Targeted genome editing in grape using multiple CRISPR-guided editing systems

Abstract

The CRISPR/Cas9 system, together with newly developed CRISPR technologies such as CRISPR/LbCpf1 and base editors, have expanded the scope of targeted genome editing in plants. However, in grape, applications of these novel CRISPR-guided tools have not been reported. Here, we employed EGFP (enhanced green fluorescent protein) and RUBY to help to screen transformed grape cells based on fluorescence and red betalain and tested the activities of CRISPR/LbCpf1, CRISPR/xCas9 and cytidine base editor (CBE) in grape, respectively. The grape TMT1 (tonoplastic monosaccharide transporter1) and TMT2 genes were simultaneously edited by using LbCpf1, resulting in an efficiency of 16-48%. Furthermore, high temperature (34{degrees}C) could enhance editing efficiencies at most of the designed targets. The CRISPR/xCas9 could induce targeted mutagenesis at the target with NGG PAM, but the efficiencies were very low (< 1.9%). The targets with GAA and GAT PAMs that are reported in mammalian cells and rice were not recognized by xCas9 in our study. Moreover, successful C-to-T substitutions were achieved in GAI1 (gibberellin insensitive1) gene by using CBE. The editing efficiencies ranged from 2.4 to 15% at the two targets in GAI1 in grape cells. Analysis of independent embryos revealed a C-to-T efficiency of 12.5% at the first target of GAI1. Taken together, our results demonstrate the efficacy of these CRISPR-guided tools in grape and provide evidence for further application of these editing tools in this economically important species.