Table 1. Photoperiod induced changes in the pattern of gene expression over time in candidate flowering time loci.
| ZT0 | ZT2 | ZT4 | |||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Interaction | Mean | Log2 | Log2 | adj. | Mean | Log2 | Log2 | adj. | Meam | Log2 | Log2 | adj. | |||||
| Gene identifier | Name | Description (Mt4.0 annotation) | adj. p-value | read counts | fold-change | s.e | p-value | read counts | fold-change | s.e | p-value | read counts | fold-change | s.e | p-value | Cluster | Membership |
| Medtr1g085160 | MtPHYA | phytochrome protein A | 3.20 ×10−24 | 1100 | −0.13 | 0.10 | 2.30 ×10−01 | 1000 | −0.71 | 0.10 | 5.80 ×10−12 | 1900 | −1.60 | 0.10 | 6.90 ×10−60 | 11 | 0.41 |
| Medtr2g034040 | MtPHYB | phytochrome protein B | 2.70 ×10−08 | 790 | −0.38 | 0.08 | 7.60 ×10−06 | 800 | 0.06 | 0.08 | 5.50 ×10−01 | 590 | 0.34 | 0.08 | 1.50 ×10−04 | 18 | 0.74 |
| Medtr2g049520 | MtPHYE | phytochrome protein | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr5g063920 | MtCRY1 | cryptochrome protein | 1.70 ×10−13 | 5500 | −0.85 | 0.07 | 1.40 ×10−29 | 3600 | −0.04 | 0.07 | 6.30 ×10−01 | 4700 | −0.26 | 0.07 | 1.00 ×10−03 | 10 | 0.53 |
| Medtr1g076190 | MtCrRY2A | cryptochrome 2B apoprotein | 3.60 ×10−21 | 2500 | −0.68 | 0.08 | 1.40 ×10−16 | 1200 | 0.35 | 0.08 | 8.50 ×10−05 | 2000 | −0.65 | 0.08 | 6.30 ×10−15 | 15 | 0.47 |
| Medtr1g043190 | MtCRY2B | cryptochrome 2B apoprotein | 4.60 ×10−21 | 300 | −0.96 | 0.14 | 8.50 ×10−12 | 140 | −1.60 | 0.16 | 7.50 ×10−22 | 250 | −3.10 | 0.17 | 1.30 ×10−73 | 10 | 0.18 |
| Medtr7g118330 | MtLHY | late elongated hypocotyl-like protein | 3.00 ×10−70 | 37000 | −1.90 | 0.18 | 2.00 ×10−25 | 28000 | 0.57 | 0.18 | 2.60 ×10−03 | 18000 | 2.90 | 0.18 | 7.40 ×10−58 | 18 | 0.27 |
| Medtr4g108880 | MtTOC1a | two-component response regulator-like APRR7 protein | 1.50 ×10−58 | 75 | 4.40 | 0.36 | 2.10 ×10−31 | 63 | 2.00 | 0.23 | 5.10 ×10−17 | 120 | −0.97 | 0.18 | 2.60 ×10−07 | 2 | 0.69 |
| Medtr3g037390 | MtTOC1b | timing of cab expression 1/PRR response regulator | 2.00 ×10−22 | 100 | 1.70 | 0.19 | 4.10 ×10−18 | 100 | 0.88 | 0.18 | 2.30 ×10−06 | 190 | −0.71 | 0.15 | 1.70 ×10−05 | 2 | 0.37 |
| Medtr4g061360 | MtPRR37a | PRR response regulator | 1.20 ×10−11 | 580 | −4.40 | 0.21 | 1.80 ×10−97 | 1600 | −3.40 | 0.18 | 5.30 ×10−77 | 4400 | −2.40 | 0.17 | 1.10 ×10−40 | 12 | 0.41 |
| Medtr1g067110 | MtPRR37b | two-component response regulator-like APRR7 protein | 1.90 ×10−03 | 350 | −2.00 | 0.14 | 3.30 ×10−46 | 820 | −1.40 | 0.12 | 5.20 ×10−30 | 2700 | −2.10 | 0.12 | 5.60 ×10−66 | 9 | 0.34 |
| Medtr3g092780 | MtPRR59a | PRR response regulator | 4.20 ×10−30 | 22 | 0.28 | 0.32 | 4.60 ×10−01 | 150 | −2.30 | 0.24 | 4.40 ×10−20 | 1400 | −4.30 | 0.21 | 4.20 ×10−88 | 9 | 0.5 |
| Medtr8g024260 | MtPRR59b | PRR response regulator | 1.40 ×10−05 | 54 | −2.30 | 0.24 | 5.20 ×10−21 | 210 | −1.20 | 0.15 | 1.50 ×10−14 | 1300 | −2.00 | 0.13 | 5.50 ×10−56 | 9 | 0.33 |
| Medtr7g118260 | MtPRR59c | PRR response regulator | 9.50 ×10−34 | 200 | −6.20 | 0.38 | 8.60 ×10−57 | 710 | −2.00 | 0.18 | 3.30 ×10−26 | 2100 | −1.90 | 0.18 | 4.30 ×10−25 | 12 | 0.59 |
