Gene targeting and transgene stacking using intra genomic homologous recombination in plants
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- 作者：Sandeep Kumar ; Pierluigi Barone ; Michelle Smith
- 关键词：Gene targeting ; Plant transformation ; Transgene stacking ; Designed nuclease ; Intra genomic homologous recombination ; Somatic recombination
- 刊名：Plant Methods
- 出版年：2016
- 出版时间：December 2016
- 年：2016
- 卷：12
- 期：1
- 全文大小：1,119 KB
- 参考文献：1.Dockter C, Hansson M. Improving barley culm robustness for secured crop yield in a changing climate. J Exp Bot. 2015;66(12):3499–509. doi:10.1093/jxb/eru521 .CrossRef PubMed
2.Parry MA, Hawkesford MJ. An integrated approach to crop genetic improvement. J Integr Plant Biol. 2012;54(4):250–9. doi:10.1111/j.1744-7909.2012.01109.x .CrossRef PubMed
3.Bohra A, Sahrawat KL, Kumar S, Joshi R, Parihar AK, Singh U, et al. Genetics- and genomics-based interventions for nutritional enhancement of grain legume crops: status and outlook. J Appl Genet. 2015. doi:10.1007/s13353-014-0268-z .PubMed
4.Que Q, Chilton MD, de Fontes CM, He C, Nuccio M, Zhu T, et al. Trait stacking in transgenic crops: challenges and opportunities. GM Crops. 2010;1(4):220–9. doi:10.4161/gmcr.1.4.13439 .CrossRef PubMed
5.Siebert MW, Nolting SP, Hendrix W, Dhavala S, Craig C, Leonard BR, et al. Evaluation of corn hybrids expressing Cry1F, Cry1A.105, Cry2Ab2, Cry34Ab1/Cry35Ab1, and Cry3Bb1 against southern United States insect pests. J Econ Entomol. 2012;105(5):1825–34. doi:10.1603/Ec12155 .CrossRef PubMed
6.Zhang F, Maeder ML, Unger-Wallace E, Hoshaw JP, Reyon D, Christian M, et al. High frequency targeted mutagenesis in Arabidopsis thaliana using zinc finger nucleases. Proc Natl Acad Sci U S A. 2010;107(26):12028–33. doi:10.1073/pnas.0914991107 .PubMedCentral CrossRef PubMed
7.Liang Z, Zhang K, Chen K, Gao C. Targeted mutagenesis in Zea mays using TALENs and the CRISPR/Cas system. J Genet Genomics. 2014;41(2):63–8. doi:10.1016/j.jgg.2013.12.001 .CrossRef PubMed
8.Gao J, Wang G, Ma S, Xie X, Wu X, Zhang X, et al. CRISPR/Cas9-mediated targeted mutagenesis in Nicotiana tabacum. Plant Mol Biol. 2015;87(1–2):99–110. doi:10.1007/s11103-014-0263-0 .CrossRef PubMed
9.Gao HR, Smith J, Yang MZ, Jones S, Djukanovic V, Nicholson MG, et al. Heritable targeted mutagenesis in maize using a designed endonuclease. Plant J. 2010;61(1):176–87. doi:10.1111/j.1365-313X.2009.04041.x .CrossRef PubMed
10.Camerini-Otero RD, Hsieh P. Homologous recombination proteins in prokaryotes and eukaryotes. Annu Rev Genet. 1995;29:509–52. doi:10.1146/annurev.ge.29.120195.002453 .CrossRef PubMed
11.Wood RD. DNA repair in eukaryotes. Annu Rev Biochem. 1996;65:135–67. doi:10.1146/annurev.bi.65.070196.001031 .CrossRef PubMed
12.Lieberman-Lazarovich M, Levy AA. Homologous recombination in plants: an antireview. Methods Mol Biol. 2011;701:51–65. doi:10.1007/978-1-61737-957-4_3 .CrossRef PubMed
13.Waterworth WM, Drury GE, Bray CM, West CE. Repairing breaks in the plant genome: the importance of keeping it together. New Phytol. 2011;192(4):805–22. doi:10.1111/j.1469-8137.2011.03926.x .CrossRef PubMed
14.Puchta H, Fauser F. Synthetic nucleases for genome engineering in plants: prospects for a bright future. Plant J. 2014;78(5):727–41. doi:10.1111/tpj.12338 .CrossRef PubMed
15.Weeks DP, Spalding MH, Yang B. Use of designer nucleases for targeted gene and genome editing in plants. Plant Biotechnol J. 2015;. doi:10.1111/pbi.12448 .PubMed
16.Puchta H, Fauser F. Synthetic nucleases for genome engineering in plants: prospects for a bright future. Plant J. 2013;. doi:10.1111/tpj.12338 .PubMed
17.Osman K, Higgins JD, Sanchez-Moran E, Armstrong SJ, Franklin FC. Pathways to meiotic recombination in Arabidopsis thaliana. New Phytol. 2011;190(3):523–44. doi:10.1111/j.1469-8137.2011.03665.x .CrossRef PubMed
