Table S1. List of primers used for the amplification of DNA fragments that were used as probes for Northern blot analysis.

Primer name Sequence 5`-3` cDNA Product size (bp)

Accession number

Gene

AtNPR1-F GAGGACACACTGGTTATACTC 691 EF470707 non-expressor of PR1 (NPR1)AtNPR1-R CCAGATCGAGCAGCGTCATCTT

PR1-F TGCCCAAGACTCACAACAAG 238 CK988133.1 Putative PR1

PR1-R GGCCTTCTCATTAACCCACA

PR10-F TACTATTGAAGCCGCCAAGG 399 AF305067 PR10

PR10-R TCGGGATTAGCCAAGAGGTA

Thaumatin-F CAAGCTTGTTGGGTCATCCT 357 DN828172 Thaumatin like

Thaumatin-R GTCCTCGAATGCAAGGGATA

Glucanase-F CATTGATATGACCTTGATCG 173 CD486342 Glucanase

Glucanase-R GTGAGATATCCCTTGGATTG

CAD1C-F ATAAGGATGAAATGCGTCC 433 AF270425.1 (+)-Delta-cadinene synthaseCAD1C-R GAAGCTTGGTAAAGTTCCA

LOX1-F GCATGGAGGACTGATGAAGAGTT 1060 AF361893 Pathogen induced lipoxygenaseLOX1-R GACTGGAAGGCTGAAGCCACCCATAT

Chitinase-F ACCAAGCTACTCGCAAGAGG 156 CD485880 Chitinase

Chitinase-R CGGAAGCGCAGTAAGATGA

POD10-F CACTGTTTCCTGCGCTGATA 413 ES831865 Peroxidase

POD10-R CGAAACCATCAGGTGTTGTG

MIC3-F TACCAAGGTGCTCCGGTAAC 290 GQ231922 MIC3

MIC3-R GGGCTGAAGGATGCTCACTA

GST13-F TTTTTGGATACTGGGCAAGC 566 DT464022 Glutathione S-transferase

GST13-R GCTGCAATTTGCGAAATCTT

Primer name

Sequence 5`-3` cDNA Product size bp

Accession number

Gene

OXRED-F AATTGAGTTCCCAGCCATT 495 CO123294 Oxidoreductase

OXRED-R TATTTCATCATCCGCACCAA

MPD-F TGGACATAAGGGCAAAAAGG 635 CO118999 Mevalonate Pyrophosphate DecarboxylaseMPD-R TGCAAAATTAGCCTGTGCTG

HIST3-F GAAGCCTCATCGATACCGTC 412 AF024716 Histone 3

HIST3-R CTACCACTACCATCATGGC

Table S1. (Continued)

Fig. S1. Disease severity in wild-type (WT) and transgenic cotton plants expressing AtNPR1 gene, one month following inoculation with Thielaviopsis basicola. The image shown is at the termination of experiment #2 conducted under growth chamber conditions.

0

1

2

3

4

5

6

7

8

9

WT 68L-19 68L-20 68L-5 WT 68L-19 68L-20 68L-5

Sh

oo

t wei

gh

t (g

)

Uninfected Infected

**

Fig. S2. Resistance to Thielaviopsis basicola in transgenic cotton lines (#68L-19, #68L-20, and #68L-5) expressing AtNPR1. WT: wild-type. Shoot weight was used as a parameter to score disease-severity in experiment #2, conducted under growth chamber conditions, one month following inoculation with the pathogen. Data represent mean±SE, **P<0.01; n=10.

0

0.5

1

1.5

2

2.5

3

3.5

4

4.5

5

WT 68L-19 68L-20 68L-5 WT 68L-19 68L-20 68L-5

Ro

ot

wei

gh

t (g

)

Uninfected Infected

***

*

Fig. S3. Resistance to Thielaviopsis basicola in transgenic cotton lines (#68L-19, #68L-20, and #68L-5) expressing AtNPR1. WT: wild-type. Root weight was used as a parameter to score disease-severity in experiment #2, conducted under growth chamber conditions, one month following inoculation with the pathogen. Data represent mean±SE, *P<0.05, **P<0.01; n=10.

0

100

200

300

400

WT 68L-19 68L-20 68L-5

Chl

amyd

ospo

res/

mg

root

***

***

*

Fig. S4. Resistance to Thielaviopsis basicola in transgenic cotton lines (#68L-19, #68L-20, and #68L-5) expressing AtNPR1. WT: wild-type. Chlamydospore count was obtained from the roots of WT and transgenic cotton plants, one month following inoculation with the pathogen in experiment # 2. Data represent mean±SE; *P<0.05, ***P<0.001; n=3; each replicate is a representative sample obtained from roots pooled from 3-4 infected plants.

WT 68L-20 WT 68L-20

Uninfected Infected

Fig. S5. Stunting of growth caused by Thielaviopsis basicola in wild-type (WT) and transgenic cotton plants expressing AtNPR1 gene. The image depicted is of plants three months following inoculation with the pathogen from experiment #4 conducted under greenhouse conditions.