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Table 1 Compiled subset of constructs approved by the BESC Transformation Committee for overexpression or knockdown of target genes to modify cell wall traits

From: Development and use of a switchgrass (Panicum virgatum L.) transformation pipeline by the BioEnergy Science Center to evaluate plants for reduced cell wall recalcitrance

Gene name

BESC ID

Transgene origin

Expression system

Gene in expression vector

Expression vector

Eventsa

Target expression levelb

Visual phenotype

Comments

PIc

Ref.

4-Coumarate: coenzyme A ligase (4CL)

180

Switchgrass

KD

Yes

pVT1629

100

80% decrease

Brown and red pigment in shootsd

 

2

[48, 62]

Cinnamic acid 4-hydroxylase (C4H)

182

Switchgrass

KD

Yes

pANIC 4B

9

50% decrease

Normal growth

No change in lignin or S/G monomer ratio

2

[48]

Hydroxycinnamoyl CoA: shikimate hydroxycinnamoyl transferase (HCT1)

184-1e

Switchgrass

KD

Yes

pANIC 8A

28

0–95% decrease

Normal growth

Revised to target HCT1. No change in lignin content or composition

7

This report

Hydroxycinnamoyl CoA: shikimate hydroxycinnamoyl transferase (HCT2)

184-2e

Switchgrass

KD

Yes

pANIC 8A

41

0–90% decrease

Normal growth

Revised to target HCT2. Increase in H lignin monomer in majority of transgenic lines analyzed. No change in lignin content.

7

This report

Caffeoyl CoA 3-O-methyl transferase (CCoAOMT)

186

Switchgrass

KD

Yes

pANIC8A

17

0–90% decrease

Normal growth

No change in lignin content or composition

7

[48]

Coumaroyl shikimate 3′-hydroxylase (C3′H)

264

Switchgrass

KD

Yes

pANIC 4A

48

0–80% decrease

Normal growth

No change in lignin content or composition

7

 

VirE2-interactor protein (VIP2)

266

Arabidopsis

OE

No

Not applicable (see comment)

Not applicable (see comment)

Not applicable (see comments)

Not applicable (see comment)

Gene not clonable

7

 

Arabinosyl transferase 1 (Rra1 reduced residual arabinose)

274

Switchgrass

KD

No

Not applicable (see comment)

Not applicable (see comment)

Not applicable (see comments)

Not applicable (see comment)

Gene not clonable

3

 

Endoxylanase (PttXyn10A) /Endoxylanase

282

Switchgrass

OE

No

Not applicable (see comment)

Not applicable (see comment)

Not applicable (see comments)

Not applicable (see comment)

Gene not clonable

3

 

LIM transcription factor (LIM 1)

292

Switchgrass

OE

No

Not applicable (see comment)

Not applicable (see comment)

Not applicable (see comments)

Not applicable (see comment)

Gene not clonable

2

 

R2R3-MYB transcription factor (MYB4)

294

Switchgrass

OE

Yes

pANIC 2B

5

ninefold to 11-fold increase

Varying impacts on growth, from reduced to increased yield

 

2

[33, 34, 36]

Gibberellin 20-oxidase (GA20-ox)

318

Foxtail millet

OE

Yes

pANIC 10A

3

No change

Normal growth. No change in biomass yield

No change in lignin content, S/G monomer ratio or sugar release

4

 

Gibberellin 20-oxidase (GA20-ox)

319

Switchgrass

KD

Yes

pANIC 12A

6

No change

Normal growth. No change in biomass yield

No change in lignin content, S/G monomer ratio or sugar release

4

 

NAC transcription factor (NAC 2)

321

Switchgrass

OE

No

Not applicable (see comment)

Not applicable (see comment)

Not applicable (see comment)

Not applicable (see comment)

Gene not clonable

1

 

Peroxidase-30

324

Switchgrass

OE

Yes

pANIC 6A

52

Not done

Normal growth

No change in lignin content or composition

5

 

Dirigent protein

327

Switchgrass

OE

Yes

pANIC 6A

23

Not done

Normal growth

No change in lignin content or composition

5

 

