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Figure legends of supplementary figures Figure 1. Phenotypic analysis of rice early flowering1 () plants and enhanced expression of floral identity genes in.. Leaf emergence of,, and plants with complementary expression of EL1 (pel1:el1, lines L1 and L2). Leaf numbers were calculated when a new blade tip is emerged from the sheath of the previous leaf.. Semi-quantitative RT-PCR analysis on the transcripts of selected floral initiation genes indicated the stimulated expressions of OsCK2, Hd1 and OsMDS1 in plants. Total RNs were extracted from rice meristems at the heading stage (4, 45, 5, and 55 days). Rice CTIN gene was amplified and used as an internal positive control. Experiments were repeated twice. Figure 2. Phylogenetic and structural analysis of EL1.. Phylogenetic analysis of plant casein kinase I.. The conserved motifs of casein kinase I in EL1, compared with that of rice OsCKI1. EL1 contains four short conserved peptides: LLGPSLEDLF, HIPXR, EXSRRDD, LPWQGLK. The black box indicates an SV4 T antigen putative nuclear localization sequence. Figure 3. Expression pattern analysis of EL1. Semi-quantitative RT-PCR analysis revealed the constitutive expression of EL1 in stem (St), leaf (Le), flower (Fl), sheath (Sh), glume (Gl), seedling (Se), shoot apical meristem (4 days, SM), and root. Detailed analysis showed that EL1 is mainly expressed at the P2 stage during floral development (lower panel). The rice CTIN gene was amplified and used as an internal positive control. Figure 4. EL1 overexpression in plants. Semi-quantitative RT-PCR analysis revealed the enhanced expression of EL1 in plants. The rice CTIN gene was amplified and used as an internal positive control. Figure 5. has increased response to G.. Measurement of the length of 2 nd leaf sheaths of 7-day-old seedlings in the presence of exogenous G 3 (,.1, 1 or 1 µm). Error bars represent SD (n=15-

2). Heteroscedastic t-test analysis showed a significant difference (**, p<.1).. Measurement of the length of 2 nd leaf sheaths of 7-day-old seedlings in the presence of exogenous uniconazole (, 1, 1 or 1 µm). Error bars represent SD (n=15-2). Heteroscedastic t-test analysis showed a significant difference (**, p<.1). C. Measurement of the length of 2 nd leaf sheaths of 7-day-old transgenic seedlings overexpressing EL1 (ps:el1) in the presence of exogenous G 3 (,.1, 1 or 1 µm). Error bars represent SD (n=15). Heteroscedastic t-test analysis showed a significant difference (**, p<.1). ar=1 cm. D. Measurement of the length of 2 nd leaf sheaths of 7-day-old, plants and with complementary expression of EL1 (pel1:el1, lines L1 and L2) in the presence of exogenous G 3 (,.1, 1 or 1 µm). Error bars represent SD (n=15-2). Heteroscedastic t-test analysis revealed a significant difference (**, p<.1). Figure 6. nalysis of α-amylase activities employing starch-containing plates in the presence of G 3 (1 mm) or (1 µm) for 2 days.. The starch was stained with I 2 -KI. Production and secretion of α-amylase from embryo-less half-seeds were observed as cleared zones (plaques).. seeds could secret α-amylase even in the presence of, confirming the enhanced G 3 response of. Figure 7. Prediction of phosphorylation sites in SLR1. Two putative phosphorylation sites in SLR1, S 196 and S 51, were predicted with the help of http://scansite.mit.edu/motifscan_seq.phtml. Figure 8. Overexpression of SLR1 in and seedlings.. Semi-quantitative RT-PCR analysis of the stimulated SLR1 transcripts in or plants transformed with ps:slr1.. Observation of the lengths of 7-day-old seedlings (upper panel) and various internodes of mature plants (lower panel) indicated the negative effects of SLR1 on plant growth were suppressed under EL1 deficiency. ar=1 cm. Figure 9. Suppressed expression of various Hd genes does not delay the flowering time of rice under EL1 deficiency.

