BİTKİ ISLAHINDA CRISPR/CAS9 UYGULAMALARI

Year 2020, Volume: 3 Issue: 2, 32 - 40, 02.11.2020

Anıl Mehmet Baltacı , Mehmet Arslan

Abstract

Bitkiler için genom dizilerinin mevcudiyeti ve genom düzenleme teknolojisindeki ilerlemeler, hemen hemen her türlü istenilen özellik açısından ıslah olanaklarını artırmıştır. ZFN (Zinc Finger Nucleas) ve TALEN (Transcription Activator-Like Effector Nuclease) gibi genom düzenleme teknolojilerindeki gelişmeler moleküler düzeyde ilgilenilen herhangi bir genin düzenlenmesini mümkün kılmıştır. Bunların aksine CRISPR / Cas9 genom düzenleme yöntemi basit tasarım ve kolay klonlama yöntemlerini içermektedir. Cas9 genomdaki birden fazla bölgeyi hedefleyen farklı kılavuz (guide) RNA'lar ile farklı birden fazla gen bölgesine müdahale edilebilmektedir. CRISPR-Cas9 modülünde hedef özgüllüğünü geliştirmek ve hedef dışı bölünmeyi azaltmak birkaç farklı modifiye Cas9 kaseti kullanılmaktadır. Ayrıca farklı bakteri türlerinden elde edilen Cas9 enzimlerinin mevcudiyeti gen düzenleme yöntemlerinin özgüllüğünü ve verimliliğini arttırmak için yeni seçenekler sunmaktadır. Bu çalışmada, bitki ıslahçılarının CRISPR / Cas9 temelli genom düzenleme araçlarını kullanarak moleküler düzyde bitki ıslahı için mevcut durumu özetlemekte ve CRISPR / Cas9'un biyotik ve abiyotik stres toleransını artırmak için kullanıldığı çalışmaları sunmaktadır.

Keywords

TALEN, ZFN, biyotik stres, abiyotik stres, bitki ıslahı, CRISPR

CRISPR / Cas9 Applications In Plant Breeding

Abstract

The availability of genome sequences for plants and advances in genome editing technology have increased breeding possibilities for almost all kinds of desired traits. Advances in genome editing technologies such as ZFN (Zinc Finger Nucleas) and TALEN (Transcription Activator-Like Effector Nuclease) have made it possible to edit any gene of interest at the molecular level. On the contrary, the CRISPR / Cas9 genome editing method includes simple design and easy cloning methods. With different guide RNAs targeting more than one region in the Cas9 genome, multiple different gene regions can be intervened. Several different modified Cas9 cassettes are used in the CRISPR-Cas9 module to improve target specificity and reduce off-target cleavage. In addition, the availability of Cas9 enzymes from different bacterial species offers new options to increase the specificity and efficiency of gene editing methods. This study summarizes the current situation for plant breeding at the molecular level using the genome editing tools of plant breeders based on CRISPR / Cas9 and presents studies using CRISPR / Cas9 to increase biotic and abiotic stress tolerance.

