Supplementary Table S1: Different Tissues of Plant Life Cycle Used for Microarry Analysis

Supplementary Table S1: Different Tissues of Plant Life Cycle Used for Microarry Analysis

Supplementary Table S1 Different tissues of plant life cycle used for microarry analysis

Sample No. / Developmental stage / Tissue / Treatment
1 / embryo and radicle after germination / calli
2 / 15 days after subculture / calli
3 / screening stage / resistant calli
4 / 5 days after regeneration / calli
5 / 72h after imbibition / seed
6 / root and leaf at three leave stage / seedling
7 / 5 days before heading / leaf
8 / seedling with 2 tillers / root
9 / 5 days before heading / stem
10 / 5 days before heading / flag leaf
11 / heading stage / stem
12 / heading stage / panicle
13 / 14 days after heading / flag leaf
14 / young panicle at stage 3 / leaf
15 / young panicle at stage 3 / sheath
16 / young panicle at stage 3 / panicle
17 / young panicle at stage 4 / panicle
18 / young panicle at stage 5 / panicle
19 / 4-5cm young panicle / leaf
20 / 4-5cm young panicle / sheath
21 / 4-5cm young panicle / panicle
22 / one day before flowering / hull
23 / one day before flowering / stamen
24 / 3 days after pollination / spikelet
25 / 7 days after pollination / endosperm
26 / 14 days after pollination / endosperm
27 / 21 days after pollination / endosperm
28 / trefoil stage, mixture of 5,15,30,60 min after treatment / seedling / GA3
29 / trefoil stage, mixture of 5,15,30,60 min after treatment / seedling / NAA
30 / trefoil stage, mixture of 5,15,30,60 min after treatment / seedling / KT
31 / 48h after emergence / plumule / light
32 / 48h after emergence / radicle / light
33 / 48h after emergence / plumule / dark
34 / 48h after emergence / radicle / dark

Supplementary Table S2 Gene primers used for RT-PCR

Gene name / Forward primer (5'–3') / Reverse primer (5'–3')
OsTrx1 / TGGGAAAGGAACGCAGTG / TGCTGGCAACGTCTGAAC
OsTrx2 / GCCCTCGTCGAGTTCTA / CCGCCATCGTAATCTTC
OsTrx3 / GGAGGTGAACAAGGATAC / TCATGACGTTGGAAATAG
OsTrx4 / AGGCGATAAGATTCAAGT / TAAATGGTGCCCAGAGGT
OsTrx5 / CCGTCCTTAGTCCTGCTC / GTTCCTGACAATGCCCAC
OsTrx6 / TGAGCCCATCATAGTTGCC / GAAGCAGGGATTGCCGTAT
OsTrx7 / TCTCAGGGTGCTTTCCAG / GGAGCCCTTGTTCTTGGT
OsTrx9 / GAAGCGAAGAGGAGCAAG / GGGATTTAGGATGAGGAGG
OsTrx13 / TGGTGTTTGGGTATGTCG / CAGGTCCTTCAGGATTGC
OsTrx14 / TCCTTGTTGGATACTGGGCTAC / AGGCTTCCTTGCGACTTTCA
OsTrx17 / GCCGTGATTCAAAGGGTC / ATGCCGGGCAGTGGGATA
OsTrx18 / CCTCATTTGGTGGGATT / TCGACCTGCTTCTCGTT
OsTrx19 / AAGGCCCATGCAGCCGTCT / ATGTGCTGGATAGCCCTGAG
OsTrx20 / CTCTTGCAGAGTGGAG CAGA / TCAGTAGAATGAGCTCTC
OsTrx22 / CCGCAATCCGAGTCATC / CGTCAGCTCCACGGTAA
OsTrx23 / ATCGCCTGCCACAACAAG / ACACCCAAGCCAAACTGA
OsTrx24 / AAGCGAAGAGGAGCAAG / GGATTTAGGATGAGGAGGAT
OsTrx25 / CAGGATAGGATTATCTCTCC / ATCGCTAGGATATAGGGACA
OsTrx30 / TGCTGGTGCCAAGAAGA / CAAACATCCGAAGACTGA
Actin / TGCTATGTACGTCGCCATCCAG / AATGAGTAACCACGCTCCGTCA

