Fig. 1

Experimental design and work flow. a Genome editing efficiency at selected 12 Cas9 and three Cpf1 target sites in T0 rice plants. The x-axis shows the names of sgRNAs and crRNAs which are denoted as Cas9-A to Cas9-K and Cpf1-A to Cpf1-C. The numbers of T0 and/or T1 lines that are subjected to whole-genome sequencing (WGS) are indicated. The y-axis shows genome editing frequencies calculated based on genotyping data in T0 generation. Cas9-J* and Cas9-K* samples each express a dual-sgRNA construct, targeting two genes simultaneously. b Selection of plants for WGS. Left: four groups of controls are included for assessing different background mutations. Middle: three generations of wild-type plants are included for assessing parent–progeny spontaneous mutations. Right: multiple T0 and T1 lines edited by Cas9 and Cpf1 are chosen for assessing off-targeting by WGS. c Workflow of whole-genome detection of SNV and indel mutations. SNV analysis involves using three computer programs: LoFreq, VarScan2, and MuTect2. Indel analysis also involves using three programs: VarScan2, MuTect2, and Pindel