| Medtr3g103970 | MtELF3a | early flowering protein | 1.30 ×10−43 | 250 | 3.70 | 0.24 | 7.30 ×10−50 | 43 | 2.00 | 0.30 | 1.60 ×10−10 | 110 | −1.00 | 0.22 | 2.20 ×10−05 | 4 | 0.37 |
| Medtr1g016920 | MtELF3b | EARLY flowering protein, putative | 9.20 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr8g015470 | ELF3-like | hypothetical protein | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr8g015480 | ELF3-like | early flowering protein, putative | 4.50 ×10−12 | 160 | 1.50 | 0.23 | 4.20 ×10−10 | 56 | −0.38 | 0.26 | 2.00 ×10−01 | 150 | −0.86 | 0.23 | 4.40 ×10−04 | 16 | 0.34 |
| Medtr4g064730 | MtLUXa | myb-like DNA-binding domain, shaqkyf class protein | 1.60 ×10−07 | 11 | 3.80 | 0.79 | 6.10 ×10−06 | 12 | 0.36 | 0.45 | 5.00 ×10−01 | 21 | −0.62 | 0.38 | 1.50 ×10−01 | 7 | 0.57 |
| Medtr7g089010 | MtLUXb | MYB-like transcription factor family protein | 2.90 ×10−02 | 180 | −1.60 | 0.14 | 6.60 ×10−28 | 310 | −1.10 | 0.12 | 4.90 ×10−19 | 330 | −1.10 | 0.12 | 7.70 ×10−17 | 12 | 0.37 |
| Medtr3g070490 | MtELF4 | early flowering protein | 2.10 ×10−71 | 53 | 3.60 | 0.35 | 2.40 ×10−22 | 24 | 1.80 | 0.33 | 4.20 ×10−07 | 56 | −4.00 | 0.37 | 2.30 ×10−25 | 16 | 0.32 |
| Medtr8g020200 | ELF4-like | early flowering protein | 5.80 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr4g125590 | ELF4-like | early flowering protein | 9.20 ×10−02 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr2g041310 | ELF4-like | early flowering protein | 2.60 ×10−02 | 160 | −1.40 | 0.20 | 8.50 ×10−11 | 120 | −0.55 | 0.20 | 1.20 ×10−02 | 200 | −0.67 | 0.19 | 1.10 ×10−03 | 10 | 0.17 |
| Medtr1g098160 | MtGI | gigantea protein 1B | 2.60 ×10−14 | 35 | −3.40 | 0.36 | 5.90 ×10−20 | 3300 | −0.86 | 0.12 | 8.40 ×10−12 | 4100 | −1.70 | 0.12 | 1.20 ×10−45 | 9 | 0.23 |
| Medtr8g105590 | MtFKF1 | flavin-binding kelch repeat F-box protein, putative | 4.60 ×10−56 | 14 | 3.30 | 0.60 | 1.50 ×10−07 | 24 | −1.40 | 0.33 | 5.40 ×10−05 | 250 | −5.00 | 0.29 | 1.70 ×10−64 | 11 | 0.78 |
| Medtr2g036510 | MtZTL | galactose oxidase/kelch repeat protein | 6.90 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr2g058520 | MtE1 | E1 protein | 2.20 ×10−03 | 1.8 | −2.30 | 1.20 | 8.60 ×10−02 | 23 | 2.20 | 0.51 | 6.20 ×10−05 | 23 | 1.40 | 0.49 | 7.10 ×10−03 | 8 | 0.16 |
| Medtr7g084970 | MtFTa1 | flowering locus protein T | 5.70 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr7g085020 | MtFTa2 | flowering locus protein T | 2.80 ×10−03 | 17 | 1.00 | 0.44 | 3.80 ×10−02 | 11 | −1.10 | 0.49 | 4.90 ×10−02 | 28 | −0.97 | 0.39 | 2.30 ×10−02 | 11 | 0.3 |
| Medtr6g033040 | MtFTa3 | flowering locus protein T | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr7g006630 | MtFTb1 | flowering locus protein T | 2.00 ×10−03 | 0 | −0.16 | 1.70 | 9.40 ×10−01 | 3 | 5.00 | 1.30 | 2.10 ×10−04 | 90 | 9.90 | 1.20 | 2.60 ×10−15 | 3 | 0.4 |
| Medtr7g006690 | MtFTb2 | flowering locus protein T | 6.70 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr2g461760 | MtFULa | MADS-box transcription factor | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr4g109830 | MtFULb | MADS-box transcription factor | 3.00 ×10−02 | 10 | 1.70 | 0.60 | 8.00 ×10−03 | 24 | −0.27 | 0.46 | 6.30 ×10−01 | 15 | 1.40 | 0.52 | 1.60 ×10−02 | 8 | 0.39 |
