Key Points
-
There are several emerging genetic tools that will have increasingly important roles in the future of plant biotechnology and crop genetics.
-
Precise transgene or endogenous gene expression can be regulated at the transcriptional level by novel synthetic promoters, as well as synthetic transcriptional activators and repressors, for increased spatio-temporal control.
-
The recent development of several advanced DNA construction and assembly methods will allow the production of long DNA constructs and vectors that are needed for multigene transformation into plants.
-
Plant transformation with large constructs that are needed for metabolic pathway engineering is enabled by several techniques, including plant artificial chromosomes. There is no clear 'winner' among the several techniques presented.
-
Plant-genome editing using a host of new tools, including zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats (CRISPRs), is poised to have, perhaps, the greatest effect on precisely changing DNA sequences in crops in novel ways.
-
Tools for transgene removal and confinement are crucial for the commercialization of certain crops and crop–transgene combinations to ensure biosafety and government regulatory compliance.
Abstract
Basic research has provided a much better understanding of the genetic networks and regulatory hierarchies in plants. To meet the challenges of agriculture, we must be able to rapidly translate this knowledge into generating improved plants. Therefore, in this Review, we discuss advanced tools that are currently available for use in plant biotechnology to produce new products in plants and to generate plants with new functions. These tools include synthetic promoters, 'tunable' transcription factors, genome-editing tools and site-specific recombinases. We also review some tools with the potential to enable crop improvement, such as methods for the assembly and synthesis of large DNA molecules, plant transformation with linked multigenes and plant artificial chromosomes. These genetic technologies should be integrated to realize their potential for applications to pressing agricultural and environmental problems.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Buy this article
- Purchase on SpringerLink
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
![](http://media.springernature.com/m312/springer-static/image/art%3A10.1038%2Fnrg3583/MediaObjects/41576_2013_Article_BFnrg3583_Fig1_HTML.jpg)
![](http://media.springernature.com/m312/springer-static/image/art%3A10.1038%2Fnrg3583/MediaObjects/41576_2013_Article_BFnrg3583_Fig2_HTML.jpg)
![](http://media.springernature.com/m312/springer-static/image/art%3A10.1038%2Fnrg3583/MediaObjects/41576_2013_Article_BFnrg3583_Fig3_HTML.jpg)
![](http://media.springernature.com/m312/springer-static/image/art%3A10.1038%2Fnrg3583/MediaObjects/41576_2013_Article_BFnrg3583_Fig4_HTML.jpg)
![](http://media.springernature.com/m312/springer-static/image/art%3A10.1038%2Fnrg3583/MediaObjects/41576_2013_Article_BFnrg3583_Fig5_HTML.jpg)
Similar content being viewed by others
Change history
26 November 2013
In Figure 4d, e of this article, the products of transgene excision and marker gene removal were shown incorrectly. The article has been corrected online. The authors apologize for the error.
References
Collins, N. C., Tardieu, F. & Tuberosa, R. Quantitative trait loci and crop performance under abiotic stress: where do we stand? Plant Physiol. 147, 469–486 (2008).
Wollenweber, B., Porter, J. R. & Lubberstedt, T. Need for multidisciplinary research towards a second green revolution. Curr. Opin. Plant Biol. 8, 337–341 (2005).
Naqvi, S. et al. When more is better: multigene engineering in plants. Trends Plant Sci. 15, 48–56 (2010).
Venter, M. Synthetic promoters: genetic control through cis engineering. Trends Plant Sci. 12, 118–124 (2007).
De Wilde, C. et al. Plants as bioreactors for protein production: avoiding the problem of transgene silencing. Plant Mol. Biol. 43, 347–359 (2000).
Kooter, J. M., Matzke, M. A. & Meyer, P. Listening to the silent genes: transgene silencing, gene regulation and pathogen control. Trends Plant Sci. 4, 340–347 (1999).
Venter, M. & Botha, F. C. in Plant Developmental Biology — Biotechnological Perspectives Vol. 2 (eds Pua, E. C. & Davey, M. R.) 393–408 (Springer, 2010).
Liu, W., Mazarei, M., Rudis, M. R., Fethe, M. H. & Stewart, C. N. Jr. Rapid in vivo analysis of synthetic promoters for plant pathogen phytosensing. BMC Biotechnol. 11, 108 (2011).
