Red light induction of IR is misregulated in the phytochrome-deficient and -knockout mutants. (A) Expression profiles of top 1,000 red light-regulated IR isoforms and total transcripts of corresponding genes in wild type (WT) and pubs hy2 mutant are shown. IR level (IR) and corresponding gene expression level (Gene expression) for the top 1,000 IR events were normalized by mean across WT and mutant samples. Heat maps of these events in dark-grown (D) and 1-h red light-treated (R1) samples are generated. Events were arranged according to the fold-change of IR level comparing 1-h red light-treated to dark-grown samples in WT. The scale of expression is shown in the bottom. (B) IR of PpRPP3A and PpSCL42 in WT and phytochrome-knockout mutants. Quantitative RT-PCR analysis of IR level in samples from WT and four phytochrome-knockout mutants (phy1, phy2, phy3, phy4) grown under dark (D), 1-h (R1), and 4-h (R4) of red light. Both genes were tested in triplicate with primer sets designed for IR isoforms, total transcripts of the corresponding genes, and PpACT2 (see Additional file 7).