ECA-PGR: Somatic Genetic and Epigenetic Variations in Long-lived Perennial Trees and their Interactions with the Environment

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Long-lived woody trees are rooted in place and must cope with environments that change daily and over long timescales. With no where to go, trees are remarkably resilient to these environmental assaults; but how is this accomplished? What features of the genome confer the ability to thrive in these ever-changing environments? One hypothesis is that that random changes in DNA accumulate throughout the lifespan of trees and this provides potential new ways to adapt. Another possibility is that a sudden change occurs in how a gene that confers an adaptive trait is expressed. This project tests these hypotheses using long-lived poplar trees as an ideal study system. Due to their fast growth, poplars are used as short-rotation woody biomass crops for composites, pulp and biofuels. Poplars can also be propagated sexually by seeds, or asexually by stem cuttings, so genomic changes and inheritance patterns can be studied in progeny from variously aged trees. This project investigates how poplar genes respond to changing environments and determines if newly formed gene expression states are inherited after stem cutting. Undergraduate students will work directly with researchers and graduate students by participating in summer research projects in poplar genomics. As a keystone ecological species, poplars are broadly distributed in the Northern Hemisphere and are associated with significant ecosystem services; therefore, understanding the genomic response to the environment will provide powerful tools for expanding the genetic potential of this important tree species. The project aims to characterize the genomes and epigenomes of two ~300-year old Populus trichocarpa trees to understand the proportion of tree genomes that are subjected to environmentally-induced and spontaneous genetic and epigenetic variation. One key aspect is the ability to collect tissues from five ontogenetic sectors of each tree spaced ~25 years apart, which represent distinct times since divergence from the original germ line. It is expected that certain genes from different ontogenetic sectors may respond differently to the present-day environments due to prior exposure to environments experienced by one ontogenetic sector of the tree and not by another. These experiments will enable an assessment of the timescale on which cellular memory can persist in the absence of sexual reproduction. To address if sexual reproduction serves as a mechanism to reprogram epigenomes to the original germ line status, maternal-specific epigenomes will be evaluated in seedlings collected from two different ontogenetic sectors of a female tree. Lastly, controlled greenhouse experiments will be used to understand if poplar trees can be primed by acute stresses for similar future environments by clonal propagation. Research from this proposal will lead to a better understanding of how plants interact with the environment and how they use cellular memory to cope with changing environments.