Roots and Root Hairs: Comparative Molecular Studies Across Land Plants

Regents Of The University Of Michigan - Ann Arbor, Ann Arbor MI

Investigators

Abstract

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/).