Have a personal or library account? Click to login
Selection and validation of reference genes for real-time qRT-PCR normalization in different tissues of Eucalyptus tereticornis Cover

Selection and validation of reference genes for real-time qRT-PCR normalization in different tissues of Eucalyptus tereticornis

Open Access
|Aug 2017

References

  1. ALVAREZ, C., L. VALLEDOR, R. HASBÚN, M. SANCHEZ-OLATE and D. RÍOS (2011): Variation in gene expression profile with aging of Pinus radiata D. Don. BMC Proceedings 2011, 5 (Suppl 7): P62.
  2. ANDERSEN, C. L., J. L. JENSEN and T. F. ORNTOFT (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 (15): 5245-5250.10.1158/0008-5472.CAN-04-049615289330
  3. ARIOLI, T., L. PENG, A. S. BETZNER, J. BURN, W. WITTKE, W. HERTH, C. CAMILLERI, H. HOFTE, J. PLAZINSKI, R. BIRCH, A. CORK, J. GLOVER, J. REDMOND and R. E. WILLIAMSON (1998): Molecular analysis of cellulose biosynthesis in Arabidopsis. Science 279: 717-720.10.1126/science.279.5351.7179445479
  4. BALASARAVANAN, T., P. CHEZHIAN, R. KAMALAKANNAN, M. GHOSH, R. YASODHA, M. VARGHESE and K. GURUMURTHI (2005): Determination of inter- and intra-species genetic relationships among six Eucalyptus species based on inter-simple sequence repeats (ISSR). Tree Physiol 25: 1295-1302.10.1093/treephys/25.10.129516076778
  5. BALASARAVANAN , T., P. CHEZHIAN, R. KAMALAKANNAN, VARGHESE YASODHA, M. VARGHESE, K. GURUMURTHI and M. GHOSH (2006): Identification of species-diagnostic ISSR markers for six Eucalyptus species. Silvae Genet 55(3): 119-122.10.1515/sg-2006-0017
  6. BOAVA, L. P., M. L. LAIA, T. R. JACOB, K. M. DABBAS, J. F. GONÇALVES, J. A. FERRO, M. I. T. FERRO and E. L. FUR - TADO (2010): Selection of endogenous genes for gene expression studies in Eucalyptus under biotic (Puccinia psidii) and abiotic (acibenzolar-S-methyl) stresses using QRT-PCR. BMC Res Notes 3: 43. 10.1186/1756-0500-3-43285410720181283
  7. BRUNNER, A. M., I. A. YAKOVLEV and S. H. STRAUSS (2004): Validating internal controls for quantitative plant gene expression studies. BMC Plant Biol 4: 14.10.1186/1471-2229-4-1451530115317655
  8. BUSTIN, S. A. (2002): Quantification of mRNA using realtime reverse transcription PCR (RT-PCR) trends and problems. J Mol Endocrinol 29: 23-39.10.1677/jme.0.029002312200227
  9. BUSTIN, S. A. and T. NOLAN (2004): Pitfalls of quantitative real-time reverse transcription polymerase chain reaction. J Biomol Tech 15(3): 155-166.
  10. CHEN, C. Y., M. H. HSIEH, C. C. YANG, C. S LIN and A. WANG (2010): Analysis of the cellulose synthase genes associated with primary cell wall synthesis in Bambusa oldhamii. Phytochemistry 71: 1270-1279.10.1016/j.phytochem.2010.05.01120541781
  11. CHEZHIAN, P., R. YASODHA and M. GHOSH (2010): Genetic diversity analysis in a seed orchard of Eucalyptus tereticornis. New Forest 40(1): 85-99.10.1007/s11056-009-9184-1
  12. CZECHOWSKI, T., M. STITT, T. ALTMAN, M. K. UDVARDI and W. R. SCHEIBLE (2005): Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis. Plant Physiol 139(1): 5-17.10.1104/pp.105.063743120335316166256
  13. DAY, M. E., M. S. GREENWOOD and C. DIAZ-SALA (2002): Age- and size-related trends in woody plant shoot development: regulatory pathways and evidence for genetic control. Tree Physiol 22: 507-513.10.1093/treephys/22.8.507
  14. DE ALMEIDA, M. R., C. M. RUEDELL, F. K. RICACHENEVSKY, R. A. SPEROTTO, G. PASQUALI and A. G. FETT-NETO (2010): Reference gene selection for quantitative reverse transcription-polymerase chain reaction-normalization during in vitro adventitious rooting in Eucalyptus globulus Labill. BMC Mol Biol 11: 73.10.1186/1471-2199-11-73
  15. DOBLIN, M. S., I. KURECK, D. JACOB-WILK and D. P. DELMER (2002): Cellulose biosynthesis in plants: from genes to rosettes. Plant Cell Physiol 43: 1407-1420.10.1093/pcp/pcf164
