RESEARCH-PGR: Deciphering the link between RNA directed DNA methylation and reproduction in Brassicaceae

种子是人类和牲畜的主要热量来源，因此，农业生产力最关键的方面之一是种子开发。即使是种子发育中的微小变化也会对生产力产生深远影响，并通过整个食物链产生连锁反应。该提案解决了DNA甲基化的作用，DNA上的化学标记，在种子的发展，特别是那些影响种子集，大小和活力的标记。我们最近在重要的油料作物芜菁中发现了三个DNA甲基化途径的突变。每一种突变在种子生产中都有严重和特定的缺陷。使用先进的DNA测序技术，我们将确定这些突变的遗传，分子和基因组后果。这些发现将有助于了解调节种子发育的内部机制。该项目还将为多名研究生和本科生提供培训机会。这项培训将发展他们在基因组编辑和高通量测序等尖端技术方面的专业知识。这项工作建立在将小RNA指导的DNA甲基化（RdDM）与适当的种子发育联系起来的几个关键观察基础上，可能通过建立和维护：1）基因组印记（等位基因表达中的起源亲本偏差），和/或2）基因组平衡（在全基因组复制后从显性亚基因组优先表达）。该项目将首先通过分析芜菁中RNA指导的DNA甲基化突变体的小RNA，转录组和表观基因组来探索RdDM在种子发育中的转录和发育后果，其中每一个都大大减少了结实。此外，我们将调查基因组印记和基因组优势之间的联系在B。拉帕。最后，我们将测试的假设，即RdDM影响种子集通过改变基因组印记和/或基因组优势产生同源突变在其他成员的拟南芥科。这项研究的结果将提供一个更好的理解印迹和基因组的优势，可以翻译到密切相关的物种在家庭油菜科，包括种子作物B。油菜。

Seeds are the primary source of calories for humans and livestock, and thus one of the most critical aspects of agricultural productivity is seed development. Even small changes in seed development can have profound impacts on productivity with cascading repercussions through the entire food chain. This proposal addresses the role of DNA methylation, a chemical mark placed on DNA, in the development of seeds, particularly those marks that impact seed set, size, and viability. We have recently uncovered three mutations of a DNA methylation pathway in the important oil crop Brassica rapa. Each mutation has severe and specific defects in seed production. Using advanced DNA sequencing technologies, we will identify the genetic, molecular, and genomic consequences of these mutations. These findings will help understand the internal mechanisms that regulate seed development. This project will also provide training opportunities for multiple graduate and undergraduate students. This training will develop their expertise in cutting-edge techniques such as genome editing and high-throughput sequencing.This work builds on several key observations that link small-RNA directed DNA methylation (RdDM) with proper seed development, likely through establishment and maintenance of: 1) genomic imprinting (parent-of-origin bias in allele expression), and/or 2) genome balance (preferential expression from a dominant subgenome following whole genome duplication). This project will first explore the transcriptional and developmental consequences of RdDM in seed development by profiling small RNAs, transcriptomes, and epigenomes of RNA-directed DNA methylation mutants in Brassica rapa, each of which dramatically reduces seed set. In addition, we will investigate links between genomic imprinting and genome dominance in B. rapa. Finally, we will test the hypothesis that RdDM influences seed set by altering genomic imprinting and/or genome dominance by generating cognate mutations in other members of the Brassicaceae family. Results from this study will provide a better understanding of both imprinting and genome dominance that can be translated to closely related species in the family Brassicaceae, including the seed crop B. napus.