Supplemental Data

Files in this Data Supplement:

• Supplemental Table 1 - Genes whose function has been previously experimentally addressed and are expressed specifically in the embryo or endosperm one day after imbibition. To qualify, genes must be called present in one tissue, but called absent in at least two of the three replicates in the other by MAS5. Values represent the mean and standard error of expression in the three replicate experiments.
• Supplemental Table 2 - Expression of genes involved in lipid storage reserve mobilization in Arabidopsis. Abbreviations: CTS – comatose; KAT - 3-L-ketoacyl-CoA thiolase; MFP –Multifunctional Protein; ACX –acyl-CoA oxidase; LACS –long chain acyl-CoA synthetase; CSY – citrate synthase; ICL – isocitrate lyase; MDH – malate dehydrogenase; MLS – malate synthase; PCK – phosphorenolpyruvate carboxykinase.
• Supplemental Table 3 - The identification of a core set of ABA responsive probesets in embryo, endosperm (both this study), 24h imbibed seeds and 7 day old seedlings. A. 8 probesets two-fold or greater repressed by ABA in all tissues. B. 52 probsets two-fold or greater up-regulated by ABA in all tissues. C. The expression ratio in dry seed (abi4-1 and abi5-1; data from Nakabayashi et al., 2005) or imbibed seed (abi3; http://affymetrix.arabidopsis.info/narrays/experimentbrowse.pl) of the identified core set of ABA responsive probes in abi3-4, abi4-1 and abi5-1 versus wild type. Boxed cells indicate those probesets whose expression is twofold or more increased in the abi mutants compared to wild type for ABA repressed genes, or those probesets twofold or greater decreased in the abi mutants compared to wild type for the ABA induced genes.
• Supplemental Table 4 - Cell wall modifying genes expressed in the endosperm during germination and their regulation by PAC and ABA. Inhibition of expression by ABA and PAC was determined by SAM analysis at an FDR of 1% (see methods). Only genes with mean expression >50 are shown. ¹xyloglucan endotransglycosidase.
• Supplemental Figure 1 - The MapMan visualization tool’s overview of the differences in metabolism related gene expression between embryo and endosperm one day after imbibition. Scale refers to the natural log ratio of the mean of three embryo experiments versus the mean of three endosperm experiments. Blue- expression increased in endosperm relative to embryo; red- expression increased in embryo relative to endosperm. Highlighted bins indicate pathways involved in the flow of carbon in the endosperm from oil bodies to sucrose synthesis and export to the embryo. 1. β-oxidation. 2. glyoxylate cycle/gluconeogenesis. 3. TCA cycle. 4. glycolysis (operating in reverse). 5. sucrose synthesis. 6. carbohydrate transporters.
• Supplemental Figure 2 - The MapMan metabolism visualization tool’s overview of the differential affect of applied ABA on the transcriptome of the embryo (A) and endosperm (B). Scale refers to the natural log ratio of the mean of three control versus three ABA treated samples. Red – repressed by ABA; blue –induced by ABA. The five most significantly differentially regulated bins are highlighted: 1. Photosynthetic reaction centres. 2. Calvin cycle. 3. cellulose synthesis. 4. tetrapyrolle biosynthesis. 5. Fatty acid synthesis and elongation. Also highlighted in yellow is the bin for oleosins (6), induced by ABA in both embryo and endosperm.
• Supplemental Figure 3 - The embryo and endosperm eicosenoic acid content five days after imbibition on control media, 20μM ABA or 400mM mannitol. Data points represent mean and standard deviation of four replicate determinations.