCR data: the necessity of adopting a systematic, experimental conditions-specific, validation of references. J Exp Bot 60: 487- 493.
10. Huggett J, Dheda K, Bustin S, Zumla A (2005) Real-time RT-PCR normalisation; strategies and considerations. Genes Immun 6: 279-284. (Pubitemid 40903399)
11. Udvardi MK, Czechowski T, Scheible W-R (2008) Eleven Golden Rules of Quantitative RT-PCR. The Plant Cell Online 20: 1736-1737. (Pubitemid 352844528)
12. Czechowski T, Stitt M, Altmann T, Udvardi MK, Scheible WR (2005) Genomewide identification and testing of superior reference genes for transcript normalization in Arabidopsis. Plant Physiol 139: 5-17. (Pubitemid 43951587)
13. Jain M, Nijhawan A, Tyagi AK, Khurana JP (2006) Validation of housekeeping genes as internal control for studying gene expression in rice by quantitative realtime PCR. Biochem Biophys Res Commun 345: 646-651. (Pubitemid 43776982)
14. Hong S-Y, Seo P, Yang M-S, Xiang F, Park C-M (2008) Exploring valid reference genes for gene expression studies in Brachypodium distachyon by realtime PCR. BMC Plant Biology 8: 112.
15. Petit C, Pernin F, Heydel JM, Delye C (2012) Validation of a set of reference genes to study response to herbicide stress in grasses. BMC Res Notes 5: 18.
16. Gutierrez L, Mauriat M, Guenin S, Pelloux J, Lefebvre JF, et al. (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. (Pubitemid 351989484)
17. Fan C, Ma J, Guo Q, Li X, Wang H, et al. (2013) Selection of Reference Genes for Quantitative Real-Time PCR in Bamboo (Phyllostachys edulis). PLoS ONE 8: e56573.
18. Ovesná J, Kučera L, Vaculová K, Š trymplová K, Svobodová I, et al. (2012) Validation of the β-amy1 Transcription Profiling Assay and Selection of Reference Genes Suited for a RT-qPCR Assay in Developing Barley Caryopsis. PLoS ONE 7: e41886.
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. Kumar K, Muthamilarasan M, Prasad M (2013) Reference genes for quantitative real-time PCR analysis in the model plant foxtail millet (Setaria italica L.) subjected to abiotic stress conditions. Plant Cell, Tissue and Organ Culture (PCTOC) 115: 13-22.
21. Chandna R, Augustine R, Bisht NC (2012) Evaluation of Candidate Reference Genes for Gene Expression Normalization in Brassica juncea Using Real Time Quantitative RT-PCR. PLoS ONE 7: e36918.
22. Chi X, Hu R, Yang Q, Zhang X, Pan L, et al. (2012) Validation of reference genes for gene expression studies in peanut by quantitative real-time RT-PCR. Mol Genet Genomics 287: 167-176.
23. Paolacci A, Tanzarella O, Porceddu E, Ciaffi M (2009) Identification and validation of reference genes for quantitative RT-PCR normalization in wheat. BMC Molecular Biology 10: 11.
24. Tenea G, Peres Bota A, Cordeiro Raposo F, Maquet A (2011) Reference genes for gene expression studies in wheat flag leaves grown under different farming conditions. BMC Research Notes 4: 373.
25. Gimeno J, Eattock N, Van Deynze A, Blumwald E (2014) Selection and Validation of Reference Genes for Gene Expression Analysis in Switchgrass (Panicum virgatum) Using Quantitative Real-Time RT-PCR. PLoS ONE 9: e91474.
26. 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: 291-295. (Pubitemid 29486627)
27. Zhu J, Zhang L, Li W, Han S, Yang W, et al. (2013) Reference gene selection for quantitative real-time PCR normalization in Caragana intermedia under different abiotic stress conditions. PLoS One 8: e53196.
28. Brunner AM, Yakovlev IA, Strauss SH (2004) Validating internal controls for quantitative plant gene expression studies. BMC Plant Biol 4: 14.
29. Silver N, Best S, Jiang J, Thein SL (2006) Selection of housekeeping genes for gene expression studies in human reticulocytes using real-time PCR. BMC Mol Biol 7: 33.
30. 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: 509-515. (Pubitemid 38448421)
31. 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: Research0034.