Supplementary TableS3 General information about Trx protein–encoding genes in rice

Gene name / TIGR locus / Genomic locusa / Nearest markerb / Fl-cDNA Accession No.c / Deduced polypeptided / Trx domaine
BAC/PAC / Accession no. / cM position / Length / MW / PI
OsTrx01 / Os01g07376 / OJ1276_B06 / AP003339 / 16.1 / R1613 / AK103756 / 132 / 14.67 / 4.64 / 1
OsTrx02 / Os01g23740 / B1088D01 / AP003331 / 69.3 / S11337 / AK066111 / 372 / 40.74 / 6.86 / 2
OsTrx03 / Os01g68480 / P0470A12 / AP003436 / 157.6 / L1082 / AK101264 / 188 / 19.74 / 8.76 / 1
OsTrx04 / Os01g73234 / P0483G10 / AP003263 / 176.3 / R117 / AK062343 / 169 / 18.18 / 9.78 / 1
OsTrx05 / Os02g01010 / OSJNOa183H18 / AP006851 / 0.111 / C135 / AK071514 / 562 / 62.13 / 4.76 / 2
OsTrx06 / Os02g34530 / OSJNBa0084A10 / AL606458 / 62.6 / R2406 / AK069367 / 426 / 47.10 / 4.47 / 1
OsTrx07 / Os02g34940 / P0470G10 / AP004876 / 81.7 / R447 / AK072252 / 546 / 59.60 / 4.52 / 2
OsTrx08 / Os02g42700 / P0408D11 / AP004788 / sequencing in progress / NF / AK099517 / 174 / 16.39 / 5.30 / 1
OsTrx09 / Os03g17860 / OSJNBb0022M22 / AC137074 / 44.4 / C12534S / AK063663 / 148 / 16.28 / 5.07 / 1
OsTrx10 / Os03g58630 / OSJNBa0052F07 / AC104321 / 151.5 / C50771S / AK062383 / 135 / 14.79 / 5.47 / 1
OsTrx11 / Os04g35150 / OSJNBa0084A10 / AL606458 / 62.6 / R2406 / NF / 267 / 29.93 / 9.78 / 1
OsTrx12 / Os04g35290 / OSJNBa0084A10 / AL606458 / 62.6 / R2406 / AK069367 / 424 / 47.05 / 4.57 / 1
OsTrx13 / Os04g35600 / OSJNBa0006B20 / AL606592 / 65 / R2921 / AK101074 / 518 / 57.33 / 4.43 / 2
OsTrx14 / Os04g44830 / OSJNBa0081C01 / AL662984 / 81.7 / R374 / AK069195 / 181 / 19.14 / 9.25 / 1
OsTrx15 / Os04g53740 / OSJNBa0089N06 / AL662988 / 109.9 / R78 / AK121437 / 134 / 14.67 / 4.51 / 1
OsTrx16 / Os04g57930 / OSJNBa0064G10 / AL606668 / 128.5 / C107 / NF / 181 / 19.12 / 8.47 / 1
OsTrx17 / Os05g06430 / P0431G05 / AC087551 / 27.7 / R1838 / AK099341 / 368 / 40.05 / 7.00 / 2
OsTrx18 / Os05g07690 / P0419C04 / AC084817 / 31.5 / E61210S / AK060918 / 133 / 14.81 / 5.79 / 1
OsTrx19 / Os05g11090 / OSJNBa0017O06 / AC136520 / 42.2 / E11303S / AK099199 / 217 / 23.79 / 8.96 / 1
OsTrx20 / Os05g40190 / OSJNBa0018K15 / AC144737 / 96.4 / R2117A / AK071198 / 136 / 15.25 / 4.13 / 1
OsTrx21 / Os06g06790 / P0681F10 / AB026295 / 12.3 / E10921 / AK073970 / 534 / 59.03 / 4.59 / 2
OsTrx22 / Os06g45510 / P0473H04 / AP003628 / 105.6 / E4392S / NF / 175 / 18.68 / 9.91 / 1
OsTrx23 / Os07g08840 / P0506C07 / AP004384 / 35.7 / R2401 / AK121423 / 123 / 13.15 / 4.94 / 1
OsTrx24 / Os07g09310 / OSJNBb0003E08 / AC104321 / 38.4 / S4774 / AK062383 / 139 / 14.89 / 5.00 / 1
OsTrx25 / Os08g29110 / OSJNBb0011E04 / AP005443 / 60.4 / E61839S / AK066851 / 190 / 20.52 / 4.86 / 1
OsTrx26 / Os09g23650 / P0650H04 / AP005321 / 49.3 / R1751 / AK063980 / 318 / 34.98 / 6.03 / 1
OsTrx27 / Os09g27830 / OJ1163_C07 / AP005559 / 62.4 / C1227 / AK062254 / 442 / 47.33 / 5.25 / 2
OsTrx28 / Os11g09280 / OSJNBa0058P12 / AC139170 / 27.8 / S20163S / AK068268 / 513 / 56.85 / 4.76 / 2
OsTrx29 / Os12g08730 / OSJNBa0042N11 / AL954157 / 30.0 / G124A / AK061678 / 173 / 18.52 / 8.05 / 1
OsTrx30 / Os12g18360 / OJ1115_G02 / AL772419 / 50.4 / C53024S / AK071926 / 1034 / 11.69 / 6.96 / 1

