Evaluation and Validation of Reference Genes for Normalization of Quantitative Real-Time PCR Based Gene Expression Studies in Peanut

PLoS ONE

Volumn 8, Issue 10, 2013, Pages

  Reddy, Dumbala Srinivas ^a   Bhatnagar Mathur, Pooja ^a   Cindhuri, Katamreddy Sri ^a   Sharma, Kiran K ^a  

^a INTERNATIONAL CROPS RESEARCH INSTITUTE FOR THE SEMI ARID TROPICS ICRISAT   (India)

Author keywords

[No Author keywords available]

Indexed keywords

GLUCOSE 6 PHOSPHATE DEHYDROGENASE;

ABIOTIC STRESS; ACT11 GENE; ADH3 GENE; ARTICLE; ATPSYN GENE; BIOTIC STRESS; CYP2 GENE; ELF1B GENE; G6PD GENE; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENETIC STABILITY; GENETIC VARIABILITY; LEC GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; PEANUT; PLANT GENE; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; STANDARD; TILLAGE; UBC1 GENE; VALIDATION STUDY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PHYSIOLOGY; PROCEDURES;

ARACHIS HYPOGAEA; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; REAL-TIME POLYMERASE CHAIN REACTION;

EID: 84885969794     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0078555     Document Type: Article

References (54)

