Epigenetically stable hypomethylated plants to exploit epigenetic diversity

Epigenetics studies biological traits which are not dependent on changes in DNA sequence. In plants, many of these epigenetic changes are stable and are transmitted very efficiently from parent to offspring. Therefore, epigenetic variability represents an important source of biological variation, including traits potentially able to improve crop plants and develop sustainable agriculture. However, the main limitation of using epigenetic traits in agriculture is our inability to induce sufficient epigenetic diversity in plants without interfering with critical developmental pathways. My working hypothesis is that these epigenetic negative effects on plant development could be associated with the epigenetic alteration of a single gene called IBM1. In the model plant Arabidopsis thaliana, if the IBM1 sequence loses DNA methylation (a strong epigenetic mark) in a crucial region located in one of its introns, a shorter non-functional transcript is produced. Since a functional IBM1 is essential to maintain correct epigenetic regulation at many genes, the lack of IBM1 function allows the accumulation of epigenetic defects and reduces plant fitness across generations.
In stable Arabidopsis plant lines with identical genome sequence but different degrees of reduction in DNA methylation, I observed that IBM1 gene was always inherited in its methylated version, suggesting that the removal of DNA methylation at this locus has a negative impact on plant fitness. To test this hypothesis I will investigate the relationship between plant epigenetic stability, decrease of fitness, and different epigenetic regulation of the IBM1 gene. I will also test if the artificial generation of an IBM1 allele insensitive to DNA methylation can be a suitable approach to avoid the negative effects associated to the generation of epigenetic variability.
Obviously, the possibility to generate new epigenetic variation in plants without affecting their fitness will generate a larger impact if directly explored into crops, where new traits could be exploited into breeding programs. In this direction my preliminary investigation suggests that the epigenetic regulation of IBM1 is conserved in wheat. Therefore, in this project I will also transform wheat with an IBM1 allele insensitive to epigenetic regulation, and I will test if the modified plants will be a suitable genetic material for the generation of new stable epigenetic traits. With the use of genome wide genomics approaches, I will be able to quantify and compare the IBM1 contribution to phenotypes induced by epigenetic alteration in wheat. As wheat is a model crop for monocots and target of intensive breeding, the achievement of this project will allow both to extend IBM1 epigenetic function into monocots, and to test directly its epigenetic complementation as method to facilitate the introduction of epigenetic variation into crops. Wheat is the most extensive cultivated crop worldwide and a target of intense breeding programs, it is used as critical food resource for more than 2.5 billion people, and it is strategically important for the UK economy. Therefore, the genetic material produced in this project will have direct relevance to breeders, allowing the investigation and screening of epigenetic traits relevant to the generation of new wheat varieties.
In short, with the proposed project I want to characterize IBM1's role in the epigenetic stability of plant phenotypes, and to develop a strategy to increase fitness of plants with induced epigenetic variation. Following the achievement of the project objectives, it will become possible to generate epigenetic variability without affecting plant development, strongly facilitating the use of epigenetic traits in crop breeding programs.

In plants, changes in DNA methylation generate transgenerationally stable epigenetic alleles (also called epialleles), which can interact with many biological processes and generate new plant traits. Therefore, epigenetic variation is considered a powerful resource to improve crop production and food security in a controlled way, without altering the DNA sequence. However, efficient generation of epigenetic diversity is associated with strong developmental defects in many plants, representing a strong limitation to the use of epigenetic traits in agriculture. My preliminary investigation showed that in Arabidopsis hypomethylated lines (epiRILs) the viability problems are strongly associated with epigenetic misregulation of the histone demethylatse IBM1. With this New Investigator project, I will characterize the impact of the IBM1 epiallele on epigenetic stability in Arabidopsis, and I will test the use of an IBM1 allele resistant to epigenetic regulation as effective tool to avoid the negative phenotype induced by genome hypomethylaton. I will investigate this point directly in crops, using wheat as a model, a crop of high importance for food production worldwide and target of intense breeding programs. Therefore, this work will not only expand our understanding on plant epigenetic stability, but will also facilitate the direct generation and the use of epigenetic variability in crops.