Time of bloom

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Austin Mudd - Spring 2013
Shortened URL: http://goo.gl/zuTkP


Introduction to Flowering

The Process of Flowering

  • Flowering is the "switch from vegetative growth (the production of stems and leaves) to reproductive growth (the production of flowers)" (Higgins et al., 2010)
  • The “shoot apical meristem starts to produce flowers instead of leaves” (Fornara et al., 2010)
  • Occurs “when conditions for pollination and seed development are optimal and consequently most plants restrict flowering to a specific time of year” (Higgins et al., 2010)
  • ”The genes and molecular mechanisms controlling flowering have been extensively studied in the model dicot Arabidopsis thaliana” (Higgins et al., 2010)
  • In Arabidopsis thaliana, “180 genes have been implicated in flowering-time control based on isolation of loss-of-function mutations or analysis of transgenic plants ... Strikingly, several genes act more than once and in several tissues during floral induction” (Fornara et al., 2010)
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The major pathways in the timing of flowering from Turck and Adrian at the Max Planck Institute for Plant Breeding Research; permission granted

The Timing of Flowering

  • Flowering is controlled by several “major pathways: the photoperiod and vernalization pathways control flowering in response to seasonal changes in day length and temperature; the ambient temperature pathway responds to daily growth temperatures; and the age, autonomous, and gibberellin pathways act more independently of environmental stimuli.” (Fornara et al., 2010)
  • These “pathways converge to regulate a small number of ‘floral integrator genes,’ ... which govern flowering time by merging signals from multiple pathways” (Fornara et al., 2010)

The Importance of Flowering

  • ”Flowering is one of the most important agronomic traits influencing crop yield” (Jung et al., 2012)
  • ”Flowering time is important for adaptation to specific environments and the world's major crop species provide a particularly interesting opportunity for study because they are grown in areas outside the ecogeographical limits of their wild ancestors” (Higgins et al., 2010)
  • “Adaptation to different environments and practices has been achieved by manipulation of flowering time responses” (Higgins et al., 2010)
  • The study of flowering is ”critical for the breeding of climate change resilient crop varieties” (Jung et al., 2012)
  • Flowering is “an excellent system for comparison between and within domestic and wild species” (Higgins et al., 2010)


Pathways Controlling Flowering

Age Pathway

  • "The miR156–SPL interaction constitutes an evolutionarily conserved, endogenous cue for both vegetative phase transition and flowering ... The age-dependent decrease in miR156 results in an increase in SPLs that promote juvenile to adult phase transition and flowering through activation of miR172, MADS box genes, and LFY" (Yu et al., 2012)
  • 5 Arabidopsis genes are involved in the age pathway: SPL3, SPL4, SPL5, SPL9, SPL10 (Amasino, 2010)

Ambient Temperature Pathway

  • Unlike "the photoperiod and vernalisation pathways [which] monitor seasonal changes in day length or temperature and ... [respond] to exposure to long days or prolonged cold temperatures, the ambient temperature pathway coordinates the response to daily growth temperatures" (Jung et al., 2012)
  • 16 Arabidopsis genes are involved in the ambient temperature pathway: AGL31, ATARP6, ATBZIP27, FCA, FD, FLC, FLD, FT, FVE, MAF1, MAF3, MAF4, MAF5, SVP, TFL1, TSF (Jung et al., 2012)

Autonomous Pathway

  • The autonomous pathway is "activated in response to endogenous changes that are independent from the environmental cues leading to flowering", such as the plant's circadian rhythm (Jung et al., 2012)
  • 17 Arabidopsis genes are involved in the autonomous pathway: CLF, FCA, FIE1, FLD, FLK, FPA, FVE, FY, LD, MSI1, SWN, VEL1, VEL2, VEL3, VIN3, VRN2, VRN5 (Jung et al., 2012)

Gibberellin Pathway

  • Gibberellin "is essential for floral induction in short-day conditions." In fact, plants with a "mutation in a GA biosynthetic gene, such as GA1, fail to flower" (Yu et al., 2012)
  • 5 Arabidopsis genes are involved in the gibberellin pathway: GAI, GID1, RGA, RGL1, RGL2 (Yu et al., 2012)

Light Signaling Pathway

  • "Light is one of the main environmental regulators of flowering in plants. Plants sense the time of day and season of year by monitoring the light environment through light signalling pathways." Furthermore, the light signalling pathway is comprised of the "photoperiod pathway genes together with photoreceptor genes and circadian clock components" (Jung et al., 2012)
  • 48 Arabidopsis genes are involved in the light signaling pathway: APRR3, APRR5, APRR9, AT1G26790, AT1G29160, AT2G34140, AT3G21320, AT3G25730, ATCOL4, ATCOL5, CCA1, CDF1, CDF2, CDF3, CDF5, CHE, CIB1, CO, COL1, COL2, COL9, COP1, CRY1, CRY2, ELF3, ELF4, ELF4-L3, FKF1, GI, LHY, LKP2, LUX, PHYA, PHYB, PHYC, PHYD, PHYE, PRR7, RAV1, RFI2, SPA1, SPA2, SPA3, SPA4, TEM1, TEM2, TOC1, ZTL (Jung et al., 2012)

