MaizeCode - An Initial Analysis of Functional Elements in the Maize Genome

PI: Thomas Gingeras（冷泉港实验室）CoPIs: David Jackson, Robert Martienssen， W. Richard McCombie, Michael Schatz, David Micklos（冷泉港实验室），Doreen Ware （USDA-ARS/冷泉港实验室）；玉米（玉米）是世界上最重要的经济和农业作物之一。经过几个世纪的精心遗传育种，以提高其许多生长和营养特性，它才获得了这一地位。高质量的基因组序列与不同的分子数据相结合，使科学家能够更好地了解这种选择性育种在遗传和表观遗传水平上的影响。MaizeCODE项目旨在为育种家和植物科学家创建一个全面的参考百科全书，其中包含非常有用的基因组参考序列资源，用于提高经济上重要的作物性状，如抗病性和产量。此外，该项目将通过具体的课程和研讨会，为学生、育种者和实践科学家提供广泛而全面的培训机会，这些课程和研讨会将讨论获取和分析MaizeCODE数据的各种方法。教育、外展和培训（EOT）工作将使主要本科院校（PUIs）的教师准备好与本科生一起分析MaizeCODE，并将为研究生提供旅行奖励，以参加MaizeCODE专业会议的培训。EOT项目将通过预测和鼓励本科生和研究生广泛参与初级数据分析，在促进科学、技术、工程和数学（STEM）学科方面发挥独特作用。改进的玉米基因组组合将为鉴定在该工作草案序列中编码的生物化学活性和生物功能元件提供基础。在玉米这一经典遗传系统中，这些元素的全面目录将是将基因型与重要性状联系起来的关键组成部分。这是MaizeCODE项目的首要目标。人类ENCODE项目就是这样一个全面目录的模型。基于ENCODE项目团队的领导经验，这个类似的集成和多学科项目有三个主要目标：1)为两个自交系迷宫系和一个大刍动物自交系建立高质量的工作草图；2)鉴定玉米基因组中6种细胞类型中被特异性修饰组蛋白转录、甲基化和结合的区域，这些细胞类型是根和茎系统的主要祖细胞（重点研究3种根细胞类型中的组蛋白修饰）和5种不相关组织中的转录因子；展示和传播的数据，更广泛的社区植物生物学家全世界。鉴于玉米“基因组到表型”研究的丰富，以及人们逐渐认识到选择下的许多变异在基因调控水平上起作用，预计该项目将对玉米遗传学研究和育种产生广泛而重大的影响，并有可能为其他禾本科作物的类似研究提供信息。该项目预计将显著扩展功能注释和目前对玉米基因活性调控的理解，为已建立的数据库和图形基因组展示中心增加关键内容。本项目产生的信息将利用公开的数据库和CyVerse （www.cyverse.org）在线资源迅速和广泛地传播。

PI: Thomas Gingeras (Cold Spring Harbor Laboratory)CoPIs: David Jackson, Robert Martienssen, W. Richard McCombie, Michael Schatz, and David Micklos (Cold Spring Harbor Laboratory), Doreen Ware (USDA-ARS/Cold Spring Harbor Laboratory); and Ken Birnbaum (New York University)Maize (corn) is one of the most economically and agriculturally important crops grown in the world. It has assumed this position after centuries of careful genetic breeding to enhance many of its growth and nutritional properties. The generation of high quality genome sequences paired with diverse molecular data allows scientists to better understand the effects of this selective breeding at both the genetic and epigenetic levels. The MaizeCODE project aims to create a comprehensive reference encyclopedia of highly useful genomic reference sequence resources for breeders and plant scientists to use to improve economically important crop traits like disease resistance and yield. In addition, this project will provide broad and comprehensive training opportunities for students, breeders and practicing scientists through specific courses and workshops that will address various approaches to obtain and analyze MaizeCODE data. The Education, Outreach, and Training (EOT) effort will prepare faculty from primarily undergraduate institutions (PUIs) to analyze MaizeCODE with undergraduate students and will provide travel awards for graduate students to attend MaizeCODE training at professional meetings. The EOT program will be unique in promoting Science, Technology, Engineering and Math (STEM) disciplines by anticipating and encouraging broad participation in primary data analysis by undergraduate and graduate students. Improved assemblies of the maize genome will provide a foundation for the identification of biochemically active and biologically functional elements encoded in this working-draft sequence. A comprehensive catalog of these elements will be a critical component in strategies to link genotype with important traits in maize, a classical genetic system. This is the overarching goal of the MaizeCODE project. The human ENCODE project is a model for such a comprehensive catalog. Building on the project team's leadership experience with ENCODE, this similarly integrated and multi-disciplinary project has three main objectives: 1) to develop high-quality working drafts for two inbred maze lines and one teosinte inbred line, 2) to identify regions of the maize genome that are transcribed, methylated, bound by specific modified histones in six cell types that are the major progenitors of the root and shoot systems (focusing on histone modification in three root cell types) and transcription factors in five unrelated tissues and 3) to store, collate, display and disseminate the data to the broader community of plant biologists worldwide. Given the wealth of "genome to phenome" studies in maize, and the emerging realization that much of the variation under selection acts at the level of gene regulation, it is expected that this project will have broad and significant impact on maize genetics research and breeding, with the potential to inform similar research in other grass crops. The project expects to extend significantly the functional annotations and the current understanding of the regulation of gene activity in maize, adding critical content to established databases and graphical genome display centers. Information generated in this project will be rapidly and broadly disseminated using publically available databases and the CyVerse (www.cyverse.org) online resource.