Keywords

CRISPR, TALEN, ZFN, biotic stress, abiotic stress, plant breeding

References

• Ali, Z., Abul-Faraj, A., Li, L., Ghosh, N., Piatek, M., Mahjoub, A., ... & Dinesh-Kumar, S. 2015. Efficient virus-mediated genome editing in plants using the CRISPR/Cas9 system. Molecular plant, 8(8), 1288-1291.
• Butler, N. M., Baltes, N. J., Voytas, D. F., and Douches, D. S. 2016. Geminivirus-mediated genome editing in potato (Solanum tuberosum L.) using sequence-specific nucleases. Frontiers in plant science, 7, 1045.
• Chen, K., and Gao, C. 2013. TALENs: customizable molecular DNA scissors for genome engineering of plants. Journal of Genetics and Genomics, 40(6), 271-279.
• Cermak, T., Doyle, E. L., Christian, M., Wang, L., Zhang, Y., Schmidt, C., ... and Voytas, D. F. 2011. Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic acids research, 39(12), e82-e82.
• Engler, C., Kandzia, R., and Marillonnet, S. 2008. A one pot, one step, precision cloning method with high throughput capability. PloS one, 3(11), e3647.
• Feng, Z., Mao, Y., Xu, N., Zhang, B., Wei, P., Yang, D. L., ... and Zeng, L. 2014. Multigeneration analysis reveals the inheritance, specificity, and patterns of CRISPR/Cas-induced gene modifications in Arabidopsis. Proceedings of the National Academy of Sciences, 111(12), 4632-4637.
• Fauser, F., Schiml, S., and Puchta, H. 2014. Both CRISPR/C as‐based nucleases and nickases can be used efficiently for genome engineering in Arabidopsis thaliana. The Plant Journal, 79(2), 348-359.
• Feng, Z., Zhang, B., Ding, W., Liu, X., Yang, D. L., Wei, P., ... and Zhu, J. K. 2013. Efficient genome editing in plants using a CRISPR/Cas system. Cell research, 23(10), 1229-1232.
• Gaj, T., Gersbach, C. A., and Barbas III, C. F. 2013. ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends in biotechnology, 31(7), 397-405.
• Govindan, G., and Ramalingam, S. 2016. Programmable site‐specific nucleases for targeted genome engineering in higher eukaryotes. Journal of cellular physiology, 231(11), 2380-2392.
• Gao, Y., and Zhao, Y. 2014. Self‐processing of ribozyme‐flanked RNAs into guide RNAs in vitro and in vivo for CRISPR‐mediated genome editing. Journal of integrative plant biology, 56(4), 343-349.
• Gibson, D. G., Young, L., Chuang, R. Y., Venter, J. C., Hutchison, C. A., and Smith, H. O. 2009. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nature methods, 6(5), 343-345.
• Gil‐Humanes, J., Wang, Y., Liang, Z., Shan, Q., Ozuna, C. V., Sánchez‐León, S., ... and Voytas, D. F. 2017. High‐efficiency gene targeting in hexaploid wheat using DNA replicons and CRISPR/Cas9. The Plant Journal, 89(6), 1251-1262.
• Hiei, Y., and Komari, T. 2008. Agrobacterium-mediated transformation of rice using immature embryos or calli induced from mature seed. Nature protocols, 3(5), 824-834.
• Ishino, Y., Shinagawa, H., Makino, K., Amemura, M., and Nakata, A. 1987. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. Journal of bacteriology, 169(12), 5429-5433.
• Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., and Charpentier, E. 2012. A programmable dual-RNA–guided DNA endonuclease in adaptive bacterial immunity. science, 337(6096), 816-821.
• Jiang, W., Zhou, H., Bi, H., Fromm, M., Yang, B., and Weeks, D. P. 2013. Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice. Nucleic acids research, 41(20), e188-e188.
• Janga, M. R., Campbell, L. M., and Rathore, K. S. 2017. CRISPR/Cas9-mediated targeted mutagenesis in upland cotton (Gossypium hirsutum L.). Plant Molecular Biology, 94(4-5), 349-360.
• Jaganathan, D., Ramasamy, K., Sellamuthu, G., Jayabalan, S., and Venkataraman, G. 2018. CRISPR for crop improvement: an update review. Frontiers in plant science, 9, 985.
• Kim, D., Alptekin, B., and Budak, H. 2018. CRISPR/Cas9 genome editing in wheat. Functional and integrative genomics, 18(1), 31-41.
