Submitted Successfully!
To reward your contribution, here is a gift for you: A free trial for our video production service.
Thank you for your contribution! You can also upload a video entry or images related to this topic.
Version Summary Created by Modification Content Size Created at Operation
1
Kejian Wang
 + 2320 word(s) 2320 2021-06-15 05:04:09 |
2 format correct
Vivi Li
 Meta information modification 2320 2021-06-16 04:28:50 |

Video Upload Options

We provide professional Video Production Services to translate complex research into visually appealing presentations. Would you like to try it?
No, upload directly Yes

Confirm

Are you sure to Delete?
Yes No
Cite
If you have any further questions, please contact Encyclopedia Editorial Office.
Wang, K. CRISPR/Cas and Herbicide Resistance. Encyclopedia. Available online: https://encyclopedia.pub/entry/10881 (accessed on 17 November 2024).
Wang K. CRISPR/Cas and Herbicide Resistance. Encyclopedia. Available at: https://encyclopedia.pub/entry/10881. Accessed November 17, 2024.
Wang, Kejian. "CRISPR/Cas and Herbicide Resistance" Encyclopedia, https://encyclopedia.pub/entry/10881 (accessed November 17, 2024).
Wang, K. (2021, June 16). CRISPR/Cas and Herbicide Resistance. In Encyclopedia. https://encyclopedia.pub/entry/10881
Wang, Kejian. "CRISPR/Cas and Herbicide Resistance." Encyclopedia. Web. 16 June, 2021.
CRISPR/Cas and Herbicide Resistance
Edit
This entry is adapted from the peer-reviewed paper 10.3390/genes12060912

The rapid increase in herbicide-resistant weeds creates a huge challenge to global food security because it can reduce crop production, causing considerable losses. Combined with a lack of novel herbicides, cultivating herbicide-resistant crops becomes an effective strategy to control weeds because of reduced crop phytotoxicity, and it expands the herbicidal spectrum. Recently developed clustered regularly interspaced short palindromic repeat/CRISPR-associated protein (CRISPR/Cas)-mediated genome editing techniques enable efficiently targeted modification and hold great potential in creating desired plants with herbicide resistance.

CRISPR/Cas genome editing herbicide resistance application

1. Introduction

The world population is expected to reach 10 billion by the year 2050, an increase of 34%. As a result, the global grain yield needs to increase by 70%, according to the Food and Agriculture Organization of the United Nations, to meet the demand of the world population [1][2]. However, global food security has suffered other challenges because of climate change, reduced arable land, scarcity of water, and biotic and abiotic stresses [3], which could affect crop production and cause enormous losses.

The presence of weeds in farmland will compete with crops for growth space, water, fertilizer, sunlight, and spread pests and diseases directly or indirectly [4][5], thereby inhibiting crop growth, reducing crop yields, and even seriously affecting the quality of crops [6][7]. Additionally, several weed seeds or pollen contain toxins; adulteration in crop seeds can cause poisoning to humans and animals. Cultivation of herbicide-resistant crops is an effective measure to control weeds, which can reduce crop phytotoxicity due to herbicide application [8], expand the herbicidal spectrum [9], and reduce the cost of weeding [10]. Thus, developing herbicide resistance crops is the most efficient strategy to control weed proliferation and tremendously increase crop productivity [11].

Previously, traditional mutagenesis breeding played an important role in improving herbicide-resistant crops, but it is labor-intensive and time-consuming. After the transgenic techniques became available, it has been successfully used for crop improvement in the past few decades [12][13]. Moreover, transgenic herbicide-resistant crops have also increased dramatically [14]. However, due to the transfer of foreign genes, the promotion and use of genetically modified products are restricted, and the wide application of this approach is also limited [15].

Since the clustered regularly interspaced short palindromic repeats/CRISPR-associated (CRISPR/Cas) genetic scissors were discovered in 2012 [16][17], CRISPR/Cas-based techniques have been successfully used to accelerate plant breeding for desirable traits. These traits include increased yield and nutritional value, stress tolerance, and pest and herbicide resistance because of its simplicity, flexibility, and high specificity. The CRISPR/Cas system generates double-strand breaks (DSBs) at target loci [17], and two main pathways can repair the DSBs, namely, nonhomologous end-joining (NHEJ), an error-prone repair system that often allows the introduction of deletions, insertions, or substitutions [18], and homology-directed repair (HDR) when a donor template with the homologous sequence is available [19]. If the target sequence is near microhomologous sequences, then the DSBs may be repaired through microhomology-mediated end-joining, resulting in fragment deletions of the plant genome with higher efficiency [20][21].