  16. EVANS, J. (1992): Plantation forestry in the tropics: In: Tree planting for industrial, social, environmental, and agro forestry purposes, (2nd ed.) Oxford Science Publications, Oxford, New York.
  17. FAGARD, M., T. DESONS, D. F. GOUBET, G. REFREGIER, G. MOUILLE, M. MCCANN, C. RAYON, S. VERNHETTES and H. HOFTE (2000): PROCUSTE1 encodes a cellulose synthase required for normal cell elongation specifically in roots and dark-grown hypocotyls of Arabidopsis. Plant Cell 12: 2409-2423.10.1105/tpc.12.12.2409
  18. F.A.O. (2005): Global forest resources assessment 2005 - main report. FAO Forestry Paper, 2005; available online: ftp://ftp.fao.org/docrep/fao/008/A0400E/A0400E00.pdf.
  19. FERNANDEZ, M., C. VILLARROEL, C. BALBONTIN and S. VALENZUELA (2010): Validation of reference genes for real-time QRT-PCR normalization during cold acclimation in Eucalyptus globulus. Trees 24: 1109-1116.10.1007/s00468-010-0483-0
  20. GAN, S., J. SHI, M. LI, K. WU, J. WU and J. BAI (2003): Moderate density molecular maps of Eucalyptus urophylla S.T. Blake and E. tereticornis Smith genomes based on RAPD markers. Genetica 118: 59-67. 10.1023/A:1022966018079
  21. GINZINGER, D. G. (2002): Gene quantification using realtime quantitative PCR: an emerging technology hits the mainstream. Exp Hematol 30(6): 503-512.10.1016/S0301-472X(02)00806-8
  22. GOICOECHEA, M., E. LACOMBE, S. LEGAY, S. MIHALJEVIC, P. RECH, A. JAUNEAU, C. LAPIERRE, B. POLLET, D. VERHAEGEN, N. C. GIGOT and J. G. PETTENATI (2005): EgMYB2, a new transcriptional activator from Eucalyptus xylem, regulates secondary cell wall formation and lignin biosynthesis Plant J 43: 553-567.10.1111/j.1365-313X.2005.02480.x16098109
  23. GUTIERREZ, L., M. MAURIAT, J. PELLOUX, C. BELLINI and O. van WUYTSWINKEL (2008): Towards a systematic validation of references in Real-Time RT-PCR. Plant Cell 20: 1734-1735.10.1105/tpc.108.059774251824118664615
  24. HUGGETT, J., K. DHEDA, S. BUSTIN and A. ZUMLA (2005): Real-time RT-PCR normalization; strategies and considerations. Genes Immun 6(4): 279-284.10.1038/sj.gene.636419015815687
  25. IGLESIAS TRABADO, G. and D. WILSTERMANN (2008): Eucalyptus universalis. Global cultivated eucalypt forests map 2008. In: GIT Forestry Consulting’s Eucalyptologics: Information resources on Eucalyptus cultivation worldwide. Retrieved from http://www.git-forestry.com
  26. ISHITANI, R., K. SUNAGA, A. HIRANO, P. SAUNDERS, N. KATSUBE and D. M. CHUANG (1996): Evidence that glyceraldehyde- 3-phosphate dehydrogenase is involved in ageinduced apoptosis in mature cerebellar neurons in culture. J Neurochem 66(3): 928-935.
  27. JOSHI, C. P. (2003): Molecular biology of cellulose biosynthesis in plants. In: PANDALAI, R. (ed) Recent research developments plant molecular biology. Research Signpost, Kerala, India. p. 19-38.
  28. JOSHI, C. P., S. BHANDARI, P. RANJAN, U. C. KALLURI, X. LIANG, T. FUJINO and A. SAMUGA (2004): Genomics of cellulose biosynthesis in poplars. New Phytol 164: 53-61.10.1111/j.1469-8137.2004.01155.x33873484
  29. KIMA, H. J., A. BARBARA, TRIPLETTA, H. B. ZHANGB, M. K. LEEB, D. J. C. HINCHLIFFEA, P. LIA and D. D. FANGA (2012): Cloning and characterization of homeologous cellulose synthase catalytic subunit 2 genes from allotetraploid cotton (Gossypium hirsutum L.) Gene 494(2): 181-189.10.1016/j.gene.2011.12.01822200568
  30. LEE, P. D., R. SLADEK, C. M. T. GREENWOOD and T. J. HUDSON (2001): Control genes and variability: absence of ubiquitous reference transcripts in diverse mammalian expression studies. Genome Res 12: 292-297.10.1101/gr.21780215527311827948
  31. LEGAY, S., E. LACOMBE, M. GOICOECHEA, C. BRIERE, A. SEGUIN, J. MACKAY and J. GRIMA-PETTENATI (2007): Molecular characterization of EgMYB1, a putative transcriptional repressor of the lignin biosynthetic pathway. Plant Sci 173: 542-549.10.1016/j.plantsci.2007.08.007
