Figure legends for Supporting Information
Figure S1. Comparison of three HCF152 protein sequences among rice and Arabidopsis
Figure S2. The heat maps of three duplicated gene pairs with positive, irrelevant, and negative expression correlations.
The color scale indicates the relative expression levels (Z-scores) of genes in all the organs. Each horizontal line represents a gene in each variety (m, Minghui 63; s, Shanyou 63; z, Zhenshan 97). Each portrait line represents one of the 36 tissues at different stages or treatments. LOC_Os11g06020.1 and LOC_Os12g06340.1 have an expression correlation of 0.672, with a P value of 1.6E-15; LOC_Os11g06690.1 and LOC_Os12g06800.1 are irrelevant; LOC_Os11g06680.1 and LOC_Os12g07110.1 have an expression correlation of –0.401 with a P value of 1.5E-5.
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Table S1. Pearson correlation analysis among the expression levels of duplicated genes in the distal region of chromosomes 11 and 12
No. / Duplicated genes on Chr 11 / Duplicated genes on Chr 12 / Wu-blast / Pearson correlation / No expression signal aGenes / Probe sets / Genes / Probe sets / P value / Coefficient / P value
1 / LOC_Os11g01300.1 / OsAffx.30763.1.S1_s_at / LOC_Os12g01260.1 / Os.12962.1.S1_at / 1.50E-51 / 0.259 / 0.00689
2 / LOC_Os11g01320.1 / OsAffx.30764.1.S1_at / LOC_Os12g01350.1 / OsAffx.30764.2.S1_at / 1.90E-87 / 0.206 / 0.03240
3 / LOC_Os11g01400.1 / OsAffx.31538.2.S1_at / LOC_Os12g01410.1 / OsAffx.31538.1.S1_at / 9.90E-46 / Chr 11
4 / LOC_Os11g01410.1 / OsAffx.31539.2.S1_at / LOC_Os12g01420.1 / OsAffx.31539.1.S1_at / 3.10E-154 / 0.103 / 0.28726
5 / LOC_Os11g01480.1 / OsAffx.30765.1.S1_at / LOC_Os12g01490.1 / Os.18448.1.S1_at / 1.70E-135 / 0.852 / 0.00000
6 / LOC_Os11g01540.1 / OsAffx.31540.2.S1_at / LOC_Os12g01540.1 / OsAffx.31540.1.S1_at / 5.60E-43 / 0.467 / 0.00000
7 / LOC_Os11g01660.1 / OsAffx.6959.1.S1_x_at / LOC_Os12g01720.1 / OsAffx.7457.1.S1_at / 1.50E-51 / 0.277 / 0.00376
8 / LOC_Os11g01830.1 / Os.51935.1.S1_at / LOC_Os12g01830.1 / Os.16506.1.A1_at / 4.20E-125 / 0.900 / 0.00000
9 / LOC_Os11g01836.1 / OsAffx.31545.1.S1_at / LOC_Os12g01850.1 / Os.54332.1.S1_at / 1.00E-250 / 0.231 / 0.01595
10 / LOC_Os11g02210.1 / OsAffx.31551.2.S1_at / LOC_Os12g02160.1 / OsAffx.31551.1.S1_at / 8.30E-81 / 0.335 / 0.00040
11 / LOC_Os11g02300.1 / Os.28385.1.S1_x_at / LOC_Os12g02250.1 / Os.28385.3.S1_at / 1.00E-250 / 0.855 / 0.00000
12 / LOC_Os11g02330.1 / Os.37860.1.S1_at / LOC_Os12g02290.1 / Os.28462.1.S1_s_at / 3.10E-58 / 0.858 / 0.00000
13 / LOC_Os11g02440.1 / Os.37295.1.S1_at / LOC_Os12g02370.1 / Os.6354.1.S1_at / 7.30E-105 / 0.909 / 0.00000