a Name, accession number, and approximate cM position of BAC/PAC clone in which the Trx protein–encoding gene.

b Nearest marker to the Trx protein–encoding gene.

c Corresponding full-length cDNA is available or not; NF, not found.

d Length (number of amino acids), molecular weight (kDa), and isoelectric point (PI) of the deduced polypeptide.

e Trx domain of Trx protein–encoding genes.

Note. Accession no. (AK062383) is same as two LOC_ (Os03g58630 and Os07g09310)

Supplementary Table S4 Putative type and subcellualar location of OsTrx gene family

Type of Thioredoxin / TIGR ID / Gene name / Subcellular location
M / Os02g42700 / OsTrx8 / chlo: 14.0
M / Os04g44830 / OsTrx14 / chlo: 14.0
M / Os12g08730 / OsTrx29 / chlo: 11.0, vacu: 2.0
M / Os04g35150 / OsTrx11 / chlo: 12.0, mito: 2.0
X / Os01g73234 / OsTrx4 / chlo: 14.0
X / Os04g57930 / OsTrx16 / chlo: 14.0
X / Os08g29110 / OsTrx25 / chlo: 14.0
F / Os05g11090 / OsTrx19 / chlo: 12.0, mito: 1.0, cyto 1.0
F / Os01g68480 / OsTrx3 / chlo: 14.0
F / Os06g45510 / OsTrx22 / chlo: 9.0, mito: 5.0
H / Os01g07376 / OsTrx1 / cyto:8.5.0, 2.5, nucl: 2.5, chlo: 2.0, extr: 2.0
H / Os05g07690 / OsTrx18 / nucl: 7.5, cyto: 5.0, nucl: 1.5
H / Os05g40190 / OsTrx20 / chlo: 7.0, cyto: 4.0, extr: 3.0
H / Os04g53740 / OsTrx15 / chlo: 11.0, cyto: 2, mito: 1.0
H / Os07g08840 / OsTrx23 / cyto: 11.0, chlo: 2.0
H / Os12g18360 / OsTrx30 / cyto: 7.0, chlo: 5.0, nucl: 1.0
H / Os09g23650 / OsTrx26 / nucl: 8.0, cyto: 3.0,extr: 3.0
H / Os03g58630 / OsTrx10 / cyto: 8.0, extr: 5.0
H / Os07g09310 / OsTrx24 / chlo: 8.0, cyto: 4.0, mito: 1.0
PDIL1-3 / Os02g34940 / OsTrx7 / chlo: 12.0, mito: 2.0
PDIL1-2 / Os04g35600 / OsTrx13 / chlo: 4.0, extr: 4.0, E.R.: 3.0, vacu: 2.0
PDIL1-1 / Os11g09280 / OsTrx28 / chlo: 10.0, nucl: 1.0, extr: 1.0, vacu: 1.0
PDIL5-3 / Os02g34530 / OsTrx6 / extr: 7.0, chlo: 2.0, cyto: 2.0, golg: 2.0
PDIL5-2 / Os04g35290 / OsTrx12 / plas: 10.0, vacu: 2.0, E.R.: 2.0
PDIL1-4 / Os02g01010 / OsTrx5 / chlo: 7.0, extr: 2.0, E.R.: 2.0, nucl: 1.0, mito: 1.0
PDIL1-5 / Os06g06790 / OsTrx21 / chlo: 11.0, E.R.: 2.0
PDIL2-3 / Os09g27830 / OsTrx27 / chlo: 4.0, vacu: 4.0, extr: 3.0, mito: 2.0
PDIL2-2 / Os01g23740 / OsTrx2 / chlo: 4.0, extr: 3.0, vacu: 3.0, nucl: 1.0, mito: 1.0, plas: 1.0
PDIL2-1 / Os05g06430 / OsTrx17 / chlo: 11.0, nucl: 1.0, mito: 1.0

cyto, chytosol; chlo, chloroplast; mito, mitochondria; nucl, nucleus; E.R. endoplasmic reticulum. plas, plastid; golg, golgi apparatus; vacu, cacuole; extr, extra

Supplementary Table S6 The average signal values (two biological repeats) of 29 Trx protein–encoding genes differentially expressed seedling, at trefoil stage under different hormonal treatment conditions in the three cultivars.

