CRISPR-Based Genome Editing Tools: Insights into Technological Breakthroughs and Future Challenges

. 2021 May 24 ; 12 (6) : . [epub] 20210524

Jazyk angličtina Země Švýcarsko Médium electronic

Typ dokumentu časopisecké články, práce podpořená grantem, přehledy

Perzistentní odkaz   https://www.medvik.cz/link/pmid34073848

Genome-editing (GE) is having a tremendous influence around the globe in the life science community. Among its versatile uses, the desired modifications of genes, and more importantly the transgene (DNA)-free approach to develop genetically modified organism (GMO), are of special interest. The recent and rapid developments in genome-editing technology have given rise to hopes to achieve global food security in a sustainable manner. We here discuss recent developments in CRISPR-based genome-editing tools for crop improvement concerning adaptation, opportunities, and challenges. Some of the notable advances highlighted here include the development of transgene (DNA)-free genome plants, the availability of compatible nucleases, and the development of safe and effective CRISPR delivery vehicles for plant genome editing, multi-gene targeting and complex genome editing, base editing and prime editing to achieve more complex genetic engineering. Additionally, new avenues that facilitate fine-tuning plant gene regulation have also been addressed. In spite of the tremendous potential of CRISPR and other gene editing tools, major challenges remain. Some of the challenges are related to the practical advances required for the efficient delivery of CRISPR reagents and for precision genome editing, while others come from government policies and public acceptance. This review will therefore be helpful to gain insights into technological advances, its applications, and future challenges for crop improvement.

Centre of Research for Development University of Kashmir Srinagar 190006 India

Department of Agronomy Faculty of Agriculture Kafrelsheikh University Kafrelsheikh 33516 Egypt

Department of Bioresources University of Kashmir Srinagar 190006 India

Department of Biotechnology BGSB University Jammu 185234 India

Department of Botany and Plant Physiology Faculty of Agrobiology Food and Natural Resources Czech University of Life Sciences Prague Kamycka 129 165 00 Prague Czech Republic

Department of Crop Science Institute of Crop Science and Resource Conservation University Bonn 53115 Bonn Germany

Department of Field Crops Faculty of Agriculture Siirt University Siirt 56100 Turkey

Department of Horticulture Faculty of Agriculture Siirt University Siirt 56100 Turkey

Department of Plant Physiology Slovak University of Agriculture Nitra Tr A Hlinku 2 949 01 Nitra Slovakia

Division of Plant Pathology Sher e Kashmir University of Agricultural Sciences and Technology of Jammu Jammu 180009 India

ICAR National Institute for Plant Biotechnology New Delhi 110012 India

Mountain Research Centre for Field Crops Khudwani Sher e Kashmir University of Agricultural Sciences and Technology of Kashmir Jammu 192101 India

Plant Physiology and Biochemistry Section Department of Botany Aligarh Muslim University Aigarh 202002 India

School of Biotechnology Sher e Kashmir University of Agricultural Sciences and Technology of Jammu Jammu 180009 India

School of Biotechnology University of Jammu Jammu 180006 India

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Hickey L.T., Hafeez A.N., Robinson H., Jackson S.A., Leal-Bertioli S.C.M., Tester M., Gao C., Godwin I.D., Hayes B.J., Wulff B.B.H. Breeding crops to feed 10 billion. Nat. Biotechnol. 2019;37:744–754. doi: 10.1038/s41587-019-0152-9. PubMed DOI

Clarke J.L., Zhang P. Plant biotechnology for food security and bioeconomy. Plant Mol. Biol. 2013;83:1–3. doi: 10.1007/s11103-013-0097-1. PubMed DOI

Haque E., Taniguchi H., Hassan M., Bhowmik P., Karim M.R., Śmiech M., Zhao K., Rahman M., Islam T. Application of CRISPR/Cas9 genome editing technology for the improvement of crops cultivated in tropical climates: Recent progress, prospects, and challenges. Front. Plant Sci. 2018;9:617. doi: 10.3389/fpls.2018.00617. PubMed DOI PMC

Chen K., Wang Y., Zhang R., Zhang H., Gao C. CRISPR/Cas genome editing and precision plant breeding in agriculture. Annu. Rev. Plant Biol. 2019;70:667–697. doi: 10.1146/annurev-arplant-050718-100049. PubMed DOI

Zhang C., Xu W., Wang F., Kang G., Yuan S., Lv X., Li L., Liu Y., Yang J. Expanding the base editing scope to GA and relaxed NG PAM sites by improved xCas9 system. Plant Biotechnol. J. 2020;18:884. doi: 10.1111/pbi.13259. PubMed DOI PMC

Adamu A.K., Aliyu H. Morphogical effects of sodium azide on tomato (Lycopersicon esculentum Mill) Sci. World J. 2007;2:777–780. doi: 10.4314/swj.v2i4.51755. DOI

Mba C., Afza R., Bado S., Jain S.M. Induced mutagenesis in plants using physical and chemical agents. Plant Cell Cult. Essent. Methods. 2010;20:111–130.

Mostafa G.G. Effect of Sodium Azide on the Grovvth and Variability Induction in. Int. J. Plant Breed. Genet. 2011;5:76–85. doi: 10.3923/ijpbg.2011.76.85. DOI

Pacher M., Puchta H. From classical mutagenesis to nuclease-based breeding–directing natural DNA repair for a natural end-product. Plant J. 2017;90:819–833. doi: 10.1111/tpj.13469. PubMed DOI

Chaudhary J., Alisha A., Bhatt V., Chandanshive S., Kumar N., Mir Z., Kumar A., Yadav S.K., Shivaraj S.M., Sonah H. Mutation breeding in tomato: Advances, applicability and challenges. Plants. 2019;8:128. doi: 10.3390/plants8050128. PubMed DOI PMC

Wright I.J., Reich P.B., Cornelissen J.H.C., Falster D.S., Groom P.K., Hikosaka K., Lee W., Lusk C.H., Niinemets Ü., Oleksyn J. Modulation of leaf economic traits and trait relationships by climate. Glob. Ecol. Biogeogr. 2005;14:411–421. doi: 10.1111/j.1466-822x.2005.00172.x. DOI

Maggio I., Goncalves M.A.F.V. Genome editing at the crossroads of delivery, specificity, and fidelity. Trends Biotechnol. 2015;33:280–291. doi: 10.1016/j.tibtech.2015.02.011. PubMed DOI

Mishra R., Zhao K. Genome editing technologies and their applications in crop improvement. Plant Biotechnol. Rep. 2018;12:57–68. doi: 10.1007/s11816-018-0472-0. DOI

Mushtaq M., Sakina A., Wani S.H., Shikari A.B., Tripathi P., Zaid A., Galla A., Abdelrahman M., Sharma M., Singh A.K. Harnessing genome editing techniques to engineer disease resistance in plants. Front. Plant Sci. 2019;10:550. doi: 10.3389/fpls.2019.00550. PubMed DOI PMC

Bao W., Wan Y., Baluška F. Nanosheets for delivery of biomolecules into plant cells. Trends Plant Sci. 2017;22:445–447. doi: 10.1016/j.tplants.2017.03.014. PubMed DOI

Li H., Li J., Chen J., Yan L., Xia L. Precise modifications of both exogenous and endogenous genes in rice by prime editing. Mol. Plant. 2020;13:671–674. doi: 10.1016/j.molp.2020.03.011. PubMed DOI

El-Mounadi K., Morales-Floriano M.L., Garcia-Ruiz H. Principles, applications, and biosafety of plant genome editing using CRISPR-Cas9. Front. Plant Sci. 2020;11:56. doi: 10.3389/fpls.2020.00056. PubMed DOI PMC

Jaganathan D., Ramasamy K., Sellamuthu G., Jayabalan S., Venkataraman G. CRISPR for crop improvement: An update review. Front. Plant Sci. 2018;9:985. doi: 10.3389/fpls.2018.00985. PubMed DOI PMC

