CRISPR/Cas9 genome editing of rubber producing dandelion Taraxacum kok-saghyz using Agrobacterium rhizogenes without selection

Abstract

CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR associated protein 9) is a highly accessible genome editing tool. Here we demonstrate its potential for use in Taraxacum species. Taraxacum kok-saghyz (TK, Rubber Dandelion) is notable for its ability to produce high molecular weight rubber in its roots and promise as an alternative source of natural rubber. In order to accelerate the domestication of TK, we have established a simple strategy to deploy CRISPR/Cas9 in this species. A critical gene encoding fructan:fructan 1-fructosyltransferase (1-FFT), implicated in inulin biosynthesis was selected as the target, as inulin is an expected antagonist of rubber production. TK plantlets were inoculated with Agrobacterium rhizogenes harboring a plasmid encoding a Cas9 and sgRNA (single guide RNA) targeting TK 1-FFT. We were able to rapidly induce hairy roots harboring knockout alleles without the selection of stable, herbicide or antibiotic resistant transformants. Mutagenesis was affirmed by observing a loss of restriction sites within 1-FFT, followed by sequencing. Of 11 hairy root samples tested, 10 showed the presence of genome editing, with mutation rates as high as 88.9%, suggesting a high efficiency mutagenesis induced by CRISPR/Cas9 via A. rhizogenes-mediated transformation. Whole TK plants were regenerated from hairy roots harboring knockout alleles. The regenerated plants contained knockout alleles, with mutation rates as high as 80.0%. TK plants with edited genomes were obtained within 10 weeks. By omitting a selection step, it was possible to generate edited TK plants lacking stably transformed CRISPR elements, which may potentially reduce off-target mutagenesis. Application of high efficiency CRISPR/Cas9 genome editing will facilitate the domestication and commercialization of TK as a rubber producing crop, and may accelerate basic research on the regulation of rubber biosynthesis.