SDRP Journal of Plant Science

ISSN: 2573-7988

VOLUME: 2 ISSUE: 1

Application of precise genome editing in plants


Co-Authors

Muhamed Adem, Tileye Feyissa, Dereje Beyene

Citation

Muhamed Adem, Application of precise genome editing in plants(2017)SDRP Journal of Plant Science 2(1)

Abstract

Genome engineering, the ability to manipulate and alter DNA sequences in living cells is entering to its golden age. This is due to the advent of quickly advancing techniques that enable to engineer the genome with significant impact. Many of the plants, yeast strains and filamentous fungi industrially relevant for enormous biotechnological applications are non-domesticated difficult to engineer, have intricate genomes and have little molecular tools, making their genome engineering a complex task.  But precise genome editing which mimics the naturally occurring mutations has been used to overcome the biological engineering challenges posed by these organisms. Application areas of precise genome editing are diverse and potentially limitless as it is capable of altering any component of any genome.  The technique enables to open the genome like a book and proceed to words; in this case the DNA sequences then engineer the sequences to end up with the desired product. Focus areas of precise genome editing includes but not limited to; genome engineering, knockout, activation, RNA editing, in disease models, gene drive, biomedicine, gene function and in vitro gene depletion. With precise genome editing approach particularly Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR), there are visions of another green revolution - where plant yields could be improved significantly and worries might fade about how to feed the world in 2050 with projected population of nine billion people. For various applications precise genome editing has been successfully employed in several plants including; Arabidopsis thaliana, Nicotiana tobacum, sweet orange, rice, wheat, tomato, soybean, maize, sorghum and popular. Although CRISPR/Cas9 is a rising star in genome editing taking the technology to its full potential requires tackling off-target mutations among others. 

Key words:  CRISPR/Cas9, Double strand breaks, Genome engineering, Targeted mutagenesis

References

  1. Dimas J. Precise genome editing may improve rice crops, 2015. Source

    View Article           

  2. Walsh R, Hochedlinger, K. A variant CRISPR-Cas9 system adds versatility to genome engineering. PNAS , 2013;110:39, 15514-15515. doi: 10.1073/pnas.1314697110

    View Article           

  3. Boch J, Sholze H, Schornack S, Landgraf A, and Hahn S. Breaking the code of DNA binding specificity of TAL-type III effectors. Science. 2009;326:1509-12. doi: 10.1126/science.1178811.

    View Article           

  4. Kim H and Kim JS.2014.A guide to genome engineering with programmable nucleases. Nat.Rev.Genet. 2014; 15: 321?334. doi:10.1038/nrg3686

    View Article           

  5. Segal D, Meckler J. Genome Engineering at the Dawn of the Golden Age . 2003. doi: 10.1146/annurev-genom-091212-153435

    View Article           

  6. Estrela R, Cate J.H.D. Energy biotechnology in the CRISPR-Cas9 era. Elsevier Current Opinion in Biotechnology 2016; 38:79?84. doi: 10.1016/j.copbio.2016.01.005.

    View Article           

  7. Ran F, Hsu P, Lin CY, Gootenberg J, Konermann S, Trevino A. Double Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing Specificity. Cell. 2013; 154:1380-1389. doi:10.1016/j.cell.2013.08.021

    View Article           

  8. Gaj T, Gersbach CA, Barbas CF. ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol. 2013; 31:397?405. doi: 10.1016/j.tibtech.2013.04.004. Epub 2013 May 9.

    View Article           

  9. Christian M, Targeted mutagenesis of Arabidopsis thaliana using engineered TAL effector nucleases. G3 (Bethesda). 2013 3:1697?1705. PMid:23979944 PMCid:PMC3789794

    View Article      PubMed/NCBI     

  10. Liang Z, Zhang K, Chen KL, Gao CX. Targeted mutagenesis in Zea mays using TALENs and the CRISPR/Cas system, J. Genet. Genomics. 2014; 41: 63?68. doi: 10.1016/j.jgg.2013.12.001. Epub 2013 Dec 14.

    View Article           

  11. Fan D, Liu T, Li C, Jiao B, Li S, Hou Y, et al. Efficient CRISPR/Cas9-mediated Targeted Mutagenesis in Populus in the First Generation. Sci. Rep.2015; 5: 12217. doi: 10.1038/srep12217.

