Difference between revisions of "Time of bloom"
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==105 Flowering Genes== | ==105 Flowering Genes== | ||
| − | + | This table lists all of the genes involved in the ambient temperature, autonomous, light signaling, and vernalization pathways. All <i>Arabidopsis</i> genes are compiled from [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung et al., 2012]. All potential orthologs are found via [http://www.uniprot.org/uniprot/?query=taxonomy%3A%22Vitis+vinifera+%28Grape%29+%5B29760%5D%22&sort=score UniProt Grape] or [http://www.uniprot.org/uniprot/?query=taxonomy%3A%22Fragaria+vesca+%5B57918%5D%22&sort=score UniProt Strawberry] nomenclature search. | |
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Revision as of 22:55, 5 March 2013
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 pathway | |
| AT1G02580 | EMB173, EMBRYO DEFECTIVE 173, FERTILIZATION INDEPENDENT SEED 1, FIS1, MEA, MEDEA, SDG5, SET DOMAIN-CONTAINING PROTEIN 5 | TAIR | Autonomous pathway, Vernalization pathway | |
| AT1G04400 | AT-PHH1, ATCRY2, CRY2, CRYPTOCHROME 2, FHA, PHH1 | TAIR | Light signaling pathway | |
| AT1G09570 | ELONGATED HYPOCOTYL 8, FAR RED ELONGATED 1, FAR RED ELONGATED HYPOCOTYL 2, FHY2, FRE1, HY8, PHYA, PHYTOCHROME A | TAIR | Light signaling pathway | Grape |
| AT1G13260 | EDF4, ETHYLENE RESPONSE DNA BINDING FACTOR 4, RAV1, RELATED TO ABI3/VP1 1 | TAIR | Light signaling pathway | |
| AT1G20330 | COTYLEDON VASCULAR PATTERN 1, CVP1, FRILL1, FRL1, SMT2, STEROL METHYLTRANSFERASE 2 | TAIR | Vernalization pathway | |
| AT1G22770 | FB, GI, GIGANTEA | TAIR | Light signaling pathway | |
| AT1G25560 | EDF1, ETHYLENE RESPONSE DNA BINDING FACTOR 1, TEM1, TEMPRANILLO 1 | TAIR | Light signaling pathway | |
| AT1G26790 | TAIR | Light signaling pathway | ||
| AT1G29160 | TAIR | Light signaling pathway | ||
| AT1G30970 | SUF4, SUPPRESSOR OF FRIGIDA4 | TAIR | Vernalization pathway | |
| AT1G31814 | FRIGIDA LIKE 2, FRL2 | TAIR | Vernalization pathway | |
| AT1G47250 | 20S PROTEASOME ALPHA SUBUNIT F2, PAF2 | TAIR | Vernalization pathway | |
| AT1G53090 | SPA1-RELATED 4, SPA4 | TAIR | Light signaling pathway | |
| AT1G62830 | ARABIDOPSIS LYSINE-SPECIFIC HISTONE DEMETHYLASE, ATLSD1, ATSWP1, LDL1, LSD1, LSD1-LIKE 1, LYSINE-SPECIFIC HISTONE DEMETHYLASE, SWP1 | TAIR | Ambient temperature pathway, Autonomous pathway | |
| AT1G65480 | FLOWERING LOCUS T, FT | TAIR | Ambient temperature pathway, Flowering pathway integrator | Grape, Strawberry |
| AT1G68050 | "FLAVIN-BINDING, KELCH REPEAT, F BOX 1", ADO3, FKF1 | TAIR | Light signaling pathway | |
| 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 pathway | |
| AT1G77080 | AGAMOUS-LIKE 27, AGL27, FLM, FLOWERING LOCUS M, MADS AFFECTING FLOWERING 1, MAF1 | TAIR | Ambient temperature pathway, Flowering pathway integrator, Vernalization pathway | |
| 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 pathway | |
