Details of methods: Rice (Oryza sativa L. japonica cv. Nipponbare) plants were grown in a paddy field under normal conditions. Ovaries at 2, 3 and 4 days after pollination (DAP)

were collected and fixed in 75% ethanol and 25% aceate. Each sample was embedded in paraffin, cut into 10 µm sections with a microtome, and used for laser microdissection.

For ‘Temporal sub-dataset’, the entire embryonic tissue at 2, 3 and 4 DAP was collected by laser microdissection (Figure 1). For ‘Spatial sub-dataset’, 3 DAP embryos were separated into 2 parts along the apical-basal axis and the

dorsal-ventral axis of the embryo by laser microdissection (Figure 2).

Figure 1. Tissues of embryos collected by laser microdissection for temporal sub-dataset. A: Mature embryo; B: 2DAP embryo; C: 3DAP embryo; D: 4DAP embryo. Yellow dotted lines indicate regions dissected in this analysis. Arrow in the panel A and

D indicates shoot apical meristem. Black and white arrowheads in the panel D indicate primordium of the coleoptile and the radicle, respectively. SC: Scutellum; CO: Coleoplile; EP: Epiblast; RA: Radicle. Figures are reproduced

with permission from Itoh et al. (2005).

B C D A

Figure 2. Tissues of 3DAP embryos collected by laser microdissection for spatial sub-dataset.

Yellow dotted lines indicate regions dissected in this analysis. A: Apical region; B: Basal region; C: Ventral region; D: Dorsal region. Figures are reproduced with permission from Itoh et al. (2005).

B C D A