Deletion of a target gene in Indica rice via CRISPR/Cas9

Plant Cell Reports

Volumn 36, Issue 8, 2017, Pages 1333-1343

  Wang, Ying ^a   Geng, Lizhao ^a   Yuan, Menglong ^a   Wei, Juan ^a   Jin, Chen ^a   Li, Min ^a   Yu, Kun ^a   Zhang, Ya ^a   Jin, Huaibing ^a   Wang, Eric ^a   Chai, Zhijian ^a   Fu, Xiangdong ^b   Li, Xianggan ^a  

^a Zhongguancun Life Science Park   (China)

^b INSTITUTE OF GENETICS AND DEVELOPMENTAL BIOLOGY   (China)

Author keywords

CRISPR Cas9; DEP1; Indica rice; sgRNA; Target gene deletion

Indexed keywords

PLANT PROTEIN;

CRISPR CAS SYSTEM; GENETICS; METABOLISM; ORYZA; TRANSGENIC PLANT;

CRISPR-CAS SYSTEMS; ORYZA; PLANT PROTEINS; PLANTS, GENETICALLY MODIFIED;

EID: 85020164984     PISSN: 07217714     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00299-017-2158-4     Document Type: Article

References (45)

1. Bedell VM, Wang Y, Campbell JM, Poshusta TL, Starker CG, Krug RG II, Tan W, Penheiter SG, Ma AC, Leung AY (2012) In vivo genome editing using a high-efficiency TALEN system. Nature 491:114–118
2. Bikard D, Jiang W, Samai P, Hochschild A, Zhang F, Marraffini LA (2013) Programmable repression and activation of bacterial gene expression using an engineered CRISPR–Cas system. Nucleic Acids Res 41:7429–7437
3. Bitinaite J, Wah DA, Aggarwal AK, Schildkraut I (1998) FokI dimerization is required for DNA cleavage. Proc Natl Acad Sci 95:10570–10575
4. Brooks C, Nekrasov V, Lippman ZB, Van Eck J (2014) Efficient gene editing in tomato in the first generation using the clustered regularly interspaced short palindromic repeats/CRISPR-associated 9 system. Plant Physiol 166:1292–1297
5. Cho SW, Kim S, Kim JM, Kim J-S (2013) Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nat Biotechnol 31:230–232
6. Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA (2013) Multiplex genome engineering using CRISPR/Cas systems. Science 339:819–823
7. Ding Q, Regan SN, Xia Y, Oostrom LA, Cowan CA, Musunuru K (2013) Enhanced efficiency of human pluripotent stem cell genome editing through replacing TALENs with CRISPRs. Cell Stem Cell 12:393
8. Essletzbichler P, Konopka T, Santoro F, Chen D, Gapp BV, Kralovics R, Brummelkamp TR, Nijman SM, Bürckstümmer T (2014) Megabase-scale deletion using CRISPR/Cas9 to generate a fully haploid human cell line. Genome Res 24:2059–2065
9. Fauser F, Schiml S, Puchta H (2014) Both CRISPR/Cas-based nucleases and nickases can be used efficiently for genome engineering in Arabidopsis thaliana. Plant J 79:348–359
10. Feng Z, Zhang B, Ding W, Liu X, Yang D-L, Wei P, Cao F, Zhu S, Zhang F, Mao Y (2013) Efficient genome editing in plants using a CRISPR/Cas system. Cell Res 23:1229
11. Feng Z, Mao Y, Xu N, Zhang B, Wei P, Yang D-L, Wang Z, Zhang Z, Zheng R, Yang L (2014) Multigeneration analysis reveals the inheritance, specificity, and patterns of CRISPR/Cas-induced gene modifications in Arabidopsis. Proc Natl Acad Sci 111:4632–4637
12. Fujii W, Onuma A, Sugiura K, Naito K (2014) Efficient generation of genome-modified mice via offset-nicking by CRISPR/Cas system. Biochem Biophys Res Commun 445:791–794
