Aim 3 examines how epigenomic patterns develop in young vines over the course of their acclimation to a new environment. In aims 1 and 2 of our project, we study the grape epigenome in vines that were established several years ago. It is likely that the methylation of DNA in such well-established vines is already in a steady state with minimal or no change from season to season. In order to gain insight into the dynamics of DNA methylation in young vines as they acclimate to their environment, this spring we are planting a new experimental vineyard of two grapevine scions, each grafted on two different rootstocks at three of our sites (South Dakota, New York, and Missouri). In this, and two subsequent growing seasons, we will extract genomic DNA from leaf and root samples and construct enzymatic Methyl-seq libraries. Methylome sequencing of these libraries will reveal which genomic regions receive epigenetic marks in the scion and the rootstock over a three-year period.
This experiment will answer a range of questions related to molecular mechanisms underlying the development of phenotypic plasticity in grafted grapevine. Performing the experiment in diverse environments in four shoot-root combinations (2 scions x 2 rootstocks) will offer a glimpse of which genomic regions are modified differentially under various climatic conditions, and to what extent these epigenetic modifications depend on the genotype of the scion and the rootstock. Importantly, using scion and rootstock cultivars for which phased diploid genome sequences are/will be available, we can track the deposition of epigenetic marks in an allele-specific manner.
This experiment will answer a range of questions related to molecular mechanisms underlying the development of phenotypic plasticity in grafted grapevine. Performing the experiment in diverse environments in four shoot-root combinations (2 scions x 2 rootstocks) will offer a glimpse of which genomic regions are modified differentially under various climatic conditions, and to what extent these epigenetic modifications depend on the genotype of the scion and the rootstock. Importantly, using scion and rootstock cultivars for which phased diploid genome sequences are/will be available, we can track the deposition of epigenetic marks in an allele-specific manner.
Thumbs up to the Danforth Center Field Crew for preparing the Missouri „epivineyard” site, designed for tracking changes in the epigenome of both scion and rootstock.
Before planting, root samples are collected from all 216 vines to measure and characterize base-line methylation of the rootstock genome.
Planting the entire epivinyard is snap when the full force of the Miller Lab is applied to the task.
Newly planted vines with three-to-five-node shoots in early June (left) fill their grow-tubes by late July at the New York epivineyard site.