14 / LOC_Os11g02660.1 / Os.26742.1.S1_at / LOC_Os12g02589.1 / Os.10374.2.S1_at / 7.10E-139 / Chr 12
15 / LOC_Os11g02730.1 / Os.51048.1.S1_at / LOC_Os12g02700.1 / Os.50992.1.S1_at / 1.30E-114 / 0.827 / 0.00000
16 / LOC_Os11g02760.1 / Os.40337.1.S1_at / LOC_Os12g02730.1 / Os.17056.1.A1_at / 3.80E-101 / Chr 12
17 / LOC_Os11g03200.1 / Os.52764.1.S1_at / LOC_Os12g02950.1 / Os.52945.1.S1_at / 1.20E-143 / 0.252 / 0.00839
18 / LOC_Os11g03210.1 / OsAffx.18651.1.S1_at / LOC_Os12g02960.1 / OsAffx.19460.1.S1_at / 1.80E-23 / Chr 11
19 / LOC_Os11g03370.1 / Os.35343.1.A1_at / LOC_Os12g03050.1 / OsAffx.31559.1.S1_at / 6.30E-138 / 0.704 / 0.00000
20 / LOC_Os11g03380.1 / Os.11848.1.S1_at / LOC_Os12g03060.1 / Os.37912.1.S1_at / 4.10E-159 / 0.583 / 0.00000
21 / LOC_Os11g03390.1 / Os.8564.1.S1_at / LOC_Os12g03070.1 / Os.10524.2.S1_at / 1.90E-104 / 0.964 / 0.00000
22 / LOC_Os11g03400.1 / Os.9193.1.S1_at / LOC_Os12g03090.1 / Os.37737.1.S1_at / 1.10E-76 / 0.827 / 0.00000
23 / LOC_Os11g03430.1 / Os.54171.1.S1_at / LOC_Os12g03130.1 / Os.48443.1.S1_at / 1.00E-250 / 0.965 / 0.00000
24 / LOC_Os11g03640.1 / OsAffx.30800.2.S1_at / LOC_Os12g03410.1 / OsAffx.30800.1.S1_at / 1.00E-250 / -0.050 / 0.60508
25 / LOC_Os11g03750.1 / OsAffx.31565.1.S1_at / LOC_Os12g03510.1 / OsAffx.7472.1.S1_at / 1.10E-46 / Chr 11
26 / LOC_Os11g04030.1 / Os.6142.1.S1_s_at / LOC_Os12g03860.1 / Os.21635.1.S1_at / 1.40E-243 / 0.885 / 0.00000
27 / LOC_Os11g04360.1 / OsAffx.19482.2.S1_x_at / LOC_Os12g04150.1 / Os.5943.1.S1_at / 4.40E-130 / 0.579 / 0.00000
28 / LOC_Os11g04480.1 / Os.10842.2.S1_at / LOC_Os12g04240.1 / Os.10842.1.S1_at / 2.60E-157 / 0.726 / 0.00000
29 / LOC_Os11g04680.1 / OsAffx.19490.1.S1_at / LOC_Os12g04450.1 / OsAffx.19490.2.S1_at / 7.30E-66 / Chr 12
30 / LOC_Os11g04930.1 / Os.50597.1.S1_at / LOC_Os12g04930.1 / Os.14713.1.S1_at / 5.70E-208 / 0.187 / 0.05257
31 / LOC_Os11g04950.1 / Os.18447.1.S2_at / LOC_Os12g04940.1 / Os.18732.1.S1_at / 1.00E-250 / -0.148 / 0.12527
32 / LOC_Os11g04990.1 / Os.53519.1.S1_at / LOC_Os12g05000.1 / OsAffx.31586.1.S1_s_at / 6.10E-117 / 0.436 / 0.00000
33 / LOC_Os11g05050.1 / Os.9392.1.S1_at / LOC_Os12g05050.1 / Os.7801.1.S1_at / 1.50E-111 / 0.132 / 0.17469
34 / LOC_Os11g05080.1 / Os.7417.1.S1_at / LOC_Os12g05080.1 / Os.12064.1.S1_at / 1.70E-192 / -0.199 / 0.03879
35 / LOC_Os11g05090.1 / Os.10515.1.S1_s_at / LOC_Os12g05090.1 / Os.52139.1.S1_at / 2.00E-182 / -0.065 / 0.50288
36 / LOC_Os11g05100.1 / Os.47960.1.S1_at / LOC_Os12g05100.1 / OsAffx.19502.1.S1_at / 1.70E-60 / Chr 12
37 / LOC_Os11g05110.1 / Os.49493.1.S1_at / LOC_Os12g05110.1 / Os.28109.1.S1_at / 1.00E-250 / 0.241 / 0.01213
