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

Pi：David R.Gang(华盛顿州立大学)Copis：Carol A.Soderlund(亚利桑那大学)和Jay Thelen，密苏里-哥伦比亚大学根茎是维管植物谱系的原始茎。在植物发育直立茎之前，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类型。根状茎是世界上许多最重要的杂草的侵入性、耐寒性，甚至是严酷的原因。这些根茎杂草植物通过地下入侵新领域的能力导致了它们在世界范围内的巨大成功，这直接归功于它们的根茎。相比之下，世界上许多最重要的药用植物，如生姜和姜黄，在它们的根茎中生产药用活性成分。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。该项目的目的是确定在根茎中唯一表达的基因和蛋白质，并确定在整个植物界的植物中在根茎功能中发挥重要作用的特定基因的功能。通过构建特定根茎植物根茎发育过程中的cDNA文库，并对文库中的随机克隆进行测序，以提供大量的表达序列标签(EST)，从而识别出在根茎中唯一或主要表达的基因。基因转录本的根状茎特异表达将使用DNA微阵列来确定。根茎相对于其他组织中的蛋白质水平将使用互补的蛋白质组学技术来确定。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有基因和个别物种特有的基因。然后将使用多种方法验证特定基因在根茎分化、生长和发育中的作用，包括更详细的表达谱和通过基因敲除或在其他物种中异源表达进行功能分析。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束植物的茎，并且仍然被许多物种用作其主要的茎类型，这个项目也将影响我们对直立茎进化的理解。由于世界上许多最严重的杂草通过根茎传播，其中三个最重要的杂草物种将成为调查对象，该项目还将产生信息，可用于更好地量身定做控制全球重要经济杂草的努力。该项目的更广泛影响是，它将在多学科研究方法方面交叉培训本科生、研究生和博士后研究人员。该项目将以两种主要方式将研究和教育结合起来：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.为本科生和高中教师提供暑期研究经验。将高度重视招聘和培训任职人数不足的少数群体和妇女，特别是教师、实习生和本科生职位，以及博士后和研究生职位。将开发一个EST、微阵列和蛋白质组学数据的网络数据库，并在项目网站(www.PLANT-ROUTOME.org)上向公众开放。

PI: David R. Gang (Washington State University)CoPIs: Carol A. Soderlund (University of Arizona) and Jay Thelen, University of Missouri - ColumbiaThe 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).