Table 2. Photoperiod induced changes in the magnitude of gene expression in candidate flowering time loci not observed to alter their pattern over time (see Table 1).
| ZT0 | ZT2 | ZT4 | |||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Condition | Mean | Log2 | Log2 | adj. | Mean | Log2 | Log2 | adj. | Mean | Log2 | Log2 | adj. | |||||
| Gene identifier | Name | Description (Mt4.0 annotation) | adj. p-value | read count | fold-change | s.e | p-value | read count | fold-change | s.e | p-value | read count | fold-change | s.e | p-value | Cluster | Membership |
| Medtr2g049520 | MtPHYE | phytochrome protein | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr1g016920 | MtELF3b | EARLY flowering protein, putative | 5.50 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr8g015470 | ELF3-like | hypothetical protein | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr8g020200 | ELF4-like | early flowering protein | 1.60 ×10−20 | 100 | −0.88 | 0.18 | 1.50 ×10−05 | 98 | −1.2 | 0.19 | 7.40 ×10−09 | 210 | −0.94 | 0.16 | 1.70 ×10−07 | 13 | 0.43 |
| Medtr4g125590 | ELF4-like | early flowering protein | 1.60 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr2g036510 | MtZTL | galactose oxidase/kelch repeat protein | 8.20 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr7g084970 | MtFTa1 | flowering locus protein T | 1.80 ×10−27 | 28 | 5.2 | 0.79 | 1.20 ×10−09 | 16 | 6.4 | 1.2 | 1.90 ×10−06 | 55 | 6.8 | 0.89 | 2.10 ×10−12 | 1 | 0.32 |
| Medtr6g033040 | MtFTa3 | flowering locus protein T | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr7g006690 | MtFTb2 | flowering locus protein T | 5.20 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr2g461760 | MtFULa | MADS-box transcription factor | 2.90 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr7g016630 | MtFULc | MADS-box transcription factor | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr8g033250 | MtSOC1b | MADS-box transcription factor | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr8g033220 | MtSOC1c | MADS-box transcription factor | 9.80 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr2g016030 | MtCDFa | Dof domain zinc finger protein | 7.60 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr5g041380 | MtCDFd | DOF domain, zinc finger protein | 4.40 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr6g027450 | MtCDFf | Dof zinc finger DOF5.2-like protein | 2.10 ×10−09 | 12 | 3.1 | 0.67 | 4.10 ×10−05 | 9.8 | 1.8 | 0.57 | 5.50 ×10−03 | 2.7 | 3.7 | 1.3 | 9.70 ×10−03 | 2 | 0.53 |
| Medtr7g086780 | MtCDFg | Dof zinc finger DOF5.2-like protein | 5.00 ×10−02 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr8g044220 | MtCDFh | DOF-type zinc finger DNA-binding family protein | 9.50 ×10−05 | 65 | 0.93 | 0.21 | 1.10 ×10−04 | 60 | 0.49 | 0.21 | 4.00 ×10−02 | 63 | 0.26 | 0.21 | 2.80 ×10−01 | 2 | 0.4 |
| Medtr5g009530 | SPA1-like | ubiquitin ligase cop1, putative | 1.90 ×10−06 | 890 | −0.22 | 0.062 | 1.40 ×10−03 | 980 | −0.28 | 0.061 | 3.50 ×10−05 | 850 | −0.096 | 0.063 | 1.70 ×10−01 | 18 | 0.52 |
| Medtr2g085210 | SPA1-like | ubiquitin ligase cop1, putative | 2.40 ×10−03 | 4100 | 0.075 | 0.086 | 4.30 ×10−01 | 4600 | 0.36 | 0.086 | 1.80 ×10−04 | 4700 | 0.18 | 0.086 | 6.20 ×10−02 | 6 | 0.45 |
| Medtr4g009840 | TPL-like | topless-like protein | 9.00 ×10−11 | 3200 | −0.35 | 0.11 | 3.30 ×10−03 | 3000 | −0.51 | 0.11 | 1.40 ×10−05 | 2000 | −0.49 | 0.11 | 4.30 ×10−05 | 18 | 0.88 |
| Medtr4g114980 | TPL-like | topless-like protein | 1.20 ×10−05 | 840 | −0.25 | 0.14 | 9.90 ×10−02 | 960 | −0.42 | 0.13 | 6.30 ×10−03 | 1200 | −0.59 | 0.13 | 8.90 ×10−05 | 9 | 0.57 |