. Semi-quantitative RT-PCR analysis confirms the suppressed expressions of Hd1, Hd3a, Hd6 in or plants transformed with ps:-hd1, ps:-hd3, or ps:-hd6. The leaves of plants at tilling stage were used for analysis.. Heading date of,, overexpressing SLR1 (ps:slr1), or plants with suppressed expression of HD1 (ps:-hd1), HD3a (ps:-hd3a) or HD6 (ps:-hd6). The heading time was calculated after seed germination and statistically analyzed using a heteroscedastic t-test (*, p<.5, n=15). Figure 1. Recombinant protein expression of EL1, tpip5k9, OsCKI1, SLR1, SLR1-N, and SLR1-C. Coomassie brilliant blue (C) staining indicated the recombinantly expressed EL1, tpip5k9, and OsCKI1. Proteins were extracted from cultures in the presence (lane 2, 4, 6) or absence of 1 mm IPTG (lane 1, 3, 5). The inducement was performed by incubation at o C for 3 h.. C staining revealed the recombinantly expressed SLR1. Proteins were extracted from cultures in the presence (lane 2) or absence of IPTG (lane 1). C. C staining indicated the recombinantly expressed C-terminus of SLR1 (SLR1- C, a position 329 to 626) and N-terminus of SLR1 (SLR1-N, a position 1 to 3). Proteins were extracted from cultures in the presence (lane 2, 3) or absence of IPTG (lane 1).

Dai and Xue, Supp Figure 1 12 1 f Leaf Number o 8 6 4 2 pel1:el1 L1 pel1:el1 L2 8 24 26 3 32 34 36 38 4 42 46 days CTIN Hd6 Hd1 OsMDS1 4 45 5 55 4 45 5 55 Cycles 3 3 3

Dai and Xue, Supp Figure 2 77 34 24 46 98 41 1 OsCKI 84 Os2g486 64 Os4g4349 3 Os1g3365 86 Os2g5656 84 tcki2 98 1 tcki1 CKL11 88 CKL6 98 CKL9a CKL7 84 Os1g136 1 Os2g1791 1 CKL3 CKL4 85 CKL2 1 CKL1 67 Os1g512 99 Os1g3895 Os5g5156 1 CKIepsilon CKIdelta CKIbeta CKIalpha 7 Hhp1 Hhp2 7 CKIgamma 99 CKI YCK2 EL1 OsCKI1 N 16 a S/T Kinase domain 259 a 24 a I II III IV C LLGPSLEDLF HIPXR EXSRRDD LPWQGLK EL1 N 138 a I II III IV S/T Kinase domain 271 a 298 a C

Dai and Xue, Supp Figure 3 CTIN EL1 St Le Fl Sh Gl Se SM Cycles 3 Root P1 P2 P3 P4 P5 Cycles CTIN EL1 3

Dai and Xue, Supp Figure 5 Length of 2nd l eaf sheath (cm) Length of 2 nd leaf sheath (c cm) C 14 12 1 8 6 4 2 5 4 3 2 1.1 1 1.1 1 1 G 3 (μm).1 1 1 G 3 (μm) 1 1 1 Uni (μm) 1 1 1 1 1 1 Uni (μm) Length of 2 nd leaf sheath (cm) D (cm) Length of 2 nd leaf sheath ( 12 1 8 6 4 2 14 12 1 8 6 4 2 * ps:el1-l8 ps:el1-l1.1 1 1 ** G 3 (μm) ** ** pel1:el1-l1 pel1:el1-l2 1.1 1 1 G 3 (μm).1 1 1.1 1 1.1 1 1 G 3 (μm) ps:el1-l8 ps:el1-l1

Dai and Xue, Supp Figure 6 G 3 1 μm 1 μm

Dai and Xue, Supp Figure 7 S196 S51

Dai and Xue, Supp Figure 8 CTIN SLR1 p:slr1 L1 L2 L3 L4 L5 L6 ps:slr1 L6 L7 L15 Cycles L2 L4 L6 L15 Internode length hs (cm) 4 3 2 1 * * Panicle I II III IV V L1 L7

Dai and Xue, Supp Figure 9 CTIN HD1 ps:-hd1 L1 L3 L4 L5 L6 L7 L8 L9 L1 Cycles L5 L4 L3 L2 L1 Cycles CTIN HD1 ps:-hd1 ps:-hd3a L3 L4 L5 L8 L1 L11 L12 L16 L17 Cycles CTIN HD3a ps:-hd6 L1 L2 L3 L6 L8 L1 L11 L12 L14 Cycles CTIN HD6 CTIN HD3a CTIN HD6 ps:-hd3a L5 L4 L3 L2 L1 Cycles ps:-hd6 L5 L4 L3 L1 L2 Cycles Heading time (day) 8 7 6 5 4 3 2 1 * * * * * * * ps:slr1-yfp ps:-hd1-l8 ps:-hd1-l9 ps:-hd3a-l3 ps:-hd6-l14 ps:-hd1-l2 ps:-hd3a-l3 ps:-hd1-l1

Dai and Xue, Supp Figure 1 M 1 2 3 4 5 6 * tpip5k9 EL1 OsCKI1 1 2 M SLR1 C M 1 2 3 * SLR1-C SLR1-N

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