Liu, W. et al. Bacterial pathogen phytosensing in transgenic tobacco and Arabidopsis. Plant Biotechnol. J. 11, 43–52 (2013). References 8 and 9 provide good examples of the use of synthetic promoters for the phytosensing of bacterial pathogen in plants.
Mehrotra, R. et al. Designer promoter: an artwork of cis engineering. Plant Mol. Biol. 75, 527–536 (2011).
Hu, J., Li, B. & Kihara, D. Limitations and potentials of current motif discovery algorithms. Nucleic Acids Res. 33, 4899–4913 (2005).
Tompa, M. et al. Assessing computational tools for the discovery of transcription factor binding sites. Nature Biotech. 23, 137–144 (2005). This paper provides an excellent comparison of the effectiveness of 13 computational tools for de novo motif discovery.
Koschmann, J. et al. Intergration of bioinformatics and synthetic promoters leads to the discovery of novel elicitor-responsive cis-regulatory sequences in Arabidopsis. Plant Physiol. 160, 178–191 (2012).
Mukherji, S. & van Oudenaarden, A. Synthetic biology: understanding biological design from synthetic circuits. Nature Rev. Genet. 10, 859–871 (2009).
Sawant, S., Singh, P. K., Madanala, R. & Tuli, R. Designing of an artificial expression cassette for the high-level expression of transgenes in plants. Theor. Appl. Genet. 102, 635–644 (2001).
Comai, L., Moran, P. & Maslyar, D. Novel and useful properties of a chimeric plant promoter combining CaMV 35S and MAS elements. Plant Mol. Biol. 15, 373–381 (1990).
Petolino, J. F. & Davies, J. P. Designed transcriptional regulators for trait development. Plant Sci. 201–202, 128–136 (2013).
Bogdanove, A. J. & Voytas, D. F. TAL effectors: customizable proteins for DNA targeting. Science 333, 1843–1846 (2011).
Guan, X. et al. Heritable endogenous gene regulation in plants with designed polydactyl zinc finger transcription factors. Proc. Natl Acad. Sci. USA 99, 13296–13301 (2010).
Sanchez, J.-P., Ullman, C., Moore, M., Choo, Y. & Chua, N.-H. Regulation of gene expression in Arabidopsis thaliana by artificial zinc finger chimeras. Plant Cell Physiol. 43, 1465–1472 (2002).
Li, J. et al. Activation domains for controlling plant gene expression using designed transcription factors. Plant Biotechnol. J. 11, 671–680 (2013).
Sanchez, J.-P., Ullman, C., Moore, M., Choo, Y. & Chua, N.-H. Regulation of Arabidopsis thaliana 4-coumarate: coenzyme-A ligase-1 expression by artificial zinc finger chimeras. Plant Biotechnol. J. 4, 103–114 (2006).
Lindhout, B. I., Pinas, J. E., Hooykaas, P. J. J. & van der Zaal, B. J. Employing libraries of zinc finger artificial transcription factors to screen for homologous recombination mutants in Arabidopsis. Plant J. 48, 475–483 (2006).
Holmes-Davis, R. et al. Gene regulation in planta by plant-derived engineered zinc finger protein transcription factors. Plant Mol. Biol. 57, 411–423 (2005).
Van Eenennaam, A. L. et al. Elevation of seed α-tocopherol levels using plant-based transcription factors targeted to an endogenous locus. Metabol. Eng. 6, 101–108 (2004).
Gupta, M. et al. Transcriptional activation of Brassica napus β-ketoacyl-ACP synthase II with an engineered zinc finger protein transcription factor. Plant Biotechnol. J. 10, 783–791 (2012).
Ordiz, M. I., Magnenat, L., Barbas, C. F. 3rd. & Beachy, R. N. Negative regulation of the RTBV promoter by designed zinc finger proteins. Plant Mol. Biol. 72, 621–630 (2010).
Moscou, M. J. & Bogdanove, A. J. A simple cipher governs DNA recognition by TAL effectors. Science 326, 1501 (2009).
Boch, J. & Bonas, U. Xanthomonas AvrBs3 family-type III effectors: discovery and function. Annu. Rev. Phytopathol. 48, 419–436 (2010).
