Current and Future Prospects of Plant Breeding with CRISPR/Cas
Current Journal of Applied Science and Technology,
Page 1-17
DOI:
10.9734/cjast/2019/v38i330360
Abstract
Innovative plant breeding technology is an absolute necessity to enhance agriculture production in order to have an ambition of feeding nutritious food to the ever-increasing population. Current advances in CRISPR/Cas genome editing technology have led to effective targeted changes in most plants that promise to accelerate crop improvement. Here we discussed the discovery of CRISPR/Cas technology, associated manipulations for plant genome editing and its potential applications in the plant breeding. We emphasized mainly on the most essential applications of CRISPR/Cas genome editing in crop improvement, such as crop trait improvement (yield and biotic/abiotic stress tolerance), developments in optimizing gene regulation, strategies for generating virus resistance in plants, and the use of high throughput mutant libraries. Finally, the challenges and opportunities for plant breeding in precision agriculture and its bright future discussed.
Keywords:
- Genome editing
- CRISPR/Cas
- precision plant breeding
- trait improvement
- future plant breeding.
How to Cite
Wagh, S. G., & Pohare, M. B. (2019). Current and Future Prospects of Plant Breeding with CRISPR/Cas. Current Journal of Applied Science and Technology, 38(3), 1-17. https://doi.org/10.9734/cjast/2019/v38i330360
References
Tilman D, Balzer C, Hill J, Befort BL. Global food demand and the sustainable intensification of agriculture. PNAS. 2011;108:260-64.
Scheben A, Wolter F, Batley J, Puchta H, Edwards D. Towards CRISPR/Cas crops—bringing together genomics and genome editing. New Phytol. 2017;216:682-98.
Pacher M, Puchta H. From classical mutagenesis to nuclease-based breeding-directing natural DNA repair for a natural end-product. Plant J. 2017;90:819-33.
Pohare MB, Rathod HP, Shahakar SB, Kelatkar SK, Suryawanshi PP. Effects of UV radiations on morphological characters in In vitro regenerated Polianthes tuberosa. Research Journal of Agricultural Sciences. 2012;3:1307-1308.
Pohare MB, Batule BS, Bhor SA, Shahakar SB, Kelatkar SK, Varandani SP. Effect of Gamma radiations on the morphological characters in in vitro regenerated Polianthes tuberosa. Indian Horticulture Journal. 2013;3:95-97.
Li JF, Norville JE, Aach J, McCormack M, Zhang D, Bush J, et al. Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9. Nat. Biotechnol. 2013;31:688-91.
Nekrasov V, Staskawicz B, Weigel D, Jones JD, Kamoun S. Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease. Nat. Biotechnol. 2013;31: 691-93.
Shan Q, Wang Y, Li J, Zhang Y, Chen K, Liang Z, et al. Targeted genome modification of crop plants using a CRISPR/Cas system. Nat. Biotechnol. 2013;31:686-88.
Zetsche B, Gootenberg Jonathan S, Abudayyeh Omar O, Slaymaker Ian M, Makarova Kira S, Essletzbichler P, et al. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR/Cas system. Cell. 2015;163:759-71.
Shimatani Z, Kashojiya S, Takayama M, Terada R, Arazoe T, Ishii H, et al. Targeted base editing in rice and tomato using a CRISPR/Cas9 cytidine deaminase fusion. Nat. Biotechnol. 2013;35:441-43.
Makarova KS, Aravind L, Grishin NV, Rogozin IB, Koonin EV. A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis. Nucleic Acids Research. 2002;30:482-496.
Horvath P, Barrangou R. CRISPR/Cas, the immune system of bacteria and archaea. Science. 2010;327:167-170.
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;169:5429-5433.
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:E2579-E2586.
Hsu PD, Lander ES, Zhang F. Development and applications of CRISPR/Cas9 for genome engineering. Cell. 2014;157(6):1262-1278.
Brouns SJ, Jore MM, Lundgren M, Westra ER, Slijkhuis RJ, Snijders AP, et al. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science. 2008;321:960-964.
Deveau H, Barrangou R, Garneau JE, Labonté J, Fremaux C, Boyaval P, el al. Phage response to CRISPR-encoded resistance in Streptococcus thermophilus. Journal of Bacteriology. 2008;190:1390-1400.
Deveau H, Garneau JE, Moineau S. CRISPR/Cas system and its role in phage-bacteria interactions. Annual Review of Microbiology. 2010;64:475-493.
Bhaya D, Davison M, Barrangou R. CRISPR/Cas systems in bacteria and archaea: Versatile small RNAs for adaptive defense and regulation. Annual Review of Genetics. 2011;45:273-297.
Koonin EV, Makarova KS, Zhang F. Diversity classification and evolution of CRISPR/Cas systems. Curr. Opin. Microbiol. 2017;37:67-78.
Deltcheva E, Chylinski K, Sharma CM, Gonzales K, Chao Y, Pirzada ZA, el al. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature. 2011;471:602-608.
Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier EA. Programmable dual-RNA–guided DNA endonuclease in adaptive bacterial immunity. Science. 2012;12:258-59.
Doudna JA, Charpentier E. The new frontier of genome engineering with CRISPR/Cas9. Science. 2014;346(6213): 1258096.
Jiang F, Doudna JA. CRISPR/Cas9 structures and mechanisms. Annual Review of Biophysics. 2017;46:505-529.
Chen H, Choi J, Bailey S. Cut site selection by the two nuclease domains of the Cas9 RNA-guided endonuclease. Journal of Biological Chemistry. 2014;jbc-M113.
Cristea S, Freyvert Y, Santiago Y, Holmes MC, Urnov FD, Gregory PD, el al. In vivo cleavage of transgene donors promotes nuclease mediated targeted integration. Biotechnology and Bioengineering. 2013;110:871-880.
Cristea S, Freyvert Y, Santiago Y, Holmes MC, Urnov FD, Gregory PD. In vivo cleavage of transgene donors promotes nuclease mediated targeted integration. Biotechnology and Bioengineering. 2012;121:671-680.
Maresca M, Lin VG, Guo N, Yang Y. Obligate ligation-gated recombination (ObLiGaRe): custom-designed nuclease-mediated targeted integration through nonhomologous end joining. Genome Research. 2013;23:539-546.
Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N. Multiplex genome engineering using CRISPR/Cas systems. Science. 2013;339:819-23.
Gasiunas G, Barrangou R, Horvath P, Siksnys V. Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. PNAS. 2012;109:E2579-86.
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;337:816-21.
Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, et al. RNA-guided human genome engineering via Cas9. Science. 2013;339:823-26.
Wagh SG, Alam MM, Kobayashi K, Yaeno T, Yamaoka N, Toriba T, Hirano HY, Nishiguchi M. Analysis of rice RNA-dependent RNA polymerase 6 (OsRDR6) gene in response to viral, bacterial and fungal pathogens. J Gen Plant Pathol. 2016a;82:12-17.
