Sample No Abbreviation Tissues or organ Developmental stages

1 Calli 1 Calli 15 DAS (days after subculture)

2 Calli 2 Calli 5 DAR (days after regeneration)

3 Calli 3 Calli Screening stage

4 Calli 4 Calli 15 DAI T2 (days after induction)

5 Calli 5 Calli 15 DAI T3 (days after induction)

6 Seed imbibition Seed 72 h after imbibition

7 Seed germination Embryo bud and radicle 3 days after germination

8 Plumule/Dark Plumule 48 hours after emergence, Dark

9 Plumule/Light Plumule 48 hours after emergence, Light

10 Radicle/Dark Radicle 48 hours after emergence, Dark

11 Radicle/Light Radicle 48 hours after emergence, Light

12 Seedlings Seedling Three-leaf stage

13 Young shoot Shoot Seedlings with 2 tillers

14 Young root Root Seedlings with 2 tillers

15 Mature leaf Leaf Stage 3 (secondary branch primordium differentiation stage)

16 Old leaf Leaf 4– young panicle

17 Mature sheath Sheath Stage 3

18 Old sheath Sheath 4– young panicle

19 Young flag leaf Flag leaf 5 DBH (5 days before heading)

20 Old flag leaf Flag leaf 14 DAH (14 days after heading)

21 Panicle, stage 3 Young Panicle Stage 3

22 Panicle, stage 4 Young Panicle Stage 4 (pistil/stamen primordium differentiation stage)

23 Panicle, stage 5 Young Panicle Stage 5 (pollen-mother cell formation stage)

24 Young panicle Panicle 4– young panicle

25 Old panicle Panicle Heading stage

26 Young stem Stem 5 DBH

27 Old stem Stem Heading stage

28 Hull Hull 1 DBF (1 day before flowering)

29 Spikelet Spikelet 3 DAP (3 days after pollination)

30 Stamen Stamen 1 DBF

31 Endosperm 1 Endosperm 7 DAP (7 days after pollination)

32 Endosperm 2 Endosperm 14 DAP (14 days after pollination)

33 Endosperm 3 Endosperm 21 DAP (21 days after pollination)

Table S1. Tissues and developmental stages throughout the life cycles of two rice varieties.

Table S2. Gene primers used for PCR amplification.

Genes Purpose Forward primer (5’-3’) Reverse primer (5’-3’)

OsSUS3 Gene clone TCCCCCGGGATGGGGGAAACTACTGGAG TCCCCCGGGCATTGCCCATTCTTTTCAC

OsSUS3 Q-PCR GTGAGACACGCCGCTACCTGGAGA CCCTGAAATCAACTAAACCCT

OsCESA1 Q-PCR GGCATGGTGGCGGGTATAT AGGCGACGGCTTTCTGAGT

OsCESA3 Q-PCR GTGTAGATAGAAACACGAAAGGTG CAATGGGCACCCACACACGT

OsCESA4 Q-PCR CCATCGTCTACCCGTTCACC TCCAGCCCAGCAATCATCTT

OsCESA7 Q-PCR TTAACGGGGTTCAAGATGC ATGGTGTTGGTGTAGGCGA

OsCESA8 Q-PCR TGGTCGGTGTTGTTGCTGG ATGGTCGGAGTGCGGTTTT

OsCESA9 Q-PCR TACAAGAACGGCAACCTCA AAGAACAAACTCGCAAACG

OsIRX9 Q-PCR ACAAGGAGATGATGATTTTAGCA AGGCGGAGGTCGTAGATGTCG

OsIRX14 Q-PCR GATGGATGGTGTGATTGTG TTGAACTGGAAGAGGCATA

OsGH9B1 Q-PCR ACTTCCTCTACAAAACCCCAAC ATAATCCACTCGCTGAACCATA

OsGH9B3 Q-PCR TCCGATCTCCTCTACGACTGA CCCCGTTCCTGCCATTT

OsGH9B16 Q-PCR CGGAACCACCAAGTAGCCAT GAATACACGACAAAGTCAACGAAC

OsXAT2 Q-PCR GGCGAAGAGGATAATAAGAAC TCACGGATGGTATAATTGGA

OsXAT3 Q-PCR AAGCAAGAAGGTATGAATAATGT AGTGGCAGTTGGATGAAT

OsGSL1 Q-PCR TGAGGACCTGCCACGATT CACGCTGATTGCGAACAT

OsGSL3 Q-PCR TGGCAAGCGACCACATAG AGACCTTAGCACGGACTG

OsGSL5 Q-PCR GTGGTGTCCCTGCTATGA GTTGTTTGCTATTCTCCC

OsSG1 Q-PCR GGCGTATGGGACAAAGGA TTCAGAGGCGAAGGATGG

OsGNS5 Q-PCR TTGCGGCCATTCCTACAGT TGGTGAGGGCGATGCTTG

OsUBQ1 Q-PCR CAGTAAGTCCTCAGCCAT AGACCAGACAACCATAGC

Transgenic

line

Biomass production (g/plant)