| Medtr2g435370 | TPL-like | transducin family protein/WD-40 repeat protein | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr2g435440 | TPL-like | topless-like protein | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr7g112460 | TPL-like | topless-like protein | 1.60 ×10−18 | 570 | −0.57 | 0.12 | 1.20 ×10−05 | 430 | −0.65 | 0.12 | 1.40 ×10−06 | 450 | −0.73 | 0.12 | 3.40 ×10−08 | 10 | 0.5 |
| Medtr2g065670 | TPL-like | topless-like protein | 6.70 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr2g435380 | TPL-like | topless-like protein | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr1g012820 | TPL-like | topless-like protein | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr1g082660 | NF-YC like | nuclear transcription factor Y protein | 6.40 ×10−03 | 370 | −0.38 | 0.094 | 2.90 ×10−04 | 490 | −0.14 | 0.089 | 1.60 ×10−01 | 530 | −0.065 | 0.088 | 5.10 ×10−01 | 12 | 0.34 |
| Medtr7g113680 | NF-YC like | nuclear transcription factor Y protein | 1.10 ×10−10 | 490 | 0.37 | 0.1 | 1.40 ×10−03 | 380 | 0.46 | 0.11 | 1.40 ×10−04 | 400 | 0.41 | 0.11 | 6.30 ×10−04 | 4 | 0.69 |
| Medtr8g104190 | MtCOLi | zinc finger constans-like protein | 2.00 ×10−02 | 5800 | −0.032 | 0.07 | 6.90 ×10−01 | 4100 | −0.092 | 0.071 | 2.50 ×10−01 | 6100 | −0.29 | 0.07 | 1.80 ×10−04 | 15 | 0.28 |
| Medtr5g072780 | MtCMF3 | CCT motif protein | 6.10 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr3g100040 | MtCMF5 | GATA transcription factor | 4.50 ×10−02 | 240 | −0.4 | 0.13 | 8.00 ×10−03 | 180 | −0.14 | 0.14 | 3.80 ×10−01 | 210 | −0.063 | 0.14 | 6.80 ×10−01 | 14 | 0.83 |
| Medtr3g100050 | MtCMF6 | GATA transcription factor | 1.20 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr5g066510 | MtCMF7 | GATA transcription factor | 2.40 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr4g093730 | MtCMF8 | GATA transcription factor | 1.70 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr4g061910 | MtCMF11a | CCT motif protein | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr4g061823 | MtCMF11b | CCT motif protein | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr2g096080 | MtCMF12 | CCT motif protein | 1.50 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr8g098725 | MtCMF13 | CCT motif protein | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr5g010120 | MtCMF14 | CCT motif protein | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr2g068730 | MtCMF15 | CCT motif protein | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr1g044785 | MtCMF17 | CCT motif protein | 1.80 ×10−02 | 2.3 | -2 | 1 | 8.70 ×10−02 | 4.5 | −1.6 | 0.76 | 6.80 ×10−02 | 13 | −0.51 | 0.54 | 4.00 ×10−01 | 16 | 0.54 |
| Medtr4g008090 | MtCMF18 | GATA transcription factor, putative | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr3g113070 | CCT domain gene | salt tolerance-like protein | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr4g071200 | CCT domain gene | salt tolerance-like protein | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr8g012290 | MtCBL4 | BHLH transcription factor | 1.40 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr5g048860 | MtCBL6 | BHLH transcription factor | 4.20 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr8g065740 | MtCBL7 | transcription factor | 6.20 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr8g099880 | MtCBL9 | basic helix loop helix protein BHLH8 | 5.40 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr8g062240 | MtCBL10 | transcription factor | 8.90 ×10−03 | 110 | 0.066 | 0.16 | 7.20 ×10−01 | 64 | 0.28 | 0.19 | 1.90 ×10−01 | 82 | 0.72 | 0.18 | 3.60 ×10−04 | 4 | 0.31 |
| Medtr1g069155 | MtPIF1b | transcription factor | 9.30 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| Medtr7g111320 | MtPIF3b | phytochrome-interacting factor 3.1 | 5.80 ×10−01 | – | – | – | – | – | – | – | – | – | – | – | – | – | – |
| 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 MtCOLi 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.