2. Site Mutations Confer Resistance to Herbicides in Plants

Herbicides can interfere with and inhibit the metabolic processes of plants, thus causing plant death. Therefore, they are widely used for weed control in crop fields. However, the prolonged and extensive use of certain herbicides or groups of herbicides has consequently led to the evolution of resistance in many weed species, and the resistance to herbicides in weeds is increasing rapidly worldwide. Tolerance to acetolactate synthase (ALS)-inhibiting herbicides, acetyl-CoA carboxylase (ACCase)-inhibiting herbicides and 5-enolpyruvylshikimate-3-phosphate (EPSPS) synthase-inhibiting herbicides have been reported more frequently, especially ALS-inhibiting herbicides, which account for one-third of all weed resistance [22].
Generally, herbicide resistance can be achieved through several mechanisms, such as target site mutation, target site gene amplification, increased herbicide detoxification, and metabolism [23]. Target site mutation is the primary resistance mechanism and has been successfully applied to creating herbicide-resistant germplasm in many crop species. For the development of herbicide-resistant plants, it is very important to select target genes associated with important resistance traits. Notably, the ALS gene, ACCase gene, and EPSPS gene have provided a wealth of potential genes to produce herbicide-resistant crops.
ALS (EC 4.1.3.18) is the key enzyme that catalyzes the first step in the biosynthesis of the three branched-chain amino acids (leucine, isoleucine, and valine) [24]. This is the target enzyme of ALS-inhibiting herbicides with dissimilar chemistries, including sulfonylureas (SU), imidazolinones (IMI), pyrimidinylthiobenzoates (PTB), sulfonylaminocarbonyl-triazoli-nones (SCT), and triazolopyrimidines (TP) [25]. So far, eight variant ALS genes have been discovered in weeds as natural mutations conferring tolerance to ALS-inhibiting herbicides involve the amino acids residues Ala122, Pro197, Ala205, Asp376, Arg377, Trp574, Ser653, and Gly654, in which the amino acid number is based on the Arabidopsis ALS gene [22].
ACCase (EC 6.4.1.2) is a crucial enzyme for fatty acid biosynthesis pathways. ACCase-inhibiting herbicides such as aryloxyphenoxypropionate (APP), cyclohexanedione (CHD), and phenylpyrazoline (PPZ) inhibit fatty acid synthesis in plants leading to plant death [26]. Many weeds acquire resistance to ACCase inhibitors due to amino acid mutations at seven positions: Ile1781, Trp1999, Trp2027, Ile2041, Asp2078, Cys2088, and Gly2096 [27].
Glyphosate is a broad-spectrum, non-selective herbicide that has become the globally dominant herbicide [28] that inhibits EPSPS (EC 2.5.1.19), a critical enzyme involved in the biosynthesis of aromatic amino acids [29]. As a result of intense glyphosate use, resistance to this herbicide has been confirmed in many weed species. Target site mutations occurring at Thr102, Ala103, and Pro106 of the EPSPS gene are known to endow glyphosate resistance in several fields that evolved resistant weed species [30].

3. Herbicide-Resistant Crops Generated by CRISPR/Cas System

With the advent of modern molecular biology, more recently developed CRISPR/Cas-mediated genome editing techniques offer an effective alternative method for inducing genetic modification in various crops [31], exhibiting great potential in accelerating the development of improved crop varieties (Table 1). Thus, genome editing technology could improve precise modifications of DNA sequences that correlated with herbicide resistance (Figure 1C,D).
Table 1. The herbicide-resistant plants generated by CRISPR/Cas9-mediated gene editing.
Gene Mutation Sites Herbicide Resistance Plants Repair Pathway References
ALS Ala96 rice CBE [32][33]
Pro165 maize HDR [34]
Pro178 soybean HDR [35]
Pro165 maize CBE [36]
Pro174 wheat CBE [37][38]
Pro174 watermelon CBE [39]
Pro197 oilseed rape CBE [40]
Pro194 tobacco CBE [41]
Pro197 tomato and potato CBE [42]
Trp548 rice HDR [43]
Gly628 rice CBE [44]
Ser627 rice ABE [45]
/ rice CDE [46]
Pro171/Gly628 rice CBE [47]
Trp574/Ser653 Arabidopsis NHEJ [48]
Trp548/Ser627 rice HDR [49][50][51][52][53][54]
Trp542/Ser621 maize HDR [55]
ACCase Trp2038 Arabidopsis NHEJ [48]
Cys2186 rice ABE [45][56]
Ala1992 wheat CBE [37]
/ rice CDE [57][58]
EPSPS Thr102/Pro106 rice NHEJ-HDR [59]
Thr102/Pro106 rapeseed HDR [60]
Thr178/Pro182 flax HDR [61]
TubA2 Met268 rice ABE [62]
Met268 rice ABE [45]
SF3B1 / rice CDE [63][64]
LsGGP uORF lettuce NHEJ [65]
Abbreviations: NHEJ-HDR means targeting gene replacement strategy via the NHEJ pathway using CRISPR–Cas9; CBE means cytosine base editor; ABE means adenine base editor; CDE means CRISPR/Cas-mediated direction evolution.