1. Tsai HF, Sammons LR, Zhang X, Suffis SD, Su Q, et al. (2010) Microarray and molecular analyses of the azole resistance mechanism in Candida glabrata oropharyngeal isolates. Antimicrob Agents Chemother 54: 3308-3317. doi:10.1128/AAC.00535-10. PubMed: 20547810.
2. Bustin SA, Benes V, Nolan T, Pfaffl MW, (2005) Quantitative real-time RT-PCR-a perspective. J Mol Endocrinol 34: 597-601. doi:10.1677/jme.1.01755. PubMed: 15956331.
3. Kubista M, Andrade JM, Bengtsson M, Forootan A, Jonák J, et al. (2006) The real-time polymerase chain reaction. Mol Aspects Med 27: 95-125. doi:10.1016/j.mam.2005.12.007. PubMed: 16460794.
4. VanGuilder HD, Vrana KE, Freeman WM, (2008) Twenty-five years of quantitative PCR for gene expression analysis. BioTechniques 44: 619-626. PubMed: 18474036.
5. Bustin SA, (2000) Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J Mol Endocrinol 25: 169-193. doi:10.1677/jme.0.0250169. PubMed: 11013345.
6. Giulietti A, Overbergh L, Valckx D, Decallonne B, Bouillon R, et al. (2001) An overview of real-time quantitative PCR: applications to quantify cytokine gene expression. Methods 25: 386-401. doi:10.1006/meth.2001.1261. PubMed: 11846608.
7. Mason G, Provero P, Vaira AM, Accotto GP, (2002) Estimating the number of integrations in transformed plants by quantitative real-time PCR. BMC Biotechnol 2: 20-30. doi:10.1186/1472-6750-2-20. PubMed: 12398792.
8. Weng H, Pan A, Yang L, Zhang C, Liu Z, Zhang D, (2004) Estimating number of transgene copies in transgenic rapeseed by real-time PCR assay with HMG I/Y as an endogenous reference gene. Plant Mol Biol Rep 22: 289-300. doi:10.1007/BF02773139.
9. 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. doi:10.1371/journal.pone.0036918. PubMed: 22606308.
10. Radonić 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. doi:10.1016/j.bbrc.2003.11.177. PubMed: 14706621.
11. 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. doi:10.1016/S0168-1656(99)00163-7. PubMed: 10617337.
12. 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. doi:10.1104/pp.105.063743. PubMed: 16166256.
13. 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. PubMed: 20302670.
14. 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. doi:10.1007/s00425-008-0706-4. PubMed: 18273637.
15. 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. doi:10.1093/jxb/eri285. PubMed: 16188960.
16. 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: 93-104. doi:10.1186/1471-2199-10-93. PubMed: 19785741.
17. Garg R, Sahoo A, Tyagi AK, Jain M, (2010) Validation of internal control genes for quantitative gene expression studies in chickpea. Biochem Biophys Res Commun 396: 283-288. doi:10.1016/j.bbrc.2010.04.079. PubMed: 20399753.
18. 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: 15-27. doi:10.1186/1471-2199-11-15. PubMed: 20156357.
19. Gu C, Chen S, Liu Z, Shan H, Luo H, et al. (2011) Reference gene selection for quantitative real-time PCR in Chrysanthemum subjected to biotic and abiotic stress. Mol Biotechnol 49: 192-197. doi:10.1007/s12033-011-9394-6. PubMed: 21416201.
20. 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: 1-11. PubMed: 12184808.
21. 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: R23. doi:10.1186/gb-2007-8-2-r23. PubMed: 17316440.
22. 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. doi:10.1016/j.bbrc.2006.04.140. PubMed: 16690022.
23. Long XY, Wang JR, Ouellet T, Rocheleau L, Wei YM, et al. (2010) Genome-wide identification and evaluation of novel internal control genes for Q-PCR based transcript normalization in wheat. Plant Mol Biol 74: 307-311. doi:10.1007/s11103-010-9666-8. PubMed: 20658259.
24. Manoli A, Sturaro A, Trevisan S, Quaggiotti S, Nonis A, (2012) Evaluation of candidate reference genes for qPCR in maize. J Plant Physiol 169(8):: 807-815. doi:10.1016/j.jplph.2012.01.019. PubMed: 22459324.
25. Expósito-Rodríguez M, Borges AA, 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: 131-142. doi:10.1186/1471-2229-8-131. PubMed: 19102748.
26. 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. doi:10.1186/1471-2229-6-27. PubMed: 17105665.
27. 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.
28. Chen X, Truksa M, Shah S, Weselake RJ, (2010) A survey of quantitative realtime polymerase chain reaction internal reference genes for expression studies in Brassica napus. Anal Biochem 405: 138-140. doi:10.1016/j.ab.2010.05.032. PubMed: 20522329.
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. doi:10.1186/1471-2199-9-59. PubMed: 18573215.
30. Libault M, Thibivilliers S, Bilgin DD, Radwan O, Benitez M, et al. (2008) Identification of four soybean reference genes for gene expression normalization. Plants Genome 1: 44-54. doi:10.3835/plantgenome2008.02.0091.
31. Li Q, Fan CM, Zhang XM, Fu YF, (2012) Validation of reference genes for real-time quantitative PCR normalization in soybean developmental and germinating seeds. Plant Cell Rep 31: 1789-1798. doi:10.1007/s00299-012-1282-4. PubMed: 22588479.
