CRISPR/Cas9 activity in the rice OsBEIIb gene does not induce off-target effects in the closely related paralog OsBEIIa

Molecular Breeding

Volumn 36, Issue 8, 2016, Pages

  Baysal, Can ^a   Bortesi, Luisa ^b   Zhu, Changfu ^a   Farré, Gemma ^a   Schillberg, Stefan ^c   Christou, Paul ^a,d  

^a UNIVERSITY OF LLEIDA   (Spain)

^b RWTH AACHEN UNIVERSITY   (Germany)

^c FRAUNHOFER INSTITUTE FOR MOLECULAR BIOLOGY AND APPLIED ECOLOGY IME   (Germany)

^d INSTITUCIÓ CATALANA DE RECERCA I ESTUDIS AVANÇATS ICREA   (Spain)

Author keywords

Genome editing; Isozyme; Mutation frequency; Off target activity; Oryza sativa; Starch branching enzyme; Targeted mutation

Indexed keywords

EFFICIENCY; ENZYMES; STARCH;

GENOME EDITING; ISOZYME; MUTATION FREQUENCY; OFF-TARGET ACTIVITY; ORYZA SATIVA; PARALOGS; STARCH-BRANCHING ENZYMES; TARGET ACTIVITY; TARGET SITES; TARGETED MUTATION;

GENES;

EID: 84983086751     PISSN: 13803743     EISSN: 15729788     Source Type: Journal    
DOI: 10.1007/s11032-016-0533-4     Document Type: Article

References (37)

