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

长寿的木本树木扎根于当地，必须科普每天和长期变化的环境。 由于无处可去，树木对这些环境攻击具有显著的适应力;但这是如何实现的呢？基因组的哪些特征赋予了在这些不断变化的环境中茁壮成长的能力？一种假设是，DNA的随机变化在树木的整个生命周期中积累，这提供了潜在的新方法来适应。另一种可能性是，赋予适应性特征的基因的表达方式发生了突然变化。本计画以长寿白杨为理想的研究系统，来验证这些假设。由于其快速生长，杨树被用作短轮伐期木质生物质作物，用于生产复合材料、纸浆和生物燃料。杨树也可以通过种子进行有性繁殖，或者通过扦插进行无性繁殖，因此可以研究不同树龄树木后代的基因组变化和遗传模式。该项目研究白杨基因如何响应变化的环境，并确定新形成的基因表达状态是否在茎切割后遗传。本科生将通过参加白杨基因组学的夏季研究项目直接与研究人员和研究生合作。杨树作为一种重要的生态物种，广泛分布于北方，具有重要的生态系统服务功能，因此，了解杨树基因组对环境的响应将为扩大这一重要树种的遗传潜力提供强有力的工具。该项目旨在表征两棵~300年树龄的大叶杨的基因组和表观基因组，以了解受环境诱导和自发遗传和表观遗传变异影响的树木基因组的比例。一个关键方面是能够从每棵树间隔约25年的五个个体发育部分收集组织，这代表了从原始种系分化以来的不同时间。预计来自不同个体发育部门的某些基因可能对当今环境的反应不同，这是由于先前暴露于树的一个个体发育部门而不是另一个个体发育部门所经历的环境。这些实验将能够评估细胞记忆在没有有性生殖的情况下能够持续的时间尺度。为了解决有性生殖是否可以作为将表观基因组重新编程为原始种系状态的机制，将在从母树的两个不同个体发育部分收集的幼苗中评估母株特异性表观基因组。最后，控制温室实验将被用来了解白杨是否可以引发类似的未来环境的克隆繁殖的急性压力。这项研究将有助于更好地了解植物如何与环境相互作用，以及它们如何使用细胞记忆来科普不断变化的环境。

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.