In this review, we analyze progress in understanding the mechanisms of root meristem development and function. The formation of embryonic and lateral roots, together with the remarkable regenerative ability of roots, seems to be linked to an auxin-dependent patterning mechanism, the "reflux loop," that can act at least partly independently of cellular context. A major feature of root formation is the production of the "structural initials," the center of the developing root. These cells form an organizing center (OC), the quiescent center (QC), which is needed for meristem activity. The exact role of the QC remains somewhat unclear, though it maintains a stem cell (SC) state in adjacent cells and acts as a long-term SC pool itself. SCs in the root can be defined on an operational basis, but a molecular definition for SC identity remains elusive. Instead, the behavior of cells in the proximal root might better be understood as the result of a "potential" gradient in the meristem, which confers cellular characteristics with respect to proximity to the QC. This potential gradient also seems to be auxin-dependent, possibly as a result of the effect of auxin on the expression of PLETHORA genes, key regulators of meristem function. Only in the root cap (RC) has distinct SC identity been proposed; but increasingly, evidence suggests that regulation of RC development is rather different from that in the proximal meristem; interestingly, a similar dichotomy can also be observed in the shoot meristem. Cell cycle progression must lie at the core of meristematic activity, and recent work has begun to uncover how hormonal regulation feeds forward into various aspects of the cell cycle. The emergent picture is one of coordinate regulation of cell division and elongation by a hormonal signaling network that is integrated by the auxin reflux loop to control root growth.
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