Dirigent protein

328

Switchgrass

KD

Yes

pANIC 8A

30

Not done

Normal growth

Full length construct in antisense orientation. No change in lignin content or composition

5

 

Peroxidase-1

343

Switchgrass

FKD

Yes

pANIC 8A

19

Not done

Normal growth

No change in lignin content or composition

5

 

NAC transcription factor (NAC-AP2)

348

Switchgrass

OE

Yes

pCAMBIA 1305

65

21-fold to 65-fold increase

Increased biomass yield in greenhouse

 

6

[63]

NAC transcription factor (NAC-AP2)

349

Switchgrass

FKD

Yes

pSTARGATE

6

No change

 

Discontinued (regenerated plants were false positive)

6

 

NAC transcription factor (NAC 033)

350

Switchgrass

OE

No

Not applicable (see comment)

Not applicable (see comment)

Not applicable (see comment)

Not applicable (see comment)

Gene not clonable

2

 

Dirigent protein-2

356

Switchgrass

KD

Yes

pANIC 8A

23

Not done

Normal growth

 

5

 

Sucrose synthase 1 (SUS1)

413

Switchgrass

OE

Yes

pANIC 10A

5

twofold to sevenfold increase

Increased plant height, tiller number and biomass yield.

Increased lignin

4

[64]

Cellulose synthase-like; subfamily D (CslD4)

540

Switchgrass

OE

Yes

pANIC 10A

10

Not done

Normal growth

Under further analysis

3

 

Cellulose synthase-like; subfamily J (CslJ)

543

Switchgrass

OE

Yes

pANIC 10A

11

Not done

Normal growth

Under further analysis

3

 

Cellulose synthase-like; subfamily F (CslF6)

549

Switchgrass

OE

Yes

pANIC 10A

23

Not done

Normal growth

Under further analysis

3

 

Cellulose synthase-like; subfamily F (CslF9)

552

Switchgrass

OE

No

Not applicable (see comment)

Not applicable (see comment)

Not applicable (see comment)

Not applicable (see comment)

Gene not clonable

3

 

Cellulose synthase 8 (CesA8)

558

Switchgrass

OE

Yes

pANIC 10A

10

Not done

Normal growth

Under further analysis

4

 

NAC transcription factor (NAC-AP2)

692

Switchgrass

OE

Yes

modified pER8

30

No change

Not determined

Discontinued as plants unresponsive to estradiol treatment

6

 

Laccase 4 (Lac 4)

693

Switchgrass

KD

Yes

pANIC 8A

30

Not done

Normal growth

No change in lignin amount or composition

5

 

R2R3-MYB transcription factor (MYB63-like2)

721

Switchgrass

OE

No

Not applicable (see comment)

Not applicable (see comment)

Not applicable (see comment)

Not applicable (see comment)

Gene not clonable

2

 

R2R3-MYB transcription factor (MYB63-like3)

722

Switchgrass

OE

No

Not applicable (see comment)

Not applicable (see comment)

Not applicable (see comment)

Not applicable (see comment)

Gene not clonable

2

 

Knotted-like homeobox protein 1 (KN1)

833

Switchgrass

KD

Yes

pANIC 12A

8

No change

Normal growth. No change in biomass yield

Discontinued

4

 

Knotted-like homeobox protein 1 (KN1)

834

Switchgrass

OE

Yes

pANIC 10A

5

Up to sevenfold increase

Normal growth. No change in biomass yield

 

4

[65]

Gibberellin 2-oxidase (GA2-ox)

835-1e

Switchgrass

OE

Yes

pANIC 10A

14

Up to 14-fold increase

Dwarf to semi-dwarf growth

 

4

[66]

Gibberellin 2-oxidase (GA2-ox)

835-2e

Switchgrass

OE

Yes

pANIC 10A

7

Up to fourfold increase

Dwarf growth

 

4

[66]

Ethylene response factor/SHINE transcription factor (ERF/SHN 1)

837

Switchgrass

OE

Yes

pANIC 10A

6

Up to ninefold increase

Normal growth. Increased biomass dry weight

 

