Table 3.
qRT–PCR validation of the RNA-seq data.
| Gene Name | Functional Annotation | Fold Change (P3A vs. P3B) | ||
|---|---|---|---|---|
| Methylation | Transcriptome | qRT–PCR | ||
| atp8 | Phospholipid-transporting atpase 8 | 2.18 | 0.49 | 0.47 |
| COX2 | Cytochrome c oxidase subunit II | 2.19 | 4.53 | 6.39 |
| DDM1 | ATP-dependent DNA helicase DDM1 | 0 | 0.49 | 0.86 |
| DME | Transcriptional activator DEMETER | 2.16 | 0.48 | 0.6 |
| DRM1 | DNA(cytosine-5)-methyltransferase DRM1 | 2.04 | 0.47 | 0.35 |
| DRM2 | DNA(cytosine-5)-methyltransferase DRM2 | 0.72 | 0.47 | 0.72 |
| FAAH | Fatty acid amide hydrolase | 2.81 | 0.09 | 0.12 |
| FRU | Acid beta-fructofuranosidase | 5.59 | 0.19 | 0.14 |
| GA2ox6 | Gibberellin 2-oxidase | 0.03 | 104.5 | 100 |
| GLU | Beta-glucosidase bogh3b-like | 3.34 | 0.18 | 0.12 |
| IAA32 | Auxin-responsive protein IAA32 | 4.49 | 3.32 | 1.52 |
| ILR1 | IAA-amino acid hydrolase ILR1 | 0.67 | 0.1 | 0.48 |
| LIM2 | LIM domain-containing protein WLIM2b | 5.88 | 0.04 | 0.03 |
| LSD | Lysine-specific demethylase | 2.02 | 0.49 | 0.33 |
| MADS2 | MADS-box transcription factor 2 | 6.38 | 0.45 | 0.49 |
| MADS23 | MADS-box transcription factor 23 | 0.63 | 0.45 | 0.25 |
| AGL29 | MADS-box gene, AGL29 | 0.81 | 0.37 | 0.2 |
| AGL30 | MADS-box gene, AGL30 | 0.84 | 0.19 | 0.13 |
| AGL61 | MADS-box gene, AGL61 | 0.79 | 0/15.6 | 0.03 |
| AGL62 | MADS-box gene, AGL62 | 6.78 | 0.42 | 0.17 |
| AGL104 | MADS-box gene, AGL104 | 0.54 | 0.29 | 0.27 |
| MET1 | DNA methylation 1 | 1.46 | 0.5 | 0.58 |
| MYB21 | Myb21 | 0/2.1 | 14.08 | 2.81 |
| MYB26 | Myb26 | 0/1 | 0.5 | 0.47 |
| PHY | Phytochrome B | 0.58 | 0.46 | 0.33 |
| PK | Pyruvate kinase, cytosolic isozyme | 1.53 | 0.12 | 0.16 |
| ROS1 | ROS1, Repressor of silencing 1 | 1.34 | 0.46 | 0.3 |
Note: 0/2.1 means that the DNA methylation of P3A and P3B was 0 and 2.1, respectively.