Zhang J, Zhang H, Botella JR, Zhu JK. Generation of new glutinous rice by CRISPR/Cas9- targeted mutagenesis of the Waxy gene in elite rice varieties. J. Integr. Plant Biol. 2018;60:369-75.
Wang M, Lu Y, Botella JR, Mao Y, Hua K, Zhu JK. Gene targeting by homology-directed repair in rice using a geminivirus-based CRISPR/Cas9 system. Mol. Plant. 2017;10:1007-10.
Sun Y, Jiao G, Liu Z, Zhang X, Li J, Guo X, et al. Generation of high-amylose rice through CRISPR/Cas9- mediated targeted mutagenesis of starch branching enzymes. Front. Plant Sci. 2017;8:1298.
Shan Q, Zhang Y, Chen K, Zhang K, Gao C. Creation of fragrant rice by targeted knockout of the OsBADH2 gene using TALEN technology. Plant Biotechnol. J. 2015;13:791-800.
Sanchez-Leon S, Gil-Humanes J, Ozuna CV, Gimenez MJ, Sousa C, Voytas DF, et al. Low-gluten, nontransgenic wheat engineered with CRISPR/Cas9. Plant Biotechnol. J. 2018;16:902-10.
Jiang WZ, Henry IM, Lynagh PG, Comai L, Cahoon EB, Weeks DP. Significant enhancement of fatty acid composition in seeds of the allohexaploid, Camelina sativa, using CRISPR/Cas9 gene editing. Plant Biotechnol. J. 2017;15:648-57.
Morineau C, Bellec Y, Tellier F, Gissot L, Kelemen Z, Nogué F, et al. Selective gene dosage by CRISPR/Cas9 genome editing in hexaploid Camelina sativa. Plant Biotechnol. J. 2017;15:729-39.
Okuzaki A, Ogawa T, Koizuka C, Kaneko K, Inaba M, Imamura J, et al. CRISPR/Cas9-mediated genome editing of the fatty acid desaturase 2 gene in Brassica napus. Plant Physiol. Biochem. 2018;131:63-69.
Ito Y, Nishizawa-Yokoi A, Endo M, Mikami M, Toki S. CRISPR/Cas9-mediated mutagenesis of the RIN locus that regulates tomato fruit ripening. Biochem. Biophys. Res. Commun. 2015;467:76-82.
Li R, Fu D, Zhu B, Luo Y, Zhu H. CRISPR/Cas9-mediated mutagenesis of lncRNA1459 alters tomato fruit ripening. Plant J. 2018;94:513-24.
Li X, Wang Y, Chen S, Tian H, Fu D, Zhu B, et al. Lycopene is enriched in tomato fruit by CRISPR/Cas9- mediated multiplex genome editing. Front. Plant Sci. 2018;9: 559.
Li R, Li R, Li X, Fu D, Zhu B, Tian H, et al. Multiplexed CRISPR/Cas9-mediated metabolic engineering of γ-aminobutyric acid levels in Solanumly copersicum. Plant Biotechnol. J. 2018;16:415-27.
Nonaka S, Arai C, Takayama M, Matsukura C, Ezura H. Efficient increase of γ-aminobutyric acid (GABA) content in tomato fruits by targeted mutagenesis. Sci Rep. 2017;7:7057.
Nakayasu M, Akiyama R, Lee HJ, Osakabe K, Osakabe Y, Watanabe B. Generation of α-solanine-free hairy roots of potato by CRISPR/Cas9 mediated genome editing of the St16DOX gene. Plant Physiol. Biochem. 2018;131:70-77.
Wang Y, Cheng X, Shan Q, Zhang Y, Liu J, Guo C. Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew. Nat. Biotechnol. 2014;32:947-51.
Nekrasov V, Wang C, Win J, Lanz C, Weigel D, Kamoun S. Rapid generation of a transgene-free powdery mildew resistant tomato by genome deletion. Sci. Rep. 2017;7:482.
Wang F, Wang C, Liu P, Lei C, Hao W, Gao Y, et al. Enhanced rice blast resistance by CRISPR/Cas9- targeted mutagenesis of the ERF transcription factor gene OsERF922. PLOS ONE. 2016;11:e0154027.
Macovei A, Sevilla NR, Cantos C, Jonson GB, Slamet-Loedin I, Čermák T, et al. Novel alleles of rice eIF4G generated by CRISPR/Cas9-targeted mutagenesis confer resistance to rice tungro spherical virus. Plant Biotechnol. J. 2018;16:1918- 27.
Iqbal Z, Sattar MN, Shafiq M. CRISPR/Cas9: A tool to circumscribe cotton leaf curl disease. Front. Plant Sci. 2016;7:475.
Lu HP, Luo T, Fu HW, Wang L, Tan YY, Huang JZ, et al. Resistance of rice to insect pests mediated by suppression of serotonin biosynthesis. Nat. Plants. 2018;4:338-44.
Nieves-Cordones M, Mohamed S, Tanoi K, Kobayashi NI, Takagi K, Vernet A, et al. Production of low- Cs+ rice plants by inactivation of the K+ transporter OsHAK1 with the CRISPR/Cas system. Plant J. 2017;92:43-56.
Tang L, Mao B, Li Y, Lv Q, Zhang L, Chen C, et al. Knockout of OsNramp5 using the CRISPR/Cas9 system produces low Cd-accumulating indica rice without compromising yield. Sci. Rep. 2017;7: 14438.
Wang FZ, Chen MX, Yu LJ, Xie LJ, Yuan LB, Qi H, et al. OsARM1, an R2R3 MYB transcription factor, is involved in regulation of the response to arsenic stress in rice. Front. Plant Sci. 2017;8:1868.
Zhou H, He M, Li J, Chen L, Huang Z, Zheng S, et al. Development of commercial thermo-sensitive genic male sterile rice accelerates hybrid rice breeding using the CRISPR/Cas9-mediated TMS5 editing system. Sci. Rep. 2016;6:37395.
Li J, Zhang H, Si X, Tian Y, Chen K, Liu J, et al. Generation of thermosensitive male-sterile maize by targeted knockout of the ZmTMS5 gene. J. Genet. Genom. 2017;44:465-68.
Li Q, Zhang D, Chen M, Liang W, Wei J, Qi Y, et al. Development of japonica photo-sensitive genic male sterile rice lines by editing carbon starved anther using CRISPR/Cas9. J. Genet. Genom. 2016;43: 415-19.
Singh M, Kumar M, Albertsen MC, Young JK, Cigan AM. Concurrent modifications in the three homologs of Ms45 gene with CRISPR/Cas9 lead to rapid generation of male sterile bread wheat (Triticum aestivum L.). Plant Mol. Biol. 2018;97:371-83.
Xie Y, Niu B, Long Y, Li G, Tang J, Zhang Y, et al. Suppression or knockout of SaF/SaM overcomes the Sa-mediated hybrid male sterility in rice. J. Integr. Plant Biol. 2017;59:669-79.
Xie Y, Xu P, Huang J, Ma S, Xie X, Tao D, et al. Interspecific hybrid sterility in rice is mediated by OgTPR1 at the S1 locus encoding a peptidase-like protein. Mol. Plant. 2017;10:1137-40.
