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
This table lists all of the genes involved in the ambient temperature, autonomous, light signaling, and vernalization pathways. All Arabidopsis genes are compiled from Jung et al., 2012. All potential orthologs are found via UniProt Grape or UniProt Strawberry nomenclature search.
| Arabidopsis Locus | Other Names | AA Sequence | Pathway | Potential Ortholog |
|---|---|---|---|---|
| AT1G01060 | LATE ELONGATED HYPOCOTYL, LATE ELONGATED HYPOCOTYL 1, LHY, LHY1 | TAIR | Light signaling | |
| AT1G02580 | EMB173, EMBRYO DEFECTIVE 173, FERTILIZATION INDEPENDENT SEED 1, FIS1, MEA, MEDEA, SDG5, SET DOMAIN-CONTAINING PROTEIN 5 | TAIR | Autonomous, Vernalization | |
| AT1G04400 | AT-PHH1, ATCRY2, CRY2, CRYPTOCHROME 2, FHA, PHH1 | TAIR | Light signaling | |
| AT1G09570 | ELONGATED HYPOCOTYL 8, FAR RED ELONGATED 1, FAR RED ELONGATED HYPOCOTYL 2, FHY2, FRE1, HY8, PHYA, PHYTOCHROME A | TAIR | Light signaling | Grape |
| AT1G13260 | EDF4, ETHYLENE RESPONSE DNA BINDING FACTOR 4, RAV1, RELATED TO ABI3/VP1 1 | TAIR | Light signaling | |
| AT1G20330 | COTYLEDON VASCULAR PATTERN 1, CVP1, FRILL1, FRL1, SMT2, STEROL METHYLTRANSFERASE 2 | TAIR | Vernalization | |
| AT1G22770 | FB, GI, GIGANTEA | TAIR | Light signaling | |
| AT1G25560 | EDF1, ETHYLENE RESPONSE DNA BINDING FACTOR 1, TEM1, TEMPRANILLO 1 | TAIR | Light signaling | |
| AT1G26790 | TAIR | Light signaling | ||
| AT1G29160 | TAIR | Light signaling | ||
| AT1G30970 | SUF4, SUPPRESSOR OF FRIGIDA4 | TAIR | Vernalization | |
| AT1G31814 | FRIGIDA LIKE 2, FRL2 | TAIR | Vernalization | |
| AT1G47250 | 20S PROTEASOME ALPHA SUBUNIT F2, PAF2 | TAIR | Vernalization | |
| AT1G53090 | SPA1-RELATED 4, SPA4 | TAIR | Light signaling | |
| AT1G62830 | ARABIDOPSIS LYSINE-SPECIFIC HISTONE DEMETHYLASE, ATLSD1, ATSWP1, LDL1, LSD1, LSD1-LIKE 1, LYSINE-SPECIFIC HISTONE DEMETHYLASE, SWP1 | TAIR | Ambient temperature, Autonomous | |
| AT1G65480 | FLOWERING LOCUS T, FT | TAIR | Ambient temperature, Flowering integrator | Grape, Strawberry |
| AT1G68050 | "FLAVIN-BINDING, KELCH REPEAT, F BOX 1", ADO3, FKF1 | TAIR | Light signaling | |
| 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 | Light signaling | |
| AT1G77080 | AGAMOUS-LIKE 27, AGL27, FLM, FLOWERING LOCUS M, MADS AFFECTING FLOWERING 1, MAF1 | TAIR | Ambient temperature, Flowering integrator, Vernalization | |
| AT1G77300 | ASH1 HOMOLOG 2, ASHH2, CAROTENOID CHLOROPLAST REGULATORY1, CCR1, EARLY FLOWERING IN SHORT DAYS, EFS, LAZ2, LAZARUS 2, SDG8, SET DOMAIN GROUP 8 | TAIR | Vernalization | |
| AT2G06255 | ELF4-L3, ELF4-LIKE 3 | TAIR | Light signaling | |
