The development is expected to revolutionize the improvement processes of agricultural crops
For the first time in the world, researchers from Tel Aviv University succeeded in developing a technology that makes it possible to reveal the role of genes and traits that have been hidden until now. The researchers point out that since the agricultural revolution, man has been in the habit of improving plant varieties for agricultural purposes by creating genetic diversity. But until today it was only possible to examine the functions of 20% of the genes (which are single genes). For 80% of the other genes (which are grouped in families) there was no effective way, on a large scale of the whole genome, to find out what their role is in the plant.
As a result of the unique development, the team of researchers from Tel Aviv University managed to isolate and identify dozens of new features that had been overlooked until now. This development is expected to revolutionize the improvement processes of agricultural crops because it is suitable for the improvement of most crops and most agricultural traits, such as increasing yield, resistance to drought or pests. The research was conducted under the leadership of the post-doctoral student, Dr. Yangzhe Hu, under the guidance of Prof. Elon Shani and Prof. Itai Miroz from the School of Plant Sciences and Food Security at Tel Aviv University. Researchers from France, Denmark, and Switzerland also participated in the study. The study was published in the prestigious journal Nature Plants.
Using the CRISPR technology for gene editing
Prof. Shani: "For thousands of years, since the agricultural revolution, man has been in the habit of improving varieties of plants for agricultural purposes by creating genetic diversity. But until a few years ago, it was not possible to intervene in a targeted manner in the genetic changes, but only to identify and encourage desired traits that were randomly generated. The development of gene editing technologies now allows precise changes to be made in a large number of plants."
As part of the research, the team of researchers used the innovative technology 'CRISPR' for gene editing and methods from the field of bioinformatics and molecular genetics to develop a new method for locating genes responsible for specific traits in plants.
The researchers explain that despite the development of genetic editing technology, several challenges remain that limit its application in agriculture. One of them is the need to identify as precisely as possible which genes in the plant's genome are responsible for a specific trait that we wish to cultivate. The accepted method for this matter is to produce mutations, that is, to change genes in different ways, then to examine the change in the plant created by the DNA containing the mutation, and to learn from this about the activity of the gene.
Thus, for example, if a plant with sweeter fruits develops, it can be learned that the altered gene is needed to determine the sweetness of the fruit. This method has been used for decades, and has been very successful, but it also has a fundamental problem: an average plant such as a tomato or rice has about 30,000 genes, but about 80% of them do not work alone but are grouped in families of similar genes. Therefore, if a single gene from a certain gene family is damaged, there is a high chance that another gene from the same family (actually a copy very similar to the damaged gene) will mask the damage and function in place of the damaged gene. This phenomenon, called genetic redundancy, means that we will most likely not be able to create a change in the plant itself, and we will not be able to understand the activity of the gene and its link to a specific trait.
Improving the control of mutations for improvement
The current study sought to find a solution to the problem of genetic redundancy throughout the genome, using an innovative gene editing method called 'Crisper'. Prof. Miroz explains: "The CRISPR method is based on an enzyme called Cas9 found naturally in bacteria, whose function is to cut foreign DNA sequences. An sgRNA sequence is attached to the enzyme, which identifies the DNA sequence that the enzyme is required to cut. The gene editing method allows us to design sgRNA sequences as we wish so that Cas9 will cut almost any gene we want to change. We sought to apply this technique to improve control over the creation of mutations in plants for the purposes of agricultural improvement, and specifically to overcome the difficulty posed by genetic redundancy."
In the first stage, a bioinformatics study was carried out on a computer, which, unlike most studies in the field, initially covered the entire genome. The researchers chose to focus on the Arabidopsis plant, which is used as a model plant in many studies and has about 30,000 genes. First, they swept about 8,000 individual genes, which have no family members, and therefore also have no additional copies in the genome to sweep over them. The remaining 22,000 genes were divided into families, and for each family appropriate sgRNA sequences were computationally designed: each sgRNA sequence is designed to lead the Cas9 cutting enzyme to a specific genetic sequence that characterizes the entire family, with the aim of creating mutations in all family members, so that they can no longer overlap each other. In this way, a library was built that totaled approximately 59,000 sgRNA sequences, which allow simultaneous damage to 10-2 genes in each gene family, thereby effectively neutralizing the phenomenon of genetic redundancy.
Arrange the gardens in the libraries
In addition, the sequences were divided into 10 sublibraries of approximately 6,000 sequences each, according to the presumed role of the genes - genes that code for enzymes, receptors, transcription proteins, etc. According to the researchers, building the libraries is a tool that allows to focus and optimize the search for genes responsible for desired traits, a search that until now has been largely random.
In the next step, the researchers moved from the computer to the laboratory. Here they generated all 59,000 sgRNA sequences identified by the computational method and engineered them into new plasmid libraries (ie, circular DNA segments) in combination with the cutting enzyme. The researchers then created thousands of new plants containing the libraries - with each plant having a single sgRNA sequence directed against a specific gene family.
The researchers followed the phenomena that were discovered in the plants following the changes in the genome, and when some new feature was observed in a particular plant, it was easy to know, based on the sequence of the sgRNA that was inserted into it, which genes had undergone a change. Also, through DNA sequencing of the identified genes, it was possible to find out the nature of the mutation that caused the change and what its contribution to the plant's properties was. In this way, many new traits were mapped that until now were blocked due to genetic redundancy. Specifically, the researchers identified unique proteins that make up a mechanism related to the transport of the hormone cytokinin, which is essential for the normal development of the plant.
Prof. Shani concludes: "The new method we developed is expected to be of great help to basic research to understand mechanisms in plants, but beyond that, it has enormous significance for agriculture: 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 or for diseases, or increasing crops. We believe this is the future of agriculture: controlled and targeted crop improvement operating on a large scale. Today we apply the method we developed with great success to rice and tomato plants, and in the future we intend to apply it to other crops as well."
For this purpose, Tel Aviv University's technology trading company (Ramot), in collaboration with the AgChimedes group, established the DisTree company. The 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 the climate crisis.
More of the topic in Hayadan:
- Garden Lab Teva
- Winners of the 2014 Wolf Prize for Agriculture: Bringing back genes lost from wild to domesticated animals and from wild to domesticated plants is essential to improving the food supply
- Researchers from Ben-Gurion University have identified genes that may increase the resistance of plants to desert conditions
