Roots and Root Hairs: Comparative Molecular Studies Across Land Plants

作物产量取决于根部对水分和养分的有效吸收。目前的一个挑战是了解作物如何调节其根的形成和功能。对在这一水平上控制根的基因的了解将有助于植物育种者定制根特征，以适应新的农业实践、土地利用模式和次优土壤。在这个项目中，将从多种作物及其近缘植物的根和根毛中定义在不同环境条件下的全基因组基因表达。这些基因表达模式将被分析，以确定控制根的形成和功能的关键基因。此外，这些大型基因表达数据集将为科学家研究根生物学的许多方面提供有价值的工具。从这个项目中获得的知识有望为调节植物根和根毛的形成和功能的分子机制的起源、多样化和保护提供新的见解。此外，鉴于根/根毛对植物生长和环境响应的重要作用，这些发现有望帮助合理设计操纵作物根和根毛结构的策略，鉴于对养分贫乏的土壤和环境变化的影响，这是一个特别重要的目标。该项目将为参与的本科生、研究生和博士后研究员提供强有力的跨学科培训。该项目的一个主要推广活动是与查尔斯顿学院(SC)的合作研究访客交流计划，该学院主要是一所本科院校，为无法在本国机构获得这种培训的学生提供大规模的基因组和计算生物学体验。该项目将参与密歇根生物学者计划，这是一个帮助生命科学一年级本科生，特别是未被充分代表的少数族裔的过渡计划。最后，这项研究的各个方面将被纳入密歇根大学为期一学期的实验室练习中，作为高级分子开发课程的一部分。随着植物中基因和基因组序列的迅速扩展，现在可以考虑定义整个植物界物种中每个器官和细胞类型中存在的基因活动的最终目标。这一知识将极大地提高对植物过程及其多样性的理解，并可能带来操纵作物的新机会。该项目旨在通过定义简单的植物器官(根)和简单的植物细胞类型(根毛)在不同植物物种中的基因表达，作为迈向这一最终目标的第一步。在初步研究中，已经产生了七个物种(水稻、玉米、大豆、黄瓜、番茄、拟南芥和卷柏)的表达数据，证明了拟议研究的可行性和潜在影响。这个项目有两个主要目标。第一个是通过定义初级根的三个主要活动区的转录本和来自不同作物的其他根类型的转录本，确定与特定的根结构和功能特征相关的调控基因集。在第二个目标中，将通过将正常和营养胁迫条件下生长的这些相同植物的根毛细胞中的基因表达和细胞特征联系起来，来定义细胞特有的调控基因。该项目的结果预计将对植物研究社区产生重大影响，通过产生来自许多不同物种的根区特定和根毛特定的表达数据，这将有助于为未知基因分配功能，预测功能同源基因，并评估基因进化历史。该项目产生的数据和材料将在项目网站(http://sites.lsa.umich.edu/PGRP-roots)，)上查阅(美国国家生物信息学研究所序列读取档案(sRa，http://trace.ncbi.nlm.nih.gov/Traces/sra/)，)和基因表达总览(geo，http://www.ncbi.nlm.nih.gov/geo/).

Crop yields depend on effective uptake of water and nutrients by the roots. A current challenge is to understand how crop plants regulate the formation and function of their roots. An understanding of the genes that control roots at this level would help plant breeders tailor root traits to match new agricultural practices, land use patterns, and suboptimal soils. In this project, genome-wide gene expression will be defined from roots and root hairs from a wide range of crop plants and their relatives under various environmental conditions. These gene expression patterns will be analyzed to identify key genes that control the formation and function of roots. Further, these large gene expression datasets will provide a valuable tool for scientists studying many aspects of root biology. The knowledge obtained from this project is expected to provide new insight into the origin, diversification, and conservation of molecular mechanisms used to regulate the formation and function of roots and root hairs of plants. Further, given the important roles of roots/root hairs for plant growth and environmental response, these findings are expected to assist the rational design of strategies to manipulate root and root hair architecture in crop plants, a particularly important goal given concerns about nutrient-poor soils and the impact of environmental change. This project will provide strong interdisciplinary training for the participating undergraduates, graduate students, and postdoctoral fellows. A major outreach activity of this project is a collaborative research visitor exchange program with the College of Charleston (SC), a primarily undergraduate institution, to provide large-scale genomic and computational biology experiences to students who are unable to obtain this training at their home institution. The project will participate in the Michigan Biological Scholars Program, a bridging program assisting first-year undergraduates in the life sciences, especially underrepresented minorities. Finally, aspects of this research will be incorporated into a semester-long laboratory exercise as part of an advanced molecular development course at the University of Michigan. With the rapidly expanding gene and genome sequences available in plants, it is now possible to consider the ultimate goal of defining the gene activities present in every organ and cell type in species throughout the plant kingdom. This knowledge would dramatically improve the understanding of plant processes and their diversity, and will likely lead to new opportunities for manipulating crop plants. This project is designed as a first step toward this ultimate goal by defining gene expression in a simple plant organ (the root) and a simple plant cell type (the root hair) in diverse plant species. In a preliminary study, expression data has been generated from seven species (rice, maize, soybean, cucumber, tomato, Arabidopsis, and Selaginella), demonstrating the feasibility and potential impact of the proposed research. This project has two major objectives. The first is to identify sets of regulatory genes associated with specific root structural and functional traits, by defining transcriptomes from the three major zones of activity for the primary roots and other root types from a diverse set of crop plants. In the second objective, cell-specific regulatory genes will be defined by linking gene expression and cell characteristics in the root hair cells from these same plant species grown under normal and nutrient stress conditions. The results of this project are expected to have a significant impact on the plant research community, through the generation of root-zone-specific and root-hair-specific expression data from many diverse species, which will assist efforts to assign function to unknown genes, predict functional homologs, and assess gene evolutionary history. The data and materials produced by this project will be available at the project website (http://sites.lsa.umich.edu/PGRP-roots), the NCBI Sequence Read Archive (SRA, http://trace.ncbi.nlm.nih.gov/Traces/sra/), and the Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/).