Rice Gene Knockout or Downregulation through CRISPR-Cas9

Part of the Springer Protocols Handbooks book series (SPH)


Precise genome modification via clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein (Cas)9 in rice plants, is a powerful tool for improving abiotic and biotic stress tolerance and increasing yield in rice. Valuable agronomical traits and functional study of a novel gene can be obtained by targeting single or multiple mutations in the rice genome. Here we describe the sgRNA design, cloning, and assembly of CRISPR constructs for specific gene knockout and the variant analysis in the rice plant.

Key words

CRISPR-Cas9 sgRNA design Knockout Mutagenesis Rice 



2,4-Dichlorophenoxyacetic acid




CRISPR-associated protein 9


Clustered regularly interspaced short palindromic repeats


Deoxyadenosine triphosphate


Deoxyribonucleic acid


Genetically modified organism


Hygromycin phosphotransferase gene


Immature embryo


Insertions and deletions


Luria broth


2-(N-Morpholino)ethanesulfonic acid

MS medium

Murashige and Skoog medium


1-Naphthaleneacetic acid.


Protospacer adjacent motif


Polymerase chain reaction


Plasmid DNA


Polynucleotide kinase


Room temperature


Single-guide ribonucleic acid

SOC medium

Super optimal broth


T7 Endonuclease 1


Yeast extract peptone dextrose



We want to thank Daniel Voytas Laboratory for providing us the modular vector system.


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© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  1. 1.Strategic Innovation PlatformInternational Rice Research InstituteLos BanosPhilippines

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