3.1. NHEJ Pathway to Improve Herbicide Resistance in Crops

Despite the dominance of NHEJ pathway during the DSBs repair, only a handful of editing events about creating herbicide-resistant crops have been reported in which endogenous plant genes were accurately modified this way.
Zhang et al. [66] obtained the paraquat-resistant lettuce with small or large deletion through editing the uORF of LsGGP2, a gene link to the production of ascorbic acid that increases oxidative stress tolerance in plant cells. This indicated that the gene editing introduced by the NHEJ repair pathway has measurable effects on the creation of herbicide-resistant crops. Except for the multiple base deletions, small insertions or deletions (indels), such as +1/−1 bp indels, often occurred in the period of the NHEJ repair pathway. Fortunately, resistance to ALS-inhibiting herbicide and ACCase-inhibiting herbicide were improved in Arabidopsis via the deletion of a base followed by the insertion of a different one [67], and the NHEJ repair strategy for the improvement of herbicide-resistant germplasm may also be applicable to crops.
Efficient intron-mediated site-specific gene replacement and insertion can also be generated through the NHEJ pathway using the CRISPR/Cas9 system. Depending on double amino acid substitution, T102I and P106S (TIPS) in the conserved motif of the endogenous EPSPS gene lead to resistance to glyphosate in goosegrass [65]. Scientists developed TIPS double amino acid substitutions in rice plants harboring the OsEPSPS gene, and the intended substitutions demonstrated resistance to glyphosate using the NHEJ pathway to generate gene replacements and insertions [48].
Herbicide resistance reported in plants indicated that the NHEJ pathway is suitable for developing important traits in crops. Nevertheless, their applications in crop improvements are rather limited, because they often yielded insertions or deletions that largely resulted in loss-of-function mutations [68], and many agriculturally important traits are conferred by point mutations, gene replacements, or gene knock-in by homologous recombination. Thus, the development of genome editing that enables gene replacement rather than gene inactivation will greatly facilitate plant breeding [59].

3.2. Development of Herbicide Resistance Crops via HDR Pathway

In contrast to NHEJ, the HDR pathway can modify endogenous genes precisely with targeted gene insertion or gene replacements, whereas HDR events remain much lower than that of NHEJ [69]. The recent application of HDR-dependent genome editing using the CRISPR system can potentially provide a feasible approach in plant breeding.
The resistant herbicide maize and soybeans were obtained through the HDR pathway mediated by the CRISPR/Cas9 technology [70][71]. Additionally, novel rice germplasms with bispyribac-sodium resistance were obtained by introducing point mutations at the 548th and 627th amino acid positions of the rice ALS gene [34][35]. Besides, a chimeric Cas9-VirD2 protein that combines Cas9 and VirD2, a Vir protein that cleaves the bottom strands of the Ti plasmid in the left and right border, was developed to enhance HDR efficiency in plants. Furthermore, precise OsALS allele modification that yields herbicide-resistant rice was successfully gained by employing this system [49]. Similarly, the glyphosate-resistant trait was optimized in rapeseed by introducing the donor template and a geminiviral replicon into plant cells [50]. Otherwise, the ALS inhibitor-resistant rice was generated with chimeric single-guide RNA (cgRNA) molecules composed of target site-specificity and repair template sequences [51]. The herbicide resistance trait in flax was also discovered owing to the combination of single-stranded oligonucleotides (ssODN) and CRISPR/Cas9 [60].
The development of the CRISPR/Cpf1 system has further expanded the application scope of genome editing technology based on the HDR pathway because of its long 5′-protruding ends [52], which may facilitate the pairing and insertion of repair templates, although the system has the disadvantage that nonspecific cleavage activity of single-stranded DNAs [61]. Scientists performed allelic replacement of the wild-type ALS gene with the intended mutations that carries two discrete point mutations, thereby conferring herbicide resistance in rice plants [72]. However, the efficiency is still very low through homology-mediated repair pathways. They improved the CRISPR/Cpf1 system and successfully the high-efficiency editing, simultaneously obtaining herbicide-resistant rice plants [53]. Prime editing is a novel and universal CRISPR/Cas-derived precision genome editing technology without exogenous donor DNA repair templates [54]. Jiang et al. [73] and Butt et al. [55] obtained herbicide resistance maize and rice through this editing system, respectively.
Notwithstanding the above reports, several limitations are still present, including the dominance of the NHEJ repair pathway, the difficulty in delivering sufficient repair templates [43][74], and susceptibility to degradation by cellular nucleases [75].

