Rapid generation of genetic diversity by multiplex CRISPR/Cas9 genome editing in rice

logo

SCIENCE CHINA Life Sciences, Volume 60, Issue 5: 506-515(2017) https://doi.org/10.1007/s11427-017-9008-8

Rapid generation of genetic diversity by multiplex CRISPR/Cas9 genome editing in rice

More info
  • ReceivedDec 1, 2016
  • AcceptedDec 20, 2016
  • PublishedMar 24, 2017

Abstract

The clustered regularly interspaced short palindromic repeats (CRISPR)-associated endonuclease 9 (CRISPR/Cas9) system has emerged as a promising technology for specific genome editing in many species. Here we constructed one vector targeting eight agronomic genes in rice using the CRISPR/Cas9 multiplex genome editing system. By subsequent genetic transformation and DNA sequencing, we found that the eight target genes have high mutation efficiencies in the T0 generation. Both heterozygous and homozygous mutations of all editing genes were obtained in T0 plants. In addition, homozygous sextuple, septuple, and octuple mutants were identified. As the abundant genotypes in T0 transgenic plants, various phenotypes related to the editing genes were observed. The findings demonstrate the potential of the CRISPR/Cas9 system for rapid introduction of genetic diversity during crop breeding.


Funded by

the Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences

National Natural Science Foundation of China(31271681)

Jiangsu Agriculture Science and Technology Innovation Fund(CX(135075)


Acknowledgment

This work was supported by the National Natural Science Foundation of China (31271681, 3140101312), the Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences, and Jiangsu Agriculture Science and Technology Innovation Fund (CX(13)5075).


Open access

This article is distributed under the terms of the Creative Commons Attribution License, which permits any use, distribution, and reproduction in any medium, provided the original author(s) and source are credited.


Interest statement

The author(s) declare that they have no conflict of interest.


Supplement

Figure S1 Mutation types at the eight target sites in the T0 generation.

Table S1 Mutations detected in putative CRISPR/Cas9 off-target sites

Table S2 Primers used in this study.

The supporting information is available online at life.scichina.com and www.springerlink.com. The supporting materials are published as submitted, without typesetting or editing. The responsibility for scientific accuracy and content remains entirely with the authors.


References

[1] Ashikari M., Sakakibara H., Lin S., Yamamoto T., Takashi T., Nishimura A., Angeles E.R., Qian Q., Kitano H., Matsuoka M.. Cytokinin oxidase regulates rice grain production. Science, 2005, 309: 741-745 CrossRef PubMed ADS Google Scholar

[2] Casini A., Storch M., Baldwin G.S., Ellis T.. Bricks and blueprints: methods and standards for DNA assembly. Nat Rev Mol Cell Biol, 2015, 16: 568-576 CrossRef PubMed Google Scholar

[3] Chen S., Yang Y., Shi W., Ji Q., He F., Zhang Z., Cheng Z., Liu X., Xu M.. Badh2, encoding betaine aldehyde dehydrogenase, inhibits the biosynthesis of 2-acetyl-1-pyrroline, a major component in rice fragrance. Plant Cell, 2008, 20: 1850-1861 CrossRef PubMed Google Scholar

[4] Cho Y.G., Eun M.Y., McCouch S.R., Chae Y.A.. The semidwarf gene, sd-1, of rice (Oryza sativa L.). II. molecular mapping and marker-assisted selection. Theoret Appl Genet, 1994, 89: 54 CrossRef PubMed Google Scholar

[5] Doench J.G., Fusi N., Sullender M., Hegde M., Vaimberg E.W., Donovan K.F., Smith I., Tothova Z., Wilen C., Orchard R., Virgin H.W., Listgarten J., Root D.E.. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat Biotechnol, 2016, 34: 184-191 CrossRef PubMed Google Scholar

[6] Fan C., Xing Y., Mao H., Lu T., Han B., Xu C., Li X., Zhang Q.. GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor Appl Genet, 2006, 112: 1164-1171 CrossRef PubMed Google Scholar

[7] Fukuma M., Ganmyo Y., Miura O., Ohyama T., Shimizu N.. Cloning and characterization of a human genomic sequence that alleviates repeat-induced gene silencing. PLoS One, 2016, 11: e0153338 CrossRef PubMed ADS Google Scholar

