Selectable marker genes and unintended changes to the plant transcriptome

Plant Biotechnology Journal

Volumn 7, Issue 3, 2009, Pages 211-218

  Miki, Brian ^a   Abdeen, Ashraf ^a   Manabe, Yuzuki ^a   MacDonald, Phil ^b  

^a AGRICULTURE AND AGRI FOOD CANADA   (Canada)

^b CANADIAN FOOD INSPECTION AGENCY   (Canada)

Author keywords

Phenotype; Pleiotropic effects; Position effects; Selectable marker genes; Transcriptome; Transgenic plants; Unintended effects

Indexed keywords

GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC MARKER; GENETICS; PLANT GENOME; REVIEW; TRANSGENE; TRANSGENIC PLANT;

GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENETIC MARKERS; GENOME, PLANT; MUTAGENESIS, INSERTIONAL; PLANTS, GENETICALLY MODIFIED; TRANSGENES;

EID: 62149095662     PISSN: 14677644     EISSN: 14677652     Source Type: Journal    
DOI: 10.1111/j.1467-7652.2009.00400.x     Document Type: Review

References (53)

1. Abdeen A. Miki B. (2009) The pleiotropic effects of the bar gene and glufosinate on the Arabidopsis transcriptome. Plant Biotechnol. J. 7, 266 282.
2. Aragao, F.J.L., Sarokin, L., Vianna, G.R. Rech, E.L. (2000) Selection of transgenic meristematic cells utilizing a herbicidal molecule results in the recovery of fertile transgenic soybean [Glycine max (L.) Merril] plants at a high frequency. Theor. Appl. Genet. 101, 1 6.
3. Baker, J.M., Hawkins, N.D., Ward, J.L., Lovegrove, A., Napier, J.A., Shewry, P.R. Beale, M.H. (2006) A metabolomics study of substantial equivalence of field-grown genetically modified wheat. Plant Biotechnol. J. 4, 381 392.
4. Baudo, M.M., Lyons, R., Powers, S., Pastori, G.M., Edwards, K.J., Holdsworth, M.J. Shewry, P.R. (2006) Transgenesis has less impact on the transcriptome of wheat grain than conventional breeding. Plant Biotechnol. J. 4, 369 380.
5. Bregitzer, P., Cooper, L.D., Hayes, P.M., Lemaux, P.G., Singh, J. Sturbaum, A.K. (2007) Viability and bar expression are negatively correlated in Oregon Wolfe Barley dominant hybrids. Plant Biotechnol. J. 5, 381 388.
6. Catchpole, G.S., Beckmann, M., Enot, D.P., Mondhe, M., Zywicki, B., Taylor, J., Hardy, N., Smith, A., King, R.D., Kell, D.B., Fiehn, O. Draper, J. (2005) Hierarchical metabolomics demonstrates substantial compositional similarity between genetically modified and conventional potato crops. Proc. Natl. Acad. Sci. USA, 102, 14 458 14 462.
7. Causier, B., Castillo, R., Zhou, J., Ingram, R., Xue, Y., Schwarz-Sommer, Z. Davies, B. (2005) Evolution in Action: following function in duplicated floral homeotic genes. Curr. Biol. 15, 1508 1512.
8. Cellini, F., Chesson, A., Coquhoun, I., Constable, A., Davies, H.V., Engel, K.H., Gatehouse, A.M.R., Kärenlampi, S., Kok, E.J., Leguay, J.-J., Lehesranta, S., Noteborn, H.P.J.M., Pederson, J. Smith, M. (2004) Unintended effects and their detection in genetically modified crops. Food Chem. Toxicol. 42, 1089 1125.
9. Cheng, K.C., Beaulieu, J., Iquira, E., Belzile, F.J., Fortin, M.G. Stromvik, M.V. (2008) Effect of transgenes on global gene expression in soybean is within the natural range of variation of conventional cultivars. J. Agric. Food Chem. 56, 3057 3067.
10. Corpillo, D., Gardini, G., Vaira, A.M., Basso, M., Aime, S., Accotto, G.P. Fasano, M. (2004) Proteomics as a tool to improve investigation of substantial equivalence in genetically modified organisms: the case of a virus-resistant tomato. Proteomics, 4, 193 200.
11. Coutu, C., Brandle, J., Brown, D., Brown, K., Miki, B., Simmonds, J. Hegedus, D.D. (2007) pORE; a modular binary vector series suited for both monocot and dicot plant transformation. Transgenic Res. 16, 771 781.
12. Darbani, B., Eimanifar, A., Stewart, C.N. Camargo, W.N. (2007) Methods to produce marker-free transgenic plants. Biotechnol. J. 2, 83 90.
13. Daxinger, L., Hunter, B., Sheikh, M., Jauvion, V., Gasciolli, V., Vaucheret, H., Matzke, M. Furner, I. (2007) Unexpected silencing effects from T-DNA tags in Arabidopsis. Trends Plant Sci. 13, 4 6.
