Epigenetic Landscapes and Transcriptomes in Two Maize Inbred Lines and Their Heterotic Hybrids

杂种优势（或杂种优势）是一种现象，即一个物种内不同近交亲本的后代比任何一个近交亲本具有更优越的生物量、身高和/或育性。虽然杂种优势在作物生产中被广泛利用，但其分子基础在很大程度上是未知的。本研究将探讨小rna和表观遗传修饰（如组蛋白修饰和DNA甲基化）是否参与玉米杂种优势的调控。该项目将采用下一代测序技术，对两个自交系及其杂交后代的信使RNA和小RNA转录组进行全基因组分析，并选择表观遗传修饰。对这些数据的系统分析将提供玉米自交系及其互交杂交种的DNA甲基化、组蛋白修饰模式、序列多态性、小RNA丰度和基因表达水平的全基因组图谱。对选定的典型玉米品系的深入分析将有助于实现理解玉米杂种优势的分子机制的长期目标。了解杂种优势背后的分子事件有可能改善作物和牲畜育种计划。此外，由于杂种优势是一种潜在的进化驱动力，阐明其分子基础将有助于我们对物种进化的理解。该项目将为博士后、研究生和本科层次的年轻研究人员提供培训。此外，该项目还将支持一项外展计划，将本科生暑期研究项目与学年期间的本科生课程和项目结合起来。本计画将透过课堂作业与专案课程，整合到本科生物资讯学与分子生物学课程中。项目人员还将参加针对年轻学生的各种外展活动。将建立一个网站（http://plantgenomics.biology.yale.edu），供公众查阅数据并提供该项目的摘要。所有数据集将存放在NIH GEO存储库（http://www.ncbi.nlm.nih.gov/geo）和植物基因表达数据库（PLEXdb） http://plexdb.org。

Heterosis (or hybrid vigor) is the phenomenon where the progeny of diverse inbred parents within a species have superior biomass, stature and/or fertility compared to either of the inbred parental lines. Although heterosis is commonly exploited in crop production, the molecular basis is largely unknown. This proposal will address whether small RNAs and epigenetic modifications (such as histone modifications and DNA methylation) are involved in regulation of heterosis in maize. This project will employ next-generation sequencing to provide genome-wide profiling of messenger RNA and small RNA transcriptomes and selected epigenetic modifications in two inbred lines and their reciprocal hybrid offspring. A systematic analysis of these data will provide genome-wide maps of DNA methylation, histone modification patterns, sequence polymorphisms, small RNA abundance, and gene expression levels in the maize inbred lines and their reciprocal hybrids. This in-depth analysis of a selected model pair of maize lines will aid in achieving the long-term goal of understanding the molecular mechanisms of heterosis in maize. Understanding the molecular events underlying heterosis has the potential to improve crop and livestock breeding programs. In addition, because heterosis is potentially a driving evolutionary force, elucidating its molecular basis will contribute to our understanding of the evolution of species. This project will provide training to young researchers at the postdoctoral, graduate, and undergraduate levels. In addition, the project will support an outreach program that couples undergraduate summer research projects with undergraduate classes and projects during the academic year. This project will be integrated into undergraduate bioinformatics and molecular biology curricula through class assignments and project-based lessons. Project personnel will also participate in various outreach events targeting younger students. A website (http://plantgenomics.biology.yale.edu) will be developed to provide public access to the data and provide a summary of the project. All datasets will be deposited at the NIH GEO repository (http://www.ncbi.nlm.nih.gov/geo) and the Plant Gene Expression database (PLEXdb) at http://plexdb.org.