The main goal of our research is to identify molecular mechanisms underlying the establishment of the basic body organization in the Arabidopsis early embryo. The asymmetric division of the zygote generates a small apical (embryogenic) cell and a large basal (extra-embryogenic) cell that differ from one another in gene expression, cell division pattern and developmental fate. How these differences are initially set up is analyzed from several perspectives. One approach makes use of fluorescent markers that are differentially expressed between the two cell lineages and enables sorting of nuclei followed by expression profiling. This is to yield inventories of genes that are specifically expressed in the embryonic or extra-embryonic lineages, and to eventually lead to the identification and functional analysis of relevant transcriptional regulators. Another approach focuses on the role of auxin response in early embryogenesis, notably in cell-communication resulting in cell fate specification events. A well known example is the interaction of ARF transcription factor MP and its AUX/IAA inhibitor BDL in the embryonic lineage. This interaction regulates auxin transport via the efflux carrier PIN1 to the future basal pole and activates the expression of a mobile transcription factor TMO7, both of which together mediate the specification of the founder cell for the root stem-cell system (Schlereth et al., 2010). A different auxin-response machinery acts in the basal lineage, and one of the challenges is to analyze how the two systems are initially set up and how they might be interrelated. Finally, the goal is to determine when and how the initial apical-basal polarity of the embryo is established.