Genomic disease control

Harvests face a constant barrage of plagues. Over time, crops have lost a large proportion of their natural defence arsenal as breeders have long focused mainly on increasing yield. This has made them far more vulnerable to attack and it is now urgent to equip plants with advanced weaponry to protect them against the wide variety of pathogenic organisms.

These war-like analogies are used by Pierre de Wit, Professor of Phytopathology, who even speaks of an arms race. Triggered by Rachel Carson’s book ‘Silent Spring’, he has been working on improving the natural resistance of plants against pathogens since starting his studies in Wageningen in 1968. These pathogens – fungi, bacteria and viruses – attack plants and affect their growth physiology, sometimes leading to death. Over recent decades most plant pathogens have been controlled by means of chemicals. Wouldn’t it be better if the plants were able to protect themselves against plagues and disease?

Variation increases the chance of identifying specific pathogenic weapons, allowing crops to protect themselves against their main pathogens

Natural resistance has often been a secondary consideration in plant breeding compared to increasing crop production, especially after it was discovered that many plagues and diseases could easily be controlled by means of chemicals. The downside of this increasing viability has been a loss of genetic variation relevant for protection. Genetic deterioration often affects resistance, allowing pathogens to strike without mercy. The highly aggressive stem rust fungus Uganda 99, for example, is a major threat to the wheat fields in East Africa because the crops are not sufficiently armed against the weapons of their attackers.

Interactions of fungi with plants

A mould that comes into contact with a plant can create a symbiotic, necrotrophic or biotrophic relationship with it. In many plants, no gene-for-gene interaction is possible, and the plant is defenceless against the attack of the fungus. If the plant has built up a natural defence through gene-for-gene complementarity, an R-protein can neutralise the harmful effect of the fungus.
A mould that comes into contact with a plant can create a symbiotic, necrotrophic or biotrophic relationship with it. In many plants, no gene-for-gene interaction is possible, and the plant is defenceless against the attack of the fungus. If the plant has built up a natural defence through gene-for-gene complementarity, an R-protein can neutralise the harmful effect of the fungus.

Gene-for-gene interaction

De Wit and his research group are studying the interaction between tomato and the Cladosporium fulvum fungus at the genetic and molecular level; the so-called gene-for-gene interaction. A tomato plant recognises the products of specific effector genes from the fungus causing the leaf mould disease. It does so by means of receptor proteins which are coded in its genetic reservoir by receptor genes. The fungus, however, uses genetic mutations in the effector genes to escape recognition by the plant.

In the early 1990s, Wageningen phytopathologists led by De Wit achieved a breakthrough when they found the effector gene of the fungus that affects the tomato, and, shortly thereafter, the gene in the plant that recognises this effector gene. It marked the unravelling of the first gene-for-gene relationship. Armed with this knowledge they were able to identify resistance genes and their products in tomato to keep the fungus at bay. This marked the transition from ‘trial and error’ to the fundamental understanding of the response capacity of the natural plant resistance system. It made the knowledge applicable for a wide range of interactions between plants and pathogens.

Meanwhile, De Wit and his research group have developed the tools to map the entire arsenal of pathogens. One of the most important tools is next generation sequencing, which enables a quick search for the DNA of the genes that code for the weapons of the pathogen and the defence genes of the plant, respectively.

Infection of tomato leaves by C. fulvum


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Advanced defence systems

The next step is the development of plants with advanced defence systems. This starts, with unravelling the basal recognition mechanisms; a plant recognises a fungus by components of its cell wall material (chitin) and bacteria via the flagella that contain the protein flagellin. Some of these basic defence mechanisms may have been lost during the yield-improving breeding programs. In addition, it is important to maintain as much genetic variation as possible in plants. The variation increases the chance of identifying specific pathogenic weapons, allowing crops to protect themselves against their main pathogenic attackers. The markers for resistance genes can be identified with various sequencing technologies (genomics). By combining these markers it is possible to simultaneously build multiple barriers, making it more difficult for pathogens to breach the resistance. In this way chemical pathogen control can be replaced by the development of varieties with natural resistance in their genetic material. These types of biological control always strengthen resistance, although they never provide 100 percent protection against pathogens, according to De Wit.

The scientists are currently working on the possibilities for building in new barriers against pathogens; either through crossbreeding or genetic modification. From a scientific perspective, it is disappointing that the social opposition to Genetically Modified Organisms (GMO) in some parts of the world is thwarting breakthroughs in this field. The feared resistance genes and their products are commonly present in all organisms, including plants and animals (and humans).

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More sustainable

The (re-)introduction of natural resistance in crops will come at the cost of the yield. By making plants more resistant to natural enemies, their yield will be reduced as part of their energy is used for defence. It does, however, make the total system less vulnerable and the costs of the investments will be recovered due to the reduced occurrence of diseases and plagues. If pressure from consumers and the processing industry would increase the focus on the total range of qualities, including nutritional value and health, the overall balance could become even more sustainable.

The industry continues to join forces in the fight against pathogens to protect crops. Sometimes protection will be based on chemicals, but increasingly it is based on enhancing the crops’ natural resistance. New dynamics are gradually developing, which is also resulting in shifting partnerships. While in the past phytopathologists were mainly approached on research issues by the chemical sector, now it are the breeding companies who are showing interest. Although this does not mean they will determine the research agenda, it does indicate what type of knowledge is most in demand.

There is a constant battle against (new) diseases and plagues. The evolutionary development of viruses, bacteria and fungi is rapid and they are always looking for new ways to attack plants. For a long time we have given our crops insufficient protection against these enemies, as a result of which we have had to protect them using chemicals. The strongest weapon against pathogens, however, is the natural resistance of the plant. It may seem expensive and time-consuming, but ultimately this is the most sustainable option. Chemical control can be cut back significantly, preventing Rachel Carson’s ‘Silent Spring’ from becoming a reality."