Crop Biotech Update

Scientists Use Open-Source Genetic Analysis Method in Plant Cells for the First Time

May 22, 2019

Scientists at the U.S. Department of Energy's Lawrence Berkeley National Lab (Berkeley Lab) have successfully used an open-source RNA analysis platform for the first time in an effort that could help engineer more efficient food and biofuel crops.

Drop-seq, developed at Harvard Medical School in 2015, is a popular method for measuring the RNA present in individual cells, allowing scientists to see what genes are being expressed and how this relates to the specific functions of different cell types. However, the freely shared protocol has only been used in animal cells. Diane Dickel, a scientist from Berkeley Lab pointed out that this is important in understanding plant biology. Dickel said that plants, like humans and mice, have multiple cell and tissue types, but unlike animals, plants have cell walls, which make it hard to open the cells up for genetic study.

While Dickel was interested in using Drop-seq in plants, some were skeptical. To run plants cells through a single-cell RNA-seq analysis, they must be protoplasted, a process that will strip their cell walls using enzymes. Dickel and her colleagues at DOE Joint Genome Institute (JGI) teamed up with researchers from UC Davis who had perfected a protoplasting technique for root tissue from Arabidopsis thaliana. After preparing samples of more than 12,000 Arabidopsis root cells, the group was thrilled when the Drop-seq process went smoother than expected.

For more details, read the news release from the Berkeley Lab.