The discovery of the genome editing tool CRISPR/Cas in 2012 marks a turning point in research and plant breeding: thanks to its practical properties – precise, user-friendly, and inexpensive – the method has spread to laboratories worldwide. In plant breeding, these “gene scissors” are now indispensable, although the term “new genomic techniques” (NGTs) is more appropriate, as a wide range of different editing tools with varying capabilities is now available.

The number of scientific studies can serve as an indicator of progress: the EU-SAGE database, a network of 134 European research institutes, lists around 1,000 peer-reviewed genome editing studies from 58 countries covering 76 plant species. Among the crops studied, rice leads, followed by tomato, wheat, maize, and soybean. Most applications aim to make plants more resistant to abiotic stress factors such as drought, salinity, or extreme temperatures, as well as to diseases and pests. Other key areas include increasing yield and improving quality – such as taste, nutritional value, and shelf life.

This shift is also reflected in regulation: countries such as the United States, Canada, India, and China have adapted their legal frameworks. Simple genome-edited plants (SDN1, SDN2) are no longer subject to the strict regulations of classical genetic engineering. The European Commission has also presented a revised law, which is currently being negotiated with European institutions – Member States and the European Parliament.

A look back

To understand why gene editing is often described as a “revolution,” it is worth taking a look back at the history of plant breeding. The fundamental goals have hardly changed over thousands of years: it has always been about making crops more productive and more resilient.

The three most important crops for humans are maize, wheat, and rice. They originate from wild grasses with tiny seed heads and were domesticated around 10,000 years ago through artificial selection: humans selectively propagated plants with larger seed heads and gradually achieved better yields. This was possible because plants of the same species differ, both in appearance and in their genetic makeup. This genetic diversity is what makes breeding possible in the first place.

Plant breeding received a major boost in the mid-20th century when it was discovered that mutations could also be induced artificially: exposing plant seeds to radiation or chemicals triggers numerous DNA changes that can lead to new traits. Most mutations are neutral, some are negative, and very few are positive. Since this process always produces a mixture of traits, it is referred to as random mutagenesis. To remove undesirable traits, complex backcrossing is required. In this way, more than 3,000 varieties were created, including durum wheat for pasta or pink grapefruits.

Precision instead of chance

With new genomic techniques (NGTs), a new era of plant breeding begins: the genome can now be modified in a targeted and direct way, without introducing foreign DNA. NGTs include zinc finger nucleases, TALENs, and CRISPR/Cas systems, which have become established thanks to their ease of use. Classical genetic engineering pursued a targeted approach for the first time: genes for specific traits, such as pest resistance, are inserted directly into the genome of plants. One example is Bt maize, which repels insects through a bacterial gene. Critics point to the crossing of species barriers and the element of chance: no one can predict where the additional gene will integrate into the genome.

Through modifications of the Cas9 enzyme, the guide RNA, and the discovery of new Cas proteins, the possibilities of genome editing have expanded significantly in recent years: variants such as base editing, prime editing, and multiplex editing increase the number of editable sites in the genome and enable even more precise interventions.

In addition to basic research, practical applications are increasingly coming to the fore: a key focus is on disease resistance; in addition, vitamin content in tomatoes and bananas is being increased, or allergens in wheat, soy, and peanuts are being eliminated. Some genome-edited varieties have already been approved, many more are in the pipeline, but no variety is yet cultivated on a large scale.

United States: several plants have been approved, such as soybeans with an improved fatty acid profile, mustard greens that taste less bitter, camelina, and rapeseed.
Japan: two tomato varieties, one maize variety and one potato variety, as well as three fish species have been approved. One tomato variety and the three fast-growing fish species are already being sold.
China: five genome-edited varieties (wheat, maize, soybean, and rice) were approved at the end of 2024; cultivation is expected to begin shortly.
India: in 2025, two genome-edited, climate-resilient rice varieties were approved. The seeds are being multiplied, and cultivation is expected to begin soon.

What is possible

Altered gene activity. A large proportion of all studies conducted use CRISPR to introduce point mutations and small insertions into specific genes. In this way, genes can be quickly and easily switched off (knock-outs), and researchers can observe how this affects the plant. CRISPR has thus become a central tool in basic research: in systematic mutagenesis, a target region – usually a gene or part of it – is mutated at every position to determine which changes preserve function and which are harmful. This provides a rapid overview of which mutations can lead to desirable traits such as disease resistance.