Gene name / Probe sets / Minghui 63 / Shanyou 63 / Zhenshan 97
Control / GA3 / NAA / KT / Control / GA3 / NAA / KT / Control / GA3 / NAA / KT
OsTrx01 / Os.16494.1.S1_at / 1206 / 707 / 729 / 678 / 1214 / 599 / 672 / 558 / 664 / 599 / 525 / 388
OsTrx02 / Os.17269.1.S1_at / 4123 / 5196 / 5729 / 5387 / 3728 / 5795 / 5495 / 5689 / 4547 / 6046 / 6061 / 5697
OsTrx03 / Os.9880.1.S1_a_at / 30500 / 10205 / 10743 / 12101 / 27586 / 10753 / 10220 / 10885 / 23517 / 7960 / 7036 / 7537
OsTrx05 / Os.13477.1.S1_at / 711 / 1034 / 988 / 1047 / 754 / 1253 / 1278 / 1127 / 739 / 1137 / 975 / 1013
OsTrx06 / OsAffx.12349.1.S1_at / 48 / 27 / 11 / 15 / 19 / 18 / 13 / 4 / 79 / 11 / 11 / 28
OsTrx07 / Os.53357.1.S1_at / 93 / 106 / 109 / 112 / 91 / 132 / 128 / 183 / 146 / 106 / 99 / 85
OsTrx08 / Os.37995.1.S1_at / 2217 / 2364 / 2766 / 2744 / 1890 / 2303 / 2651 / 2265 / 1876 / 4237 / 2930 / 2538
OsTrx09 / Os.51769.1.S1_at / 2921 / 3029 / 2586 / 2440 / 3096 / 3173 / 2940 / 3234 / 3115 / 3933 / 2991 / 2921
OsTrx10 / Os.12826.1.S1_at / 8387 / 5313 / 5733 / 5960 / 9765 / 6681 / 6333 / 6891 / 8598 / 6646 / 5234 / 4638
OsTrx11 / OsAffx.14142.1.S1_at / 286 / 249 / 256 / 205 / 264 / 207 / 241 / 276 / 215 / 201 / 237 / 248
OsTrx12 / Os.9630.1.S1_at / 1375 / 1285 / 1082 / 770 / 954 / 1077 / 865 / 906 / 980 / 1007 / 874 / 878
OsTrx13 / Os.53966.1.S1_at / 126 / 105 / 127 / 118 / 125 / 169 / 138 / 156 / 81 / 165 / 223 / 186
OsTrx14 / Os.7403.1.S1_at / 6716 / 5463 / 5257 / 6292 / 4854 / 5200 / 4968 / 5298 / 4498 / 4900 / 4328 / 4220
OsTrx15 / Os.10512.1.S1_at / 8417 / 7494 / 7465 / 8315 / 7044 / 5689 / 5912 / 5760 / 6351 / 9879 / 7809 / 7030
