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

RESEARCH-PGR：破译十字花科中 RNA 指导的 DNA 甲基化与繁殖之间的联系

• 批准号: 1546825
• 负责人: Rebecca Mosher
• 金额: $ 227.1万
• 依托单位: University of Arizona
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-09-15 至 2022-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1546825&HistoricalAwards=false
• 关键词: RESEARCH; PGR; Deciphering; link; between

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.

种子是人类和牲畜热量的主要来源，因此农业生产力最关键的方面之一就是种子的发育。即使是种子发育的微小变化也会对生产力产生深远影响，并在整个食物链中产生连锁反应。该提案解决了DNA甲基化（放置在DNA上的化学标记）在种子发育中的作用，特别是那些影响种子形成、大小和生存能力的标记。我们最近在重要的油料作物油菜中发现了DNA甲基化途径的三个突变。每种突变在制种过程中都有严重和特殊的缺陷。利用先进的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。这些发现将有助于理解调控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。该培训将培养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。这项工作建立在几个关键观察的基础上，这些观察将小rna导向的DNA甲基化（RdDM）与适当的种子发育联系起来，可能通过建立和维持：1)基因组印记（等位基因表达的亲本起源偏见）和/或2)基因组平衡（全基因组复制后优势亚基因组的优先表达）。该项目将首先通过分析油菜中rna导向的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，每个突变体都会显著减少种子的结实率。此外，我们将研究rapa基因组印迹与基因组显性之间的联系。最后，我们将验证RdDM通过改变基因组印迹和/或通过在其他十字花科成员中产生同源突变来影响种子形成的假设。该研究结果将有助于更好地理解印迹和基因组优势，这些印迹和优势可以翻译为芸苔科近亲物种，包括种子作物甘蓝型油菜。