32. Le DT, Aldrich DL, Valliyodan B, Watanabe Y, Ha CV, et al. (2012) Evaluation of candidate reference genes for normalization of quantitative RT-PCR in soybean tissues under various abiotic stress conditions. PLOS ONE 7(9):: e46487. doi:10.1371/journal.pone.0046487. PubMed: 23029532.
33. Wang Y, Yu K, Poysa V, Shi C, Zhou Y, (2012) Selection of reference genes for normalization of qRT-PCR analysis of differentially expressed genes in soybean exposed to cadmium. Mol Biol Rep 39: 1585-1594. doi:10.1007/s11033-011-0897-9. PubMed: 21625860.
34. FAO (2009) Food and Agricultural Organization of the United Nation. FAO statistical database. Available: http://faostat.fao.org/ faostat/collections?Subset= agriculture.
35. Sharma KK, Ortiz R, (2000) Program for the application of genetic transformation for crop improvement in the semi-arid tropics. In Vitro Cell Dev Biol-Plant 36: 83-92. doi:10.1007/s11627-000-0019-1.
36. Sharma HC, Crouch JH, Sharma KK, Seetharama N, Hash CT, (2002) Applications of biotechnology for crop improvement: prospects and constraints. Plant Sci 163: 381-395. doi:10.1016/S0168-9452(02)00133-4.
37. Brand Y, Hovav R, (2010) Identification of suitable internal control genes for quantitative real-time PCR expression analyses in peanut (Arachis hypogaea). Peanut Sci 37: 12-19. doi:10.3146/PS09-014.1.
38. Morgante CV, Guimarães PM, Martins ACQ, Araújo ACG, Leal-Bertioli SCM, et al. (2011) Reference genes for quantitative reverse transcription-polymerase chain reaction expression studies in wild and cultivated peanut. BMC Res Notes 4: 339-350. doi:10.1186/1756-0500-4-339. PubMed: 21906295.
39. 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. doi:10.1007/s00438-011-0665-5. PubMed: 22203160.
40. Kumar PL, Waliyar F, (2007) iagnosis and detection of viruses infecting ICRISAT mandate crops: methods manual. Patancheru 502 324, Andhra Pradesh, India, International Crops Research Institute for the Semi-Arid Tropics.
41. Subrahmanyam P, Moss JP, McDonald D, Subba Rao PV, Rao VR, (1985) Resistance to leaf spot caused by Cercosporidium personatum in wild Arachis species. Plant Dis 69: 951-954. doi:10.1094/PD-69-951.
42. Schmidt MA, Parrott WA, (2001) Quantitative detection of transgenes in soybean [Glycine max (L.) Merrill] and peanut (Arachis hypogaea L.) by real-time polymerase chain reaction. Plant Cell Rep 20: 422-428. doi:10.1007/s002990100326.
43. Peterhansel C, Hahnen S, Kalamajka R, Offermann S, Miedl B, et al. (2004) Quantitative detection of transgenic and endogenous DNA sequences in seeds after automated DNA preparation. Biomed Eng Appl Basis Comm 16: 1-6.
44. Yi CX, Zhang J, Chan KM, Liu XK, Hong Y, (2008) Quantitative real-time PCR assay to detect transgene copy number in cotton (Gossypium hirsutum). Anal Biochem 375: 150-152. doi:10.1016/j.ab.2007.11.022. PubMed: 18078801.
45. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, (1990) Basic local alignment search tool. J Mol Biol 215: 403-410. doi:10.1016/S0022-2836(05)80360-2. PubMed: 2231712.
46. Tunbridge EM, Eastwood SL, Harrison PJ, (2011) Changed relative to what? House-keeping genes and normalization strategies in human brain gene expression studies. Biol Psychiatry 69: 173-179. doi:10.1016/j.biopsych.2010.05.023. PubMed: 20673871.
47. Andersen CL, Jensen JL, Ørntoft TF, (2004) Normalization of real-time quantitative reverse transcription-PCR data: A modelbased variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer Res 64: 5245-5250. doi:10.1158/0008-5472.CAN-04-0496. PubMed: 15289330.
48. Bhatnagar-Mathur P, Devi MJ, Srinivas Reddy D, Lavanya M, Vadez V, et al. (2007) Stress-inducible expression of AtDREB1A in transgenic peanut (Arachis hypogaea L.) increases transpiration efficiency under water limiting conditions. Plant Cell Rep 26: 2071-2082. doi:10.1007/s00299-007-0406-8. PubMed: 17653723.
49. Hruz T, Wyss M, Docquier M, Pfaffl MW, Masanetz S, et al. (2011) RefGenes: identification of reliable and condition specific reference genes for RT-qPCR data normalization. BMC Genomics 12: 156. doi:10.1186/1471-2164-12-156. PubMed: 21418615.
50. 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. Plants Methods 3: 7. doi:10.1186/1746-4811-3-7.
51. Boava LP, Laia ML, Jacob TR, Dabbas KM, Gonçalves J, et al. (2010) Selection of endogenous genes for gene expression studies in Eucalyptus under biotic (Puccinia psidii) and abiotic (acibenzolar-Smethyl) stresses using RT-qPCR. BMC Res Notes 3: 43. doi:10.1186/1756-0500-3-43. PubMed: 20181283.
52. Yokoyama S, Harry DE, (1993) Molecular phylogeny and evolutionary rates of alcohol dehydrogenases in vertebrates and plants. Mol Biol Evol 10: 1215-1226. PubMed: 8277852.
53. 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 6: 1. PubMed: 19126214.
54. Gutierrez N, Gimenez MJ, Palomino C, Avila CM, (2011) Assessment of candidate reference genes for expression studies in Vicia faba L. by real-time quantitative PCR. Mol Breed 28: 13-24.