Boch, J. et al. Breaking the code of DNA binding specificity of TAL-type III effectors. Science 326, 1509–1512 (2009). References 28 and 30 are the two studies that first reported the molecular mechanisms of bacterial TALEs.
Morbitzer, R., Romer, P., Boch, J. & Lahaye, T. Regulation of selected genome loci using de novo-engineered transcription activator-like effector (TALE)-type transcription factors. Proc. Natl Acad. Sci. USA 107, 21617–21622 (2010).
Mahfouz, M. M. et al. Targeted transcriptional repression using a chimeric TALE–SRDX repressor protein. Plant Mol. Biol. 78, 311–321 (2012).
Knight, T. Idempotent vector design for standard assembly of Biobricks. DSpace@MIT [online], (2003).
Anderson, J. C. et al. BglBricks: a flexible standard for biological part assembly. J. Biol. Eng. 4, 1 (2010).
Engler, C., Kandzia, R. & Marillonnet, S. A one pot, one step, precision cloning method with high throughput capability. PLoS ONE 3, e3647 (2008).
Sasaki, Y. Evidence for high specificity and efficiency of multiple recombination signals in mixed DNA cloning by the MultiSite Gateway system. J. Biotechnol. 107, 233 (2004).
Nour-Eldin, H. H., Geu-Flores, F. & Halkier, B. A. USER cloning and USER fusion: the ideal cloning techniques for small and big laboratories. Methods Mol. Biol. 643, 185–200 (2010).
Sleight, S., Bartley, B., Lieviant, J. & Sauro, H. In-fusion BioBrick assembly and re-engineering. Nucleic Acids Res. 38, 2624 (2010).
Li, M. Z. & Elledge, S. J. Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC. Nature Methods 4, 251–256 (2007).
Gibson, D. G. et al. Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329, 52–56 (2010). This study reports the largest de novo synthesized and assembled genome.
Hillson, N. J., Rosengarten, R. D. & Keasling, J. D. j5 DNA assembly design automation software. ACS Synth. Biol. 1, 14–21 (2012).
Sarrion-Perdigones, A. et al. GoldenBraid: an iterative cloning system for standardized assembly of reusable genetic modules. PLoS ONE 6, e21622 (2011).
Cardi, T., Lenzi, P. & Maliga, P. Chloroplasts as expression platforms for plant-produced vaccines. Expert Rev. Vaccines 9, 893–911 (2010).
Scotti, N., Rigano, M. M. & Cardi, T. Production of foreign proteins using plastid transformation. Biotechnol. Adv. 30, 387–397 (2012).
Maliga, P. & Bock, R. Plastid biotechnology: food, fuel, and medicine for the 21st century. Plant Physiol. 155, 1501–1510 (2011).
Clarke, J. L. & Daniell, H. Plastid biotechnology for crop production: present status and future perspectives. Plant Mol. Biol. 76, 211–220 (2011).
Dufourmantel, N. et al. Generation and analysis of soybean plastid transformants expressing Bacillus thuringiensis Cry1 Abprotoxin. Plant Mol. Biol. 58, 659–668 (2006).
Sidorov, V. A. et al. Stable chloroplast transformation in potato: use of green fluorescent protein as a plastid marker. Plant J. 19, 209–216 (1999).
Apel, W. & Bock, R. Enhancement of carotenoid biosynthesis in transplastomic tomatoes by induced lycopene-to-provitamin A conversion. Plant Physiol. 151, 59–66 (2009).
Lelivelt, C. L. C. et al. Stable plastid transformation in lettuce (Lactuca sativa L.). Plant Mol. Biol. 58, 763–774 (2005).
Kanamoto, H. et al. Efficient and stable transformation of Lactuca sativa L. cv. Cisco (lettuce) plastids. Transgen. Res. 15, 205–217 (2006).
Marchis, F. D., Wang, Y., Stevanato, P., Arcioni, S. & Bellucci, M. Genetic transformation of the sugar beet plastome. Transgen. Res. 18, 17–30 (2009).
Singh, A. K., Verma, S. S. & Bansal, K. C. Plastid transformation in eggplant (Solanum melongena L.). Transgen. Res. 19, 113–119 (2010).
