Table I. Genes regulated upon DEX induction.
| Gene Number | Gene Name | Putative Function | Callus 3 h | Roots 3 h | Callus 24 h | Roots 24 h | References |
|---|---|---|---|---|---|---|---|
| Transcription Factors Putatively Involved in the Epidermal Cell Fate | |||||||
| Solyc09g065100 | SlbHLH150 | — | 63 | 199 | 1259 | 2512 | (Sun et al., 2015) |
| Rosea 1 | Rosea 1 | Anthocyanin biosynthesis | 234 | 316 | 63 | 100 | (Goodrich et al., 1992) |
| Delila | Delila | Anthocyanin biosynthesis | 63 | 398 | 40 | 199 | (Schwinn et al., 2006) |
| Solyc07g052490 | MYB-CPC-like | Trichome and root hair regulation | 20 | 316 | 79 | 158 | — |
| Solyc03g120620 | GL2 | Cuticle regulation | 6 | 39 | 5 | 31 | (Lashbrooke et al., 2015) |
| Solyc01g109120 | WD40 repeat | — | 12 | 16 | 25 | 6 | — |
| Solyc10g055410 | SlTHM27 | Anthocyanin biosynthesis | 31 | 6 | 79 | 2 | (Matus et al., 2009) |
| Solyc04g072890 | WD40 repeat | — | 16 | 10 | 8 | 4 | — |
| Solyc03g098200 | HDG11-like/GL2- like | — | 2.5 | 6 | 2.5 | 10 | (Yu et al., 2008) |
| Solyc02g088190 | MIXTA-like | Epidermis and cuticle development | 2 | 3 | 4 | 8 | (Lashbrooke et al., 2015) |
| Solyc03g097340 | TTG1-like | Trichome and root hair regulation | 5 | 4 | 2.5 | 3 | (Galway et al., 1994) |
| Solyc10g081320 | SlMYB69 | — | −4 | −5 | −2 | −2 | (Stracke et al., 2001) |
| Solyc09g057710 | SlbHLH057 | — | 4 | 5 | 2 | 2 | (Sun et al., 2015) |
| Solyc04g074170 | SlMYB39 | — | −3 | −2.5 | −3 | −5 | — |
| Solyc05g051550 | SlMYB | — | −5 | −2.5 | −5 | −6 | — |
| Solyc09g018500 | SlbHLH | — | −20 | −10 | −20 | −32 | — |
| Cutin Pathway | |||||||
| Solyc00g278110 | CER1-like | Cutin synthesis | 29 | 252 | 17 | 199 | — |
| Solyc01g079240 | SlLACS1 | Cutin synthesis | 100 | 422 | 4.3 | 17 | (Girard et al., 2012) |
| Flavonoid Pathway | |||||||
| Solyc09g091510 | CHS2 | Chalcone synthase | 4 | 398 | 125 | 5011 | (Tohge et al., 2015) |
| Solyc05g052240 | CHIL | Chalcone isomerase | 20 | 316 | 100 | 631 | (Tohge et al., 2015) |
| Solyc05g010320 | CHI | Chalcone isomerase | 2.5 | 3.1 | 7.9 | 7.9 | (Tohge et al., 2015) |
| Solyc02g083860 | F3H | Flavanone 3-hydroxylase | 12 | 158 | 16 | 251 | (Tohge et al., 2015) |
| Solyc11g066580 | F3′5’H | Flavonoid-3′-monooxygenase | 501 | 1585 | 25,118 | 31,623 | (Tohge et al., 2015) |
| Solyc02g085020 | DFR | Dihydroflavonol 4-reductase | 15,849 | 5012 | 19,953 | 5012 | (Butelli et al., 2008) |
| Solyc08g080040 | ANS | Leucoanthocyanidin dioxygenase | 126 | 251 | 251 | 251 | (Tohge et al., 2015) |
| Solyc09g082660 | AnthOMT | Anthocyanin-O-methyltransferase | 501 | 100 | 5012 | 1995 | (Gomez Roldan et al., 2014) |
| Solyc10g083440 | A3GT | Anthocyanin-3-O-Glucosyltransferase | 501 | 630 | 398 | 501 | (Butelli et al., 2008) |
