1. A B 6 h 24 h 12277 462 Supplemental Fig. S1 Genes that are predominantly expressed in the endosperms of germinating seeds (A). A Venn diagram of endosperm-specific genes at 6 h and 24 h. (B). Temporal expression patterns of the endosperm-specific genes during germination. Expression intensities of 54 out of 59 endosperm-specific genes (the Endo/Emb ratios are more than 50-fold at 24 h) were extracted from the data published in Nakabayashi et al. (2005). Group A, genes up-regulated during germination; Group B, genes with constant expression during germination; Group C, genes down-regulated during germination. The top column indicates hours after the start of seed imbibition: 0, dry seed; 6, 6-h-imbibed seed, 12, 12-h-imbibed seed; 24, 24-h-imbibed seed. A scale of the expression intensity is shown in the right side at bottom. Group AGroup B MIPS code061224MIPS code061224 AT1G73220 340833447064 AT4G08290 2741205528484950 AT5G05290 1222841309215402 AT1G29195 38112371021676 AT1G29080 5332806 AT1G79520 1236229316581459 AT3G44990 2678300611279 AT5G06330 3962390528252496 AT4G34135 42012501665 AT2G43590 2523475025401504 AT4G21490 1718910446546 AT2G27380 26785138591418315611 AT2G27920 1153523387 AT4G15380 6321087854364 AT4G36540 44058151105 AT3G25260 91516941270526 AT1G74670 341193109489152 AT1G71250 8831571883310 AT4G01700 81361324 AT1G43160 32931321111068 AT1G02900 131298271463 AT3G20210 6124515456552 AT1G28650 1328511851255 AT4G12910 16275231580116043 AT1G44800 28114330692297MIPS code061224 AT1G13080 82284444525824 AT2G02930 1679313060120083852 AT3G45010 12517222606341 AT1G14930 197631436481112420 AT4G31330 9734214503312 AT5G59170 2808012976122833239 AT4G01450 15297421164992 AT1G47980 195821012889661518 AT5G17480 41955110 AT3G21370 2739613084110771589 AT2G39420 291800772157075 AT1G14940 278401401894021406 AT3G25290 165189355233211 AT1G14950 30700153017559845 AT4G39950 210491133610 AT2G33070 2657153895350722 AT4G19030 132702702228 AT1G70840 1995154653508468 AT1G09380 1962639663262 AT3G21380 2858572514008583 AT5G39580 13894917412246 AT2G17710 17989010922814 >10,000 AT3G06750 11238011381330 >5,000 AT4G37580 255280027012625 >3,000 AT5G24150 4367277513839 >1,000 AT5G55930 2831983351433 >500 AT1G68510 7954119388 >300 AT2G23620 794163021212902 >100 AT5G43150 919189418262146 <100 Group C Supplemental Fig. S1

2. 6 h24 h FL BF FL BF FL 6 h24 h Supplemental Fig. S2 Flavonol accumulation in Cvi seeds. Dissected endosperm (A) and embryo (B). Left, 6-h imbibed seed; right, 24-h imbibed seed. From top to bottom, DPBA fluorescence (FL), bright field (BF), and DPBA fluorescence (FL) with a larger magnification. Bars in 1 st and 3 rd lines indicate 300  m and 50  m, respectively. Subcellular localization of flavonols in the endosperm. Supplemental Fig. S2 AB

3. Coltt4 FL BF FL BF endosperm embryo Supplemental Fig. S3 Supplemental Fig. S3 DPBA staining in wild-type and tt4 seeds. FL and BF indicates DPBA fluorescence and bright field, respectively. A bar indicates 300  m.

4. Supplemental Fig. S4 6 h24 h Col 6 h24 h Cvi endosperm FL BF embryo FL BF FL BF

5. Supplemental Fig. S4 Non-DPBA-treated seeds. From left to right, 6-h imbibed Columbia seed, 24-h imbibed Columbia seed, 6-h imbibed Cvi seed, 24-h imbibed Cvi seed. From top to bottom, line 1~4 show dissected endosperm and line 5~8 show dissected embryo. Images were obtained under same conditions as Fig. 4 without DPBA staining (FL) or under bright field (BF). Bars in 1 st and 5 th lines indicate 300  m, and bars in 3 rd and 7 th lines indicate 50  m.