With the rapidly expanding genome technologies and information available, 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.

This project has two major objectives. The first is to define transcriptomes from the three major zones of activity (meristematic zone, elongation zone, and differentiation zone) for the primary roots and other root types from a diverse set of plant species.  In the second objective, cell-type specific transcriptome data will be obtained from the root hair cells from these diverse plant species.  For each of these objectives, transcriptome data is obtained from bulk RNA-seq and from single-cell RNA-seq experiments. 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 also provide broader scientific benefits.  It will offer 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 PUI, to provide large-scale genomic and computational biology experiences to students not able to obtain this training at their home institution. The project activities will also be incorporated into formal coursework and laboratory exercises. The results of this project research are expected to have a significant impact on the plant science community, through information garnered from the comparative analysis of developmental zone-specific and cell-type-specific expression data from many diverse species, assisting efforts to assign function to unknown genes, predict functional homologs, and assess gene evolutionary history.

Sources of Transcript Data for this Project. RNA will be isolated from sections of roots corresponding to the three major developmental zones (Meristematic, Elongation, and Differentiation Zones, as indicated in the figure) and RNA will be obtained from isolated root hairs (hair-like single-cell projections from the root surface).