    View Article           

  12. Jiang WZ, Zhou HB, Bi HH, Fromm M, Yang B, Weeks DP. 2013. Demonstration of RISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice, Nucleic Acids Res.2013; 41: 1?12. doi: 10.1093/nar/gkt780

    View Article           

  13. Xing HL, Dong L, Wang ZP, Zhang HY, Han CY, Liu B, et al. A CRISPR/Cas9 toolkit for multiplex genome editing in plants. BMC Plant Biol. 2014; 14:327. doi: 10.1186/s12870-014-0327-y.

    View Article           

  14. Jacobs TB, LaFayette PR, Schmitz RJ, Parrott WA. Targeted genome modifications in soybean with CRISPR/Cas9. BMC Biotechnology. 2015; 15:16. doi 10.1186/s12896-015-0131-2

    View Article           

  15. Visk D. CRISPR Applications in Plants, A Report from the Plant and Animal Genomics Conference, January 14-18, 2017 San Diego, Ca, USA.

  16. Yong E . "The Revolutionary Gene Editing Technique That Reveals Cancer's Weaknesses". The Atlantic. 2015

  17. Kumar V and Jain M. 2015. The CRISPR?Cas system for plant genome editing: advances and opportunities. Journal of Experimental Botany. 2015; 66: 1 . 47?57. doi:10.1093/jxb/eru429.

    View Article           

  18. Stovicek V, Borodina I, Forster J. CRISPR?Cas9 system enables fast and simple genome editing of industrial Saccharomyces cerevisiae strains. Metab Eng Commun. 2015; 2:13-22. https://doi.org/10.1016/j.meteno.2015.03.001

    View Article           

  19. Ishino Y, Shinagawa H, Makino K, Amemura M, Nakata A. 1987. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product, J. Bacteriol. 169: 5429?5433. PMid:3316184 PMCid:PMC213968

    View Article      PubMed/NCBI     

  20. Horvath P, Barrangou R. 2010. CRISPR/Cas, the immune system of bacteria and archaea, Science. 2010; 327:167?170. doi: 10.1126/science.1179555.

    View Article           

  21. Barrangou R.CRISPR-Cas systems and RNA-guided interference. Wiley Interdiscip. Rev. RNA. 2013; 4:267?278. doi: 10.1002/wrna.1159.

    View Article           

  22. Jinek M, East A, Cheng,A, Li,S. RNA-programmed genome editing in human cells. Elife. 2013. 2:e00471. doi: 10.7554/eLife.00471.

    View Article           

  23. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2012; 337(6096):816?21. doi: 10.1126/science.1225829.

    View Article           

  24. Gasiunas G, Barrangou R, Horvath P, Siksnys V. Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc Natl Acad Sci U S A. 2012; 109(39):E2579?86. doi: 10.1073/pnas.1208507109

    View Article           

  25. Ali Z, Abulfaraj A, Idris A, Ali S, Tashkandi M, and Mahfouz M. CRISPR/Cas9- mediated viral interference in Plants. Genome biology. 2015; 16:238. doi: 10.1186/s1305901507996

  26. Ding Y, Li H, Chen L-L, Xie K. Recent Advances in Genome Editing Using CRISPR/Cas9. Front. Plant Sci.2016; 7:703. doi: 10.3389/fpls.2016.00703

    View Article           

  27. Pennisi, E. The CRISPR Craze. Science. 2013; 341, 833-836. doi: 10.1126/science.341.6148.833.

    View Article           

  28. Gomaa AA, Klumpe HE, Luo ML, Selle K, Barrangou R, Beisel CL. Programmable removal of bacterial strains by use of genome targeting CRISPRCas systems. mBio. 2014; 5 (1): e00928?13. doi: 10.1128/mBio.00928-13

    View Article           

  29. Shalem O, Sanjana NE, Hartenian E, Shi X, Scott DA, Mikkelson T, et al. Genomescale CRISPRCas9 knockout screening in human cells. Science.2014; 343 (6166): 84?7. doi: 10.1126/science.1247005

    View Article           

  30. Abrahimi P, Chang WG, Kluger MS, Qyang Y, Tellides G, Saltzman WM, et al . Efficient gene disruption in cultured primary human endothelial cells by CRISPR/Cas9. Circulation Research.2015; 117 (2): 121?8. doi: 10.1161/CIRCRESAHA.117.306290.

    View Article           

  31. Freedman BS, Brooks CR, Lam AQ et al., Modelling kidney disease with CRISPR mutant kidney organoids derived from human pluripotent epiblast spheroids. Nature Communications. 2015; 6: 8715. doi: 10.1038/ncomms9715.