| Medtr7g016630 | MtFULc | MADS-box transcription factor | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr7g075870 | MtSOC1a | MADS-box transcription factor | 7.40 ×10−04 | 110 | −0.16 | 0.18 | 4.60 ×10−01 | 120 | 0.53 | 0.18 | 5.30 ×10−03 | 150 | 0.86 | 0.17 | 1.90 ×10−06 | 3 | 0.35 |
| Medtr8g033250 | MtSOC1b | MADS-box transcription factor | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr8g033220 | MtSOC1c | MADS-box transcription factor | 9.80 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr2g059540 | MtCDF1 | Dof domain zinc finger protein | 8.80 ×10−03 | 0 | −0.16 | 1.70 | 9.40 ×10−01 | 8.7 | −4.70 | 1.10 | 4.30 ×10−05 | 96 | −8.20 | 1.10 | 1.00 ×10−13 | 11 | 0.4 |
| Medtr5g041420 | MtCDF2 | DOF zinc finger protein | 1.40 ×10−05 | 11 | −1.10 | 0.54 | 5.70 ×10−02 | 9.5 | 2.40 | 0.65 | 7.60 ×10−04 | 2.7 | 3.80 | 1.30 | 7.30 ×10−03 | 5 | 0.19 |
| Medtr5g041530 | MtCDF3 | cycling DOF factor 2 | 3.10 ×10−19 | 220 | 0.29 | 0.16 | 9.30 ×10−02 | 170 | 1.30 | 0.17 | 8.80 ×10−14 | 99 | 2.80 | 0.23 | 1.20 ×10−34 | 1 | 0.58 |
| Medtr6g012450 | MtCDF4 | DOF-type zinc finger DNA-binding family protein | 3.40 ×10−77 | 860 | −1.40 | 0.14 | 1.60 ×10−21 | 350 | 1.90 | 0.16 | 5.40 ×10−31 | 270 | 2.40 | 0.17 | 1.30 ×10−45 | 5 | 0.34 |
| Medtr6g027460 | MtCDF5 | Dof zinc finger DOF5.2-like protein | 1.40 ×10−18 | 370 | 1.40 | 0.19 | 4.40 ×10−13 | 350 | 2.00 | 0.19 | 2.30 ×10−24 | 100 | 4.90 | 0.37 | 1.30 ×10−37 | 1 | 0.69 |
| Medtr7g010950 | MtCDF6 | DOF-type zinc finger DNA-binding family protein | 6.40 ×10−30 | 360 | −0.40 | 0.16 | 2.50 ×10−02 | 260 | 1.60 | 0.17 | 1.10 ×10−19 | 200 | 2.40 | 0.19 | 2.40 ×10−36 | 1 | 0.32 |
| Medtr2g016030 | MtCDFa | Dof domain zinc finger protein | 8.90 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr3g435480 | MtCDFb | DOF-type zinc finger DNA-binding family protein | 2.60 ×10−22 | 1400 | −3.10 | 0.24 | 2.40 ×10−35 | 800 | −0.33 | 0.24 | 2.30 ×10−01 | 1400 | 0.33 | 0.24 | 2.20 ×10−01 | 12 | 0.23 |
| Medtr4g082060 | MtCDFc | DOF-type zinc finger DNA-binding family protein | 1.90 ×10−41 | 970 | −1.90 | 0.15 | 5.40 ×10−35 | 720 | 0.73 | 0.15 | 2.80 ×10−06 | 760 | 0.69 | 0.15 | 1.10 ×10−05 | 13 | 0.26 |
| Medtr5g041380 | MtCDFd | DOF domain, zinc finger protein | 6.00 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr5g041400 | MtCDFe | DOF domain, zinc finger protein | 2.70 ×10−06 | 8.3 | −2.70 | 0.71 | 2.80 ×10−04 | 8.7 | 1.00 | 0.58 | 1.20 ×10−01 | 3.5 | 2.50 | 0.98 | 1.70 ×10−02 | 18 | 0.21 |
| Medtr6g027450 | MtCDFf | Dof zinc finger DOF5.2-like protein | 3.30 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr7g086780 | MtCDFg | Dof zinc finger DOF5.2-like protein | 1.80 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr8g044220 | MtCDFh | DOF-type zinc finger DNA-binding family protein | 1.50 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr5g085250 | MtCOP1 | E3 ubiquitin-protein ligase COP1 | 1.70 ×10−02 | 1200 | −0.48 | 0.09 | 3.20 ×10−07 | 1800 | −0.26 | 0.09 | 6.10 ×10−03 | 1600 | −0.08 | 0.09 | 4.50 ×10−01 | 8 | 0.17 |
