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Epigenetics describes different mechanisms that allow transmission of gene expression states through cell division and from one generation to another. This is very important because it means that not only the DNA sequence can be inherited but also “memories” of environmental influences (e.g. abiotic and biotic stresses) that have led to transmissible changes of the chromatin structure. The chromatin structure can be influenced by DNA methylation and histone modifications. While a lot of knowledge has been acquired in model plants (such as Arabidopsis), little is currently known in crops and it is therefore not yet being used in breeding.

In the last decades plant breeding has made great advances with the help of genetic markers. However, the existence of epigenetic control of important traits in crops can make that the genotype does not always explain fully the phenotype and thus may limit the informative value of genetic markers. That is why it is now important to assess the epigenotype of crops (consisting of a map of genome-wide DNA methylation and histone modification patterns) to further accelerate breeding. This is particularly important in Rosaceae because they are predominately multiplied asexually by vegetative propagation (cloning). In comparison to sexual reproduction, vegetative reproduction hugely increases the likelihood of inheritance of epigenetic marks from one plant to another. Therefore, all adaptations of plants to their environment that involves an epigenetic mark will represent a “memory” of the cultivar that will be transmitted to the next generation by cutting or grafting. Such populations will evolve as the clonal generations go by to develop different phenotypes without changes at the DNA sequence level. 

The main questions that are being addressed by VALEMA are of basic biological nature but with a direct link to applications:

1-    What is the role of epigenetics in the control of plant’s development in response to biotic or abiotic stress?

2-    Can epigenetic marks be memorized by the plants, and by which mechanism?

3-    Can epigenetic marks be transmitted by clonal propagation?

4-    What are the effects of epigenetically primed rootstocks on scion’s development?

5-    Can epigenetics be developed as a tool to help improve plant breeding?

6-    What is the extent of natural epigenetic variation in perennial plants?