    View Article           

  32. Maggio I, Gon?alves MA . Genome editing at the crossroads of delivery, specificity, and fidelity. Trends in Biotechnology. 2015;33 (5): 280?91. PMid:25819765

    View Article      PubMed/NCBI     

  33. Rath D, Amlinger L, Rath A, Lundgren M . The CRISPR/Cas immune system: biology, mechanisms and applications. Biochimie.2015; 117: 119?28. doi: 10.1016/j.biochi.2015.03.025

    View Article           

  34. Yong E . 2015. "The Revolutionary Gene Editing Technique That Reveals Cancer's Weaknesses". The Atlantic.

  35. Gu W, Crawford ED, Donovan BD, Wilson MR, Chow ED, Retallack H, DeRisi JL. Depletion of Abundant Sequences by Hybridization (DASH): using Cas9 to remove unwanted high abundance species in sequencing libraries and molecular counting applications. Genome Biology. 2016; 17: 41. doi: 10.1186/s13059-016-0904-5.

    View Article           

  36. Liu Y, Zhan Y, Chen Z, He A, Li J, Wu H, et al. Directing cellular information flow via CRISPR signal conductors". Nature Methods. 2016;13: 938?944. doi: 10.1038/nmeth.3994

    View Article           

  37. MaoY, Zhang H, Xu N, Zhang B, Gou F, Zhu JK. Application of the CRISPR-Cas system for efficient genome engineering in plants. Mol. Plant. 2013; 6: 2008?2011. doi: 10.1093/mp/sst121

    View Article           

  38. Feng ZY, Mao YF, Xu NF, Zhang BT, Wei PL, Wang Z, et al. Multi-generation analysis reveals the inheritance, specificity, and patterns of CRISPR/Cas-induced gene modifications in Arabidopsis, Proc. Natl. Acad. Sci. U. S. A. 2014; 111: 4632?4637. PMid:24550464 PMCid:PMC3970504

    View Article      PubMed/NCBI     

  39. Schiml S, Fauser F, Puchta H. The CRISPR/Cas system can be used as nuclease for in plant a gene targeting and as paired nickases for directed mutagenesis in Arabidopsis resulting in heritable progeny. Plant J. 2014; 80: 1139?1150. doi:10.1111/tpj.12704.

    View Article           

  40. Hyun Y, Kim J, Cho SW, Choi Y, Kim JS, Coupland G. Site-directed mutagenesisin Arabidopsis thaliana using dividing tissue-targete region of the CRISPR/Cas system to generate heritable null alleles. Planta. 2015; 241: 271?284. doi: 10.1007/s00425-014-2180-5.

    View Article           

  41. Shan Q, Wang Y, Li J, Yi Zhang, Kunling Chen, Zhen Liang, et al. Targeted genome modification of crop plants using a CRISPR-Cas system. Nat. Biotechnol. 2013; 31: 686?688. doi:10.1038/nbt.2650

    View Article           

  42. Zhou HB, 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; 42:10903?10914. doi: 10.1093/nar/gku806.

    View Article           

  43. Ma XL, Zhang QY, Zhu QL, Liu W, Chen Y, Qiu R, et al. A robust CRISPR/Cas9 system for convenient high-efficiency multiplex genome editing in monocot and dicot plants, Mol. Plant. 2015; 8: 1274?1284.

    View Article           

  44. Xu R, Yang Y, Qin R, Li H, Qiu C, Li L, et al. Rapid improvement of grain weight via highly efficient CRISPR/Cas9mediated multiplex genome editing in rice. Journal of Genetics and Genomics. 2016;43: 8, 529?532. ttp://dx.doi.org/10.1016/j.jgg.2016.07.003

  45. Haun W, Coffman A, Clasen BM, Demorest ZL, Lowy A, Ray E, et al. Improved soybean oil quality by targeted mutagenesis of the fatty acid desaturase 2 gene family. Plant Biotechnol J. 2014; 12(7):934?40. doi: 10.1111/pbi.12201

    View Article           

  46. Zhu J, Song N, Sun S, Yang W, Zhao H, Song W, et al. Efficiency and Inheritance of Targeted Mutagenesis in Maize Using CRISPRCas9. Journal of Genetics and Genomics. 2016; 43:1, 25?36. https://doi.org/10.1016/j.jgg.2015.10.006

    View Article           

  47. Fenga C, Yuana J, Wanga R, Liua Y, Birchlerc J, Hana F. Efficient Targeted Genome Modification in Maize Using CRISPR/Cas9 System. Journal of Genetics and Genomics. 2016; 43:1, 37?43. . https://doi.org/10.1016/j.jgg.2015.10.002

    View Article           

  48. Jia H, Wang N. Targeted genome editing of sweet orange using Cas9/sgRNA. PLoS ONE. 2014; 9:e93806. https://doi.org/10.1371/journal.pone.0093806

    View Article           

  49. Svitashev S, Young JK, Schwartz C, Gao HR, Falco SC, Cigan AM. Targeted mutagenesis, precise gene editing, and site-specific gene insertion in maize using Cas9 and guide RNA, Plant Physiol. 2015; 169: 931?945. doi: 10.1104/pp.15.00793.