Puchta H., Dujon B., Hohn B. Two different but related mechanisms are used in plants for the repair of genomic double-strand breaks by homologous recombination. Proc. Natl. Acad. Sci. USA. 1996;93:5055–5060. doi: 10.1073/pnas.93.10.5055. PubMed DOI PMC

Symington L.S., Gautier J. Double-strand break end resection and repair pathway choice. Annu. Rev. Genet. 2011;45:247–271. doi: 10.1146/annurev-genet-110410-132435. PubMed DOI

Sedeek K.E.M., Mahas A., Mahfouz M. Plant genome engineering for targeted improvement of crop traits. Front. Plant Sci. 2019;10:114. doi: 10.3389/fpls.2019.00114. PubMed DOI PMC

Mali P., Esvelt K.M., Church G.M. Cas9 as a versatile tool for engineering biology. Nat. Methods. 2013;10:957–963. doi: 10.1038/nmeth.2649. PubMed DOI PMC

Bortesi L., Fischer R. The CRISPR/Cas9 system for plant genome editing and beyond. Biotechnol. Adv. 2015;33:41–52. doi: 10.1016/j.biotechadv.2014.12.006. PubMed DOI

Gaj T., Gersbach C.A., Barbas Iii C.F. ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol. 2013;31:397–405. doi: 10.1016/j.tibtech.2013.04.004. PubMed DOI PMC

Lozano-Juste J., Cutler S.R. Plant genome engineering in full bloom. Trends Plant Sci. 2014;19:284–287. doi: 10.1016/j.tplants.2014.02.014. PubMed DOI

Jiang W.Z., Henry I.M., Lynagh P.G., Comai L., Cahoon E.B., Weeks D.P. Significant enhancement of fatty acid composition in seeds of the allohexaploid, Camelina sativa, using CRISPR/Cas9 gene editing. Plant Biotechnol. J. 2017;15:648–657. doi: 10.1111/pbi.12663. PubMed DOI PMC

Mohanta T.K., Bashir T., Hashem A., Abd_Allah E.F., Bae H. Genome editing tools in plants. Genes. 2017;8:399. doi: 10.3390/genes8120399. PubMed DOI PMC

Vats S., Kumawat S., Kumar V., Patil G.B., Joshi T., Sonah H., Sharma T.R., Deshmukh R. Genome editing in plants: Exploration of technological advancements and challenges. Cells. 2019;8:1386. doi: 10.3390/cells8111386. PubMed DOI PMC

Bannikov A.V., Lavrov A.V. CRISPR/CAS9, the king of genome editing tools. Mol. Biol. 2017;51:514–525. doi: 10.1134/S0026893317040033. PubMed DOI

Karimian A., Azizian K., Parsian H., Rafieian S., Shafiei-Irannejad V., Kheyrollah M., Yousefi M., Majidinia M., Yousefi B. CRISPR/Cas9 technology as a potent molecular tool for gene therapy. J. Cell. Physiol. 2019;234:12267–12277. doi: 10.1002/jcp.27972. PubMed DOI

Nussenzweig P.M., Marraffini L.A. Molecular Mechanisms of CRISPR-Cas Immunity in Bacteria. Annu. Rev. Genet. 2020;54:93–120. doi: 10.1146/annurev-genet-022120-112523. PubMed DOI

Murugan K., Babu K., Sundaresan R., Rajan R., Sashital D.G. The revolution continues: Newly discovered systems expand the CRISPR-Cas toolkit. Mol. Cell. 2017;68:15–25. doi: 10.1016/j.molcel.2017.09.007. PubMed DOI PMC

Steinert J., Schiml S., Fauser F., Puchta H. Highly efficient heritable plant genome engineering using Cas9 orthologues from Streptococcus thermophilus and Staphylococcus aureus. Plant J. 2015;84:1295–1305. doi: 10.1111/tpj.13078. PubMed DOI

Zetsche B., Gootenberg J.S., Abudayyeh O.O., Slaymaker I.M., Makarova K.S., Essletzbichler P., Volz S.E., Joung J., Van Der Oost J., Regev A. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell. 2015;163:759–771. doi: 10.1016/j.cell.2015.09.038. PubMed DOI PMC

Zetsche B., Heidenreich M., Mohanraju P., Fedorova I., Kneppers J., DeGennaro E.M., Winblad N., Choudhury S.R., Abudayyeh O.O., Gootenberg J.S. Erratum: Multiplex gene editing by CRISPR–Cpf1 using a single crRNA array. Nat. Biotechnol. 2017;35:178. doi: 10.1038/nbt0217-178b. PubMed DOI

Mitsunobu H., Teramoto J., Nishida K., Kondo A. Beyond native Cas9: Manipulating genomic information and function. Trends Biotechnol. 2017;35:983–996. doi: 10.1016/j.tibtech.2017.06.004. PubMed DOI

Nishimasu H., Shi X., Ishiguro S., Gao L., Hirano S., Okazaki S., Noda T., Abudayyeh O.O., Gootenberg J.S., Mori H. Engineered CRISPR-Cas9 nuclease with expanded targeting space. Science. 2018;361:1259–1262. doi: 10.1126/science.aas9129. PubMed DOI PMC

Endo M., Mikami M., Endo A., Kaya H., Itoh T., Nishimasu H., Nureki O., Toki S. Genome editing in plants by engineered CRISPR–Cas9 recognizing NG PAM. Nat. Plants. 2019;5:14–17. doi: 10.1038/s41477-018-0321-8. PubMed DOI

Mao Y., Botella J.R., Liu Y., Zhu J.K. Gene editing in plants: Progress and challenges. Natl. Sci. Rev. 2019;6:421–437. doi: 10.1093/nsr/nwz005. PubMed DOI PMC

Baltes N.J., Gil-Humanes J., Cermak T., Atkins P.A., Voytas D.F. DNA replicons for plant genome engineering. Plant Cell. 2014;26:151–163. doi: 10.1105/tpc.113.119792. PubMed DOI PMC

Lin S., Staahl B., Alla R.K., Doudna J.A. Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery. Elife. 2014;3:e04766. doi: 10.7554/eLife.04766. PubMed DOI PMC

Zheng X., Qi C., Yang L., Quan Q., Liu B., Zhong Z., Tang X., Fan T., Zhou J., Zhang Y. The Improvement of CRISPR-Cas9 system With Ubiquitin-Associated Domain Fusion for Efficient Plant Genome Editing. Front. Plant Sci. 2020;11:621. doi: 10.3389/fpls.2020.00621. PubMed DOI PMC

Wolabu T.W., Park J., Chen M., Cong L., Ge Y., Jiang Q., Debnath S., Li G., Wen J., Wang Z. Improving the genome editing efficiency of CRISPR/Cas9 in Arabidopsis and Medicago truncatula. Planta. 2020;252:15. doi: 10.1007/s00425-020-03415-0. PubMed DOI PMC

Bortesi L., Zhu C., Zischewski J., Perez L., Bassié L., Nadi R., Forni G., Lade S.B., Soto E., Jin X. Patterns of CRISPR/Cas9 activity in plants, animals and microbes. Plant Biotechnol. J. 2016;14:2203–2216. doi: 10.1111/pbi.12634. PubMed DOI PMC

Abdelrahman M., Al-Sadi A.M., Pour-Aboughadareh A., Burritt D.J., Tran L.-S.P. Genome editing using CRISPR/Cas9–targeted mutagenesis: An opportunity for yield improvements of crop plants grown under environmental stresses. Plant Physiol. Biochem. 2018;131:31–36. doi: 10.1016/j.plaphy.2018.03.012. PubMed DOI