3.3. Improving Herbicide Resistance through Base Editing

Base editing enables irreversible conversion of base-pair without requiring double-stranded DNA breaks or donor repair templates [76]. So far, the base editors to convert C:G > T:A mutations and A:T > G:C base pairs at target loci have been developed and named cytidine-deaminase-mediated base editor (CBE) or adenine-deaminase-mediated base editor (ABE), respectively [76][77]. Base editors make it possible to correct a substantial fraction of herbicide resistance-associated SNPs. The two base editors have been introduced into several genes, including the ALS gene, ACCase gene, EPSPS genes, and other genes related to herbicide resistance in crops.
Fortunately, developing crop varieties harboring herbicide-resistant mutations that render crop tolerance to ALS-inhibiting herbicides by the CBE has been successfully applied in various crop species, including rice [44][78], maize [47], wheat [36][37], watermelon [38], oilseed rape [39], tobacco [40], tomato, and potato [41]. Similarly, crop tolerance to ACCase-inhibiting herbicides was also found in wheat via the CBE editor [36]. To improve the editing efficiency of CRISPR/Cas technology, the target-activation induced cytidine deaminase (Target-AID) was developed for improving multiplex traits that could accelerate crop improvement at one time in combination with targeted base editing. Furthermore, this base editing system has been applied to produce herbicide-resistant germplasm in rice plant [32][42].
Conversely, the ABEs also exhibited powerful potential for developing novel germplasms to confer resistance to herbicides. Li et al. [33] optimized an ABE for application in plant systems with an evolved tRNA adenosine deaminase, achieved targeted conversion of adenine to guanine, and produced a haloxyfop-R-methyl-resistant rice plant [33]. Additionally, the mutation of the OsTubA2 gene can also be rapidly introduced to confer resistance to both trifluralin and pendimethalin herbicides in rice using CRIPSR-mediated adenine base editors [56]. Recently, Yan et al. [62] simultaneously developed novel SNPs in four endogenous herbicide target genes (OsALS1, OsGS1, OsTubA2, OsACC) with induced efficient A-to-G conversion using new TadA variants, named TadA9.
Directed evolution has proved to be an effective strategy for accelerating the improvement of crop traits, because genetic diversity is artificially increased. Combined with a sgRNA library, the CRISPR/Cas9 system can generate considerable gene variants, thus driving the directed evolution of proteins [45]. Butt et al. [79] developed a CRISPR/Cas-based directed evolution system in rice, and the spliceosome component SF3B1 mutant variants conferred variable levels of resistance to herboxidiene (GEX1A) [63][79][80]. Moreover, a base editing-mediated gene evolution method was present with both the CBE editor and ABE editor alongside a sgRNA library to generate various nucleotide changes in target genomic regions. Consequently, four different novel amino acid substitutions that have never been reported formerly were identified in OsALS, exhibiting various resistance levels to bispyribac-sodium belonging to the ALS inhibitor [64]. Meanwhile, a dual base editing system that fused cytidine deaminase with adenosine deaminase named STEMEs was developed, enabling C:G > T:A and A:T > G:C substitutions in the same target sequence, provided directed evolution of endogenous genes by improved saturated mutagenesis. The saturated mutagenesis of the ACCase gene in rice plants by this dual base editing system can generate mutations associated with ACCase inhibitor, haloxyfop [46]. Accordingly, to exploit dominant mutations endowing resistance to ACCase-inhibiting herbicide, 141 sgRNAs were designed in the carboxyltransferase domain of the ACCase gene. As a result, a novel W2125S mutation was produced by CRISPR-mediated directed evolution to confer APP herbicide resistance in rice [57].