  32. MARQUES, C. M., J. A. ARAUJO, J. G. FERREIRA, R. WHETTEN, D. M. O’MALLEY, H. LIB and R. SEDEROFF (1998): AFLP genetic maps of Eucalyptus globulus and E. tereticornis. Theoret Appl Genet 96: 727-737.10.1007/s001220050795
  33. MARUM, L., A. MIGUEL, P. C. RICARDO and C. MIGUEL (2012): Reference Gene Selection for Quantitative Realtime PCR Normalization in Quercus suber. PLoS ONE 7(4): e35113. doi:10.1371/journal.pone.0035113.
  34. MAXWELL, A. (2004): The taxonomy, phylogeny and impact of Mycosphaerella species on eucalypts in south-western Australia. Dissertation, Perth, Murdoch University.
  35. NAIRN, J. and T. HASELKORN (2005): Three loblolly pine CesA genes expressed in developing xylem are orthologous to secondary cell wall CesA genes of angiosperms. New Phytol 166: 907-915. 10.1111/j.1469-8137.2005.01372.x15869651
  36. OBEMBE, O. O., E. JACOBSEN, J. P. VINCKEN and R. G. F. VISSER (2009): Differential expression of cellulose synthase (CesA) gene transcripts in potato as revealed by QRT-PCR. Plant Physiol Biochem 47: 1116-1118.10.1016/j.plaphy.2009.07.00619646886
  37. OLBRICH, M., E. GERSTNER, G. WELZL, F. FLEISCHMANN, W. OSSWALD, G. BAHNWEG and D. Z. Ernst (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(7-8): 574-82.
  38. PFAFFL, M. W., A. TICHOPAD, C. PRGOMET and T. P. NEUVIANS (2004): Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper - Excel-based tool using pair-wise correlations. Biotechnol Lett 26(6): 509-515.10.1023/B:BILE.0000019559.84305.47
  39. POKE, F. S. (2004): Summary of world-wide research in eucalypt genomics. Prof. R. GRIFFIN, Prof. J. B. REID, Assoc Prof R. Vaillancourt [Consultants Report].
  40. RANIK, M. and A. A. MYBURG (2006): Six new cellulose synthase genes from Eucalyptus are associated with primary and secondary cell wall biosynthesis. Tree Physiol 26: 545-556.10.1093/treephys/26.5.54516452068
  41. REID, K. E., N. OLSSON, J. SCHLOSSER, F. PENG and S. T. LUND (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: 27.10.1186/1471-2229-6-27165415317105665
  42. SELVEY, S., E.W. THOMPSON, K. MATTHAEI, R. A. LEA, M. G. IRVING and L. R. GRIFFITHS (2001): Beta-actin an unsuitable internal control for RT-PCR. Mol Cell Probes 15(5): 307-311.10.1006/mcpr.2001.037611735303
  43. SUZUKI, T., P. J. HIGGINS and D. R. CRAWFORD (2000): Control selection for RNA quantitation. Biotechniques 29: 332-337.10.2144/00292rv0210948434
  44. TONG, Z., Z. GAO, F. WANG, J. ZHOU and Z. ZHANG (2009): Selection of reliable reference genes for gene expression studies in peach using real-time PCR. BMC Mol Biol 10:71 doi:10.1186/1471-2199-10-71.
  45. TURNBULL, J.W. (1999): Eucalypt plantations. New Forest 17: 37-52.10.1023/A:1006524911242
  46. VANDESOMPELE, J., K. DE PRETER, F. PATTYN, B. POPPE, N. VAN ROY, A. de PAEPE and F. SPELEMAN (2002): Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 3: 1-11.10.1186/gb-2002-3-7-research003412623912184808
  47. XU, M., B. ZHANG, S. X. ZHANG and M. HUANG (2011): Reference gene selection for quantitative real-time polymerase chain reaction in Populus. Anal Biochem 408: 337-339.10.1016/j.ab.2010.08.04420816740
  48. ZOBEL, B. J., G. V. WYK and P. STAHL (1987): Growing Exotic Forests, pp. 508 in John Wiley and Sons, New York.
DOI: https://doi.org/10.1515/sg-2012-0035 | Journal eISSN: 2509-8934 | Journal ISSN: 0037-5349
Language: English
Page range: 280 - 286
Submitted on: Jun 12, 2012
Published on: Aug 1, 2017
Published by: Johann Heinrich von Thünen Institute
In partnership with: Paradigm Publishing Services
Publication frequency: 1 issue per year

© 2017 B. Karpaga Raja Sundari, M. Ghosh Dasgupta, published by Johann Heinrich von Thünen Institute
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.