32. 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. (Pubitemid 39006544)
33. Chen D, Pan X, Xiao P, Farwell MA, Zhang B (2011) Evaluation and identification of reliable reference genes for pharmacogenomics, toxicogenomics, and small RNA expression analysis. J Cell Physiol 226: 2469-2477.
34. Untergasser A, Nijveen H, Rao X, Bisseling T, Geurts R, et al. (2007) Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res 35: W71-74.
35. Saha P, Majumder P, Dutta I, Ray T, Roy SC, et al. (2006) Transgenic rice expressing Allium sativum leaf lectin with enhanced resistance against sapsucking insect pests. Planta 223: 1329-1343.
36. Saha P, Ray T, Tang Y, Dutta I, Evangelous NR, et al. (2013) Self-rescue of an EXTENSIN mutant reveals alternative gene expression programs and candidate proteins for new cell wall assembly in Arabidopsis. The Plant Journal 75: 104- 116.
37. Ramakers C, Ruijter JM, Deprez RH, Moorman AF (2003) Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data. Neurosci Lett 339: 62-66. (Pubitemid 36263221)
38. 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 Biology 8: R19.
39. Pfaffl MW, Horgan GW, Dempfle L (2002) Relative expression software tool (REST) for group-wise comparison and statistical analysis of relative expression results in real-time PCR. Nucleic Acids Res 30: e36.
40. Jefferson RA, Kavanagh TA, Bevan MW (1987) GUS fusions: beta-glucuronidase as a sensitive and versatile gene fusion marker in higher plants. Embo j 6: 3901-3907.
41. Wang Y, Barbacioru C, Hyland F, Xiao W, Hunkapiller KL, et al. (2006) Large scale real-time PCR validation on gene expression measurements from two commercial long-oligonucleotide microarrays. BMC Genomics 7: 59.
42. Chomczynski P, Sacchi N (1987) Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162: 156-159. (Pubitemid 17064313)
43. Caldana C, Scheible W-R, Mueller-Roeber B, Ruzicic S (2007) A quantitative RT-PCR platform for high-throughput expression profiling of 2500 rice transcription factors. Plant Methods 3: 7.
44. Bustin SA (2002) Quantification of mRNA using real-time reverse transcription PCR (RT-PCR): trends and problems. J Mol Endocrinol 29: 23-39.
45. Ruijter JM, Ramakers C, Hoogaars WMH, Karlen Y, Bakker O, et al. (2009) Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data. Nucleic Acids Research 37: e45.
46. Borges A, Tsai SM, Caldas DG (2012) Validation of reference genes for RTqPCR normalization in common bean during biotic and abiotic stresses. Plant Cell Rep 31: 827-838.
47. Karlen Y, McNair A, Perseguers S, Mazza C, Mermod N (2007) Statistical significance of quantitative PCR. BMC Bioinformatics 8: 131.
48. Gimenez MJ, Piston F, Atienza SG (2011) Identification of suitable reference genes for normalization of qPCR data in comparative transcriptomics analyses in the Triticeae. Planta 233: 163-173.
49. Amil-Ruiz F, Garrido-Gala J, Blanco-Portales R, Folta KM, Munoz-Blanco J, et al. (2013) Identification and Validation of Reference Genes for Transcript Normalization in Strawberry (Fragaria x ananassa) Defense Responses. PLoS One 8: e70603.
50. Chao WS, Doǧramaci M, Foley ME, Horvath DP, Anderson JV (2012) Selection and Validation of Endogenous Reference Genes for qRT-PCR Analysis in Leafy Spurge (Euphorbia esula). PLoS ONE 7: e42839.
51. Chollet R, Vidal J, O'Leary MH (1996) PHOSPHOENOLPYRUVATE CARBOXYLASE: A Ubiquitous, Highly Regulated Enzyme in Plants. Annu Rev Plant Physiol Plant Mol Biol 47: 273-298.
52. Agarwal PK, Agarwal P, Reddy MK, Sopory SK (2006) Role of DREB transcription factors in abiotic and biotic stress tolerance in plants. Plant Cell Rep 25: 1263-1274. (Pubitemid 44786606)
53. Cheng MC, Liao PM, Kuo WW, Lin TP (2013) The Arabidopsis ETHYLENE RESPONSE FACTOR1 regulates abiotic stress-responsive gene expression by binding to different cis-acting elements in response to different stress signals. Plant Physiol 162: 1566-1582. Development