• Kapusi, E., Corcuera-Gómez, M., Melnik, S., and Stoger, E. 2017. Heritable genomic fragment deletions and small indels in the putative ENGase gene induced by CRISPR/Cas9 in barley. Frontiers in plant science, 8, 540.
• Li, T., Liu, B., Spalding, M. H., Weeks, D. P., and Yang, B. 2012. High-efficiency TALEN-based gene editing produces disease-resistant rice. Nature biotechnology, 30(5), 390.
• Liu, X., Wu, S., Xu, J., Sui, C., and Wei, J. 2017. Application of CRISPR/Cas9 in plant biology. Acta pharmaceutica sinica B, 7(3), 292-302. Li, J. F., Norville, J. E., Aach, J., McCormack, M., Zhang, D., Bush, J., ... and Sheen, J. 2013. Multiplex and homologous recombination–mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9. Nature biotechnology, 31(8), 688-691.
• Lawrenson, T., Shorinola, O., Stacey, N., Li, C., Østergaard, L., Patron, N., ... and Harwood, W. 2015. Induction of targeted, heritable mutations in barley and Brassica oleracea using RNA-guided Cas9 nuclease. Genome biology, 16(1), 258.
• Lloyd, A., Plaisier, C. L., Carroll, D., and Drews, G. N. 2005. Targeted mutagenesis using zinc-finger nucleases in Arabidopsis. Proceedings of the National Academy of Sciences, 102(6), 2232-2237.
• Lowder, L. G., Zhang, D., Baltes, N. J., Paul, J. W., Tang, X., Zheng, X., ... and Qi, Y. 2015. A CRISPR/Cas9 toolbox for multiplexed plant genome editing and transcriptional regulation. Plant physiology, 169(2), 971-985.
• Liu, D., Chen, X., Liu, J., Ye, J., and Guo, Z. 2012. The rice ERF transcription factor OsERF922 negatively regulates resistance to Magnaporthe oryzae and salt tolerance. Journal of experimental botany, 63(10), 3899-3911.
• Liang, Z., Chen, K., Li, T., Zhang, Y., Wang, Y., Zhao, Q., ... and Gao, C. 2017. Efficient DNA-free genome editing of bread wheat using CRISPR/Cas9 ribonucleoprotein complexes. Nature communications, 8(1), 1-5.
• Liang, Z., Chen, K., Zhang, Y., Liu, J., Yin, K., Qiu, J. L., and Gao, C. 2018. Genome editing of bread wheat using biolistic delivery of CRISPR/Cas9 in vitro transcripts or ribonucleoproteins. Nature protocols, 13(3), 413.
• Li, F., Fan, G., Lu, C., Xiao, G., Zou, C., Kohel, R. J., ... and Liang, X. 2015. Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution. Nature biotechnology, 33(5), 524-530.
• Ma, X., Zhu, Q., Chen, Y., and Liu, Y. G. 2016. CRISPR/Cas9 platforms for genome editing in plants: developments and applications. Molecular plant, 9(7), 961-974.
• Malzahn, A., Lowder, L., and Qi, Y. 2017. Plant genome editing with TALEN and CRISPR. Cell and bioscience, 7(1), 21. Mojica, F. J., García-Martínez, J., and Soria, E. 2005. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. Journal of molecular evolution, 60(2), 174-182.
• Mao, Y., Zhang, H., Xu, N., Zhang, B., Gou, F., and Zhu, J. K. 2013. Application of the CRISPR–Cas system for efficient genome engineering in plants. Molecular plant, 6(6), 2008-2011.
• Ma, X., Chen, L., Zhu, Q., Chen, Y., and Liu, Y. G. 2015a. Rapid decoding of sequence-specific nuclease-induced heterozygous and biallelic mutations by direct sequencing of PCR products. Molecular plant, 8(8), 1285-1287.
• Ma, X., Zhang, Q., Zhu, Q., Liu, W., Chen, Y., Qiu, R., ... and Xie, Y. 2015b. A robust CRISPR/Cas9 system for convenient, high-efficiency multiplex genome editing in monocot and dicot plants. Molecular plant, 8(8), 1274-1284.
• Nishimasu, H., Ran, F. A., Hsu, P. D., Konermann, S., Shehata, S. I., Dohmae, N., ... and Nureki, O. 2014. Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell, 156(5), 935-949. Nekrasov, V., Staskawicz, B., Weigel, D., Jones, J. D., and Kamoun, S. 2013. Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease. Nature biotechnology, 31(8), 691-693.