In addition to switching off genes, the targeted modification of gene regulation is increasingly coming into focus. Even small changes in promoters – the regulatory regions – can fine-tune gene activity and thereby create new plant traits.

Breeding accelerator. CRISPR/Cas systems open up new pathways in plant breeding. By comparing wild and cultivated plants, it is possible to identify the genomic regions that were altered during domestication. Many modern crops are genetically depleted because breeding has primarily focused on yield. With CRISPR/Cas, the domestication process can be restarted and accelerated. This could lead to plants that combine the robustness and often better taste of wild species with the yield traits of cultivated crops.

A well-known example is the wild tomato Solanum pimpinellifolium: researchers used multiplex editing to switch off six genes and obtained plants after just one generation with improved growth, more flowers, larger fruits, and higher lycopene content. Similar approaches are also being pursued with wild strawberries and wild rice species.

New genomic techniques (NGTs) are also gaining importance in hybrid breeding: hybrid plants often deliver higher yields and are more resistant to diseases and environmental stress. The production of hybrid seeds requires male sterile lines, i.e., plants without fertile pollen. While such traits previously had to be laboriously introduced into elite varieties, NGTs now allow the genes responsible for pollen formation to be switched off in a targeted manner. This enables the creation of stable male sterile lines, making hybrid production simpler, faster, and applicable to more plant species than before.

Sustainable and targeted plant protection. Genome editing is particularly well suited to making plants resistant to viruses, bacteria, or fungi, as modifying a single gene is often sufficient. A prominent example – recently approved in China – is powdery mildew-resistant wheat, in which the MLO gene has been knocked out. This prevents the fungus from infecting plant cells. Other examples demonstrate the broad potential of the method: knocking out the DMR6 gene causes tomato plants to activate their defense systems more strongly. As a result, the tomatoes show broad resistance to several bacteria and fungi. Many plant viruses require specific host genes to replicate. If these genes are knocked out in tomatoes, cucumbers, and potatoes, the viruses can no longer multiply effectively and the plants remain healthy. There is also promising research in bananas and citrus fruits for combating fungal and bacterial diseases.

Unlike chemical plant protection, genome editing approaches are highly targeted: they act only against specific pathogens and have little effect on other organisms. This could significantly reduce the use of plant protection products.

What is (not yet) possible

As promising as genome editing is, the methods have their limits. Complex traits such as salt or drought tolerance cannot simply be “created” in this way. Such traits usually involve many genes, often including transcription factors that regulate central metabolic and signaling pathways. Switching such genes on or off can easily lead to unwanted side effects in growth or yield.

Recent studies show, however, that certain metabolic and regulatory networks can be specifically influenced – for example through multiplex editing or targeted changes in gene regulation. In this way, researchers have already been able to improve drought tolerance in rice, tomatoes, and wheat without major negative effects. Such approaches could help gradually adapt plants to increasing environmental and climate stresses.

Another challenge is the development of resistance to animal pests such as herbivorous insects. Plants typically defend themselves through complex metabolic pathways and produce defense compounds such as tannins or glycoalkaloids. These defense mechanisms involve many genes and signaling pathways, often linked to growth and quality traits. If these defenses are permanently activated, they can inhibit growth or increase toxic compounds. For this reason, genome editing reaches its limits here, and classical genetic engineering continues to play a role.

The targeted insertion of larger DNA sequences using CRISPR/Cas is still inefficient. Although the method creates a precise cut at a defined location in the genome, the insertion of new sequences depends on the cell’s natural repair mechanisms. In plants, the required repair pathway (homologous recombination) is unreliable, so larger DNA fragments can only be inserted with low efficiency.

Looking ahead

New genomic techniques are not miracle tools that can solve all challenges in plant breeding at once. Nevertheless, they have the potential to fundamentally transform breeding: new varieties can be developed more quickly, and genetic changes can be made more precisely than with conventional methods.

After achieving the editing goal, however – as with conventionally bred plants – several years of breeding work usually follow, during which the new variety is tested for its traits and must prove itself in field trials.

In the future, the combination of precision breeding and artificial intelligence will play a central role. AI can help identify the genes responsible for important agronomic traits more quickly within complex genomes. In addition, molecular tools such as nucleases or recombinases could be designed using AI, enabling even more flexible and broadly applicable approaches in plant modification.