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CRISPR/Cas9-mediated genome editing is a next-generation strategy for genetic modifications and crop improvement.Not only for single gene kocck out, but also for multiple targeted mutagenesis and functional nucleotide substitution technology will be mostly employed for elite allele creation, especially for the numberous quantitative trait locuses.To make the multiplexity of CRISPR/Cas9, We tested different type Ⅱ CRISPR/Cas systems and demonstrate that they worked very well in rice.In the best system, we realized 6 loci mutation one time with above 30% efficiency.To develop functional nucleotide substitution technology, we employed CRISPR/Cas9, positive-negtive selection to realized two fuction nucleotide subtitution in one important trait gene with a not very high efficiency.When we used homolog recombination improving effect, the efficiency can be improved above 2%, which should be engouth for some important genes testing in crop improvement.Combine these two methods for multi-trait impromovment or special quantitative trait locus editing will be carried out in nect step.