    View Article           

  50. Fauser F, Schiml S, Puchta H. Both CRISPR/Cas-based nucleases and nickases can be used efficiently for genome engineering in Arabidopsis thaliana. Plant J. 2014; 79, 348?359. doi: 10.1111/tpj.12554.

    View Article           

  51. Jiang W, Yang B, Weeks DP. Efficient CRISPR/Cas9-mediated gene editing in Arabidopsis thaliana and inheritance of modified genes in the T2 and T3 generations. PLoS ONE. 2014; 9:e99225. https://doi.org/10.1371/journal.pone.0099225

    View Article           

  52. Johnson RA, Gurevich V, Filler S, Samach A, Levy A. Comparative assessments of CRISPR-Cas nucleases' cleavage efficiency in planta. Plant Mol.Biol. 2015; 87: 143?156. doi: 10.1007/s11103-014-0266-x

    View Article           

  53. Upadhyay SK, Kumar J, Alok A, Tuli R. RNA-guided genome editing for target gene mutations in wheat. G3(Bethesda). 2013;3:2233?2238. doi: 10.1534/g3.113.008847.

    View Article           

  54. Yin K, Han T, Liu G, Chen T, Wang Y, Yu AY, et al. Ageminivirus- based guide RNA delivery system for CRISPR/Cas9 mediated plant genome editing. Sci.Rep. 2015; 5:14926. doi: 10.1038/srep14926

    View Article           

  55. Feng Z, Zhang B, Ding W, Liu X, Yang DL, Wei P, et al. Efficient genome editing in plants using aCRISPR/Cas system. Cell Res.2013; 23:1229?1232. doi: 10.1038/cr.2013.114.

    View Article           

  56. Xie K, Yang Y. RNA-guided genome editing in plants using a CRISPR-Cas system. Mol. Plant. 2013; 6: 1975?1983. doi: 10.1093/mp/sst119.

    View Article           

  57. Endo M, Mikami M, Toki S. Multigene knockout utilizing off-target mutations of the CRISPR/Cas9 system in rice. Plant Cell Physiol. 2014; 1:1?7. doi: 10.1093/pcp/pcu154

    View Article           

  58. Baltes NJ, Gil-Humanes J, Cermak T, Atkins PA, Voytas DF. DNA replicons for plant genome engineering. Plant Cell. 2014; 26:151?163. doi: 10.1105/tpc.113.119792.

    View Article           

  59. Gao J, Wang G, Ma S.2014.CRISPR/Cas9- mediated targeted mutagenesis in Nicotiana tabacum. Plant Mol.Biol. 2014; 87: 99?110. doi: 10.1007/s11103-014-0263-0.

    View Article           

  60. Butler NM, Atkins PA, Voytas DF, Douches DS. Generation and inheritance of targeted mutations in potato (Solanum tuberosum L.) Using the CRISPR/CasSystem. PLoS ONE. 2015; 10:e0144591.

    View Article           

  61. Wang S, Zhang S, Wang W, Xiong X, Men F. Efficient targeted mutagenesis in potato by the CRISPR/Cas9system. Plant Cell Rep. 2015;34, 1473?1476. doi: 10.1007/s00299-015-1816-7

    View Article           

  62. Michno JM, Wang X, Liu J, Curtin SJ, KonoTJ, Stupar RM. CRISPR/Cas mutagenesis of soybean and Medicago truncatula using a new web-tool and a modifiedCas9enzyme. GM Crops Food. 2015; 6:243?252 PMid:26479970 PMCid:PMC5033229

    View Article      PubMed/NCBI     

  63. Zhou X, Jacobs TB, Xue LJ, Harding SA, Tsai CJ. 2015. Exploiting SNPs for biallelic CRISPR mutations in the out crossing woody perennial Populus reveals4-coumarate:CoA ligase specificity and redundancy. New Phytol. 2015; 208: 298?301. doi: 10.1111/nph.13470.

    View Article           

  64. Sun, X, Hu Z, Chen R, Jiang Q, Song S, Zhang H, et al. Targeted mutagenesis in soybean using the CRISPR-Cas9 system. Sci.Rep. 2015; 5:103-42. doi: 10.1038/srep10342.

