To establish a rapid high-throughput evaluation system for the enhanced plant growth-inhibitory activity caused by modifications of cis-cinnamic acid’s (cis-CA’s) chemical structure, a DNA microarray assay was used to analyze the changes in early gene responses of Arabidopsis thaliana seedlings. After a 6-hr exposure to (Z)-3-(3-iodophenyl)acrylic acid, we observed an upregulation in three classes of early auxin-responsive genes, which was similar to the transcriptional response to indole-3-acetic acid (IAA), together with an upregulation of the genes related to environmental stress and toxin detoxification responses. Gene responses to 2-(3,4-dihydronaphthalen-1-yl)acetic acid were similar to those to IAA. In contrast, fewer genes were upregulated in response to its double-bond isomer, (Z)-2-[3,4-dihydronaphthalen-1(2H)-ylidene]acetic acid, than to cis-CA. DNA microarray data suggest that the structurally different cis-CA analogues trigger diverse gene responses.