[8] Generoso W.C., Gottardi M., Oreb M., Boles E.. Simplified CRISPR-Cas genome editing for Saccharomyces cerevisiae. J Microbiol Methods, 2016, 127: 203-205 CrossRef PubMed Google Scholar

[9] Hiei Y., Ohta S., Komari T., Kumashiro T.. Efficient transformation of rice (Oryza sativa L.) mediated by Agrobacterium and sequence analysis of the boundaries of the T-DNA. Plant J, 1994, 6: 271-282 CrossRef Google Scholar

[10] Hu X., Wang C., Fu Y., Liu Q., Jiao X., Wang K.. Expanding the range of CRISPR/Cas9 genome editing in rice. Mol Plant, 2016, 9: 943-945 CrossRef PubMed Google Scholar

[11] Huang X., Qian Q., Liu Z., Sun H., He S., Luo D., Xia G., Chu C., Li J., Fu X.. Natural variation at the DEP1 locus enhances grain yield in rice. Nat Genet, 2009, 41: 494-497 CrossRef PubMed Google Scholar

[12] Jiang L., Liu X., Xiong G., Liu H., Chen F., Wang L., Meng X., Liu G., Yu H., Yuan Y., Yi W., Zhao L., Ma H., He Y., Wu Z., Melcher K., Qian Q., Xu H.E., Wang Y., Li J.. DWARF 53 acts as a repressor of strigolactone signalling in rice. Nature, 2013, 504: 401-405 CrossRef PubMed ADS Google Scholar

[13] Li M., Li X., Zhou Z., Wu P., Fang M., Pan X., Lin Q., Luo W., Wu G., Li H.. Reassessment of the four yield-related genes Gn1a, DEP1, GS3, and IPA1 in rice using a CRISPR/Cas9 system. Front Plant Sci, 2016, 7: 377 CrossRef PubMed Google Scholar

[14] Li T., Huang S., Zhao X., Wright D.A., Carpenter S., Spalding M.H., Weeks D.P., Yang B.. Modularly assembled designer TAL effector nucleases for targeted gene knockout and gene replacement in eukaryotes. Nucleic Acids Res, 2011, 39: 6315-6325 CrossRef PubMed Google Scholar

[15] Liu X., Zhang Y., Cheng C., Cheng A.W., Zhang X., Li N., Xia C., Wei X., Liu X., Wang H.. CRISPR-Cas9-mediated multiplex gene editing in CAR-T cells. Cell Res, 2017, 27: 154-157 CrossRef PubMed Google Scholar

[16] Ma X., Liu Y.G.. CRISPR/Cas9-based multiplex genome editing in monocot and dicot plants. Curr Protoc Mol Biol, 2016, 115: 31.6.1-31.6.21 CrossRef Google Scholar

[17] Ma X., Zhu Q., Chen Y., Liu Y.G.. CRISPR/Cas9 platforms for genome editing in plants: developments and applications. Mol Plant, 2016, 9: 961-974 CrossRef PubMed Google Scholar

[18] Ma X., Chen L., Zhu Q., Chen Y., Liu Y.G.. Rapid decoding of sequence-specific nuclease-induced heterozygous and biallelic mutations by direct sequencing of PCR products. Mol Plant, 2015a, 8: 1285-1287 CrossRef PubMed Google Scholar

[19] Ma X., Zhang Q., Zhu Q., Liu W., Chen Y., Qiu R., Wang B., Yang Z., Li H., Lin Y., Xie Y., Shen R., Chen S., Wang Z., Chen Y., Guo J., Chen L., Zhao X., Dong Z., Liu Y.G.. A robust CRISPR/Cas9 system for convenient, high-efficiency multiplex genome editing in monocot and dicot plants. Mol Plant, 2015b, 8: 1274-1284 CrossRef PubMed Google Scholar

[20] Mao H., Sun S., Yao J., Wang C., Yu S., Xu C., Li X., Zhang Q.. Linking differential domain functions of the GS3 protein to natural variation of grain size in rice. Proc Natl Acad Sci USA, 2010, 107: 19579-19584 CrossRef PubMed ADS Google Scholar

[21] Mitsuda S.H., Shimizu N.. Epigenetic repeat-induced gene silencing in the chromosomal and extrachromosomal contexts in human cells. PLoS One, 2016, 11: e0161288 CrossRef PubMed ADS Google Scholar

