BACKGROUND: The type II clustered, regularly interspaced, short palindromic 
repeat (CRISPR)/ CRISPR-associated protein 9 (Cas9) system is a novel molecular 
tool for site-specific genome modification. The CRISPR-Cas9 system was recently 
introduced into plants by transient or stable transformation.
FINDINGS: Here, we report gene targeting in rice via the Agrobacterium 
tumefaciens-mediated CRISPR-Cas9 system. Three 20-nt CRISPR RNAs were designed 
to pair with diverse sites followed by the protospacer adjacent motif (PAM) of 
the rice herbicide resistance gene BEL. After integrating the single-guide RNA 
(sgRNA) and Cas9 cassette in a single binary vector, transgenic rice plants 
harboring sgRNA:Cas9 were generated by A. tumefaciens-mediated stable 
transformation. By analyzing the targeting site on the genome of corresponding 
transgenic plants, the mutations were determined. The mutagenesis efficiency was 
varied from ~2% to ~16%. Furthermore, phenotypic analysis revealed that the 
biallelic mutated transgenic plant was sensitive to bentazon.
CONCLUSIONS: Our results indicate that the agricultural trait could be purposely 
modified by sgRNA:Cas9-induced gene targeting. CRISPR-Cas9 system could be 
exploited as a powerful tool for trait improvements in crop breeding.