Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

High-Throughput Genome Editing and Phenotyping of Plant Cells Using a Scalable and Automated Pipeline


Jia Dong1,2* (, Seth W. Croslow2, Stephan T. Lane1,2, Jantana Blanford3, Kiyoul Park1,4, Edgar Cahoon1,4, John Shanklin1,3, Jonathan Sweedler1,2, Huimin Zhao1,2, Matthew E. Hudson1,2, Andrew Leakey1,2


1DOE Center for Advanced Bioenergy and Bioproducts Innovation; 2University of Illinois Urbana-Champaign; 3Brookhaven National Laboratory; 4University of Nebraska–Lincoln



This project aims to: (1) enhance bioproduct lipid production using CRISPR activation system in crops; (2) accelerate the design-build-test-learn plant bioengineering cycle through using a biofoundry (iBioFAB); and (3) improve high-throughput genome editing and metabolic engineering in crops to reduce labor and time during the process of plant bioengineering.


In plant synthetic biology, one challenge arises from the laborious and time-consuming bioengineering process. To address this, researchers established a fast, automated, scalable, and high-throughput pipeline for plant bioengineering (FAST-PB), which significantly, efficiently, and cost-effectively streamlines gene cloning, genotyping, and phenotyping processes. This pipeline not only enhances lipid production up to 6-fold, but also significantly accelerates the design-build-test-learn cycle in plant synthetic biology and facilitates plant regeneration. The other challenge lies in the fact that the synergistic fusion of biofoundry automation and single-cell MALDI has not been applied in plant research, which is a critical area for high-throughput metabolic engineering and cell biology. This study bridges this knowledge gap by successfully uniting automation techniques with MALDI methodology, enabling high-throughput single-cell lipid profiling. The pipeline demonstrates high versatility, with main applications in synthetic biology, genome editing, metabolic engineering, single-cell metabolomics, and plant regeneration.

Funding Information

This work was funded by the DOE Center for Advanced Bioenergy and Bioproducts Innovation (U.S. DOE, Office of Science, BER Program under Award Number DE-SC0018420).