[22] Miura K., Ikeda M., Matsubara A., Song X.J., Ito M., Asano K., Matsuoka M., Kitano H., Ashikari M.. OsSPL14 promotes panicle branching and higher grain productivity in rice. Nat Genet, 2010, 42: 545-549 CrossRef PubMed Google Scholar

[23] Monna L., Kitazawa N., Yoshino R., Suzuki J., Masuda H., Maehara Y., Tanji M., Sato M., Nasu S., Minobe Y.. Positional cloning of rice semidwarfing gene, sd-1: rice “green revolution gene” encodes a mutant enzyme involved in gibberellin synthesis. DNA Res, 2002, 9: 11-17 CrossRef Google Scholar

[24] Patron N.J.. DNA assembly for plant biology: techniques and tools. Curr Opin Plant Biol, 2014, 19: 14-19 CrossRef PubMed Google Scholar

[25] Piao R., Jiang W., Ham T.H., Choi M.S., Qiao Y., Chu S.H., Park J.H., Woo M.O., Jin Z., An G., Lee J., Koh H.J.. Map-based cloning of the ERECT PANICLE 3 gene in rice. Theor Appl Genet, 2009, 119: 1497-1506 CrossRef PubMed Google Scholar

[26] Qi W., Zhu T., Tian Z., Li C., Zhang W., Song R.. High-efficiency CRISPR/Cas9 multiplex gene editing using the glycine tRNA-processing system-based strategy in maize. BMC Biotechnol, 2016, 16: 58 CrossRef PubMed Google Scholar

[27] Sakuma T., Masaki K., Abe-Chayama H., Mochida K., Yamamoto T., Chayama K.. Highly multiplexed CRISPR-Cas9-nuclease and Cas9-nickase vectors for inactivation of hepatitis B virus. Genes Cells, 2016, 21: 1253-1262 CrossRef PubMed Google Scholar

[28] Shan Q., Wang Y., Li J., Gao C.. Genome editing in rice and wheat using the CRISPR/Cas system. Nat Protoc, 2014, 9: 2395-2410 CrossRef PubMed Google Scholar

[29] Shan Q., Wang Y., Li J., Zhang Y., Chen K., Liang Z., Zhang K., Liu J., Xi J.J., Qiu J.L., Gao C.. Targeted genome modification of crop plants using a CRISPR-Cas system. Nat Biotechnol, 2013, 31: 686-688 CrossRef PubMed Google Scholar

[30] Shen L., Wang C., Fu Y., Wang J., Liu Q., Zhang X., Yan C., Qian Q., Wang K.. QTL editing confers opposing yield performance in different rice varieties. J Integr Plant Biol, 2016, in press: doi: 10.1111/jipb.12501 CrossRef PubMed Google Scholar

[31] Si L., Chen J., Huang X., Gong H., Luo J., Hou Q., Zhou T., Lu T., Zhu J., Shangguan Y., Chen E., Gong C., Zhao Q., Jing Y., Zhao Y., Li Y., Cui L., Fan D., Lu Y., Weng Q., Wang Y., Zhan Q., Liu K., Wei X., An K., An G., Han B.. OsSPL13 controls grain size in cultivated rice. Nat Genet, 2016, 48: 447-456 CrossRef PubMed Google Scholar

[32] Song X.J., Huang W., Shi M., Zhu M.Z., Lin H.X.. A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet, 2007, 39: 623-630 CrossRef PubMed Google Scholar

[33] Sood, B.C., and Sidiq, E.A. (1978). A rapid technique for scent determination in rice. Indian J Genet Plant Breed 38, 268?275. Google Scholar

[34] Spielmeyer W., Ellis M.H., Chandler P.M.. Semidwarf (sd-1), “green revolution” rice, contains a defective gibberellin 20-oxidase gene. Proc Natl Acad Sci USA, 2002, 99: 9043-9048 CrossRef PubMed ADS Google Scholar

[35] Wang C., Shen L., Fu Y., Yan C., Wang K.. A Simple CRISPR/Cas9 system for multiplex genome editing in rice. J Genets Genomics, 2015a, 42: 703-706 CrossRef PubMed Google Scholar

[36] Wang S., Li S., Liu Q., Wu K., Zhang J., Wang S., Wang Y., Chen X., Zhang Y., Gao C., Wang F., Huang H., Fu X.. The OsSPL16-GW7 regulatory module determines grain shape and simultaneously improves rice yield and grain quality. Nat Genet, 2015b, 47: 949-954 CrossRef PubMed Google Scholar

