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Research Topics

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? 

Evolution of duplicated genes in Apple

Malus domestica has a recent and well preserved WGD. This massive event makes the apple tree an organism of choice to study duplicate genes.
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The apple Genome and Epigenome

The apple Genome and Epigenome

A major limitation in the study of epigenetics in non-model organisms is the availability and the quality of the reference genome. In order to...
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MAESTRO

MAESTRO - Memorisation et Acquisition de marques Epigenetiques suite à un STRess abiOtique

Plants are continuously exposed to environmental perturbations such as pests/pathogens infestation, extreme temperature, modification in light...
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TEMA

TEMA - Transmission of Epigenetic Marks in Apple

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JOLLY JUMPER

Plants are constantly required to adapt to various biotic and abiotic constrains. They have developed various strategies allowing them to (i) detect...
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IMMODUS

IMMODUS - Genetic and epigenetic regulation of apple skin color variation in “Gala” apple (epi)mutants

This project aims to increase the efficiency and reliability of DUS testing of apple mutants. Its final goal is to develop genetic and epigenetic...
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INVITE - INnovations in plant VarIety Testing in Europe

INVITE European project: INnovations in plant VarIety Testing in Europe to foster the introduction of new varieties better adapted to varying biotic...
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BEEP (CRISPR-Cas9 Based Epigenome Editing in Plants)

Inactivation of nuclease defective Cas9 (dCas9) can be fused to catalytic domains of proteins that are involved in setting and maintaining epigenetic...
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VERO

VERO - Vernalisation of Rose plant

The objective of this project is to understand the molecular mechanisms (genetic and epigenetic) controlling flowering and branching in response to...
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