This excerpt is from an article published in the most recent edition (No. 9) of Buitenstebinnen, Naktuinbouw's biannual magazine. It can be read here.
Analysing genetic fingerprints is not something new to Naktuinbouw. DNA research has been done in this laboratory since the turn of the century. For example, determining the identity of a plant or identifying pathogens. But, there has been a flurry of activity in this area in recent years. Sequencing - determining the order of the four building blocks that make up DNA - has advanced in leaps and bounds.
One of the ways it can be applied is in determining the distinctness of plants for varietal research. "A plant's appearance - its phenotype - remains crucial to breeders' rights and admission examinations. DNA research can provide good support for this", says Dons. Currently, Naktuinbouw only occasionally uses DNA analysis. Specifically, it provides a definitive confirmation when a plant's identity is in question.
Left: Thomas van Gurp, bio-information scientist at Naktuinbouw. Right: Hans Dons (photo source: www.caln.nl)
One of the proposals is to set up a databank for this. Not for all crops yet; it suggests doing so for about 15 of the varieties that receive the most DUS testing requests. Sequencing techniques not only improve and speed up the processes used for this but will also reduce costs. A databank will be especially helpful for crops that are hard to distinguish morphologically (with the naked eye). These include crops such as tomatoes, roses, beans, onions and cucumber. DNA analysis is also a quick and useful tool for determining breed-specific resistances. A living collection is needed for vegetatively propagated crops. The DNA information for this could be recorded in a databank. The maintenance of a living collection is costly and replacing an accidentally lost plant is not always an easy matter. There are, after all, already databanks available for potatoes and Phalaenopsis, as well as for various large and small fruit crops.
In the field of disease research, a lot can also be gained by using DNA methods. Traditional testing takes up a lot of time. In the identification of viruses and viroids, complete DNA, so-called 'Whole Genome Sequencing' is recorded. When it comes to bacterias, fungi and nematodes, SNP - DNA variations - can be used, just as in plant identification. Here too, the entire DNA sequence will be analysed. This will indicate with greater certainty whether pathogens are present, or not, in the plant material. The DNA research does not only show if a plant is infected with a pathogen. It can even distinguish between the pathogen's various strains. Even if the plant appears healthy a DNA test can indicate if there are pathogens present. It reveals the still-invisible disease symptoms. Sequencing can provide valuable support during examinations and certifications. When it comes to determining varietal purity and identification, DNA analysis provides the Inspectorate with additional information, in addition to the visual examination. In the next five years, DNA techniques will likely be less beneficial for work involving the inspection of the quality of breeding materials. Theoretically, you could use it to determine uniformity. A large number of plants are, however, needed to get a reliable result. The cost of this does not (yet) outweigh the benefits.
Some of the DNA analyses can be outsourced to specialised laboratories. Naktuinbouw still has to purchase the necessary equipment. One of the consequences of the increased sequencing is that a massive amount of data is generated. As some of this information is confidential, this data has to be stored in an accessible, secure manner. It is expected that plant breeding companies will make the information about their varieties available. Their confidential data must, of course, not be made public. This large amount of data requires a large storage capacity. There must, therefore, also be invested in computer storage capacity. Specialised personnel are also needed to deal with the flow of data. Bio-information scientist, Thomas van Gurp, has been working at Naktuinbouw for a few months now. He maps and compares the available genetic information and draws conclusions from the similarities and differences. A bio-information scientist also develops analytic methods and standardises and automates the processes.
This excerpt is from an article published in the latest edition (No. 9) of Buitenstebinnen, Naktuinbouwś biannual magazine. This can be seen here.