What has been the biggest challenge during the apple genome sequencing and mapping?
The real problem in our case was that the variety, Golden Delicious, we had chosen is heterozygous. Golden Delicious is the most cultivated variety in the area where we work. As for other heterozygous genomes, including the human genome, the two chromosomes differ at several positions. This makes it more difficult to align the DNA along the chromosomes.

In what way can the apple genome map benefit society?
There are several reasons behind the efforts to sequence the genome. One of the major reasons is that plants such as apples and grapes need lots of chemicals to be protected. This chemical treatment has an influence on the surrounding environment. It will be better to produce varieties which are resistant to some diseases. The breeding of new apple varieties is complex - because it takes a long time from one generation to the next generation. If you want to select for a resistance to a disease you find a wild species that is resistant. Then you have to cross back to the cultivated one. This is complex because you bring in one positive gene and eliminate negative genes. If you want to accelerate time you may use genetic markers and if you have an available genome you have many genetic markers available. You can use those markers to predict the outcome of your breeding work. This should shorten the time and give you a better genetic gain.

What implications will the apple genome map have for applied breeding?
Availability of many markers will change all apple breeding paradigms. The real achievement on the plant breeding side is that we now have an incredible number of molecular markers available where we want them to be. We have marked the genome so finely that now you can develop any marker that you want. But the important point is to correlate the marker position with the character. That will take generations.

What reactions have you met from breeders?
Good reactions. We have already applied some of our discoveries to apple breeding in-house and have genotypes which can be interesting. But we’ll see the major impact of molecular markers in our breeding programme within four to seven years.

When will we see new breeds that have reached the market thanks to your research?
The real problem in apple breeding is resistance to diseases; but at the very end the apple must have the capacity to resist degradation in the chambers for at least eight to ten months. This characteristic is extremely important. So very few of our varieties have the capacity to resist for such a long time before being introduced into the market. Apples are ripening in autumn, but they are sold all winter, spring and early in the summer. If an apple cannot last for more than five months it is not an apple, because you have to sell them the next year. Many of those varieties which have been bred using molecular markers for disease resistance cannot reach the market because they are defective in this characteristic. It’s a difficult characteristic. We now have markers which are able to monitor at least six to eight genes important for the conservation so we ought to be able to overcome this problem in five to six years.

What other projects are being developed at the Edmund Mach Foundation?
Apples are grown in very dense stands with one plant every 60 to 80 centimeter. We select for genes which give the plant a columnar apperance that we need in practical apple production. The second characteristic is disease resistance. Apple scab is due to the attack of a fungus called venturia inequalis. Sixty percent of our chemical treatments are meant to eradicate one single fungus. The idea is to have as much of natural resistance against parasites as possible to drastically reduce the chemical input in agriculture. We also participate in the worldwide strawberry initiative and would like to do more for the raspberry.