Rhizomics - Comparative Functional Genomic and Proteomic Analysis of Rhizome Specificity Across the Plant Kingdom

大卫河Gang（PI），亚利桑那大学Carol A. Soderlund（CoPI），亚利桑那大学Jay Thelen（CoPI），密苏里大学项目摘要根茎是维管植物谱系的原始茎。在植物发育出直立的茎之前，它们通过根茎水平生长。所有现存的原始维管植物和许多高级被子植物仍然使用根茎作为其唯一的茎型。根茎是负责入侵，耐寒，甚至苛刻的许多世界上最重要的杂草。这些根茎杂草植物通过地下侵入新领域的能力导致了它们在世界范围内的巨大成功，这直接归因于它们的根茎。相反，世界上许多最重要的药用植物，如生姜和姜黄，在其根茎中产生其药用活性成分。尽管它们很重要，但人们对哪些基因参与根茎的生长和功能知之甚少。该项目的目的是鉴定仅在根茎中表达的基因和蛋白质，并表征在整个植物王国的植物根茎功能中发挥重要作用的特定基因的功能。将通过从所选根茎物种的发育根茎构建cDNA文库并对来自这些文库的随机克隆进行测序以提供大量表达序列标签（EST）来鉴定仅在根茎中表达或主要在根茎中表达的基因。基因转录物的根茎特异性表达将使用DNA微阵列测定。将使用互补蛋白质组学技术测定根茎与其他组织中的蛋白质水平。这些数据集将被整合到一个数据库中，然后进行比较分析，以确定所有物种共有的根茎特异性基因和个别物种特有的基因。具体基因在根茎分化，生长和发育中的作用，然后将使用一些方法进行验证，包括更详细的表达谱和功能分析的基因敲除或异源表达在其他物种。这个项目将影响我们对根茎生长和功能的理解。由于根茎是原始的维管植物茎，并且仍然被许多物种用作其主要的茎类型，因此该项目也将影响我们对直立茎进化的理解。因为世界上很多？世界上最严重的杂草是通过根茎传播的，其中三种最重要的杂草将成为调查的对象，该项目还将提供信息，用于更好地控制全球经济上重要的杂草。该项目将在两个主要方面整合研究和教育：1。培训学生在跨学科和地理分散的环境中进行研究的成功方法，这对生物科学的成功变得越来越重要; 2.本科生和高中教师的暑期研究经验。将大力强调征聘和培训代表性不足的少数民族和妇女，特别是实习教师和本科生职位，以及博士后和研究生职位。将开发一个基于网络的EST、微阵列和蛋白质组学数据库，并在项目网站www.plant-rhizomy.org上向公众开放。

David R. Gang (PI), University of ArizonaCarol A. Soderlund (CoPI), University of ArizonaJay Thelen (CoPI), University of MissouriSummary of the ProjectThe rhizome is the original stem of the vascular plant lineage. Before plants developed upright stems, they grew horizontally via rhizomes. All extant primitive vascular plants and many advanced angiosperms still use rhizomes as their sole stem type. Rhizomes are responsible for the invasiveness, hardiness, and even harshness of many of the world's most significant weeds. The ability of these rhizomatous weedy plants to invade new territory via the underground has led to their great success world-wide, and is directly attributable to their rhizomes. In contrast, many of the world's most important medicinal plants, such as ginger and turmeric, produce their medicinally active components in their rhizomes. Despite their importance, very little is known about what genes are involved in the growth and function of rhizomes. The aim of this project is to identify genes and proteins that are expressed exclusively in the rhizome and to characterize the function of specific genes that play important roles in rhizome function from plants across the plant kingdom. Genes that are expressed exclusively or predominantly in rhizomes will be identified by constructing cDNA libraries from developing rhizomes from selected rhizomatous species and sequencing random clones from these libraries to provide a large set of expressed sequence tags (ESTs). Rhizome-specific expression of gene transcripts will be determined using DNA microarrays. Protein levels in the rhizomes versus other tissues will be determined using complementary proteomics technologies. These datasets will be integrated into one database, and will then be comparatively analyzed to identify rhizome-specific genes common to all species and specific to individual species. The roles of specific genes in rhizome differentiation, growth and development will then be validated using a number of approaches, including more detailed expression profiling and functional analysis by gene knock out or heterologous expression in other species. This project will impact our understanding of rhizome growth and function. Because the rhizome is the original vascular plant stem, and is still used by many species as their major stem type, this project will impact our understanding of the evolution of upright stems as well. Because many of the world?s worst weeds spread via their rhizomes and three of the most important of these weedy species will be the subject of investigation, this project will also produce information that could be used to better tailor efforts to control economically important weeds worldwide.The broader impacts of this project is that it will cross-train undergraduate and graduate students and postdoctoral researchers in multidisciplinary research approaches. This project will integrate research and education in two major ways: 1. Training of students in successful approaches to doing research in an interdisciplinary and geographically dispersed environment, which is becoming more important for success in the biological sciences; 2. Summer research experiences for undergraduate students and high school teachers. A strong emphasis will be placed on recruitment and training of underrepresented minorities and women, especially for teacher intern and undergraduate student positions, but also for the post-doctoral and graduate student positions. A web-based database of EST, microarray and proteomics data will be developed and made publicly accessible at the project web site: www.plant-rhizome.org.