Information on changes in the plant transcriptome during early interaction with arbuscular mycorrhizal (AM) fungi is still limited since infections are usually not synchronized and plant markers for early stages of colonization are not yet available. A prepenetration apparatus (PPA), organized in epidermal cells during appressorium development, has been reported to be responsible for assembling a trans-cellular tunnel to accommodate the invading fungus. Here, we used PPAs as markers for cell responsiveness to fungal contact to investigate gene expression at this early stage of infection with minimal transcript dilution. PPAs were identified by confocal microscopy in transformed roots of Medicago truncatula expressing green fluorescent protein-HDEL, colonized by the AM fungus Gigaspora margarita. A PPA-targeted suppressive-subtractive cDNA library was built, the cDNAs were cloned and sequenced, and, consequently, 107 putative interaction-specific genes were identified. The expression of a subset of 15 genes, selected by reverse northern dot blot screening, and five additional genes, potentially involved in PPA formation, was analyzed by real-time reverse transcription-polymerase chain reaction and compared with an infection stage, 48 h after the onset of the PPA. Comparison of the expression profile of G. margarita-inoculated wild type and the mycorrhiza-defective dmi3-1 mutant of M. truncatula revealed that an expansin-like gene, expressed in wild-type epidermis during PPA development, can be regarded as an early host marker for successful mycorrhization. A putative Avr9/Cf-9 rapidly elicited gene, found to be up-regulated in the mutant, suggests novel regulatory roles for the DMI3 protein in the early mycorrhization process.Arbuscular mycorrhizal (AM) symbiosis represents a unique interaction between a symbiotic fungus and its host plant. The fungus, an obligate biotroph belonging to Glomeromycota (Schü ßler et al., 2001), is provided by the host plant with carbon sources required to complete its life cycle, whereas it facilitates the plant with the uptake of nutrients, such as phosphate (Smith and Read, 1997). Cellular, physiological, biochemical, and molecular research on mycorrhization is currently performed in many laboratories because positive effects of symbiotic fungi on the metabolism of their host plants are recognized as being beneficial to many ecosystems.The AM-plant associations are a result of a long coevolutionary process (Karandashov and Bucher, 2005) that required profound morphological readjustments in the plant to accommodate the fungus and to facilitate the exchange of nutrients between the two partners. In both epidermal and cortical cells, the fungus is surrounded by a membrane of host origin. The formation of this apoplastic interface causes a dramatic structural re-organization of the plant cells with all their organelles (Bonfante, 1984;Bonfante and Perotto, 1995).Development of new technological (in vivo confocal microscopy) and molecular (transformed plants expressing GUS or GFP marke...