The impact of somatic and epigenetic DNA variation on tree adaptation and evolution

In virtually all living organisms, mutations of genomic DNA allow the generation of new traits that, if positively selected, drive adaptation to changing environments and contribute to evolution. In most multicellular organisms, these DNA mutations are propagated only if passed to next generations by creating a mutated progeny. In addition, intra-organism DNA changes also occur and are known as somatic mutations. However, in most cases, somatic mutations are not biologically relevant, as they do not proliferate in adult cells. An important exception to this principle occurs in trees: although all tree adult tissues derive from a single egg cell, different tree branches contain cells that separated and proliferated independently for long time, spanning several tens, or even hundreds of years. Therefore, somatic DNA genetic and epigenetic variation can be propagated clonally in the cell lineage of a new branch, affecting vast tree areas and producing visible phenotypes. This phenomenon is well documented in artificially mutagenized herbaceous plants and clonally propagated fruit trees, and was recently observed occurring in natural forest trees. However, its relevance as a natural mechanism of tree evolution remains deeply unknown. To fill this gap, this project will search for genomic variants generated in different braches of forest trees, dating and mapping them onto the tree’s branching architecture. Then, we will characterize the impact of DNA mutations on gene expression, and their relevance on genome adaptation to environmental changes and stress. Moreover, for each analysed tree, we will estimate the DNA mutation rate and we will investigate possible correlation of DNA mutations with past documented environmental changes and stress.

The selected student will apply ground-breaking newly established methods for efficient detection of genomic variations, constituted by Single Nucleotide Polymorphisms (SNPs), indels, genome rearrangements and transposable element (TE) mobilizations. Interesting variants identified will be validated with standard molecular biology techniques, and their relation to environmental stresses will be evaluated, including disease pressure, high temperature, drought and increased atmospheric CO2 concentration. With this project, we will be able to estimate tree genome plasticity operating in natural conditions, and predict the impact of a changing climate to genome evolution and adaptation of forest trees.