4

[67]

UTR6

838

Switchgrass

FKD

Yes

pANIC 8A

30

18–70% decrease

 

No consistent correlation in lignin content, S/G monomer ratio or sugar release with gene expression levels

2

 

UTR6

839

Switchgrass

OE

Yes

pANIC 10A

50

Up to 38-fold increase

 

No consistent correlation in lignin content, S/G monomer ratio or sugar release with gene expression levels

2

 

Laccase 17-like gene A (LAC17a)

844

Switchgrass

FKD

Yes

pANIC 8A

40

No change

Normal growth

No change in lignin content

7

 

Laccase 17-like gene A (LAC17a)

845

Switchgrass

OE

Yes

pANIC 6A

40

No change

Normal growth

No change in lignin content

7

 

Laccase 17-like gene B (LAC17b)

846

Switchgrass

OE

Yes

pANIC 6A

40

No change

Normal growth

No change in lignin content

7

 

Purple acid phosphatase 2 (PAP2)

847

Switchgrass

OE

Yes

pMDC32

40

No change

Normal growth

No change in lignin content

7

 

Caffeoyl CoA 3-O-methyl transferase 2 (CCoAOMT2)

848

Switchgrass

KD

Yes

pANIC 8A

30

40–90% decrease

Normal growth

No change in lignin content.

7

[48]

Coumaroyl shikimate 3′-hydroxylase 2 (C3′H2)

849

Switchgrass

KD

Yes

pANDA

30

10–85% decrease

Normal growth

No change in lignin content

7

 

Basic helix-loop-helix transcription factor (bHLH1)

859

Switchgrass

OE

Yes

pANIC 10A

7

No change

Normal growth. No change in biomass yield

Discontinued

4

 

p-coumarate 3-hydroxylase 2 (C3H2)

861

Switchgrass

KD

No

Not applicable (see comment)

Not applicable (see comment)

Not applicable (see comment)

Not applicable (see comment)

Gene not clonable

2

 

p-coumarate 3-hydroxylase 2 (C3H2)

862

Switchgrass

OE

No

Not applicable (see comment)

Not applicable (see comment)

Not applicable (see comment)

Not applicable (see comment)

Gene not clonable

2

 

Xyloglucan endotransglucosylase/hydrolase (XTH-like2a)

863

Switchgrass

KD

Yes

pANIC 8A

30

40–80% decrease

Not observed

No change in lignin content

2

This report

Xyloglucan endotransglucosylase/hydrolase (XTH-like2a)

864

Switchgrass

OE

Yes

pANIC 10A

40

15–70% increase

Semidwarf to normal growth

No change in lignin content

2

This report

Xyloglucan endotransglucosylase/hydrolase (XTH-like1b)

870

Switchgrass

KD

Yes

pANIC 8A

30

10–80% decrease

Semidwarf to normal growth

No change in lignin content

2

This report

Xyloglucan endotransglucosylase/hydrolase (XTH-like1b)

871

Switchgrass

OE

Yes

pANIC 10A

40

20–150% increase

Semidwarf to normal growth

No change in lignin content

2

This report

Caffeic acid 3-O-methyltransferase (COMT)

930

Switchgrass

KD

Yes

pANDA

9

90% decrease

Normal growth. Increased biomass yield

 

7

[21, 35, 47, 48, 68,69,70]

  1. ID identification number, OE overexpression, KD knockdown, FKD family knockdown, Ref. References
  2. aNumber of independent events
  3. bDetermined by RT-qPCR
  4. cPrincipal Investigator associated with construct: (1) Fang Chen; (2) Richard A. Dixon; (3) Debra Mohnen; (4) C. Neal Stewart, Jr.; (5) Yuhong Tang; (6), Michael Udvardi; (7) Zeng-Yu Wang
  5. dBrown coloration in parts of leaf veins; brown patches in stems; reddish-brown coloration on the inner sides of basal stems and brownish color in the mature roots
  6. eHomologs of HCT or GA2-ox genes targeted after initial TP submission, designated by dashed numeral after BESC ID number