Ron M., Kajala K., Pauluzzi G., Wang D., Reynoso M.A., Zumstein K., Garcha J., Winte S., Masson H., Inagaki S. Hairy root transformation using Agrobacterium rhizogenes as a tool for exploring cell type-specific gene expression and function using tomato as a model. Plant Physiol. 2014;166:455–469. doi: 10.1104/pp.114.239392. PubMed DOI PMC

Lloyd A.H., Wang D., Timmis J.N. Single molecule PCR reveals similar patterns of non-homologous DSB repair in tobacco and Arabidopsis. PLoS ONE. 2012;7:e32255. doi: 10.1371/journal.pone.0032255. PubMed DOI PMC

Lawrenson T., Harwood W.A. Barley. Springer; Amsterdam, The Netherlands: 2019. Creating targeted gene knockouts in barley using CRISPR/Cas9; pp. 217–232. PubMed

Manova V., Gruszka D. DNA damage and repair in plants–from models to crops. Front. Plant Sci. 2015;6:885. doi: 10.3389/fpls.2015.00885. PubMed DOI PMC

Nambiar T.S., Billon P., Diedenhofen G., Hayward S.B., Taglialatela A., Cai K., Huang J.-W., Leuzzi G., Cuella-Martin R., Palacios A. Stimulation of CRISPR-mediated homology-directed repair by an engineered RAD18 variant. Nat. Commun. 2019;10:1–13. doi: 10.1038/s41467-019-11105-z. PubMed DOI PMC

Puchta H. The repair of double-strand breaks in plants: Mechanisms and consequences for genome evolution. J. Exp. Bot. 2005;56:1–14. doi: 10.1093/jxb/eri025. PubMed DOI

Miki D., Zhang W., Zeng W., Feng Z., Zhu J.-K. CRISPR/Cas9-mediated gene targeting in Arabidopsis using sequential transformation. Nat. Commun. 2018;9:1–9. doi: 10.1038/s41467-018-04416-0. PubMed DOI PMC

Wolter F., Klemm J., Puchta H. Efficient in planta gene targeting in Arabidopsis using egg cell-specific expression of the Cas9 nuclease of Staphylococcus aureus. Plant J. 2018;94:735–746. doi: 10.1111/tpj.13893. PubMed DOI

Begemann M.B., Gray B.N., January E., Gordon G.C., He Y., Liu H., Wu X., Brutnell T.P., Mockler T.C., Oufattole M. Precise insertion and guided editing of higher plant genomes using Cpf1 CRISPR nucleases. Sci. Rep. 2017;7:1–6. doi: 10.1038/s41598-017-11760-6. PubMed DOI PMC

Wang M., Mao Y., Lu Y., Tao X., Zhu J.-k. Multiplex gene editing in rice using the CRISPR-Cpf1 system. Mol. Plant. 2017;10:1011–1013. doi: 10.1016/j.molp.2017.03.001. PubMed DOI

Li J., Zhang X., Sun Y., Zhang J., Du W., Guo X., Li S., Zhao Y., Xia L. Efficient allelic replacement in rice by gene editing: A case study of the NRT1. 1B gene. J. Integr. Plant Biol. 2018;60:536–540. doi: 10.1111/jipb.12650. PubMed DOI

Svitashev S., Schwartz C., Lenderts B., Young J.K., Cigan A.M. Genome editing in maize directed by CRISPR–Cas9 ribonucleoprotein complexes. Nat. Commun. 2016;7:1–7. doi: 10.1038/ncomms13274. PubMed DOI PMC

Li Z., Liu Z.-B., Xing A., Moon B.P., Koellhoffer J.P., Huang L., Ward R.T., Clifton E., Falco S.C., Cigan A.M. Cas9-guide RNA directed genome editing in soybean. Plant Physiol. 2015;169:960–970. doi: 10.1104/pp.15.00783. PubMed DOI PMC

Gil-Humanes J., Wang Y., Liang Z., Shan Q., Ozuna C.V., Sánchez-León S., Baltes N.J., Starker C., Barro F., Gao C. High-efficiency gene targeting in hexaploid wheat using DNA replicons and CRISPR/Cas9. Plant J. 2017;89:1251–1262. doi: 10.1111/tpj.13446. PubMed DOI PMC

Butler N.M., Douches D.S. Sequence-specific nucleases for genetic improvement of potato. Am. J. Potato Res. 2016;93:303–320. doi: 10.1007/s12230-016-9513-9. DOI

Gasparis S., Kała M., Przyborowski M., Łyżnik L.A., Orczyk W., Nadolska-Orczyk A. A simple and efficient CRISPR/Cas9 platform for induction of single and multiple, heritable mutations in barley (Hordeum vulgare L.) Plant Methods. 2018;14:1–14. doi: 10.1186/s13007-018-0382-8. PubMed DOI PMC

Li J.-F., Norville J.E., Aach J., McCormack M., Zhang D., Bush J., Church G.M., Sheen 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. PubMed DOI PMC

Li C., Unver T., Zhang B. A high-efficiency CRISPR/Cas9 system for targeted mutagenesis in Cotton (Gossypium hirsutum L.) Sci. Rep. 2017;7:1–10. doi: 10.1038/srep43902. PubMed DOI PMC

Sauer N.J., Mozoruk J., Miller R.B., Warburg Z.J., Walker K.A., Beetham P.R., Schöpke C.R., Gocal G.F.W. Oligonucleotide-directed mutagenesis for precision gene editing. Plant Biotechnol. J. 2016;14:496–502. doi: 10.1111/pbi.12496. PubMed DOI PMC

Zhao Y., Zhang C., Liu W., Gao W., Liu C., Song G., Li W.-X., Mao L., Chen B., Xu Y. An alternative strategy for targeted gene replacement in plants using a dual-sgRNA/Cas9 design. Sci. Rep. 2016;6:1–11. doi: 10.1038/srep23890. PubMed DOI PMC

Nishizawa-Yokoi A., Endo M., Ohtsuki N., Saika H., Toki S. Precision genome editing in plants via gene targeting and piggy B ac-mediated marker excision. Plant J. 2015;81:160–168. doi: 10.1111/tpj.12693. PubMed DOI PMC

Čermák T., Curtin S.J., Gil-Humanes J., Čegan R., Kono T.J.Y., Konečná E., Belanto J.J., Starker C.G., Mathre J.W., Greenstein R.L. A multipurpose toolkit to enable advanced genome engineering in plants. Plant Cell. 2017;29:1196–1217. doi: 10.1105/tpc.16.00922. PubMed DOI PMC

Butt H., Eid A., Ali Z., Atia M.A.M., Mokhtar M.M., Hassan N., Lee C.M., Bao G., Mahfouz M.M. Efficient CRISPR/Cas9-mediated genome editing using a chimeric single-guide RNA molecule. Front. Plant Sci. 2017;8:1441. doi: 10.3389/fpls.2017.01441. PubMed DOI PMC

Komor A.C., Kim Y.B., Packer M.S., Zuris J.A., Liu D.R. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature. 2016;533:420–424. doi: 10.1038/nature17946. PubMed DOI PMC

Mushtaq M., Bhat J.A., Mir Z.A., Sakina A., Ali S., Singh A.K., Tyagi A., Salgotra R.K., Dar A.A., Bhat R. CRISPR/Cas approach: A new way of looking at plant-abiotic interactions. J. Plant Physiol. 2018;224:156–162. doi: 10.1016/j.jplph.2018.04.001. PubMed DOI

Lo A., Qi L. Genetic and epigenetic control of gene expression by CRISPR–Cas systems. F1000Research. 2017;6 doi: 10.12688/f1000research.11113.1. PubMed DOI PMC

Lowder L.G., Zhang D., Baltes N.J., Paul J.W., Tang X., Zheng X., Voytas D.F., Hsieh T.-F., Zhang Y., Qi Y. A CRISPR/Cas9 toolbox for multiplexed plant genome editing and transcriptional regulation. Plant Physiol. 2015;169:971–985. doi: 10.1104/pp.15.00636. PubMed DOI PMC