Shen R, Wang L, Liu X, Wu J, Jin W, et al. Genomic structural variation-mediated allelic suppression causes hybrid male sterility in rice. Nat. Commun. 2017;8:1310.
Yu X, Zhao Z, Zheng X, Zhou J, Kong W, Zhao X, et al. A selfish genetic element confers Non-Mendelian inheritance in rice. Science. 2018;360:1130-32.
Khanday I, Skinner D, Yang B, Mercier R, Sundaresan V. A male-expressed rice embryogenic trigger redirected for asexual propagation through seeds. Nature. 2018;565:91-95.
Wang C, Liu Q, Shen Y, Hua Y, Wang J, Lin J, et al. Clonal seeds from hybrid rice by simultaneous genome engineering of meiosis and fertilization genes. Nat. Biotechnol. (In Press)
Available:https://doi.org/10.1038/s41587-018-0003-0
Li X, Zhou W, Ren Y, Tian X, Lv T, Wang Z, et al. High-efficiency breeding of early-maturing rice cultivars via CRISPR/Cas9-mediated genome editing. J. Genet. Genom. 2017;44:175-78.
Ye M, Peng Z, Tang D, Yang Z, Li D, et al. Generation of self-compatible diploid potato by knockout of S-R Nase. Nat. Plants. 2018;4:651-54.
Dong L, Li L, Liu C, Liu C, Shuaifeng G, Li X, et al. Genome editing and double fluorescence proteins enable robust maternal haploid induction and identification in maize. Mol. Plant. 2018;11:P1214-17.
Yao L, Zhang Y, Liu C, Liu Y, Wang Y, Liang D, et al. Os MATL mutation induces haploid seed formation in indica rice. Nat. Plants. 2018;4:530-33.
Luo M, Gilbert B, Ayliffe M. Applications of CRISPR/Cas9 technology for targeted mutagenesis, gene replacement and stacking of genes in higher plants. Plant Cell Rep. 2016;35:1439-50.
Shi J, Gao H,Wang H, Lafitte HR, Archibald RL, Yang M, et al. ARGOS8 variants generated by CRISPR/Cas9 improve maize grain yield under field drought stress conditions. Plant Biotechnol. J. 2017;15:207-16.
Yu QH, Wang B, Li N, Tang Y, Yang S, Yang T, et al. CRISPR/Cas9-induced targeted mutagenesis and gene replacement to generate long-shelf life tomato lines. Sci. Rep. 2017;7:11874.
Butler NM, Baltes NJ, Voytas DF, Douches DS. Geminivirus-mediated genome editing in potato (Solanum tuberosum L.) using sequence-specific nucleases. Front. Plant Sci. 2016;7:1045.
Cermák T, Baltes NJ, Cegan R, Zhang Y, Voytas DF. High-frequency, precise modification of the tomato genome. Genome Biol. 2015;16:232.
Dahan-Meir T, Filler-Hayut S, Melamed-Bessudo C, Bocobza S, Czosnek H, Aharoni A, et al. Efficient in planta gene targeting in tomato using geminiviral replicons and the CRISPR/Cas9 system. Plant J. 2018;95:5-16.
Wang M, Lu Y, Botella JR, Mao Y, Hua K, Zhu JK. Gene targeting by homology-directed repair in rice using a geminivirus-based CRISPR/Cas9 system. Mol. Plant. 2017;10:1007-10.
Gil-Humanes J, Wang Y, Liang Z, Shan Q, Ozuna CV, Sánchez-León S, et al. High-efficiency gene targeting in hexaploid wheat using DNA replicons and CRISPR/Cas9. Plant J. 2017;89:1251-62.
Hummel AW, Chauhan RD, Cermak T, Mutka AM, Vijayaraghavan A, Boyher A, et al. Allele exchange at the EPSPS locus confers glyphosate tolerance in cassava. Plant Biotechnol. J. 2017;16:1275-82.
Cermák T, Baltes NJ, Cegan R, Zhang Y, Voytas DF. High-frequency, precise modification of the tomato genome. Genome Biol. 2015;16:232.
Li Z, Liu ZB, Xing A, Moon BP, Koellhoffer JP, Huang L, et al. Cas9-guide RNA directed genome editing in soybean. Plant Physiol. 2015;169:960-70.
Svitashev S, Schwartz C, Lenderts B, Young JK, Mark Cigan A. Genome editing in maize directed by CRISPR/Cas9 ribonucleoprotein complexes. Nat. Commun. 2016;7:13274.
Svitashev S, Young JK, Schwartz C, Gao H, Falco SC, Cigan AM. Targeted mutagenesis, precise gene editing, and site-specific gene insertion in maize using Cas9 and guide RNA. Plant Physiol. 2015;169:931-45.
Butt H, Eid A, Ali Z, Atia MAM, Mokhtar MM, Hassan N, et al. Efficient CRISPR/Cas9-mediated genome editing using a chimeric single-guide RNA molecule. Front. Plant Sci. 2017;8:1441.
Endo M, Mikami M, Toki S. Biallelic gene targeting in rice. Plant Physiol. 2016;170: 667-77.
Sun Y, Zhang X, Wu C, He Y, Ma Y, Hou H, et al. Engineering herbicide-resistant rice plants through CRISPR/Cas9-mediated homologous recombination of Acetolactate synthase. Mol. Plant. 2016;9:628-31.
Sauer NJ, Narvaez-Vasquez J, Mozoruk J, Miller RB, Warburg ZJ, Gao C, et al. Oligonucleotide-mediated genome editing provides precision and function to engineered nucleases and antibiotics in plants. Plant Physiol. 2016;170:1917- 28.
Hummel AW, Chauhan RD, Cermak T, Mutka AM, Vijayaraghavan A, Boyher A, et al. Allele exchange at the EPSPS locus confers glyphosate tolerance in cassava. Plant Biotechnol. J. 2017;16:1275-82.
Li J, Meng X, Zong Y, Chen K, Zhang H, Li J, et al. Gene replacements and insertions in rice by intron targeting using CRISPR/Cas9. Nat. Plants. 2016;2:16139.
Li C, Zong Y, Wang Y, Jin S, Zhang D, Gao S, et al. Expanded base editing in rice and wheat using a Cas9-adenosine deaminase fusion. Genome Biol. 2018;19:59.
Shimatani Z, Kashojiya S, Takayama M, Terada R, Arazoe T, Isshi H, et al. Targeted base editing in rice and tomato using a CRISPR/Cas9 cytidine deaminase fusion. Nat. Biotechnol. 2017;35:441-43.
Zong Y, Song Q, Li C, Jin S, Zhang D, Wang Y, et al. Efficient C-to-T base editing in plants using a fusion of nCas9 and human APOBEC3A. Nat. Biotechnol. 2018;36:950-53.
Chen YY, Wang ZP, Ni HW, Xu Y, Chen QJ, Jiang LJ. CRISPR/Cas9-mediated base-editing system efficiently generates gain-of-function mutations in Arabidopsis. Sci. China Life Sci. 2017;60:520-23.
