The role of DNA methylation in transgenerational stress resistance in a clonal plant

DNA甲基化在克隆植物跨代抗逆性中的作用

• 批准号: 512079118
• 负责人: Professorin Dr. Meret Huber, Ph.D.
• 金额: --
• 依托单位: Institut für Organismische und Molekulare Evolutionsbiologie
• 依托单位国家: 德国
• 项目类别: Independent Junior Research Groups
• 资助国家: 德国
• 项目状态: 未结题
• 来源: https://gepris.dfg.de/gepris/projekt/512079118?language=en
• 关键词: role; DNA; methylation; transgenerational; stress

Dwindling intraspecific diversity and global environmental change are threatening ecosystem functioning and human society. Assessing whether species may acquire stress resistance across generations in the absence of genetic change has thus never been more urgent. DNA methylation is hypothesized to facilitate rapid adaptation, particularly in clonal plants. Experimental evidence for this controversial hypothesis is however scarce. In my previous work, I found that the duckweed Spirodela polyrhiza – a clonally reproducing aquatic angiosperm – can acquire resistance to copper excess across generations in the absence of genetic change. Based on these results and the state of the art, I propose to use S. polyrhiza to address three fundamental questions on the role of DNA methylation in transgenerational stress resistance in clonal plants: 1) How common and stable are spontaneous and stress-induced methylome variants? 2) Do stress-induced methylome variants mediate transgenerational resistance? 3) Can populations adapt via selection on methylome variants? To answer these questions, we will first assess the accumulation of spontaneous methylome changes across generations in S. polyrhiza and investigate whether two contrasting stresses – copper excess and herbivory of the aphid Rhopalosiphum nymphaeae – induce methylome variants that are passed on to offspring using whole-genome bisulfite sequencing. Next, we will assess whether S. polyrhiza exhibits transgenerational resistance not only to copper excess but also to aphid herbivory and identify traits and genes that are associated with transgenerational resistance and stress-induced methylome variants using targeted metabolite analysis, transcriptomics and whole-genome bisulfite sequencing. We will manipulate the identified genes and the DNA methylation machinery with CRISPR-Cas9 and chemical inhibition to infer causation between stress-induced methylome variants and transgenerational resistance. Finally, we will assess whether S. polyrhiza adapts via selection on methylome variants by manipulating both the methylome and the efficacy of selection: a wild type and a knockout mutant deficient in the DNA methylation machinery will be grown for 80 generations under control, copper excess and aphid herbivory in minimally small (evolving through drift) and large (evolution with selection) populations. Assessing variation in resistance between small and large populations and between wild type and mutant under chemical inhibition of the methylome will allow us to infer whether selection on methylome variants facilitates rapid adaptation. Together, these experiments will provide novel insights into the sources of methylome variation and its contribution to adaptation, thereby testing a controversial hypothesis in evolutionary ecology. Considering the importance of clonal plants in natural and agricultural ecosystems and the rapid pace of global change, the results will be relevant to diverse biological fields.

种内多样性的减少和全球环境变化正在威胁生态系统的功能和人类社会。因此，评估物种是否可以在没有遗传变化的情况下获得跨代的抗逆性从未如此紧迫。DNA甲基化被假设为促进快速适应，特别是在克隆植物中。然而，这个有争议的假设的实验证据是稀缺的。在我以前的工作中，我发现浮萍螺旋藻-一种克隆繁殖的水生被子植物-可以在没有遗传变化的情况下获得对铜过量的抗性。基于这些结果和现有技术，我建议使用S。多根来解决三个基本问题的作用，DNA甲基化的跨代胁迫抗性克隆植物：1）如何常见和稳定的自发和胁迫诱导的甲基化变异？2)应激诱导的甲基化变异介导跨代抗性吗？3)种群可以通过选择甲基化变异体来适应吗？为了回答这些问题，我们将首先评估S.多根和调查是否两个对比的压力-铜过量和草食性的蚜虫Rhopalosiphum nymphaeae -诱导甲基化变异，通过使用全基因组亚硫酸氢盐测序后代。接下来，我们将评估S。Polyrhiza不仅对铜过量而且对蚜虫植食性表现出跨代抗性，并使用靶向代谢物分析、转录组学和全基因组亚硫酸氢盐测序来鉴定与跨代抗性和胁迫诱导的甲基化变体相关的性状和基因。我们将使用CRISPR-Cas9和化学抑制来操纵已鉴定的基因和DNA甲基化机制，以推断应激诱导的甲基化变异与跨代抗性之间的因果关系。最后，我们将评估S。通过操纵甲基化组和选择的效力，多根属通过对甲基化组变体的选择来适应：在DNA甲基化机制中缺陷的野生型和敲除突变体将在控制、铜过量和蚜虫食草性下在最小的（通过漂移进化）和大的（选择进化）群体中生长80代。评估小群体和大群体之间以及甲基化组的化学抑制下野生型和突变体之间的抗性变化将使我们能够推断甲基化组变体的选择是否有利于快速适应。总之，这些实验将提供新的见解甲基化变异的来源及其对适应的贡献，从而测试进化生态学中有争议的假设。考虑到克隆植物在自然和农业生态系统中的重要性以及全球变化的快速步伐，其结果将与不同的生物学领域相关。