[37] Wang X., Niu Y., Zhou J., Yu H., Kou Q., Lei A., Zhao X., Yan H., Cai B., Shen Q., Zhou S., Zhu H., Zhou G., Niu W., Hua J., Jiang Y., Huang X., Ma B., Chen Y.. Multiplex gene editing via CRISPR/Cas9 exhibits desirable muscle hypertrophy without detectable off-target effects in sheep. Sci Rep, 2016, 6: 32271 CrossRef PubMed ADS Google Scholar

[38] Wood A.J., Lo T.W., Zeitler B., Pickle C.S., Ralston E.J., Lee A.H., Amora R., Miller J.C., Leung E., Meng X., Zhang L., Rebar E.J., Gregory P.D., Urnov F.D., Meyer B.J.. Targeted genome editing across species using ZFNs and TALENs. Science, 2011, 333: 307-307 CrossRef PubMed ADS Google Scholar

[39] Wu X., Tang D., Li M., Wang K., Cheng Z.. Loose plant architecture1, an INDETERMINATE DOMAIN protein involved in shoot gravitropism, regulates plant architecture in rice. Plant Physiol, 2013, 161: 317-329 CrossRef PubMed Google Scholar

[40] Xing H.L., Dong L., Wang Z.P., Zhang H.Y., Han C.Y., Liu B., Wang X.C., Chen Q.J.. A CRISPR/Cas9 toolkit for multiplex genome editing in plants. BMC Plant Biol, 2014, 14: 327 CrossRef PubMed Google Scholar

[41] Yano M., Katayose Y., Ashikari M., Yamanouchi U., Monna L., Fuse T., Baba T., Yamamoto K., Umehara Y., Nagamura Y., Sasaki T.. Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the arabidopsis flowering time gene CONSTANS. Plant Cell, 2000, 12: 2473-2484 CrossRef Google Scholar

[42] Yu H., Murchie E.H., González-Carranza Z.H., Pyke K.A., Roberts J.A.. Decreased photosynthesis in the erect panicle 3 (ep3) mutant of rice is associated with reduced stomatal conductance and attenuated guard cell development. J Exp Bot, 2015, 66: 1543-1552 CrossRef PubMed Google Scholar

[43] Zhang Z., Mao Y., Ha S., Liu W., Botella J.R., Zhu J.K.. A multiplex CRISPR/Cas9 platform for fast and efficient editing of multiple genes in Arabidopsis. Plant Cell Rep, 2016, 35: 1519-1533 CrossRef PubMed Google Scholar

[44] Zhou Y., Zhu J., Li Z., Yi C., Liu J., Zhang H., Tang S., Gu M., Liang G.. Deletion in a quantitative trait gene qPE9-1 associated with panicle erectness improves plant architecture during rice domestication. Genets, 2009, 183: 315-324 CrossRef PubMed Google Scholar

  • Figure 1

    Schematic diagram of the targeted sites in eight genes. A–H, The targeted sites are labeled in black uppercase letters. The initiation codons are underlined twice. The protospacer adjacent motif (PAM) sequences are underlined once. The arrows show the regions around the editing sites.

  • Figure 2

    Flow diagram of an octuple CRISPR/Cas9 system for multiplex gene editing in rice. The restriction sites used for cloning are labeled. BamH I+Bgl II, Nhe I+Xba I, and Sal I+Xho I are isocaudamer pairs and are highlighted in blue, green, and yellow, respectively.

  • Figure 3

    PCR/RE assay of mutations at eight loci in rice protoplast. BADH2, DEP1, Gn1a, GW2, Hd1, EP3, LPA1, and GS3 products were digested with MscI, NarI, MscI, T7E1, T7E1, HinfI, T7EI, and T7EI, respectively. Lane M, DNA marker. Lane 1, results of PCR/RE assay co-transformed in the single sgRNA (SK-gRNA-BADH2 SK-gRNA-DEP1 SK-gRNA-Gn1a SK-gRNA-GW2 SK-gRNA-Hd1 SK-gRNA-EP3 SK-gRNA-LPA1, and SK-gRNA-GS3, respectively) and Cas9 protein using the transient expression system in rice protoplast. Lane 2, results of PCR/RE assay co-transformed in the four sgRNAs (SK-gRNA-DEP1-Gn1a-GW2-EP3 and SK-gRNA-BADH2-LPA1-GS3-Hd1, respectively) and Cas9 protein using the transient expression system in rice protoplast. Lane 3, results of PCR/RE assay co-transformed in the eight sgRNAs (SK-gRNA-DEP1-Gn1a-GW2-EP3-BADH2-LPA-GS3-Hd1) and Cas9 protein using the transient expression system in rice protoplast. Lane 4, results of PCR/RE assay co-transformed in the control sgRNA (SK-gRNA) and Cas9 protein by using the transient expression system in rice protoplast.