| Medtr5g009530 | SPA1-like | ubiquitin ligase cop1, putative | 1.90 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr8g027985 | SPA1-like | ubiquitin ligase cop1, putative | 8.90 ×10−170 | 310 | 3.40 | 0.16 | 5.10 ×10−96 | 1000 | −1.10 | 0.11 | 4.10 ×10−20 | 2400 | −1.60 | 0.11 | 1.60 ×10−47 | 17 | 0.46 |
| Medtr2g085210 | SPA1-like | ubiquitin ligase cop1, putative | 1.30 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr2g104140 | TPL-like | topless-like protein | 9.70 ×10−05 | 1700 | −0.89 | 0.12 | 3.30 ×10−13 | 1800 | −0.48 | 0.12 | 1.50 ×10−04 | 1500 | −0.11 | 0.12 | 4.20 ×10−01 | 18 | 0.2 |
| Medtr4g009840 | TPL-like | topless-like protein | 6.50 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr4g114980 | TPL-like | topless-like protein | 3.50 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr2g435370 | TPL-like | transducin family protein/WD-40 repeat protein | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr2g435440 | TPL-like | topless-like protein | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr4g120900 | TPL-like | topless-like protein | 1.10 ×10−04 | 980 | −0.48 | 0.07 | 9.70 ×10−12 | 1200 | −0.22 | 0.07 | 1.70 ×10−03 | 1400 | −0.05 | 0.06 | 5.40 ×10−01 | 12 | 0.34 |
| Medtr7g112460 | TPL-like | topless-like protein | 7.60 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr2g065670 | TPL-like | topless-like protein | 8.50 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr2g435380 | TPL-like | topless-like protein | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr1g012820 | TPL-like | topless-like protein | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr6g444980 | MtFE | myb-like transcription factor family protein | 3.00 ×10−04 | 430 | 0.46 | 0.10 | 6.50 ×10−06 | 380 | 0.03 | 0.10 | 7.90 ×10−01 | 440 | 0.61 | 0.10 | 8.50 ×10−10 | 1 | 0.29 |
| Medtr3g058980 | NF-YB like | nuclear transcription factor Y protein | 3.60 ×10−04 | 910 | 0.09 | 0.09 | 3.80 ×10−01 | 540 | −0.42 | 0.09 | 1.30 ×10−05 | 820 | −0.31 | 0.09 | 8.40 ×10−04 | 15 | 0.21 |
| Medtr5g095740 | NF-YB like | nuclear transcription factor Y protein | 2.40 ×10−09 | 570 | −0.80 | 0.17 | 4.70 ×10−06 | 160 | 0.69 | 0.18 | 5.00 ×10−04 | 430 | −0.74 | 0.17 | 3.30 ×10−05 | 15 | 0.54 |
| Medtr1g082660 | NF-YC like | nuclear transcription factor Y protein | 8.80 ×10−02 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr3g099180 | NF-YC like | nuclear transcription factor Y protein | 5.10 ×10−03 | 1800 | 0.51 | 0.12 | 5.40 ×10−05 | 1200 | 0.84 | 0.12 | 3.20 ×10−11 | 1900 | 0.22 | 0.12 | 9.40 ×10−02 | 4 | 0.23 |
| Medtr7g113680 | NF-YC like | nuclear transcription factor Y protein | 9.00 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr1g093600 | MtTEM1 | AP2/ERF and B3 domain transcription factor | 3.00 ×10−09 | 2600 | −1.50 | 0.16 | 3.90 ×10−20 | 560 | −0.15 | 0.17 | 4.50 ×10−01 | 360 | −1.50 | 0.17 | 1.30 ×10−16 | 14 | 0.46 |
| Medtr5g053920 | MtTEM2 | AP2/ERF and B3 domain transcription factor | 7.40 ×10−03 | 1900 | −1.20 | 0.17 | 2.10 ×10−11 | 1000 | −0.35 | 0.18 | 7.60 ×10−02 | 550 | −0.79 | 0.18 | 3.30 ×10−05 | 14 | 0.23 |