| AT2G16780 | MSI2, NFC2, NUCLEOSOME/CHROMATIN ASSEMBLY FACTOR GROUP C 2 | TAIR | Autonomous, Vernalization | |
| AT2G17770 | ATBZIP27, BASIC REGION/LEUCINE ZIPPER MOTIF 27, BZIP27, FD PARALOG, FDP | TAIR | Ambient temperature, Meristem identity | |
| AT2G18790 | HY3, OOP1, OUT OF PHASE 1, PHYB, PHYTOCHROME B | TAIR | Light signaling | Grape |
| AT2G18870 | VEL3, VERNALIZATION5/VIN3-LIKE 3, VIL4, VIN3-LIKE 4 | TAIR | Autonomous | |
| AT2G18880 | VEL2, VERNALIZATION5/VIN3-LIKE 2, VIL3, VIN3-LIKE 3 | TAIR | Autonomous | |
| AT2G18915 | ADAGIO 2, ADO2, LKP2, LOV KELCH PROTEIN 2 | TAIR | Light signaling | |
| AT2G19520 | ACG1, ATMSI4, FVE, MSI4, MULTICOPY SUPPRESSOR OF IRA1 4, NFC04, NFC4 | TAIR | Ambient temperature, Autonomous | |
| AT2G22540 | AGAMOUS-LIKE 22, AGL22, SHORT VEGETATIVE PHASE, SVP | TAIR | Ambient temperature, Vernalization | Grape |
| AT2G23380 | CLF, CURLY LEAF, ICU1, INCURVATA 1, SDG1, SET1, SETDOMAIN 1, SETDOMAIN GROUP 1 | TAIR | Autonomous, Vernalization | |
| AT2G25930 | EARLY FLOWERING 3, ELF3, PYK20 | TAIR | Light signaling | |
| AT2G32950 | ARABIDOPSIS THALIANA CONSTITUTIVE PHOTOMORPHOGENIC 1, ATCOP1, CONSTITUTIVE PHOTOMORPHOGENIC 1, COP1, DEETIOLATED MUTANT 340, DET340, EMB168, EMBRYO DEFECTIVE 168, FUS1, FUSCA 1 | TAIR | Light signaling | |
| AT2G33835 | FES1, FRIGIDA-ESSENTIAL 1 | TAIR | Vernalization | |
| AT2G34140 | TAIR | Light signaling | ||
| AT2G40080 | EARLY FLOWERING 4, ELF4 | TAIR | Light signaling | |
| AT2G43410 | FPA | TAIR | Autonomous | |
| AT2G46340 | SPA1, SUPPRESSOR OF PHYA-105 1 | TAIR | Light signaling | |
| AT2G46670 | TAIR | Light signaling | ||
| AT2G46790 | APRR9, ARABIDOPSIS PSEUDO-RESPONSE REGULATOR 9, PRR9, PSEUDO-RESPONSE REGULATOR 9, TL1, TOC1-LIKE PROTEIN 1 | TAIR | Light signaling | |
| AT2G46830 | ATCCA1, CCA1, CIRCADIAN CLOCK ASSOCIATED 1 | TAIR | Light signaling | |
| AT2G47700 | RED AND FAR-RED INSENSITIVE 2, RFI2 | TAIR | Light signaling | |
| AT3G02380 | ATCOL2, B-BOX DOMAIN PROTEIN 3, BBX3, COL2, CONSTANS-LIKE 2 | TAIR | Flowering integrator, Light signaling | |
| AT3G04610 | FLK, FLOWERING LOCUS KH DOMAIN | TAIR | Autonomous | |
| AT3G07650 | B-BOX DOMAIN PROTEIN 7, BBX7, COL9, CONSTANS-LIKE 9 | TAIR | Light signaling | |
| AT3G10390 | FLD, FLOWERING LOCUS D | TAIR | Ambient temperature, Autonomous | |
| AT3G12810 | CHR13, PHOTOPERIOD-INDEPENDENT EARLY FLOWERING 1, PIE1, SRCAP | TAIR | Vernalization | |
| AT3G13682 | LDL2, LSD1-LIKE2 | TAIR | Ambient temperature, Autonomous | |
| AT3G15354 | SPA1-RELATED 3, SPA3 | TAIR | Light signaling | |
| AT3G15620 | UV REPAIR DEFECTIVE 3, UVR3 | TAIR | Light signaling | |
