An Efficient Targeted Mutagenesis System Using CRISPR/Cas in Monocotyledons

Zhen Liang1, Yuan Zong1, Caixia Gao2

1 University of Chinese Academy of Sciences, Beijing, China, 2 State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
Publication Name:  Current Protocols in Plant Biology
Unit Number:   
DOI:  10.1002/cppb.20021
Online Posting Date:  June, 2016
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Precise genome modification using artificial nucleases is a powerful tool for in‐depth understanding of gene functions and for creating new varieties. The CRISPR/Cas system, derived from an adaptive immunity system in bacteria and archaea, can introduce DNA double‐strand breaks (DSBs) into pre‐selected genomic loci and lead to loss of gene function due to error‐prone non‐homologous end joining (NHEJ). RNA‐guided nucleases have been widely used in several eukaryotic organisms. In this article, we provide a detailed protocol for designing and constructing gRNA targets, detecting nuclease activity in transient protoplast assays, and identifying mutations in transgenic plants (including rice, wheat and maize). Targeted mutations in T0 plants can be generated in 14 to 18 weeks. © 2016 by John Wiley & Sons, Inc.

Keywords: CRISPR/Cas; gene knock‐out; maize; rice; wheat

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Table of Contents

  • Introduction
  • Basic Protocol 1: CRISPR/Cas‐Mediated Genome Modifications in Monocotyledons
  • Support Protocol 1: Protoplast Transformation Assay
  • Reagents and Solutions
  • Commentary
  • Literature Cited
  • Figures
  • Tables
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Basic Protocol 1: CRISPR/Cas‐Mediated Genome Modifications in Monocotyledons

  • pEasy‐Blunt cloning vector (TransGen Biotech)
  • pEasy‐TI cloning vector (TransGen Biotech)
  • gRNA expression plasmids:
  • pOsU3‐gRNA (Addgene, Plasmid #53063)
  • pTaU6‐gRNA (Addgene, Plasmid #53062)
  • pZmU3‐gRNA (Addgene, Plasmid #53061)
  • 10× annealing buffer (OriGene)
  • AarI (Fermentas/Thermo Scientific) and corresponding 10× buffer
  • BbsI (Fermentas/Thermo Scientific) and corresponding 10× buffer
  • 10× Fast Green buffer(Fermentas/Thermo Scientific, supplied with FastDigest restriction enzyme)
  • DNA gel purification kit (Axygen)
  • T4 DNA ligase (Fermentas/Thermo Scientific) and 10× T4 DNA ligase buffer
  • Chemically competent E coli DH5α (TransGen Biotech)
  • LB medium and plates (see reciperecipes) containing 100 μg/ml ampicillin
  • 50% (v/v) glycerol
  • Primers (Table 20.2.1000; prepared by DNA synthesis facility, e.g., BGI; also see Ellington and Pollard, ):
  • OsU3‐F
  • TaU6‐F
  • ZmU3‐F
  • gRNA‐R 5′‐AAACN( 19)‐3′
  • Plasmid miniprep kit (Axygen)
  • Wizard Plus midiprep kit (Promega)
  • pJIT163‐Ubi‐rCas9 (this plasmid can be obtained from the authors on request)
  • DNAquick plant system (Tiangen Biotech)
  • 10× FastDigest buffer (Thermo Fisher Scientific)
  • T7 Endonuclease I (T7EI, ViewSolid Biotech) and 10× T7EI buffer
  • PCR thermal cycler (BioRad; also see Kramer and Coen, )
  • NanoDrop spectrophotometer (Thermo Scientific)
  • Digital gel imaging system (BioDoc‐It; UVP, cat. no. 97‐0256‐02)
  • Gel quantification software (e.g., ImageJ from the NIH)
  • Additional reagents and equipment for PCR (Kramer and Coen, ), general cloning techniques including sequencing (Ausubel et al., ), oligonucleotide synthesis (Ellington and Pollard, ), agarose gel electrophoresis (Voytas, ), and colony PCR (Woodman, )
Table 0.2.1   MaterialsPrimers Used for gRNA Cloning and Validation

Name Sequence Purpose
OsU3F 5′‐AAGGAATCTTTAAACATACGA‐3′ Colony PCR and sequencing to validate the gRNA
TaU6F 5′‐CATCTAAGTATCTTGGTAAAG‐3′ Colony PCR and sequencing to validate the gRNA
ZmU3F 5′‐CCCAAGCTTGACCAAGCCCG‐3′ Colony PCR and sequencing to validate the gRNA
gRNA‐R 5′‐AAACNNNNNNNNNNNNNNNNNNN‐3′ gRNA cloning and colony PCR and sequencing to validate the gRNA

NOTE: The plasmid map and sequence for each of the plasmids listed above can be found in the supplementary materials file for this unit at

Support Protocol 1: Protoplast Transformation Assay

  • Rice cultivar: Nipponbare (IGDB, CAS)
  • Wheat cultivar: Kenong 199 (IGDB, CAS)
  • Maize cultivar: Hi‐II (IGDB, CAS)
  • 75% ethanol
  • 2.55 (w/v) sodium hypochlorite
  • 1/2 MS solid medium (see recipe)
  • Nutrient‐rich soil (Pindstrup sphagnum)
  • 0.6 M mannitol, sterilized with a 0.45‐μm filter (store at room temperature)
  • Enzyme solution (for rice and wheat or for maize; see reciperecipes)
  • W5 solution (for rice and wheat or for maize; see reciperecipes)
  • MMG solution (see recipe)
  • gRNA expression plasmids:
  • pOsU3‐gRNA (Addgene, Plasmid #53063)
  • pTaU6‐gRNA (Addgene, Plasmid #53062)
  • pZmU3‐gRNA (Addgene, Plasmid #53061)
  • pJIT163‐Ubi‐rCas9 (this plasmid can be obtained from the authors on request)
  • PEG solution (see recipe)
  • Environmentally controlled incubators (Eppendorf)
  • Shaker
  • Round glass cup with diameter 66 mm and height 180 mm
  • 9‐cm Petri dishes
  • Blotting paper
  • Single‐edge razor blade (Feiying)
  • 150‐ml conical flask
  • Vacuum desiccator and vacuum pump
  • 40‐μm nylon mesh (BD Falcon)
  • 50‐ml round‐bottom centrifuge tubes (Haimeng)
  • 2‐ml round‐bottom microcentrifuge tubes
  • 6‐well tissue culture plates
  • Fluorescence microscope (Olympus)
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Supplementary Material