    View Article           

  65. Brooks C, Nekrasov V, Lippman Z, Eck J. Efficient gene editing in tomato in the first generation using the clustered regularly interspaced short palindromic repeats/CRISPR associated 9 system. Plant Physiol.2014; 166:1292?1297 PMid:25225186 PMCid:PMC4226363

    View Article      PubMed/NCBI     

  66. Ron M, Kajala K, Pauluzzi G, Wang D, Reynoso MA, Zumstein K, et al. Hairy root transformation using Agrobacterium rhizogenes as a tool for exploring celltype-specific gene expression and function using tomato as a model. Plant Physiol.2014; 166:455?469. doi: 10.1104/pp.114.239392.

    View Article           

  67. ItoY, Nishizawa-Yokoi A, Endo M, Mikami M, Toki S. CRISPR/Cas9-mediated mutagenesis of the RIN locus that regulates tomato fruit ripening. Biochem. Biophy.Res .Commun.2015; 467:76?82. doi: 10.1016/j.bbrc.2015.09.117.

    View Article           

  68. Sugano SS, Shirakawa M, Takagi J, Matsuda Y, Shimada T, Hara-Nishimura I, et al. .2014. CRISPR/Cas9-mediated targeted mutagenesis in the liverwort Marchantia polymorpha L. Plant Cell Physiol. 2014; 55:475?481. doi: 10.1093/pcp/pcu014.

    View Article           

  69. Wang Y, Cheng X, Shan Q, Zhang Y, Liu J, Gao C, et al. Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew. Nat.Biotechnol. 2014; 32: 947?951. doi: 10.1038/nbt.2969.

    View Article           

  70. Tingting L, Di F, Lingyu R, Yuanzhong J, Rui L, Keming L. Highly efficient CRISPR/Cas9?mediated targeted mutagenesis of multiple genes in Populus. Yi Chuan 2015; 37: 1044?1052 PMid:26496757

  71. Li JF, Norville J E, Aach J. Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9. Nat.Biotechnol. 2013; 31: 688?691. doi: 10.1038/nbt.2654.

    View Article           

  72. Xie K, Minkenberg B. Yang Y. Boosting CRISPR/Cas9 multiplex editing capability with the endogenous tRNA-processing system. Proc. Natl. Acad.Sci.U.S.A. 2015; 112: 3570?3575. PMid:25733849 PMCid:PMC4371917

    View Article      PubMed/NCBI     

  73. Cai Y, Chen L, Liu X, Sun S, Wu C, Jiang B, et al. CRISPR/Cas9-Mediated Genome Editing in Soybean Hairy Roots. PLoS ONE. 2015; 10(8): e0136064. doi:10.1371/journal.pone.0136064

    View Article           

  74. Nelles A, Fang MY. Aigner SW, Yeo GW, Applications of Cas9 as an RNA-programmed RNA-binding protein, BioEssays. 2015; 37 :732?739. doi:10.1002/bies.201500001.

    View Article           

  75. O'Connell M, Oakes BL, Sternberg SH, East-Seletsky A, Kaplan M, Doudna JA. Programmable RNA recognition and cleavage by CRISPR/Cas9. Nature. 2014; 516: 263?266. doi: 10.1038/nature13769.

    View Article           

  76. Qi L, Larson M, Gilbert L, Doudna J, Weissman J, Arkin A, et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression, Cell. 2013; 152:1173?1183. https://doi.org/10.1016/j.cell.2013.02.022

    View Article           

  77. Piatek A, Ali Z, Baazim H, Li L, Abulfaraj A, Al-Shareef S, et al. RNA-guided transcriptional regulation in planta via synthetic dCas9-based transcription factors, Plant Biotechnol. J. 2015; 13: 578?589. doi: 10.1111/pbi.12284

    View Article           

  78. Kanchiswamy CN, DNA-free genome editing methods for targeted crop improvement. Plant Cell Rep. 2016; doi:10.1007/s00299- 016-1982-2

  79. Nogue F, Mara K, Collonnier C, Casacuberta JM. Genome engineering and plant breeding: impact on trait discovery and development. Plant Cell Rep. 2016; doi:10.1007/s00299-016-1993-z.

    View Article           

  80. Morineau C, Bellec Y, Tellier F, Gissot L, Kelemen Z, Nogu? F et al. Selective gene dosage by CRISPR-Cas9 genome editing in hexaploid Camelina sativa. Plant biotechnology J. 2016. doi: 10.1111/pbi.12671.

    View Article           

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