References

  1. Food and Agriculture Organization (FAO) of the United Nations. Agriculture and Climate Change-Challenges and Opportunities at the Global and Local Level-Collaboration on Climate-Smart Agriculture; FAO: Rome, Italy, 2019.
  2. Godfray, H.C.; Beddington, J.R.; Crute, I.R.; Haddad, L.; Lawrence, D.; Muir, J.F.; Pretty, J.; Robinson, S.; Thomas, S.M.; Toulmin, C.; et al. Food security: The challenge of feeding 9 billion people. Science 2010, 327, 812–818.
  3. Sundström, J.; Albihn, A.; Boqvist, S.; Ljungvall, K.; Marstorp, H.; Martiin, C.; Nyberg, K.; Vågsholm, I.; Yuen, J.; Magnusson, U.; et al. Future threats to agricultural food production posed by environmental degradation, climate change, and animal and plant diseases-a risk analysis in three economic and climate settings. Food. Secur. 2014, 6, 201–215.
  4. Délye, C.; Jasieniuk, M.; Le Corre, V.L. Deciphering the evolution of herbicide resistance in weeds. Trends. Genet. 2013, 29, 649–658.
  5. Quareshy, M.; Prusinska, J.; Li, J.; Napier, R. A cheminformatics review of auxins as herbicides. J. Exp. Bot. 2018, 69, 265–275.
  6. Akbar, N.; Jabran, K.; Ali, M.A. Weed management improves yield and quality of direct seeded rice. Aust. J. Crop Sci. 2011, 5, 688–694.
  7. Rao, A.N.; Johnson, D.E.; Sivaprasad, B.; Ladha, J.K.; Mortimer, A.M. Weed management in direct-seeded rice. Adv. Agron. 2007, 93, 153–255.
  8. Glick, H.L. Herbicide tolerant crops: A review of agronomic, economic and environmental impacts. BCPC Conf. Weeds 2001, 1, 359–366.
  9. Shaner, D.L. The impact of glyphosate-tolerant crops on the use of other herbicides and on resistance management. Pest Manag. Sci. 2000, 56, 320–326.
  10. Green, J.M. The benefits of herbicide-resistant crops. Pest Manag. Sci. 2012, 68, 1323–1331.
  11. Kumar, V.; Bellinder, R.R.; Gupta, R.K.; Malik, R.K.; Brainard, D.C. Role of herbicide-resistant rice in promoting resource conservation technologies in rice–wheat cropping systems of India: A review. Crop Prot. 2008, 27, 290–301.
  12. Ogawa, T.; Kawahigashi, H.; Toki, S.; Handa, H. Efficient transformation of wheat by using a mutated rice acetolactate synthase gene as a selectable marker. Plant Cell. Rep. 2008, 27, 1325–1331.
  13. Alibhai, M.F.; Stallings, W.C. Closing down on glyphosate inhibition--with a new structure for drug discovery. Proc. Nat. Acad. Sci. USA 2001, 98, 2944–2946.
  14. James, C. Global Status of Commercialized Transgenic Crops (GMO): 2003. Int. Serv. Acquis. Agribiotech Appl. 2003, 41, 175–176.
  15. Sanvido, O.; Romeis, J.; Gathmann, A.; Gielkens, M.; Raybould, A.; Bigler, F. Evaluating environmental risks of genetically modified crops: Ecological harm criteria for regulatory decision-making. Environ. Sci. Policy 2012, 15, 82–91.
  16. Deltcheva, E.; Chylinski, K.; Sharma, C.M.; Gonzales, K.; Chao, Y.; Pirzada, Z.A.; Eckert, M.R.; Vogel, J.; Charpentier, E. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 2011, 471, 602–607.
  17. Jinek, M.; Chylinski, K.; Fonfara, I.; Hauer, M.; Doudna, J.A.; Charpentier, E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 2012, 337, 816–821.
  18. Belhaj, K.; Chaparro-Garcia, A.; Kamoun, S.; Nekrasov, V. Plant genome editing made easy: Targeted mutagenesis in model and crop plants using the CRISPR/Cas system. Plant Methods 2013, 9, 39.
  19. Symington, L.S.; Gautier, J. Double-strand break end resection and repair pathway choice. Annu. Rev. Genet. 2011, 45, 247–271.
  20. Owens, D.D.G.; Caulder, A.; Frontera, V.; Harman, J.R.; Allan, A.J.; Bucakci, A.; Greder, L.; Codner, G.F.; Hublitz, P.; McHugh, P.J.; et al. Microhomologies are prevalent at Cas9-induced larger deletions. Nucleic Acids. Res. 2019, 47, 7402–7417.
  21. Tan, J.; Zhao, Y.; Wang, B.; Hao, Y.; Wang, Y.; Li, Y.; Luo, W.; Zong, W.; Li, G.; Chen, S.; et al. Efficient CRISPR/Cas9-based plant genomic fragment deletions by microhomology-mediated end joining. Plant Biotechnol. J. 2020, 18, 2161–2163.
  22. Tranel, P.J.; Wright, T.R.; Heap, I.M. Mutations in Herbicide-Resistant Weeds to ALS Inhibitors. Available online: (accessed on 5 May 2021).