Kumar, S., Dhingra, A. & Daniell, H. Plastid expressed betaine aldehyde dehydrogenase gene in carrot cultured cells, roots and leaves confers enhanced salt tolerance. Plant Physiol. 136, 2843–2854 (2004).
Hou, B. K. et al. Chloroplast transformation in oilseed rape. Transgen. Res. 12, 111–114 (2003).
Liu, C. W., Lin, C. C., Chen, J. J. & Tseng, M. J. Stable chloroplast transformation in cabbage (Brassica oleracea L. var. Capitata L.) by particle bombardment. Plant Cell Rep. 26, 1733–1744 (2007).
Werner, S., Breus, O., Symonenko, Y., Marillonnet, S. & Gleba, Y. High-level recombinant protein expression in transgenic plants by using a double-inducible viral vector. Proc. Natl Acad. Sci. USA 108, 14061–14066 (2011).
Marton, I. et al. Nontransgenic genome modification in plant cells. Plant Physiol. 154, 1079–1087 (2010).
Mozes-Koch, R. et al. Expression of an entire bacterial operon in plants. Plant Physiol. 158, 1883–1892 (2012).
Liu, Y. G. et al. Complementation of plant mutants with large genomic DNA fragments by a transformation-competent artificial chromosome vector accelerates positional cloning. Proc. Natl Acad. Sci. USA 96, 6535–6540 (1999).
Lin, L., Liu, Y.-G., Xu, X. & Li, B. Efficient linking and transfer of multiple genes by a multigene assembly and transformation vector system. Proc. Natl Acad. Sci. USA 100, 5962–5967 (2003).
Hamilton, C. M., Frary, A., Lewis, C. & Tanksley, S. D. Stable transfer of intact high molecular weight DNA into plant chromosomes. Proc. Natl Acad. Sci. USA 93, 9975–9979 (1996).
Chen, Q.-J. et al. MISSA is a highly efficient in vivo DNA assembly method for plant multiple-gene transformation. Plant Physiol. 153, 41–51 (2010).
Ananiev, E. V. et al. Artificial chromosome formation in maize (Zea mays L.). Chromosoma 118, 157–177 (2009).
Carlson, S. R. et al. Meiotic transmission of an in vitro-assembled autonomous maize minichromosome. PLoS Genet. 3, 1965–1974 (2007). This paper is the first report of the bottom-up approach for minichromosome generation in plants.
Kapusi, E. et al. Telomere-mediated truncation of barley chromosomes. Chromosoma 121, 181–190 (2012).
Nelson, A. D., Lamb, J. C., Kobrossly, P. S. & Shippen, D. E. Parameters affecting telomere-mediated chromosomal truncation in Arabidopsis. Plant Cell 23, 2263–2272 (2011).
Teo, C. H. et al. Induction of telomere-mediated chromosomal truncation and stability of truncated chromosomes in Arabidopsis thaliana. Plant J. 68, 28–39 (2011).
Yu, W., Lamb, J. C., Han, F. & Birchler, J. A. Telomere-mediated chromosomal truncation in maize. Proc. Natl Acad. Sci. USA 103, 17331–17336 (2006).
Yu, W., Han, F., Gao, Z., Vega, J. M. & Birchler, J. A. Construction and behavior of engineered minichromosomes in maize. Proc. Natl Acad. Sci. USA 104, 8924–8929 (2007). References 69 and 70 are the first reports of the top-down approach for minichromosome generation in plants.
Frary, A. & Hamilton, C. M. Efficiency and stability of high molecular weight DNA transformation: an analysis in tomato. Transgen. Res. 10, 121–132 (2001).
Houben, A., Dawe, R. K., Jiang, J. & Schubert, I. Engineered plant minichromosomes: a bottom-up success? Plant Cell 20, 8–10 (2008).
Gaeta, R. T. & Krishnaswamy, L. in Plant Chromosome Engineering: Methods and Protocols, Methods in Molecular Biology Vol. 701 (ed. Birchler, J. A.) 131–146 (Springer, 2011).
Gaeta, R. T., Masonbrink, R. E., Krishnaswamy, L., Zhao, C. & Birchler, J. A. Synthetic chromosome platforms in plants. Annu. Rev. Plant Biol. 63, 307–330 (2012).
