CRISPR/Cas9 in rice can induce new mutations in later generations, leading to chimerism and unpredicted segregation of the targeted mutation

CRISPR/Cas9 is a novel tool for targeted mutagenesis and is applicable to plants, including rice. Previous reports on CRISPR/Cas9 in rice have demonstrated that target mutations are transmitted to the next generation in accordance with Mendelian law, but heritability of the target mutation and the role of inherited Cas9 gene have not been fully elucidated. Here, we targeted the rice phytoene desaturase gene, mutants of which exhibit an albino phenotype, by using CRISPR/Cas9 and analyzed segregation of target mutations. Agrobacterium-mediated methods using immature embryos successfully transformed a CRISPR/Cas9 system into five rice cultivars and subsequently induced mutation. Unpredicted segregations, with more mutants than theoretically predicted, were frequently found in T-1 plants from monoallelic T-0 mutants. Chimeric plants with both biallelic and monoallelic mutated cells were also observed in the T-1 . Next, we followed segregation of a target mutation in the T-2 from monoallelic T-1 mutants. When T-1 mutants possessed Cas9, unpredicted segregations of the target mutation and chimeric plants were observed again in the T-2. When T-1 mutants did not possess Cas9, segregation of the target mutations followed Mendelian law and no chimeric plants appeared in the T-2. T-2 mutants with Cas9 had mutations different from the original ones found in T-0. Our results indicated that inherited Cas9 was still active in later generations and could induce new mutations in the progeny, leading to chimerism and unpredicted segregation. We conclude that Cas9 has to be eliminated by segregation in T-1 to generate homozygous mutants without chimerism or unpredicted segregation.