| Medtr4g061200 | MtTOE1a | AP2-like ethylene-responsive transcription factor | 1.90 ×10−05 | 42 | 1.10 | 0.28 | 1.90 ×10−04 | 37 | 0.61 | 0.28 | 4.80 ×10−02 | 70 | −0.67 | 0.25 | 1.30 ×10−02 | 2 | 0.25 |
| Medtr2g093060 | MtTOE1b | AP2-like ethylene-responsive transcription factor | 1.20 ×10−04 | 1200 | −0.15 | 0.08 | 1.00 ×10−01 | 1100 | −0.64 | 0.08 | 2.20 ×10−14 | 1600 | −0.24 | 0.08 | 4.90 ×10−03 | 9 | 0.2 |
| Medtr7g100590 | MtTOE1c | AP2 domain transcription factor | 1.90 ×10−02 | 49 | 0.82 | 0.27 | 6.00 ×10−03 | 28 | 0.30 | 0.30 | 4.00 ×10−01 | 64 | −0.36 | 0.26 | 2.10 ×10−01 | 16 | 0.38 |
| Medtr1g049140 | MtTOE2 | AP2 domain transcription factor | 2.50 ×10−17 | 1600 | −1.60 | 0.13 | 4.00 ×10−33 | 2500 | −0.65 | 0.13 | 8.40 ×10−07 | 2900 | 0.06 | 0.13 | 6.80 ×10−01 | 12 | 0.71 |
| Medtr5g016810 | MtAP2a | AP2 domain transcription factor | 2.30 ×10−14 | 510 | 0.57 | 0.11 | 2.80 ×10−07 | 880 | −0.61 | 0.10 | 4.30 ×10−09 | 730 | −0.24 | 0.10 | 3.30 ×10−02 | 6 | 0.46 |
| Medtr4g094868 | MtAP2b | AP2 domain transcription factor | 1.50 ×10−12 | 260 | 1.00 | 0.13 | 7.80 ×10−14 | 390 | −0.17 | 0.12 | 2.30 ×10−01 | 280 | −0.24 | 0.13 | 9.70 ×10−02 | 6 | 0.21 |
| Medtr7g018170 | MtCOLa | zinc finger constans-like protein | 5.90 ×10−104 | 4400 | −2.30 | 0.11 | 3.60 ×10−105 | 1500 | 0.79 | 0.11 | 1.50 ×10−12 | 2200 | 0.38 | 0.11 | 8.10 ×10−04 | 13 | 0.36 |
| Medtr1g013450 | MtCOLb | zinc finger constans-like protein | 1.60 ×10−47 | 5000 | −0.82 | 0.07 | 8.30 ×10−27 | 3800 | 0.16 | 0.08 | 5.50 ×10−02 | 3100 | 0.76 | 0.08 | 1.20 ×10−22 | 18 | 0.37 |
| Medtr3g105710 | MtCOLc | zinc finger constans-like protein | 1.30 ×10−28 | 1700 | −0.48 | 0.05 | 8.30 ×10−22 | 860 | 0.19 | 0.06 | 1.40 ×10−03 | 1200 | 0.28 | 0.05 | 5.00 ×10−07 | 14 | 0.32 |
| Medtr4g128930 | MtCOLd | zinc finger constans-like protein | 1.10 ×10−38 | 2400 | −2.60 | 0.14 | 6.10 ×10−81 | 1500 | −0.34 | 0.14 | 2.00 ×10−02 | 2300 | −0.35 | 0.13 | 1.50 ×10−02 | 12 | 0.19 |
| Medtr3g082630 | MtCOLe | B-box type zinc finger protein | 1.50 ×10−54 | 48 | 7.90 | 1.20 | 3.80 ×10−10 | 5 | 2.30 | 0.75 | 5.20 ×10−03 | 39 | −3.90 | 0.46 | 4.60 ×10−16 | 16 | 0.47 |
| Medtr5g069480 | MtCOLf | zinc finger constans-like protein | 9.40 ×10−12 | 490 | 4.20 | 0.21 | 1.40 ×10−88 | 130 | 2.20 | 0.21 | 4.50 ×10−24 | 110 | 2.40 | 0.23 | 4.10 ×10−25 | 4 | 0.57 |
| Medtr7g108150 | MtCOLg | zinc finger constans-like protein | 6.10 ×10−03 | 880 | −0.36 | 0.09 | 7.50 ×10−05 | 510 | 0.08 | 0.09 | 4.40 ×10−01 | 650 | −0.20 | 0.09 | 3.60 ×10−02 | 14 | 0.38 |
| Medtr7g083540 | MtCOLh | zinc finger constans-like protein | 6.20 ×10−07 | 57 | 0.14 | 0.24 | 6.30 ×10−01 | 69 | −0.19 | 0.23 | 5.00 ×10−01 | 61 | −1.70 | 0.26 | 8.40 ×10−11 | 16 | 0.1 |
| Medtr8g104190 | MtCOLi | zinc finger constans-like protein | 5.50 ×10−02 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr2g088900 | MtCOLj | zinc finger constans-like protein | 2.50 ×10−02 | 79 | −0.81 | 0.29 | 1.10 ×10−02 | 83 | 0.28 | 0.29 | 4.00 ×10−01 | 75 | 0.30 | 0.29 | 3.80 ×10−01 | 18 | 0.28 |
