Jerusalem, 10 June, 2025 (TPS-IL) — Israeli and Chines scientists have developed a groundbreaking genetic editing method that has successfully modified complex traits in tomato plants such as size, shape, flavor, nutrient use and resistance to disease.
taste, nutrient usage, and resistance to heat and drought, Tel Aviv University announced on Tuesday.
The method, which uses a refined form of CRISPR-Cas9 technology, allows for the simultaneous editing of multiple genes, a long-standing challenge in agricultural science due to the complex and redundant nature of plant genomes. In a study recently published in the peer-reviewed Nature Communications journal, the researchers demonstrated the ability to influence key characteristics in tomatoes, such as taste, shape, and nutrient utilization.
“Genetic editing in crop plants is a complex process. Our method overcomes major challenges and may be used to study and influence a variety of traits, such as resistance to diseases and drought, in different field crops,” the researchers said.
The project was led by Professors Eilon Shani and Itay Mayrose, along with PhD student Amichai Berman from Tel Aviv University’s School of Plant Sciences and Food Security. They collaborated with Ning Su and Dr. Yuqin Zhang from the University of Chinese Academy of Sciences in Beijing, and Dr. Osnat Yanai of Israeli agri-tech company NetaGenomiX.
CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats. It is a powerful tool that enables scientists to edit genes precisely and efficiently. It works like molecular scissors: a specialized protein (often Cas9) is guided by a small piece of RNA to a specific location in the DNA. Once it finds its target, it makes a cut, allowing researchers to remove, disable, or replace specific genes.
However, in complex organisms like plants, many genes belong to families of similar genes that perform overlapping functions. This creates a challenge known as genetic redundancy — when one gene is edited, another in the same family may compensate, making it hard to see any change.
The breakthrough centers on two major innovations. First, the researchers improved the scalability of CRISPR-Cas9 by developing a system that can target thousands of genes at once.
To tackle the second problem of genetic redundancy, “We aimed to simultaneously alter entire families of similar genes,” said Berman. “In a previous study, we developed a dedicated algorithm that takes a list of target genes and identifies a unique CRISPR unit for each one — or for a group of similar genes — to induce the desired modification. That allowed us to build comprehensive CRISPR libraries.”
In this research, the scientists created a CRISPR library — a large collection of customized gene-editing tools, each designed to target a specific gene or group of similar genes in the tomato genome. This CRISPR library allowed scientists to overcome the redundancy problem by simultaneously edit thousands of genes across hundreds of plants. Each plant had a unique genetic alteration, allowing the researchers to observe which changes led to differences in traits like sweetness, fruit shape, or disease resistance.
While earlier tests of the algorithm were successful in the model plant Arabidopsis thaliana, the new study marks its first application in a crop species. The team constructed 10 CRISPR libraries containing roughly 15,000 unique gene-editing units designed for the tomato genome. They then introduced these edits into about 1,300 tomato plants, each one modified in a different gene group.
The Israeli company NetaGenomiX has received a license to commercialize the technology. The goal is to develop improved, non-GMO crops that can better withstand climate change and provide tangible benefits for both farmers and consumers.
“We believe our research opens the door to breeding improved varieties for a wide range of crops, and also advances the field of plant science as a whole,” added Berman. “In follow-up studies, we are working on developing additional selected traits in tomato and in rice.”