13. Gao J, Wang G, Ma S, Xie X, Wu X, Zhang X, Wu Y, Zhao P, Xia Q (2015) CRISPR/Cas9-mediated targeted mutagenesis in Nicotiana tabacum. Plant Mol Biol 87:99–110
14. García-Almodóvar R, Petri C, Padilla I, Burgos L (2014) Combination of site-specific recombination and a conditional selective marker gene allows for the production of marker-free tobacco plants. Plant Cell Tissue Organ Cult (PCTOC) 116:205–215
15. Gui H, Li X, Liu Y, Han K, Li X (2014) The relationship between PMI (manA) gene expression and optimal selection pressure in Indica rice transformation. Plant Cell Rep 33:1081–1090
16. Huang X, Qian Q, Liu Z, Sun H, He S, Luo D, Xia G, Chu C, Li J, Fu X (2009) Natural variation at the DEP1 locus enhances grain yield in rice. Nat Genet 41:494–497
17. Hyun Y, Kim J, Cho SW, Choi Y, Kim J-S, Coupland G (2015) Site-directed mutagenesis in Arabidopsis thaliana using dividing tissue-targeted RGEN of the CRISPR/Cas system to generate heritable null alleles. Planta 241:271–284
18. Jacobs TB, LaFayette PR, Schmitz RJ, Parrott WA (2015) Targeted genome modifications in soybean with CRISPR/Cas9. BMC Biotechnol 15:16
19. Jiang WZ, Zhou HB, Bi HH, Fromm L, Yang B, Weeks DP (2013) Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice. Nucleic Acids Res 41:20
20. Jiang W, Yang B, Weeks DP (2014) Efficient CRISPR/Cas9-mediated gene editing in Arabidopsis thaliana and inheritance of modified genes in the T2 and T3 generations. PLoS One 9(6):e99225
21. Li D, Qiu Z, Shao Y, Chen Y, Guan Y, Liu M, Li Y, Gao N, Wang L, Lu X (2013a) Heritable gene targeting in the mouse and rat using a CRISPR–Cas system. Nat Biotechnol 31:681–683
22. Li W, Teng F, Li T, Zhou Q (2013b) Simultaneous generation and germline transmission of multiple gene mutations in rat using CRISPR–Cas systems. Nat Biotechnol 31:684–686
23. Li Z, Liu Z-B, Xing A, Moon BP, Koellhoffer JP, Huang L, Ward RT, Clifton E, Falco SC, Cigan AM (2015) Cas9-guide RNA directed genome editing in soybean. Plant Physiol 169:960–970
24. Li J, Meng X, Zong Y, Chen K, Zhang H, Liu J, Li J, Gao C (2016a) Gene replacements and insertions in rice by intron targeting using CRISPR–Cas9. Nat Plants 2:16139
25. Li M, Li X, Zhou Z, Wu P, Fang M, Pan X, Lin Q, Luo W, Wu G, Li H (2016b) Reassessment of the four yield-related genes Gn1a, DEP1, GS3, and IPA1 in rice using a CRISPR/Cas9 system. Front Plant Sci 7:377
26. Ma X, Zhang Q, Zhu Q, Liu W, Chen Y, Qiu R, Wang B, Yang Z, Li H, Lin Y (2015) A robust CRISPR/Cas9 system for convenient, high-efficiency multiplex genome editing in monocot and dicot plants. Mol Plant 8:1274–1284
27. Mao Y, Zhang H, Xu N, Zhang B, Gou F, Zhu J-K (2013) Application of the CRISPR–Cas system for efficient genome engineering in plants. Mol Plant 6:2008–2011
28. Miao J, Guo D, Zhang J, Huang Q, Qin G, Zhang X, Wan J, Gu H, Qu L-J (2013) Targeted mutagenesis in rice using CRISPR–Cas system. Cell Res 23:1233