Xu, C., Cheng, Z. & Yu, W. Construction of rice mini-chromosome by telomere-mediated chromosomal truncation. Plant J. 70, 1070–1079 (2012).
Vega, J. M. et al. Agrobacterium-mediated transformation of maize (Zea mays L.) with Cre–lox site specific recombination cassettes in BIBAC vectors. Plant Mol. Biol. 66, 587–598 (2008).
Bibikova, M., Golic, M., Golic, K. G. & Carroll, D. Targeted chromosomal cleavage and mutagenesis in Drosophila using zinc-finger nucleases. Genetics 161, 1169–1175 (2002). This is the first report of using ZFN for genome engineering by linking the cleavage domain of the Fok I restriction enzyme to designed ZFPs.
Porteus, M. H. & Baltimore, D. Chimeric nucleases stimulate gene targeting in human cells. Science 300, 763 (2003).
Urnov, F. D. et al. Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature 435, 646–651 (2005).
Lloyd, A., Plaisier, C. L., Carroll, D. & Drews, G. N. Targeted mutagenesis using zinc-finger nucleases in Arabidopsis. Proc. Natl Acad. Sci. USA 102, 2232–2237 (2005). This paper is the first report of the use of ZFNs in plants.
Christian, M. et al. Targeting DNA double-strand breaks with TAL effector nucleases. Genetics 186, 757–761 (2010).
Li, T. et al. TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain. Nucleic Acids Res. 39, 359–372 (2010). References 81 and 82 are the first reports of the potential use of TALENs as site-specific endonucleases for selective genome cleavage.
Osakabe, K., Osakabe, Y. & Toki, S. Site-directed mutagenesis in Arabidopsis using custom-designed zinc finger nucleases. Proc. Natl Acad. Sci. USA 107, 12034–12039 (2010).
Zhang, F. et al. High frequency targeted mutagenesis in Arabidopsis thaliana using zinc finger nucleases. Proc. Natl Acad. Sci. USA 107, 12028–12033 (2010).
Townsend, J. A. et al. High-frequency modification of plant genes using engineered zinc-finger nucleases. Nature 459, 442–445 (2009).
Shukla, V. K. et al. Precise genome modification in the crop species Zea mays using zinc-finger nucleases. Nature 459, 437–443 (2009).
Curtin, S. J. et al. Targeted mutagenesis of duplicated genes in soybean with zinc-finger nucleases. Plant Physiol. 156, 466–473 (2011).
Mahfouz, M. M. et al. De novo-engineered transcription activator-like effector (TALE) hybrid nuclease with novel DNA binding specificity creates double-strand breaks. Proc. Natl Acad. Sci. USA 108, 2623–2628 (2011).
Zhang, Y. et al. Transcription activator-like effector nucleases enable efficient plant genome engineering. Plant Physiol. 161, 20–27 (2013).
Cermak, T. et al. Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Res. 39, e82 (2011).
Shan, Q. et al. Rapid and efficient gene modification in rice and Brachypodium using TALENs. Mol. Plant 6, 1365–1368 (2013).
Li, T., Liu, B., Spalding, M. H., Weeks, D. P. & Yang, B. High-efficiency TALEN-based gene editing produces disease-resistant rice. Nature Biotech. 30, 390–392 (2012).
De Pater, S., Neuteboom, L. W., Pinas, J. E., Hooykaas, P. J. J. & Van Der Zaal, B. J. ZFN-induced mutagenesis and gene-targeting in Arabidopsis through Agrobacterium-mediated floral dip transformation. Plant Biotechnol. J. 7, 821–835 (2009).
Puchta, H., Dujon, B. & Hohn, B. Two different but related mechanisms are used in plants for the repair of genomic double-strand breaks by homologous recombination. Proc. Natl Acad. Sci. USA 93, 5055–5060 (1996).
Gao, H. et al. Heritable targeted mutagenesis in maize using a designed endonuclease. Plant J. 61, 176–187 (2010).
D'Halluin, K., Vanderstraeten, C., Stals, E., Cornelissen, M. & Ruiter, R. Homologous recombination: a basis for targeted genome optimization in crop species such as maize. Plant Biotechnol. J. 6, 93–102 (2008).