  23. Sammons, R.D.; Gaines, T.A. Glyphosate resistance: State of knowledge. Pest. Manag. Sci. 2014, 70, 1367–1377.
  24. Devine, M.; Shukla, A. Altered target sites as a mechanism of herbicide resistance. Crop Prot. 2000, 19, 881–889.
  25. Zhou, Q.; Liu, W.; Zhang, Y.; Liu, K. Action mechanisms of acetolactate synthase-inhibiting herbicides. Pestic. Biochem. Physiol. 2007, 89, 89–96.
  26. Kaundun, S.S. Resistance to acetyl-CoA carboxylase-inhibiting herbicides. Pest. Manag. Sci. 2014, 70, 1405–1417.
  27. Délye, C.; Zhang, X.; Michel, S.; Matéjicek, A.; Powles, S.B. Molecular bases for sensitivity to acetyl-coenzyme A carboxylase inhibitors in black-grass. Plant Physiol. 2005, 137, 794–806.
  28. Funke, T.; Yang, Y.; Han, H.; Healyfried, M.; Olesen, S.; Becker, A.; Schönbrunn, E. Structural basis of glyphosate resistance resulting from the double mutation Thr⁹⁷→Ile and Pro¹⁰¹→Ser in 5-enolpyruvylshikimate-3-phosphate synthase from Escherichia coli. J. Biol. Chem. 2009, 284, 9854–9860.
  29. Achary, V.; Sheri, V.; Manna, M.; Panditi, V.; Borphukan, B.; Ram, B.; Agarwal, A.; Fartyal, D.; Teotia, D.; Masakapalli, S.K.; et al. Overexpression of improved EPSPS gene results in field level glyphosate tolerance and higher grain yield in rice. Plant Biotechnol. J. 2020, 18, 2504–2519.
  30. Gaines, T.A.; Heap, I.M. Mutations in Herbicide-Resistant Weeds to EPSP Synthase Inhibitors. Available online: (accessed on 5 May 2021).
  31. Zhou, H.; Liu, B.; Weeks, D.P.; Spalding, M.H.; Yang, B. Large chromosomal deletions and heritable small genetic changes induced by CRISPR/Cas9 in rice. Nucleic Acids. Res. 2014, 42, 10903–10914.
  32. Shimatani, Z.; Fujikura, U.; Ishii, H.; Matsui, Y.; Suzuki, M.; Ueke, Y.; Taoka, K.I.; Terada, R.; Nishida, K.; Kondo, A.; et al. Inheritance of co-edited genes by CRISPR-based targeted nucleotide substitutions in rice. Plant Physiol. Biochchem. 2018, 131, 78–83.
  33. 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, 59.
  34. Endo, M.; Mikami, M.; Toki, S. Biallelic gene targeting in rice. Plant Physiol. 2016, 170, 667–677.
  35. Sun, Y.; Zhang, X.; Wu, C.; He, Y.; Ma, Y.; Hou, H.; Guo, X.; Du, W.; Zhao, Y.; Xia, L.; et al. Engineering herbicide-resistant rice plants through CRISPR/Cas9-mediated homologous recombination of acetolactate synthase. Mol. Plant 2016, 9, 628–631.
  36. Zhang, R.; Liu, J.; Chai, Z.; Chen, S.; Bai, Y.; Zong, Y.; Chen, K.; Li, J.; Jiang, L.; Gao, C.; et al. Generation of herbicide tolerance traits and a new selectable marker in wheat using base editing. Nat. Plants 2019, 5, 480–485.
  37. Zong, Y.; Song, Q.; Li, C.; Jin, S.; Zhang, D.; Wang, Y.; Qiu, J.; Gao, C. Efficient C-to-T base editing in plants using a fusion of nCas9 and human APOBEC3A. Nat. Biotechnol. 2018, 36, 950–953.
  38. Tian, S.; Jiang, L.; Cui, X.; Zhang, J.; Guo, S.; Li, M.; Zhang, H.; Ren, Y.; Gong, G.; Zong, M.; et al. Engineering herbicide-resistant watermelon variety through CRISPR/Cas9-mediated base-editing. Plant Cell. Rep. 2018, 37, 1353–1356.
  39. Wu, J.; Chen, C.; Xian, G.; Liu, D.; Lin, L.; Yin, S.; Sun, Q.; Fang, Y.; Zhang, H.; Wang, Y.; et al. Engineering herbicide-resistant oilseed rape by CRISPR/Cas9-mediated cytosine base-editing. Plant Biotechnol. J. 2020, 18, 1857–1859.
  40. Kang, B.C.; Woo, J.W.; Kim, S.T.; Bae, S.J.; Kim, S.G. Guidelines for C to T base editing in plants: Base-editing window, guide RNA length, and efficient promoter. Plant Biotechnol. Rep. 2019, 13, 533–541.
  41. Veillet, F.; Perrot, L.; Chauvin, L.; Kermarrec, M.P.; Guyon-Debast, A.; Chauvin, J.E.; Nogué, F.; Mazier, M. Transgene-free genome editing in tomato and potato plants using agrobacterium-mediated delivery of a CRISPR/Cas9 cytidine base editor. Int. J. Mol. Sci. 2019, 20, 402.
  42. Shimatani, Z.; Kashojiya, S.; Takayama, M.; Terada, R.; Arazoe, T.; Ishii, H.; Teramura, H.; Yamamoto, T.; Komatsu, H.; Miura, K.; et al. Targeted base editing in rice and tomato using a CRISPR-Cas9 cytidine deaminase fusion. Nat. Biotechnol. 2017, 35, 441–443.
