The early post-pollination phase of maize (Zea mays) development is particularly sensitive to water deficit stress. Using cDNA microarray, we studied transcriptional profiles of endosperm and placenta/pedicel tissues in developing maize kernels under water stress. At 9 d after pollination (DAP), placenta/pedicel and endosperm differed considerably in their transcriptional responses. In placenta/pedicel, 79 genes were significantly affected by stress and of these 89% were up-regulated, whereas in endosperm, 56 genes were significantly affected and 82% of these were down-regulated. Only nine of the stress-regulated genes were in common between these tissues. Hierarchical cluster analysis indicated that different sets of genes were regulated in the two tissues. After rewatering at 9 DAP, profiles at 12 DAP suggested that two regulons exist, one for genes responding specifically to concurrent imposition of stress, and another for genes remaining affected after transient stress. In placenta, genes encoding recognized stress tolerance proteins, including heat shock proteins, chaperonins, and major intrinsic proteins, were the largest class of genes regulated, all of which were up-regulated. In contrast, in endosperm, genes in the cell division and growth category represented a large class of down-regulated genes. Several cell wall-degrading enzymes were expressed at lower levels than in controls, suggesting that stress delayed normal advance to programmed cell death in the central endosperm. We suggest that the responsiveness of placenta to whole-plant stress factors (water potential, abscisic acid, and sugar flux) and of endosperm to indirect factors may play key roles in determining the threshold for kernel abortion.Water deficit during pollination and grain formation causes severe losses in crop production. In maize (Zea mays), the early reproductive stages of kernel development have long been recognized as being particularly vulnerable to water deficit (Claassen and Shaw, 1970); however, the mechanistic bases of cellular response are still not fully understood. Stresses that occur soon after pollination coincide with the period of endosperm cell division. This phase is particularly sensitive to water deficit, whereas later phases of kernel development, when starch and zein synthesis are at their maximum, are usually less affected (Grant et al., 1989; Artlip et al., 1995; Mambelli and Setter, 1998). Water deficit during the first few days after pollination inhibits endosperm cell proliferation, which is well correlated with kernel size at maturity (Nicolas et al., 1985; Ober et al., 1991). During this period, the development of placenta and vascular tissue of the pedicel creates capacity for influx of sugar and signaling molecules. Such development also occurs during the late phases of floral growth, which is also highly sensitive to stresses (Otegui et al., 1995; Edmeades et al., 2000).Previous studies of maize have indicated that reproductive abortion in stress environments involves the plant hormone abscisic a...