Selection of reliable reference genes for gene expression studies using real-time PCR in tung tree during seed development

PLoS ONE

Volumn 7, Issue 8, 2012, Pages

  Han, Xiaojiao ^a   Lu, Mengzhu ^a   Chen, Yicun ^a   Zhan, Zhiyong ^a   Cui, Qinqin ^a   Wang, Yangdong ^a  

^a RESEARCH INSTITUTE OF FORESTRY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSYLMETHIONINE DECARBOXYLASE; ALBUMIN; ELONGATION FACTOR 1ALPHA; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; UBIQUITIN; UBIQUITIN CONJUGATING ENZYME E2;

ACT7 GENE; ALB GENE; ARTICLE; COMPUTER PROGRAM; CULTIVAR; DECIDUOUS PLANT; EF1ALPHA GENE; FAD2 GENE; FADX GENE; GADPH GENE; GENE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETIC SELECTION; GENETIC STABILITY; GENETIC VARIABILITY; HOUSEKEEPING GENE; LCR69 GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT TISSUE; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; REFERENCE GENE; RELIABILITY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SAMDC GENE; SEED DEVELOPMENT; TCTP GENE; TEF1 GENE; TUNG TREE; UBC GENE; UBQ GENE;

ACTINS; ALEURITES; DNA PRIMERS; GENE EXPRESSION PROFILING; GENES, ESSENTIAL; GENES, PLANT; GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASES; PEPTIDE ELONGATION FACTOR 1; REAL-TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SEEDS; UBIQUITIN;

EID: 84865073418     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0043084     Document Type: Article

References (45)

