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Plant gene targeting and gene replacement: application to crop genetic improvement

Published online by Cambridge University Press:  01 October 2008

Zhang Xiao-hui
Affiliation:
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
Ye Zhi-biao
Affiliation:
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China National Center for Vegetable Improvement (Central China), Huazhong Agricultural University, Wuhan 430070, China
Zhang Yu-yang
Affiliation:
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China National Center for Vegetable Improvement (Central China), Huazhong Agricultural University, Wuhan 430070, China
Hou Zheng
Affiliation:
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
Li Han-xia*
Affiliation:
National Center for Vegetable Improvement (Central China), Huazhong Agricultural University, Wuhan 430070, China
*
*Corresponding author. E-mail: hxli@mail.hzau.edu.cn

Abstract

Recent advances and limitations of using zinc finger nuclease to stimulate a high efficiency of homologous recombination, and chimeric oligonucleotides to promote single base replacement in functional genomic research and plant genetic breeding, are systematically reviewed. Approaches to improve gene targeting efficiency through molecular modification of key pathways in plant homologous recombination are also discussed.

Type
Review Article
Copyright
Copyright © China Agricultural University 2008

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Footnotes

First published in Journal of Agricultural Biotechnology 2007, 15(6): 1058–1065

References

Beetham, PR, Kipp, PB, Sawycky, XL, Arntzen, CJ and May, GD (1999) A tool for functional plant genomics: chimeric RNA/DNA oligonucleotides cause in vivo gene-specific mutations. Proceedings of the National Academy of Sciences of the USA 96: 87748778.CrossRefGoogle ScholarPubMed
Beumer, K, Bhattacharyya, G, Bibikova, M, Trautman, JK and Carroll, D (2006) Efficient gene targeting in Drosophila with zinc-finger nucleases. Genetics 172: 23912403.CrossRefGoogle ScholarPubMed
Bibikova, M, Carroll, D, Segal, DJ, et al. (2001) Stimulation of homologous recombination through targeted cleavage by chimeric nucleases. Molecular and Cellular Biology 21: 289297.CrossRefGoogle ScholarPubMed
Burma, S, Chen, BP and Chen, DJ (2006) Role of non-homologous end joining (NHEJ) in maintaining genomic integrity. DNA Repair 5: 10421048.Google Scholar
Choo, Y and Isalan, M (2000) Advances in zinc finger engineering. Current Opinion in Structure Biology 10: 411416.Google Scholar
Cole-Stauss, A, Yoon, K, Xiang, Y, et al. (1996) Correction of the mutation responsible for sickle cell anemia by an RNA-DNA oligonucleotide. Science 273: 13861389.Google Scholar
Comai, L, Young, K, Till, BJ, et al. (2004) Efficient discovery of DNA polymorphisms in natural populations by Ecotilling. The Plant Journal 37: 778786.Google Scholar
Dong, C, Beetham, P, Vincent, K and Sharp, P (2006) Oligonucleotide-directed gene repair in wheat using a transient plasmid gene repair assay system. Plant Cell Report 25: 457465.Google Scholar
Flint-Garcia, SA, Thornsberry, JM and Buckler, ESt (2003) Structure of linkage disequilibrium in plants. Annual Review of Plant Biology 54: 357374.CrossRefGoogle ScholarPubMed
Hartung, F and Puchta, H (2006) The RecQ gene family in plants. Journal of Plant Physiology 163: 287296.Google Scholar
Hohn, B and Puchta, H (1999) Gene therapy in plants. Proceedings of the National Academy of Sciences of the USA 96: 83218323.Google Scholar