OsTrx16 / OsAffx.14459.1.S1_at / 4752 / 3997 / 3537 / 4232 / 2674 / 2812 / 2451 / 2667 / 2981 / 2714 / 2921 / 3368
OsTrx17 / Os.39053.1.A1_s_at / 6067 / 4633 / 4771 / 3865 / 6646 / 5243 / 5196 / 4777 / 7076 / 4974 / 5392 / 4666
OsTrx18 / Os.35448.1.S1_at / 62 / 89 / 59 / 92 / 65 / 89 / 73 / 66 / 57 / 16 / 55 / 74
OsTrx19 / Os.17917.1.S1_at / 1476 / 3003 / 3716 / 3807 / 1414 / 2883 / 2911 / 2894 / 1364 / 4158 / 2726 / 3174
OsTrx20 / Os.51130.1.S1_at / 1316 / 1766 / 1774 / 1924 / 1493 / 1527 / 1713 / 1436 / 1360 / 2305 / 1714 / 1801
OsTrx21 / Os.4371.1.S1_a_at / 733 / 517 / 490 / 477 / 846 / 654 / 647 / 682 / 777 / 501 / 585 / 524
OsTrx22 / OsAffx.15938.1.S1_s_at / 905 / 1589 / 1799 / 1811 / 930 / 1687 / 1715 / 1708 / 919 / 2184 / 1913 / 1845
OsTrx23 / Os.11037.1.S1_a_at / 41790 / 15891 / 17964 / 20164 / 36484 / 16325 / 15836 / 16554 / 30954 / 14772 / 12692 / 14115
OsTrx24 / OsAffx.28360.1.S1_at / 118 / 81 / 163 / 65 / 162 / 117 / 125 / 123 / 146 / 83 / 116 / 47
OsTrx25 / Os.35567.1.S1_at / 1081 / 2234 / 2109 / 2059 / 1061 / 1797 / 1754 / 2184 / 1232 / 2353 / 2058 / 2612
OsTrx26 / Os.15565.1.A1_at / 3533 / 2336 / 2320 / 2397 / 2596 / 2395 / 2459 / 2149 / 2443 / 2475 / 2607 / 2248
OsTrx27 / Os.6625.1.S1_x_at / 4080 / 3884 / 4220 / 4331 / 2478 / 3827 / 4067 / 4264 / 2329 / 2759 / 2903 / 3204
OsTrx28 / Os.10985.1.S1_at / 16798 / 11143 / 11493 / 13357 / 13552 / 12129 / 11478 / 11809 / 13498 / 11313 / 10966 / 11413
OsTrx29 / Os.38257.1.S1_x_at / 14804 / 10075 / 9437 / 10689 / 13021 / 8304 / 7744 / 8373 / 16257 / 9178 / 8438 / 8816
OsTrx30 / Os.9565.1.S1_x_at / 147 / 159 / 155 / 150 / 140 / 167 / 175 / 134 / 259 / 134 / 261 / 156