Tian S, Jiang L, Cui X, Zhang J, Guo S, Li M, et al. Engineering herbicide-resistant watermelon variety through CRISPR/Cas9-mediated base-editing. Plant Cell Rep. 2018;37:1353-56.
Kang BC, Yun JY, Kim ST, Shin Y, Ryu J, Choi M, et al. Precision genome engineering through adenine base editing in plants. Nat. Plants. 2018;4:427-431.
Xue C, Zhang H, Lin Q, Fan R, Gao C. Manipulating mRNA splicing by base editing in plants. Sci. China Life Sci. 2018;61:1293-300.
Li Z, Xiong X, Wang F, Li JF. Gene disruption through base-editing-induced mRNAmis-splicing in plants. New Phytol; 2018.
Available:https://doi.org/10.1111/nph.15647
Peng A, Chen S, Lei T, Xu L, He Y, Wu L, et al. Engineering canker-resistant plants through CRISPR/Cas9-targeted editing of the susceptibility gene CsLOB1 promoter in citrus. Plant Biotechnol. J. 2017;15: 1509-19.
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;13:578-89.
Rodríguez-Leal D, Lemmon ZH, Man J, Bartlett ME, Lippman ZB. Engineering quantitative trait variation for crop improvement by genome editing. Cell. 2017;171:470-80.
Von Arnim AG, Jia Q, Vaughn JN. Regulation of plant translation by upstream open reading frames. Plant Sci. 2014;214: 1-12.
Liang XH, Shen W, Sun H, Migawa MT, Vickers TA, Crooke ST. Translation efficiency of mRNAs is increased by antisense Oligonucleotides targeting upstream open reading frames. Nat. Biotechnol. 2016;34:875-80.
Zhang H, Si X, Ji X, Fan R, Liu J, Chen K, et al. Genome editing of upstream open reading frames enables translational control in plants. Nat. Biotechnol. 2018;36: 894-98.
Zhu B, Zhang W, Zhang T, Liu B, Jiang J. Genome-wide prediction and validation of intergenic enhancers in Arabidopsis using open chromatin signatures. Plant Cell. 2015;27:2415-26.
Zaidi SS, Tashkandi M, Mansoor S, Mahfouz MM. Engineering plant immunity: Using CRISPR/Cas9 to generate virus resistance. Front. Plant Sci. 2016;7:1673.
Ali Z, Abulfaraj A, Idris A, Ali S, Tashkandi M, Mahfouz M. CRISPR/Cas9-mediated viral interference in plants. Genome Biol. 2015;16:238.
Baltes NJ, Hummel AW, Konecna E, Cegan R, Bruns AN, Aaron N, et al. Conferring resistance to Gemini viruses with the CRISPR/Cas prokaryotic immune system. Nat. Plants. 2015;1:15145.
Ji X, Zhang H, Zhang Y, Wang Y, Gao C. Establishing a CRISPR/Cas-like immune system conferring DNA virus resistance in plants. Nat. Plants. 2015;1:15144.
Mehta D, Sturchler A, Hirsch-Hoffmann M, Gruissem W, Vanderschuren H. CRISPR/Cas9 interference in cassava linked to the evolution of editing-resistant geminiviruses. Bio Rxiv 314542.
Available:https://doi.org/10.1101/314542
Ji X, Si X, Zhang Y, Zhang H, Zhang F, Gao C. Conferring DNA virus resistance with high specificity in plants using a virus-inducible genome editing system. Genome Biol. 2018;19:197.
Zhang T, Zheng Q, Yi X, An H, Zhao Y, Ma S, et al. Establishing RNA virus resistance in plants by harnessing CRISPR immune system. Plant Biotechnol. J. 2018;16:1415-23.
Price AA, Sampson TR, Ratner HK, Grakoui A, Weiss DS. Cas9-mediated targeting of viral RNA in eukaryotic cells. PNAS. 2015;112:6164-69.
Nayak A, Tassetto M, Kunitomi M, Andino R. RNA interference-mediated intrinsic antiviral immunity in invertebrates. Curr. Top. Microbiol. Immunol. 2013;371:183-200.
Meng X, Yu H, Zhang Y, Zhuang F, Song X, Gao S, et al. Construction of a genome-wide mutant library in rice using CRISPR/Cas9. Mol. Plant. 2017;10:1238-41.
Jacobs TB, Zhang N, Patel D, Martin GB. Generation of a collection of mutant tomato lines using pooled CRISPR libraries. Plant Physiol. 2017;174:2023.
Osterberg JT, Xiang W, Olsen LI, Edenbrandt AK, Vedel SE, Christiansen A, et al. Accelerating the domestication of new crops: Feasibility and approaches. Trends Plant Sci. 2017;22:373-84.
Wang H, Studer AJ, Zhao Q, Meeley R, Doebley JF. Evidence that the origin of naked kernels during maize domestication was caused by a single amino acid substitution in tga1. Genetics. 2015;200: 965-74.
Komatsuda T, Pourkheirandish M, He C, Azhaguvel P, Kanamori H, Perovic D, et al. Six-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene. PNAS. 2007;104:1424-29.
Wagh SG, Kobayashi K, Yaeno T, Yamaoka N, Masuta C, Nishiguchi M. Rice necrosis mosaic virus, a fungal transmitted Bymovirus: Complete nucleotide sequence of the genomic RNAs and subgrouping of bymoviruses. J Gen Plant Pathol. 2016b;82:38-43.
Sedbrook JC, Phippen WB, Marks MD. New approaches to facilitate rapid domestication of a wild plant to an oilseed crop: Example pennycress (Thlaspi arvense L.). Plant Sci. 2014;227:122-32.
Li T, Yang X, Yu Y, Si X, Zhai X, Zhang H, et al. Domestication of wild tomato is accelerated by genome editing. Nat. Biotechnol. 2018;36:1160-63.
Zsogon A, Cermak T, Naves ER, Notini MM, Edel KH, Weinl S, et al. De novo domestication of wild tomato using genome editing. Nat. Biot. 2018;36;1211-1216.
Lemmon ZH, Reem NT, Dalrymple J, Soyk S, Swartwood KE, Weinl S, et al. Rapid improvement of domestication traits in an orphan crop by genome editing. Nat. Plants. 2018;4:766-70.
Nemhauser JL, Torii KU. Plant synthetic biology for molecular engineering of signalling and development. Nat. Plants. 2016;2:16010.
Temme K, Zhao D, Voigt CA. Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca. PNAS. 2012;109:7085-90.
Jusiak B, Cleto S, Perez-Piñera P, Lu TK. Engineering synthetic gene circuits in living cells with CRISPR technology. Trends Biotechnol. 2016;34:535-47.
Pohare MB, Akita M. Development of a precursor in a soluble form for protein import into chloroplasts. International Journal of Bio-Technology and Research. 2016;6(5):918.
