The stem, consisting of nodes and internodes, is one of the major organs in seed plants. In contrast to other organs, however, processes of stem development remain elusive, especially when nodes and internodes are initiated. By introducing an intron into the Cre recombinase gene, we established a heat-shock inducible clonal analysis system in a single binary vector and applied it to the stem in the flag leaf phytomer of rice. With detailed characterizations of stem development, we show that cell fate acquisition for each domain of the stem occurs stepwise. Cell fates for a single phytomer and the foot (non-elongating domain at the stem base) were established in the shoot apical meristem by one plastochron before the leaf initiation. The fate acquisition for the node occurred just before the leaf initiation, separating cell lineages for leaves and stems. Subsequently, fates for the axillary bud were established in early leaf primordia. Finally, cells committed to the internode emerged from, at most, a few tiers of cells when the stem epidermis was at the 12~25 celled stage. Thus, the internode is the last part of the stem whose cell fate is established. This study provides a groundwork to unveil underlying molecular mechanisms in stem development and a useful tool for clonal analysis, which can be applied to various species.