18.Puchta H. The repair of double-strand breaks in plants: mechanisms and consequences for genome evolution. J Exp Bot. 2005;56(409):1–14. doi:10.1093/jxb/eri025 .PubMed
19.Weinthal DM, Taylor RA, Tzfira T. Nonhomologous end joining-mediated gene replacement in plant cells. Plant Physiol. 2013;162(1):390–400. doi:10.1104/pp.112.212910 .PubMedCentral CrossRef PubMed
20.Chilton MD, Que Q. Targeted integration of T-DNA into the tobacco genome at double-stranded breaks: new insights on the mechanism of T-DNA integration. Plant Physiol. 2003;133(3):956–65. doi:10.1104/pp.103.026104 .PubMedCentral CrossRef PubMed
21.D’Halluin K, Ruiter R. Directed genome engineering for genome optimization. Int J Dev Biol. 2013;57(6–8):621–7. doi:10.1387/ijdb.130217kd .CrossRef PubMed
22.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 U S A. 1996;93(10):5055–60.PubMedCentral CrossRef PubMed
23.Paszkowski J, Baur M, Bogucki A, Potrykus I. Gene targeting in plants. EMBO J. 1988;7(13):4021–6.PubMedCentral PubMed
24.Cai CQ, Doyon Y, Ainley WM, Miller JC, Dekelver RC, Moehle EA, et al. Targeted transgene integration in plant cells using designed zinc finger nucleases. Plant Mol Biol. 2009;69(6):699–709. doi:10.1007/s11103-008-9449-7 .CrossRef PubMed
25.Nishizawa-Yokoi A, Nonaka S, Osakabe K, Saika H, Toki S. A universal positive-negative selection system for gene targeting in plants combining an antibiotic resistance gene and its antisense rna. Plant Physiol. 2015;169(1):362–70. doi:10.1104/pp.15.00638 .PubMedCentral CrossRef PubMed
26.Shimatani Z, Nishizawa-Yokoi A, Endo M, Toki S, Terada R. Positive-negative-selection-mediated gene targeting in rice. Front Plant Sci. 2014;5:748. doi:10.3389/fpls.2014.00748 .PubMedCentral PubMed
27.Kumar S, AlAbed D, Worden A, Novak S, Wu H, Ausmus C, et al. A modular gene targeting system for sequential transgene stacking in plants. J Biotechnol. 2015;207:12–20. doi:10.1016/j.jbiotec.2015.04.006 .CrossRef PubMed
28.Petolino JF, Kumar S. Transgenic trait deployment using designed nucleases. Plant Biotechnol J. 2015;. doi:10.1111/pbi.12457 .PubMed
29.Rivera AL, Gomez-Lim M, Fernandez F, Loske AM. Physical methods for genetic plant transformation. Phys Life Rev. 2012;9(3):308–45. doi:10.1016/j.plrev.2012.06.002 .CrossRef PubMed
30.Tzfira T, Citovsky V. Agrobacterium-mediated genetic transformation of plants: biology and biotechnology. Curr Opin Biotech. 2006;17(2):147–54. doi:10.1016/j.copbio.2006.01.009 .CrossRef PubMed
31.Taylor NJ, Fauquet CM. Microparticle bombardment as a tool in plant science and agricultural biotechnology. DNA Cell Biol. 2002;21(12):963–77. doi:10.1089/104454902762053891 .CrossRef PubMed
32.Pitzschke A. Agrobacterium infection and plant defense—transformation success hangs by a thread. Front Plant Sci. 2013;4:519. doi:10.3389/fpls.2013.00519 .PubMedCentral CrossRef PubMed
33.Arias RS, Filichkin SA, Strauss SH. Divide and conquer: development and cell cycle genes in plant transformation. Trends Biotechnol. 2006;24(6):267–73. doi:10.1016/j.tibtech.2006.04.007 .CrossRef PubMed
34.Delporte F, Jacquemin JM, Masson P, Watillon B. Insights into the regenerative property of plant cells and their receptivity to transgenesis: wheat as a research case study. Plant Signal Behav. 2012;7(12):1608–20.PubMedCentral CrossRef PubMed
35.Szabados L, Kovács I, Oberschall A, Ábrahám E, Kerekes I, Zsigmond L, et al. Distribution of 1000 sequenced T-DNA tags in the Arabidopsis genome. Plant J. 2002;32(2):233–42. doi:10.1046/j.1365-313X.2002.01417.x .CrossRef PubMed
36.Gelvin SB, Kim S-I. Effect of chromatin upon agrobacterium T-DNA integration and transgene expression. Biochimica et Biophysica Acta (BBA)—Gene Structure and Expression. 2007;1769(5–6):410–21. doi:http://dx.doi.org/10.1016/j.bbaexp.2007.04.005 .