Hurt, JA, Thibodeau, SA, Hirsh, AS, Pabo, CO and Joung, JK (2003) Highly specific zinc finger proteins obtained by directed domain shuffling and cell-based selection. Proceedings of the National Academy of Sciences of the USA 100: 1227112276.Google Scholar
Igoucheva, O, Alexeev, V and Yoon, K (2001) Targeted gene correction by small single-stranded oligonucleotides in mammalian cells. Gene Therapy 8: 391399.Google Scholar
Igoucheva, O, Alexeev, V and Yoon, K (2004) Oligonucleotide-directed mutagenesis and targeted gene correction: a mechanistic point of view. Current Molecular Medicine 4: 445463.Google Scholar
Igoucheva, O, Alexeev, V, Scharer, O and Yoon, K (2006) Involvement of ERCC1/XPF and XPG in oligodeoxynucleotide-directed gene modification. Oligonucleotides 16: 94104.Google Scholar
Iida, S and Terada, R (2005) Modification of endogenous natural genes by gene targeting in rice and other higher plants. Plant Molecular Biology 59: 205219.CrossRefGoogle ScholarPubMed
Kim, YG and Chandrasegaran, S (1994) Chimeric restriction endonuclease. Proceedings of the National Academy of Sciences of the USA 91: 883887.Google Scholar
Kim, YG, Cha, J and Chandrasegaran, S (1996) Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. Proceedings of the National Academy of Sciences of the USA 93: 11561160.Google Scholar
Kochevenko, A and Willmitzer, L (2003) Chimeric RNA/DNA oligonucleotide-based site-specific modification of the tobacco acetolactate synthase gene. Plant Physiology 132: 174184.Google Scholar
Kumar, S, Allen, GC and Thompson, WF (2006) Gene targeting in plants: fingers on the move. Trends in Plant Science 11: 159161.Google Scholar
Lettier, G, Feng, Q, de Mayolo, AA, et al. (2006) The role of DNA double-strand breaks in spontaneous homologous recombination in S. cerevisiae. PLoS Genetics 2: e194.Google Scholar
Li, HQ, Terada, R, Li, MR and Iida, S (2004) RecQ helicase enhances homologous recombination in plants. FEBS Letters 574: 151155.Google Scholar
Lloyd, A, Plaisier, CL, Carroll, D and Drews, GN (2005) Targeted mutagenesis using zinc-finger nucleases in Arabidopsis. Proceedings of the National Academy of Sciences of the USA 102: 22322237.Google Scholar
Moerschell, RP, Tsunasawa, S and Sherman, F (1988) Transformation of yeast with synthetic oligonucleotides. Proceedings of the National Academy of Sciences of the USA 85: 524528.Google Scholar
Morton, J, Davis, MW, Jorgensen, EM and Carroll, D (2006) Induction and repair of zinc-finger nuclease-targeted double-strand breaks in Caenorhabditis elegans somatic cells. Proceedings of the National Academy of Sciences of the USA 103: 1637016375.Google Scholar
Okuzaki, A and Toriyama, K (2004) Chimeric RNA/DNA oligonucleotide-directed gene targeting in rice. Plant Cell Report 22: 509512.Google Scholar
Olsen, KM, Halldorsdottir, SS, Stinchcombe, JR, Weinig, C, Schmitt, J and Purugganan, MD (2004) Linkage disequilibrium mapping of Arabidopsis CRY2 flowering time alleles. Genetics 167: 13611369.Google Scholar
Pabo, CO, Peisach, E and Grant, RA (2001) Design and selection of novel Cys2His2 zinc finger proteins. Annual Review of Biochemistry 70: 313340.Google Scholar
Pacher, M, Schmidt-Puchta, W and Puchta, H (2007) Two unlinked double-strand breaks can induce reciprocal exchanges in plant genomes via homologous recombination and nonhomologous end joining. Genetics 175: 2129.Google Scholar
Paszkowski, J, Baur, M, Bogucki, A and Potrykus, I (1988) Gene targeting in plants. EMBO Journal 7: 40214026.Google Scholar
Porteus, MH and Baltimore, D (2003) Chimeric nucleases stimulate gene targeting in human cells. Science 300: 763.Google Scholar