Polycomb Pathway

  • The polycomb pathway centers on “epigenetic [repression] … [of] various developmental and cellular processes … [through two] multi-subunit protein complexes: Polycomb Repressor Complex 1 (PRC1)” and Polycomb Repressor Complex 2 (PRC2) (Kim et al., 2012)
  • 10 Arabidopsis genes are involved in the polycomb pathway: CLF, EMF1, EMF2, FIE1, FIS2, LHP1, MEA, MSI1, SWN, VRN2 (Kim et al., 2012)

Vernalization Pathway

  • The vernalization pathway is the response to "prolonged periods of low temperature [that are required] to initiate flowering" (Jung et al., 2012)
  • 32 Arabidopsis genes are involved in the vernalization pathway: AGL14, AGL19, AGL24, AGL31, ATARP6, ATSWC6, CLF, EFS, FES1, FIE1, FLC, FRI, FRL1, FRL2, HUA2, MAF1, MAF3, MAF4, MAF5, MSI1, PAF1, PAF2, PEP, PIE1, SUF4, SVP, SWN, VEL1, VIN3, VRN1, VRN2, VRN5 (Jung et al., 2012)


Gallery of Arabidopsis Flowering Pathways

Additional figures:


Methods

Finding Genes

  • I examined a variety of journal articles related to time of flowering in Arabidopsis thaliana and found a number of pathways related to flowering (see the gallery above). I came across a genomic analysis of soybean by Jung et al., 2012. In this paper, they listed the "183 Arabidopsis genes that are known to take part in flowering regulatory pathways [taken] from previous studies." These 183 genes, plus "24 additional Arabidopsis genes that are grouped into the same [homolog groups] as known flowering genes," provided a solid foundation for my study. All 207 total genes from Jung et al., 2012 can be viewed here: File:Jung 207 Arabidopsis Flowering Genes.pdf.
  • These 207 total genes fell into two categories: 1) flowering pathway integrators/meristem identity genes and 2) condition pathway genes (responding to the photoperiod pathway, the vernalization pathway, the ambient temperature pathway, the autonomous pathway, and other pathways). Per the direction of Dr. Jeannie Rowland of the USDA Genetic Improvement for Fruits and Vegetables Laboratory, I focused on the condition pathway genes.
  • I identified a total of seven different pathways controlling flowering: the age pathway, the ambient temperature pathway, the autonomous pathway, the gibberellin pathway, the light signaling pathway, the polycomb pathway, and the vernalization pathway. Descriptions and primary genes involved in these pathways were taken from Amasino, 2010, Jung et al., 2012, Kim et al., 2012, and Yu et al., 2012.
  • A total of 108 genes were examined, almost all of which "have been implicated in flowering-time control based on isolation of loss-of-function mutations or analysis of transgenic plants." (Fornara et al., 2010)

Finding SSRs

  • A local database of the blueberry genome was created using the following coding:
./bin/makeblastdb -in BlueberryGenome.txt -input_type fasta -dbtype nucl -title blueberry_Genome
{ echo bin/tblastn -query AASequence.txt -db BlueberryGenome.txt; bin/tblastn -query 
AASequence.txt -db BlueberryGenome.txt; } >> AAOutput.txt
  • For each gene result, the best match was presumed to be the ortholog of the Arabidopsis gene in Vaccinium corymbosum. A maximum E value cutoff of e-04 was established. Although all of the results fell within this cutoff, if a tBLASTn result had not fallen below the E value limit, attempts would have been made to find and tBLASTn a Vitis vinifera ortholog of the Arabidopsis gene from UniProtKB (UniProt Consortium, 2012) nomenclature search.
  • SSRs were determined by importing the best match scaffold into the SSR Tool at the Genome Database for Vaccinium. Three di/trinucleotide SSRs near the gene location on the scaffold were chosen for each gene.


