Time of bloom
From GcatWiki
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
The factors affecting time of flowering from the Max Planck Institute for Plant Breeding Research
- 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 |
|---|---|---|---|---|
| AT1G01060 | LATE ELONGATED HYPOCOTYL, LATE ELONGATED HYPOCOTYL 1, LHY, LHY1 | TAIR | L | |
| AT1G02580 | EMB173, EMBRYO DEFECTIVE 173, FERTILIZATION INDEPENDENT SEED 1, FIS1, MEA, MEDEA, SDG5, SET DOMAIN-CONTAINING PROTEIN 5 | TAIR | Au, V | |
| AT1G04400 | AT-PHH1, ATCRY2, CRY2, CRYPTOCHROME 2, FHA, PHH1 | TAIR | L | |
| AT1G09570 | ELONGATED HYPOCOTYL 8, FAR RED ELONGATED 1, FAR RED ELONGATED HYPOCOTYL 2, FHY2, FRE1, HY8, PHYA, PHYTOCHROME A | TAIR | L | Grape |
| AT1G13260 | EDF4, ETHYLENE RESPONSE DNA BINDING FACTOR 4, RAV1, RELATED TO ABI3/VP1 1 | TAIR | L | |
| AT1G20330 | COTYLEDON VASCULAR PATTERN 1, CVP1, FRILL1, FRL1, SMT2, STEROL METHYLTRANSFERASE 2 | TAIR | V | |
| AT1G22770 | FB, GI, GIGANTEA | TAIR | L | |
| AT1G25560 | EDF1, ETHYLENE RESPONSE DNA BINDING FACTOR 1, TEM1, TEMPRANILLO 1 | TAIR | L | |
| AT1G26790 | TAIR | L | ||
| AT1G29160 | TAIR | L | ||
| AT1G30970 | SUF4, SUPPRESSOR OF FRIGIDA4 | TAIR | V | |
| AT1G31814 | FRIGIDA LIKE 2, FRL2 | TAIR | V | |
| AT1G47250 | 20S PROTEASOME ALPHA SUBUNIT F2, PAF2 | TAIR | V | |
| AT1G53090 | SPA1-RELATED 4, SPA4 | TAIR | L | |
| AT1G62830 | ARABIDOPSIS LYSINE-SPECIFIC HISTONE DEMETHYLASE, ATLSD1, ATSWP1, LDL1, LSD1, LSD1-LIKE 1, LYSINE-SPECIFIC HISTONE DEMETHYLASE, SWP1 | TAIR | Am, Au | |
| AT1G65480 | FLOWERING LOCUS T, FT | TAIR | Am, FPI | Grape, Strawberry |
| AT1G68050 | "FLAVIN-BINDING, KELCH REPEAT, F BOX 1", ADO3, FKF1 | TAIR | L | |
| AT1G68840 | ATRAV2, EDF2, ETHYLENE RESPONSE DNA BINDING FACTOR 2, RAP2.8, RAV2, RELATED TO ABI3/VP1 2, RELATED TO AP2 8, TEM2, TEMPRANILLO 2 | TAIR | L | |
| AT1G77080 | AGAMOUS-LIKE 27, AGL27, FLM, FLOWERING LOCUS M, MADS AFFECTING FLOWERING 1, MAF1 | TAIR | Am, FPI, V | |
| AT1G77300 | ASH1 HOMOLOG 2, ASHH2, CAROTENOID CHLOROPLAST REGULATORY1, CCR1, EARLY FLOWERING IN SHORT DAYS, EFS, LAZ2, LAZARUS 2, SDG8, SET DOMAIN GROUP 8 | TAIR | V | |