Yang, M. et al. Targeted mutagenesis in the progeny of maize transgenic plants. Plant Mol. Biol. 70, 669–679 (2009).
Prieto, J. et al. The C terminal loop of the homing endonuclease I CreI is essential for site recognition, DNA binding and cleavage. Nucleic Acids Res. 35, 3262–3271 (2007).
Haurwitz, R. E., Jinek, M., Wiedenheft, B., Zhou, K. & Doudna, J. A. Sequence- and structure-specific RNA processing by a CRISPR endonuclease. Science 329, 1355–1358 (2010).
Deltcheva, E. et al. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 471, 602–607 (2011).
Jinek, M. et al. A programmable dual-RNA-Guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816–821 (2012). The first report that the engineered fusion of mature crRNAs to tracrRNA forms a two-RNA structure which directs dual RNA-guided genome editing.
Li, J.-F. et al. Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9. Nature Biotech. 31, 688–691 (2013).
Nekrasov, V., Staskawicz, B., Weigel, D., Jones, J. D. G. & Kamoun, S. Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease. Nature Biotech. 31, 691–693 (2013).
Shan, Q. et al. Targeted genome modification of crop plants using a CRISPR–Cas system. Nature Biotech. 31, 686–688 (2013). References 102–104 are the first reports of the application of the CRISPR–Cas system for targeted genome modification in plants.
Daniell, H. Molecular strategies for gene containment in transgenic crops. Nature Biotech. 20, 581–586 (2002).
Yau, Y. Y. & Stewart, C. N. Jr. Less is more: strategies to remove marker genes from transgenic plants. BMC Biotechnol. 13, 36 (2013).
Akbudak, M. A. & Srivastava, V. Improved FLP recombinase, FLPe, efficiently removes marker gene from transgene locus developed by Cre–lox mediated site-specific gene integration in rice. Mol. Biotechnol. 49, 82–89 (2011).
Khan, R. S., Nakamura, I. & Mii, M. Development of disease-resistant marker-free tomato by R/RS site-specific recombination. Plant Cell Rep. 30, 1041–1053 (2011).
Lloyd, A. M. & Davis, R. W. Functional expression of the yeast FLP/FRT site-specific recombination system in Nicotiana tabacum. Mol. Gen. Genet. 242, 653–657 (1994).
Luo, K. et al. 'GM-gene-deletor': fused loxP–FRT recognition sequences dramatically improve the efficiency of FLP or CRE recombinase on transgene excision from pollen and seed of tobacco plants. Plant Biotechnol. J. 5, 263–274 (2007).
Nandy, S. & Srivastava, V. Site-specific gene integration in rice genome mediated by the FLP–FRT recombination system. Plant Biotechnol. J. 9, 713–721 (2011).
Kolodii, G. The shuffling function of resolvases. Gene 269, 121–130 (2001).
Rao, M. R. et al. FLP/FRT recombination from yeast: application of a two gene cassette scheme as an inducible system in plants. Sensors 10, 8526–8535 (2010).
Zuo, J., Niu, Q. W., Moller, S. G. & Chua, N.-H. Chemical-regulated, site-specific DNA excision in transgenic plants. Nature Biotech. 19, 157–161 (2001).
Thomson, J. G. & Ow, D. W. Site-specific recombination systems for the genetic manipulation of eukaryotic genomes. Genesis 44, 465–476 (2006).
Wang, Y., Yau, Y. Y., Perkins-Balding, D. & Thomson, J. G. Recombinase technology: applications and possibilities. Plant Cell Rep. 30, 267–285 (2011).
Thomason, L. C., Calendar, R. & Ow, D. W. Gene insertion and replacement in Schizosaccharomyces pombe mediated by the Streptomyces bacteriophage phiC31 site-specific recombination system. Mol. Genet. Genomics 265, 1031–1038 (2001).
Moon, H. S. et al. Transgene excision in pollen using a codon optimized serine resolvase CinH–RS2 site-specific recombination system. Plant Mol. Biol. 75, 621–631 (2011).
Petolino, J. F. et al. Zinc finger nuclease-mediated transgene deletion. Plant Mol. Biol. 73, 617–628 (2010).
