Next-generation multi-targeted CRISPR genetic toolbox uncovers hidden breeding traits

Project Information

Multi-Crop

Grant agreement ID: 101113412

DOI

10.3030/101113412

Project closed

EC signature date 20 February 2023

Start date 1 August 2023

End date 31 July 2025

Funded under

• European Research Council (ERC)

Total cost

No data

EU contribution

€ 150 000,00

Coordinated by

TEL AVIV UNIVERSITY
Israel

Periodic Reporting for period 1 - Multi-Crop (Next-generation multi-targeted CRISPR genetic toolbox uncovers hidden breeding traits)

Reporting period: 2023-08-01 to 2025-07-31

Summary of the context and overall objectives of the project

Food demand is rising while arable land and water are constrained. Many agronomic traits remain “genetically hidden” because gene duplication has created families of related genes that buffer one another; therefore, editing a single member often has little or no effect. This redundancy benefits plants by adding robustness and fine control of environmental responses, but it limits breeding and slows discovery. To overcome this bottleneck, we developed Multi-Crop: a genome-scale, multi-target CRISPR platform that edits several members of a gene family at once. Our objective was to bypass functional redundancy and rapidly reveal useful traits in major crops, with an initial focus on drought-relevant mechanisms in tomato and rice. By enabling systematic, family-level editing and forward screening, Multi-Crop shortens the path from gene discovery to breeding and expands the range of traits accessible for crop improvement.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

We designed, synthesized and quality-controlled large multi-target sgRNA libraries for tomato and rice, deep-sequenced them to confirm coverage, and generated extensive edited plant populations. In tomato, a transportome sub-library was cloned and transformed; in rice, ~1,000 independent edited lines were produced. Screening identified multiple previously hidden phenotypes relevant to growth and stress responses. The tomato work has been peer-reviewed and published, demonstrating that multiplex editing of gene families can unlock fruit-quality and other agronomic traits that single-gene edits could not access. In parallel, the rice pipeline has been completed and advanced towards dissemination. To support exploitation, a spin-out company (NetaGenomiX) was launched to further develop and commercialize the technology with partners.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

Multi-Crop delivers a step change over one-gene-at-a-time methods by enabling genome-scale, redundant-free editing and forward genetics directly in crops. This reveals trait variation masked by redundancy, provides higher hit-rates in phenotypic screens with unique phenotypic variation, and creates an efficient route to validate complex traits at scale. The published tomato study confirms that multi-genic editing exposes valuable, heritable traits that conventional editing missed, underscoring the platform’s potential for breeding and product development. For widespread adoption, the key requirements are continued transformation capacity in target crops, sustained partnerships with seed companies, and public institutions for field validation. Overall, the project delivers a validated technology, crop libraries, and initial application results that open up new avenues for drought resilience and other complex traits in major crops.