| AT2G06255 | ELF4-L3, ELF4-LIKE 3 | TAIR | L | |
| AT2G16780 | MSI2, NFC2, NUCLEOSOME/CHROMATIN ASSEMBLY FACTOR GROUP C 2 | TAIR | Au, V | |
| AT2G17770 | ATBZIP27, BASIC REGION/LEUCINE ZIPPER MOTIF 27, BZIP27, FD PARALOG, FDP | TAIR | Am, MI | |
| AT2G18790 | HY3, OOP1, OUT OF PHASE 1, PHYB, PHYTOCHROME B | TAIR | L | Grape |
| AT2G18870 | VEL3, VERNALIZATION5/VIN3-LIKE 3, VIL4, VIN3-LIKE 4 | TAIR | Au | |
| AT2G18880 | VEL2, VERNALIZATION5/VIN3-LIKE 2, VIL3, VIN3-LIKE 3 | TAIR | Au | |
| AT2G18915 | ADAGIO 2, ADO2, LKP2, LOV KELCH PROTEIN 2 | TAIR | L | |
| AT2G19520 | ACG1, ATMSI4, FVE, MSI4, MULTICOPY SUPPRESSOR OF IRA1 4, NFC04, NFC4 | TAIR | Am, Au | |
| AT2G22540 | AGAMOUS-LIKE 22, AGL22, SHORT VEGETATIVE PHASE, SVP | TAIR | Am, V | Grape |
| AT2G23380 | CLF, CURLY LEAF, ICU1, INCURVATA 1, SDG1, SET1, SETDOMAIN 1, SETDOMAIN GROUP 1 | TAIR | Au, V | |
| AT2G25930 | EARLY FLOWERING 3, ELF3, PYK20 | TAIR | L | |
| AT2G32950 | ARABIDOPSIS THALIANA CONSTITUTIVE PHOTOMORPHOGENIC 1, ATCOP1, CONSTITUTIVE PHOTOMORPHOGENIC 1, COP1, DEETIOLATED MUTANT 340, DET340, EMB168, EMBRYO DEFECTIVE 168, FUS1, FUSCA 1 | TAIR | L | |
| AT2G33835 | FES1, FRIGIDA-ESSENTIAL 1 | TAIR | V | |
| AT2G34140 | TAIR | L | ||
| AT2G40080 | EARLY FLOWERING 4, ELF4 | TAIR | L | |
| AT2G43410 | FPA | TAIR | Au | |
| AT2G46340 | SPA1, SUPPRESSOR OF PHYA-105 1 | TAIR | L | |
| AT2G46670 | TAIR | L | ||
| AT2G46790 | APRR9, ARABIDOPSIS PSEUDO-RESPONSE REGULATOR 9, PRR9, PSEUDO-RESPONSE REGULATOR 9, TL1, TOC1-LIKE PROTEIN 1 | TAIR | L | |
| AT2G46830 | ATCCA1, CCA1, CIRCADIAN CLOCK ASSOCIATED 1 | TAIR | L | |
| AT2G47700 | RED AND FAR-RED INSENSITIVE 2, RFI2 | TAIR | L | |
| AT3G02380 | ATCOL2, B-BOX DOMAIN PROTEIN 3, BBX3, COL2, CONSTANS-LIKE 2 | TAIR | FPI, L | |
| AT3G04610 | FLK, FLOWERING LOCUS KH DOMAIN | TAIR | Au | |
| AT3G07650 | B-BOX DOMAIN PROTEIN 7, BBX7, COL9, CONSTANS-LIKE 9 | TAIR | L | |
| AT3G10390 | FLD, FLOWERING LOCUS D | TAIR | Am, Au | |
| AT3G12810 | CHR13, PHOTOPERIOD-INDEPENDENT EARLY FLOWERING 1, PIE1, SRCAP | TAIR | V | |
| AT3G13682 | LDL2, LSD1-LIKE2 | TAIR | Am, Au | |
| AT3G15354 | SPA1-RELATED 3, SPA3 | TAIR | L | |