Zhou, Y., Yau, Y.-Y., Ow, D. W. & Wang, Y. Site-specific deletions in the tomato genome by the CinH–RS2 and ParA–MRS recombination systems. Plant Biotechnol. Rep. 6, 225–232 (2012).
Thomson, J. G. et al. ParA resolvase catalyzes site-specific excision of DNA from the Arabidopsis genome. Transgen. Res. 18, 237–248 (2009).
Thomson, J. G. et al. The Bxb1 recombination system demonstrates heritable transmission of site-specific excision in Arabidopsis. BMC Biotechnol. 12, 9 (2012).
Thomson, J. G., Chan, R., Thilmony, R., Yau, Y.-Y. & Ow, D. W. PhiC31 recombination system demonstrates heritable germinal transmission of site-specific excision from the Arabidopsis genome. BMC Biotechnol. 10, 17 (2010).
Antunes, M. S., Smith, J. J., Jantz, D. & Medford, J. I. Targeted DNA excision in Arabidopsis by a re-engineered homing endonuclease. BMC Biotechnol. 12, 86 (2012).
Blechl, A., Lin, J., Shao, M., Thilmony, R. & Thomson, J. The Bxb1 recombinase mediates site-specific deletion in transgenic wheat. Plant Mol. Biol. Rep. 30, 1357–1366 (2012).
Kempe, K. et al. Transgene excision from wheat chromosome by phage phiC31 integrase. Plant Mol. Biol. 72, 673–387 (2010).
Sang, Y., Millwood, R. J. & Stewart, C. N. Jr. Gene use restriction technologies for transgenic plant bioconfinement. Plant Biotechnol. J. 11, 649–658 (2013).
Schwille, P. Bottom-up synthetic biology: engineering in a tinkerer's world. Science 333, 1252–1254 (2011).
Antunes, M. S. et al. Programmable ligand detection system in plants through a synthetic signal transduction pathway. PLoS ONE 6, e16292 (2011).
Borak, B., Ort, D. R. & Burbaum, J. J. Energy and carbon accounting to compare bioenergy crops. Curr. Opin. Biotechnol. 24, 369–375 (2013).
Bradford, K. J. et al. Regulating transgenic crops sensibly: lessons from plant breeding, biotechnology and genomics. Nature Biotech. 23, 439–444 (2005).
Dhar, M. K., Kaul, S. & Kour, J. Towards the development of better crops by genetic transformation using engineered plant chromosomes. Plant Cell Rep. 30, 799–806 (2011).
Hirano, N. et al. Site-specific recombination system based on actinophage TG1 integrase for gene integration into bacterial genomes. Appl. Microbiol. Biotechnol. 89, 1877–1884 (2011).
Ghosh, P., Pannunzio, N. R. & Hatfull, G. F. Synapsis in phage Bxb1 integration: selection mechanism for the correct pair of recombination sites. J. Mol. Biol. 349, 331–348 (2005).
Blake, W. et al. Pairwise selection assembly for sequence-independent construction of long-length DNA. Nucleic Acids Res. 38, 2594 (2010).
Cha-aim, K., Fukunaga, T., Hoshida, H. & Akada, R. Reliable fusion PCR mediated by GC-rich overlap sequences. Gene 434, 43–49 (2009).
Quan, J. & Tian, J. Circular polymerase extension cloning of complex gene libraries and pathways. PLoS ONE 4, e6441 (2009).
Acknowledgements
The authors thank J. Haseloff, who provided much feedback on earlier drafts. They appreciate their respective universities for the freedom and resources to undertake this Review, including funding by Advanced Research Projects Agency-Energy to J.S.Y. and by the BioEnergy Science Center to C.N.S. The BioEnergy Science Center is a US Department of Energy (DOE) Bioenergy Research Center supported by the Office of Biological and Environmental Research in the DOE Office of Science. The authors appreciate the work of multiple anonymous reviewers. They thank J. Hinds and M. Rudis for their assistance on various drafts of the paper.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Competing interests
J.S.Y. is a principal in a start-up company. C.N.S.Jr and J.S.Y. have received grants and contracts from the private sector, which has an interest in plant biotechnology.