Supplementary Table S7 The average signal values (two biological repeats) of 29 Trx protein–encoding genes differentially expressed under light and dark treatment at the plumule stage (48 h after emergence) in three cultivars

Gene name / Probe set / Minghui 63 / Shanyou 63 / Zhenshan 97
Light / Dark / Light / Dark / Light / Dark
OsTrx01 / Os.16494.1.S1_at / 580 / 472 / 531 / 415 / 279 / 322
OsTrx02 / Os.17269.1.S1_at / 8432 / 9895 / 6789 / 7233 / 7425 / 9972
OsTrx03 / Os.9880.1.S1_a_at / 1713 / 717 / 2248 / 1697 / 2423 / 901
OsTrx05 / Os.13477.1.S1_at / 1986 / 2732 / 1520 / 1523 / 1683 / 2566
OsTrx06 / OsAffx.12349.1.S1_at / 14 / 23 / 24 / 12 / 7 / 30
OsTrx07 / Os.53357.1.S1_at / 64 / 23 / 57 / 50 / 77 / 60
OsTrx08 / Os.37995.1.S1_at / 2906 / 1758 / 3490 / 3207 / 3201 / 1501
OsTrx09 / Os.51769.1.S1_at / 5481 / 7177 / 5070 / 6098 / 4314 / 6711
OsTrx10 / Os.12826.1.S1_at / 6122 / 5741 / 8251 / 7247 / 5618 / 5554
OsTrx11 / OsAffx.14142.1.S1_at / 210 / 178 / 188 / 180 / 146 / 152
OsTrx12 / Os.9630.1.S1_at / 2166 / 2164 / 1501 / 1737 / 1286 / 1904
OsTrx13 / Os.53966.1.S1_at / 120 / 155 / 61 / 78 / 73 / 91
OsTrx14 / Os.7403.1.S1_at / 5393 / 5536 / 5953 / 5948 / 6004 / 4743
OsTrx15 / Os.10512.1.S1_at / 5324 / 4248 / 8109 / 6983 / 5268 / 2880
OsTrx16 / OsAffx.14459.1.S1_at / 369 / 162 / 571 / 739 / 549 / 210
OsTrx17 / Os.39053.1.A1_s_at / 6500 / 6774 / 5808 / 5897 / 6350 / 7018
OsTrx18 / Os.35448.1.S1_at / 52 / 35 / 18 / 10 / 40 / 49
OsTrx19 / Os.17917.1.S1_at / 1357 / 542 / 904 / 920 / 1573 / 629
OsTrx20 / Os.51130.1.S1_at / 377 / 50 / 359 / 265 / 677 / 86
OsTrx21 / Os.4371.1.S1_a_at / 1233 / 1526 / 907 / 966 / 1000 / 1497
OsTrx22 / OsAffx.15938.1.S1_s_at / 2572 / 2901 / 2234 / 2445 / 2194 / 3075
OsTrx23 / Os.11037.1.S1_a_at / 3115 / 2641 / 8895 / 9401 / 6168 / 3984
OsTrx24 / OsAffx.28360.1.S1_at / 7 / 8 / 40 / 53 / 19 / 54
OsTrx25 / Os.35567.1.S1_at / 2733 / 1071 / 2121 / 2308 / 2689 / 1414
OsTrx26 / Os.15565.1.A1_at / 1744 / 1796 / 2703 / 2721 / 2225 / 1519
OsTrx27 / Os.6625.1.S1_x_at / 1407 / 1340 / 6943 / 6570 / 4415 / 1482
OsTrx28 / Os.10985.1.S1_at / 15202 / 19886 / 18518 / 18226 / 15694 / 15526
OsTrx29 / Os.38257.1.S1_x_at / 1090 / 290 / 889 / 687 / 1386 / 292
OsTrx30 / Os.9565.1.S1_x_at / 44 / 17 / 64 / 69 / 108 / 64