1. Baltes NJ, Voytas DF (2015) Enabling plant synthetic biology through genome engineering. Trends Biotechnol 33:120–131
2. Bassie L, Zhu C, Romagosa I, Christou P, Capell T (2008) Transgenic wheat plants expressing an oat arginine decarboxylase cDNA exhibit increases in polyamine content in vegetative tissue and seeds. Mol Breed 22:39–50
3. Belhaj K, Chaparro-Garcia A, Kamoun S, Nekrasov V (2013) Plant genome editing made easy: targeted mutagenesis in model and crop plants using the CRISPR/Cas system. Plant Methods 9:39–49
4. Belhaj K, Chaparro-Garcia A, Kamoun S, Patron NJ, Nekrasov V (2015) Editing plant genomes with CRISPR/Cas9. Curr Opin Biotechnol 32:76–84
5. Bortesi L, Fischer R (2015) The CRISPR/Cas9 system for plant genome editing and beyond. Biotechnol Adv 33:41–52
6. Brinkman EK, Chen T, Amendola M, Van Steensel B (2014) Easy quantitative assessment of genome editing by sequence trace decomposition. Nucl Acids Res 42:e168
7. Christian M, Cermak T, Doyle EL, Schmidt C, Zhang F, Hummel A, Bogdanove AJ, Voytas DF (2010) Targeting DNA double-strand breaks with TAL effector nucleases. Genetics 186:756–761
8. Dian W, Jiang H, Wu P (2005) Evolution and expression analysis of starch synthase III and IV in rice. J Exp Bot 56:623–632
9. Doudna JA, Charpentier E (2014) The new frontier of genome engineering with CRISPR-Cas9. Science 346:1077–1086
10. Endo M, Mikami M, Toki S (2015) Multigene knockout utilizing off-target mutations of the CRISPR/cas9 system in rice. Plant Cell Physiol 56:41–47
11. Farré G, Sudhakar D, Naqvi S, Sandmann G, Christou P, Capell T, Zhu C (2012) Transgenic rice grains expressing a heterologous ρ-hydroxyphenylpyruvate dioxygenase shift tocopherol synthesis from the γ to the α isoform without increasing absolute tocopherol levels. Transgenic Res 21:1093–1097
12. Fu Y, Foden JA, Khayter C, Maeder ML, Reyon D, Joung JK, Sander JD (2013) High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat Biotechnol 31:822–826
13. Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, Agarwala V, Li Y, Fine EJ, Wu X, Shalem O, Cradick TJ, Marrafini LA, Bao G, Zhang F (2013) DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol 31:827–832
14. Jinek M, Chylinski K, Fonfara I, Hauer M, Charpentier E, Doudna JA (2012) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337:816–821
15. Kang T-J, Yang M-S (2004) Rapid and reliable extraction of genomic DNA from various wild-type and transgenic plants. BMC Biotechnol 4:20
16. Kim YG, Cha J, Chandrasegaran S (1996) Hybrid restriction enzymes: zinc finger fusions to FokI cleavage domain. Proc Natl Acad Sci USA 93:1156–1160
17. Konieczny A, Ausubel FM (1993) A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. Plant J 4:403–410
18. Li J, Zhang B, Ren Y, Gu S, Xiang Y, Huang C, Du J (2015) Intron targeting-mediated and endogenous gene integrity-maintaining knockin in zebrafish using the CRISPR/Cas9 system. Cell Res 25:634–637
19. Li M, Li X, Zhou Z, Wu P, Fang M, Pan X, Lin Q, Luo W, Wu G, Li H (2016) Reassessment of the four yield-related genes Gn1a, IPA1, DEP1 and GS3 in rice using a CRISPR/cas9 system. Front Plant Sci 7:377
20. Liang G, Zhang H, Lou D, Yu D (2016) Selection of highly efficient sgRNAs for CRISPR/Cas9-based plant genome editing. Sci Rep 6:21451
21. Liu L, Fan X-D (2014) CRISPR–Cas system: a powerful tool for genome engineering. Plant Mol Biol 85:209–218
22. Ma X, Zhang Q, Zhu Q, Liu W, ChenY Qiu R, Wang B, Yang Z, Li H, Xie Y, Shen R, Chen S, Wang Z, Chen Y, Guo J, Chen L, Zhao X, Dong Z, Liu Y (2015) A robust CRISPR/Cas9 system for convenient, high-efficiency multiplex genome editing in monocot and dicot plants. Mol Plant 8:1274–1284
23. Milbury CA, Li J, Makrigiorgos GM (2011) Ice-COLD-PCR enables rapid amplification and robust enrichment for low-abundance unknown DNA mutations. Nucl Acids Res 39:1–10
24. Mizuno K, Kobayashi E, Tachibana M, Tachibana M, Kawasaki T, Fujimura T, Funane K, Kobayashi M, Baba T (2001) Characterization of an isoform of rice starch branching enzyme, RBE4, in developing seeds. Plant Cell Physiol 42:349–357
25. Nakamura Y (2002) Towards a better understanding of the metabolic system for amylopectin biosynthesis in plants: rice endosperm as a model tissue. Plant Cell Physiol 43:718–725
26. Nishi A, Nakamura Y, Tanaka N, Satoh H (2001) Biochemical and genetic analysis of the effects of amylose-extender mutation in rice endosperm. Plant Physiol 127:459–472
27. Osakabe Y, Osakabe K (2015) Genome editing with engineered nucleases in plants. Plant Cell Physiol 56:389–400
28. Rahman S, Regina A, Li Z, Mukai Y, Yamamoto M, Kosar-Hasemi B, Abrahams S, Morell MK (2015) Comparison of starch-branching enzyme genes reveals evolutionary relationships among isoforms. characterization of a gene for starch-branching enzyme IIa from the wheat D genome donor Aegilops tauschii 1. Plant Physiol 125:1314–1324
29. Semenova E, Jore MM, Datsenko KA, Semenova A, Westra ER, Wanner B, Van Der Ost J, Brouns SJJ, Severinov K (2011) Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence. Proc Natl Acad Sci USA 108:10098–10103
30. Shan Q, Wang Y, Li J, Zhang Y, Chen K, Liang Z, Zhang K, Liu J, Xi J, Qiu J, Gao C (2013) Targeted genome modification of crop plants using a CRISPR-Cas system. Nat Biotechnol 31:686–688
31. Smith AM, Denyer K, Martin C (1999) The synthesis of the starch granule. Plant Physiol 48:67–87
32. Sudhakar D, Duc LT, Bong BB, Tinjuangjun P, Maqbool SB, Valdez M, Jefferson R, Christou P (1998) An efficient rice transformation system utilizing mature seed-derived explants and a portable, inexpensive particle bombardment device. Transgenic Res 7:289–294
33. Valdez M, Cabrera-Ponce JL, Sudhakar D, Herrera-Estrella L, Christou P (1998) Transgenic Central American, West African and Asian Elite rice varieties resulting from particle bombardment of foreign DNA into mature seed-derived explants utilizing three different bombardment devices. Ann Bot 82:795–801
34. Weeks DP, Spalding MH, Yang B (2016) Use of designer nucleases for targeted gene and genome editing in plants. Plant Biotechnol J 14:483–495
35. Xie K, Yang Y (2013) RNA-guided genome editing in plants using a CRISPR-Cas system. Mol Plant 6:1975–1983
36. Xie K, Zhang J, Yang Y (2014) Genome-wide prediction of highly specific guide RNA spacers for CRISPR-Cas9-mediated genome editing in model plants and major crops. Mol Plant 7:923–926
37. Zhang H, Zhang J, Wei P, Zhang B, Gou F, Feng Z, Mao Y, Yang L, Zhang H, Xu N, Zhu JK (2014) The CRISPR/Cas9 system produces specific and homozygous targeted gene editing in rice in one generation. Plant Biotechnol J 12:797–807