Researchers from Tel Aviv University (TAU) have developed a genome-scale technology that makes it possible to reveal the role of genes and traits in plants that have been hidden by functional redundancy. They isolated and identified dozens of new features that had been overlooked until now. The development is expected to revolutionize the way agricultural crops are improved, as it can be applied to most crops and agricultural traits, such as increased yield and resistance to drought or pests.

The research was performed by postdoctoral student Dr. Yangjie Hu under the guidance of Professor Eilon Shani and Professor Itay Mayrose from the School of Plant Sciences and Food Security at TAU’s Wise Faculty of Life Sciences. Scientists from France, Denmark, and Switzerland also participated in the research. The research was published on March 27, 2023, in the journal Nature Plants.

Since the agricultural revolution, human beings have improved plant varieties for agricultural purposes by creating genetic diversity. But until this recent development, it was only possible to examine the functions of single genes, which make up only 20% of the genome. For the remaining 80% of the genome, made up of genes grouped in families, there was no effective way, on the large scale of the whole genome, to determine their role in the plant.

The research team used the innovative CRISPR technology for gene editing as well as methods from the field of bioinformatics and molecular genetics to develop a new method for locating genes responsible for specific traits in plants.

“For thousands of years, since the agricultural revolution, man has been improving different plant varieties for agriculture by promoting genetic variation,” Professor Shani says. “But until a few years ago it was not possible to genetically intervene in a targeted manner, but only to identify and promote desirable traits that were created randomly. The development of gene editing technologies now allows precise changes to be made in a large number of plants.”

The researchers explain that despite the development of genetic editing technologies, such as CRISPR, several challenges remained that limited its application to agriculture. One of them was the need to identify as precisely as possible which genes in the plant’s genome are responsible for a specific desired trait to cultivate. The accepted method to address this challenge is to produce mutations — that is, to modify genes in different ways — and then to examine changes in the plant’s traits as a result of the mutation in the DNA and to learn from this about the function of the gene.

If a plant with sweeter fruit develops, for example, it can be concluded that the altered gene determines the sweetness of the fruit. This strategy has been used for decades and has been very successful, but it also has a fundamental problem: an average plant such as tomato or rice has about 30,000 genes, but about 80% of them do not work alone. They are grouped in families of similar genes. Therefore, if a single gene from a certain gene family is mutated, there is a high probability that another gene from the same family (actually a copy very similar to the mutated gene) will mask the phenotypes in place of the mutated gene. Due to this phenomenon, called genetic redundancy, it is difficult to create a change in the plant itself, and to determine the function of the gene and its link to a specific trait.

The current study sought to find a solution to the problem of genetic redundancy by using an innovative gene editing method called CRISPR. “The CRISPR method is based on an enzyme called Cas9 found naturally in bacteria, whose role is to cut foreign DNA sequences,” Professor Mayrose explains. “This genetic editing method allows us to design different sgRNA sequences to allow Cas9 to cut almost any gene that we want to change. We wanted to apply this technique to improve the control of creating mutations in plants for the purposes of agricultural improvement, and specifically to overcome the common limitation posed by genetic redundancy.”

“The new method we developed is expected to be of great help to basic research in understanding processes in plants, but beyond that, it has enormous significance for agriculture,” Professor Shani concludes. “It allows us to efficiently and accurately reveal the pool of genes responsible for traits we seek to improve, such as resistance to drought, pests, and diseases, or increasing yields. We believe that this is the future of agriculture: controlled and targeted crop improvement on a large scale. Today we are applying the method we developed to rice and tomato plants with great success, and we intend to apply it to other crops as well.”

To this end, Ramot, TAU’s technology commercialization company, established the DisTree company in collaboration with the AgChimedes group. This financial investment, combined with the business and professional support of Agchimedes, will allow DisTree to apply the new technology to a variety of crops, with the aim of revolutionizing the genetics of the world of agriculture and enabling nutritional security in the age of climate crisis.