Time of bloom
By Austin Mudd - Spring 2013
Contents
To Do
- Write introduction and procedure sections
- Aggregate all sequences into a single document in proper FASTA format
Introduction
- Higgins et al., 2010
- Jung et al., 2012
- General plant anatomy / process of flowering
- Why flowering is important to study / general impact
- Factors affecting time of flowering
Procedure
- Overall procedure for finding the genes, running with GenSAS, determining SSRs, etc
Gallery of Arabidopsis Flowering Pathways
105 Flowering Genes
The below table lists all of the genes involved in the ambient temperature, autonomous, light signaling, and vernalization pathways.
Note: All Arabidopsis genes are compiled from Jung et al., 2012. All potential orthologs are found via UniProt Grape or UniProt Strawberry nomenclature search. Formatting is the same as Jung et al., 2012 where a * indicates 1 of "24 Arabidopsis genes, which had not been previously investigated for their roles in flowering, [that] belong to [paralog groups] with known Arabidopsis flowering genes." Moreover, for pathways, "Am: Ambient temperature pathway, Au: Autonomous pathway, FPI: Flowering Pathway [Integrators], L: Light signaling pathway, MI: Meristem Identity, V: Vernalization pathway."
| Arabidopsis Locus | Other Names | AA Sequence | Pathway | Potential Ortholog |
|---|---|---|---|---|
| PEP | TAIR | V | ||
| FD | TAIR | Am, MI | ||
| FRI | TAIR | V | ||
| VEL1 | TAIR | Au, V | ||
| FCA | TAIR | Am, Au | Grape | |
| SWN | TAIR | Au, V | ||
| NFC5* | TAIR | Am, Au | ||
| SPA2 | TAIR | L | ||
| CRY1 | TAIR | L | Grape | |
| CIB1 | TAIR | L | ||
| CO | TAIR | FPI, L | ||
| COL1 | TAIR | FPI, L | ||
| MAF3 | TAIR | Am, FPI, V | ||
| MAF4 | TAIR | Am, FPI, V | ||
| MAF5 | TAIR | Am, FPI, V | ||
| ATCOL4 | TAIR | L | ||
| TFL1 | TAIR | Am, FPI | Grape, Strawberry | |
| PRR7 | TAIR | L | ||
| MSI1 | TAIR | Au, V | ||
| TOC1 | TAIR | L | ||
| PHYC | TAIR | L | Grape | |
| PAF1 | TAIR | V | ||
| ATCOL5 | TAIR | L | ||
| ZTL | TAIR | L | ||
| VIN3 | TAIR | Au, V | ||
| HUA2 | TAIR | V | ||
| FLC | TAIR | Am, FPI, V | Grape | |
| FY | TAIR | Au | ||
| EFS | TAIR | V | ||
| MEA* | TAIR | Au, V | ||
| GI | TAIR | L | ||
| FKF1 | TAIR | L | ||
| LHY | TAIR | L | ||
| RAV1 | TAIR | L | ||
| FRL2 | TAIR | V | ||
| VRN2 | TAIR | Au, V | ||
| CLF | TAIR | Au, V | ||
| PHYB | TAIR | L | Grape | |
| TSF | TAIR | Am, FPI | ||
| LD | TAIR | Au | ||
| PHYD | TAIR | L | ||
| PHYE | TAIR | L | Grape | |
| PHYA | TAIR | L | Grape | |
| TEM2 | TAIR | L | ||
| FRL1 | TAIR | V | ||
| SUF4 | TAIR | V | ||
| CRY2 | TAIR | L | ||
| MAF1 | TAIR | Am, FPI, V | ||
| LDL1* | TAIR | Am, Au | ||
| TEM1 | TAIR | L | ||
| FT | TAIR | Am, FPI | Grape, Strawberry | |
| PAF2 | TAIR | V | ||
| SPA4 | TAIR | L | ||
| SPA1 | TAIR | L | ||
| SVP | TAIR | Am, V | Grape | |
| RFI2 | TAIR | L | ||
| ELF3 | TAIR | L | ||
| VEL2 | TAIR | Au | ||
| VEL3 | TAIR | Au | ||
| FVE | TAIR | Am, Au | ||
| FPA | TAIR | Au | ||
| COP1 | TAIR | L | ||
| ELF4 | TAIR | L | ||
| COL2 | TAIR | FPI, L | ||
| LUX | TAIR | L | ||
| FLD | TAIR | Am, Au | ||
| FLK | TAIR | Au | ||
| VRN1 | TAIR | V | ||
| PIE1 | TAIR | V | ||
| COL9 | TAIR | L | ||
| LDL2* | TAIR | Am, Au | ||
| FIE1 | TAIR | Au, V | ||
| UVR3* | TAIR | L | ||
| VRN5 | TAIR | Au, V | ||
| SPA3 | TAIR | L | ||
| FES1 | TAIR | V | ||
| ELF4-L3 | TAIR | L | ||
| LKP2 | TAIR | L | ||
| ATSWC6 | TAIR | V | ||
| ATBZIP27 | UniProtKB | Am, MI | ||
| MSI2* | UniProtKB | Au, V | ||
| MSI3* | UniProtKB | Au, V | ||
| AT2G34140 | UniProtKB | L | ||
| AGL19 | UniProtKB | V | ||
| AGL24 | UniProtKB | V | ||
| AT1G29160 | UniProtKB | L | ||
| CCA1 | UniProtKB | L | ||
| AGL14 | UniProtKB | V | ||
| CDF2 | UniProtKB | L | ||
| CDF1 | UniProtKB | L | ||
| AT3G21320 | UniProtKB | L | ||
| AT2G46670* | UniProtKB | L | ||
| APRR5 | UniProtKB | L | ||
| APRR9 | UniProtKB | L | ||
| ATARP6 | UniProtKB | Am, V | ||
| AT5G23280* | UniProtKB | L | ||
| AGL31 | UniProtKB | Am, FPI, V | ||
| CHE | UniProtKB | L | ||
| AT5G08230* | UniProtKB | V | ||
| AT1G26790 | UniProtKB | L | ||
| AT3G25730 | UniProtKB | L | ||
| AT5G59570* | UniProtKB | L | ||
| AT5G48250* | UniProtKB | L | ||
| APRR3 | UniProtKB | L | ||
| CDF3 | UniProtKB | L |
