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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