38 / LOC_Os11g05160.1 / Os.47918.1.S1_at / LOC_Os12g05200.1 / OsAffx.31589.1.S1_at / 7.30E-105 / 0.470 / 0.00000
39 / LOC_Os11g05170.1 / OsAffx.18681.1.S1_s_at / LOC_Os12g05210.1 / Os.51775.1.S1_at / 1.30E-50 / 0.798 / 0.00000
40 / LOC_Os11g05190.1 / Os.1307.1.S1_a_at / LOC_Os12g05260.1 / Os.2218.1.S1_at / 5.20E-24 / 0.517 / 0.00000
41 / LOC_Os11g05230.1 / OsAffx.30825.1.S1_at / LOC_Os12g05270.1 / OsAffx.31592.1.S1_at / 5.90E-24 / Both
42 / LOC_Os11g05300.1 / OsAffx.18684.1.S1_at / LOC_Os12g05370.1 / OsAffx.31594.1.S1_at / 1.30E-75 / Chr 12
43 / LOC_Os11g05320.1 / OsAffx.31595.1.S1_at / LOC_Os12g05394.1 / Os.50606.1.S1_at / 1.60E-132 / Chr 11
44 / LOC_Os11g05380.1 / Os.14105.1.S1_at / LOC_Os12g05440.1 / Os.51923.1.S1_at / 1.40E-236 / 0.786 / 0.00000
45 / LOC_Os11g05430.1 / OsAffx.18688.1.S1_at / LOC_Os12g05560.1 / OsAffx.7491.1.S1_x_at / 6.10E-14 / Chr 12
46 / LOC_Os11g05450.1 / OsAffx.18689.1.S1_at / LOC_Os12g05580.1 / OsAffx.7492.1.S1_at / 1.50E-17 / 0.396 / 0.00002
47 / LOC_Os11g05470.1 / Os.49726.1.S1_at / LOC_Os12g05590.1 / Os.57548.1.S1_at / 5.90E-87 / 0.088 / 0.36712
48 / LOC_Os11g05480.1 / Os.49126.1.S1_at / LOC_Os12g05680.1 / Os.54058.1.S1_at / 5.20E-198 / 0.712 / 0.00000
49 / LOC_Os11g05490.1 / Os.16214.1.S1_at / LOC_Os12g05690.1 / Os.55494.1.S1_at / 3.70E-23 / 0.658 / 0.00000
50 / LOC_Os11g05530.1 / Os.51005.1.S1_at / LOC_Os12g05770.1 / OsAffx.19509.1.S1_at / 2.50E-79 / 0.110 / 0.25581
51 / LOC_Os11g05550.1 / Os.55491.1.S1_at / LOC_Os12g05890.1 / Os.51098.1.S1_at / 3.80E-53 / 0.452 / 0.00000
52 / LOC_Os11g05580.1 / OsAffx.18690.1.S1_at / LOC_Os12g05970.1 / OsAffx.7496.1.S1_at / 3.40E-14 / Both
53 / LOC_Os11g05614.1 / Os.54623.1.S1_at / LOC_Os12g05990.1 / Os.19369.1.S1_at / 2.80E-89 / 0.183 / 0.05855
54 / LOC_Os11g05650.1 / Os.8763.1.S1_at / LOC_Os12g06020.1 / Os.18097.1.S1_at / 2.00E-159 / 0.743 / 0.00000
55 / LOC_Os11g05740.1 / Os.53019.1.S1_at / LOC_Os12g06080.1 / Os.5875.1.S1_at / 6.10E-117 / 0.693 / 0.00000
56 / LOC_Os11g05770.1 / Os.54938.1.S1_at / LOC_Os12g06150.1 / OsAffx.19516.1.S1_at / 2.20E-50 / 0.538 / 0.00000
57 / LOC_Os11g05780.1 / OsAffx.19517.2.S1_at / LOC_Os12g06160.1 / OsAffx.7498.1.S1_at / 1.30E-57 / -0.128 / 0.18592
58 / LOC_Os11g05810.1 / Os.6844.1.S1_at / LOC_Os12g06190.1 / OsAffx.31611.1.S1_s_at / 7.00E-45 / 0.620 / 0.00000
59 / LOC_Os11g05860.1 / Os.9519.1.S1_at / LOC_Os12g06260.1 / Os.9526.1.S1_at / 5.80E-96 / 0.518 / 0.00000
60 / LOC_Os11g06010.1 / Os.31883.1.A1_at / LOC_Os12g06330.1 / Os.48567.1.S1_at / 1.00E-250 / 0.622 / 0.00000
61 / LOC_Os11g06020.1 / Os.11805.1.A1_s_at / LOC_Os12g06340.1 / Os.27423.1.S1_x_at / 1.70E-70 / 0.672 / 0.00000