Chen B., Gilbert L.A., Cimini B.A., Schnitzbauer J., Zhang W., Li G.-W., Park J., Blackburn E.H., Weissman J.S., Qi L.S. Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell. 2013;155:1479–1491. doi: 10.1016/j.cell.2013.12.001. PubMed DOI PMC

Dreissig S., Schiml S., Schindele P., Weiss O., Rutten T., Schubert V., Gladilin E., Mette M.F., Puchta H., Houben A. Live-cell CRISPR imaging in plants reveals dynamic telomere movements. Plant J. 2017;91:565–573. doi: 10.1111/tpj.13601. PubMed DOI PMC

Duan J., Lu G., Hong Y., Hu Q., Mai X., Guo J., Si X., Wang F., Zhang Y. Live imaging and tracking of genome regions in CRISPR/dCas9 knock-in mice. Genome Biol. 2018;19:1–7. doi: 10.1186/s13059-018-1530-1. PubMed DOI PMC

Dominguez A.A., Lim W.A., Qi L.S. Beyond editing: Repurposing CRISPR–Cas9 for precision genome regulation and interrogation. Nat. Rev. Mol. Cell Biol. 2016;17:5. doi: 10.1038/nrm.2015.2. PubMed DOI PMC

Arora L., Narula A. Gene editing and crop improvement using CRISPR-Cas9 system. Front. Plant Sci. 2017;8:1932. doi: 10.3389/fpls.2017.01932. PubMed DOI PMC

Malzahn A., Lowder L., Qi Y. Plant genome editing with TALEN and CRISPR. Cell Biosci. 2017;7:1–18. doi: 10.1186/s13578-017-0148-4. PubMed DOI PMC

Rodríguez-Leal D., Lemmon Z.H., Man J., Bartlett M.E., Lippman Z.B. Engineering quantitative trait variation for crop improvement by genome editing. Cell. 2017;171:470–480. doi: 10.1016/j.cell.2017.08.030. PubMed DOI

McGillivray P., Ault R., Pawashe M., Kitchen R., Balasubramanian S., Gerstein M. A comprehensive catalog of predicted functional upstream open reading frames in humans. Nucleic Acids Res. 2018;46:3326–3338. doi: 10.1093/nar/gky188. PubMed DOI PMC

Mao Y., Zhang Z., Feng Z., Wei P., Zhang H., Botella J.R., Zhu J.K. Development of germ-line-specific CRISPR-Cas9 systems to improve the production of heritable gene modifications in Arabidopsis. Plant Biotechnol. J. 2016;14:519–532. doi: 10.1111/pbi.12468. PubMed DOI PMC

Sanford J.C. Biolistic plant transformation. Physiol. Plant. 1990;79:206–209. doi: 10.1111/j.1399-3054.1990.tb05888.x. DOI

Husaini A.M., Abdin M.Z., Parray G.A., Sanghera G.S., Murtaza I., Alam T., Srivastava D.K., Farooqi H., Khan H.N. Vehicles and ways for efficient nuclear transformation in plants. Gm Crop. 2010;1:276–287. doi: 10.4161/gmcr.1.5.14660. PubMed DOI

Lacroix B., Citovsky V. Pathways of DNA transfer to plants from Agrobacterium tumefaciens and related bacterial species. Annu. Rev. Phytopathol. 2019;57:231–251. doi: 10.1146/annurev-phyto-082718-100101. PubMed DOI PMC

Kujur S., Senthil-Kumar M., Kumar R. Plant viral vectors: Expanding the Possibilities of Precise Gene Editing in Plant Genomes. Plant Cell Rep. 2021;17:1–4. PubMed

Yang N.-S., Christou P. Particle Bombardment Technology for Gene Transfer. Oxford University Press; Oxford, UK: 1994.

Christou P. Transformation technology. Trends Plant Sci. 1996;1:423–431. doi: 10.1016/S1360-1385(96)10047-9. DOI

Porta C., Lomonossoff G.P. Viruses as vectors for the expression of foreign sequences in plants. Biotechnol. Genet. Eng. Rev. 2002;19:245–292. doi: 10.1080/02648725.2002.10648031. PubMed DOI

Roy I., Mitra S., Maitra A., Mozumdar S. Calcium phosphate nanoparticles as novel non-viral vectors for targeted gene delivery. Int. J. Pharm. 2003;250:25–33. doi: 10.1016/S0378-5173(02)00452-0. PubMed DOI

Manghwar H., Lindsey K., Zhang X., Jin S. CRISPR/Cas system: Recent advances and future prospects for genome editing. Trends Plant Sci. 2019;24:1102–1125. doi: 10.1016/j.tplants.2019.09.006. PubMed DOI

Mookkan M., Nelson-Vasilchik K., Hague J., Zhang Z.J., Kausch A.P. Selectable marker independent transformation of recalcitrant maize inbred B73 and sorghum P898012 mediated by morphogenic regulators BABY BOOM and WUSCHEL2. Plant Cell Rep. 2017;36:1477–1491. doi: 10.1007/s00299-017-2169-1. PubMed DOI PMC

Lozano-Durán R. Geminiviruses for biotechnology: The art of parasite taming. New Phytol. 2016;210:58–64. doi: 10.1111/nph.13564. PubMed DOI

Zaidi S.S.-E.-A., Mansoor S. Viral vectors for plant genome engineering. Front. Plant Sci. 2017;8:539. doi: 10.3389/fpls.2017.00539. PubMed DOI PMC

Liu Y., Gao Y., Gao Y., Zhang Q. Targeted deletion of floral development genes in Arabidopsis with CRISPR/Cas9 using the RNA endoribonuclease Csy4 processing system. Hortic. Res. 2019;6:1–10. doi: 10.1038/s41438-019-0179-6. PubMed DOI PMC

Martin-Ortigosa S., Wang K. Proteolistics: A biolistic method for intracellular delivery of proteins. Transgenic Res. 2014;23:743–756. doi: 10.1007/s11248-014-9807-y. PubMed DOI

Bilang R., Klöti A., Schrott M., Potrykus I. Plant Molecular Biology Manual. Springer; Berlin/Heidelberg, Germany: 1994. PEG-mediated direct gene transfer and electroporation; pp. 1–16.

Roest S., Gilissen L.J.W. Plant regeneration from protoplasts: A literature review. Acta Bot. Neerl. 1989;38:1–23. doi: 10.1111/j.1438-8677.1989.tb01907.x. DOI

Roest S., Gilissen L.J.W. Regeneration from protoplasts—A supplementary literature review. Acta Bot. Neerl. 1993;42:1–23. doi: 10.1111/j.1438-8677.1993.tb00674.x. DOI

Yin X., Biswal A.K., Dionora J., Perdigon K.M., Balahadia C.P., Mazumdar S., Chater C., Lin H.-C., Coe R.A., Kretzschmar T. CRISPR-Cas9 and CRISPR-Cpf1 mediated targeting of a stomatal developmental gene EPFL9 in rice. Plant Cell Rep. 2017;36:745–757. doi: 10.1007/s00299-017-2118-z. PubMed DOI

Nakade S., Yamamoto T., Sakuma T. Cas9, Cpf1 and C2c1/2/3―What’s next? Bioengineered. 2017;8:265–273. doi: 10.1080/21655979.2017.1282018. PubMed DOI PMC

Kaya H., Mikami M., Endo A., Endo M., Toki S. Highly specific targeted mutagenesis in plants using Staphylococcus aureus Cas9. Sci. Rep. 2016;6:1–9. doi: 10.1038/srep26871. PubMed DOI PMC

Langner T., Kamoun S., Belhaj K. CRISPR crops: Plant genome editing toward disease resistance. Annu. Rev. Phytopathol. 2018;56:479–512. doi: 10.1146/annurev-phyto-080417-050158. PubMed DOI