2013 2014 2015

ZH11 ZH11 31.81±0.96 27.95±1.37 24.73±1.29

Vector EV 31.63±1.18 26.58±1.93 23.92±0.63

SUS3-OE

1 35.27±1.39** +11%† 34.49±1.55** +30% 27.10±1.11** +13%

2 33.89±1.01* +7% 32.43±1.56** +22% 26.73±0.88** +12%

3 35.77±1.12** +13% 33.78±1.73** +27% 26.87±1.06** +12%

4 36.55±2.13** +15% 35.57±1.77** +34% 28.62±1.30** +20%

Table S3. Biomass production in three-year field experiments.

* and **, Indicated significant difference between transgenic lines and EV control by t-test as P < 0.05 and 0.01 (n=10).†Percentage of increased or decreased level between transgenic line and EV by subtraction of two values divided by EV.

Transgenic

line

Total grain yield (g/plant)

2013 2014 2015

ZH11 ZH11 34.01±1.69 27.82±1.14 23.58±0.90

Vector EV 33.56±2.24 28.44±2.21 23.42±1.25

SUS3-OE

1 37.56±2.83* +12%† 33.91±0.77** +19% 25.43±0.86* +9%

2 36.26±1.47* +8% 33.90±3.65** +19% 25.22±0.33* +8%

3 36.68±2.98 +9% 31.07±1.27 +9% 25.53±0.87* +9%

4 35.72±1.80* +6% 31.39±3.03* +10% 27.68±1.60** +18%

Table S4. Total grain yield in three-year field experiments.

* and **, Indicated significant difference between transgenic lines and EV control by t-test as P < 0.05 and 0.01 (n=10).†Percentage of increased or decreased level between transgenic line and EV by subtraction of two values divided by EV.

Transgenic

line

Leaves Stems

Cellulose Hemicelluloses Lignin Cellulose Hemicelluloses Lignin

ZH11 ZH11 19.02±0.19 16.21±0.12 12.55±0.16 22.35±0.13 16.34±0.10 12.85±0.17

Vector EV 18.98±0.44 16.16±0.37 12.61±0.19 22.42±0.44 16.36±0.10 12.79±0.95

SUS3-

OE

1 23.92±0.73** +26%@ 17.57±0.38** +9% 12.86±0.20 25.02±0.28** +12% 18.10±0.28** +11% 12.38±0.83

2 21.67±0.29** +14% 17.06±0.31** +6% 12.08±0.19 24.41±0.17** +9% 17.41±0.18** +6% 12.11±0.43

3 21.50±0.44** +13% 17.28±0.32** +7% 12.70±0.27 24.43±0.28** +9% 18.22±0.28** +11% 13.76±0.44

4 22.88±0.38* +21% 18.26±0.44** +13% 12.02±0.19 25.74±0.23* +15% 17.69±0.23** +8% 13.67 ±0.37

Table S5. Three major wall polymer contents (% dry matter) in leaves and mature stems of transgenic rice lines.

* and **, Indicated significant difference between transgenic lines and EV control by t-test as P < 0.05 and 0.01 (n=3);@ Percentage of increased or decreased level between transgenic line and EV by subtraction of two values divided by EV.

Transgenic

lineDP

Monosaccharides of hemicelluloses (% total, mol/mol)

Rha Fuc Ara Xyl Man Glu Gal

ZH11 ZH11 1207±11 0.14 0.04 8.42 88.16 0.07 1.00 2.17

Vector EV 1223±8 0.25 0.03 8.11 87.78 0.08 1.15 2.60

SUS3-OE

1 1401±10** +15%@ 0.27 0.04 10.03 85.59 0.10 0.69 3.28

2 1323±10** +8% 0.20 0.03 9.11 87.06 0.08 0.62 2.91

3 1350±11** +10% 0.16 0.06 9.14 87.32 0.09 0.81 2.43

4 1411±12** +15% 0.25 0.04 11.39 84.33 0.11 0.71 3.18

Table S6. Wall polymer features in mature stems of transgenic rice lines.

* and **, Indicated significant difference between transgenic lines and EV control by t-test as P < 0.05 and 0.01 (n=3);@ Percentage of increased or decreased level between transgenic line and EV by subtraction of two values divided by EV.

Rha, Rhamnose; Fuc, Fucose; Ara, Arabinose; Xyl, Xylose; Man, Mannose; Glu, Glucose; Gal, Galactose.