14. Day, C.D., Lee, E., Kobayashi, J., Holappa, L.D., Albert, H. Ow, D.W. (2000) Transgene integration into the same chromosome location can produce alleles that express at a predictable level, or alleles that are differentially silenced. Genes Devel. 14, 2869 2880.
15. El Ouakfaoui, S. Miki, B. (2005) The stability of the Arabidopsis transcriptome in transgenic plants expressing the marker genes nptII and uidA. Plant J. 41, 791 800.
16. Endo, S., Kasahara, T., Sugita, K., Matsunaga, E. Ebinuma, H. (2001) The isopentyl transferase gene is effective as a selectable marker gene for plant transformation in tobacco (Nicotiana tabacum cv Petite Havana SR1). Plant Cell Rep. 20, 60 66.
17. Fobert, P.R., Labbe, H., Cosmopolous, J., Gottlob-McHugh, S., Ouellet, T., Hattori, J., Sunohara, G., Iyer, V.N. Miki, B. (1994) T-DNA tagging of a seed coat-specific cryptic promoter in tobacco. Plant J. 6, 567 577.
18. Foster, E., Hattori, J., Labbe, H., Ouellet, T., Fobert, P., James, L. Miki, B. (1999) A tobacco cryptic promoter, tCUP, revealed by T-DNA tagging. Plant Mol. Biol. 41, 45 55.
19. Gudynaite-Savitch, L., Johnson, D. Miki, B. (in press) Strategies to mitigate transgene - promoter interactions. Plant Biotechnol. J.
20. Kakimoto, T. (1996) CKI1, a histidine kinase homolog implicated in cytokinin signal transduction. Science, 8, 982 985.
21. Kim, S.I., Veena Gelvin, S.B. (2007) Genome-wide analysis of Agrobacterium T-DNA integration sites in the Arabidopsis genome generated under non-selective conditions. Plant J. 51, 779 791.
22. Koncz, C., Martini, N., Mayerhofer, R., Koncz-Kalman, Z., Korber, H., Redei, G.P. Schell, J. (1989) High-frequency T-DNA-mediated gene tagging in plants. Proc. Natl. Acad. Sci. USA, 86, 8467 8471.
23. Kristensen, C., Morant, M., Olsen, C.E., Ekstrom, C.T., Galbraith, D.W., Moller, B.L. Bak, S. (2005) Metabolic engineering of dhurrin in transgenic Arabidopsis plants with marginal inadvertent effects on the metabolome and transcriptome. Proc. Natl. Acad. Sci. USA, 102, 1779 1784.
24. Kuiper, H.A., Kleter, G.A., Noteborn, H.P.J.M. Kok, E.J. (2001) Assessment of the food safety issues related to genetically modified foods. Plant J. 27, 503 528.
25. Lehesranta, S.J., Davies, H.V., Shepherd, L.V.T., Nunan, N., McNicol, J.W., Auriola, S., Koistinen, K.M., Suomalainen, S., Kokko, H.I. Karenlampi, S.O. (2005) Comparison of tuber proteomes of potato varieties, landraces and genetically modified lines. Plant Physiol. 138, 1690 1699.
26. Lin, R., Ding, L., Casola, C., Ripoli, D.R., Feschotte, C. Wang, H. (2007) Transposase-derived transcription factors regulate light signalling in Arabidopsis. Science, 318, 1302 1305.
27. Louwerse, J.D., van Lier, M.C.M., van der Steen, D.M., de Vlaam, C.M.T., Hooykaas, P.J.J. Vergunst, A.C. (2007) Stable recombinase-mediated cassette exchange in Arabidopsis using Agrobacterium tumefaciens. Plant Physiol. 145, 1282 1293.
28. Malik, K., Wu, K., Li, X.-Q., Martin-Heller, T., Hu, M., Foster, E., Tian, L., Wang, C., Ward, K., Jordan, M., Brown, D., Gleddie, S., Simmonds, D., Zheng, S., Simmonds, J. Miki, B. (2002) A constitutive gene expression system derived from the tCUP cryptic promoter elements. Theor. Appl. Genet. 105, 505 514.
29. Manabe, Y., Tinker, N., Colville, A. Miki, B. (2007) CSR1, the sole target of imidazolinone herbicide in Arabidopsis thaliana. Plant Cell Physiol. 48, 1340 1358.
30. Mathews, H., Clendennen, S.K., Caldwell, C.G., Liu, X.L., Connors, K., Matheis, N., Schuster, D.K., Menasco, D.J., Wagoner, W., Lightner, J. Wagner, D.R. (2003) Activation tagging in tomato identifies a transcriptional regulator of anthocyanin biosynthesis, modification, and transport. Plant Cell, 15, 1689 1703.
31. Mentewab, A. Stewart, C.N. (2005) Overexpression of an Arabidopsis thaliana ABC transporter confers kanamycin resistance to transgenic plants. Nat. Biotechnol. 23, 1177 1180.
32. Miki, B. (2008) Marker genes and promoters. In : Plant Biotechnology and Genetics: Principles, Techniques and Applications (Neal Stewart Jr., C.N., ed. pp. 217 243. Hoboken, NJ : John Wiley and Sons.