| Solyc09g059170 | A3G2”GT | Anthocyanin-3-O-gluc-2″ GT | 148 | 631 | 631 | 1000 | (Tohge et al., 2015) |
| Solyc12g098590 | A5GT | Anthocyanin-5-O- Glucosyltransferase | 1585 | 630 | 25,119 | 10,000 | (Tohge et al., 2015) |
| Solyc12g088170 | SlFdAT1 | Anthocyanin acyltransferase | 794 | 3162 | 1585 | 10,000 | (Tohge et al., 2015) |
| Solyc08g068700 | THT7-1 | Acyltransferase | 4 | 2.5 | 10 | 2.5 | (Von Roepenack et al., 2003) |
| Solyc03g097500 | HCT-like | Acyltransferase | −2 | −2.5 | −2.5 | −3 | — |
| Solyc08g078030 | HCT-like | Acyltransferase | −12 | −3 | −12 | −5 | — |
| Solyc10g078240 | C3H | p-Coumarate 3-hydroxylase | 5 | 4 | 4 | 2.5 | (Butelli et al., 2008) |
| Solyc02g081340 | GST | Glutathione-S-transferase | 1585 | 10,000 | 2511 | 10,000 | (Butelli et al., 2008) |
| Solyc10g084960 | GST | Glutathione-S-transferase | 10 | 10 | 6 | 5 | — |
| Solyc07g056510 | GST | Glutathione-S-transferase | 6 | 8 | 3 | 3 | — |
| Solyc06g009020 | GST | Glutathione-S-transferase | 4 | 5 | 3 | 2.5 | — |
| Solyc03g025190 | FFT | Flower flavonoid transporter/putative anthocyanin permease | 316 | 10,000 | 2000 | 50,119 | (Mathews et al., 2003) |
| Pentose Phosphate Pathway | |||||||
| Solyc10g018300 | Tansketolase | Transketolase | −2.5 | −4 | 2 | 2.5 | — |
| Solyc09g008840 | Pyruvate kinase | Pyruvate kinase | 3.4 | 2.5 | 4 | 2.6 | — |
| Solyc12g056940 | Acetyl-CoA carboxylase | Acetyl-CoA carboxylase | 17 | 12 | 12 | 9 | — |
| Shikimate Pathway | |||||||
| Solyc04g051860 | SK1 | Shikimate kinase | 4 | 4 | 2.5 | 2 | (Schmid et al., 1992) |
| Phenylpropanoid Pathway | |||||||
| Solyc02g086770 | CCR | Cinnamoyl CoA reductase | 40 | 32 | 20 | 10 | (Tohge et al., 2015) |
| Solyc08g005120 | CCR | Cinnamoyl CoA reductase | 4 | 8 | 5 | 5 | — |
| Solyc03g036480 | PAL | Phe ammonia lyase | 6 | 8 | 5 | 5 | — |
| Solyc03g036470 | PAL | Phe ammonia lyase | 6 | 8 | 6 | 4 | — |
| Solyc05g056170 | PAL6 | Phe ammonia lyase | 5 | 3 | 10 | 3 | (Tohge et al., 2015) |
| Solyc09g007910 | PAL3 | Phe ammonia lyase | 10 | 2 | 5 | 2 | (Tohge et al., 2015) |
| Solyc03g042560 | PAL | Phe ammonia lyase | 5 | 6 | 6 | 3 | (Butelli et al., 2008) |
| Solyc01g079240 | 4CL6 | 4-Coumaroyl CoA ligase | 16 | 4 | 398 | 16 | (Tohge et al., 2015) |
Shown are accession numbers (1st column), gene abbreviation (2nd column), putative function (3rd column), fold-change induction upon DEX application in callus after 3 h (4th column), in roots after 3 h (5th column), in callus after 24 h (6th column), in roots after 24 h (7th column), and a reference for the function of the gene (8th column). Only genes for which a t test indicates that expression upon DEX induction is significantly different from noninducing conditions (t test n = 3; P ≤ 0.05) are shown. More genes can be found in Supplemental Table S2.