Genome engineering has advanced tremendously during the last decades, and applied not only in model species, but also crops, to transfer desirable traits between varieties quickly and more accurately than by conventional breeding. However, these techniques are still limited to a small number of genes that have been functionally assessed, and to species amendable to genetic modification. In addition, genetically modified organisms are not widely accepted by the public.
Besides genetic modification, epigenetic modifications, e.g. though the addition or removal of methyl groups on the DNA, can also have an impact on plant traits - without changing the sequence of the DNA itself. In the model plant Arabidopsis thaliana, changes in DNA methylation can affect a range of phenotypes, such as flowering time, biomass and response to stresses. And importantly, at least some of those changes can be induced experimentally. A knowledge gap that prevents a broad use of this approach to modify plant traits is that it is most often unclear which region and modifications in the (epi)genome control a trait of interest. Also, epigenetic modifications introduced during a plant’s lifetime are reset during sexual reproduction, thus limiting the inheritance of the newly introduced epigenetic modification and the associated phenotypic traits.
We have developed a novel method to create stable epigenetic variants in plants. We discovered that A.thaliana plants clonally propagated from different tissue types through the manipulation of zygotic transcription factors could retain a substantial fraction of the epigenetic characteristics of the origin tissue. Plants regenerated from roots could stably pass on many aspects of root-specific DNA methylation as well as gene expression patterns to the clonal progeny – not just to their roots, but also their leaves. As a consequence, in one A. thaliana accession, plants regenerated from roots showed altered interaction with beneficial and pathogenic microbes. In another accession, we observed elevated levels of a hormone that regulates defense to pathogens, which, as a by-product, also leads to lower biomass in the regenerants.
Depending on the species, plants can be clonally propagated from different tissues by different regeneration protocols. We found that tissue of origin and regeneration protocol can both distinctly affect the epigenetic landscape in the regenerants. DNA methylation is affected more by the regeneration protocol than by tissue type. Plants that were regenerated using the manipulation of zygotic transcription factors have less epimutations and also genetic mutations compared to plants that were regenerated using tissue culture. Therefore, the rate of epigenetic and genetic variation in clonal plants can be adjusted based on the choice of explants and protocols used during regeneration.
Our findings are fundamental for understanding the significance of epigenetic variability arising from clonal propagation, and have implications for future biotechnological applications. They not only provide us with novel methods to create stable epigenetic and phenotypic diversity in plants, but also provide us with new and exciting possibilities for increasing or limiting epigenetic, genetic and phenotypic variation in clonal lines.
