A Review on Revolutionary Strategy for Crop Improvement: Genome Editing

Unnati Vaghela *

Department of Genetics and Plant Breeding, B. A. College of Agriculture, Anand Agricultural University, Anand, 388 110, India.

Mayur Kumar Sonagara

Department of Genetics and Plant Breeding, B. A. College of Agriculture, Anand Agricultural University, Anand, 388 110, India.


Department of Genetics and Plant Breeding, B. A. College of Agriculture, Anand Agricultural University, Anand, 388 110, India.

Ankit Yadav

Department of Agricultural Biotechnology, Anand Agricultural University, Anand, 388 110, India.

*Author to whom correspondence should be addressed.


Genome editing technology revolutionized crop improvement technology through sequence-specific, precise, site-directed, safe genetic manipulation and combat the major 21st century challenge such as achieving world food security meeting rising global food demand and improving food nutrition in the face of rapidly changing climate conditions. Crop improvement using conventional and molecular breeding approaches takes time, causing biosafety concerns and cannot equipoise with raising demand. Genome editing system like zinc finger nuclease (ZFN), transcription activator-like effector nucleases (TALEN), and clustered regularly interspaced short palindromic repeats (CRISPR) made a desirable targeted modification in crops for improving crop yield, nutraceutical quality and also enhance tolerance to environmental stress (biotic or abiotic) through add the desirable trait(s) and remove the undesirable. Genome manipulation tools progression creates new breakthroughs and speeds up crop improvement through site-directed mutagenesis efficiently for crop improvements to meet the ever-increasing global demand for food and produce more resilient crop with great flexibility to combat climate change.

Keywords: Genome editing, crop improvement, targeted gene, CRISPR/Cas9, TALENs, ZFNs, homology-dependent repair, nonhomologous end-joining modification

How to Cite

Vaghela , Unnati, Mayur Kumar Sonagara, Pratibha, and Ankit Yadav. 2023. “A Review on Revolutionary Strategy for Crop Improvement: Genome Editing”. International Journal of Environment and Climate Change 13 (8):2005-18. https://doi.org/10.9734/ijecc/2023/v13i82158.


Download data is not yet available.


Ray DK, Mueller ND, West PC, Foley JA. Yield trends are insufficient to double global crop production by 2050. PloS One. 2013;8(6):e66428.

Tilman D, Balzer C, Hill J, Befort BL. Global food demand and the sustainable intensification of agriculture. Proceedings of the National Academy of Sciences. 2011;108(50):20260-20264.

Ray DK, Mueller ND, West PC, Foley JA. Yield trends are insufficient to double global crop production by 2050. PloS One. 2013;8(6):e66428.

Röös E, Bajželj B, Smith P, Patel M, Little D, Garnett T. Greedy or needy? Land use and climate impacts of food in 2050 under different livestock futures. Global Environmental Change. 2017;47:1-2.

Miglani GS. Genome editing in crop improvement: Present scenario and future prospects. Journal of Crop Improvement. 2017;31(4):453-559.

Georges F, Ray H. Genome editing of crops: a renewed opportunity for food security. GM Crops & Food. 2017;8(1):1-2.

Osakabe Y, Osakabe K. Genome editing with engineered nucleases in plants. Plant and Cell Physiology. 2015;56(3):389-400.

Chen K, Gao C. Targeted genome modification technologies and their applications in crop improvements. Plant Cell Reports. 2014;33(4):575-83.

Puchta H. The repair of double-strand breaks in plants: mechanisms and consequences for genome evolution. Journal of Experimental Botany. 2005;56(409):1-4.

Mladenov E, Iliakis G. Induction and repair of DNA double strand breaks: The increasing spectrum of non-homologous end joining pathways. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis. 2011;711(1-2):61-72.

Carroll D. Genome engineering with targetable nucleases (467.1). The FASEB Journal. 2014;28:467-1.

Pâques F, Duchateau P. Meganucleases and DNA double-strand break-induced recombination: perspectives for gene therapy. Current gene therapy. 2007;7(1):49-66.

Mishra R, Joshi RK, Zhao K. Genome editing in rice: recent advances, challenges, and future implications. Frontiers in Plant Science. 2018;9:1361.

Smith HO, Nathans D. A suggested nomenclature for bacterial host modification and restriction systems and their enzymes. Journal of Molecular Biology. 1973;81(3):419-23.

Lloyd A, Plaisier CL, Carroll D, Drews GN. Targeted mutagenesis using zinc-finger nucleases in Arabidopsis. Proceedings of the National Academy of Sciences. 2005; 102(6):2232-7.

