“The method of genome editing should not be opposed to traditional selection methods. “This is rather a new tool,” emphasizes the head of the laboratory of plant stress resistance All-Russian Research Institute of Agricultural Biotechnology (VNIISB) Vasily Taranov. – Once upon a time, surgeons performed operations with a knife, then they appeared scalpels, then lasers. Completely different options became available to surgery. So genetic engineering offers a tool with which you can take and improve something, but it does not cancel or replace everything that was used previously.”
The All-Russian Research Institute of Agricultural Biotechnology (VNIISB) operates a laboratory for plant stress resistance, the work of which is carried out in two main directions: the search for genes that determine plant resistance to abiotic and biotic stress, and editing the genome of cultivated plants in order to increase their stress resistance. The scientists' research area includes potatoes and open-ground vegetables.
We talk with the head of the laboratory Vasily Taranov and senior researcher Marina Lebedeva about what the features and advantages of the latest technologies are, what results they can achieve and what problems of Russian agricultural producers they are used by laboratory scientists to solve.
– Today there is a lot of talk about the need to speed up the selection process. It is believed that the method of genome editing allows this to be done. This is true?
V.T.: It would be more correct to say that biotechnological methods help not so much to speed up selection as to expand the capabilities of scientists. The process of working on a variety still remains quite lengthy, since we are talking about plants that have a certain life cycle.
But it becomes possible for specialists to obtain results that would be extremely difficult (if not impossible) to achieve using traditional breeding methods.
With the help of genomic editing, we can purposefully introduce a mutation that directly affects a specific characteristic of a variety, while keeping the rest of the complex of economically valuable traits unchanged.
M.L.: Imagine that we want to introduce a resistance gene from a wild potato into our cultivated variety using traditional breeding methods. To do this, the breeder carries out a series of crosses of the “savage” with certain cultural lines. The problem is that along with the resistance gene, all other “wild” genes are transferred to the variety, which is most often extremely undesirable. Genetic engineering allows you to take/change only one desired gene.
– There is a point of view that despite the fact that the method of genome editing has been known for about 10 years, it has not yet produced noticeable commercial results.
V.T.: This is not entirely true. The world's leading breeding companies use genome editing and do not hide it. But we don't know what exactly they do and what results they get.
Achievements are not advertised because it is more expensive to bring to market a plant that has been processed using genetic engineering methods than one that was obtained traditionally. And sometimes this is simply impossible to do.
At the same time, it is very difficult to prove that genome editing was used to create a particular variety using existing methods.
During the test, specialists will look for a marker sequence in the genome of the organism; if it is present, the plant will be recognized as genetically modified. But with genomic editing, nothing is introduced into the genome, so nothing can be found.
Changes often affect not just one gene, but a specific place in the gene, literally one nucleotide, one letter. And the remaining billions of letters remain as they were. To determine that a plant has been edited, you need to actually read its entire genome, with a coverage ten times higher than the standard to eliminate error. No one will do such a voluminous and very expensive analysis, and the breeder can always say that he obtained the plant using mutagenesis or traditional selection.
– M.L.: Genome editing in general, and especially the experience of using these technologies on plants, is a fairly recent story.
Not least because to change a feature you need to know what exactly and how to edit it. Plant traits are determined by genes, most often a set of genes, from which suitable targets for editing must be selected. But elucidating the functions and regulation of specific genes that contribute to traits of interest requires complex and often lengthy studies. When compared with animals and humans, we can say that we do not know many of the molecular mechanisms of plant traits (for example, resistance, productivity, etc.) very well. At the same time, plant genomes are larger and more complex, which does not simplify the task at all. However, much is already known through basic research in plant biology, and the more we understand this, the more our possibilities for modification increase.
In addition, we are talking about a method that makes it possible to correct certain characteristics, but not to introduce new varieties to the market, work on which, despite some acceleration, still takes years.
– Do biotechnologists do gene editing? How do they determine the actual direction of the work (the purpose for editing)?
V.T.: The biotechnologist must work in tandem with a successful breeder of the chosen crop and, ideally, involve other specialist producers. The breeder, together with the farmers, sets the task, the breeder helps to select suitable genotypes. We, in turn, consult with biochemists and geneticists, we think what we can offer on this basis (the necessary characteristics are not always sufficiently studied from a biological point of view). We look at what we can actually do, carry out our stage of work, return the resulting line to the breeder, and the breeder brings the result to the variety.
- Is genome editing an expensive technology?
V.T.: The cost of obtaining a plant depends on the crop and whether the resulting plant is edited or transgenic.
If we talk about equipment, then for a company that is already engaged in obtaining virus-free material and microcloning, the purchase of equipment and reagents for genome editing will cost a relatively small amount. The obstacle to starting such work may not be the overwhelming amount of investment, but the lack of qualified personnel. There are very few people who can take on and perform such a specialized task.