| AT2G06255 | ELF4-L3, ELF4-LIKE 3 | TAIR | Light signaling pathway | |
| AT2G16780 | MSI2, NFC2, NUCLEOSOME/CHROMATIN ASSEMBLY FACTOR GROUP C 2 | TAIR | Autonomous pathway, Vernalization pathway | |
| AT2G17770 | ATBZIP27, BASIC REGION/LEUCINE ZIPPER MOTIF 27, BZIP27, FD PARALOG, FDP | TAIR | Ambient temperature pathway, Meristem identity | |
| AT2G18790 | HY3, OOP1, OUT OF PHASE 1, PHYB, PHYTOCHROME B | TAIR | Light signaling pathway | Grape |
| AT2G18870 | VEL3, VERNALIZATION5/VIN3-LIKE 3, VIL4, VIN3-LIKE 4 | TAIR | Autonomous pathway | |
| AT2G18880 | VEL2, VERNALIZATION5/VIN3-LIKE 2, VIL3, VIN3-LIKE 3 | TAIR | Autonomous pathway | |
| AT2G18915 | ADAGIO 2, ADO2, LKP2, LOV KELCH PROTEIN 2 | TAIR | Light signaling pathway | |
| AT2G19520 | ACG1, ATMSI4, FVE, MSI4, MULTICOPY SUPPRESSOR OF IRA1 4, NFC04, NFC4 | TAIR | Ambient temperature pathway, Autonomous pathway | |
| AT2G22540 | AGAMOUS-LIKE 22, AGL22, SHORT VEGETATIVE PHASE, SVP | TAIR | Ambient temperature pathway, Vernalization pathway | Grape |
| AT2G23380 | CLF, CURLY LEAF, ICU1, INCURVATA 1, SDG1, SET1, SETDOMAIN 1, SETDOMAIN GROUP 1 | TAIR | Autonomous pathway, Vernalization pathway | |
| AT2G25930 | EARLY FLOWERING 3, ELF3, PYK20 | TAIR | Light signaling pathway | |
| 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 pathway | |
| AT2G33835 | FES1, FRIGIDA-ESSENTIAL 1 | TAIR | Vernalization pathway | |
| AT2G34140 | TAIR | Light signaling pathway | ||
| AT2G40080 | EARLY FLOWERING 4, ELF4 | TAIR | Light signaling pathway | |
| AT2G43410 | FPA | TAIR | Autonomous pathway | |
| AT2G46340 | SPA1, SUPPRESSOR OF PHYA-105 1 | TAIR | Light signaling pathway | |
| AT2G46670 | TAIR | Light signaling pathway | ||
| AT2G46790 | APRR9, ARABIDOPSIS PSEUDO-RESPONSE REGULATOR 9, PRR9, PSEUDO-RESPONSE REGULATOR 9, TL1, TOC1-LIKE PROTEIN 1 | TAIR | Light signaling pathway | |
| AT2G46830 | ATCCA1, CCA1, CIRCADIAN CLOCK ASSOCIATED 1 | TAIR | Light signaling pathway | |
| AT2G47700 | RED AND FAR-RED INSENSITIVE 2, RFI2 | TAIR | Light signaling pathway | |
| AT3G02380 | ATCOL2, B-BOX DOMAIN PROTEIN 3, BBX3, COL2, CONSTANS-LIKE 2 | TAIR | Flowering pathway integrator, Light signaling pathway | |
| AT3G04610 | FLK, FLOWERING LOCUS KH DOMAIN | TAIR | Autonomous pathway | |
| AT3G07650 | B-BOX DOMAIN PROTEIN 7, BBX7, COL9, CONSTANS-LIKE 9 | TAIR | Light signaling pathway | |
| AT3G10390 | FLD, FLOWERING LOCUS D | TAIR | Ambient temperature pathway, Autonomous pathway | |
| AT3G12810 | CHR13, PHOTOPERIOD-INDEPENDENT EARLY FLOWERING 1, PIE1, SRCAP | TAIR | Vernalization pathway | |
| AT3G13682 | LDL2, LSD1-LIKE2 | TAIR | Ambient temperature pathway, Autonomous pathway | |
| AT3G15354 | SPA1-RELATED 3, SPA3 | TAIR | Light signaling pathway | |
| AT3G15620 | UV REPAIR DEFECTIVE 3, UVR3 | TAIR | Light signaling pathway | |
| AT3G18990 | REDUCED VERNALIZATION RESPONSE 1, REM39, REPRODUCTIVE MERISTEM 39, VRN1 | TAIR | Vernalization pathway | |