  • Figure 4

    Characterization of targeted editing in T0 rice plants. A, Editing efficiencies of eight agronomic genes in T0 plants. B, Editing efficiencies of wild type (WT), homozygous mutations, and heterozygous mutations in each gene. C, Numbers of plants with different mutation genes. D, Editing efficiencies of off-target genes in T0 plants.

  • Figure 5

    Comparison of panicle traits among Nipponbare (NIP), Mutant 1, and Mutant 2. A, The morphology of the panicles of the NIP, Mutant 1, and Mutant 2. Scale bar, 1 cm. B, Comparison of panicle length among NIP, Mutant 1, and Mutant 2. C, Comparison of grain number per panicle among NIP, Mutant 1, and Mutant 2. Values in B and C are means±standard deviations (SD), n=5. The genotype of mutant-1 and mutant-2 are aabbccddeeffgghh and AABBccDdEEFFGGHH. The letters (a–h), represent BADH2, DEP1, Gn1a, GS3, GW2, Hd1, EP3, LPA1, respectively.

  • Figure 6

    Comparison of seed size among Nipponbare (NIP), Mutant 3, and Mutant 4. Aand B, Grain shape of the NIP, Mutant 3, and Mutant 4. Scale bar, 1 cm. C, Comparison of grain length among NIP, Mutant 3, and Mutant 4. D, Domparison of grain width among NIP, Mutant 3, and Mutant 4. E, Comparison of 1,000-grain weight among NIP, Mutant 3, and Mutant 4. Values in C, D, and F are means±standard deviation (s.d.), n=20, and three replicates. The genotype of mutant-3 and mutant-4 are aabbccddeeffgghh and aaBBccddEEFFGgHh. The letters (a–h), represent BADH2, DEP1, Gn1a, GS3, GW2, Hd1, EP3, LPA1, respectively.

  • Figure 7

    Phenotypes of plants with different gene combinations. A–F, Nipponbare (NIP). The letters (a–h), up from the plants represent BADH2, DEP1, Gn1a, GS3, GW2, Hd1, EP3, LPA1, respectively. Lowercase letters represent the modifed genes, whereas the uppercase letters indicate the normal genes. Scale bar, 10 cm.

  • Table 1   Combination patterns of eight agronomic genesa)

    Type of gene mutation

    Genotype

    No. of plants

    Sum

    Double mutations

    AABBccDdEEFFGGHH

    3

    3

    Quintuple mutations

    AabbccddEEffGGHH

    2

    8

    aaBbCcddEEffGGHH

    1

    aaBBccddEEFFGgHh

    2

    AABbccddEEffGgHH

    1

    AABbccddEEffGGHh

    1

    AABBCcDdeeffGGHh

    1

    Sextuple mutations

    aabbCcddeeffGGHH

    1

    6

    aaBbCcddeeffGGHH

    2

    aabbccddeeFfGGHH

    1

    aabbccddeeffGGHH

    1

    AaBbCCddEeFfGgHH

    1

    Septuple mutations

    aabbccddEEffGgHh

    1

    10

    aaBbccddEEFfGgHh

    1

    aabbccddeeFFGghh

    2

    aaBbccddEeFFGgHh

    1

    aabbccddeeFfGGhh

    1

    aabbccddeeffGGhh

    1

    aaBbccddeeFfGGhh

    2

    aabbccddeeffGGHh

    1

    Octuple mutations

    AaBbccddEeFfGgHh

    1

    9

    aabbccddeeFfGghh

    4

    aaBbccddEeFfGgHh

    1

    Aabbccddeeffgghh

    2

    AabbccddeeFfGgHh

    1

    a)The letters (a–h), represent BADH2, DEP1, Gn1a, GS3, GW2, Hd1, EP3, LPA1, respectively.

Copyright 2019 Science China Press Co., Ltd. 科学大众杂志社有限责任公司 版权所有

京ICP备18024590号-1