Research: New CRISPR Method Boosts Tomato Traits

Researchers at Tel Aviv University, in collaboration with the University of Chinese Academy of Sciences and Israeli Agri-Tech company NetaGenomiX, have developed a groundbreaking genetic editing method using CRISPR technology that promises to significantly advance crop improvement, particularly for tomatoes. Published in Nature Communications, this innovation directly addresses two major challenges in traditional plant breeding: the limited scale of gene editing and the issue of "genetic redundancy."

Traditionally, while CRISPR offers precise gene modification, it has been difficult to apply on a large scale, limiting the number of genes that could be studied simultaneously. Furthermore, many plants, including tomatoes, exhibit "genetic redundancy" – where multiple similar genes perform the same function, masking the effect if only one is altered. This means that even if a gene is edited, its function might still be performed by another similar gene, preventing the desired trait from appearing.

To overcome this, the Tel Aviv University team, led by Prof. Eilon Shani, Prof. Itay Mayrose, and PhD student Amichai Berman, developed a multi-targeted CRISPR approach. Using a dedicated algorithm, they designed extensive "CRISPR libraries" (over 15,000 unique CRISPR units) specifically to target and alter entire families of similar genes at once.

PhD Student Amichai Berman

After initial success in the model plant Arabidopsis, they successfully applied this innovative method to the tomato.

The researchers used these CRISPR units to induce mutations in approximately 1,300 tomato plants, each altered in a different gene group. By tracking the development of these plants, they successfully identified mutants with desirable changes in crucial traits for the processing tomato industry, including:

• Fruit size and shape: Enabling tailored physical characteristics.
• Fruit flavor and sweetness: Directly impacting product quality and consumer appeal.
• Nutrient utilization: Leading to more efficient plant growth.
• Pathogen resistance: Enhancing resilience against diseases, reducing crop loss.

This new approach allows for the large-scale identification and modification of genes, enabling the precise selection and influence of specific traits. The technology holds immense potential for cultivating new and improved tomato varieties that are better adapted to changing climates, more efficient in resource use, and possess enhanced characteristics for processing.

NetaGenomiX, an Israeli Agri-Tech company, has secured a license to commercialize this technology. The aim is to develop non-GMO crops that will benefit both farmers through improved yields and resilience, and consumers through enhanced product quality, ultimately contributing to global food security. The researchers are already working on developing additional selected traits in tomatoes and rice for future applications.

Reference: Berman, A., Su, N., Li, Z. et al. Construction of multi-targeted CRISPR libraries in tomato to overcome functional redundancy at genome-scale level. Nat Commun 16, 4111 (2025).

Full text at: https://doi.org/10.1038/s41467-025-59280-6

Sources: HortiDaily, Tel Aviv University Canada. Nature.com