| AT3G20740 | FERTILIZATION-INDEPENDENT ENDOSPERM, FERTILIZATION-INDEPENDENT ENDOSPERM 1, FIE, FIE1, FIS3 | TAIR | Autonomous pathway, Vernalization pathway | |
| AT3G21320 | TAIR | Light signaling pathway | ||
| AT3G24440 | VERNALIZATION 5, VIL1, VIN3-LIKE 1, VRN5 | TAIR | Autonomous pathway, Vernalization pathway | |
| AT3G25730 | EDF3, ETHYLENE RESPONSE DNA BINDING FACTOR 3 | TAIR | Light signaling pathway | |
| AT3G33520 | ACTIN-RELATED PROTEIN 6, ARP6, ATARP6, EARLY IN SHORT DAYS 1, ESD1, SUF3, SUPPRESSOR OF FRI 3 | TAIR | Ambient temperature pathway, Vernalization pathway | |
| AT3G46640 | LUX, LUX ARRHYTHMO, PCL1, PHYTOCLOCK 1 | TAIR | Light signaling pathway | |
| AT3G47500 | CDF3, CYCLING DOF FACTOR 3 | TAIR | Light signaling pathway | |
| AT4G00650 | FLA, FLOWERING LOCUS A, FRI, FRIGIDA | TAIR | Vernalization pathway | |
| AT4G02020 | EZA1, SDG10, SET DOMAIN-CONTAINING PROTEIN 10, SWINGER, SWN | TAIR | Autonomous pathway, Vernalization pathway | |
| AT4G02560 | LD, LUMINIDEPENDENS | TAIR | Autonomous pathway | |
| AT4G08920 | ATCRY1, BLU1, BLUE LIGHT UNINHIBITED 1, CRY1, CRYPTOCHROME 1, ELONGATED HYPOCOTYL 4, HY4, OOP2, OUT OF PHASE 2 | TAIR | Light signaling pathway | Grape |
| AT4G11110 | SPA1-RELATED 2, SPA2 | TAIR | Light signaling pathway | |
| AT4G11880 | AGAMOUS-LIKE 14, AGL14 | TAIR | Vernalization pathway | |
| AT4G16250 | PHYD, PHYTOCHROME D | TAIR | Light signaling pathway | |
| AT4G16280 | FCA | TAIR | Ambient temperature pathway, Autonomous pathway | Grape |
| AT4G16845 | REDUCED VERNALIZATION RESPONSE 2, VRN2 | TAIR | Autonomous pathway, Vernalization pathway | |
| AT4G18130 | PHYE, PHYTOCHROME E | TAIR | Light signaling pathway | Grape |
| AT4G20370 | TSF, TWIN SISTER OF FT | TAIR | Ambient temperature pathway, Flowering pathway integrator | |
| AT4G22950 | AGAMOUS-LIKE 19, AGL19, GL19 | TAIR | Vernalization pathway | |
| AT4G24540 | AGAMOUS-LIKE 24, AGL24 | TAIR | Vernalization pathway | |
| AT4G26000 | PEP, PEPPER | TAIR | Vernalization pathway | |
| AT4G29730 | MSI5, NFC5, NUCLEOSOME/CHROMATIN ASSEMBLY FACTOR GROUP C5 | TAIR | Ambient temperature pathway, Autonomous pathway | |
| AT4G30200 | VEL1, VERNALIZATION5/VIN3-LIKE 1, VIL2, VIN3-LIKE 2 | TAIR | Autonomous pathway, Vernalization pathway | |
| AT4G34530 | CIB1, CRYPTOCHROME-INTERACTING BASIC-HELIX-LOOP-HELIX 1 | TAIR | Light signaling pathway | |
| AT4G35050 | MSI3, NFC3, NUCLEOSOME/CHROMATIN ASSEMBLY FACTOR GROUP C 3 | TAIR | Autonomous pathway, Vernalization pathway | |
| AT4G35900 | ATBZIP14, FD, FD-1 | TAIR | Ambient temperature pathway, Meristem identity | |
| AT5G02810 | APRR7, PRR7, PSEUDO-RESPONSE REGULATOR 7 | TAIR | Light signaling pathway | |
| AT5G03840 | TERMINAL FLOWER 1, TFL1 | TAIR | Ambient temperature pathway, Flowering pathway integrator | Grape, Strawberry |
| AT5G08230 | TAIR | Vernalization pathway | ||
| AT5G08330 | CCA1 HIKING EXPEDITION, CHE, TRANSCRIPTION FACTOR TCP21, TCP21 | UniProtKB | Light signaling pathway | |