| AT3G18990 | REDUCED VERNALIZATION RESPONSE 1, REM39, REPRODUCTIVE MERISTEM 39, VRN1 | TAIR | Vernalization | |
| AT3G20740 | FERTILIZATION-INDEPENDENT ENDOSPERM, FERTILIZATION-INDEPENDENT ENDOSPERM 1, FIE, FIE1, FIS3 | TAIR | Autonomous, Vernalization | |
| AT3G21320 | TAIR | Light signaling | ||
| AT3G24440 | VERNALIZATION 5, VIL1, VIN3-LIKE 1, VRN5 | TAIR | Autonomous, Vernalization | |
| AT3G25730 | EDF3, ETHYLENE RESPONSE DNA BINDING FACTOR 3 | TAIR | Light signaling | |
| AT3G33520 | ACTIN-RELATED PROTEIN 6, ARP6, ATARP6, EARLY IN SHORT DAYS 1, ESD1, SUF3, SUPPRESSOR OF FRI 3 | TAIR | Ambient temperature, Vernalization | |
| AT3G46640 | LUX, LUX ARRHYTHMO, PCL1, PHYTOCLOCK 1 | TAIR | Light signaling | |
| AT3G47500 | CDF3, CYCLING DOF FACTOR 3 | TAIR | Light signaling | |
| AT4G00650 | FLA, FLOWERING LOCUS A, FRI, FRIGIDA | TAIR | Vernalization | |
| AT4G02020 | EZA1, SDG10, SET DOMAIN-CONTAINING PROTEIN 10, SWINGER, SWN | TAIR | Autonomous, Vernalization | |
| AT4G02560 | LD, LUMINIDEPENDENS | TAIR | Autonomous | |
| AT4G08920 | ATCRY1, BLU1, BLUE LIGHT UNINHIBITED 1, CRY1, CRYPTOCHROME 1, ELONGATED HYPOCOTYL 4, HY4, OOP2, OUT OF PHASE 2 | TAIR | Light signaling | Grape |
| AT4G11110 | SPA1-RELATED 2, SPA2 | TAIR | Light signaling | |
| AT4G11880 | AGAMOUS-LIKE 14, AGL14 | TAIR | Vernalization | |
| AT4G16250 | PHYD, PHYTOCHROME D | TAIR | Light signaling | |
| AT4G16280 | FCA | TAIR | Ambient temperature, Autonomous | Grape |
| AT4G16845 | REDUCED VERNALIZATION RESPONSE 2, VRN2 | TAIR | Autonomous, Vernalization | |
| AT4G18130 | PHYE, PHYTOCHROME E | TAIR | Light signaling | Grape |
| AT4G20370 | TSF, TWIN SISTER OF FT | TAIR | Ambient temperature, Flowering integrator | |
| AT4G22950 | AGAMOUS-LIKE 19, AGL19, GL19 | TAIR | Vernalization | |
| AT4G24540 | AGAMOUS-LIKE 24, AGL24 | TAIR | Vernalization | |
| AT4G26000 | PEP, PEPPER | TAIR | Vernalization | |
| AT4G29730 | MSI5, NFC5, NUCLEOSOME/CHROMATIN ASSEMBLY FACTOR GROUP C5 | TAIR | Ambient temperature, Autonomous | |
| AT4G30200 | VEL1, VERNALIZATION5/VIN3-LIKE 1, VIL2, VIN3-LIKE 2 | TAIR | Autonomous, Vernalization | |
| AT4G34530 | CIB1, CRYPTOCHROME-INTERACTING BASIC-HELIX-LOOP-HELIX 1 | TAIR | Light signaling | |
| AT4G35050 | MSI3, NFC3, NUCLEOSOME/CHROMATIN ASSEMBLY FACTOR GROUP C 3 | TAIR | Autonomous, Vernalization | |
| AT4G35900 | ATBZIP14, FD, FD-1 | TAIR | Ambient temperature, Meristem identity | |
| AT5G02810 | APRR7, PRR7, PSEUDO-RESPONSE REGULATOR 7 | TAIR | Light signaling | |
| AT5G03840 | TERMINAL FLOWER 1, TFL1 | TAIR | Ambient temperature, Flowering integrator | Grape, Strawberry |
| AT5G08230 | TAIR | Vernalization | ||
