CRISPR/Cas9-mediated Genome Engineering and Its Application in Plant Variety Improvement

doi:10.11924/j.issn.1000-6850.casb15080140

Abstract

Abstract: Genome editing using targetable nucleases is an emerging technology for the precise genome modification. The CRISPR (clustered regularly interspaced short palindromic repeats) system, which appeared in 2013, has been modified to serve as RNA-guided endonuclease (known as CRISPR/Cas9). CRISPR/Cas9 has been developed into the third generation of genome editing technology, which is widely used in genome editing among varieties of species including plants with high efficiency and specificity. Furthermore, owing to its simplicity, convenience, and flexibility, CRISPR/Cas9 technology has dramatically accelerated genetic engineering and functional genomics, brought a revolutionary change in every research field of life science studies. This review briefly introduced the emergence and developing of CRISPR/Cas9, described the mechanism of CRISPR/Cas9 mediated genome editing, summarized the application of this tool in crop breeding that aimed at improving crop quality and yield. Finally, we discussed the prospect and application value of CRISPR/Cas9 in crop breeding, so as to provide a theory basis for its use in novel germplasm innovation and crop breeding improvement.

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References

[1] Yamamoto, T., Targeted Genome Editing Using Site-Specific Nucleases. Japan: Springer Tokyo Heidelberg New York Dordrecht London.2014.
[2] Capecchi, M.R., Altering the genome by homologous recombination. Science, 1989. 244(4910): 1288-92.
[3] Hsu, P.D., E.S. Lander, and F. Zhang, Development and applications of CRISPR-Cas9 for genome engineering. Cell, 2014. 157(6): 1262-78.
[4] Urnov, F.D., et al., Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature, 2005. 435(7042): 646-51.
[5] Miller, J.C., et al., An improved zinc-finger nuclease architecture for highly specific genome editing. Nat Biotechnol, 2007. 25(7): 778-85.
[6] Christian, M., et al., Targeting DNA double-strand breaks with TAL effector nucleases. Genetics, 2010. 186(2): 757-61.
[7] Miller, J.C., et al., A TALE nuclease architecture for efficient genome editing. Nat Biotechnol, 2011. 29(2): 143-8.
[8] Boch, J., et al., Breaking the code of DNA binding specificity of TAL-type III effectors. Science, 2009. 326(5959): 1509-12.
[9] Cong, L., et al., Multiplex genome engineering using CRISPR/Cas systems. Science, 2013. 339(6121): 819-23.
[10] Mali, P., et al., RNA-guided human genome engineering via Cas9. Science, 2013. 339(6121): 823-6.
[11] Mali, P., et al., CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat Biotechnol, 2013. 31(9): 833-8.
[12] Li, J.F., et al., Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9. Nat Biotechnol, 2013. 31(8): 688-91.
[13] Nekrasov, V., et al., Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease. Nature Biotechnology, 2013. 31(8): 691-693.
[14] Konermann, S., et al., Optical control of mammalian endogenous transcription and epigenetic states. Nature, 2013. 500(7463): 472-6.
[15] Mendenhall, E.M., et al., Locus-specific editing of histone modifications at endogenous enhancers. Nat Biotechnol, 2013. 31(12): 1133-6.
[16] Ishino, Y., et al., NUCLEOTIDE-SEQUENCE OF THE IAP GENE, RESPONSIBLE FOR ALKALINE-PHOSPHATASE ISOZYME CONVERSION IN ESCHERICHIA-COLI, AND IDENTIFICATION OF THE GENE-PRODUCT. Journal of Bacteriology, 1987. 169(12): 5429-5433.
[17] Nakata, A., M. Amemura, and K. Makino, Unusual nucleotide arrangement with repeated sequences in the Escherichia coli K-12 chromosome. Journal of Bacteriology, 1989. 171(6): 3553-3556.
[18] Groenen, P.M.A., et al., Nature of DNA polymorphism in the direct repeat cluster of Mycobacterium-tuberculosis; application for strain differentiation by a novel typing method. Molecular Microbiology, 1993. 10(5): 1057-1065.
[19] Mojica, F.J.M., G. Juez, and F. Rodriguezvalera, TRANSCRIPTION AT DIFFERENT SALINITIES OF HALOFERAX-MEDITERRANEI SEQUENCES ADJACENT TO PARTIALLY MODIFIED PSTI SITES. Molecular Microbiology, 1993. 9(3): 613-621.