| AT3G15620 | UV REPAIR DEFECTIVE 3, UVR3 | TAIR | L | |
| AT3G18990 | REDUCED VERNALIZATION RESPONSE 1, REM39, REPRODUCTIVE MERISTEM 39, VRN1 | TAIR | V | |
| AT3G20740 | FERTILIZATION-INDEPENDENT ENDOSPERM, FERTILIZATION-INDEPENDENT ENDOSPERM 1, FIE, FIE1, FIS3 | TAIR | Au, V | |
| AT3G21320 | TAIR | L | ||
| AT3G24440 | VERNALIZATION 5, VIL1, VIN3-LIKE 1, VRN5 | TAIR | Au, V | |
| AT3G25730 | EDF3, ETHYLENE RESPONSE DNA BINDING FACTOR 3 | TAIR | L | |
| AT3G33520 | ACTIN-RELATED PROTEIN 6, ARP6, ATARP6, EARLY IN SHORT DAYS 1, ESD1, SUF3, SUPPRESSOR OF FRI 3 | TAIR | Am, V | |
| AT3G46640 | LUX, LUX ARRHYTHMO, PCL1, PHYTOCLOCK 1 | TAIR | L | |
| AT3G47500 | CDF3, CYCLING DOF FACTOR 3 | TAIR | L | |
| AT4G00650 | FLA, FLOWERING LOCUS A, FRI, FRIGIDA | TAIR | V | |
| AT4G02020 | EZA1, SDG10, SET DOMAIN-CONTAINING PROTEIN 10, SWINGER, SWN | TAIR | Au, V | |
| AT4G02560 | LD, LUMINIDEPENDENS | TAIR | Au | |
| AT4G08920 | ATCRY1, BLU1, BLUE LIGHT UNINHIBITED 1, CRY1, CRYPTOCHROME 1, ELONGATED HYPOCOTYL 4, HY4, OOP2, OUT OF PHASE 2 | TAIR | L | Grape |
| AT4G11110 | SPA1-RELATED 2, SPA2 | TAIR | L | |
| AT4G11880 | AGAMOUS-LIKE 14, AGL14 | TAIR | V | |
| AT4G16250 | PHYD, PHYTOCHROME D | TAIR | L | |
| AT4G16280 | FCA | TAIR | Am, Au | Grape |
| AT4G16845 | REDUCED VERNALIZATION RESPONSE 2, VRN2 | TAIR | Au, V | |
| AT4G18130 | PHYE, PHYTOCHROME E | TAIR | L | Grape |
| AT4G20370 | TSF, TWIN SISTER OF FT | TAIR | Am, FPI | |
| AT4G22950 | AGAMOUS-LIKE 19, AGL19, GL19 | TAIR | V | |
| AT4G24540 | AGAMOUS-LIKE 24, AGL24 | TAIR | V | |
| AT4G26000 | PEP, PEPPER | TAIR | V | |
| AT4G29730 | MSI5, NFC5, NUCLEOSOME/CHROMATIN ASSEMBLY FACTOR GROUP C5 | TAIR | Am, Au | |
| AT4G30200 | VEL1, VERNALIZATION5/VIN3-LIKE 1, VIL2, VIN3-LIKE 2 | TAIR | Au, V | |
| AT4G34530 | CIB1, CRYPTOCHROME-INTERACTING BASIC-HELIX-LOOP-HELIX 1 | TAIR | L | |
| AT4G35050 | MSI3, NFC3, NUCLEOSOME/CHROMATIN ASSEMBLY FACTOR GROUP C 3 | TAIR | Au, V | |
| AT4G35900 | ATBZIP14, FD, FD-1 | TAIR | Am, MI | |
| AT5G02810 | APRR7, PRR7, PSEUDO-RESPONSE REGULATOR 7 | TAIR | L | |
| AT5G03840 | TERMINAL FLOWER 1, TFL1 | TAIR | Am, FPI | Grape, Strawberry |
