Differential Patterns of Genome-Wide Methylation within and between Eucalyptus Clones across Variable Environments

Phenotypic plasticity, the ability to display a range of phenotypes as a function of variable environments, is a key feature of long-lived forest trees. Nevertheless, knowledge of the extent and underlying mechanisms of phenotypic plasticity in response to abiotic stresses is fragmentary. Besides genetic diversity, epigenetic variation is believed to contribute to tree phenotypic plasticity and adaptive potential. While clonal eucalypt plantations are the preferred deployment system due to higher productivities, they are intrinsically more prone to genotype x environment interaction such that plasticity becomes a key feature to select an elite clone. We set out to profile methylation patterns of Eucalyptus clones that display variable adaptive plasticity across environments. After using MSAP (Methylation-sensitive amplification polymorphism) as an exploratory method, sequence-based genome-wide differential methylation analysis of Eucalyptus clones planted in replicated trials across locations in Brazil was performed using genome complexity reduction with PstI-MspI (methylation insensitive) and PstI-HpaII (sensitive). Following a rigorous analytical pipeline that accounts for the sequence variation between these hybrid clones and the reference genome, uniquely mapped reads to the reference genome provided reproducible, genome-scale methylation measurements at ~20,000 genomic sites across biological replicates. Comparative data within and between five clones classified as plastic or interactive, revealed differential methylation profiles across environments for leaf and cambium tissues. Annotation of these sites is under development, focusing on the distinctive patterns of transposon and gene body methylation, in an attempt to describe the differential patterns of epigenetic marks within and between clones that may be contributing to phenotypic plasticity.