1. Brown K, Keeler W, (2005) The history of tung oil. Wildland Weeds 9: 4-24.
2. Shang Q, Jiang W, Lu H, Liang B, (2010) Properties of tung oil biodiesel and its blends with 0# diesel. Bioresource technol 101: 826-828.
3. Sonntag N, (1979) Composition and characteristics of individual fats and oils. Bailey's industrial oil and fat products 1: 289-477.
4. Thanamongkollit N, Soucek MD (2008) Modification of tung oil for bio-based coating [The Graduate Faculty of the University of Akron In Partial Fulfillment of the Requirements for the Degree Master of Science]. Akron (Ohio): Department of Science, University of Akron.
5. Fang JX, He F, (1998) Tung oil trees in China. China Forestry Publishing House, Beijing pp. 104-127.
6. Chen Y, Zhou G, Wang Y, Xu L, (2010) F-BOX and oleosin: additional target genes for future metabolic engineering in tung trees? Ind Crop Prod 32: 684-686.
7. Shockey JM, Gidda SK, Chapital DC, Kuan J-C, Dhanoa PK, et al. (2006) Tung tree DGAT1 and DGAT2 have nonredundant functions in triacylglycerol biosynthesis and are localized to different subdomains of the endoplasmic reticulum. Plant Cell 18: 2294-2313.
8. Bustin SA, (2002) Quantification of mRNA using real-time reverse transcription PCR (RT-PCR): trends and problems. J Mol Endocrinol 29: 23-39.
9. Bustin SA, Benes V, Nolan T, Pfaffl MW, (2005) Quantitative real-time RT-PCR-a perspective. J Mol Endocrinol 34: 597-601.
10. Nolan T, Hands RE, Bustin SA, (2006) Quantification of mRNA using real-time RT-PCR. Nat Protoc 1: 1559-1582.
11. Huggett J, Dheda K, Bustin S, Zumla A, (2005) Real-time RT-PCR normalisation; strategies and considerations. Genes and Immun 6: 279-284.
12. Udvardi MK, Czechowski T, Scheible WR, (2008) Eleven golden rules of quantitative RT-PCR. Plant Cell 20: 1736-1737.
13. Banda M, Bommineni A, Thomas RA, Luckinbill LS, Tucker JD, (2008) Evaluation and validation of housekeeping genes in response to ionizing radiation and chemical exposure for normalizing RNA expression in real-time PCR. Mutat Res 649: 126-134.
14. Dheda K, Huggett JF, Bustin SA, Johnson MA, Rook G, et al. (2004) Validation of housekeeping genes for normalizing RNA expression in real-time PCR. Biotechniques 37: 112-119.
15. Kim BR, Nam HY, Kim SU, Kim SI, Chang YJ, (2003) Normalization of reverse transcription quantitative-PCR with housekeeping genes in rice. Biotechnol Lett 25: 1869-1872.
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.
17. Luo H, Chen S, Wan H, Chen F, Gu C, et al. (2010) Candidate reference genes for gene expression studies in water lily. Anal biochem 404: 100-102.
18. Qi J, Yu S, Zhang F, Shen X, Zhao X, et al. (2010) Reference gene selection for real-time quantitative polymerase chain reaction of mRNA transcript levels in Chinese cabbage (Brassica rapa L. ssp pekinensis). Plant Mol Biol Rep 28: 597-604.
19. Kumar V, Sharma R, Trivedi PC, Vyas GK, Khandelwal V, (2011) Traditional and novel references towards systematic normalization of qRT-PCR data in plants. Aust J Crop Sci 5: 1455-1468.
20. Demidenko NV, Logacheva MD, Penin AA, (2011) Selection and validation of reference genes for quantitative real-time PCR in buckwheat (Fagopyrum esculentum) based on transcriptome sequence data. PLoS One 6: e19434.
21. Pastor S (2011) Determining biological roles of four unique Vernicia fordii acyl-CoA Binding Proteins. University of New Orleans Theses and Dissertations Paper 1337.
22. 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: RESEARCH0034.1-0034.11.
23. 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.
24. 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.
25. 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: 27-37.
26. Czechowski T, Stitt M, 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.
27. 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 pp. 2907-2914.
28. Remans T, Smeets K, Opdenakker K, Mathijsen D, Vangronsveld J, et al. (2008) Normalisation of real-time RT-PCR gene expression measurements in Arabidopsis thaliana exposed to increased metal concentrations. Planta 227: 1343-1349.
29. Jian B, Liu B, Bi Y, Hou W, Wu C, et al. (2008) Validation of internal control for gene expression study in soybean by quantitative real-time PCR. BMC Mol Biol 9: 59-72.
30. Kuijk EW, Du Puy L, Van Tol HTA, Haagsman HP, Colenbrander B, et al. (2007) Validation of reference genes for quantitative RT-PCR studies in porcine oocytes and preimplantation embryos. BMC Dev Biol 7: 58.
31. 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 9: 4066-4069.
32. Fernandez P, Di Rienzo JA, Moschen S, Dosio GAA, Aguirrezábal LAN, et al. (2011) Comparison of predictive methods and biological validation for qPCR reference genes in sunflower leaf senescence transcript analysis. Plant Cell Rep 30: 63-74.
33. Chen X, Truksa M, Shah S, Weselake RJ, (2010) A survey of quantitative real-time polymerase chain reaction internal reference genes for expression studies in Brassica napus. Anal Biochem 405: 138-140.
34. Maroufi A, Bockstaele Ev, Loose Md, 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: 15-26.
35. 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.
36. Martin RC, Hollenbeck VG, Dombrowski JE, (2008) Evaluation of Reference Genes for Quantitative RT-PCR in Lolium perenne. Crop Sci 48: 1881-1887.
37. Basa B, Solti A, Sarvari E, Tamas L, (2009) Housekeeping gene selection in poplar plants under Cd-stress: comparative study for real-time PCR normalisation. Funct Plant Biol 36: 1079-1087.
38. Wan H, Zhao Z, Qian C, Sui Y, Malik AA, et al. (2009) Selection of appropriate reference genes for gene expression studies by quantitative real-time polymerase chain reaction in cucumber. Anal Biochem 399: 257-261.
39. 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 bioph res commun 345: 646-651.
40. Hochstrasser M, (2000) Evolution and function of ubiquitin-like protein-conjugation systems. Nat Cell Biol 2: E153-157.
41. Mafra V, Kubo KS, Alves-Ferreira M, Ribeiro-Alves M, Stuart RM, et al. (2012) Reference genes for accurate transcript normalization in citrus genotypes under different experimental conditions. PLoS One 7: e31263.
42. Dyer JM, Chapital DC, Kuan JC, Mullen RT, Turner C, et al. (2002) Molecular analysis of a bifunctional fatty acid conjugase/desaturase from tung. Implications for the evolution of plant fatty acid diversity. Plant Physiol 130: 2027-2038.
43. Dyer JM, Mullen RT, (2008) Engineering plant oils as high-value industrial feedstocks for biorefining: the need for underpinning cell biology research. Physiol Plantarum 132: 11-22.
44. Phillips MA, D'Auria JC, Luck K, Gershenzon J, (2009) Evaluation of candidate reference genes for real-time quantitative PCR of plant samples using purified cDNA as template. Plant Mol Biol Rep 27: 407-416.
45. Radonic A, Thulke S, Mackay IM, Landt O, Siegert W, et al. (2004) Guideline to reference gene selection for quantitative real-time PCR. Biochem Biophys Res Commun 313: 856-862.