Kim YG, Cha J, Chandrasegaran S. Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. Proceedings of the National Academy of Sciences. 1996;93(3):1156-60.

Petolino JF. Genome editing in plants via designed zinc finger nucleases. In Vitro Cellular & Developmental Biology-Plant. 2015;51(1):1-8.

Petolino JF, Srivastava V, Daniell H. Editing plant genomes: A new era of crop improvement. Plant Biotechnology Journal. 2016;14(2):435-6.

Rebar EJ, Huang Y, Hickey R, Nath AK, Meoli D, Nath S, Chen B, Xu L, Liang Y, Jamieson AC, Zhang L. Induction of angiogenesis in a mouse model using engineered transcription factors. Nature Medicine. 2002;8(12):1427-32.

Bitinaite J, Wah DA, Aggarwal AK, Schildkraut I. Fok I dimerization is required for DNA cleavage. Proceedings of the National Academy of Sciences. 1998;95(18):10570-5.

Ramirez CL, Foley JE, Wright DA, Müller-Lerch F, Rahman SH, Cornu TI, Winfrey RJ, Sander JD, Fu F, Townsend JA, Cathomen T. Unexpected failure rates for modular assembly of engineered zinc fingers. Nature Methods. 2008;5(5): 374-5.

Cermak T, Doyle EL, Christian M, Wang L, Zhang Y, Schmidt C, Baller JA, Somia NV, Bogdanove AJ, Voytas DF. Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Research. 2011;39(12):e82.

Mahfouz MM, Li L, Shamimuzzaman M, Wibowo A, Fang X, Zhu JK. De novo-engineered transcription activator-like effector (TALE) hybrid nuclease with novel DNA binding specificity creates double-strand breaks. Proceedings of the National Academy of Sciences. 2011;108(6):2623-8.

Miller JC, Tan S, Qiao G, Barlow KA, Wang J, Xia DF, Meng X, Paschon DE, Leung E, Hinkley SJ, Dulay GP. A TALE nuclease architecture for efficient genome editing. Nature Biotechnology. 2011;29(2): 143-8.

Li T, Liu B, Spalding MH, Weeks DP, Yang B. High-efficiency TALEN-based gene editing produces disease-resistant rice. Nature Biotechnology. 2012;30(5):390-2.

Zhang Y, Zhang F, Li X, Baller JA, Qi Y, Starker CG, Bogdanove AJ, Voytas DF. Transcription activator-like effector nucleases enable efficient plant genome engineering. Plant Physiology. 2013;161(1):20-7.

Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA, Horvath P. CRISPR provides acquired resistance against viruses in prokaryotes. Science. 2007;315(5819):1709-1712.

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):816-821.

Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F. Multiplex genome engineering using CRISPR/Cas systems. Science. 2013;339(6121):819-23.

Ishino Y, Shinagawa H, Makino K, Amemura M, Nakata A. 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):5429-33.

Datsenko KA, Pougach K, Tikhonov A, Wanner BL, Severinov K, Semenova E. Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system. Nature Communications. 2012;3(1):1-7.

Gasiunas G, Barrangou R, Horvath P, Siksnys V. Cas9–crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proceedings of the National Academy of Sciences. 2012;109(39):E2579-86.

Nishimasu H, Ran FA, Hsu PD, Konermann S, Shehata SI, Dohmae N, Ishitani R, Zhang F, Nureki O. Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell. 2014;156(5):935-49.

Shukla VK, Doyon Y, Miller JC, DeKelver RC, Moehle EA, Worden SE, Mitchell JC, Arnold NL, Gopalan S, Meng X, Choi VM. Precise genome modification in the crop species Zea mays using zinc-finger nucleases. Nature. 2009;459(7245):437-41.

Mao Y, Zhang H, Xu N, Zhang B, Gou F, Zhu JK. Application of the CRISPR–Cas system for efficient genome engineering in plants. Molecular Plant. 2013;6(6):2008-11.

Zetsche B, Volz SE, Zhang F. A split-Cas9 architecture for inducible genome editing and transcription modulation. Nature Biotechnology. 2015;33(2):139-42.

Kim D, Kim J, Hur JK, Been KW, Yoon SH, Kim JS. Genomewide analysis reveals specificities of Cpf1 endonucleases in human cells. Nat Biotechnol. 2016;34:863-868.

Zaidi SS, Mahfouz MM, Mansoor S. CRISPR-Cpf1: a new tool for plant genome editing. Trends in Plant Science. 2017;22(7):550-3.

Kim H, Kim ST, Ryu J, Kang BC, Kim JS, Kim SG. CRISPR/Cpf1-mediated DNA-free plant genome editing. Nat Commun; 2017;8:1-7.

