Optimization of multiplexed CRISPR/Cas9 system for highly efficient genome editing in Setaria viridis

Trevor Weiss, Chunfang Wang, Xiaojun Kang, Hui Zhao, Maria Elena Gamo, Colby G. Starker, Peter A. Crisp, Peng Zhou, Nathan M. Springer, Daniel F. Voytas, Feng Zhang

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33 Scopus citations


In recent years, Setaria viridis has been developed as a model plant to better understand the C4 photosynthetic pathway in major crops. With the increasing availability of genomic resources for S. viridis research, highly efficient genome editing technologies are needed to create genetic variation resources for functional genomics. Here, we developed a protoplast assay to rapidly optimize the multiplexed clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas9) system in S. viridis. Targeted mutagenesis efficiency was further improved by an average of 1.4-fold with the exonuclease, Trex2. Distinctive mutation profiles were found in the Cas9_Trex2 samples, with 94% of deletions larger than 10 bp, and essentially no insertions at all tested target sites. Further analyses indicated that 52.2% of deletions induced by Cas9_Trex2, as opposed to 3.5% by Cas9 alone, were repaired through microhomology-mediated end joining (MMEJ) rather than the canonical non-homologous end joining DNA repair pathway. Combined with a robust Agrobacterium-mediated transformation method with more than 90% efficiency, the multiplex CRISPR/Cas9_Trex2 system was demonstrated to induce targeted mutations in two tightly linked genes, svDrm1a and svDrm1b, at a frequency ranging from 73% to 100% in T0 plants. These mutations were transmitted to at least 60% of the transgene-free T1 plants, with 33% of them containing bi-allelic or homozygous mutations in both genes. This highly efficient multiplex CRISPR/Cas9_Trex2 system makes it possible to create a large mutant resource for S. viridis in a rapid and high throughput manner, and has the potential to be widely applicable in achieving more predictable and deletion-only MMEJ-mediated mutations in many plant species.

Original languageEnglish (US)
Pages (from-to)828-838
Number of pages11
JournalPlant Journal
Issue number3
StatePublished - Nov 1 2020

Bibliographical note

Funding Information:
We thank all members of Voytas Lab and Zhang Lab for helpful discussions and feedback, as well as Meredith Song for assisting with the genomic DNA extractions, genotyping and caring for plants. FZ was supported by a startup fund (to FZ) from the College of Biological Sciences, University of Minnesota. DV, CS and MG were supported in part by grant DE‐SC0018277 from the DOE. HZ was supported by the grant ZDYF2017017 from the key research and development project of Hainan. PZ, PC and NMS were supported in part by a grant from NSF (IOS‐1802848). The University of Minnesota is part of a team supporting DARPA's LiSTENS Program.


  • Cas9
  • NHEJ and MMEJ DNA repair
  • Setaria viridis
  • Trex2 exonuclease
  • multiplexed genome editing
  • technical advance


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