Maresca M., Lin V.G., Guo N., Yang Y. Obligate ligation-gated recombination (ObLiGaRe): Custom-designed nuclease-mediated targeted integration through nonhomologous end joining. Genome Res. 2013;23:539–546. doi: 10.1101/gr.145441.112. PubMed DOI PMC

Tang X., Lowder L.G., Zhang T., Malzahn A.A., Zheng X., Voytas D.F., Zhong Z., Chen Y., Ren Q., Li Q. A CRISPR–Cpf1 system for efficient genome editing and transcriptional repression in plants. Nat. Plants. 2017;3:1–5. PubMed

Lowder L., Malzahn A., Qi Y. Rapid evolution of manifold CRISPR systems for plant genome editing. Front. Plant Sci. 2016;7:1683. doi: 10.3389/fpls.2016.01683. PubMed DOI PMC

Zhang D., Zhang H., Li T., Chen K., Qiu J.-L., Gao C. Perfectly matched 20-nucleotide guide RNA sequences enable robust genome editing using high-fidelity SpCas9 nucleases. Genome Biol. 2017;18:1–7. doi: 10.1186/s13059-017-1325-9. PubMed DOI PMC

Aman R., Ali Z., Butt H., Mahas A., Aljedaani F., Khan M.Z., Ding S., Mahfouz M. RNA virus interference via CRISPR/Cas13a system in plants. Genome Biol. 2018;19:1–9. doi: 10.1186/s13059-017-1381-1. PubMed DOI PMC

Krenek P., Samajova O., Luptovciak I., Doskocilova A., Komis G., Samaj J. Transient plant transformation mediated by Agrobacterium tumefaciens: Principles, methods and applications. Biotechnol. Adv. 2015;33:1024–1042. doi: 10.1016/j.biotechadv.2015.03.012. PubMed DOI

Hwang H.-H., Yu M., Lai E.-M. Agrobacterium-mediated plant transformation: Biology and applications. Arab. Book. 2017;15:e0186. doi: 10.1199/tab.0186. PubMed DOI PMC

Nekrasov V., Staskawicz B., Weigel D., Jones J.D.G., Kamoun S. Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease. Nat. Biotechnol. 2013;31:691–693. doi: 10.1038/nbt.2655. PubMed DOI

Chen L., Li W., Katin-Grazzini L., Ding J., Gu X., Li Y., Gu T., Wang R., Lin X., Deng Z. A method for the production and expedient screening of CRISPR/Cas9-mediated non-transgenic mutant plants. Hortic. Res. 2018;5:1–12. doi: 10.1038/s41438-018-0023-4. PubMed DOI PMC

Zhang Y., Liang Z., Zong Y., Wang Y., Liu J., Chen K., Qiu J.-L., Gao C. Efficient and transgene-free genome editing in wheat through transient expression of CRISPR/Cas9 DNA or RNA. Nat. Commun. 2016;7:1–8. doi: 10.1038/ncomms12617. PubMed DOI PMC

Kim S., Kim D., Cho S.W., Kim J., Kim J.-S. Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins. Genome Res. 2014;24:1012–1019. doi: 10.1101/gr.171322.113. PubMed DOI PMC

Yubing H.E., Min Z.H.U., Lihao W., Junhua W.U., Qiaoyan W., Rongchen W., Yunde Z. Improvements of TKC technology accelerate isolation of transgene-free CRISPR/Cas9-edited rice plants. Rice Sci. 2019;26:109–117. doi: 10.1016/j.rsci.2018.11.001. DOI

Metje-Sprink J., Menz J., Modrzejewski D., Sprink T. DNA-free genome editing: Past, present and future. Front. Plant Sci. 2019;9:1957. doi: 10.3389/fpls.2018.01957. PubMed DOI PMC

Liang Z., Chen K., Li T., Zhang Y., Wang Y., Zhao Q., Liu J., Zhang H., Liu C., Ran Y. Efficient DNA-free genome editing of bread wheat using CRISPR/Cas9 ribonucleoprotein complexes. Nat. Commun. 2017;8:1–5. doi: 10.1038/ncomms14261. PubMed DOI PMC

Woo J.W., Kim J., Kwon S.I., Corvalán C., Cho S.W., Kim H., Kim S.-G., Kim S.-T., Choe S., Kim J.-S. DNA-free genome editing in plants with preassembled CRISPR-Cas9 ribonucleoproteins. Nat. Biotechnol. 2015;33:1162–1164. doi: 10.1038/nbt.3389. PubMed DOI

Lowe K., Wu E., Wang N., Hoerster G., Hastings C., Cho M.-J., Scelonge C., Lenderts B., Chamberlin M., Cushatt J. Morphogenic regulators Baby boom and Wuschel improve monocot transformation. Plant Cell. 2016;28:1998–2015. doi: 10.1105/tpc.16.00124. PubMed DOI PMC

Toda E., Koiso N., Takebayashi A., Ichikawa M., Kiba T., Osakabe K., Osakabe Y., Sakakibara H., Kato N., Okamoto T. An efficient DNA-and selectable-marker-free genome-editing system using zygotes in rice. Nat. Plants. 2019;5:363–368. doi: 10.1038/s41477-019-0386-z. PubMed DOI

Stoddard T.J., Clasen B.M., Baltes N.J., Demorest Z.L., Voytas D.F., Zhang F., Luo S. Targeted mutagenesis in plant cells through transformation of sequence-specific nuclease mRNA. PLoS ONE. 2016;11:e0154634. doi: 10.1371/journal.pone.0154634. PubMed DOI PMC

Baek K., Kim D.H., Jeong J., Sim S.J., Melis A., Kim J.-S., Jin E., Bae S. DNA-free two-gene knockout in Chlamydomonas reinhardtii via CRISPR-Cas9 ribonucleoproteins. Sci. Rep. 2016;6:1–7. doi: 10.1038/srep30620. PubMed DOI PMC

Gan S.Y., Maggs C.A. Random mutagenesis and precise gene editing technologies: Applications in algal crop improvement and functional genomics. Eur. J. Phycol. 2017;52:466–481. doi: 10.1080/09670262.2017.1358827. DOI

Malnoy M., Viola R., Jung M.-H., Koo O.-J., Kim S., Kim J.-S., Velasco R., Nagamangala Kanchiswamy C. DNA-free genetically edited grapevine and apple protoplast using CRISPR/Cas9 ribonucleoproteins. Front. Plant Sci. 2016;7:1904. doi: 10.3389/fpls.2016.01904. PubMed DOI PMC

Subburaj S., Chung S.J., Lee C., Ryu S.-M., Kim D.H., Kim J.-S., Bae S., Lee G.-J. Site-directed mutagenesis in Petunia× hybrida protoplast system using direct delivery of purified recombinant Cas9 ribonucleoproteins. Plant Cell Rep. 2016;35:1535–1544. doi: 10.1007/s00299-016-1937-7. PubMed DOI

Ferenczi A., Pyott D.E., Xipnitou A., Molnar A. Efficient targeted DNA editing and replacement in Chlamydomonas reinhardtii using Cpf1 ribonucleoproteins and single-stranded DNA. Proc. Natl. Acad. Sci. USA. 2017;114:13567–13572. doi: 10.1073/pnas.1710597114. PubMed DOI PMC

Montecillo J.A.V., Chu L.L., Bae H. CRISPR-Cas9 system for plant genome editing: Current approaches and emerging developments. Agronomy. 2020;10:1033. doi: 10.3390/agronomy10071033. DOI

Kim H., Kim S.-T., Ryu J., Kang B.-C., Kim J.-S., Kim S.-G. CRISPR/Cpf1-mediated DNA-free plant genome editing. Nat. Commun. 2017;8:1–7. doi: 10.1038/ncomms14406. PubMed DOI PMC