• Oliveira, M. A. C., Duarte, J. B., Morello, C. D. L., Suassuna, N. D., and Oliveira, A. B. 2016. Mixed inheritance in the genetic control of ramulosis (Colletotrichum gossypii var. cephalosporioides) resistance in cotton. Embrapa Algodão-Artigo em periódico indexado (ALICE). Ricroch, A., Clairand, P., and Harwood, W. 2017. Use of CRISPR systems in plant genome editing: toward new opportunities in agriculture. Emerging Topics in Life Sciences, 1(2), 169-182.
• Stephens, J., and Barakate, A. 2017. Gene editing technologies–ZFNs, TALENs, and CRISPR/Cas9. Shan, Q., Wang, Y., Li, J., Zhang, Y., Chen, K., Liang, Z., ... and Gao, C. 2013. Targeted genome modification of crop plants using a CRISPR-Cas system. Nature biotechnology, 31(8), 686-688.
• Svitashev, S., Young, J. K., Schwartz, C., Gao, H., Falco, S. C., and Cigan, A. M. 2015. Targeted mutagenesis, precise gene editing, and site-specific gene insertion in maize using Cas9 and guide RNA. Plant physiology, 169(2), 931-945.
• Shimatani, Z., Kashojiya, S., Takayama, M., Terada, R., Arazoe, T., Ishii, H., ... and Ezura, H. 2017. Targeted base editing in rice and tomato using a CRISPR-Cas9 cytidine deaminase fusion. Nature biotechnology, 35(5), 441-443.
• Shen, L., Hua, Y., Fu, Y., Li, J., Liu, Q., Jiao, X., ... and Wang, K. 2017. Rapid generation of genetic diversity by multiplex CRISPR/Cas9 genome editing in rice. Science China Life Sciences, 60(5), 506-515.
• Shan, Q., Wang, Y., Li, J., and Gao, C. 2014. Genome editing in rice and wheat using the CRISPR/Cas system. Nature protocols, 9(10), 2395-2410.
• Voytas, D. F. 2013. Plant genome engineering with sequence-specific nucleases. Annual review of plant biology, 64.
• Waltz, E. 2018. With a free pass, CRISPR-edited plants reach market in record time. Nature Biotechnology, 36(1), 6-8.
• Wong, G. K. S., Wang, J., Tao, L., Tan, J., Zhang, J., Passey, D. A., and Yu, J. 2002. Compositional gradients in Gramineae genes. Genome research, 12(6), 851-856.
• Wang, Z. P., Xing, H. L., Dong, L., Zhang, H. Y., Han, C. Y., Wang, X. C., and Chen, Q. J. 2015. Egg cell-specific promoter-controlled CRISPR/Cas9 efficiently generates homozygous mutants for multiple target genes in Arabidopsis in a single generation. Genome biology, 16(1), 144.
• Wang, Y., Cheng, X., Shan, Q., Zhang, Y., Liu, J., Gao, C., and Qiu, J. L. 2014. Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew. Nature biotechnology, 32(9), 947-951.
• Wang, W., Pan, Q., He, F., Akhunova, A., Chao, S., Trick, H., and Akhunov, E. 2018. Transgenerational CRISPR-Cas9 activity facilitates multiplex gene editing in allopolyploid wheat. The CRISPR journal, 1(1), 65-74.
• Xie, K., and Yang, Y. 2013. RNA-guided genome editing in plants using a CRISPR–Cas system. Molecular plant, 6(6), 1975-1983. Xing, H. L., Dong, L., Wang, Z. P., Zhang, H. Y., Han, C. Y., Liu, B., ... and Chen, Q. J. 2014. A CRISPR/Cas9 toolkit for multiplex genome editing in plants. BMC plant biology, 14(1), 327.
• Yin, K., Han, T., Liu, G., Chen, T., Wang, Y., Yu, A. Y. L., & Liu, Y. 2015. A geminivirus-based guide RNA delivery system for CRISPR/Cas9 mediated plant genome editing. Scientific reports, 5, 14926.
• Zhang, Z., Ge, X., Luo, X., Wang, P., Fan, Q., Hu, G., ... and Wu, J. 2018. Simultaneous editing of two copies of Gh14-3-3d confers enhanced transgene-clean plant defense against Verticillium dahliae in allotetraploid upland cotton. Frontiers in plant science, 9, 842.
• Zhang, Z., Mao, Y., Ha, S., Liu, W., Botella, J. R., and Zhu, J. K. 2016. A multiplex CRISPR/Cas9 platform for fast and efficient editing of multiple genes in Arabidopsis. Plant cell reports, 35(7), 1519-1533.
• Zhou, H., Liu, B., Weeks, D. P., Spalding, M. H., and Yang, B. 2014. Large chromosomal deletions and heritable small genetic changes induced by CRISPR/Cas9 in rice. Nucleic acids research, 42(17), 10903-10914.
• Zong, Y., Wang, Y., Li, C., Zhang, R., Chen, K., Ran, Y., ... and Gao, C. 2017. Precise base editing in rice, wheat and maize with a Cas9-cytidine deaminase fusion. Nature biotechnology, 35(5), 438.