SSR Results

All SSR results can be viewed on the Time of bloom SSR Results page. An abbreviated listing of the results is included below.
Flowering SSR Results Table.png


Flowering Genes Of Interest

This table lists 108 genes involved in the age, ambient temperature, autonomous, gibberellin, light signaling, polycomb, and vernalization pathways, almost all of which "have been implicated in flowering-time control based on isolation of loss-of-function mutations or analysis of transgenic plants." (Fornara et al., 2010)

Arabidopsis Locus Other Names AA Source Pathway Top Hit Vaccinium Scaffold E Value
AT1G01060 LATE ELONGATED HYPOCOTYL, LATE ELONGATED HYPOCOTYL 1, LHY, LHY1 TAIR Light Signaling Scaffold00140 (length 354209) at 234299 2e-19
AT1G02580 EMB173, EMBRYO DEFECTIVE 173, FERTILIZATION INDEPENDENT SEED 1, FIS1, MEA, MEDEA, SDG5, SET DOMAIN-CONTAINING PROTEIN 5 TAIR Polycomb Scaffold00354 (length 215005) at 64805 4e-17
AT1G04400 AT-PHH1, ATCRY2, CRY2, CRYPTOCHROME 2, FHA, PHH1 TAIR Light Signaling Scaffold00649 (length 159319) at 28296 1e-119
AT1G09570 ELONGATED HYPOCOTYL 8, FAR RED ELONGATED 1, FAR RED ELONGATED HYPOCOTYL 2, FHY2, FRE1, HY8, PHYA, PHYTOCHROME A TAIR Light Signaling Scaffold03861 (length 7403) at 3771 0.0
AT1G13260 EDF4, ETHYLENE RESPONSE DNA BINDING FACTOR 4, RAV1, RELATED TO ABI3/VP1 1 TAIR Light Signaling Scaffold00930 (length 110378) at 63069 1e-103
AT1G14920 GAI, GIBBERELLIC ACID INSENSITIVE, RESTORATION ON GROWTH ON AMMONIA 2, RGA2 TAIR Gibberellin Scaffold01360 (length 81306) at 51382 0.0
AT1G20330 COTYLEDON VASCULAR PATTERN 1, CVP1, FRILL1, FRL1, SMT2, STEROL METHYLTRANSFERASE 2 TAIR Vernalization Scaffold02142 (length 46662) at 24743 9e-06
AT1G22770 FB, GI, GIGANTEA TAIR Light Signaling Scaffold00100 (length 346620) at 198329 0.0
AT1G25560 EDF1, ETHYLENE RESPONSE DNA BINDING FACTOR 1, TEM1, TEMPRANILLO 1 TAIR Light Signaling Scaffold00930 (length 110378) at 63096 3e-99
AT1G26790 TAIR Light Signaling Scaffold00079 (length 471015) at 69048 6e-33
AT1G27370 SPL10, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 10 TAIR Age Scaffold00127 (length 336847) at 165806 5e-33
AT1G29160 TAIR Light Signaling Scaffold00270 (length 246371) at 215229 4e-50
AT1G30970 SUF4, SUPPRESSOR OF FRIGIDA4 TAIR Vernalization Scaffold00348 (length 210978) at 75279 1e-15
AT1G31814 FRIGIDA LIKE 2, FRL2 TAIR Vernalization Scaffold00289 (length 259591) at 150896 2e-19
AT1G47250 20S PROTEASOME ALPHA SUBUNIT F2, PAF2 TAIR Vernalization Scaffold00528 (length 197283) at 110933 3e-64
AT1G53090 SPA1-RELATED 4, SPA4 TAIR Light Signaling Scaffold00734 (length 158513) at 143450 3e-129
AT1G53160 FLORAL TRANSITION AT THE MERISTEM6, FTM6, SPL4, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 4 TAIR Age Scaffold00062 (length 451336) at 412489 1e-15
AT1G65480 FLOWERING LOCUS T, FT TAIR Ambient Temperature Scaffold00357 (length 260075) at 58774 6e-35
AT1G66350 RGA-LIKE 1, RGL, RGL1 TAIR Gibberellin Scaffold00134 (length 346346) at 174707 0.0
AT1G68050 "FLAVIN-BINDING, KELCH REPEAT, F BOX 1", ADO3, FKF1 TAIR Light Signaling Scaffold00110 (length 358202) at 120279 0.0
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 Scaffold00930 (length 110378) at 63096 5e-102
AT1G77080 AGAMOUS-LIKE 27, AGL27, FLM, FLOWERING LOCUS M, MADS AFFECTING FLOWERING 1, MAF1 TAIR Ambient Temperature, Vernalization Scaffold10765 (length 2447) at 744 3e-13
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 Scaffold00894 (length 114877) at 89213 1e-27
