Scientists in Israel claim to have made a “world-first breakthrough” in plant gene modification that they believe could revolutionize how crop traits are improved. The researchers say their discovery makes it possible to reveal the role of genes and traits in plants previously hidden by functional redundancy. Meaning they are able to isolate and identify dozens of new genetic features that had been overlooked until now.
The team of researchers used CRISPR and methods from the field of bioinformatics and molecular genetics to develop a new method for locating genes responsible for specific plant traits. This itself is not novel, as targeted gene editing has been around for several years now. However, CRISPR and similar technologies have challenges that limit its application in agriculture.
The problem is the genome itself. An average plant such as tomato or rice has about 30,000 genes. However, about 80% of them don’t work alone but are grouped in families of similar genes. Due to this phenomenon, which is called genetic redundancy, it’s hard to create a change in the plant itself and to determine the function of the gene and its link to a specific trait.
Professor Itay Mayrose from the School of Plant Sciences and Food Security at Tel Aviv University’s Wise Faculty of Life Sciences says the team focused on the Arabidopsis plant, a member of the mustard family that is widely used as a model organism in plant biology. The plant has about 30,000 genes, of which about 8,000 were identified and isolated. The remaining 22,000 genes were divided into families for which the researchers designed appropriate sgRNA sequences.
The science details get pretty complicated, but suffice to say that they were eventually able to create a library of approximately 59,000 sgRNA sequences, where each sgRNA by itself is able to simultaneously modify two to 10 genes at once from each gene family, thereby effectively neutralizing the phenomenon of genetic redundancy. Those were divided further into sub-libraries according to the presumed role of the genes.
The researchers then generated thousands of new plants containing the libraries and observed the traits that manifested. As each plant was implanted with a single sgRNA sequence targeting a specific gene family, it was easy to know which genes were responsible for the changes. Also, through DNA sequencing of the identified genes, it was possible to determine the nature of the mutation that caused the change and its contribution to the plant’s new properties. In this way, many new traits were mapped that until now were blocked due to genetic redundancy.
Professor Eilon Shani, also from Tel Aviv University, says the new method is expected to be of great help to basic research in understanding processes in plants. “But beyond that, it has enormous significance for agriculture: it makes it possible 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,” explains Shani. “We believe that this is the future of agriculture: controlled and targeted crop improvement on a large scale.”
Shani says they are also already applying the method to rice and tomato plants “with great success,” and intend to apply it to other crops as well. The research was performed by postdoctoral student Dr. Yangjie Hu under the guidance of Prof. Shani and Prof. Mayrose from the School of Plant Sciences and Food Security at Tel Aviv University’s Wise Faculty of Life Sciences. Scientists from France, Denmark, and Switzerland also participated in the research, which was published in Nature Plants. More details are available at Phys.org.