Akita M, Pohare MB. Chloroplastic protein import characteristics of dihydrofolate reductase (DHFR) fused recombinant precursor protein in the presence of methotrexate. Biosci., Biotechnol. Res. Asia. 2016;13(4):2351-2358.
Eberhard S, Finazzi G, Wollman FA. The dynamics of photosynthesis. Annu. Rev. Genet. 2008;42:463515.
Waters MT, Langdale JA. The making of a chloroplast. EMBO J. 2009;28:2861-73.
Von Caemmerer S, Quick WP, Furbank RT. The development of C4 rice: Current progress and future challenges. Science. 2012;336:1671.
Pohare MB, Sharma M, Wagh SG. CRISPR/Cas9 genome editing and its medical potential. Advances in Biotechnology and Biosciences; 2019. (In Press)
Scheben A, Wolter F, Batley J, Puchta H, Edwards D. Towards CRISPR/Cas crops—bringing together genomics and genome editing. New Phytol. 2017;216:682-98.
Pacher M, Puchta H. From classical mutagenesis to nuclease-based breeding-directing natural DNA repair for a natural end-product. Plant J. 2017;90:819-33.
Pohare MB, Rathod HP, Shahakar SB, Kelatkar SK, Suryawanshi PP. Effects of UV radiations on morphological characters in In vitro regenerated Polianthes tuberosa. Research Journal of Agricultural Sciences. 2012;3:1307-1308.
Pohare MB, Batule BS, Bhor SA, Shahakar SB, Kelatkar SK, Varandani SP. Effect of Gamma radiations on the morphological characters in in vitro regenerated Polianthes tuberosa. Indian Horticulture Journal. 2013;3:95-97.
Li JF, Norville JE, Aach J, McCormack M, Zhang D, Bush J, et al. Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9. Nat. Biotechnol. 2013;31:688-91.
Nekrasov V, Staskawicz B, Weigel D, Jones JD, Kamoun S. Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease. Nat. Biotechnol. 2013;31: 691-93.
Shan Q, Wang Y, Li J, Zhang Y, Chen K, Liang Z, et al. Targeted genome modification of crop plants using a CRISPR/Cas system. Nat. Biotechnol. 2013;31:686-88.
Zetsche B, Gootenberg Jonathan S, Abudayyeh Omar O, Slaymaker Ian M, Makarova Kira S, Essletzbichler P, et al. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR/Cas system. Cell. 2015;163:759-71.
Shimatani Z, Kashojiya S, Takayama M, Terada R, Arazoe T, Ishii H, et al. Targeted base editing in rice and tomato using a CRISPR/Cas9 cytidine deaminase fusion. Nat. Biotechnol. 2013;35:441-43.
Makarova KS, Aravind L, Grishin NV, Rogozin IB, Koonin EV. A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis. Nucleic Acids Research. 2002;30:482-496.
Horvath P, Barrangou R. CRISPR/Cas, the immune system of bacteria and archaea. Science. 2010;327:167-170.
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;169:5429-5433.
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:E2579-E2586.
Hsu PD, Lander ES, Zhang F. Development and applications of CRISPR/Cas9 for genome engineering. Cell. 2014;157(6):1262-1278.
Brouns SJ, Jore MM, Lundgren M, Westra ER, Slijkhuis RJ, Snijders AP, et al. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science. 2008;321:960-964.
Deveau H, Barrangou R, Garneau JE, Labonté J, Fremaux C, Boyaval P, el al. Phage response to CRISPR-encoded resistance in Streptococcus thermophilus. Journal of Bacteriology. 2008;190:1390-1400.
Deveau H, Garneau JE, Moineau S. CRISPR/Cas system and its role in phage-bacteria interactions. Annual Review of Microbiology. 2010;64:475-493.
Bhaya D, Davison M, Barrangou R. CRISPR/Cas systems in bacteria and archaea: Versatile small RNAs for adaptive defense and regulation. Annual Review of Genetics. 2011;45:273-297.
Koonin EV, Makarova KS, Zhang F. Diversity classification and evolution of CRISPR/Cas systems. Curr. Opin. Microbiol. 2017;37:67-78.
Deltcheva E, Chylinski K, Sharma CM, Gonzales K, Chao Y, Pirzada ZA, el al. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature. 2011;471:602-608.
Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier EA. Programmable dual-RNA–guided DNA endonuclease in adaptive bacterial immunity. Science. 2012;12:258-59.
Doudna JA, Charpentier E. The new frontier of genome engineering with CRISPR/Cas9. Science. 2014;346(6213): 1258096.
Jiang F, Doudna JA. CRISPR/Cas9 structures and mechanisms. Annual Review of Biophysics. 2017;46:505-529.
Chen H, Choi J, Bailey S. Cut site selection by the two nuclease domains of the Cas9 RNA-guided endonuclease. Journal of Biological Chemistry. 2014;jbc-M113.
Cristea S, Freyvert Y, Santiago Y, Holmes MC, Urnov FD, Gregory PD, el al. In vivo cleavage of transgene donors promotes nuclease mediated targeted integration. Biotechnology and Bioengineering. 2013;110:871-880.
Cristea S, Freyvert Y, Santiago Y, Holmes MC, Urnov FD, Gregory PD. In vivo cleavage of transgene donors promotes nuclease mediated targeted integration. Biotechnology and Bioengineering. 2012;121:671-680.
Maresca M, Lin VG, Guo N, Yang Y. Obligate ligation-gated recombination (ObLiGaRe): custom-designed nuclease-mediated targeted integration through nonhomologous end joining. Genome Research. 2013;23:539-546.
Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N. Multiplex genome engineering using CRISPR/Cas systems. Science. 2013;339:819-23.
Gasiunas G, Barrangou R, Horvath P, Siksnys V. Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. PNAS. 2012;109:E2579-86.
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;337:816-21.
Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, et al. RNA-guided human genome engineering via Cas9. Science. 2013;339:823-26.
Wagh SG, Alam MM, Kobayashi K, Yaeno T, Yamaoka N, Toriba T, Hirano HY, Nishiguchi M. Analysis of rice RNA-dependent RNA polymerase 6 (OsRDR6) gene in response to viral, bacterial and fungal pathogens. J Gen Plant Pathol. 2016a;82:12-17.
Zhang J, Zhang H, Botella JR, Zhu JK. Generation of new glutinous rice by CRISPR/Cas9- targeted mutagenesis of the Waxy gene in elite rice varieties. J. Integr. Plant Biol. 2018;60:369-75.
Wang M, Lu Y, Botella JR, Mao Y, Hua K, Zhu JK. Gene targeting by homology-directed repair in rice using a geminivirus-based CRISPR/Cas9 system. Mol. Plant. 2017;10:1007-10.
Sun Y, Jiao G, Liu Z, Zhang X, Li J, Guo X, et al. Generation of high-amylose rice through CRISPR/Cas9- mediated targeted mutagenesis of starch branching enzymes. Front. Plant Sci. 2017;8:1298.
