During the early stages of Arabidopsis seed development, the endosperm is syncytial and proliferates rapidly through multiple rounds of mitosis in the absence of cytokinesis and cell wall formation. This stage of endosperm development is important in determining seed viability and size. To identify genes involved in syncytial endosperm development, we analyzed the endosperm transcriptome, obtained using laser capture microdissection of developing seeds at four days after pollination. Our results support the idea that similar sets of genes are required for conventional somatic mitosis with cytokinesis and syncytial proliferation. Furthermore, we identify cytoskeleton associated genes that may act to facilitate syncytial development thereby providing an important resource for further characterization of the processes involved in syncytial endosperm development.Seed development begins with double fertilization where the haploid egg cell and the double haploid central cell are both fertilized by haploid sperm cells contributed from a single pollen grain. This generates the diploid embryo and the triploid endosperm, respectively. The embryo and the endosperm grow rapidly in a coordinated manner that is influenced by the surrounding maternal integument tissues that later form the seed coat. During these early stages, maternal resources are used for the rapid cell division and growth that occurs as seed tissues form and develop. In many plant species, including Arabidopsis, the triploid primary endosperm nucleus undergoes several rounds of free-nuclear division, growing rapidly as a syncytium. The organization of microtubule arrays during this early stage of endosperm development is markedly different from those found in vegetative tissues.1 During the syncytial phase, interphase microtubules emanate from the nucleus into the cytoplasm and this nucleus-based radial microtubule system aids in positioning of nuclei and the designation of cytoplasm into nucleo-cytoplasmic domains. At about six days after pollination, cell wall deposition is initiated by the formation of phragmoplasts at the margins of nucleocytoplasmic domains. Interestingly, interzonal arrays which resemble phragmoplasts form between nuclei after karyokinesis, but they never participate in cell plate formation.2 This unusual form of cellular development is conducive to a rapid cellular proliferation; however, the molecular mechanisms that underlie the uncoupling of cell wall formation from mitosis remain elusive.To gain further insights into the early stages of endosperm biology, we have used laser capture microdissection to obtain RNA from syncytial stage endosperm at four days after pollination. At this stage of development, the endosperm has undergone six to seven rounds of nuclear division (~200 nucleocytoplasmic domains) but has not cellularized and the embryo is at the globular phase. Endosperm RNA was amplified using two-round in vitro transcription, then labeled and used, along with similarly treated silique amplified RNA, to probe long oligonucl...