We describe mutations of three genes in Arabidopsis thaliana-extra cotyledon1 (xtc1), extra cotyledon2 (xtc2), and altered meristem programming1 (amp1)-that transform leaves into cotyledons. In all three of these mutations, this transformation is associated with a change in the timing of events in embryogenesis. xtc1 and xtc2 delay the morphogenesis of the embryo proper at the globular-to-heart transition but permit the shoot apex to develop to an unusually advanced stage late in embryogenesis. Both mutations have little or no effect on seed maturation and do not affect the viability of the shoot or the rate of leaf initiation after germination. amp1 perturbs the pattern of cell division at an early globular stage, dramatically increases the size of the shoot apex and, like xtc1 and xtc2, produces enlarged leaf primordia during seed development. These unusual phenotypes suggest that these genes play important regulatory roles in embryogenesis and demonstrate that the development of the shoot apical meristem and the development of the embryo proper are regulated by independent processes that must be temporally coordinated to ensure normal organ identity.Embryogenesis in seed plants consists of several discrete processes (1-4). During the early, morphogenetic phase of embryogenesis, the primary axis of the plant is established, one or more cotyledons are formed, and the primordia of the root and shoot systems are initiated. The embryo subsequently undergoes a process of maturation in which it acquires the capacity for autonomous growth, accumulates nutritional reserves, becomes desiccation tolerant, and then enters a period of dormancy. Upon germination, the seedling uses its stored reserves, and the shoot and root meristems resume growth. Recent work has shown that although these events usually occur in a predictable temporal sequence, they are not part of a linear developmental pathway (4). For example, in several species, precocious germination leads to the simultaneous expression of genes that are normally expressed only during embryo maturation and genes that are normally expressed only during germination (reviewed in ref. 1). Similarly, the leafy cotyledon1-2 mutation in Arabidopsis causes plants to express germination-specific genes without completely suppressing the expression of a storage protein gene that is normally expressed during the maturation phase of embryogenesis (5). Conversely, the raspberry mutant of Arabidopsis thaliana is blocked at a globular stage of embryogenesis, but expresses genes that are normally activated much later (6).To study how morphogenetic events are temporally coordinated during embryogenesis, we screened for mutations of A. thaliana that mimicked the cotyledon-leaf phenotype of precociously germinated Brassica napus embryos (7, 8). We identified three mutations that have this phenotype. Here we describe the effect of these mutations on the morphogenesis of the embryo and provide evidence that the effect of these mutations on leaf identity is the result of a change i...