Related links
Supplementary information
Supplementary information S1 (table)
Synthetic promoters that have been designed for the regulation of transgene expression in plants (PDF 227 kb)
Glossary
- Agrobacterium tumefaciens-mediated transformation
-
The most common plant transformation method. It involves the transfer of genes of interest from A. tumefaciens vectors and the subsequent integration of these genes into plant nuclear genomes.
- Biolistics
-
A commonly used transformation method in which high velocity microprojectiles coated with gene constructs are used to deliver genes into cells and tissues.
- Targeted genome modification
-
The fusion of engineered DNA-binding proteins or domains with sequence specificities to effector domains that modify genetic sequences and/or gene expression.
- Genome editing
-
Genome modification achieved by the induction of a double-strand break in a specific genome site, followed by DNA-break repair and the generation of desired modifications (gene disruption, addition or correction).
- Homology-dependent gene silencing
-
A gene silencing phenomenon induced by homologous sequences at the transcriptional or post-transcriptional levels.
- Zinc-finger proteins
-
(ZFPs). DNA-binding protein domains that consist of a tandem array of 2–9 zinc-fingers, each of which recognizes approximately three bases of DNA sequence.
- Transcription activator-like effectors
-
(TALEs). Major virulence factors (containing an amino terminus, a unique type of central DNA-binding domain and a carboxyl terminus with the activation domain) that are secreted by the pathogenic Xanthomonas spp. bacterium when it infects plants. Their DNA-binding domains can be custom-designed to specifically bind to any DNA sequences.
- Seamless assembly
-
The precise joining of DNA fragments without the addition of intervening or unwanted nucleotides at the junctions.
- De novo DNA synthesis
-
The synthesis of continuous strands of DNA molecules using a laboratory instrument without the presence of pre-existing templates.
- Plant artificial chromosome
-
An engineered non-integrating vector that harbours large amounts of DNA (including telomeres, origins of replication, a centromere and genes of interest) and is transmissible in cell division after transformation into plant cells.
- Cre–loxP recombination system
-
A site-specific recombination system mediated by the Cre recombinase in a genome that contains pre-existing or pre-engineered loxP sites which are recognized by the Cre recombinase.
- Gene stacking
-
The accumulation of multiple trangenes of interest into the same plant genome for stacked traits.
- FLP–FRT systems
-
A recombination system in which the FLP recombinase specifically recognizes the FRT site and mediates excision of any sequence that is flanked by the FRT sites.
- B chromosomes
-
Supernumerary or accessory chromosomes that are heterochromatic. They do not contain functional genes and do not to pair with A chromosomes at meiosis.
- Zinc-finger nucleases
-
(ZFNs). Fusions of engineered zinc-finger arrays (that consist of 3–6 C2H2 fingers) to a non-specific DNA-cleavage domain of the FokI endonuclease.
- TALE nucleases
-
(TALENs). Fusions of truncated TALEs (containing an amino terminus, a custom-designed DNA-binding domain and a carboxyl terminus with the activation domain being removed) to a non-specific DNA-cleavage domain of the FokI endonuclease.
- Gene targeting
-
The incorporation of a transgene (or transgenes) of interest into one or more desired specific genomic loci for the permanent modification of plant genomes using homologous recombination (or another method) followed by the selection for a rare recombination event.
- Agroinfiltration
-
The most common transient transformation method in plants which uses injection or vacuum infiltration to transform genes into cells and tissues using Agrobacterium tumefaciens.
- Apomixes
-
The replacement of normal sexual reproduction by asexual reproduction without fertilization.
- Cleistogamy
-
A phenomenon in which certain plants propagate using non-opening, self-pollinating flowers.
Rights and permissions
About this article
Cite this article
Liu, W., Yuan, J. & Stewart Jr, C. Advanced genetic tools for plant biotechnology. Nat Rev Genet 14, 781–793 (2013). https://doi.org/10.1038/nrg3583
Published:
Issue Date:
DOI: https://doi.org/10.1038/nrg3583
This article is cited by
-
An orthogonalized PYR1-based CID module with reprogrammable ligand-binding specificity
Nature Chemical Biology (2024)
-
Heterologous mogrosides biosynthesis in cucumber and tomato by genetic manipulation
Communications Biology (2023)
-
Genetic engineering of plants for phytoremediation: advances and challenges
Journal of Plant Biochemistry and Biotechnology (2023)