Comparative Analysis of Gene Expression in the Developing Roots and Root Hairs Across Vascular Plants.

Abstract

The evolution of the plant root is one of the remarkable examples of land plants’ adaptation to the terrestrial environment. The root and root hairs are found in almost all vascular plants, making them good models to study the conservation and diversification of adaptations in different vascular lineages. The molecular basis of root and root hair development has been intensively studied in the model organism Arabidopsis thaliana and many of the key regulators have been elucidated over the past 20 years. However, little is known about the molecular basis of root and root hair development in other vascular plants, which prevents a detailed understanding of root and root hair adaptation at a mechanistic level. In this thesis project, I compared the gene expression programs in seven vascular plants to find the conserved/diversified regulators in root and root hair development. First, I defined temporal transcript accumulation profiles generated from three root development zones in seven vascular plants and found significant family-wise gene expression similarity between these plants. Next, I found that most of the 133 Arabidopsis key root development genes are used in all vascular plants, including Selaginella moellendorffii, which is thought to have evolved roots independently. These results suggest broad conservation in the molecular mechanisms employed during root formation. Next, I defined the root hair transcriptome in Arabidopsis and rice and found significant conservation in the two species. However, a subset of 563 genes regulated by ROOT HAIR DEFECTIVE 6 (RHD6) exhibited less conservation compared to the total root-hair-expressed genes. This divergence in the family structure and gene expression is found in other vascular plants as well. I further analyzed the Arabidopsis root hair patterning genes in other vascular plants and identified a substantial difference in their expression patterns. These results suggest lineage specific diversification in the structure and expression of the root hair development genes in Arabidopsis. Altogether, this thesis work revealed broad conservation of gene expression programs for root formation in all vascular plants and lineage specific diversification for root-hair cell differentiation in Arabidopsis.