Xu R, Qin R, Li H, Li D, Li L, Wei P, Yang J. Generation of targeted mutant rice using a CRISPR‐Cpf1 system. Plant Biotechnology Journal. 2017;15(6):713- 7.

Zetsche B, Gootenberg JS, Abudayyeh OO, Slaymaker IM, Makarova KS, Essletzbichler P, Volz SE, Joung J, Van Der Oost J, Regev A, Koonin EV. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell. 2015;163(3):759-71.

Wędzony M, Szechyńska-Hebda M, Żur I, Dubas E, Krzewska M. Tissue culture and regeneration: a prerequisite for alien gene transfer. In Alien Gene Transfer in Crop Plants. Springer, New York, NY. 2014;1:43-75.

Altpeter F, Springer NM, Bartley LE, Blechl AE, Brutnell TP, Citovsky V, Conrad LJ, Gelvin SB, Jackson DP, Kausch AP, Lemaux PG. Advancing crop transformation in the era of genome editing. The Plant Cell. 2016;28(7):1510-20.

Tuteja N, Verma S, Sahoo RK, Raveendar S, Reddy IN. Recent advances in development of marker-free transgenic plants: Regulation and biosafety concern. Journal of Biosciences. 2012; 37(1):167-97.

Zhang Y, Liang Z, Zong Y, Wang Y, Liu J, Chen K, Qiu JL, Gao C. Efficient and transgene-free genome editing in wheat through transient expression of CRISPR/Cas9 DNA or RNA. Nature Communications. 2016;7(1):1-8.

Liang Z, Chen K, Zhang Y, Liu J, Yin K, Qiu JL, Gao C. Genome editing of bread wheat using biolistic delivery of CRISPR/Cas9 in vitro transcripts or ribonucleoproteins. Nature Protocols. 2018;13(3):413-30.

Gorbunova V, Levy AA. Non-homologous DNA end joining in plant cells is associated with deletions and filler DNA insertions. Nucleic Acids Research. 1997;25(22):4650-7.

Woo JW, Kim J, Kwon SI, Corvalán C, Cho SW, Kim H, Kim SG, Kim ST, Choe S, Kim JS. DNA-free genome editing in plants with preassembled CRISPR-Cas9 ribonucleoproteins. Nature Biotechnology. 2015;33(11):1162-1164.

Subburaj S, Chung SJ, Lee C, Ryu SM, Kim DH, Kim JS, Bae S, Lee GJ. Site-directed mutagenesis in Petunia× hybrida protoplast system using direct delivery of purified recombinant Cas9 ribonucleoproteins. Plant Cell Reports. 2016;35(7):1535-1544.

Svitashev S, Schwartz C, Lenderts B, Young JK, Cigan AM. Genome editing in maize directed by CRISPR–Cas9 ribonucleoprotein complexes. Nat Commun. 2016;7:1–7.

Liang Z, Chen K, Li T, Zhang Y, Wang Y, Zhao Q, Liu J, Zhang H, Liu C, Ran Y, Gao C. Efficient DNA-free genome editing of bread wheat using CRISPR/Cas9 ribonucleoprotein complexes. Nature Communications. 2017;8(1):1-5.

Malnoy M, Viola R, Jung MH, Koo OJ, Kim S, Kim JS, Velasco R, Nagamangala Kanchiswamy C. DNA-free genetically edited grapevine and apple protoplast using CRISPR/Cas9 ribonucleoproteins. Frontiers in Plant Science. 2016;7:1904.

Gao C. Genome engineering for crop improvement and future agriculture. Cell. 2021;184(6):1621-35.

Li JF, Norville JE, Aach J, McCormack M, Zhang D, Bush J, Church GM, Sheen J. Multiplex and homologous recombination–mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9. Nature Biotechnology. 2013;31(8):688-91.

Xie K, Minkenberg B, Yang Y. Boosting CRISPR/Cas9 multiplex editing capability with the endogenous tRNA-processing system. Proceedings of the National Academy of Sciences. 2015;112(11):3570-3575.

Zhang Z, Mao Y, Ha S, Liu W, Botella JR, Zhu JK. A multiplex CRISPR/Cas9 platform for fast and efficient editing of multiple genes in Arabidopsis. Plant Cell Reports. 2016;35(7):1519-33.

Char SN, Neelakandan AK, Nahampun H, Frame B, Main M, Spalding MH, Becraft PW, Meyers BC, Walbot V, Wang K, Yang B. An Agrobacterium‐delivered CRISPR/Cas9 system for high‐frequency targeted mutagenesis in maize. Plant Biotechnology Journal. 2017;15(2):257-68.