Transgenic

line

1% NaOH 1% H2SO4

Total sugar yield

(% dry matter)

Hexoses yield

(% dry matter)

Bioethanol yield

(% dry matter)

Sugar-ethanol

conversion rate (%)

Total sugar yield

(% dry matter)

Hexoses yield

(% dry matter)

Bioethanol yield

(% dry matter)

Sugar-ethanol

conversion rate (%)

ZH11 ZH11 24.45±0.21 16.27±0.31 10.65±0.11 65.46±0.63 10.74±0.16 9.07±0.18 5.35±0.06 58.99±0.81

Vector EV 24.47±0.37 16.29±0.24 10.52±0.26 64.58±0.78 10.98±0.29 9.32±0.29 5.41±0.26 58.05±0.89

SUS3-

OE

1 28.25±0.29** 19.44±0.23** 14.61±0.13** 75.15±0.73** 13.57±0.20** 11.85±0.24** 8.53±0.18** 71.98±0.74**

2 27.61±0.23** 18.90±0.21** 12.77±0.25** 67.57±0.45** 12.64±0.39** 10.86±0.18** 7.15±0.09** 65.84±0.76**

3 27.79±0.32** 19.03±0.14** 13.48±0.26** 70.87±0.68** 13.65±0.19** 11.68±0.20** 7.44±0.11** 63.70±0.68**

4 30.08±0.38** 20.22±0.28** 15.88±0.29** 78.54±0.73** 14.34±0.28** 12.45±0.30** 8.89±0.18** 71.41±0.73**

Table S7. Biomass enzymatic saccharification and ethanol productivity in in mature stems.

* and **, Indicated significant difference between transgenic lines and EV control by t-test as P < 0.05 and 0.01 (n=3).

Transgenic

line

Strain IV173 Strain ZH173

2014 Wuhan 2015 Wuhan 2015 Hanchuan 2015 Wuhan

Lesion length (cm) Lesion length (cm) Lesion length (cm) Lesion length (cm)

ZH11 ZH11 8.18±1.07 16.57±0.72 17.63±2.76 6.54±0.83

Vector EV 7.34±1.22 16.58±0.73 16.8±0.85 6.77±0.79

SUS3-OE

1 4.26±1.06** -48%† 14.53±1.76** -12% 13.50±0.88** -23% 5.05±0.23** -25%

2 6.12±0.96** -25% 15.07±1.06* -9% 13.56±0.79** -23% 5.63±0.49** -17%

3 3.39±2.08** -59% 15.73±0.39** -5% 14.70±0.75** -17% 4.66±0.37** -31%

4 5.10±1.41** -38% 15.35±0.93** -7% 12.98±0.43** -26% 4.57±0.41** -32%

* and ** Indicated significant difference between transgenic line and EV by Student’s t-test at P < 0.05 and 0.01 (n=30).

† Percentage of decreased level between transgenic line and EV by subtraction of two values divided EV.

Table S8. Lesion lengths of transgenic leaves infected with bacterial blight for 20 days.

Number of lesions per leaf Lesion length (cm)

Strain RB22 R01-1 MT31-3 RB22 R01-1 MT31-3

EV 21±2 30±3 19±2 0.35±0.04 0.27±0.02 0.16±0.02

SUS3-1 15±1** -29%@ 19±1** -37% 9±2** -53% 0.29±0.02** -17% 0.24±0.03** -11% 0.12±0.03** -25%

SUS3-4 15±1** -29% 17±2** -43% 11±2** -42% 0.28±0.03** -20% 0.22±0.03** -19% 0.11±0.02** -31%

* and ** Indicated significant difference between transgenic line and EV by Student’s t-test at P < 0.05 and 0.01 (n=30).@ Percentage of decreased level between transgenic line and EV by subtraction of two values divided by EV.

Table S9. Lesion number and length of transgenic leaves infected with blast strains.

Table S10. Feeding behaviors of BPH recorded by electronic penetration graph (EPG)#.

EPG waveform

Nonprobing Pathway Phloem Ingestion Xylem Ingestion

EV 23.15±7.54 99.41±7.28 205.97±14.94 56.67±4.33

SUS3-1 57.32±8.98** 2.47& 159.98±12.92** 1.61 59.54±6.16** 0.29 104.36±11.37** 1.84

SUS3-4 48.45±7.73* 2.09 204.28±1.99** 2.05 45.85±6.32 ** 0.22 67.80±5.12** 1.20

* and ** Indicated significant difference between transgenic line and EV by Student’s t-test at P < 0.05 and P < 0.01 (n=20);& Ratio of values between transgenic plants and EV.# Total duration (min) of each EPG waveform type on different host plants over 6-h recording period.