33. Miki, B. McHugh, S. (2004) Selectable marker genes in transgenic plants: applications, alternatives and biosafety. J. Biotechnol. 107 (3 193 232.
34. Nanto, K., Yamada-Watanabe, K. Ebinuma, H. (2005) Agrobacterium-mediated RMCE approach for gene replacement. Plant Biotechnol. J. 3, 203 214.
35. Nap, J.-P., Bijvoet, J. Stiekema, W.J. (1992) Biosafety of kanamycin-resistant transgenic plants. Transgenic Res. 1, 239 249.
36. Organization of Economic Co-operation and Development (OECD) (1993) Safety Evaluation of Foods Derived by Modern Biotechnology, Concepts and Principles. Paris : OECD. URL http://www.oecd.org/dsti/sti/s-t/biotech/prod/ modern.htm [accessed on 21 May 2002].
37. Olszewski, N.E., Martin, F.B. Ausubel, F.M. (1988) Specialized binary vector for plant transformation: expression of the Arabidopsis thaliana AHAS gene in Nicotiana tabacum. Nucleic Acids Res. 16, 10 765 10 781.
38. Ow, D.W. (2005) 2004 SIVB congress symposium proceeding: transgene management via multiple site-specific recombination systems. In Vitro Cell Dev Biol. Plant, 41, 2113 2219.
39. Ramessar, K., Peremarti, A., Gomez-Galera, S., Naqvi, S., Moralejo, M., Munoz, P., Capell, T. Christou, P. (2007) Biosafety and risk assessment framework for selectable marker genes in transgenic crop plants: a case of the science not supporting the politics. Transgenic Res. 16, 261 280.
40. Rijpkema, A.S., Gerats, T. Vandenbussche, M. (2007) Evolutionary complexity of MADS complexes. Curr. Opin. Plant Biol. 10, 32 38.
41. Rommens, C.M. (2006) Kanamycin resistance in plants: an unexpected trait controlled by a potentially multifaceted gene. Trends Plant Sci. 11, 317 319.
42. Shiu, S.-H. Bleecker, A.B. (2001) Receptor-like kinases from Arabidopsis form a monophyletic gene family related to animal receptor kinases. Proc. Natl. Acad. Sci. USA, 98, 10 763 10 768.
43. Singh, B.K. Shaner, D.L. (1995) Biosynthesis of branched chain amino acids: from test tube to field. Plant Cell, 7, 935 944.
44. Smyth, S. McHughen, A. (2008) Regulating innovative crop technologies in Canada: the case of regulating genetically modified crops. Plant Biotechnol. J. 6, 213 225.
45. Soltis, D.E., Ma, H., Frohlich, M.W., Soltis, P.S., Albert, V.A., Oppenheimer, D.G., Altman, N.S., dePamphilis, C. Leebens-Mack, J. (2007) The floral genome: an evolutionary history of gene duplication and shifting patterns of gene expression. Trends Plant Sci. 12, 358 367.
46. Sugita, K., Kasahara, T., Matsunaga, E. Ebinuma, H. (2000) A transformation vector for the production of marker-free transgenic plants containing a single copy transgene at high frequency. Plant J. 22, 461 469.
47. Tan, S., Evans, R.R., Dahmer, M.L., Singh, B.K. Shaner, D.L. (2005) Imidazolinone-tolerant crops: history, current status and future. Pest Manag. Sci. 61, 246 357.
48. Verma, D. Daniell, H. (2007) Chloroplast vector systems for biotechnology applications. Plant Physiol. 145, 1129 1143.
49. Weigel, D., Ahn, J.H., Blázquez, M.A., Borevitz, J.O., Christensen, S.K., Fankhauser, C., Ferrándiz, C., Kardailsky, I., Malancharuvil, E.J., Neff, M.M., Nguyen, J.T., Sato, S., Wang, Z.-Y., Xia, Y., Dixon, R.A., Harrison, M.J., Lamb, C.J., Yanofsky, M.F. Chory, J. (2000) Activation tagging in Arabidopsis. Plant Physiol. 122, 1003 1013.
50. Yoo, S.Y., Bomblies, K., Yoo, S.K., Yang, J.W., Choi, M.C., Lee, J.S., Weigel, D. Ahn, J.H. (2005) The 35S promoter used in a selectable marker gene of a plant transformation vector affects the expression of the transgene. Planta, 221, 523 530.
51. Yuan, J.S., Tranel, P.J. Stewart, C.N. Jr (2006) Non-target-site herbicide resistance: a family business. Trends Plant Sci. 12, 6 13.
52. Yuan, J.S., Galbraith, D.W., Dai, S.Y., Griffin, P. Stewart, C.N., Jr (2008) Plant systems biology comes of age. Trends Plant Sci. 13, 165 171.
53. Zuo, J., Niu, Q.-W., Ikeda, Y. Chua, N.-H. (2002) Marker-free transformation: increasing transformation frequency by the use of regeneration-promoting genes. Curr. Opin. Biotechnol. 13, 173 180.