| Medtr1g110870 | MtCOLk | zinc finger constans-like protein | 1.40 ×10−19 | 2000 | 1.70 | 0.16 | 2.20 ×10−22 | 230 | −0.05 | 0.18 | 8.20 ×10−01 | 1200 | −0.53 | 0.17 | 3.10 ×10−03 | 15 | 0.19 |
| Medtr7g032240 | MtCMF1 | CCT motif protein | 7.90 ×10−04 | 910 | −0.26 | 0.08 | 2.10 ×10−03 | 470 | 0.11 | 0.09 | 2.50 ×10−01 | 1100 | 0.16 | 0.08 | 5.40 ×10−02 | 15 | 0.34 |
| Medtr4g127420 | MtCMF2 | import apparatus protein | 2.40 ×10−19 | 180 | 0.35 | 0.13 | 1.60 ×10−02 | 660 | −0.78 | 0.11 | 6.00 ×10−12 | 840 | −1.30 | 0.11 | 3.50 ×10−31 | 9 | 0.43 |
| Medtr5g072780 | MtCMF3 | CCT motif protein | 8.60 ×10−02 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr3g100040 | MtCMF5 | GATA transcription factor | 3.00 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr3g100050 | MtCMF6 | GATA transcription factor | 6.80 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr5g066510 | MtCMF7 | GATA transcription factor | 7.30 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr4g093730 | MtCMF8 | GATA transcription factor | 4.30 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr1g008220 | MtCMF9 | CCT motif protein | 3.40 ×10−21 | 480 | 1.20 | 0.18 | 6.30 ×10−11 | 500 | −1.30 | 0.18 | 2.00 ×10−12 | 50 | −0.54 | 0.24 | 3.90 ×10−02 | 18 | 0.27 |
| Medtr3g091340 | MtCMF10 | CCT motif protein | 7.60 ×10−43 | 470 | 1.90 | 0.14 | 3.20 ×10−42 | 700 | −0.79 | 0.13 | 6.90 ×10−09 | 100 | 0.66 | 0.17 | 2.90 ×10−04 | 18 | 0.18 |
| Medtr4g061910 | MtCMF11a | CCT motif protein | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr4g061823 | MtCMF11b | CCT motif protein | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr2g096080 | MtCMF12 | CCT motif protein | 7.90 ×10−02 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr8g098725 | MtCMF13 | CCT motif protein | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr5g010120 | MtCMF14 | CCT motif protein | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr2g068730 | MtCMF15 | CCT motif protein | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr1g073350 | MtCMF16 | CCT motif protein | 4.50 ×10−02 | 42 | 0.67 | 0.39 | 1.30 ×10−01 | 16 | −0.75 | 0.46 | 1.50 ×10−01 | 36 | −0.75 | 0.40 | 9.50 ×10−02 | 16 | 0.21 |
| Medtr1g044785 | MtCMF17 | CCT motif protein | 4.50 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr4g008090 | MtCMF18 | GATA transcription factor, putative | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr1g023260 | CCT domain gene | salt tolerance-like protein | 1.20 ×10−06 | 230 | 0.71 | 0.13 | 1.10 ×10−07 | 200 | −0.28 | 0.13 | 5.30 ×10−02 | 120 | 0.43 | 0.14 | 6.10 ×10−03 | 18 | 0.2 |
| Medtr1g109350 | CCT domain gene | B-box zinc finger protein, putative | 5.10 ×10−05 | 990 | 1.30 | 0.19 | 6.60 ×10−10 | 100 | 2.40 | 0.25 | 5.90 ×10−21 | 240 | 0.92 | 0.21 | 2.80 ×10−05 | 15 | 0.28 |
| Medtr2g011450 | CCT domain gene | B-box type zinc finger protein | 1.50 ×10−05 | 11 | −1.70 | 0.52 | 2.30 ×10−03 | 30 | 0.32 | 0.38 | 4.70 ×10−01 | 10 | 1.90 | 0.54 | 8.60 ×10−04 | 8 | 0.37 |
| Medtr2g073370 | CCT domain gene | B-box type zinc finger protein | 2.70 ×10−15 | 1.8 | 4.20 | 1.30 | 3.00 ×10−03 | 24 | −0.69 | 0.42 | 1.40 ×10−01 | 66 | −4.90 | 0.53 | 4.00 ×10−19 | 9 | 0.4 |
