Science - August 30, 2012

In the throes of a revolution

For maize 3 million interesting genes have already been marked.

Today plants are still selected on appearance but that seems to be the only similarity between 2012 and 1948.
Wageningen research on plant-breeding has been going on for 100 years. For 70 years it consisted mainly of cross-breeding and selection in order to arrive at improved varieties. But now researchers and plant-breeding companies are in the throes of a DNA revolution involving dizzying quantities of genetic data. Will new crops soon be designed in the lab?
What can you say about 100 years of Dutch plant breeding when you are in the middle of a technological revolution? Rob Dirks, head of research at vegetable breeding company Rijk Zwaan, does not have to think long about this question. 'Ninety five percent of the plant technology has been developed in the last five years. For seventy years it was just a matter of cross-breeding and selecting. Breeders always needed large numbers of plants spanning several generations in order to develop a better breed. Cross-breeding and selection has been very successful and it still works but it is not terribly efficient.'
Dirks entered the Dutch plant breeding scene at a historic juncture. In 1986 he started to work for the breeding company Nunhems. At that time recombinant DNA techniques had just been developed with which you could transfer genes from one species to another. It was thought that biotechnology would replace traditional breeding and Wageningen plant breeding researchers were taken by surprise by companies that started fiddling about with plant genomes without knowing much about breeding. Dirks was one of these outsiders. 'When I started I thought plant breeders knew which characteristics were located on which chromosomes, but that was not the case. They selected on appearance, on the phenotype. I thought that was a bit vague.'
At the end of the nineteen eighties the breeding companies employed geneticists and a group of five companies formed a company called Keygene in Wageningen in order to make the new techniques applicable for the breeders. Keygene developed the AFLP technique with which you can hang 'flags' on the genes with the characteristics you want to keep for the next generation. This 'marker technology', as it is known, is a key element in the revolution now going on, says Dirks. Because it is becoming possible to insert the flags faster and more cheaply, breeders can now keep track of many characteristics of crops during the cross-breeding and selection processes. 'This has turned the selection of plants into an exercise in genetics', says Dirks. Originally it was a matter of tens or at the most hundreds of markers. But many interesting characteristics, such as taste, are determined by a lot of genes. 'I have just come from a discussion of a research in which we relate 500,000 marker genes to genetic variation in ten seconds!' says the Wageningen statistician Fred van Eeuwijk. He is helping Dirks to extract the relevant information from the vast database. Because with 500,000 flags, it can be difficult to select. Van Eeuwijk calculates how much influence each flagged gene has. The genes with the greatest influence are of course the most interesting.
Meanwhile, the explosion of genetic data goes on. Van Eeuwijk: 'For maize more the 3 million genes have already been marked. And increasingly we want to analyse DNA networks, in which several genes control a characteristic in interaction with each other. This is statistically much more complicated. And the analysis has to be done on one day, because the knowledge develops so fast.'
Yet essentially what Van Eeuwijk does today is exactly the same as what he did 20 years ago. 'I still advise people on how to set up tests so as to raise the chances of finding genetic differences. Imagine: you have a field test with three plots planted with the same genotype. Then you find the differences between these plots under the influence of environmental conditions. If the differences between two genotypes are greater that the 'environmental interference', you have the genetic variation. A well set-up test minimalizes the environmental interference.'
Many genes with a big effect, such as those that boost the harvest significantly or make a plant resistant to a disease, have already been identified in the 'old-fashioned' manner whereby the researchers selected the plants with the strong genes without looking into their DNA. 'The advantage of the DNA revolution is that we can now make small and complex genetic effects visible', says Van Eeuwijk.
Dirks foresees the end of traditional plant breeding, with crops being designed in the lab from now on instead of being selected in the field. Van Eeuwijk is less sure and sees the DNA revolution in a broader context, and so does Richard Visser, professor of Plant Breeding. Visser points out that Dirks works largely with greenhouse plants, for which the environment and the management is adapted to the plant. In the case of agricultural crops, environment and management systems are variable and complex characteristics such as drought or salt tolerance, which involve adapting to the environment, are very difficult to create. 'We shall see in ten years' time whether this revolution is the solution to our problems', says Visser diplomatically.
Visser points to previous 'revolutions' in the past 100 years, such as mutation breeding using radiation, the tissue cultivation techniques and the recombinant DNA technique. 'Those new techniques are always important for speeding things up in breeding research, but they are not the answer to complex problems with our food crops.'
The current genomics revolution is very promising, says Visser. 'Through the new knowledge, we can search in a more targeted way, and now you can create a hybrid on the computer.' One example of this designer-breeding is reverse breeding, on which Dirks published an article last year together with Wageningen geneticists. 'This means we can start breeding per chromosome', explains Dirks. 'You keep the characteristics you want to keep and change only the chromosomes which carry characteristics you want to change.'
But the new technology may prove to have its limitations, according to Visser. 'Many plants are polyploid - for example, they have four or eight copies of their chromosomes, which enables you to get very many combinations of the genetic material. We have now clarified the genome of the potato, which has four copies, but to do that we first had to make the potato monoploid. We are now doing fundamental research on how we can apply genetics in a polyploid crop - something we cannot do yet.'
Friday 31 October from 13.00 to 19.00 hours in Radix: Open Day with demonstrations, lectures and an exhibition about 100 years of Plant Breeding.
From luck to knowledge
Groningen grain farmers were behind the Institute for Plant Breeding that was set up in 1912 in Wageningen. They wanted to follow the Swedish example and establish a national breeding institute that would not only breed agricultural crops but also do scientific research. There were already individual breeders then who had developed interesting species in their back gardens. One of these was schoolteacher Kornelis de Vries, who developed the Bint potato with few seeds. Good luck played more of a role here than knowledge. 
In the early years the institute focused mainly on varieties of barley and wheat for Dutch farmers. It also provided breeding companies with breeding material, as it had been expressly tasked with supporting private plant breeders. Originally these were small breeders focusing on the Netherlands, but in the last 25 years they have become world players after the Netherlands emerged as a market leader in the field of vegetable seeds and seed potatoes. Grains are now bred elsewhere.
Twenty five years ago the Plant Breeding department had 50 staff, of whom only 10 were researchers. Most of the department's work was teaching. But at that time there were several breeding institutes in DLO. These were all brought together under the umbrella of Wageningen UR Plant Breeding, which has 250 researchers and carries out contract research for all the Dutch breeding companies.