| AT5G08230 | TAIR | V | ||
| AT5G08330 | CCA1 HIKING EXPEDITION, CHE, TRANSCRIPTION FACTOR TCP21, TCP21 | UniProtKB | L | |
| AT5G10140 | AGAMOUS-LIKE 25, AGL25, FLC, FLF, FLOWERING LOCUS C, FLOWERING LOCUS F | TAIR | Am, FPI, V | Grape |
| AT5G13480 | FY | TAIR | Au | |
| AT5G15840 | B-BOX DOMAIN PROTEIN 1, BBX1, CO, CONSTANS, FG | TAIR | FPI, L | |
| AT5G15850 | ATCOL1, B-BOX DOMAIN PROTEIN 2, BBX2, COL1, CONSTANS-LIKE 1 | TAIR | FPI, L | |
| AT5G23150 | ENHANCER OF AG-4 2, HUA2 | TAIR | V | |
| AT5G23280 | TAIR | L | ||
| AT5G24470 | APRR5, PRR5, PSEUDO-RESPONSE REGULATOR 5 | TAIR | L | |
| AT5G24930 | ATCOL4, B-BOX DOMAIN PROTEIN 5, BBX5, COL4, CONSTANS-LIKE 4 | TAIR | L | |
| AT5G35840 | PHYC, PHYTOCHROME C | TAIR | L | Grape |
| AT5G37055 | ATSWC6, SEF, SERRATED LEAVES AND EARLY FLOWERING | TAIR | V | |
| AT5G39660 | CDF2, CYCLING DOF FACTOR 2 | TAIR | L | |
| AT5G42790 | ARS5, ARSENIC TOLERANCE 5, ATPSM30, PAF1, PROTEASOME ALPHA SUBUNIT F1 | TAIR | V | |
| AT5G48250 | B-BOX DOMAIN PROTEIN 8, BBX8 | TAIR | L | |
| AT5G57360 | ADAGIO 1, ADO1, FKF1-LIKE PROTEIN 2, FKL2, LKP1, LOV KELCH PROTEIN 1, ZEITLUPE, ZTL | TAIR | L | |
| AT5G57380 | VERNALIZATION INSENSITIVE 3, VIN3 | TAIR | Au, V | |
| AT5G57660 | ATCOL5, B-BOX DOMAIN PROTEIN 6, BBX6, COL5, CONSTANS-LIKE 5 | TAIR | L | |
| AT5G58230 | ARABIDOPSIS MULTICOPY SUPRESSOR OF IRA1, ATMSI1, MATERNAL EFFECT EMBRYO ARREST 70, MEE70, MSI1, MULTICOPY SUPRESSOR OF IRA1 | TAIR | Au, V | |
| AT5G59570 | BOA, BROTHER OF LUX ARRHYTHMO | TAIR | L | |
| AT5G60100 | APRR3, PRR3, PSEUDO-RESPONSE REGULATOR 3 | TAIR | L | |
| AT5G61380 | APRR1, ATTOC1, PRR1, PSEUDO-RESPONSE REGULATOR 1, TIMING OF CAB EXPRESSION 1, TOC1 | TAIR | L | |
| AT5G62430 | CDF1, CYCLING DOF FACTOR 1 | TAIR | L | |
| AT5G65050 | AGAMOUS-LIKE 31, AGL31, MADS AFFECTING FLOWERING 2, MAF2 | TAIR | Am, FPI, V | |
| AT5G65060 | AGAMOUS-LIKE 70, AGL70, FCL3, MADS AFFECTING FLOWERING 3, MAF3 | TAIR | Am, FPI, V | |
| AT5G65070 | AGAMOUS-LIKE 69, AGL69, FCL4, MADS AFFECTING FLOWERING 4, MAF4 | TAIR | Am, FPI, V | |
| AT5G65080 | AGAMOUS-LIKE 68, AGL68, MADS AFFECTING FLOWERING 5, MAF5 | TAIR | Am, FPI, V |