  43. Wang, M.; Lu, Y.; Botella, J.R.; Mao, Y.; Hua, K.; Zhu, J. Gene targeting by homology-directed repair in rice using a geminivirus-based CRISPR/Cas9 system. Mol. Plant 2017, 10, 1007–1010.
  44. Zhang, R.; Chen, S.; Meng, X.; Chai, Z.; Wang, D.; Yuan, Y.; Chen, K.; Jiang, L.; Li, J.; Gao, C.; et al. Generating broad-spectrum tolerance to ALS-inhibiting herbicides in rice by base editing. Sci. China. Life Sci. 2020.
  45. Packer, M.S.; Liu, D.R. Methods for the directed evolution of proteins. Nat. Rev. Genet. 2015, 16, 379–394.
  46. Li, C.; Zhang, R.; Meng, X.; Chen, S.; Zong, Y.; Lu, C.; Qiu, J.; Chen, Y.; Li, J.; Gao, C.; et al. Targeted, random mutagenesis of plant genes with dual cytosine and adenine base editors. Nat. Biotechnol. 2020, 38, 875–882.
  47. Li, Y.; Zhu, J.; Wu, H.; Liu, C.; Huang, C.; Lan, J.; Zhao, Y.; Xie, C. Precise base editing of non-allelic acetolactate synthase genes confers sulfonylurea herbicide resistance in maize. Crop J. 2020, 8, 449–456.
  48. Li, J.; Meng, X.; Zong, Y.; Chen, K.; Zhang, H.; Liu, J.; Li, J.; Gao, C. Gene replacements and insertions in rice by intron targeting using CRISPR-Cas9. Nat. Plants 2016, 2, 16139.
  49. Ali, Z.; Shami, A.; Sedeek, K.; Kamel, R.; Alhabsi, A.; Tehseen, M.; Hassan, N.; Butt, H.; Kababji, A.; Hamdan, S.M.; et al. Fusion of the Cas9 endonuclease and the VirD2 relaxase facilitates homology-directed repair for precise genome engineering in rice. Commun. Biol. 2020, 3, 44.
  50. Wang, Z.; Wan, L.; Xin, Q.; Zhang, X.; Song, Y.; Wang, P.; Hong, D.; Fan, Z.; Yang, G. Optimising glyphosate tolerance in rapeseed (Brassica napus L.) by CRISPR/Cas9-based geminiviral donor DNA replicon system with Csy4-based single-guide RNA processing. J. Exp. Bot. Bot. 2021.
  51. 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.
  52. Zetsche, B.; Gootenberg, J.S.; Abudayyeh, O.O.; Slaymaker, I.M.; Makarova, K.S.; Essletzbichler, P.; Volz, S.E.; Joung, J.; Oost, J.; Regev, A.; et al. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell 2015, 163, 759–771.
  53. Li, S.; Zhang, Y.; Xia, L.; Qi, Y. CRISPR-Cas12a enables efficient biallelic gene targeting in rice. Plant Biotechnol. J. 2020, 18, 1351.
  54. 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.; et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 2019, 576, 149–157.
  55. Butt, H.; Rao, G.S.; Sedeek, K.; Aman, R.; Kamel, R.; Mahfouz, M. Engineering herbicide resistance via prime editing in rice. Plant Biotechnol. J. 2020, 18, 2370–2372.
  56. Liu, L.; Kuang, Y.; Yan, F.; Li, S.; Ren, B.; Gosavi, G.; Spetz, C.; Li, X.; Wang, X.; Zhou, X.; et al. Developing a novel artificial rice germplasm for dinitroaniline herbicide resistance by base editing of OsTubA2. Plant Biotechnol. J. 2021, 19, 5–7.
  57. Liu, X.; Qin, R.; Li, J.; Liao, S.; Shan, T.; Xu, R.; Wu, D.; Wei, P. A CRISPR-Cas9-mediated domain-specific base-editing screen enables functional assessment of ACCase variants in rice. Plant Biotechnol. J. 2020, 18, 1845–1847.
  58. Xie, K.; Yang, Y. RNA-guided genome editing in plants using a CRISPR-Cas system. Mol. Plant 2013, 6, 1975–1983.
  59. Weeks, D.P.; Spalding, M.H.; Yang, B. Use of designer nucleases for targeted gene and genome editing in plants. Plant Biotechnol. J. 2016, 14, 483–495.
  60. Sauer, N.J.; Narváez-Vásquez, J.; Mozoruk, J.; Miller, R.B.; Warburg, Z.J.; Woodward, M.J.; Mihiret, Y.A.; Lincoln, T.A.; Segami, R.E.; Sanders, S.L.; et al. Oligonucleotide-mediated genome editing provides precision and function to engineered nucleases and antibiotics in plants. Plant Physiol. 2016, 170, 1917–1928.
  61. Chen, J.S.; Ma, E.; Harrington, L.B.; Costa, M.D.; Tian, X.; Palefsky, J.M.; Doudna, J.A. CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity. Science 2018, 360, 436–439.
  62. Yan, D.; Ren, B.; Liu, L.; Yan, F.; Li, S.; Wang, G.; Sun, W.; Zhou, X.; Zhou, H. High-efficiency and multiplex adenine base editing in plants using new TadA variants. Mol. Plant 2021, 14, 722–731.
