Table 1.
Genes Displaying Rapid Responsiveness to Shade in a Robustly to Moderately PIF-Dependent Manner (Classes A and B combined [see Supplemental Figure 4B online] with a FIR >1.5; Figure 2)
| Locus | TAIR Annotation | Wild-Type FIa | pifq FIb | FR1 FIRc |
| Genes with G-Boxes in Promoter (44 Genes) | ||||
| Transcription | ||||
| AT4G32280 | IAA29 | 25.72 | 10.20 | 2.52 |
| AT4G16780 | ATHB-2 | 13.34 | 3.10 | 4.30 |
| AT1G02340 | HFR1 | 8.47 | 1.52 | 5.58 |
| AT2G42870 | PAR1 | 5.98 | 2.29 | 2.61 |
| AT3G15540 | IAA19 | 5.37 | 2.56 | 2.10 |
| AT5G39860 | PRE1 | 4.09 | 2.30 | 1.78 |
| AT4G01250 | WRKY22 | 3.84 | 2.21 | 1.73 |
| AT3G23030 | IAA2 | 3.71 | 2.37 | 1.57 |
| AT1G69570 | Dof-type Zn finger | 3.34 | 1.52 | 2.19 |
| AT1G18400 | BEE1 | 2.74 | 1.71 | 1.60 |
| AT5G15160 | bHLH 134 | 2.57 | 1.21 | 2.12 |
| AT1G14920 | GAI | 2.45 | 1.45 | 1.68 |
| AT1G01260 | bHLH 13 | 2.36 | 1.03 | 2.28 |
| AT1G69690 | TCP15 | 2.33 | 1.45 | 1.61 |
| AT3G57800 | bHLH 60 | 2.32 | 1.30 | 1.79 |
| AT5G43700 | IAA4 | 2.20 | 1.44 | 1.52 |
| AT5G28300 | Trihelix DNA binding protein | 2.15 | 1.03 | 2.09 |
| AT2G46270 | GBF3 | 2.14 | 1.27 | 1.68 |
| AT5G53980 | ATHB52 | 2.05 | 1.27 | 1.61 |
| AT1G69010 | BIM2 | 2.04 | 0.99 | 2.07 |
| AT4G30410 | Transcription factor | 2.03 | 1.18 | 1.73 |
| Hormone | ||||
| AT3G03830 | SAUR28 | 7.83 | 3.16 | 2.48 |
| AT4G13790 | SAUR25 | 5.79 | 1.38 | 4.19 |
| AT1G75450 | CKX5 | 2.68 | 1.08 | 2.48 |
| AT3G59900 | ARGOS | 2.30 | 1.22 | 1.88 |
| Cellular metabolism | ||||
| AT5G54490 | PBP1 | 3.06 | 1.77 | 1.73 |
| AT4G25260 | Invertase/pectin methylesterase inhibitor | 2.42 | 1.18 | 2.05 |
| AT1G04180 | FMO family protein | 2.37 | 1.53 | 1.55 |
| AT3G54510 | ERD protein-related | 2.27 | 1.18 | 1.92 |
| Growth/development | ||||
| AT4G14130 | XTR7 | 3.59 | 1.59 | 2.26 |
| Photosynthesis/chloroplast | ||||
| AT5G02020 | SISR | 2.14 | 1.42 | 1.50 |
| Stress/defense | ||||
| AT4G28240 | Wound-responsive protein | 2.25 | 1.43 | 1.57 |
| AT5G63650 | SNRK2.5 | 2.07 | 1.18 | 1.75 |
| Transport | ||||
| AT5G66110 | Metal ion binding | 2.08 | 1.15 | 1.80 |
| Unknown | ||||
| AT5G12050 | Unknown protein | 9.25 | 5.01 | 1.85 |
| AT3G29370 | Unknown protein | 5.48 | 2.55 | 2.15 |
| AT5G02580 | Unknown protein | 3.65 | 1.15 | 3.17 |
| AT5G50335 | Unknown protein | 3.25 | 1.55 | 2.10 |
| AT3G55840 | Unknown protein | 3.15 | 1.72 | 1.83 |
| AT5G66590 | Unknown protein | 2.65 | 1.38 | 1.93 |
| AT1G21050 | Unknown protein | 2.60 | 1.33 | 1.95 |
| AT3G29575 | Unknown protein | 2.31 | 1.09 | 2.12 |
| AT5G57760 | Unknown protein | 2.31 | 1.12 | 2.05 |
| AT3G50900 | Unknown protein | 2.05 | 1.27 | 1.61 |
| Genes with No G-Boxes in Promoter (16 Genes) | ||||
| Transcription | ||||
| AT5G44260 | Zn finger (CCCH-type) | 2.60 | 1.72 | 1.51 |
| AT3G60390 | HAT3 | 2.41 | 1.47 | 1.65 |
| Hormone | ||||
| AT5G18060 | SAUR23 | 11.26 | 4.20 | 2.68 |
| AT1G29490 | SAUR68 | 6.92 | 1.79 | 3.87 |
| AT1G29440 | SAUR63 | 4.74 | 2.41 | 1.97 |
| AT4G38850 | SAUR15 | 4.20 | 2.10 | 2.00 |
| AT1G29460 | SAUR65 | 3.65 | 2.09 | 1.75 |
| AT2G21200 | SAUR7 | 3.24 | 2.04 | 1.58 |
| AT1G02400 | GA2OX6 | 2.43 | 1.43 | 1.70 |
| Cellular metabolism | ||||
| AT5G02540 | SDR | 4.40 | 2.49 | 1.77 |
| AT4G27280 | Calcium binding EF hand | 3.33 | 2.22 | 1.50 |
| Signaling | ||||
| AT5G14470 | GHMP kinase-related | 3.23 | 2.08 | 1.55 |
| AT3G16800 | PP2C | 2.32 | 0.99 | 2.34 |
| Unknown | ||||
| AT2G28400 | Unknown protein | 2.24 | 1.37 | 1.64 |
| AT1G36940 | Unknown protein | 2.16 | 1.34 | 1.61 |
| AT4G35720 | Unknown protein | 2.05 | 0.97 | 2.10 |
Genes in boldface type were previously identified as shade responsive (Carabelli et al., 2007; Tao et al., 2008). TAIR, The Arabidopsis Information Resource.
a
FI in the wild type after exposure to 1 h of simulated shade signal.
b
FI in pifq after exposure to 1 h of simulated shade signal.