Puchta, H, Dujon, B and Hohn, B (1993) Homologous recombination in plant cells is enhanced by in vivo induction of double strand breaks into DNA by a site-specific endonuclease. Nucleic Acids Research 21: 50345040.CrossRefGoogle ScholarPubMed
Reiss, B, Klemm, M, Kosak, H and Schell, J (1996) RecA protein stimulates homologous recombination in plants. Proceedings of the National Academy of Sciences of the USA 93: 30943098.Google Scholar
Reiss, B, Schubert, I, Kopchen, K, Wendeler, E, Schell, J and Puchta, H (2000) RecA stimulates sister chromatid exchange and the fidelity of double-strand break repair, but not gene targeting, in plants transformed by Agrobacterium. Proceedings of the National Academy of Sciences of the USA 97: 33583363.Google Scholar
Ruiter, R, van den Brande, I, Stals, E, Delaure, S, Cornelissen, M and D'Halluin, K (2003) Spontaneous mutation frequency in plants obscures the effect of chimeraplasty. Plant Molecular Biology 53: 675689.Google Scholar
Segal, DJ, Dreier, B, Beerli, RR and Barbas, CF 3rd (1999) Toward controlling gene expression at will: selection and design of zinc finger domains recognizing each of the 5′-GNN-3′ DNA target sequences. Proceedings of the National Academy of Sciences of the USA 96: 27582763.Google Scholar
Shaked, H, Melamed-Bessudo, C and Levy, AA (2005) High-frequency gene targeting in Arabidopsis plants expressing the yeast RAD54 gene. Proceedings of the National Academy of Sciences of the USA 102: 1226512269.Google Scholar
Shalev, G, Sitrit, Y, Avivi-Ragolski, N, Lichtenstein, C and Levy, AA (1999) Stimulation of homologous recombination in plants by expression of the bacterial resolvase ruvC. Proceedings of the National Academy of Sciences of the USA 96: 73987402.Google Scholar
Szalma, SJ, Buckler, ESt, Snook, ME and McMullen, MD (2005) Association analysis of candidate genes for maysin and chlorogenic acid accumulation in maize silks. Theoretical and Applied Genetics 110: 13241333.Google Scholar
Terada, R, Urawa, H, Inagaki, Y, Tsugane, K and Iida, S (2002) Efficient gene targeting by homologous recombination in rice. Nature Biotechnology 20: 10301034.Google Scholar
Urnov, FD, Miller, JC, Lee, YL, et al. (2005) Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature 435: 646651.Google Scholar
West, CE, Waterworth, WM, Jiang, Q and Bray, CM (2000) Arabidopsis DNA ligase IV is induced by gamma-irradiation and interacts with an Arabidopsis homologue of the double strand break repair protein XRCC4. Plant Journal 24: 6778.Google Scholar
Wright, DA, Townsend, JA, Winfrey, RJ Jr, et al. (2005) High-frequency homologous recombination in plants mediated by zinc-finger nucleases. Plant Journal 44: 693705.CrossRefGoogle ScholarPubMed
Wright, DA, Thibodeau-Beganny, S, Sander, JD, et al. (2006) Standardized reagents and protocols for engineering zinc finger nucleases by modular assembly. Nature Protocols 1: 16371652.Google Scholar
Wu, XS, Xin, L, Yin, WX, et al. (2005) Increased efficiency of oligonucleotide-mediated gene repair through slowing replication fork progression. Proceedings of the National Academy of Sciences of the USA 102: 25082513.Google Scholar
Zhu, T, Peterson, DJ, Tagliani, L, St Clair, G, Baszczynski, CL and Bowen, B (1999) Targeted manipulation of maize genes in vivo using chimeric RNA/DNA oligonucleotides. Proceedings of the National Academy of Sciences of the USA 96: 87688773.CrossRefGoogle ScholarPubMed
Zhu, T, Mettenburg, K, Peterson, DJ, Tagliani, L and Baszczynski, CL (2000) Engineering herbicide-resistant maize using chimeric RNA/DNA oligonucleotides. Nature Biotechnology 18: 555558.CrossRefGoogle ScholarPubMed