62 / LOC_Os11g06140.1 / Os.53021.1.S1_at / LOC_Os12g06490.1 / Os.8100.1.S1_at / 1.90E-136 / 0.012 / 0.90563
63 / LOC_Os11g06170.1 / Os.53732.1.S1_a_at / LOC_Os12g06520.1 / Os.19640.1.S1_at / 8.40E-88 / 0.364 / 0.00011
64 / LOC_Os11g06180.1 / OsAffx.18704.1.S1_at / LOC_Os12g06540.1 / OsAffx.19522.1.S1_at / 2.40E-35 / -0.082 / 0.40075
65 / LOC_Os11g06690.1 / OsAffx.30846.1.S1_at / LOC_Os12g06800.1 / Os.15113.1.A1_at / 1.00E-250 / -0.002 / 0.98073
66 / LOC_Os11g06700.1 / OsAffx.30847.2.S1_at / LOC_Os12g06840.1 / Os.53000.1.S1_at / 2.00E-198 / 0.982 / 0.00000
67 / LOC_Os11g06750.1 / Os.22696.1.S1_at / LOC_Os12g07010.1 / Os.5507.1.S1_at / 1.20E-212 / 0.851 / 0.00000
68 / LOC_Os11g06880.1 / Os.23734.1.A1_at / LOC_Os12g07110.1 / Os.15600.1.S1_a_at / 1.20E-168 / -0.401 / 0.00002
69 / LOC_Os11g06900.1 / Os.14121.1.S1_at / LOC_Os12g07150.1 / Os.20118.1.A1_s_at / 1.00E-250 / 0.478 / 0.00000
70 / LOC_Os11g06910.1 / Os.9349.1.S1_at / LOC_Os12g07160.1 / Os.24613.1.S1_at / 6.40E-193 / 0.797 / 0.00000
71 / LOC_Os11g06930.1 / OsAffx.30849.1.S1_at / LOC_Os12g07190.1 / Os.21230.1.S1_at / 4.20E-196 / -0.151 / 0.11804
72 / LOC_Os11g07040.1 / Os.5879.1.S1_at / LOC_Os12g07230.1 / OsAffx.31629.1.S1_at / 1.20E-248 / 0.509 / 0.00000
73 / LOC_Os11g07360.1 / OsAffx.18723.1.S1_at / LOC_Os12g07440.1 / OsAffx.7513.1.S1_at / 3.00E-18 / Chr 11
74 / LOC_Os11g07510.1 / OsAffx.7036.1.S1_at / LOC_Os12g07540.1 / Os.21075.1.S1_at / 1.50E-123 / -0.178 / 0.06573
75 / LOC_Os11g07580.1 / OsAffx.7038.1.S1_s_at / LOC_Os12g07550.1 / Os.51529.1.S1_at / 5.70E-18 / -0.157 / 0.10480
76 / LOC_Os11g07680.1 / Os.9277.1.S1_at / LOC_Os12g07580.1 / OsAffx.7517.1.S1_x_at / 1.60E-47 / Chr 12
77 / LOC_Os11g07910.1 / Os.26444.1.S1_at / LOC_Os12g07670.1 / Os.9399.1.S1_at / 1.00E-250 / 0.626 / 0.00000
78 / LOC_Os11g07916.1 / Os.7859.1.S1_at / LOC_Os12g07700.1 / Os.5621.1.S1_s_at / 3.30E-70 / -0.150 / 0.12033
79 / LOC_Os11g08940.1 / Os.23150.1.S1_at / LOC_Os12g07980.1 / OsAffx.19547.1.S1_at / 1.80E-19 / 0.105 / 0.28008
80 / LOC_Os11g09020.1 / Os.19070.1.S1_at / LOC_Os12g08090.1 / Os.26802.2.S1_at / 4.30E-219 / 0.395 / 0.00002
81 / LOC_Os11g09030.1 / Os.51516.1.S1_at / LOC_Os12g08150.1 / OsAffx.7522.1.S1_at / 4.70E-23 / 0.812 / 0.00000
82 / LOC_Os11g09040.1 / Os.51173.1.S1_at / LOC_Os12g08160.1 / OsAffx.19549.1.S1_at / 5.90E-32 / 0.052 / 0.59074
83 / LOC_Os11g09150.1 / Os.50381.1.S1_at / LOC_Os12g08200.1 / Os.8575.1.S1_at / 1.20E-16 / 0.386 / 0.00004
a Duplicated gene had the same low expression signal as the background. “Chr 11” and “Chr 12” indicate the copy of the duplicated gene on chromosomes11 or 12. “Both” indicates both copies of the duplicated gene had no expression.
