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 A Group BMIPS code 0 6 12 24 MIPS code 0 6 12 24

AT1G73220 3 408 3344 7064 AT4G08290 2741 2055 2848 4950

AT5G05290 12 2284 13092 15402 AT1G29195 381 1237 1021 676

AT1G29080 5 3 3 2806 AT1G79520 1236 2293 1658 1459

AT3G44990 26 78 3006 11279 AT5G06330 3962 3905 2825 2496

AT4G34135 4 201 250 1665 AT2G43590 2523 4750 2540 1504

AT4G21490 17 189 1044 6546 AT2G27380 26785 13859 14183 15611

AT2G27920 11 5 352 3387 AT4G15380 632 1087 854 364

AT4G36540 4 405 815 1105 AT3G25260 915 1694 1270 526

AT1G74670 34 1193 10948 9152 AT1G71250 883 1571 883 310

AT4G01700 8 13 6 1324 AT1G43160 3293 132 111 1068

AT1G02900 13 129 827 1463

AT3G20210 61 245 1545 6552

AT1G28650 13 285 1185 1255

AT4G12910 162 7523 15801 16043

AT1G44800 28 1143 3069 2297 MIPS code 0 6 12 24

AT1G13080 82 2844 4452 5824 AT2G02930 16793 13060 12008 3852

AT3G45010 125 172 2260 6341 AT1G14930 19763 14364 8111 2420

AT4G31330 97 342 1450 3312 AT5G59170 28080 12976 12283 3239

AT4G01450 152 974 2116 4992 AT1G47980 19582 10128 8966 1518

AT5G17480 4 19 55 110 AT3G21370 27396 13084 11077 1589

AT2G39420 291 8007 7215 7075 AT1G14940 27840 14018 9402 1406

AT3G25290 165 1893 5523 3211 AT1G14950 30700 15301 7559 845

AT4G39950 210 49 113 3610 AT2G33070 26571 5389 5350 722

AT4G19030 132 70 270 2228 AT1G70840 19951 5465 3508 468

AT1G09380 196 263 966 3262 AT3G21380 28585 7251 4008 583

AT5G39580 138 949 1741 2246

AT2G17710 179 890 1092 2814 　 >10,000

AT3G06750 112 380 1138 1330 　 >5,000

AT4G37580 255 2800 2701 2625 　 >3,000

AT5G24150 436 727 751 3839 　 >1,000

AT5G55930 283 198 335 1433 　 >500

AT1G68510 79 54 119 388 　 >300

AT2G23620 794 1630 2121 2902 　 >100

AT5G43150 919 1894 1826 2146 　 <100

Group C

Supplemental Fig. S1

6 h 24 h

FL

BF

FL

BF

FL

FL

6 h 24 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 1st and 3rd lines indicate 300 m and 50 m, respectively. Subcellular localization of flavonols in the endosperm.

Supplemental Fig. S2

A B

Col tt4

FL

BF

FL

BF

end

osp

erm

emb

ryo

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.

Supplemental Fig. S4

6 h 24 h

Col

6 h 24 h

Cvien

do

sper

m

FL

BF

emb

ryo

FL

BF

FL

FL

BF

BF

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 1st and 5th lines indicate 300 m, and bars in 3rd and 7th lines indicate 50 m.