Epigenetic diversity of grassland plants in the Biodiversity Exploratories

物种内部的生物多样性是生物多样性的一个基本层面。它对物种进化和适应不断变化的环境具有重要意义，它可以以类似于物种间多样性的方式影响种群和生态系统过程。我们现在知道，这种物种内的多样性不仅可以由DNA序列的变异产生，也可以由表观遗传变异产生。因此，表观遗传多样性似乎是我们在生物多样性研究中需要考虑的一个潜在的重要但迄今为止被忽视的功能生物多样性水平。到目前为止，我们对自然植物种群表观遗传多样性的范围和分布，以及其生态原因和后果知之甚少。在此，我们建议在生物多样性探索区深入研究草原植物的表观遗传多样性。我们将利用之前在生物多样性探索项目中的工作，重点研究三个常见物种（Bromus hordeaceus， Cerastium holosteosides和Trifolium repens），这些物种已经在之前的项目中在DNA标记变异水平上进行了表征，并在表型上进行了定量遗传变异。这将使我们能够将表观遗传数据与遗传和表型数据联系起来，并测试土地利用强度和其他环境因素对表观遗传多样性的影响。我们将使用甲基化敏感（MS-）AFLP标记，量化三个目标物种发生的所有EPs内部和之间的DNA甲基化模式的可变性。我们将在田间种植的植物和它们在普通花园中生长的后代中进行这项研究，这将使我们能够解开表观遗传多样性的塑料和遗传成分。最后，我们将采用一种新的测序表观遗传型方法来验证MS-AFLP结果，并在这一重要的新一代方法中建立实验室常规。因此，我们的项目将有四个主要目标：(1)量化田间和普通花园中三个目标物种的表观遗传多样性；(2)测试土地利用强度对表观遗传多样性的影响；(3)检查三个目标物种的遗传、表观遗传和表型多样性之间的关系；(4)建立使用不同分子方法的专业知识，这些方法可用于生态-表观遗传研究。

The biological diversity within species is a fundamental level of biodiversity. It is important for evolution and adaptation of species to changing environments, and it can influence population and ecosystem processes in a similar way to the diversity among species. We now know that such within-species diversity can not only be created by variation in DNA sequence but also by epigenetic variation. Thus, epigenetic diversity appears to be a potentially important but so far overlooked level of functional biodiversity that we need to take into account in biodiversity research. So far, we know very little about the extent and distribution of epigenetic diversity in natural plant populations, or about its ecological causes and consequences.Here, we propose to thoroughly study epigenetic diversity in grassland plants in the Biodiversity Exploratories. We will take advantage of previous work in the Biodiversity Exploratories and focus on three common species (Bromus hordeaceus, Cerastium holosteosides and Trifolium repens) that have already been characterised at the level of DNA marker variation as well as quantitative genetic variation in phenotypes in previous projects. This will allow us to connect the epigenetic data to genetic and phenotypic data, and to test for the impact of land use intensity, and other environmental factors, on epigenetic diversity.We will quantify variability in DNA methylation patterns within and among all EPs in which the three target species occur, using methylation-sensitive (MS-)AFLP markers. We will do this both in plants growing in the field and in their offspring grown in a common garden, which will allow us to disentangle plastic and heritable components of epigenetic diversity. Finally, we will employ a novel epigenotyping-by-sequencing method on a subset of the samples to verify MS-AFLP results and establish a lab routine in this important new next-generation method.Thus, our project will have four main goals: (1) to quantify epigenetic diversity in three target species in the field and in a common garden, (2) to test for the effects of land use intensity on epigenetic diversity, (3) to examine associations between genetic, epigenetic and phenotypic diversity in the three target species, and (4) to build up expertise in the use of different molecular methods that can be used in ecological-epigenetic studies.