Liang Z., Chen K., Zhang Y., Liu J., Yin K., Qiu J.-L., Gao C. Genome editing of bread wheat using biolistic delivery of CRISPR/Cas9 in vitro transcripts or ribonucleoproteins. Nat. Protoc. 2018;13:413. doi: 10.1038/nprot.2017.145. PubMed DOI

Afzal S., Sirohi P., Singh N.K. A review of CRISPR associated genome engineering: Application, advances and future prospects of genome targeting tool for crop improvement. Biotechnol. Lett. 2020;42:1611–1632. doi: 10.1007/s10529-020-02950-w. PubMed DOI

Liang Z., Zhang K., Chen K., Gao C. Targeted mutagenesis in Zea mays using TALENs and the CRISPR/Cas system. J. Genet. Genom. 2014;41:63–68. doi: 10.1016/j.jgg.2013.12.001. PubMed DOI

Lu Y., Ye X., Guo R., Huang J., Wang W., Tang J., Tan L., Zhu J.-k., Chu C., Qian Y. Genome-wide targeted mutagenesis in rice using the CRISPR/Cas9 system. Mol. Plant. 2017;10:1242–1245. doi: 10.1016/j.molp.2017.06.007. PubMed DOI

Wang P., Lombi E., Zhao F.-J., Kopittke P.M. Nanotechnology: A new opportunity in plant sciences. Trends Plant Sci. 2016;21:699–712. doi: 10.1016/j.tplants.2016.04.005. PubMed DOI

Doyle C., Higginbottom K., Swift T.A., Winfield M., Bellas C., Benito-Alifonso D., Fletcher T., Galan M.C., Edwards K., Whitney H.M. A simple method for spray-on gene editing in planta. [(accessed on 20 March 2021)];bioRxiv. 2019 :805036. Available online: https://www.biorxiv.org/content/10.1101/805036v2.abstract. DOI

Scherer F., Anton M., Schillinger U., Henke J., Bergemann C., Krüger A., Gänsbacher B., Plank C. Magnetofection: Enhancing and targeting gene delivery by magnetic force in vitro and in vivo. Gene Ther. 2002;9:102–109. doi: 10.1038/sj.gt.3301624. PubMed DOI

Dobson J. Gene therapy progress and prospects: Magnetic nanoparticle-based gene delivery. Gene Ther. 2006;13:283–287. doi: 10.1038/sj.gt.3302720. PubMed DOI

Jat S.K., Bhattacharya J., Sharma M.K. Nanomaterial based gene delivery: A promising method for plant genome engineering. J. Mater. Chem. B. 2020;8:4165–4175. doi: 10.1039/D0TB00217H. PubMed DOI

Zhao X., Meng Z., Wang Y., Chen W., Sun C., Cui B., Cui J., Yu M., Zeng Z., Guo S. Pollen magnetofection for genetic modification with magnetic nanoparticles as gene carriers. Nat. Plants. 2017;3:956–964. doi: 10.1038/s41477-017-0063-z. PubMed DOI

Vejlupkova Z., Warman C., Sharma R., Scheller H.V., Mortimer J.C., Fowler J.E. No evidence for transient transformation via pollen magnetofaction in several monocot species. Nat. Plants. 2020;6:1323–1324. doi: 10.1038/s41477-020-00798-6. PubMed DOI

Chandrasekaran R., Rajiv P., Abd-Elsalam K.A. Carbon Nanomaterials for Agri-Food and Environmental Applications. Elsevier; Amsterdam, The Netherlands: 2020. Carbon nanotubes: Plant gene delivery and genome editing; pp. 279–296.

Demirer G.S., Zhang H., Matos J.L., Goh N.S., Cunningham F.J., Sung Y., Chang R., Aditham A.J., Chio L., Cho M.-J. High aspect ratio nanomaterials enable delivery of functional genetic material without DNA integration in mature plants. Nat. Nanotechnol. 2019;14:456–464. doi: 10.1038/s41565-019-0382-5. PubMed DOI PMC

Kwak S.-Y., Lew T.T.S., Sweeney C.J., Koman V.B., Wong M.H., Bohmert-Tatarev K., Snell K.D., Seo J.S., Chua N.-H., Strano M.S. Chloroplast-selective gene delivery and expression in planta using chitosan-complexed single-walled carbon nanotube carriers. Nat. Nanotechnol. 2019;14:447–455. doi: 10.1038/s41565-019-0375-4. PubMed DOI

Ghaghelestany A.B., Jahanbakhshi A., Taghinezhad E. Gene transfer to German chamomile (L chamomilla M) using cationic carbon nanotubes. Sci. Hortic. 2020;263:109106. doi: 10.1016/j.scienta.2019.109106. DOI

Demirer G.S., Zhang H., Goh N.S., González-Grandío E., Landry M.P. Carbon nanotube–mediated DNA delivery without transgene integration in intact plants. Nat. Protoc. 2019;14:2954–2971. doi: 10.1038/s41596-019-0208-9. PubMed DOI PMC

Sanzari I., Leone A., Ambrosone A. Nanotechnology in plant science: To make a long story short. Front. Bioeng. Biotechnol. 2019;7:120. doi: 10.3389/fbioe.2019.00120. PubMed DOI PMC

Gao X., Chen J., Dai X., Zhang D., Zhao Y. An effective strategy for reliably isolating heritable and Cas9-free Arabidopsis mutants generated by CRISPR/Cas9-mediated genome editing. Plant Physiol. 2016;171:1794–1800. doi: 10.1104/pp.16.00663. PubMed DOI PMC

Tang X., Liu G., Zhou J., Ren Q., You Q., Tian L., Xin X., Zhong Z., Liu B., Zheng X. A large-scale whole-genome sequencing analysis reveals highly specific genome editing by both Cas9 and Cpf1 (Cas12a) nucleases in rice. Genome Biol. 2018;19:1–13. doi: 10.1186/s13059-018-1458-5. PubMed DOI PMC

Guo J., Li K., Jin L., Xu R., Miao K., Yang F., Qi C., Zhang L., Botella J.R., Wang R. A simple and cost-effective method for screening of CRISPR/Cas9-induced homozygous/biallelic mutants. Plant Methods. 2018;14:1–10. doi: 10.1186/s13007-018-0305-8. PubMed DOI PMC

Zheng X., Yang S., Zhang D., Zhong Z., Tang X., Deng K., Zhou J., Qi Y., Zhang Y. Effective screen of CRISPR/Cas9-induced mutants in rice by single-strand conformation polymorphism. Plant Cell Rep. 2016;35:1545–1554. doi: 10.1007/s00299-016-1967-1. PubMed DOI

Grohmann L., Keilwagen J., Duensing N., Dagand E., Hartung F., Wilhelm R., Bendiek J., Sprink T. Detection and identification of genome editing in plants: Challenges and opportunities. Front. Plant Sci. 2019;10:236. doi: 10.3389/fpls.2019.00236. PubMed DOI PMC

Zischewski J., Fischer R., Bortesi L. Detection of on-target and off-target mutations generated by CRISPR/Cas9 and other sequence-specific nucleases. Biotechnol. Adv. 2017;35:95–104. doi: 10.1016/j.biotechadv.2016.12.003. PubMed DOI

Yu H., Zhao Y. Plant Genome Editing with CRISPR Systems. Springer; Berlin/Heidelberg, Germany: 2019. Fluorescence marker-assisted isolation of Cas9-free and CRISPR-edited Arabidopsis plants; pp. 147–154. PubMed

Chang Z., Chen Z., Wang N., Xie G., Lu J., Yan W., Zhou J., Tang X., Deng X.W. Construction of a male sterility system for hybrid rice breeding and seed production using a nuclear male sterility gene. Proc. Natl. Acad. Sci. USA. 2016;113:14145–14150. doi: 10.1073/pnas.1613792113. PubMed DOI PMC

He Y., Zhao Y. Technological breakthroughs in generating transgene-free and genetically stable CRISPR-edited plants. aBIOTECH. 2020;1:88–96. doi: 10.1007/s42994-019-00013-x. PubMed DOI PMC

