Supplementary Table S1: Primers used in thisstudy

Marker / Forward primer / Reverse primer / Application
RM3766 / CGCGTTCGATCGATCTCTCTCC / GGCCAGAGTACGTGCCAGATGC / Fine mapping
RM14639 / ATAAGAGGACTACGCCAAACAACACC / ATGGCTGGAATCCATTCTTTGG / Fine mapping
R-29 / GGTCAATGTGGTCCAAGGTTT / TGGCAGCACCGAGAAATG / Fine mapping
R-31 / CAGCGCCCGGTACTCCACAA / CGAGCGGCAACGGCATAAC / Fine mapping
RM14643 / CGTCGTAGTACTTGTCGCACAGC / CGTCACACCGACTTAACACTTGG / Fine mapping
RM14645 / GGTCCAATTCACACCAGAACG / TGGTGTGTAACTGCGTAATTGTCC / Fine mapping
RM14650 / GCAGGCACAAAAGCAAAGAG / AGGTGAAGGTGCATTGTGTG / Fine mapping
RM14653 / CAACCTTTCGACGGTACACACG / TTGTCTGTGGTTGAGCAGTCAGC / Fine mapping
RM14703 / AACAGTGATGGTGGTGATGAATGG / GCTCAGGGACTGATCTGCTATGG / Fine mapping
RM5944 / AAGGGCCAATCCATCCTCACC / CTGCCTCCTCGCCTTTATTCTGC / Fine mapping
Actin / TGTCTGGATTGGAGGTTCTA / CATTTCCTGTGGACGATTGA / q RT-PCR
D1352 / CATACTCATGGAGGAGAAAGGC / GCACCGATGCTAACAATCAAAC / q RT-PCR
In24 / GGTGTTCATCTGCCCGATCT / CTTGAAGCGGGTGTAGCG / Linkage analysis

Supplementary Table S2: Agronomic traits of the WT and MT

Trait / WT / MT / MT/WT Ratio（%）
Plant height（cm） / 82.80 ± 2.83 / 27.86 ± 2.72** / 33.64
Stem length（cm） / 59.06 ± 2.52 / 15.64 ± 2.00** / 26.48
Panicle length（cm） / 23.74 ± 1.54 / 12.22 ± 1.84** / 51.47
Tillering ability / 17 ± 4 / 20.36 ± 8.52 / 134.58
Flag leaf length（cm） / 41.30 ± 3.54 / 24.19 ± 4.71** / 58.57
Flag leaf width（cm） / 1.83 ± 0.20 / 2.58 ± 0.34** / 140.98
Length/width ratio of flag leaf / 22.81 ± 2.93 / 9.59 ± 2.75** / 42.04
Panicles per plant / 15 ± 3 / 12 ± 4** / 80.00
Grain length (mm) / 9.13 ± 0.34 / 5.87 ± 0.42** / 64.29
Grain width (mm) / 2.77 ± 0.10 / 3.01 ± 0.18** / 108.66
Grains per panicle / 232 ± 32 / 130 ± 19** / 56.03
Grain numbers per panicle / 147 ± 35 / 28 ± 9** / 19.04
Seed setting rate (%) / 62.84 ± 9.69 / 20.64 ± 11.39** / 32.84
1000-weight (g) / 24.80 ± 0.14 / 10.60 ± 0.28** / 42.74

All the agronomic traits are measured as mean ± SD.

* &** indicate significant difference at P<0.05 and P<0.01 level, respectively.

Supplementary Table S3: Lengths of internode of theWT and MT

Internodes / WT (cm) / Proportion (%) / MT (cm) / Proportion (%)
V / 30.54 ± 4.94 / 53.87 / 11.68 ± 0.89 / 66.70
IV / 15.60 ± 2.01 / 27.55 / 4.3 ± 0.43 / 24.56
III / 6.97 ± 1.47 / 12.31 / 0.88 ± 0.14 / 5.03
II / 2.57 ± 0.64 / 4.54 / 0.45 ± 0.11 / 2.57
I / 0.98 ± 0.22 / 1.73 / 0.20 ±0.08 / 1.14

All the agronomic traits are measured as mean ± SD

Supplementary Table S4: Segregation of dwarf and normal plants in the F2 populations

Cross combination / Normal / Dwarf / Total / χ2 (3:1) / P Value
d1352/ XS1 / 301 / 91 / 392 / 0.34 / 0.56>0.01
d1352/ MH63 / 2017 / 655 / 2672 / 0.17 / 0.68>0.01
d1352/TaiShanNuo / 158 / 62 / 220 / 0.27 / 0.60>0.01
d1352/HanMa / 146 / 63 / 209 / 0.18 / 0.67>0.01

X20.05,1= 3.84

Supplementary Table S5: Genes annotated within the mapped region

No. / Gene Functions / MSU Loci
1 / squalene monooxygenase, putative, expressed / LOC_Os03g12900
2 / squalene monooxygenase, putative, expressed / LOC_Os03g12910
3 / expressed protein / LOC_Os03g12920
4 / expressed protein / LOC_Os03g12930
5 / OsFBO13 - F-box and other domain containing protein, expressed / LOC_Os03g12940
6 / expressed protein / LOC_Os03g12945
7 / AP2-like ethylene-responsive transcription factor AINTEGUMENTA, putative, expressed / LOC_Os03g12950
8 / hypothetical protein / LOC_Os03g12960
9 / hypothetical protein / LOC_Os03g12970
10 / expressed protein / LOC_Os03g12980
11 / phytosulfokines precursor, putative, expressed / LOC_Os03g12990
12 / GTP-binding protein, putative, expressed / LOC_Os03g13000
13 / U-box domain containing protein, expressed / LOC_Os03g13010
14 / expressed protein / LOC_Os03g13020
15 / lecithin cholesterol acyltransferase, putative, expressed / LOC_Os03g13030
16 / haemolysin-III, putative, expressed / LOC_Os03g13040

(Annotated by http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice/)

Supplementary Fig.S1Stem cell morphology of the WT and MT

(a) Observations ofinternode epidermis cell. Bar: 100μm. (b) Longitudinal section observation of the third internode. Bar: 200μm.

Supplementary Fig.S2d1352 is unlikely a GA-related mutant

(a) Seeds of WT and MT were germinated on agar plates in the presence (+) or absence (−) of 20ppm GA3 (Left) or 300ppmPP333 (Right), and seedlings were examined 7 d after germination. Bar: 2cm. (b) Seedling lengths (heights) in response to GA3 treatment in WT and MT.

Supplementary Fig.S3Relative expression of BR-related genes in the WT and MT

Differentially expressed genes between the WT and MT. Six BR-related genes were confirmed to be differentially expressed by qRT-PCR analyses. Relative expression levels were measured as the mean ± SD. All P values were based on two-tailed t-tests.