Minkenberg B, Xie K, Yang Y. Discovery of rice essential genes by characterizing a CRISPR‐edited mutation of closely related rice MAP kinase genes. The Plant Journal. 2017;89(3):636-48.

Chilcoat D, Liu ZB, Sander J. Use of CRISPR/Cas9 for crop improvement in maize and soybean. Progress in Molecular Biology and Translational Science. 2017;149:27-46.

Wang M, Mao Y, Lu Y, Tao X, Zhu JK. Multiplex gene editing in rice using the CRISPR-Cpf1 system. Molecular Plant. 2017;10(7):1011-3.

Xu R, Yang Y, Qin R, Li H, Qiu C, Li L, Wei P, Yang J. Rapid improvement of grain weight via highly efficient CRISPR/Cas9-mediated multiplex genome editing in rice. Journal of Genetics and Genomics= Yi Chuan Xue Bao. 2016;43(8):529-32.

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 Research. 2014;42(17):10903-14.

Zhao C, Zhang Z, Xie S, Si T, Li Y, Zhu JK. Mutational evidence for the critical role of CBF transcription factors in cold acclimation in Arabidopsis. Plant Physiology. 2016;171(4):2744-59.

D'Halluin K, Ruiter R. Directed genome engineering for genome optimization. International Journal of Developmental Biology. 2013;57(6-7-8):621-7.

Wang Y, Cheng X, Shan Q, Zhang Y, Liu J, Gao C, Qiu JL. Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew. Nature biotechnology. 2014;32(9):947-51.

Paszkowski J, Baur M, Bogucki A, Potrykus I. Gene targeting in plants. The EMBO Journal. 1988;7(13):4021-6.

Terada R, Urawa H, Inagaki Y, Tsugane K, Iida S. Efficient gene targeting by homologous recombination in rice. Nature Biotechnology. 2002;20(10):1030-4.

Malzahn A, Lowder L, Qi Y. Plant genome editing with TALEN and CRISPR. Cell & Bioscience. 2017;7(1):1-8.

Zhang X, Wang J, Cheng Q, Zheng X, Zhao G, Wang J. Multiplex gene regulation by CRISPR-ddCpf1. Cell Discovery. 2017;3(1):1-9.

Minkenberg B, Wheatley M, Yang Y. CRISPR/Cas9-enabled multiplex genome editing and its application. Progress in Molecular Biology and Translational Science. 2017;149:111-32.

Chavez A, Scheiman J, Vora S, Pruitt BW, Tuttle M, PR Iyer E, Lin S, Kiani S, Guzman CD, Wiegand DJ, Ter-Ovanesyan D. Highly efficient Cas9-mediated transcriptional programming. Nature Methods. 2015;12(4):326-8.

Piatek A, Ali Z, Baazim H, Li L, Abulfaraj A, Al‐Shareef S, Aouida M, Mahfouz MM. RNA‐guided transcriptional regulation in planta via synthetic dC as9‐based transcription factors. Plant Biotechnology Journal. 2015;13(4):578-89.

Alagoz Y, Gurkok T, Zhang B, Unver T. Manipulating the biosynthesis of bioactive compound alkaloids for next-generation metabolic engineering in opium poppy using CRISPR-Cas 9 genome editing technology. Scientific Reports. 2016;6(1):1-9.

Li X, Zhou W, Ren Y, Tian X, Lv T, Wang Z, Fang J, Chu C, Yang J, Bu Q. High-efficiency breeding of early-maturing rice cultivars via CRISPR/Cas9-mediated genome editing. Journal of Genetics and Genomics= Yi Chuan Xue Bao. 2017;44(3):175-8.

Sun Y, Jiao G, Liu Z, Zhang X, Li J, Guo X, Du W, Du J, Francis F, Zhao Y, Xia L. Generation of high-amylose rice through CRISPR/Cas9-mediated targeted mutagenesis of starch branching enzymes. Frontiers in Plant Science. 2017;8:298.

Liang Z, Zhang K, Chen K, Gao C. Targeted mutagenesis in Zea mays using TALENs and the CRISPR/Cas system. Journal of Genetics and Genomics. 2014;41(2):63-8.

Haun W, Coffman A, Clasen BM, Demorest ZL, Lowy A, Ray E, Retterath A, Stoddard T, Juillerat A, Cedrone F, Mathis L. Improved soybean oil quality by targeted mutagenesis of the fatty acid desaturase 2 gene family. Plant Biotechnology Journal. 2014;12(7):934-40.