29. Nissim L, Perli SD, Fridkin A, Perez-Pinera P, Lu TK (2014) Multiplexed and programmable regulation of gene networks with an integrated RNA and CRISPR/Cas toolkit in human cells. Mol Cell 54:698–710
30. Qu F, Zhai WX, Chen H, Zhu LH, Morris T (1996) Cloning, characterization and transient expression of the gene encoding a rice U3 small nuclear RNA. Gene 172:217–220
31. Shan Q, Wang Y, Li J, Zhang Y, Chen K, Liang Z, Zhang K, Liu J, Xi JJ, Qiu J-L, Gao C (2013) Targeted genome modification of crop plants using a CRISPR–Cas system. Nat Biotechnol 31:686–688
32. Song Y, Yuan L, Wang Y, Chen M, Deng J, Lv Q, Sui T, Li Z, Lai L (2016) Efficient dual sgRNA-directed large gene deletion in rabbit with CRISPR/Cas9 system. Cell Mol Life Sci 73(15):2959–2968
33. Srivastava V, Underwood JL, Zhao S (2017) Dual-targeting by CRISPR/Cas9 for precise excision of transgenes from rice genome. Plant Cell Tissue Organ Cult (PCTOC) 129(1):153–160
34. Svitashev S, Young JK, Schwartz C, Gao H, Falco SC, Cigan AM (2015) Targeted mutagenesis, precise gene editing, and site-specific gene insertion in maize using Cas9 and guide RNA. Plant Physiol 169:931–945
35. Wang H, Yang H, Shivalila CS, Dawlaty MM, Cheng AW, Zhang F, Jaenisch R (2013) One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell 153:910–918
36. Wang T, Wei JJ, Sabatini DM, Lander ES (2014) Genetic screens in human cells using the CRISPR–Cas9 system. Science 343:80–84
37. Wang Z-P, Xing H-L, Dong L, Zhang H-Y, Han C-Y, Wang X-C, Chen Q-J (2015) Egg cell-specific promoter-controlled CRISPR/Cas9 efficiently generates homozygous mutants for multiple target genes in Arabidopsis in a single generation. Genome Biol 16:1
38. Xie K, Minkenberg B, Yang Y (2015) Boosting CRISPR/Cas9 multiplex editing capability with the endogenous tRNA-processing system. Proc Natl Acad Sci 112:3570–3575
39. Xing H-L, Dong L, Wang Z-P, Zhang H-Y, Han C-Y, Liu B, Wang X-C, Chen Q-J (2014) A CRISPR/Cas9 toolkit for multiplex genome editing in plants. BMC Plant Biol 14:1
40. Xu R, Li H, Qin R, Wang L, Li L, Wei P, Yang J (2014) Gene targeting using the Agrobacterium tumefaciens-mediated CRISPR–Cas system in rice. Rice 7:1
41. Yan L, Wei S, Wu Y, Hu R, Li H, Yang W, Xie Q (2015) High-efficiency genome editing in Arabidopsis using YAO promoter-driven CRISPR/Cas9 system. Mol Plant 8:1820–1823
42. Yang H, Wang H, Jaenisch R (2014) Generating genetically modified mice using CRISPR/Cas-mediated genome engineering. Nat Protoc 9:1956–1968
43. Zhang H, Zhang J, Wei P, Zhang B, Gou F, Feng Z, Mao Y, Yang L, Zhang H, Xu N (2014) The CRISPR/Cas9 system produces specific and homozygous targeted gene editing in rice in one generation. Plant Biotechnol J 12:797–807
44. Zhang Z, Mao Y, Ha S, Liu W, Botella JR, Zhu JK (2015) A multiplex CRISPR/Cas9 platform for fast and efficient editing of multiple genes in Arabidopsis. Plant Cell Rep 35(7):1519–1533
45. Zhou H, Liu B, Weeks DP, Spalding MH, Yang B (2014) Large chromosomal deletions and heritable small genetic changes induced by CRISPR/Cas9 in rice. Nucleic Acids Res 42(17):10903–10914