Defined tetra-allelic gene disruption of the 4-coumarate:coenzyme A ligase 1 (Pv4CL1) gene by CRISPR/Cas9 in switchgrass results in lignin reduction and improved sugar release

Background: The development of genome editing technologies offers new prospects in improving bioenergy crops like switchgrass (Panicum virgatum). Switchgrass is an outcrossing species with an allotetraploid genome (2n = 4x = 36), a complexity which forms an impediment to generating homozygous knock-out plants. Lignin, a major component of the plant cell wall and a contributor to cellulosic feedstock's recalcitrance to decomposition, stands as a barrier to efficient biofuel production by limiting enzyme access to cell wall polymers during the fermentation process. Results: We developed a CRISPR/Cas9 genome editing system in switchgrass to target a key enzyme involved in the early steps of monolignol biosynthesis, 4-Coumarate: coenzyme A ligase (4CL). Three 4CL genes, Pv4CL1, Pv4CL2, and Pv4CL3, were identified in switchgrass. Expression analysis revealed that Pv4CL1 transcripts were more abundant in the stem than in the leaf, while Pv4CL2 transcripts were barely detectable and Pv4CL3 was mainly expressed in the leaf. Pv4CL1 was selected as the target for CRISPR/Cas9 editing because of its preferential expression in highly lignified stem tissues. Specific guide RNA was constructed to target Pv4CL1. After introducing the construct into switchgrass calli, 39 transgenic plants were regenerated. Using two rounds of PCR screening and sequencing, four plants were confirmed to have tetra-allelic mutations simultaneously. The Pv4CL1 knock-out plants had reduced cell wall thickness, an 8-30% reduction in total lignin content, a 7-11% increase in glucose release, and a 23-32% increase in xylose release. Conclusion: This study established a successful CRISPR/Cas9 system in switchgrass with mutation efficiency reaching 10%. The system allows the precise targeting of the selected Pv4CL1 gene to create switchgrass knock-out mutant plants with decreased lignin content and reduced recalcitrance.