Shan Q, Zhang Y, Chen K, Zhang K, Gao C. Creation of fragrant rice by targeted knockout of the OsBADH2 gene using TALEN technology. Plant Biotechnol. J. 2015;13:791-800.
Sanchez-Leon S, Gil-Humanes J, Ozuna CV, Gimenez MJ, Sousa C, Voytas DF, et al. Low-gluten, nontransgenic wheat engineered with CRISPR/Cas9. Plant Biotechnol. J. 2018;16:902-10.
Jiang WZ, Henry IM, Lynagh PG, Comai L, Cahoon EB, Weeks DP. Significant enhancement of fatty acid composition in seeds of the allohexaploid, Camelina sativa, using CRISPR/Cas9 gene editing. Plant Biotechnol. J. 2017;15:648-57.
Morineau C, Bellec Y, Tellier F, Gissot L, Kelemen Z, Nogué F, et al. Selective gene dosage by CRISPR/Cas9 genome editing in hexaploid Camelina sativa. Plant Biotechnol. J. 2017;15:729-39.
Okuzaki A, Ogawa T, Koizuka C, Kaneko K, Inaba M, Imamura J, et al. CRISPR/Cas9-mediated genome editing of the fatty acid desaturase 2 gene in Brassica napus. Plant Physiol. Biochem. 2018;131:63-69.
Ito Y, Nishizawa-Yokoi A, Endo M, Mikami M, Toki S. CRISPR/Cas9-mediated mutagenesis of the RIN locus that regulates tomato fruit ripening. Biochem. Biophys. Res. Commun. 2015;467:76-82.
Li R, Fu D, Zhu B, Luo Y, Zhu H. CRISPR/Cas9-mediated mutagenesis of lncRNA1459 alters tomato fruit ripening. Plant J. 2018;94:513-24.
Li X, Wang Y, Chen S, Tian H, Fu D, Zhu B, et al. Lycopene is enriched in tomato fruit by CRISPR/Cas9- mediated multiplex genome editing. Front. Plant Sci. 2018;9: 559.
Li R, Li R, Li X, Fu D, Zhu B, Tian H, et al. Multiplexed CRISPR/Cas9-mediated metabolic engineering of γ-aminobutyric acid levels in Solanumly copersicum. Plant Biotechnol. J. 2018;16:415-27.
Nonaka S, Arai C, Takayama M, Matsukura C, Ezura H. Efficient increase of γ-aminobutyric acid (GABA) content in tomato fruits by targeted mutagenesis. Sci Rep. 2017;7:7057.
Nakayasu M, Akiyama R, Lee HJ, Osakabe K, Osakabe Y, Watanabe B. Generation of α-solanine-free hairy roots of potato by CRISPR/Cas9 mediated genome editing of the St16DOX gene. Plant Physiol. Biochem. 2018;131:70-77.
Wang Y, Cheng X, Shan Q, Zhang Y, Liu J, Guo C. Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew. Nat. Biotechnol. 2014;32:947-51.
Nekrasov V, Wang C, Win J, Lanz C, Weigel D, Kamoun S. Rapid generation of a transgene-free powdery mildew resistant tomato by genome deletion. Sci. Rep. 2017;7:482.
Wang F, Wang C, Liu P, Lei C, Hao W, Gao Y, et al. Enhanced rice blast resistance by CRISPR/Cas9- targeted mutagenesis of the ERF transcription factor gene OsERF922. PLOS ONE. 2016;11:e0154027.
Macovei A, Sevilla NR, Cantos C, Jonson GB, Slamet-Loedin I, Čermák T, et al. Novel alleles of rice eIF4G generated by CRISPR/Cas9-targeted mutagenesis confer resistance to rice tungro spherical virus. Plant Biotechnol. J. 2018;16:1918- 27.
Iqbal Z, Sattar MN, Shafiq M. CRISPR/Cas9: A tool to circumscribe cotton leaf curl disease. Front. Plant Sci. 2016;7:475.
Lu HP, Luo T, Fu HW, Wang L, Tan YY, Huang JZ, et al. Resistance of rice to insect pests mediated by suppression of serotonin biosynthesis. Nat. Plants. 2018;4:338-44.
Nieves-Cordones M, Mohamed S, Tanoi K, Kobayashi NI, Takagi K, Vernet A, et al. Production of low- Cs+ rice plants by inactivation of the K+ transporter OsHAK1 with the CRISPR/Cas system. Plant J. 2017;92:43-56.
Tang L, Mao B, Li Y, Lv Q, Zhang L, Chen C, et al. Knockout of OsNramp5 using the CRISPR/Cas9 system produces low Cd-accumulating indica rice without compromising yield. Sci. Rep. 2017;7: 14438.
Wang FZ, Chen MX, Yu LJ, Xie LJ, Yuan LB, Qi H, et al. OsARM1, an R2R3 MYB transcription factor, is involved in regulation of the response to arsenic stress in rice. Front. Plant Sci. 2017;8:1868.
Zhou H, He M, Li J, Chen L, Huang Z, Zheng S, et al. Development of commercial thermo-sensitive genic male sterile rice accelerates hybrid rice breeding using the CRISPR/Cas9-mediated TMS5 editing system. Sci. Rep. 2016;6:37395.
Li J, Zhang H, Si X, Tian Y, Chen K, Liu J, et al. Generation of thermosensitive male-sterile maize by targeted knockout of the ZmTMS5 gene. J. Genet. Genom. 2017;44:465-68.
Li Q, Zhang D, Chen M, Liang W, Wei J, Qi Y, et al. Development of japonica photo-sensitive genic male sterile rice lines by editing carbon starved anther using CRISPR/Cas9. J. Genet. Genom. 2016;43: 415-19.
Singh M, Kumar M, Albertsen MC, Young JK, Cigan AM. Concurrent modifications in the three homologs of Ms45 gene with CRISPR/Cas9 lead to rapid generation of male sterile bread wheat (Triticum aestivum L.). Plant Mol. Biol. 2018;97:371-83.
Xie Y, Niu B, Long Y, Li G, Tang J, Zhang Y, et al. Suppression or knockout of SaF/SaM overcomes the Sa-mediated hybrid male sterility in rice. J. Integr. Plant Biol. 2017;59:669-79.
Xie Y, Xu P, Huang J, Ma S, Xie X, Tao D, et al. Interspecific hybrid sterility in rice is mediated by OgTPR1 at the S1 locus encoding a peptidase-like protein. Mol. Plant. 2017;10:1137-40.
Shen R, Wang L, Liu X, Wu J, Jin W, et al. Genomic structural variation-mediated allelic suppression causes hybrid male sterility in rice. Nat. Commun. 2017;8:1310.
Yu X, Zhao Z, Zheng X, Zhou J, Kong W, Zhao X, et al. A selfish genetic element confers Non-Mendelian inheritance in rice. Science. 2018;360:1130-32.
Khanday I, Skinner D, Yang B, Mercier R, Sundaresan V. A male-expressed rice embryogenic trigger redirected for asexual propagation through seeds. Nature. 2018;565:91-95.
