TABLE 4.
List of upregulated transcription factors with potential significance to the identified putative cis-elements among upregulated genes in five genotypes from diverse background in response to submergence tolerance.
| TF Family | Locus_ID (Annotation)* | Fold increase** |
| MYB | ||
| Os12g0125000 (MYB-like DNA-binding domain-containing protein) | 5.90 | |
| Os11g0128500 (MYB-like DNA-binding domain-containing protein) | 5.57 | |
| Os05g0553400 (Putative MYB-related transcription factor) | 5.14 | |
| Os01g0298400 (Putative typical P-type R2R3 MYB protein) | 4.55 | |
| Os12g0567300 (MYB transcription factor domain-containing protein: R2R3 MYB) | 3.24 | |
| Os01g0874300 (Putative MYB-related protein; Putative MYB2) | 3.20 | |
| Os05g0140100 (R2R3 MYB transcription factor) | 2.44 | |
| bZIP | ||
| Os11g0152700 (BZIP transcription factor: transcription factor HBP-1) | 5.48 | |
| Os12g0547600 (Calmodulin-binding protein, putative, expressed) | 3.10 | |
| Os05g0129300 (bZIP transcription factor) | 2.51 | |
| ERF | ||
| Os01g0968800 (DREB transcription factor like) | Infinite | |
| Os06g0127100 (Dehydration-responsive element-binding protein 1C) | Infinite | |
| Os01g0868000 (AP2/ERF transcription factor like) | 6.86 | |
| Os09g0522100 (Similar to Dehydration-responsive element-binding protein 1H) | 6.44 | |
| Os01g0140700 (Similar to RAV family protein: AP2/ERF and B3 domain-containing protein) | 6.16 | |
| Os02g0677300 (Similar to CRT/DRE binding factor 1) | 4.71 | |
| Os02g0654700 (AP2/ERF family protein) | 4.65 | |
| Os02g0656600 (Similar to DRE binding factor 2B) | 4.52 | |
| Os05g0549800 (Similar to DNA-binding protein RAV1) | 4.17 | |
| Os03g0184500 (B3 domain-containing protein: ABIVP1 transcription factor) | 3.58 | |
| Os01g0693400 (RAV family protein) | 2.89 | |
| ARF | ||
| Os12g0601400 (Auxin-responsive protein IAA31) | 2.51 | |
| WRKY | ||
| Os05g0583000 (Similar to WRKY transcription factor 8) | Infinite | |
| Os05g0537100 (WRKY transcription factor 10, WRKY transcription factor 7) | 4.27 | |
| Os01g0750100 (Similar to WRKY transcription factor 13) | 2.71 | |
| ZnF | ||
| Os03g0437200 (C2H2-type zinc finger protein, abscisic acid-induced antioxidant defense, Water stress and oxidative stress tolerance) | 6.82 | |
| Os03g0820300 (C2H2 transcription factor protein) | 6.16 | |
| Os12g0113700 (Zinc finger, C3HC4 type family protein) | 6.04 | |
| Os02g0646200 (Zinc finger, B-box domain-containing protein) | 4.43 | |
| Os10g0456800 (CHY zinc finger family protein) | 2.81 | |
| Os01g0303600 (Zinc finger, RING/FYVE/PHD-type domain-containing protein) | 3.82 | |
| Os06g0340200 (Zinc finger, RING-CH-type domain-containing protein) | 3.33 | |
| Os03g0329200 (Zinc finger CCCH domain-containing protein 23) | 3.27 | |
| Os03g0764100 (Zinc finger transcription factor ZF1) | 2.60 | |
| Os09g0486500 (Zinc finger A20 and AN1 domain-containing stress-associated protein 1) | 2.49 | |
| Os05g0128200 (Zinc finger CCCH domain-containing protein 33) | 2.21 | |
| NAC | ||
| Os11g0154500 (No apical meristem (NAM) protein domain-containing protein; NAC-domain-containing protein 90) | 5.83 | |
| Os03g0815100 (Similar to OsNAC6 protein) | 4.94 | |
| Os01g0884300 (NAC domain-containing protein 6) | 3.50 | |
| Os07g0684800 (Similar to NAM/CUC2-like protein) | 3.33 | |
| Os07g0225300 (OsNAC3 protein; NAC domain-containing protein 67) | 3.27 | |
| MADS-box | ||
| Os04g0580700MADS-box transcription factor 17 | 6.07 | |
| HSF | ||
| Os08g0471000 (Heat stress transcription factor B-4a, HSF20) | Infinite | |
| Os09g0526600 (Heat stress transcription factor B-2c, HSF 3) | 4.51 | |
| Os09g0456800 (Heat stress transcription factor B-1) | 4.05 | |
| Os02g0232000 (Similar to Heat shock transcription factor 29, HSF 5) | 3.67 | |
| PhD-finger | ||
| Os03g0302200 (PHD-finger family protein) | 2.65 | |
| JAZ | ||
| Os10g0391400 (Jasmonate ZIM-domain (JAZ) protein, Negative regulation of JA signal transduction pathway) | 7.81 | |
| Os03g0180800 (Jasmonate ZIM-domain protein 3) | 6.04 | |
| Os08g0428400 protein (ZIM transcription factor; Jasmonate ZIM-domain protein 9) | 2.49 | |
| HD ZIP | ||
| Os05g0129700 (Homeobox protein knotted-1-like 10) | 4.82 | |
| Os06g0140400 (Homeobox-leucine zipper protein HOX28) | 4.50 | |
| Os03g0198600 (Homeodomain-leucine zipper transcription factor) | 4.46 | |
| Os06g0140700 (Homeobox-leucine zipper protein HOX2) | 3.49 | |
| Os03g0188900 (Homeobox-leucine zipper protein HOX13) | 3.21 | |
| Os09g0528200 (Similar to Homeobox-leucine zipper protein HOX6Homeobox-leucine zipper protein HOX6) | 2.83 | |
| bHLH | ||
| Os01g0773800 (Basic helix-loop-helix protein 185) | Infinite | |
| Os03g0188400 (Basic helix-loop-helix protein) | 3.84 | |
| Os07g0628500 (Basic helix-loop-helix dimerization region bHLH domain-containing protein) | 3.31 | |
| Os03g0135700 Basic helix-loop-helix transcription factor | 3.16 | |
| Os07g0143200 (Phytochrome-interacting bHLH factor) | 2.44 | |
| G-box binding protein | G-box binding protein; G-box binding protein-like (B12D-like protein); Os06g0246000 protein | 2.70 |
*Information based on RAP-DB (http://rapdb.dna.affrc.go.jp/); **based on RNA-seq data of Hsu and Tung (2017).