| AT5G10140 | AGAMOUS-LIKE 25, AGL25, FLC, FLF, FLOWERING LOCUS C, FLOWERING LOCUS F | TAIR | Ambient temperature pathway, Flowering pathway integrator, Vernalization pathway | Grape |
| AT5G13480 | FY | TAIR | Autonomous pathway | |
| AT5G15840 | B-BOX DOMAIN PROTEIN 1, BBX1, CO, CONSTANS, FG | TAIR | Flowering pathway integrator, Light signaling pathway | |
| AT5G15850 | ATCOL1, B-BOX DOMAIN PROTEIN 2, BBX2, COL1, CONSTANS-LIKE 1 | TAIR | Flowering pathway integrator, Light signaling pathway | |
| AT5G23150 | ENHANCER OF AG-4 2, HUA2 | TAIR | Vernalization pathway | |
| AT5G23280 | TAIR | Light signaling pathway | ||
| AT5G24470 | APRR5, PRR5, PSEUDO-RESPONSE REGULATOR 5 | TAIR | Light signaling pathway | |
| AT5G24930 | ATCOL4, B-BOX DOMAIN PROTEIN 5, BBX5, COL4, CONSTANS-LIKE 4 | TAIR | Light signaling pathway | |
| AT5G35840 | PHYC, PHYTOCHROME C | TAIR | Light signaling pathway | Grape |
| AT5G37055 | ATSWC6, SEF, SERRATED LEAVES AND EARLY FLOWERING | TAIR | Vernalization pathway | |
| AT5G39660 | CDF2, CYCLING DOF FACTOR 2 | TAIR | Light signaling pathway | |
| AT5G42790 | ARS5, ARSENIC TOLERANCE 5, ATPSM30, PAF1, PROTEASOME ALPHA SUBUNIT F1 | TAIR | Vernalization pathway | |
| AT5G48250 | B-BOX DOMAIN PROTEIN 8, BBX8 | TAIR | Light signaling pathway | |
| AT5G57360 | ADAGIO 1, ADO1, FKF1-LIKE PROTEIN 2, FKL2, LKP1, LOV KELCH PROTEIN 1, ZEITLUPE, ZTL | TAIR | Light signaling pathway | |
| AT5G57380 | VERNALIZATION INSENSITIVE 3, VIN3 | TAIR | Autonomous pathway, Vernalization pathway | |
| AT5G57660 | ATCOL5, B-BOX DOMAIN PROTEIN 6, BBX6, COL5, CONSTANS-LIKE 5 | TAIR | Light signaling pathway | |
| AT5G58230 | ARABIDOPSIS MULTICOPY SUPRESSOR OF IRA1, ATMSI1, MATERNAL EFFECT EMBRYO ARREST 70, MEE70, MSI1, MULTICOPY SUPRESSOR OF IRA1 | TAIR | Autonomous pathway, Vernalization pathway | |
| AT5G59570 | BOA, BROTHER OF LUX ARRHYTHMO | TAIR | Light signaling pathway | |
| AT5G60100 | APRR3, PRR3, PSEUDO-RESPONSE REGULATOR 3 | TAIR | Light signaling pathway | |
| AT5G61380 | APRR1, ATTOC1, PRR1, PSEUDO-RESPONSE REGULATOR 1, TIMING OF CAB EXPRESSION 1, TOC1 | TAIR | Light signaling pathway | |
| AT5G62430 | CDF1, CYCLING DOF FACTOR 1 | TAIR | Light signaling pathway | |
| AT5G65050 | AGAMOUS-LIKE 31, AGL31, MADS AFFECTING FLOWERING 2, MAF2 | TAIR | Ambient temperature pathway, Flowering pathway integrator, Vernalization pathway | |
| AT5G65060 | AGAMOUS-LIKE 70, AGL70, FCL3, MADS AFFECTING FLOWERING 3, MAF3 | TAIR | Ambient temperature pathway, Flowering pathway integrator, Vernalization pathway | |
| AT5G65070 | AGAMOUS-LIKE 69, AGL69, FCL4, MADS AFFECTING FLOWERING 4, MAF4 | TAIR | Ambient temperature pathway, Flowering pathway integrator, Vernalization pathway | |
| AT5G65080 | AGAMOUS-LIKE 68, AGL68, MADS AFFECTING FLOWERING 5, MAF5 | TAIR | Ambient temperature pathway, Flowering pathway integrator, Vernalization pathway |
