Fig. 1

Gene expression pattern of transcription factor, metabolic and signal transduction genes upregulated and downregulated in LM-isolated coleoptiles of rad mutant after 0, 1 and 3 days after complete submergence. Rice seeds (rad mutant and WT) were germinated under complete submergence for 0, 1 and 3 days after imbibition. Coleoptiles were isolated from rice embryo sections by using LM, and then total RNA was extracted from LM-isolated tissues. Quantitative RT-PCR analysis was performed for selected genes with appropriate primers (Additional file 5: Table S1). Upregulated genes in the rad mutant: Os01g0187900 (Similar to Transcription factor MYBS2), Os01g0797600 (ERF3), Os04g0547600 (ERF94), Os01g0826400 (WRKY 24), Os04g0605100 (WRKY 68), Os06g0193400 (PTF/bHLH), Os01g0716500 (methyltransferase type 12 domain containing protein), Os05g0194900 (PPi-PFK) and Os07g0150700 (CIPK23). Downregulated genes: Os02g0739700 (E2F Family domain containing protein), Os05g0512000 (Zinc finger/OsBRCA1), and Os10g054460 (Zinc finger, RING/FYVE/PHD-type domain containing protein). Transcript level of each gene was normalized to the transcript level of rice TF2E (Os10g0397200) gene (used as a control gene). Each data point represents the means ± SD (n = 3)