| AT5G08330 | CCA1 HIKING EXPEDITION, CHE, TRANSCRIPTION FACTOR TCP21, TCP21 | UniProtKB | Light signaling | |
| AT5G10140 | AGAMOUS-LIKE 25, AGL25, FLC, FLF, FLOWERING LOCUS C, FLOWERING LOCUS F | TAIR | Ambient temperature, Flowering integrator, Vernalization | Grape |
| AT5G13480 | FY | TAIR | Autonomous | |
| AT5G15840 | B-BOX DOMAIN PROTEIN 1, BBX1, CO, CONSTANS, FG | TAIR | Flowering integrator, Light signaling | |
| AT5G15850 | ATCOL1, B-BOX DOMAIN PROTEIN 2, BBX2, COL1, CONSTANS-LIKE 1 | TAIR | Flowering integrator, Light signaling | |
| AT5G23150 | ENHANCER OF AG-4 2, HUA2 | TAIR | Vernalization | |
| AT5G23280 | TAIR | Light signaling | ||
| AT5G24470 | APRR5, PRR5, PSEUDO-RESPONSE REGULATOR 5 | TAIR | Light signaling | |
| AT5G24930 | ATCOL4, B-BOX DOMAIN PROTEIN 5, BBX5, COL4, CONSTANS-LIKE 4 | TAIR | Light signaling | |
| AT5G35840 | PHYC, PHYTOCHROME C | TAIR | Light signaling | Grape |
| AT5G37055 | ATSWC6, SEF, SERRATED LEAVES AND EARLY FLOWERING | TAIR | Vernalization | |
| AT5G39660 | CDF2, CYCLING DOF FACTOR 2 | TAIR | Light signaling | |
| AT5G42790 | ARS5, ARSENIC TOLERANCE 5, ATPSM30, PAF1, PROTEASOME ALPHA SUBUNIT F1 | TAIR | Vernalization | |
| AT5G48250 | B-BOX DOMAIN PROTEIN 8, BBX8 | TAIR | Light signaling | |
| AT5G57360 | ADAGIO 1, ADO1, FKF1-LIKE PROTEIN 2, FKL2, LKP1, LOV KELCH PROTEIN 1, ZEITLUPE, ZTL | TAIR | Light signaling | |
| AT5G57380 | VERNALIZATION INSENSITIVE 3, VIN3 | TAIR | Autonomous, Vernalization | |
| AT5G57660 | ATCOL5, B-BOX DOMAIN PROTEIN 6, BBX6, COL5, CONSTANS-LIKE 5 | TAIR | Light signaling | |
| AT5G58230 | ARABIDOPSIS MULTICOPY SUPRESSOR OF IRA1, ATMSI1, MATERNAL EFFECT EMBRYO ARREST 70, MEE70, MSI1, MULTICOPY SUPRESSOR OF IRA1 | TAIR | Autonomous, Vernalization | |
| AT5G59570 | BOA, BROTHER OF LUX ARRHYTHMO | TAIR | Light signaling | |
| AT5G60100 | APRR3, PRR3, PSEUDO-RESPONSE REGULATOR 3 | TAIR | Light signaling | |
| AT5G61380 | APRR1, ATTOC1, PRR1, PSEUDO-RESPONSE REGULATOR 1, TIMING OF CAB EXPRESSION 1, TOC1 | TAIR | Light signaling | |
| AT5G62430 | CDF1, CYCLING DOF FACTOR 1 | TAIR | Light signaling | |
| AT5G65050 | AGAMOUS-LIKE 31, AGL31, MADS AFFECTING FLOWERING 2, MAF2 | TAIR | Ambient temperature, Flowering integrator, Vernalization | |
| AT5G65060 | AGAMOUS-LIKE 70, AGL70, FCL3, MADS AFFECTING FLOWERING 3, MAF3 | TAIR | Ambient temperature, Flowering integrator, Vernalization | |
| AT5G65070 | AGAMOUS-LIKE 69, AGL69, FCL4, MADS AFFECTING FLOWERING 4, MAF4 | TAIR | Ambient temperature, Flowering integrator, Vernalization | |
| AT5G65080 | AGAMOUS-LIKE 68, AGL68, MADS AFFECTING FLOWERING 5, MAF5 | TAIR | Ambient temperature, Flowering integrator, Vernalization |
