Epigenetic diversity of grassland plants in the Biodiversity Exploratories

物种内的生物多样性是生物多样性的一个基本层面。它对物种的进化和适应不断变化的环境很重要，它可以影响种群和生态系统的过程，就像物种之间的多样性一样。我们现在知道，这种物种内的多样性不仅可以通过DNA序列的变异来创造，也可以通过表观遗传变异来创造。因此，表观遗传多样性似乎是一个潜在的重要但迄今被忽视的功能性生物多样性水平，我们在生物多样性研究中需要考虑到这一点。到目前为止，我们对天然植物种群表观遗传多样性的范围和分布，以及其生态学原因和后果知之甚少，因此，我们建议在生物多样性探索中对草原植物的表观遗传多样性进行深入的研究。我们将利用以前在生物多样性探索中的工作，重点关注三个常见的物种(无芒雀麦、樱桃总骨苷和白三叶)，这些物种在以前的项目中已经在DNA标记变异和表型数量遗传变异的水平上进行了表征。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)标记来量化发生在三个目标物种中的所有EPs内和之间DNA甲基化模式的变异性。我们将在生长在田间的植物和生长在普通花园中的后代中做到这一点，这将使我们能够分离表观遗传多样性的可塑性和可遗传成分。最后，我们将使用一种新的表观基因分型测序方法来验证MS-AFLP结果，并在这一重要的新的下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)量化田间和公共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)检查三个目标物种中遗传、表观遗传和表型多样性之间的关联，以及(4)建立可用于生态表观遗传学研究的不同分子方法的专业知识。

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.