37.Hiei Y, Ishida Y, Komari T. Progress of cereal transformation technology mediated by Agrobacterium tumefaciens. Front Plant Sci. 2014;5:628. doi:10.3389/fpls.2014.00628 .PubMedCentral CrossRef PubMed
38.Frame B, Main M, Schick R, Wang K. Genetic transformation using maize immature zygotic embryos. Methods Mol Biol. 2011;710:327–41. doi:10.1007/978-1-61737-988-8_22 .CrossRef PubMed
39.Kita Y, Nishizawa K, Takahashi M, Kitayama M, Ishimoto M. Genetic improvement of the somatic embryogenesis and regeneration in soybean and transformation of the improved breeding lines. Plant Cell Rep. 2007;26(4):439–47. doi:10.1007/s00299-006-0245-z .CrossRef PubMed
40.Puchta H, Hohn B. In planta somatic homologous recombination assay revisited: a successful and versatile, but delicate tool. Plant Cell. 2012;24(11):4324–31. doi:10.1105/tpc.112.101824 .PubMedCentral CrossRef PubMed
41.Swoboda P, Hohn B, Gal S. Somatic homologous recombination in planta—the recombination frequency is dependent on the allelic state of recombining sequences and may be influenced by genomic position effects. Mol Gen Genet. 1993;237(1–2):33–40.PubMed
42.Swoboda P, Gal S, Hohn B, Puchta H. Intrachromosomal homologous recombination in whole plants. EMBO J. 1994;13(2):484–9.PubMedCentral PubMed
43.Chiurazzi M, Ray A, Viret JF, Perera R, Wang XH, Lloyd AM, et al. Enhancement of somatic intrachromosomal homologous recombination in Arabidopsis by the HO endonuclease. Plant Cell. 1996;8(11):2057–66. doi:10.1105/tpc.8.11.2057 .PubMedCentral CrossRef PubMed
44.Siebert R, Puchta H. Efficient repair of genomic double-strand breaks by homologous recombination between directly repeated sequences in the plant genome. Plant Cell. 2002;14(5):1121–31.PubMedCentral CrossRef PubMed
45.Petolino JF, Worden A, Curlee K, Connell J, Strange Moynahan TL, Larsen C, et al. Zinc finger nuclease-mediated transgene deletion. Plant Mol Biol. 2010;73(6):617–28. doi:10.1007/s11103-010-9641-4 .CrossRef PubMed
46.Antunes MS, Smith JJ, Jantz D, Medford JI. Targeted DNA excision in Arabidopsis by a re-engineered homing endonuclease. BMC Biotechnol. 2012;12:86. doi:10.1186/1472-6750-12-86 .PubMedCentral CrossRef PubMed
47.Qi Y, Li X, Zhang Y, Starker CG, Baltes NJ, Zhang F, et al. Targeted deletion and inversion of tandemly arrayed genes in Arabidopsis thaliana using zinc finger nucleases. G3 (Bethesda). 2013;3(10):1707–15. doi:10.1534/g3.113.006270 .PubMedCentral CrossRef
48.Zhou H, Liu B, Weeks DP, Spalding MH, Yang B. Large chromosomal deletions and heritable small genetic changes induced by CRISPR/Cas9 in rice. Nucleic Acids Res. 2014;42(17):10903–14. doi:10.1093/nar/gku806 .PubMedCentral CrossRef PubMed
49.Rong YS, Golic KG. Gene targeting by homologous recombination in Drosophila. Science. 2000;288(5473):2013–8.CrossRef PubMed
50.Rong YS, Golic KG. A targeted gene knockout in Drosophila. Genetics. 2001;157(3):1307–12.PubMedCentral PubMed
51.Maggert KA, Gong WJ, Golic KG. Methods for homologous recombination in Drosophila. Methods Mol Biol. 2008;420:155–74. doi:10.1007/978-1-59745-583-1_9 .CrossRef PubMed
52.Bi X, Rong YS. Genome manipulation by homologous recombination in Drosophila. Brief Funct Genomic Proteomic. 2003;2(2):142–6.CrossRef PubMed
53.Kumar S, Fladung M. Controlling transgene integration in plants. Trends Plant Sci. 2001;6(4):155–9. doi:10.1016/S1360-1385(01)01890-8 .CrossRef PubMed