Tang T., Yu X., Yang H., Gao Q., Ji H., Wang Y., Yan G., Peng Y., Luo H., Liu K. Development and validation of an effective CRISPR/Cas9 vector for efficiently isolating positive transformants and transgene-free mutants in a wide range of plant species. Front. Plant Sci. 2018;9:1533. doi: 10.3389/fpls.2018.01533. PubMed DOI PMC

He Y., Zhu M., Wang L., Wu J., Wang Q., Wang R., Zhao Y. Programmed self-elimination of the CRISPR/Cas9 construct greatly accelerates the isolation of edited and transgene-free rice plants. Mol. Plant. 2018;11:1210–1213. doi: 10.1016/j.molp.2018.05.005. PubMed DOI

Yu C., Wang L., Xu S., Zeng Y., He C., Chen C., Huang W., Zhu Y., Hu J. Mitochondrial ORFH79 is essential for drought and salt tolerance in rice. Plant Cell Physiol. 2015;56:2248–2258. doi: 10.1093/pcp/pcv137. PubMed DOI

McElroy D., Zhang W., Cao J., Wu R. Isolation of an efficient actin promoter for use in rice transformation. Plant Cell. 1990;2:163–171. PubMed PMC

Gao Y., Zhao Y. Self-processing of ribozyme-flanked RNAs into guide RNAs in vitro and in vivo for CRISPR-mediated genome editing. J. Integr. Plant Biol. 2014;56:343–349. doi: 10.1111/jipb.12152. PubMed DOI

Yoshioka S., Fujii W., Ogawa T., Sugiura K., Naito K. Development of a mono-promoter-driven CRISPR/Cas9 system in mammalian cells. Sci. Rep. 2015;5:1–8. doi: 10.1038/srep18341. PubMed DOI PMC

Tang X., Zheng X., Qi Y., Zhang D., Cheng Y., Tang A., Voytas D.F., Zhang Y. A single transcript CRISPR-Cas9 system for efficient genome editing in plants. Mol. Plant. 2016;9:1088–1091. doi: 10.1016/j.molp.2016.05.001. PubMed DOI

Xie K., Minkenberg B., Yang Y. Boosting CRISPR/Cas9 multiplex editing capability with the endogenous tRNA-processing system. Proc. Natl. Acad. Sci. USA. 2015;112:3570–3575. doi: 10.1073/pnas.1420294112. PubMed DOI PMC

Shi J., Gao H., Wang H., Lafitte H.R., Archibald R.L., Yang M., Hakimi S.M., Mo H., Habben J.E. ARGOS 8 variants generated by CRISPR-Cas9 improve maize grain yield under field drought stress conditions. Plant Biotechnol. J. 2017;15:207–216. doi: 10.1111/pbi.12603. PubMed DOI PMC

Ali Z., Abul-Faraj A., Piatek M., Mahfouz M.M. Activity and specificity of TRV-mediated gene editing in plants. Plant Signal. Behav. 2015;10:e1044191. doi: 10.1080/15592324.2015.1044191. PubMed DOI PMC

Molla K.A., Yang Y. CRISPR/Cas-mediated base editing: Technical considerations and practical applications. Trends Biotechnol. 2019;37:1121–1142. doi: 10.1016/j.tibtech.2019.03.008. PubMed DOI

Chen Y., Wang Z., Ni H., Xu Y., Chen Q., Jiang L. CRISPR/Cas9-mediated base-editing system efficiently generates gain-of-function mutations in Arabidopsis. Sci. China Life Sci. 2017;60:520–523. doi: 10.1007/s11427-017-9021-5. PubMed DOI

Lu H.P., Liu S.M., Xu S.L., Chen W.Y., Zhou X., Tan Y.Y., Huang J.Z., Shu Q.Y. CRISPR-S: An active interference element for a rapid and inexpensive selection of genome-edited, transgene-free rice plants. Plant Biotechnol. J. 2017;15:1371. doi: 10.1111/pbi.12788. PubMed DOI PMC

Zong Y., Wang Y., Li C., Zhang R., Chen K., Ran Y., Qiu J.-L., Wang D., Gao C. Precise base editing in rice, wheat and maize with a Cas9-cytidine deaminase fusion. Nat. Biotechnol. 2017;35:438–440. doi: 10.1038/nbt.3811. PubMed DOI

Shimatani Z., Fujikura U., Ishii H., Matsui Y., Suzuki M., Ueke Y., Taoka K.-i., Terada R., Nishida K., Kondo A. Inheritance of co-edited genes by CRISPR-based targeted nucleotide substitutions in rice. Plant Physiol. Biochem. 2018;131:78–83. doi: 10.1016/j.plaphy.2018.04.028. PubMed DOI

Ren B., Yan F., Kuang Y., Li N., Zhang D., Zhou X., Lin H., Zhou H. Improved base editor for efficiently inducing genetic variations in rice with CRISPR/Cas9-guided hyperactive hAID mutant. Mol. Plant. 2018;11:623–626. doi: 10.1016/j.molp.2018.01.005. PubMed DOI

Li J., Zhang H., Si X., Tian Y., Chen K., Liu J., Chen H., Gao C. Generation of thermosensitive male-sterile maize by targeted knockout of the ZmTMS5 gene. J. Genet. Genom. Yi Chuan Xue Bao. 2017;44:465–468. doi: 10.1016/j.jgg.2017.02.002. PubMed DOI

Yan W., Chen D., Kaufmann K. Efficient multiplex mutagenesis by RNA-guided Cas9 and its use in the characterization of regulatory elements in the AGAMOUS gene. Plant Methods. 2016;12:1–9. doi: 10.1186/s13007-016-0125-7. PubMed DOI PMC

Kang B.-C., Yun J.-Y., Kim S.-T., Shin Y., Ryu J., Choi M., Woo J.W., Kim J.-S. Precision genome engineering through adenine base editing in plants. Nat. Plants. 2018;4:427–431. doi: 10.1038/s41477-018-0178-x. PubMed DOI

Hua K., Tao X., Yuan F., Wang D., Zhu J.-K. Precise A· T to G·C base editing in the rice genome. Mol. Plant. 2018;11:627–630. doi: 10.1016/j.molp.2018.02.007. PubMed DOI

Zhang D., Zhang Z., Unver T., Zhang B. CRISPR/Cas: A powerful tool for gene function study and crop improvement. J. Adv. Res. 2020;29:207–221. doi: 10.1016/j.jare.2020.10.003. PubMed DOI PMC

Zong Y., Song Q., Li C., Jin S., Zhang D., Wang Y., Qiu J.-L., Gao C. Efficient C-to-T base editing in plants using a fusion of nCas9 and human APOBEC3A. Nat. Biotechnol. 2018;36:950–953. doi: 10.1038/nbt.4261. PubMed DOI

Li J., Sun Y., Du J., Zhao Y., Xia L. Generation of targeted point mutations in rice by a modified CRISPR/Cas9 system. Mol. Plant. 2017;10:526–529. doi: 10.1016/j.molp.2016.12.001. PubMed DOI

Li C., Zong Y., Wang Y., Jin S., Zhang D., Song Q., Zhang R., Gao C. Expanded base editing in rice and wheat using a Cas9-adenosine deaminase fusion. Genome Biol. 2018;19:1–9. doi: 10.1186/s13059-018-1443-z. PubMed DOI PMC

Gaudelli N.M., Komor A.C., Rees H.A., Packer M.S., Badran A.H., Bryson D.I., Liu D.R. Programmable base editing of A T to G C in genomic DNA without DNA cleavage. Nature. 2017;551:464–471. doi: 10.1038/nature24644. PubMed DOI PMC