| Medtr2g089310 | CCT domain gene | B-box type zinc finger protein | 2.50 ×10−62 | 690 | −2.90 | 0.17 | 2.10 ×10−67 | 750 | 0.13 | 0.16 | 5.00 ×10−01 | 590 | 0.92 | 0.16 | 4.10 ×10−08 | 12 | 0.18 |
| Medtr2g099010 | CCT domain gene | salt tolerance-like protein | 1.00 ×10−42 | 18000 | −0.59 | 0.10 | 3.40 ×10−08 | 14000 | 0.25 | 0.10 | 2.30 ×10−02 | 12000 | 1.50 | 0.10 | 2.90 ×10−45 | 1 | 0.24 |
| Medtr3g113070 | CCT domain gene | salt tolerance-like protein | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr3g117320 | CCT domain gene | salt tolerance-like protein | 2.10 ×10−04 | 26 | 3.50 | 0.64 | 2.70 ×10−07 | 3.2 | 1.90 | 0.94 | 7.20 ×10−02 | 8.3 | −0.48 | 0.62 | 5.20 ×10−01 | 4 | 0.46 |
| Medtr4g008050 | CCT domain gene | B-box type zinc finger protein, putative | 2.30 ×10−11 | 49 | −0.70 | 0.27 | 1.70 ×10−02 | 530 | −0.09 | 0.21 | 7.40 ×10−01 | 350 | 1.60 | 0.22 | 3.90 ×10−13 | 8 | 0.26 |
| Medtr4g046640 | CCT domain gene | B-box type zinc finger protein | 3.70 ×10−08 | 12 | 0.42 | 0.53 | 5.10 ×10−01 | 81 | 1.20 | 0.42 | 7.60 ×10−03 | 34 | 5.30 | 0.76 | 1.70 ×10−11 | 8 | 0.65 |
| Medtr4g067320 | CCT domain gene | salt tolerance-like protein | 6.60 ×10−33 | 1200 | −2.10 | 0.10 | 9.10 ×10−91 | 1800 | −0.45 | 0.10 | 2.00 ×10−05 | 3700 | −0.71 | 0.10 | 2.60 ×10−12 | 12 | 0.65 |
| Medtr4g071200 | CCT domain gene | salt tolerance-like protein | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr5g021580 | CCT domain gene | salt tolerance-like protein | 3.00 ×10−08 | 1200 | −1.40 | 0.17 | 4.90 ×10−15 | 1600 | −0.37 | 0.17 | 4.30 ×10−02 | 1600 | 0.09 | 0.17 | 6.60 ×10−01 | 12 | 0.48 |
| Medtr3g116770 | MtCBL1 | BHLH transcription factor | 5.20 ×10−05 | 720 | −0.76 | 0.17 | 2.00 ×10−05 | 320 | 0.29 | 0.17 | 1.30 ×10−01 | 1300 | −0.68 | 0.16 | 1.20 ×10−04 | 10 | 0.16 |
| Medtr4g070320 | MtCBL2 | transcription factor | 3.90 ×10−02 | 1200 | −0.80 | 0.15 | 1.60 ×10−07 | 420 | −1.40 | 0.16 | 1.40 ×10−17 | 1900 | −0.86 | 0.14 | 1.50 ×10−08 | 10 | 0.16 |
| Medtr7g053410 | MtCBL3 | BHLH transcription factor | 2.70 ×10−05 | 150 | 0.08 | 0.13 | 6.40 ×10−01 | 130 | −0.52 | 0.14 | 5.30 ×10−04 | 210 | 0.39 | 0.12 | 2.70 ×10−03 | 3 | 0.083 |
| Medtr8g012290 | MtCBL4 | BHLH transcription factor | 9.40 ×10−02 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr1g017350 | MtCBL5 | transcription factor | 1.70 ×10−02 | 57 | 0.67 | 0.23 | 7.00 ×10−03 | 30 | −0.26 | 0.27 | 4.10 ×10−01 | 54 | −0.24 | 0.23 | 3.60 ×10−01 | 16 | 0.2 |
| Medtr5g048860 | MtCBL6 | BHLH transcription factor | 1.40 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr8g065740 | MtCBL7 | transcription factor | 8.00 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr3g498825 | MtCBL8 | transcription factor bHLH137 | 2.80 ×10−12 | 920 | −0.04 | 0.07 | 6.30 ×10−01 | 910 | −0.41 | 0.07 | 7.80 ×10−09 | 1000 | 0.32 | 0.07 | 7.00 ×10−06 | 18 | 0.18 |
| Medtr8g099880 | MtCBL9 | basic helix loop helix protein BHLH8 | 8.30 ×10−02 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr8g062240 | MtCBL10 | transcription factor | 6.00 ×10−02 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr5g037250 | MtCBL11 | transcription factor | 5.90 ×10−14 | 170 | −0.57 | 0.18 | 3.10 ×10−03 | 180 | −1.10 | 0.18 | 3.50 ×10−09 | 70 | 1.10 | 0.21 | 9.10 ×10−07 | 18 | 0.5 |
