CRISPR pipeline for circadian cis-element editing in crop yield and defense genes
Rapid transgene-free CRISPR pipeline for targeted editing of circadian regulatory elements in plant genomes. Validated in zebrafish and Arabidopsis, with extension planned to Brassica. Enables modification of circadian gene expression to potentially improve yield, flowering, and defense traits in crops.
Overview
This offering is a transgene-free CRISPR gene-editing pipeline developed by a chronobiology group with dual expertise in medical genomics and crop science. The technology enables rapid mapping of genetic variants and generation of targeted knockouts without producing transgenic organisms. Originally developed and validated in zebrafish, the same approach has been successfully applied to plant systems, where it has recapitulated established circadian clock phenotypes such as toc1 and elf3 mutants in Arabidopsis.
The core value proposition is the ability to modify the circadian regulation of individual yield, flowering, and defense genes by editing their cis-regulatory elements (such as morning and evening elements) rather than knocking out the upstream clock proteins. This finer-grained approach allows researchers and breeders to tune the timing and amplitude of specific gene expression, which may lead to improvements in crop yield, stress resilience, and flowering time.
Technical specifications
Key features:
- Transgene-free CRISPR editing using Cas9 and sgRNA delivery, avoiding the regulatory and biosafety complications associated with transgenic plants
- Rapid variant mapping and knockout generation pipeline originally validated in zebrafish
- Successful recapitulation of circadian clock phenotypes (toc1, elf3) in Arabidopsis using the same editing principles
- Scalable targeting of cis-regulatory elements (morning and evening elements) in diurnally oscillating genes
- Applicability to any plant background and any genomic locus of interest
- Validated in zebrafish for modifying circadian outputs of SCN5A by editing cis elements
Research plan:
- Target 20 yield-, defense-, and flowering-associated genes in Arabidopsis and Brassica
- Validate effects on circadian expression of target genes via qPCR
- Transfer and adapt the pipeline from Arabidopsis to the crop Brassica
Technology readiness level
The pipeline is validated in zebrafish (pre-print available) and has been demonstrated to generate targeted elf3 and toc1 mutants in Arabidopsis without a transgenic step. Validation that cis-element knockouts can modify circadian outputs has been demonstrated in zebrafish for SCN5A. The current stage of development focuses on extending the approach from the model Arabidopsis system to the crop Brassica, and on scaling cis-element editing across 20 yield- and defense-related genes. The technology is positioned at an early-to-mid research and development stage, with demonstrated proof-of-concept in plants and an active plan for translational application in a crop species.
About University of Cambridge
Cambridge is a collegiate, comprehensive research university that combines broad academic depth with world-class facilities and strong translational activity. Industry engages through co-located labs, a major biomedical campus integrated with an NHS hospital system, and research and technology parks across the Cambridge cluster. Its location in a mature startup and scale-up ecosystem provides ready access to venture funding, prototyping resources, and collaboration with global R&D sites. Research is backed by competitive UKRI council funding and other national sources, with additional support from major charities and European programs. A dedicated technology transfer office supports IP, licensing, and seed investment to accelerate commercialization.
delivered to your inbox.