  63. Zhang, Y.; Qi, Y. CRISPR enables directed evolution in plants. Genome Biol. 2019, 20, 83.
  64. Kuang, Y.; Li, S.; Ren, B.; Yan, F.; Spetz, C.; Li, X.; Zhou, X.; Zhou, H. Base-editing-mediated artificial evolution of OsALS1 in planta to develop novel herbicide-tolerant rice germplasms. Mol. Plant 2020, 13, 565–572.
  65. Yu, Q.; Jalaludin, A.; Han, H.; Chen, M.; Sammons, R.D.; Powers, S.B. Evolution of a double amino acid substitution in the 5-enolpyruvylshikimate-3-phosphate synthase in Eleusine indica conferring high-level glyphosate resistance. Plant Physiol. 2015, 167, 1440–1447.
  66. Zhang, H.; Si, X.; Ji, X.; Fan, R.; Liu, J.; Chen, K.; Wang, D.; Gao, C. Genome editing of upstream open reading frames enables translational control in plants. Nat. Biotechnol. 2018, 36, 894–898.
  67. Yang, W.; Qi, W.; Li, Y.; Wang, J.; Jiang, L. Programmed sequential cutting endows Cas9 versatile base substitution capability in plants. Sci. China Life Sci. 2020.
  68. Tidball, A.M.; Dang, L.T.; Glenn, T.W.; Kilbane, E.G.; Klarr, D.J.; Margolis, J.L.; Uhler, M.; Parent, J.M. Rapid generation of human genetic loss-of-function iPSC lines by simultaneous reprogramming and gene editing. Stem Cell Rep. 2017, 9, 725–731.
  69. Holger, P. The repair of double-strand breaks in plants: Mechanisms and consequences for genome evolution. J. Exp. Bot. 2005, 56, 1–14.
  70. Svitashev, S.; Young, J.K.; Schwartz, C.; Gao, H.; Falco, S.C.; Cigan, A.M. Targeted Mutagenesis, Precise gene editing, and site-specific gene insertion in maize using Cas9 and guide RNA. Plant Physiol. 2015, 169, 931–945.
  71. Li, Z.; Liu, Z.; Xing, A.; Moon, B.P.; Koellhoffer, J.P.; Huang, L.; Ward, R.T.; Clifton, E.; Falco, S.C.; Cigan, A.M.; et al. Cas9-guide RNA directed genome editing in soybean. Plant Physiol. 2015, 169, 960–970.
  72. Li, S.; Li, J.; Zhang, J.; Du, W.; Fu, J.; Sutar, S.; Zhao, Y.; Xia, L. Synthesis-dependent repair of Cpf1-induced double strand DNA breaks enables targeted gene replacement in rice. J. Exp. Bot. 2018, 69, 4715–4721.
  73. Jiang, Y.; Chai, Y.; Lu, M.; Han, X.; Lin, Q.; Zhang, Y.; Zhang, Q.; Zhou, Y.; Wang, X.; Gao, C.; et al. Prime editing efficiently generates W542L and S621I double mutations in two ALS genes in maize. Genome Biol. 2020, 21, 257.
  74. Wang, M.; Wang, Z.; Mao, Y.; Lu, Y.; Zhu, J. Optimizing base editors for improved efficiency and expanded editing scope in rice. Plant Biotechnol. J. 2019, 17, 1697.
  75. Miki, D.; Zhang, W.; Zeng, W.; Feng, Z.; Zhu, J. CRISPR/Cas9-mediated gene targeting in Arabidopsis using sequential transformation. Nat. Commun. 2018, 9, 1967.
  76. 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.
  77. 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.
  78. Wang, F.; Xu, Y.; Li, W.; Chen, Z.; Yang, J.; Fan, F.; Tao, Y.; Jiang, Y.; Zhu, Q.; Yang, J.; et al. Creating a novel herbicide-tolerance OsALS allele using CRISPR/Cas9-mediated gene editing. Crop J. 2021, 9, 305–312.
  79. Butt, H.; Eid, A.; Momin, A.A.; Bazin, J.; Crespi, M.; Arold, S.T.; Mahfouz, M.M. CRISPR directed evolution of the spliceosome for resistance to splicing inhibitors. Genome Biol. 2019, 20, 73.
  80. Kotake, Y.; Sagane, K.; Owa, T.; Mimori-Kiyosue, Y.; Shimizu, H.; Uesugi, M.; Ishihama, Y.; Iwata, M.; Mizui, Y. Splicing factor SF3b as a target of the antitumor natural product pladienolide. Nat. Chem. Biol. 2007, 3, 570–575.
More
© Text is available under the terms and conditions of the Creative Commons Attribution (CC BY) license; additional terms may apply. By using this site, you agree to the Terms and Conditions and Privacy Policy.
Upload a video for this entry
Information
Subjects: Biology
Contributor MDPI registered users' name will be linked to their SciProfiles pages. To register with us, please refer to https://encyclopedia.pub/register :
Kejian Wang
View Times: 665
Revisions: 2 times (View History)
Update Date: 16 Jun 2021
Table of Contents
    1000/1000
    Hot Most Recent
    ScholarVision Creations
    Feedback