And coming back to costs: technological progress in this area is very fast. The methods of genome editing, say, in 2012, when CRISPR/Cas9 was discovered (a technology for editing the genomes of higher organisms, based on the immune system of bacteria), and what we have now are very different. Operating efficiency increases year by year, and costs decrease.
M.L.: This can be compared to the human genome sequencing project. The first human genome was sequenced by an international consortium for 10 years for 2.7 billion dollars simply because such technologies were available in the 90s. Currently, sequencing a complete human genome costs less than $1000 and takes a couple of days.
– Let’s move on to talking about your laboratory, is it focused on fundamental science or applied research?
V.T.: We try to do both. Initially, priority was given to fundamental things, but now we are trying to apply our developments to practice.
At the moment, for example, we are studying the mechanisms of potato resistance to virus Y. This is a lot of fundamental work, but if successful, the result will be very interesting for the selection of resistant varieties.
M.L.: Fundamental and applied science are closely interconnected; one cannot exist without the other. If we don't know how the virus interacts with the plant, with which specific proteins, we won't be able to change them to make the plant resistant.
We have been conducting research on virus Y since 2018 and are now approaching the fact that in the next couple of years we will obtain a formula for resistance, and in the future the necessary practical result: the potato plant will not synthesize viral proteins, it will be resistant to the virus.
– Do you cooperate with Russian breeding companies/breeders?
V.T.: On potatoes, we work with a young breeder Maria Polyakova, actively communicate with experts from the Potato Union, and maintain contacts with the Potato Federal Research Center named after. A.G. Lorja. As for cabbage, we interact with breeders and seed growers of the Russian State Agrarian University-Moscow Agricultural Academy named after. K.A. Timiryazev by Grigory and Socrates Monachos. And in what we do in this area, we are completely guided by them.
– And again about viruses. Marina Valerievna, your range of scientific interests includes not only the virus Y. In 2023, you received a grant from the Russian Science Foundation to conduct research on the project “Study of viromes of cultivated potatoes (Solanum tuberosum L.) using high-throughput sequencing methods.” Why is this topic interesting?
M.L.: Potatoes, to a greater extent than many other plants, suffer from viral diseases, since they are propagated vegetatively. Viruses accumulate in tubers and are passed on to next generations, so the viral load is constantly growing. When they say that potatoes are degenerating, this is exactly what we are talking about.
Viruses are not inert systems; they actively interact with both the host plant and each other. There are cases where a plant that is already sick with one specific virus cannot become infected with another. And there are viruses that cannot infect a plant alone; they act only in cooperation with other viruses. Just recently, a work was published describing forms of viruses that help plants survive drought. Such an unexpected transition from parasitism to mutualism.
There are no effective chemicals to combat viral diseases on potatoes. To improve its health, quite complex and, most importantly, expensive methods have been developed: through in vitro culture, obtaining microtubers. But the result only lasts for a few generations. To find other solutions, you need to study the characteristics of viruses in more detail, so the study is very, very relevant.
– GOST 33996-2016 “Seed potatoes. Technical conditions and methods for determining quality" five viruses are listed (PVK - X potato virus; SBK - S potato virus; MVK - M potato virus; YBK - Y potato virus; VSLK - leaf curl virus potato) and one viroid (PSTV – potato spindle tuber viroid). Will you focus on them?
M.L.: My project aims to use high-throughput methods to study those viromes (collections of viruses) that are present on potatoes in Russia. This is interesting both from the point of view of what complexes of different viruses are found on one plant, and from the point of view of the prevalence of these viruses.
In total, more than 50 viruses found on potatoes are known in the world. Those listed in GOST are among the most dangerous, and in addition, they have clear external signs. Thus, mosaic necrosis is a common manifestation of virus Y infection, and the presence of leaf curl virus can be determined by the characteristic deformation of leaf blades.
But there are many viruses that do not manifest themselves phenotypically, although they can also have an effect on the crop. They are rarely discovered, but only because they are not looked for.
As an example, I can cite the work of colleagues from the All-Russian Research Institute of Plant Protection (VIZR). In 2019, they published an article about the discovery of potato virus P in Russia. Previously it was believed that it was distributed exclusively in South America.
The question is what will we discover if we look not “under the streetlight” where it is light, but where we have not yet looked.
– Where will you conduct your research?
M.L.: According to the terms of the grant, the project will take two years. Last year we collaborated with a potato farm in the Tula region, collected material, worked with different varieties and reproductions. This year we will go to other regions and see what viruses are found there.
The results of the study will be summed up in 2025, and we will definitely tell Russian potato growers about them.