54.Fauser F, Roth N, Pacher M, Ilg G, Sanchez-Fernandez R, Biesgen C, et al. In planta gene targeting. Proc Natl Acad Sci U S A. 2012;109(19):7535–40. doi:10.1073/pnas.1202191109 .PubMedCentral CrossRef PubMed
55.Schiml S, Fauser F, Puchta H. The CRISPR/Cas system can be used as nuclease for in planta gene targeting and as paired nickases for directed mutagenesis in Arabidopsis resulting in heritable progeny. Plant J. 2014;80(6):1139–50. doi:10.1111/tpj.12704 .CrossRef PubMed
56.Ayar A, Wehrkamp-Richter S, Laffaire JB, Le Goff S, Levy J, Chaignon S, et al. Gene targeting in maize by somatic ectopic recombination. Plant Biotechnol J. 2013;11(3):305–14. doi:10.1111/Pbi.12014 .CrossRef PubMed
57.Even-Faitelson L, Samach A, Melamed-Bessudo C, Avivi-Ragolsky N, Levy AA. Localized egg-cell expression of effector proteins for targeted modification of the Arabidopsis genome. Plant J. 2011;68(5):929–37. doi:10.1111/j.1365-313X.2011.04741.x .CrossRef PubMed
58.Wang ZP, Xing HL, Dong L, Zhang HY, Han CY, Wang XC, et al. Egg cell-specific promoter-controlled CRISPR/Cas9 efficiently generates homozygous mutants for multiple target genes in Arabidopsis in a single generation. Genome Biol. 2015;16:144. doi:10.1186/s13059-015-0715-0 .PubMedCentral CrossRef PubMed
59.Mao Y, Zhang Z, Feng Z, Wei P, Zhang H, Botella JR, et al. Development of germ-line-specific CRISPR-Cas9 systems to improve the production of heritable gene modifications in Arabidopsis. Plant Biotechnol J. 2015. doi:10.1111/pbi.12468 . - 作者单位：Sandeep Kumar (1)
Pierluigi Barone (1)
Michelle Smith (1)
1. Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN, 46286, USA - 刊物主题：Plant Sciences; Biological Techniques;
- 出版者：BioMed Central
- ISSN：1746-4811
文摘
Modern agriculture has created a demand for plant biotechnology products that provide durable resistance to insect pests, tolerance of herbicide applications for weed control, and agronomic traits tailored for specific geographies. These transgenic trait products require a modular and sequential multigene stacking platform that is supported by precise genome engineering technology. Designed nucleases have emerged as potent tools for creating targeted DNA double strand breaks (DSBs). Exogenously supplied donor DNA can repair the targeted DSB by a process known as gene targeting (GT), resulting in a desired modification of the target genome. The potential of GT technology has not been fully realized for trait deployment in agriculture, mainly because of inefficient transformation and plant regeneration systems in a majority of crop plants and genotypes. This challenge of transgene stacking in plants could be overcome by Intra-Genomic Homologous Recombination (IGHR) that converts independently segregating unlinked donor and target transgenic loci into a genetically linked molecular stack. The method requires stable integration of the donor DNA into the plant genome followed by intra-genomic mobilization. IGHR complements conventional breeding with genetic transformation and designed nucleases to provide a flexible transgene stacking and trait deployment platform. Keywords Gene targeting Plant transformation Transgene stacking Designed nuclease Intra genomic homologous recombination Somatic recombination