Causes and Consequences of Epigenetic Variation in Maize

主要研究者：Nathan Springer（明尼苏达大学双城分校）CoPI：Damon Lisch（加州大学伯克利分校），Matt Vaughn（得克萨斯大学奥斯汀分校得克萨斯高级计算中心）和Irina Makarevitch（哈姆林大学）虽然很明显遗传变化在控制表型变异中起着重要作用，但越来越多的证据表明表观遗传变化也可能起着重要作用。 表观遗传变异的存在令人兴奋，因为它提出了一种可能性，即环境或遗传条件的记忆可以独立于DNA序列的变化而编码和传播。 这种可能性对进化生物学家和植物育种家都有明显而重要的意义，但表观遗传变异在调节表型变异中的相对作用，特别是在作物物种中，仍然知之甚少。 该项目将发展对玉米中表观等位基因的流行、起源和影响的理解，玉米是一种重要的农艺物种，可能具有丰富的表观遗传变异。 这项工作将提供一个广泛的目录表观遗传变异玉米和大刍草基因型，并将探讨在何种程度上的过程，如产生加倍单倍体或沉默的转座子可以有助于这种变化。 几个实验也将探讨表观遗传变异的产生和维持的机制。 其他的则旨在确定表观遗传变异对植物表型的影响程度。 总的来说，这些实验旨在提供一个关键作物物种表观遗传调控的全面视图。 本项目开发的基因组数据集将通过项目网站（可通过http：//www.cbs.umn.edu/labs/springer/访问）和NCBI（http：//www.ncbi.nlm.nih.gov/）、Gramene（http：gramene.org）和MaizeGDB（www.maizegdb.org）等公共储存库公开提供。精选的数据集和数据分析工具也将在iPlant上公开提供，生物材料将在公共库存中心提供。这项研究将为玉米群体中表观遗传变异的流行和影响提供更实质性的了解。 这也将有助于确定该变异在多大程度上有助于该物种的数量性状变异，这可能对植物育种过程中理想基因型（或表观基因型）的选择产生重大影响。 在更广泛的意义上，这项工作将告知目前的理解，表观遗传变异在玉米驯化中发挥的作用，以及表观遗传变化对植物进化变化的贡献。 该项目还将开发计算资源，通过集中数据和复杂数据集的解释，实现玉米中强大的表观基因组研究。 最后，该项目将为高中生、本科生和研究生在各种环境中提供培训和推广机会。 将特别强调吸收历来代表性不足的群体的成员，并将教师培训纳入研究活动。

PI: Nathan Springer (University of Minnesota - Twin Cities)CoPIs: Damon Lisch (University of California, Berkeley), Matt Vaughn (Texas Advanced Computing Center, University of Texas - Austin), and Irina Makarevitch (Hamline University)While it is clear that genetic changes play a major role in controlling phenotypic variation there is increasing evidence that epigenetic changes may also play an important role. There is considerable excitement about the existence of epigenetic variation because it raises the possibility that a memory of environmental or genetic conditions can be encoded and propagated independent of changes in DNA sequence. This possibility has obvious and important implications for both evolutionary biologists and plant breeders, but the relative role of epigenetic variation in conditioning phenotypic variation, particularly in crop species, remains poorly understood. This project will develop an understanding of the prevalence, origin and effects of epialleles in maize, an agronomically important species that is likely to be rich in epigenetic variation. This work will provide an extensive catalogue of epigenetic variation in maize and teosinte genotypes and will explore the extent to which processes such as generation of doubled haploids or silencing of transposons can contribute to that variation. Several experiments will also probe the mechanisms that underlie the creation and maintenance of epigenetic variation. Others will be aimed at determining the extent to which epigenetic variation can affect plant phenotypes. Collectively, the experiments are designed to provide a comprehensive view of epigenetic regulation in a key crop species. The genomic datasets developed in this project will be publicly available through a project website (accessible via http://www.cbs.umn.edu/labs/springer/) and at public repositories such as NCBI (http://www.ncbi.nlm.nih.gov/), Gramene (http://gramene.org), and MaizeGDB (www.maizegdb.org). Curated datasets and data analysis tools will also be publicly available at iPlant and biological materials will be available at public stock centers.The research will provide a much more substantial understanding of the prevalence and effects of epigenetic variation in populations of maize. It will also help in determining the extent to which that variation contributes to quantitative trait variation in this species, which may have a significant impact on selection of ideal genotypes (or epigenotypes) during plant breeding. In a more general sense, this work will inform the current understanding of the role that epigenetic variation has played in maize domestication and the contribution of epigenetic change to evolutionary change in plants. The project will also develop computational resources that would enable powerful epigenomic studies in maize by centralizing the data and interpretation of complex datasets. Finally, this project will provide training and outreach opportunities for high school, undergraduate and graduate students in a variety of settings. Particular emphasis will be placed on including members of historically under-represented groups and on the incorporation of teacher training into research activities.