| Medtr7g092510 | MtCBL12 | transcription factor | 3.50 ×10−07 | 270 | 0.07 | 0.11 | 6.00 ×10−01 | 210 | −0.65 | 0.12 | 2.70 ×10−07 | 360 | −0.78 | 0.11 | 2.70 ×10−12 | 11 | 0.3 |
| Medtr1g059270 | MtCBL13 | transcription factor | 2.60 ×10−06 | 320 | 0.52 | 0.09 | 3.50 ×10−08 | 320 | −0.14 | 0.09 | 1.60 ×10−01 | 230 | 0.36 | 0.10 | 6.40 ×10−04 | 1 | 0.22 |
| Medtr6g084120 | MtCBL14 | transcription factor | 3.20 ×10−11 | 92 | −1.40 | 0.25 | 1.20 ×10−07 | 80 | 1.00 | 0.25 | 8.40 ×10−05 | 25 | −1.10 | 0.32 | 2.30 ×10−03 | 18 | 0.27 |
| Medtr7g099540 | MtPIF1a | transcription factor | 5.10 ×10−25 | 1000 | 1.00 | 0.08 | 9.20 ×10−37 | 1300 | 0.13 | 0.08 | 1.40 ×10−01 | 1200 | −0.12 | 0.08 | 1.70 ×10−01 | 6 | 0.22 |
| Medtr1g069155 | MtPIF1b | transcription factor | 9.00 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr1g084980 | MtPIF3a | phytochrome-interacting factor 3.1 | 6.90 ×10−16 | 1900 | −2.70 | 0.22 | 1.00 ×10−31 | 1200 | −0.44 | 0.22 | 7.70 ×10−02 | 300 | −0.09 | 0.23 | 7.60 ×10−01 | 18 | 0.34 |
| Medtr7g111320 | MtPIF3b | phytochrome-interacting factor 3.1 | 3.20 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr7g110810 | MtPIF6 | helix loop helix DNA-binding domain protein | 1.30 ×10−04 | 18 | −2.40 | 0.54 | 1.90 ×10−05 | 27 | 0.64 | 0.45 | 2.20 ×10−01 | 12 | 0.08 | 0.52 | 9.00 ×10−01 | 18 | 0.2 |
| Medtr3g449770 | MtPIF45 | transcription factor | 4.50 ×10−32 | 2500 | −2.00 | 0.11 | 1.40 ×10−69 | 2800 | −0.34 | 0.11 | 4.20 ×10−03 | 3200 | −0.28 | 0.11 | 2.20 ×10−02 | 12 | 0.42 |
| Medtr7g039110 | MtPIF78 | transcription factor | 1.20 ×10−03 | 5000 | −0.40 | 0.09 | 5.80 ×10−05 | 3800 | −0.08 | 0.09 | 4.60 ×10−01 | 3400 | 0.13 | 0.09 | 2.20 ×10−01 | 5 | 0.43 |
| Medtr1g019240 | MtPIL | helix loop helix DNA-binding domain protein | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr5g017040 | MtSPT | helix loop helix DNA-binding domain protein | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
Notes.
The genes listed in this table are loci known or hypothesised to participate in the photoperiod pathway in legumes along with homologues of the core components of the pathway in A. thaliana.
They include potential FT promoter binding genes compiled by Ridge et al. (2016) from which the naming of MtTOE1a to MtSPT derives.
Table depicts the the adjusted p-value for the interaction between time and condition. Note that if the adjusted p-value is significant each contrast between conditions at timepoints ZT0, ZT2 and ZT4 is also given to facilitate identifying where the patterns of expression diverge. Included in these results is the mean normalised read counts for the gene at this timepoint.
If the interaction term adjusted p-value is not significant contrasts are omitted.
In all cases it is the expression in LD relative to SD which is tested. In addition the cluster assignment and membership value are listed. Differentially expressed results are in bold using an α = 0.05.