Identification of novel markers for stem-cell niche of Arabidopsis shoot apex

In Arabidopsis, shoot stem-cells give rise to all the aerial parts of plant body and are localized at the tip of the shoot apex. Feedback signaling mediated by CLAVATA3 (CLV3) and WUSCHEL (WUS), specify and maintain stem-cells in the shoot apical meristem (SAM). Although CLV3 and WUS have been used extensively as stem-cell markers, their expression levels are mutually influenced by each other. Thus, CLV3 and WUS are not ideal markers for analyzing genes that function in this feedback regulation. Here, we present the expression profiles of genes that can be used as markers for cells of the stem-cell niche based on the following criteria: (1) they are expressed in cells of the central zone (CZ) or the rib-meristem (RM)/organizing center (OC), (2) their expression levels are not influenced by alterations in CLV3 or WUS levels, and (3) their expression is initiated during embryonic stages and is maintained in post-embryonic development. By RNA in-situ hybridization, we also found that the expression of these genes follow two distinct patterns: (1) CLV3-like and (2) WUS-like. Moreover, the expression domains of these genes expand in SAMs of clv3 mutants, which accumulate higher numbers of stem-cells. A comprehensive expression patterns provided here suggests that they are ideal markers for stem-cell niche of Arabidopsis shoot apex.