Wang C, Liu Q, Shen Y, Hua Y, Wang J, Lin J, et al. Clonal seeds from hybrid rice by simultaneous genome engineering of meiosis and fertilization genes. Nat. Biotechnol. (In Press)
Available:https://doi.org/10.1038/s41587-018-0003-0
Li X, Zhou W, Ren Y, Tian X, Lv T, Wang Z, et al. High-efficiency breeding of early-maturing rice cultivars via CRISPR/Cas9-mediated genome editing. J. Genet. Genom. 2017;44:175-78.
Ye M, Peng Z, Tang D, Yang Z, Li D, et al. Generation of self-compatible diploid potato by knockout of S-R Nase. Nat. Plants. 2018;4:651-54.
Dong L, Li L, Liu C, Liu C, Shuaifeng G, Li X, et al. Genome editing and double fluorescence proteins enable robust maternal haploid induction and identification in maize. Mol. Plant. 2018;11:P1214-17.
Yao L, Zhang Y, Liu C, Liu Y, Wang Y, Liang D, et al. Os MATL mutation induces haploid seed formation in indica rice. Nat. Plants. 2018;4:530-33.
Luo M, Gilbert B, Ayliffe M. Applications of CRISPR/Cas9 technology for targeted mutagenesis, gene replacement and stacking of genes in higher plants. Plant Cell Rep. 2016;35:1439-50.
Shi J, Gao H,Wang H, Lafitte HR, Archibald RL, Yang M, et al. ARGOS8 variants generated by CRISPR/Cas9 improve maize grain yield under field drought stress conditions. Plant Biotechnol. J. 2017;15:207-16.
Yu QH, Wang B, Li N, Tang Y, Yang S, Yang T, et al. CRISPR/Cas9-induced targeted mutagenesis and gene replacement to generate long-shelf life tomato lines. Sci. Rep. 2017;7:11874.
Butler NM, Baltes NJ, Voytas DF, Douches DS. Geminivirus-mediated genome editing in potato (Solanum tuberosum L.) using sequence-specific nucleases. Front. Plant Sci. 2016;7:1045.
Cermák T, Baltes NJ, Cegan R, Zhang Y, Voytas DF. High-frequency, precise modification of the tomato genome. Genome Biol. 2015;16:232.
Dahan-Meir T, Filler-Hayut S, Melamed-Bessudo C, Bocobza S, Czosnek H, Aharoni A, et al. Efficient in planta gene targeting in tomato using geminiviral replicons and the CRISPR/Cas9 system. Plant J. 2018;95:5-16.
Wang M, Lu Y, Botella JR, Mao Y, Hua K, Zhu JK. Gene targeting by homology-directed repair in rice using a geminivirus-based CRISPR/Cas9 system. Mol. Plant. 2017;10:1007-10.
Gil-Humanes J, Wang Y, Liang Z, Shan Q, Ozuna CV, Sánchez-León S, et al. High-efficiency gene targeting in hexaploid wheat using DNA replicons and CRISPR/Cas9. Plant J. 2017;89:1251-62.
Hummel AW, Chauhan RD, Cermak T, Mutka AM, Vijayaraghavan A, Boyher A, et al. Allele exchange at the EPSPS locus confers glyphosate tolerance in cassava. Plant Biotechnol. J. 2017;16:1275-82.
Cermák T, Baltes NJ, Cegan R, Zhang Y, Voytas DF. High-frequency, precise modification of the tomato genome. Genome Biol. 2015;16:232.
Li Z, Liu ZB, Xing A, Moon BP, Koellhoffer JP, Huang L, et al. Cas9-guide RNA directed genome editing in soybean. Plant Physiol. 2015;169:960-70.
Svitashev S, Schwartz C, Lenderts B, Young JK, Mark Cigan A. Genome editing in maize directed by CRISPR/Cas9 ribonucleoprotein complexes. Nat. Commun. 2016;7:13274.
Svitashev S, Young JK, Schwartz C, Gao H, Falco SC, Cigan AM. Targeted mutagenesis, precise gene editing, and site-specific gene insertion in maize using Cas9 and guide RNA. Plant Physiol. 2015;169:931-45.
Butt H, Eid A, Ali Z, Atia MAM, Mokhtar MM, Hassan N, et al. Efficient CRISPR/Cas9-mediated genome editing using a chimeric single-guide RNA molecule. Front. Plant Sci. 2017;8:1441.
Endo M, Mikami M, Toki S. Biallelic gene targeting in rice. Plant Physiol. 2016;170: 667-77.
Sun Y, Zhang X, Wu C, He Y, Ma Y, Hou H, et al. Engineering herbicide-resistant rice plants through CRISPR/Cas9-mediated homologous recombination of Acetolactate synthase. Mol. Plant. 2016;9:628-31.
Sauer NJ, Narvaez-Vasquez J, Mozoruk J, Miller RB, Warburg ZJ, Gao C, et al. Oligonucleotide-mediated genome editing provides precision and function to engineered nucleases and antibiotics in plants. Plant Physiol. 2016;170:1917- 28.
Hummel AW, Chauhan RD, Cermak T, Mutka AM, Vijayaraghavan A, Boyher A, et al. Allele exchange at the EPSPS locus confers glyphosate tolerance in cassava. Plant Biotechnol. J. 2017;16:1275-82.
Li J, Meng X, Zong Y, Chen K, Zhang H, Li J, et al. Gene replacements and insertions in rice by intron targeting using CRISPR/Cas9. Nat. Plants. 2016;2:16139.
Li C, Zong Y, Wang Y, Jin S, Zhang D, Gao S, et al. Expanded base editing in rice and wheat using a Cas9-adenosine deaminase fusion. Genome Biol. 2018;19:59.
Shimatani Z, Kashojiya S, Takayama M, Terada R, Arazoe T, Isshi H, et al. Targeted base editing in rice and tomato using a CRISPR/Cas9 cytidine deaminase fusion. Nat. Biotechnol. 2017;35:441-43.
Zong Y, Song Q, Li C, Jin S, Zhang D, Wang Y, et al. Efficient C-to-T base editing in plants using a fusion of nCas9 and human APOBEC3A. Nat. Biotechnol. 2018;36:950-53.
Chen YY, Wang ZP, Ni HW, Xu Y, Chen QJ, Jiang LJ. CRISPR/Cas9-mediated base-editing system efficiently generates gain-of-function mutations in Arabidopsis. Sci. China Life Sci. 2017;60:520-23.
Tian S, Jiang L, Cui X, Zhang J, Guo S, Li M, et al. Engineering herbicide-resistant watermelon variety through CRISPR/Cas9-mediated base-editing. Plant Cell Rep. 2018;37:1353-56.
Kang BC, Yun JY, Kim ST, Shin Y, Ryu J, Choi M, et al. Precision genome engineering through adenine base editing in plants. Nat. Plants. 2018;4:427-431.
Xue C, Zhang H, Lin Q, Fan R, Gao C. Manipulating mRNA splicing by base editing in plants. Sci. China Life Sci. 2018;61:1293-300.