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Table S2. Primer sequences used in this study
Name / Forward primers / Reverse primerEid1 / AAGGGTGATTTATGTCATCACAAG / TGCAACAAGGCTACAAATGG
Eid15 / CAGGGTAGCTCATGTGGTGA / ACTGACAGGGTATCCATTCT
Eid19 / TCACCATTGCGCTGCTTGGA / TTGGAGAGAACTGCTGCAGG
Eid20 / TTGGACACGTCAGCGTCATC / TGGTACTAGTACTAATCTGG
Eid21 / GCAGTTGTTTGGCTTGCAAG / CTTGCAAGCCAAACAACTGC
Eid22 / TCTAGATCCGGTTGTGCCTT / GCTTGTTATCCTAACGAGCT
Eid23 / GTGCTTATCCACATTGTCAC / TGCTACTTGACTGCAGCAAC
Eid24 / GTGGCATTCTCCACGTCCTA / TTCTTCATCGGCATCTGGTC
Eid25 / GTCTTCTTCAGACTTCCCTG / GCCACATGTACATCTTACTG
Eid26 / GTGGTTTGCCAAATGTTAGG / GAACCACGTTGCTCTCTATG
Eid27 / GTGGTGGATCTGATTCCGAT / TGCATACATAGGCTAAGCGT
Eid28 / GGAAGTAACAGTAAGGTAAG / CCCAACAGGAATCGGATACG
Eid29 / CAGTAGCTACTGCTGCAATG / GGTAGAACTGTTCACAATGC
Eid30 / GATTGATGATTCCATACCAC / TTGCTCAGTTCATTCGACTC
Eid31 / ACTTATGTCCAGAACCAGGC / TGGAGTCGCTACGCTATGAG
Eid32 / TGAGTTGCGAAGGTCGATTC / TGTACGGATCGTACCTGACT
Eid33 / ACGAGGTGAACCATTAGCTC / CATTGAGCATAGGAGGTACA
Esr1 / GCGTGTGGTAAAGCAAAACTT / CTGCACTCCTTCATCCTCGT
Esr11 / CCAGCAGCAAGTAGTTGACA / CGACCAGAGACCAAGCAACA
Esr3 / CATGACCAAGCCACAGCA / AGGAGGAGGCGAGAGAGTG
de1 / CTAGTACTACCTCTGGACTA / CCAAGGTTAACACTCGTGTG
de4 / TCTAGCACTAGATGTGACGT / AGCAGAACATCTGGACTGGA
de13 / ACCCAAGGCTTTTCTTCCTC / TTTTGTGGAAAGGCGAAGAT
de15 / TCTGTGCTGAGGACATGGAC / GGCCCTCAGTGTCCTCTTTC
de19 / GATCCACCAACTTGGATTTCAG / AACCCAGTTAGGTGTAGAATGA
de23 / CATAACGCAGTTAGCCTAATC / GAACGAGAGATGATGAGTCG
de24 / CTACTTTTGTGTATCGATTGG / CATAGAGTCATGCACCTACG
de27 / TACCTGTCTATCGCATCGGA / CATACACGCTGATACTGTTG
de29 / GTGGTTGCAGCTAAACATCC / TGTCAAGCGATGACTCCAGT
de31 / ACTTGGGCTGACCAATGTTC / TGAACCCTATGGCTGCAATG
IBR2 / GGCCTCCCTATCCTCCAAT / CCCAATTCCCAACAGCATTA
MSC1 / GGGGATAGAACCCCGATAAA / CCATGCTGCGGTACCTAAAT
Table S3 Comparing sequence of Os11HCF152, the candidate genefor et11 among the wild type and etiolation types in RI184 population
Positionsa / Nipponbare / RI184 wild type / MutantNucleus / Amino acid / Nucleus / Amino acid / Nucleus / Amino acid
-1447 / G / G / A
-1445 / G / G / A
-1418 / G / G / A
-1349 / A / A / G
-1296 / C / C / T
-1273 / G / G / A
-1259 / G / G / A
-1176 / C / C / T
-1094 / A / A / G
-1044 / C / C / T
-919 / A / A / G
25 / GAC / ASP / GAC / ASP / AAC / ASN
552 / GAC / GLU / GAG / ASP / GAC / GLU
567 / CTT / LEU / CTC / LEU / CTT / LEU
594 / AGG / ARG / AGA / ARG / AGG / ARG
660 / CTG / LEU / CTT / LEU / CTG / LEU
693 / CCA / PRO / CCG / PRO / CCA / PRO
699 / AGC / SER / AGT / SER / AGC / SER
709 / CAC / HIS / TAC / LYR / CAC / HIS
867 / GGA / GLY / GGG / GLY / GGA / GLY
891 / GTA / VAL / GTG / VAL / GTA / VAL
a minus and plus numbers meant the position upstreamand downstream of the initial codon “ATG”, respectively.
Fig.S1
Figure S2
1