Liu Z., Chen M., Chen S., Deng J., Song Y., Lai L., Li Z. Highly efficient RNA-guided base editing in rabbit. Nat. Commun. 2018;9:1–10. doi: 10.1038/s41467-018-05232-2. PubMed DOI PMC

Ryu S.-M., Koo T., Kim K., Lim K., Baek G., Kim S.-T., Kim H.S., Kim D.-e., Lee H., Chung E. Adenine base editing in mouse embryos and an adult mouse model of Duchenne muscular dystrophy. Nat. Biotechnol. 2018;36:536–539. doi: 10.1038/nbt.4148. PubMed DOI

Cheng H., Hao M., Ding B., Mei D., Wang W., Wang H., Zhou R., Liu J., Li C., Hu Q. Base editing with high efficiency in allotetraploid oilseed rape by A3A-PBE system. Plant Biotechnol. J. 2021;19:87. doi: 10.1111/pbi.13444. PubMed DOI PMC

Cox D.B.T., Gootenberg J.S., Abudayyeh O.O., Franklin B., Kellner M.J., Joung J., Zhang F. RNA editing with CRISPR-Cas13. Science. 2017;358:1019–1027. doi: 10.1126/science.aaq0180. PubMed DOI PMC

Rees H.A., Wilson C., Doman J.L., Liu D.R. Analysis and minimization of cellular RNA editing by DNA adenine base editors. Sci. Adv. 2019;5:eaax5717. doi: 10.1126/sciadv.aax5717. PubMed DOI PMC

Abudayyeh O.O., Gootenberg J.S., Konermann S., Joung J., Slaymaker I.M., Cox D.B.T., Shmakov S., Makarova K.S., Semenova E., Minakhin L. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science. 2016;353:aaf5573. doi: 10.1126/science.aaf5573. PubMed DOI PMC

Xue C., Zhang H., Lin Q., Fan R., Gao C. Manipulating mRNA splicing by base editing in plants. Sci. China Life Sci. 2018;61:1293–1300. doi: 10.1007/s11427-018-9392-7. PubMed DOI

Li Z., Xiong X., Wang F., Liang J., Li J.F. Gene disruption through base editing-induced messenger RNA missplicing in plants. New Phytol. 2019;222:1139–1148. doi: 10.1111/nph.15647. PubMed DOI

Jacob P., Avni A., Bendahmane A. Translational research: Exploring and creating genetic diversity. Trends Plant Sci. 2018;23:42–52. doi: 10.1016/j.tplants.2017.10.002. PubMed DOI

Harris C.J., Slootweg E.J., Goverse A., Baulcombe D.C. Stepwise artificial evolution of a plant disease resistance gene. Proc. Natl. Acad. Sci. USA. 2013;110:21189–21194. doi: 10.1073/pnas.1311134110. PubMed DOI PMC

Liu C., Zhang L., Liu H., Cheng K. Delivery strategies of the CRISPR-Cas9 gene-editing system for therapeutic applications. J. Control. Release. 2017;266:17–26. doi: 10.1016/j.jconrel.2017.09.012. PubMed DOI PMC

Glass Z., Lee M., Li Y., Xu Q. Engineering the delivery system for CRISPR-based genome editing. Trends Biotechnol. 2018;36:173–185. doi: 10.1016/j.tibtech.2017.11.006. PubMed DOI PMC

Liu J.-J., Orlova N., Oakes B.L., Ma E., Spinner H.B., Baney K.L.M., Chuck J., Tan D., Knott G.J., Harrington L.B. CasX enzymes comprise a distinct family of RNA-guided genome editors. Nature. 2019;566:218–223. doi: 10.1038/s41586-019-0908-x. PubMed DOI PMC

Wang J., Meng X., Hu X., Sun T., Li J., Wang K., Yu H. xCas9 expands the scope of genome editing with reduced efficiency in rice. Plant Biotechnol. J. 2019;17:709. doi: 10.1111/pbi.13053. PubMed DOI PMC

Qin R., Li J., Li H., Zhang Y., Liu X., Miao Y., Zhang X., Wei P. Developing a highly efficient and wildly adaptive CRISPR-SaCas9 toolset for plant genome editing. Plant Biotechnol. J. 2019;17:706. doi: 10.1111/pbi.13047. PubMed DOI PMC

Walton R.T., Christie K.A., Whittaker M.N., Kleinstiver B.P. Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants. Science. 2020;368:290–296. doi: 10.1126/science.aba8853. PubMed DOI PMC

Ren Q., Sretenovic S., Liu S., Tang X., Huang L., He Y., Liu L., Guo Y., Zhong Z., Liu G. PAM-less plant genome editing using a CRISPR–SpRY toolbox. Nat. Plants. 2021;7:25–33. doi: 10.1038/s41477-020-00827-4. PubMed DOI

Richter M.F., Zhao K.T., Eton E., Lapinaite A., Newby G.A., Thuronyi B.W., Wilson C., Koblan L.W., Zeng J., Bauer D.E. Phage-assisted evolution of an adenine base editor with improved Cas domain compatibility and activity. Nat. Biotechnol. 2020;38:883–891. doi: 10.1038/s41587-020-0453-z. PubMed DOI PMC

Anzalone A.V., Randolph P.B., Davis J.R., Sousa A.A., Koblan L.W., Levy J.M., Chen P.J., Wilson C., Newby G.A., Raguram A. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature. 2019;576:149–157. doi: 10.1038/s41586-019-1711-4. PubMed DOI PMC

Xu R., Li J., Liu X., Shan T., Qin R., Wei P. Development of plant prime-editing systems for precise genome editing. Plant Commun. 2020;1:100043. doi: 10.1016/j.xplc.2020.100043. PubMed DOI PMC

Lin Q., Zong Y., Xue C., Wang S., Jin S., Zhu Z., Wang Y., Anzalone A.V., Raguram A., Doman J.L. Prime genome editing in rice and wheat. Nat. Biotechnol. 2020;38:582–585. doi: 10.1038/s41587-020-0455-x. PubMed DOI

Chhetri H.B., Macaya-Sanz D., Kainer D., Biswal A.K., Evans L.M., Chen J.G., Collins C., Hunt K., Mohanty S.S., Rosenstiel T., et al. Multitrait genome-wide association analysis of Populus trichocarpa identifies key polymorphisms controlling morphological and physiological traits. New Phytol. 2019;223:293–309. doi: 10.1111/nph.15777. PubMed DOI

Zhang J., Yang Y., Zheng K., Meng X., Kai F., Sara S.J., Gunter L.E., Ranjan P., Singan V.R., Engle N., et al. Genome-wide association studies and expression-based quantitative trait loci analyses reveal roles of HCT2 in caffeoylquinic acid biosynthesis and its regulation by defense-responsive transcription factors in Populus. New Phytol. 2018;220:502–516. doi: 10.1111/nph.15297. PubMed DOI

Muchero W., Sondreli K.L., Chen J.G., Urbanowicz B.R., Zhang J., Singan V., Yang Y., Brueggeman R.S., Franco-Coronado J., Abraham N., et al. Association mapping, transcriptomics, and transient expression identify candidate genes mediating plant-pathogen interactions in a tree. Proc. Natl. Acad. Sci. USA. 2018;115:11573–11578. doi: 10.1073/pnas.1804428115. PubMed DOI PMC

Induri B.R., Ellis D.R., Slavov G.T., Yin T., Zhang X., Muchero W., Tuskan G.A., DiFazio S.P. Identification of quantitative trait loci and candidate genes for cadmium tolerance in Populus. Tree Physiol. 2012;32:626–638. doi: 10.1093/treephys/tps032. PubMed DOI

McNally K.l., Childs K.L., Bohnert R., Davidson R.M., Zhao K., Ulat V.J., Zeller G., Clark R.M., Hoen D.R., Bureau T.E., et al. Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proc. Natl. Acad. Sci. USA. 2009;106:12273–12278. doi: 10.1073/pnas.0900992106. PubMed DOI PMC

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