Li Z, Xiong X, Wang F, Li JF. Gene disruption through base-editing-induced mRNAmis-splicing in plants. New Phytol; 2018.
Available:https://doi.org/10.1111/nph.15647
Peng A, Chen S, Lei T, Xu L, He Y, Wu L, et al. Engineering canker-resistant plants through CRISPR/Cas9-targeted editing of the susceptibility gene CsLOB1 promoter in citrus. Plant Biotechnol. J. 2017;15: 1509-19.
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;13:578-89.
Rodríguez-Leal D, Lemmon ZH, Man J, Bartlett ME, Lippman ZB. Engineering quantitative trait variation for crop improvement by genome editing. Cell. 2017;171:470-80.
Von Arnim AG, Jia Q, Vaughn JN. Regulation of plant translation by upstream open reading frames. Plant Sci. 2014;214: 1-12.
Liang XH, Shen W, Sun H, Migawa MT, Vickers TA, Crooke ST. Translation efficiency of mRNAs is increased by antisense Oligonucleotides targeting upstream open reading frames. Nat. Biotechnol. 2016;34:875-80.
Zhang H, Si X, Ji X, Fan R, Liu J, Chen K, et al. Genome editing of upstream open reading frames enables translational control in plants. Nat. Biotechnol. 2018;36: 894-98.
Zhu B, Zhang W, Zhang T, Liu B, Jiang J. Genome-wide prediction and validation of intergenic enhancers in Arabidopsis using open chromatin signatures. Plant Cell. 2015;27:2415-26.
Zaidi SS, Tashkandi M, Mansoor S, Mahfouz MM. Engineering plant immunity: Using CRISPR/Cas9 to generate virus resistance. Front. Plant Sci. 2016;7:1673.
Ali Z, Abulfaraj A, Idris A, Ali S, Tashkandi M, Mahfouz M. CRISPR/Cas9-mediated viral interference in plants. Genome Biol. 2015;16:238.
Baltes NJ, Hummel AW, Konecna E, Cegan R, Bruns AN, Aaron N, et al. Conferring resistance to Gemini viruses with the CRISPR/Cas prokaryotic immune system. Nat. Plants. 2015;1:15145.
Ji X, Zhang H, Zhang Y, Wang Y, Gao C. Establishing a CRISPR/Cas-like immune system conferring DNA virus resistance in plants. Nat. Plants. 2015;1:15144.
Mehta D, Sturchler A, Hirsch-Hoffmann M, Gruissem W, Vanderschuren H. CRISPR/Cas9 interference in cassava linked to the evolution of editing-resistant geminiviruses. Bio Rxiv 314542.
Available:https://doi.org/10.1101/314542
Ji X, Si X, Zhang Y, Zhang H, Zhang F, Gao C. Conferring DNA virus resistance with high specificity in plants using a virus-inducible genome editing system. Genome Biol. 2018;19:197.
Zhang T, Zheng Q, Yi X, An H, Zhao Y, Ma S, et al. Establishing RNA virus resistance in plants by harnessing CRISPR immune system. Plant Biotechnol. J. 2018;16:1415-23.
Price AA, Sampson TR, Ratner HK, Grakoui A, Weiss DS. Cas9-mediated targeting of viral RNA in eukaryotic cells. PNAS. 2015;112:6164-69.
Nayak A, Tassetto M, Kunitomi M, Andino R. RNA interference-mediated intrinsic antiviral immunity in invertebrates. Curr. Top. Microbiol. Immunol. 2013;371:183-200.
Meng X, Yu H, Zhang Y, Zhuang F, Song X, Gao S, et al. Construction of a genome-wide mutant library in rice using CRISPR/Cas9. Mol. Plant. 2017;10:1238-41.
Jacobs TB, Zhang N, Patel D, Martin GB. Generation of a collection of mutant tomato lines using pooled CRISPR libraries. Plant Physiol. 2017;174:2023.
Osterberg JT, Xiang W, Olsen LI, Edenbrandt AK, Vedel SE, Christiansen A, et al. Accelerating the domestication of new crops: Feasibility and approaches. Trends Plant Sci. 2017;22:373-84.
Wang H, Studer AJ, Zhao Q, Meeley R, Doebley JF. Evidence that the origin of naked kernels during maize domestication was caused by a single amino acid substitution in tga1. Genetics. 2015;200: 965-74.
Komatsuda T, Pourkheirandish M, He C, Azhaguvel P, Kanamori H, Perovic D, et al. Six-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene. PNAS. 2007;104:1424-29.
Wagh SG, Kobayashi K, Yaeno T, Yamaoka N, Masuta C, Nishiguchi M. Rice necrosis mosaic virus, a fungal transmitted Bymovirus: Complete nucleotide sequence of the genomic RNAs and subgrouping of bymoviruses. J Gen Plant Pathol. 2016b;82:38-43.
Sedbrook JC, Phippen WB, Marks MD. New approaches to facilitate rapid domestication of a wild plant to an oilseed crop: Example pennycress (Thlaspi arvense L.). Plant Sci. 2014;227:122-32.
Li T, Yang X, Yu Y, Si X, Zhai X, Zhang H, et al. Domestication of wild tomato is accelerated by genome editing. Nat. Biotechnol. 2018;36:1160-63.
Zsogon A, Cermak T, Naves ER, Notini MM, Edel KH, Weinl S, et al. De novo domestication of wild tomato using genome editing. Nat. Biot. 2018;36;1211-1216.
Lemmon ZH, Reem NT, Dalrymple J, Soyk S, Swartwood KE, Weinl S, et al. Rapid improvement of domestication traits in an orphan crop by genome editing. Nat. Plants. 2018;4:766-70.
Nemhauser JL, Torii KU. Plant synthetic biology for molecular engineering of signalling and development. Nat. Plants. 2016;2:16010.
Temme K, Zhao D, Voigt CA. Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca. PNAS. 2012;109:7085-90.
Jusiak B, Cleto S, Perez-Piñera P, Lu TK. Engineering synthetic gene circuits in living cells with CRISPR technology. Trends Biotechnol. 2016;34:535-47.
Pohare MB, Akita M. Development of a precursor in a soluble form for protein import into chloroplasts. International Journal of Bio-Technology and Research. 2016;6(5):918.
Akita M, Pohare MB. Chloroplastic protein import characteristics of dihydrofolate reductase (DHFR) fused recombinant precursor protein in the presence of methotrexate. Biosci., Biotechnol. Res. Asia. 2016;13(4):2351-2358.
Eberhard S, Finazzi G, Wollman FA. The dynamics of photosynthesis. Annu. Rev. Genet. 2008;42:463515.
Waters MT, Langdale JA. The making of a chloroplast. EMBO J. 2009;28:2861-73.
Von Caemmerer S, Quick WP, Furbank RT. The development of C4 rice: Current progress and future challenges. Science. 2012;336:1671.
Pohare MB, Sharma M, Wagh SG. CRISPR/Cas9 genome editing and its medical potential. Advances in Biotechnology and Biosciences; 2019. (In Press)
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