lsoflavonoids and steady-state mRNA levels of phenylalanine ammonia-lyase, chalcone isomerase, and isoflavone reductase were followed during a rapid, nearly synchronous infection of alfalfa (Medicago sativa L.) roots by the vesicular arbuscular fungus Glomus intraradices (Schenck & Smith) to test whether previously indicated suppression of the host defense response is regulated by changes in the steady-state mRNA level. Relative amounts of steadystate phenylalanine ammonia-lyase mRNA in the mycorrhizal roots doubled between d 14 and 18 and then immediately declined by 75% to reach and maintain a value lower than the control roots through d 21. Relative levels of chalcone isomerase mRNA in the inoculated roots increased 6-fold between d 14 and 17 and then decreased rapidly to the control level. lsoflavone reductase mRNA was not induced by mycorrhizal colonization. High-performance liquid chromatography, proton-nuclear magnetic resonance, and fast atom bombardment-mass spectrometry analyses showed consistent increases in formononetin levels and transient increases in medicarpin-3-Oglycoside and formononetin conjugates i n the inoculated roots when colonization began. As colonization increased, levels of formononetin conjugates declined in mycorrhizal roots below those i n uncolonized controls. Medicarpin aglycone, an alfalfa phytoalexin normally associated with pathogenic infections, was not detected at any stage. These findings supply detailed evidente that, during early colonization of plant roots by symbiotic Clomus, defense transcripts are induced and then subsequently suppressed.Plants are exposed in nature to a wide range of potentially pathogenic fungi and bacteria. Microbial plant pathogens do not generally infect a plant successfully, either because the plant is not a host species or because it is resistant to the pathogen (Koes et al., 1994). ln most cases plant resistance is associated with a hypersensitive response that is characterized by rapid, localized chemical defenses and death of plant cells surrounding the infection site (Meier et al., 1993). Most of these responses are regulated at the level of RNA transcription (Collinge and Slusarenko, 1987; Dixon and Lamb, 1990). In such interactions, the pathogens are usually sensitive to plant defense mechanisms. Alfalfa (Medicago sativa) is a host for various funga1 pathogens (Graham et al., 1979) of the isoflavonoid phytoalexin medicarpin may be involved in resistance to these pathogens (Latunde-Dada and Lucas, 1985; Dixon, 1986). The biosynthetic pathway of medicarpin is well defined (Phillips and Kapulnik, 1995), and activity of severa1 enzymes involved is regulated at the level of RNA transcription (Dixon et al., 1992). VA fungi are obligate symbionts that form mycorrhizae with alfalfa roots. Although pathogenic biotrophs generally exhibit a high degree of host specificity, VA fungi show little to none. Indeed, mycorrhizae occur in approximately 80% of a11 plants (Bonfante-Fasolo, 1987), and VA fungi do not induce typical defense responses in host p...