Figure 3.

Blocking auxin responses in the epidermis feeds back onto auxin production and gene expression. (A) Levels of free IAA in 5-d-old white light-grown Arabidopsis seedlings. Data show mean ± SEM. (**) P < 0.005; (ns) not significant, Student's t-test. (B) Box plots showing gene expression values (left) and fold change in shade (right) of 5-d-old white (W) light-grown seedlings treated for 4 h of white light or shade measured by RNA sequencing (RNA-seq). Seedlings were either hemizygous for the UAS::axr3-1::mCit transgene only (control) or expressed axr3-1::mCit under the CER6pro (hemizygous for both UAS::axr3-1::mCit and CER6pro::GAL4::VP16 transgenes). Of 104 previously identified shade-induced, SAV3-dependent genes (Li et al. 2012), 12 were significantly up-regulated by shade in our control. P < 0.005, one-sided Fisher's exact test. Expression values for these 12 genes are shown. (**) P < 0.005; (ns) not significant, Student's t-test. (C) Same as in B, except showing SAV3-independent shade-induced genes (20 of 40 such genes were significantly induced by shade in our control). P < 0.005, one-sided Fisher's exact test. (D) Same as in B, except showing BR genes. Of 1005 genes previously identified as BR-activated (Sun et al. 2010), 46 were significantly induced by shade in our control and are shown here. P < 0.005, one-sided Fisher's exact test. Of these, three were also classified as SAV3-dependent genes, and two were classified as SAV3-independent genes.