[20] Mojica, F.J.M., et al., Long stretches of short tandem repeats are present in the largest replicons of the Archaea Haloferax mediterranei and Haloferax volcanii and could be involved in replicon partitioning. Molecular Microbiology, 1995. 17(1): 85-93.
[21] Jansen, R., et al., Identification of a novel family of sequence repeats among prokaryotes. OMICS A Journal of Integrative Biology, 2002. 6(1): 23-33.
[22] Jansen, R., et al., Identification of genes that are associated with DNA repeats in prokaryotes. Molecular Microbiology, 2002. 43(6): 1565-1575.
[23] Mojica, F.J.M., et al., Biological significance of a family of regularly spaced repeats in the genomes of Archaea, bacteria and mitochondria. Molecular Microbiology, 2000. 36(1): 244-246.
[24] Juillerat, A., et al., Comprehensive analysis of the specificity of transcription activator-like effector nucleases. Nucleic Acids Res, 2014. 42(8): 5390-402.
[25] Jinek, M., et al., A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity. Science, 2012. 337(6096): 816-821.
[26] Shen, B., et al., Generation of gene-modified mice via Cas9/RNA-mediated gene targeting. Cell Research, 2013. 23(5): 720-723.
[27] Jiang, W., et al., RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nature Biotechnology, 2013. 31(3): 233-239.
[28] Hwang, W.Y., et al., Efficient genome editing in zebrafish using a CRISPR-Cas system. Nature Biotechnology, 2013. 31(3): 227-229.
[29] Yang, H., et al., One-step generation of mice carrying reporter and conditional alleles by CRISPR/Cas-mediated genome engineering. Cell, 2013. 154(6): 1370-9.
[30] Cheng, A.W., et al., Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system. Cell Res, 2013. 23(10): 1163-71.
[31] Xie, K., et al., Research Progress of Genome Editing in Plants. Journal of Chinese Biotechnology, 2013. 33(6): 99-104.
[32] Xie, K., B. Minkenberg, and Y. Yang, Boosting CRISPR/Cas9 multiplex editing capability with the endogenous tRNA-processing system. Proceedings of the National Academy of Sciences of the United States of America, 2015. 112(11): 3570-3575.
[33] Nishimasu, H., et al., Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell, 2014. 156(5): 935-49.
[34] Jinek, M., et al., A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science, 2012. 337(6096): 816-21.
[35] Wilkinson, R. and B. Wiedenheft, A CRISPR method for genome engineering. F1000Prime Rep, 2014. 6: 3.
[36] 刘思也, 夏., 一种新的由CRISPR/Cas系统介导的基因组靶向修饰技术. 中国生物工程杂志, 2013. 33(10): 117-123.
[37] Sander, J.D. and J.K. Joung, CRISPR-Cas systems for editing, regulating and targeting genomes. Nat Biotechnol, 2014. 32(4): 347-55.
[38] 郑小梅,张晓立,于建东,郑平,孙际宾, CRISPR-Cas9介导的基因组编辑技术的研究进展. 生物技术进展, 2015(01): 1-9 78-79.
[39] 刘忠松, 作物遗传育种研究进展Ⅲ.作物基因工程与基因组编辑. 作物研究, 2014(03): 332-337.
[40] 瞿礼嘉,郭冬姝,张金喆,秦跟基, CRISPR/Cas系统在植物基因组编辑中的应用. 生命科学, 2015. 27(1): 64-70.
[41] Shan, Q., et al., Targeted genome modification of crop plants using a CRISPR-Cas system. Nature Biotechnology, 2013. 31(8): 686-688.
[42] Kabin, X. and Y. Yinong, RNA-Guided Genome Editing in Plants Using a CRISPRCas System. Molecular Plant, 2013. 6(6): 1975-1983.
[43] Jiang, W., et al., Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice. Nucleic Acids Research, 2013. 41(20):e188
[44] Gao, J., et al., CRISPR/Cas9-mediated targeted mutagenesis in Nicotiana tabacum. Plant Molecular Biology, 2015. 87(1-2): 99-110.
[45] Jacobs, T.B., et al., Targeted genome modifications in soybean with CRISPR/Cas9. Bmc Biotechnology, 2015. 15:16
[46] Upadhyay, S.K., et al., RNA-Guided Genome Editing for Target Gene Mutations in Wheat. G3-Genes Genomes Genetics, 2013. 3(12): 2233-2238.
[47] Liang, Z., et al., Targeted Mutagenesis in Zea mays Using TALENs and the CRISPR/Cas System. Journal of Genetics and Genomics, 2014. 41(2): 63-68.
[48] Frampton, R.A., A.R. Pitman, and P.C. Fineran, Advances in bacteriophage-mediated control of plant pathogens. International journal of microbiology, 2012. 2012: 326452-326452.
[51] Osakabe, Y. and K. Osakabe, Genome Editing with Engineered Nucleases in Plants. Plant and Cell Physiology, 2015. 56(3): 389-400.
[49] 曾秀英,侯学文.CRISPR/Cas9 基因组编辑技术在植物基因功能研究及植物改良中的应用[J].植物生理学报,2015,51(9):1351-1358
[50] 程曦,王文义,邱金龙.基因组编辑:植物生物技术的机遇与挑战[J]. 生物技术通报,2015,4:25-33.
[52] 谢科,饶力群,李红伟,等.基因组编辑技术在植物中的研究进展与应用前景[J].中国生物工程杂志,2013,33(6):99-104.
[53] 赵欣,胡军.CRISPR/Cas9 基因编辑系统及其在植物中的研究进展 [J].中国农学通报,2015,31(12):187-192