Getting to the root of plant biology: impact of the Arabidopsis genome sequence on root research

Abstract

Prior to the availability of the genome sequence, the root of Arabidopsis had attracted a small but ardent group of researchers drawn to its accessibility and developmental simplicity. Roots are easily observed when grown on the surface of nutrient agar media, facilitating analysis of responses to stimuli such as gravity and touch. Developmental biologists were attracted to the simple radial organization of primary root tissues, which form a series of concentric cylinders around the central vascular tissue. Equally attractive was the mode of propagation, with stem cells at the tip giving rise to progeny that were confined to cell files. These properties of root development reduced the normal four-dimensional problem of development (three spatial dimensions and time) to a two-dimensional problem, with cell type on the radial axis and developmental time along the longitudinal axis. The availability of the complete Arabidopsis genome sequence has dramatically accelerated traditional genetic research on root biology, and has also enabled entirely new experimental strategies to be applied. Here we review examples of the ways in which availability of the Arabidopsis genome sequence has enhanced progress in understanding root biology.

Figure 1

Schematic representation of Arabidopsis primary and lateral root tissues. Single layers of epidermis (red), cortex (green), endodermis (yellow) and pericycle (purple) cells surround the central vascular tissue (grey). The outer layers are organized as concentric cylinders of tissues. Cells within these tissues exhibit a proximal–distal developmental gradient, originating from initial cells abutting quiescent centre cells (light blue) that transit through proximal and distal meristem zones during their division phase, then undergo rapid cell expansion in the elongation zone, prior to entering the differentiation zone. Lateral roots form from the pericyle. As lateral root primordia form (right), all of the tissues found in the primary root are generated de novo.

Figure 2

Basic features of arabidopsis root structure. This series of progressively magnified images comprises an image of 4-day-old Arabidopsis seedlings grown on vertical plates (left), a magnified view of a single seedling illustrating the abundant root hairs (centre), and a fluorescent microscopy image of an Arabidopsis root tip with the epidermis and lateral root cap (lrc) cells expressing GFP (right).

Figure 3

Pipeline for profiling mRNA expression in root cell types. Roots of transgenic lines with cell type-specific GFP expression are subjected to enzymatic digestion of the cell walls. The resulting protoplasts are analysed in a fluorescent activated cell sorter (FACS), which separates the GFP-expressing cells from the non-expressing cells. RNA from the sorted cells is then used for labelling and hybridization to microarrays.