NL: DNA technology provides new possibilities

The developments of biotechnology are going extremely fast. Ten years ago, it took millions of euros and years of work to decipher the genetic code of a living organism. Nowadays you have that information for less than a thousand euros and in a few days time. Naktuinbouw investigated what DNA technology can do for its scope of work.

Analyzing the genetic fingerprint is not new to Naktuinbouw. DNA testing has been taking place in the laboratory since the beginning of this millennium. For example to determine the identity of a plant or to identify pathogens. But in recent years quite a lot has happened in this field. In particular the sequencing, the determination of the order of the four building blocks of the DNA, has gained momentum.

A workgroup with Naktuinbouw employees investigated what new DNA techniques could mean for Naktuinbouw. They did so under the leadership of the former director of Keygene in Wageningen, Professor Hans Dons. "It is technically increasingly easier to determine the characteristics of a plant or an organism via the DNA," according to Dons. "It is therefore a logical time to look what the practical applications for Naktuinbouw are. After all, the organization wants to maintain and strengthen its leading role in the field of variety research, inspections, disease detection and diagnostics. We first looked at how DNA technology will play a role in the work of Naktuinbouw over the next five years in the area of identity, health and quality."

One of the applications is to determine the distinctness of plants for the variety research. "The appearance of a plant, the phenotype, remains decisive for the grower's right and the entrance examination. DNA research can provide a good support ", according to Hans Dons. Now Naktuinbouw only uses a DNA analysis occasionally. In particular in case of a discussion about the identity of a plant this can give a definite answer.

One of the proposals is to set up databases for this. Not yet for all crops, but the idea is to do this for about fifteen species for which many DUS applications are coming in. With sequencing techniques the processes improve and speed up and they become cheaper as well. A database helps especially for crops whose varieties are morphologically (visually) difficult to distinguish: tomato, rose, beans, onion and cucumber. This is also a handy and fast tool for determining the unique resistance DNA-analysis for a variety. A living collection is desirable for vegetative propagated crops. The DNA data of these crops should be included in a database. Maintaining a living collection is after all expensive and in case of accidental loss of a plant, replacement is not always easy. Moreover, there are already databases available for potato and Phalaenopsis, just as for various large and small fruit crops.

Also in the field of disease research there is much to be gained with DNA methods. After all, the traditional tests cost relatively a lot of time. For the identification of viruses and viroids, the complete DNA is recorded, the so-called 'Whole Genome Sequencing'. For bacteria, fungi and nematodes it is possible - just as for the identification of plants – to use SNPs: variations on the DNA. But in the future, also here the complete DNA will be examined. This gives additional certainty about the presence or absence of pathogens in the plant material. The DNA research not only shows whether a plant is infected with a pathogen. It can even distinguish the different strains and physiology. And even when the plant seems to look healthy, a DNA test can show that pathogens are present. It reveals the still invisible disease symptoms. For examinations and certifications, sequencing can provide valuable support. In the determination of varietal purity and varietal identity of propagating material, a DNA analysis provides the examiner with additional information next to the visual inspection. The work that involves inspections concerning the quality of the propagating material probably does benefit less from DNA techniques during the next five years. Theoretically, you can use it for uniformity assessment. However to get a reliable result, really a large number of plants are needed. Here, the costs do (as of yet) outweigh the benefits.

A part of the DNA analyzes can be outsourced to specialized laboratories. Naktuinbouw also has to purchase the necessary equipment itself. One of the consequences of the expansion of the sequencing is that an enormous amount of data will become available. These must be stored in a database in an accessible and secure manner, because part of the data in the database is confidential. The expectation is that breeding companies will make information available about their varieties, but confidential data must of course not become known externally. The large amount of data requires a large storage capacity. So also investment in computer capacity will be required. Special staff is also required for dealing with that data flow. Since a few months, Naktuinbouw has a bioinformatics scientist, Thomas van Gurp, on staff. He maps the available genetic information, compares the data and then draws conclusions from the similarities and differences. A bioinformatics scientist also develops analytical methods, standardizes and automates these processes.

And of course the knowledge in the field of molecular genetics must be strengthened. New staff are needed and the current researchers are in need of additional training.

The forerunner role for the Netherlands Investing in DNA technology saves money over time. In the future a part of the current work will be replaced by molecular determinations. Also new forms of international cooperation are coming within reach. Climate and test conditions are important for a great deal of phenotypic research. That is why local reference collections are necessary for DUS research and inspection standards. Molecular techniques can be applied in any country. Databases with molecular information can therefore be shared worldwide.

The most important thing is that the Dutch business community has a leading position in the field of propagating material. As a result, Naktuinbouw has a pioneering role in variety research, disease detection methods and quality assurance. "In order to continue playing this prominent role, investing in DNA technology and bioinformatics is necessary," concludes Hans Dons.