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Researchers from Tel Aviv University have developed a genetic editing method tailored to crop plants, which has influenced various traits in tomato plants, including the taste and shape of the fruit. The researchers believe this innovative technology can be applied to a wide variety of crop species and may eventually be used to cultivate new and improved plant varieties.

"We demonstrated that with our technology, it is possible to select specific traits and influence them, a capability that is essential for advancing agriculture and achieving food security," the researchers stated.

The study was led by Prof. Eilon Shani, Prof. Itay Mayrose and Ph.D. student Amichai Berman (School of Plant Sciences and Food Security at Tel Aviv University) together with Ph.D. student Ning Su and Dr. Yuqin Zhang (University of Chinese Academy of Sciences in Beijing), and Dr. Osnat Yanai from the Israeli Agri-Tech company NetaGenomiX. The article was published in the journal .

Prof. Shani explains, "Researchers around the world are engaged in advancing agriculture in order to address accelerated global changes and feed the global population in the coming decades. Among other things, genetic editing technologies are being advanced to develop new plant varieties with desirable traits such as resistance to drought, heat, and disease, improved flavor, optimized nutrient usage, and more.

"One such method is CRISPR-Cas9, which has revolutionized the field of genetic editing by enabling the precise modification of specific genes in the genome.

"However, in the realm of agricultural development, this method has encountered several fundamental challenges: Firstly, while CRISPR technology allows for targeted gene editing, until now, this capability was limited in scale—the number of genes that could be edited and studied was very small.

"In the current study, we significantly improved the method's efficiency, enabling us to examine the roles of thousands of genes. Secondly, many plants exhibit 'genetic redundancy': different genes from the same family, composed of similar amino acid sequences, compensate for one another and preserve the trait even if one gene is deactivated or edited."

Berman says, "To overcome genetic redundancy, we aimed to simultaneously alter entire families of similar genes. In a previous study, we developed a breakthrough solution to overcome the issue of genetic redundancy, a dedicated algorithm, and fed it a list of thousands of genes we wanted to edit.

"The algorithm identified a suitable CRISPR unit for each gene (or gene group) on the list that would induce the desired modification, thereby constructing CRISPR libraries. The first study achieved good results in the model plant Arabidopsis thaliana, and this time we sought to test the method in a crop plant for the first time. We chose the tomato."

In the current study, the researchers built 10 libraries comprising approximately 15,000 unique CRISPR units targeting the tomato genome—each unit designed to affect a specific gene group from the same family. They then used the CRISPR units to induce edits in around 1,300 tomato plants, each plant with an alteration in a different gene group.

The researchers then tracked the development of each plant to examine whether the selected changes appeared in fruit size, shape, taste, nutrient utilization, or pathogen resistance. Indeed, the researchers identified several lines with sweetness levels either lower or higher than the control plants.

Prof. Shani concludes, "In this study, using our innovative method, we successfully made targeted genetic changes to gene families in the tomato plant, and identified precisely which genetic edits produced the desired result." The Israeli Agri-Tech company NetaGenomiX has received a license to commercialize the new technology, with the goal of advancing food security by developing non-GMO crops adapted to the changing climate, providing benefits for both farmers and consumers.

Berman adds, "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. In follow-up studies, we are working on developing additional selected traits in tomato and in rice."