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

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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.