Roots and Root Hairs: Comparative Molecular Studies Across Land Plants

作物产量取决于根系对水分和养分的有效吸收。当前的一个挑战是了解作物植物如何调节其根的形成和功能。了解在这一水平上控制根系的基因将有助于植物育种者调整根系性状，以适应新的农业实践、土地利用模式和次优土壤。在本项目中，将从广泛的作物植物及其近缘植物的根和根毛中定义各种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。该项目所获得的知识有望为植物根和根毛的形成和功能调控的分子机制的起源、多样化和保护提供新的见解。此外，考虑到根/根毛在植物生长和环境响应中的重要作用，这些发现有望有助于合理设计作物植物根和根毛结构的策略，这是考虑到营养不良土壤和环境变化影响的一个特别重要的目标。该项目将为参与的本科生、研究生和博士后提供强有力的跨学科培训。该项目的一项主要外展活动是与查尔斯顿学院（College of Charleston，主要是一所本科院校）开展合作研究访问交流计划，为无法在本国院校获得此类培训的学生提供大规模的基因组学和计算生物学体验。该项目将参与密歇根生物学者项目，该项目是一个过渡性项目，旨在帮助生命科学专业的一年级本科生，特别是少数族裔。最后，本研究的各个方面将作为密歇根大学高级分子发展课程的一部分纳入一个学期的实验室练习。随着植物中可用的基因和基因组序列的迅速扩大，现在有可能考虑确定整个植物王国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，并可能为操纵作物植物带来新的机会。该项目旨在通过定义不同植物物种中简单植物器官（根）和简单植物细胞类型（根毛）中的基因表达，作为实现这一最终目标的第一步。在初步研究中，已经从7个物种（水稻、玉米、大豆、黄瓜、番茄、拟南芥和卷柏）中获得了表达数据，证明了该研究的可行性和潜在影响。这个项目有两个主要目标。首先是通过定义来自不同作物植物的主根和其他根类型的三个主要活动区域的转录组，确定与特定根结构和功能性状相关的一系列调控基因。在第二个目标中，细胞特异性调控基因将通过连接基因表达和细胞特性，从这些相同的植物物种生长在正常和营养胁迫条件下的根毛细胞。该项目的研究结果预计将对植物研究界产生重大影响，通过从许多不同物种中生成根区特异性和根毛特异性表达数据，这将有助于为未知基因分配功能，预测功能同源性，并评估基因进化史。本项目产生的数据和材料将在项目网站（http://sites.lsa.umich.edu/PGRP-roots）、NCBI序列读取档案（SRA, http://trace.ncbi.nlm.nih.gov/Traces/sra/）和基因表达综合数据库（GEO, http://www.ncbi.nlm.nih.gov/geo/）上提供。

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/).