Z1 Z3 Z5 Z7 Z9 Z11 Z13 Z15 Z17 Z19 Z21 Z23 Z25 Z27 Z29 Z31 Z33

0

20000

40000

60000

80000

100000 OsSUS1 OsSUS2 OsSUS3

OsSUS4 OsSUS5 OsSUS6

OsS

US

s e

xp

res

sio

n

Fig. S1

M1 M3 M5 M7 M9 M11M13M15M17M19M21M23M25M27M29M31M33

0

20000

40000

60000

80000

100000 OsSUS1 OsSUS2 OsSUS3

OsSUS4 OsSUS5 OsSUS6

OsS

US

s e

xp

ress

ion

(a) (b)

Fig. S2

0

20

40

200

300

400 **

**

**

**

OsS

US

3

exp

ressio

n

ZH11 EV SUS3-OE

1 2 3 4

0

1

2

3

4

5

**

**

*

**

**

SUS1 SUS2 SUS3 SUS4 SUS5 SUS6

Gen

e e

xp

ressio

n

(24h

/0h

)

Mock

IV173

0

1

2

3

4

5

6

7

**

****

****

**

SUS1 SUS2 SUS3 SUS4 SUS5 SUS6

Gen

e e

xp

ressio

n

(24h

/0h

)

Mock

RB22

0

1

2

3

4

*

* **

*

**

SUS1 SUS2 SUS3 SUS4 SUS5 SUS6

Gen

e e

xp

ressio

n

(6h

/0h

)

Mock

BPH

(b)(a)

(c) (d)

Fig. S3

(a) (b) (c)

0

50

100

150

200

250

300

**

**

****

**

**

EV

OE-1

OE-4

CESA1 CESA3 CESA8

CesA9

Rela

tive e

xp

ressio

n

0

30

60

90

120

150

180

** ****

**

**

**

EV

OE-1

OE-4

CESA4 CESA7 CESA9

CesA9 R

ela

tive e

xp

ressio

n

0.0

0.2

0.4

0.6

2

4

6

8

**

**

****

EV

OE-1

OE-4

IRX9 IRX14

Rela

tive e

xp

ressio

n

(d) (e)

0

5

10

15

20

25

**

**

**

**

EV

OE-1

OE-4

XAT2 XAT3

Re

lati

ve e

xp

res

sio

n

0.0

0.5

1.0

200

300

400

500

**

**

****

**

**

EV

OE-1

OE-4

GH9B1 GH9B3 GH9B16

Re

lati

ve

ex

pre

ss

ion

0

20

40

60

80

100

716466725859

10%

23%14%24%

****

****

1% H2SO

4 pretreatment

Su

ga

r-e

tha

no

l

co

nv

ers

ion

rate

(%

)

1 2 3 4ZH11 EV SUS3-OE

0

20

40

60

80

100

797168756565

10%5%

22%16%**

******

1% NaOH pretreatment

Su

gar-

eth

an

ol

co

nvers

ion

rate

(%

)

1 2 3 4

ZH11 EV SUS3-OE

0

20

40

60

80

100

484745484140

15%18%

9%17%

********

1% H2SO

4 pretreatment

He

xo

se

s r

ele

as

ed

(% c

ellu

lose

)

1 2 3 4ZH11 EV SUS3-OE

0

20

40

60

80

100

7978787872

9%9% 9%8%

********

1% NaOH pretreatment

He

xo

se

s r

ele

as

ed

(% c

ellu

los

e)

1 2 3 4

ZH11 EV SUS3-OE

72

(a)

(b)

Fig. S4

(a)

0

1

2

3

4

5

**

Ge

ne

ex

pre

ss

ion

(24

h/0

h)

EV

OE-1

OE-4

GSL1 GSL3 GSL5 SG1 GNS5

**

**

**** **

**

IV173 infection (b)

0

1

2

3

4

5

6

7

****

**

RB22 infection****

Gen

e e

xp

res

sio

n

(24

h/0

h)

EV

OE-1

OE-4

GSL1 GSL3 GSL5 SG1 GNS5

*

*

** *0

1

2

4

8

12

16

20

**

BPH attack

****

**

Gen

e e

xp

res

sio

n

(6h

/0h

)

EV

OE-1

OE-4

GSL1 GSL3 GSL5 SG1 GNS5

**

**

*

(c)

Fig. S5

Probe Amplifier

Converter

R

Ground

-+

Nonprobing

Pathway

Xylem ingestionPhloem ingestion

28 %

7 %

59 %

6 %

38 %

28 %

19 %

15 %

49 %

22 %

15 %

14 %

EV SUS3-OE-1 SUS3-OE-4 (a) (b)

Fig. S6