Wang F, Wang C, Liu P, Lei C, Hao W, Gao Y, Liu YG, Zhao K. Enhanced rice blast resistance by CRISPR/Cas9-targeted mutagenesis of the ERF transcription factor gene OsERF922. PloS One. 2016;11(4):e0154027.

Shi J, Gao H, Wang H, Lafitte HR, Archibald RL, Yang M, Hakimi SM, Mo H, Habben JE. ARGOS 8 variants generated by CRISPR‐Cas9 improve maize grain yield under field drought stress conditions. Plant Biotechnology Journal. 2017;15(2):207-16.

Zhu H, Li C, Gao C. Applications of CRISPR–Cas in agriculture and plant biotechnology. Nature Reviews Molecular Cell Biology. 2020;21(11):661-77.

Zhong Y, Liu C, Qi X, Jiao Y, Wang D, Wang Y, Liu Z, Chen C, Chen B, Tian X, Li J. Mutation of ZmDMP enhances haploid induction in maize. Nature Plants. 2019;5(6):575-80.

Kuppu S, Ron M, Marimuthu MP, Li G, Huddleson A, Siddeek MH, Terry J, Buchner R, Shabek N, Comai L, Britt AB. A variety of changes, including CRISPR/Cas9‐mediated deletions, in CENH3 lead to haploid induction on outcrossing. Plant Biotechnology Journal. 2020;18(10):2068-80.

Sailer C, Schmid B, Grossniklaus U. Apomixis allows the transgenerational fixation of phenotypes in hybrid plants. Current biology. 2016 Feb 8;26(3):331-7.

Khanday I, Skinner D, Yang B, Mercier R, Sundaresan V. A male-expressed rice embryogenic trigger redirected for asexual propagation through seeds. Nature. 2019;565(7737):91-5.

Fu Y, Foden JA, Khayter C, Maeder ML, Reyon D, Joung JK, Sander JD. High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nature Biotechnology. 2013;31(9):822-6.

Song G, Jia M, Chen K, Kong X, Khattak B, Xie C, Li A, Mao L. CRISPR/Cas9: a powerful tool for crop genome editing. The Crop Journal. 2016;4(2):75-82.

Kleinstiver BP, Tsai SQ, Prew MS, Nguyen NT, Welch MM, Lopez JM, McCaw ZR, Aryee MJ, Joung JK. Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells. Nature Biotechnology. 2016;34(8):869-74.

Niazian M, Noori SS, Galuszka P, Mortazavian SM. Tissue culture-based Agrobacterium-mediated and in planta transformation methods. Soil and Water Research. 2017;53(4):133-43.

Shah SH, Ali S, Jan SA, Ali GM. Piercing and incubation method of in planta transformation producing stable transgenic plants by overexpressing DREB1A gene in tomato (Solanum lycopersicum Mill.). Plant Cell, Tissue and Organ Culture (PCTOC). 2015;120(3):1139-57.

Verma SS, Chinnusamy V, Bansa KC. A simplified floral dip method for transformation of Brassica napus and B. carinata. Journal of Plant Biochemistry and Biotechnology. 2008;17(2):197-200.

Chen K, Gao C. Targeted genome modification technologies and their applications in crop improvements. Plant Cell Reports. 2014;33(4):575-83.

Gao C. Genome editing in crops: From bench to field. National Science Review. 2015;2(1):13-5.

Waltz E. CRISPR-edited crops free to enter market, skip regulation. Nature Biotechnology. 2016;34(6):582-3.

Zhang Y, Massel K, Godwin ID, Gao C. Applications and potential of genome editing in crop improvement. Genome Biology. 2018;19(1):1-1.

Saurabh S. Genome editing: Revolutionizing the crop improvement. Plant Molecular Biology Reporter. 2021;23:1-21.

Mishra R, Zhao K. Genome editing technologies and their applications in crop improvement. Plant Biotechnology Reports. 2018;12(2):57-68.

Zhan X, Lu Y, Zhu JK, Botella JR. Genome editing for plant research and crop improvement. Journal of Integrative Plant Biology. 2021;63(1):3-3.

Huang S, Weigel D, Beachy RN, Li J. A proposed regulatory framework for genome-edited crops. Nature Genetics. 2016;48(2):109-11.

Zhang Y, Pribil M, Palmgren M, Gao C. A CRISPR way for accelerating improvement of food crops. Nature Food. 2020;1(4):200-5.

Lassoued R, Macall DM, Smyth SJ, Phillips PW, Hesseln H. How should we regulate products of new breeding techniques? Opinion of surveyed experts in plant biotechnology. Biotechnology Reports. 2020;26:e00460.