AT2G01570 REPRESSOR OF GA, REPRESSOR OF GA1-3 1, RGA, RGA1 TAIR Gibberellin Scaffold01360 (length 81306) at 51382 0.0
AT2G06255 ELF4-L3, ELF4-LIKE 3 TAIR Light Signaling Scaffold00336 (length 230445) at 188137 1e-39
AT2G17770 ATBZIP27, BASIC REGION/LEUCINE ZIPPER MOTIF 27, BZIP27, FD PARALOG, FDP TAIR Ambient Temperature Scaffold00367 (length 240396) at 113139 7e-17
AT2G18790 HY3, OOP1, OUT OF PHASE 1, PHYB, PHYTOCHROME B TAIR Light Signaling Scaffold00751 (length 152548) at 83698 0.0
AT2G18870 VEL3, VERNALIZATION5/VIN3-LIKE 3, VIL4, VIN3-LIKE 4 TAIR Autonomous Scaffold00396 (length 187979) at 73810 7e-19
AT2G18880 VEL2, VERNALIZATION5/VIN3-LIKE 2, VIL3, VIN3-LIKE 3 TAIR Autonomous Scaffold00026 (length 499904) at 369396 6e-41
AT2G18915 ADAGIO 2, ADO2, LKP2, LOV KELCH PROTEIN 2 TAIR Light Signaling Scaffold00026 (length 499904) at 445582 0.0
AT2G19520 ACG1, ATMSI4, FVE, MSI4, MULTICOPY SUPPRESSOR OF IRA1 4, NFC04, NFC4 TAIR Ambient Temperature, Autonomous Scaffold00728 (length 157708) at 8716 6e-21
AT2G22540 AGAMOUS-LIKE 22, AGL22, SHORT VEGETATIVE PHASE, SVP TAIR Ambient Temperature, Vernalization Scaffold01187 (length 101153) at 47701 2e-24
AT2G23380 CLF, CURLY LEAF, ICU1, INCURVATA 1, SDG1, SET1, SETDOMAIN 1, SETDOMAIN GROUP 1 TAIR Autonomous, Polycomb, Vernalization Scaffold00354 (length 215005) at 64799 5e-41
AT2G25930 EARLY FLOWERING 3, ELF3, PYK20 TAIR Light Signaling Scaffold00371 (length 223748) at 73111 6e-19
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 Scaffold00734 (length 158513) at 142779 5e-62
AT2G33810 SPL3, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 3 TAIR Age Scaffold00062 (length 451336) at 412489 2e-17
AT2G33835 FES1, FRIGIDA-ESSENTIAL 1 TAIR Vernalization Scaffold00102 (length 383343) at 88264 7e-17
AT2G34140 TAIR Light Signaling Scaffold00270 (length 246371) at 215217 7e-49
AT2G35670 FERTILIZATION INDEPENDENT SEED 2, FERTILIZATION-INDEPENDENT ENDOSPERM 2, FIE2, FIS2 TAIR Polycomb Scaffold00857 (length 126644) at 55565 3e-04
AT2G40080 EARLY FLOWERING 4, ELF4 TAIR Light Signaling Scaffold00254 (length 265810) at 228805 4e-24
AT2G42200 ATSPL9, SPL9, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 9 TAIR Age Scaffold00691 (length 141413) at 61795 5e-21
AT2G43410 FPA TAIR Autonomous Scaffold01689 (length 75472) at 47663 4e-45
AT2G46340 SPA1, SUPPRESSOR OF PHYA-105 1 TAIR Light Signaling Scaffold00734 (length 158513) at 142779 3e-69
AT2G46790 APRR9, ARABIDOPSIS PSEUDO-RESPONSE REGULATOR 9, PRR9, PSEUDO-RESPONSE REGULATOR 9, TL1, TOC1-LIKE PROTEIN 1 TAIR Light Signaling Scaffold00001 (length 1030549) at 322801 1e-36
AT2G46830 ATCCA1, CCA1, CIRCADIAN CLOCK ASSOCIATED 1 TAIR Light Signaling Scaffold00140 (length 354209) at 234299 7e-20
AT2G47700 RED AND FAR-RED INSENSITIVE 2, RFI2 TAIR Light Signaling Scaffold01059 (length 101143) at 96557 1e-19
AT3G02380 ATCOL2, B-BOX DOMAIN PROTEIN 3, BBX3, COL2, CONSTANS-LIKE 2 TAIR Light Signaling Scaffold01843 (length 51900) at 40767 3e-48
AT3G03450 RGA-LIKE 2, RGL2 TAIR Gibberellin Scaffold00134 (length 346346) at 174722 0.0
AT3G04610 FLK, FLOWERING LOCUS KH DOMAIN TAIR Autonomous Scaffold01384 (length 81068) at 28309 4e-29
AT3G05120 ATGID1A, GA INSENSITIVE DWARF1A, GID1A TAIR Gibberellin Scaffold00101 (length 425332) at 398762 4e-175
AT3G07650 B-BOX DOMAIN PROTEIN 7, BBX7, COL9, CONSTANS-LIKE 9 TAIR Light Signaling Scaffold00832 (length 123094) at 89599 1e-55
AT3G10390 FLD, FLOWERING LOCUS D TAIR Ambient Temperature, Autonomous Scaffold00232 (length 253418) at 139565 0.0
AT3G12810 CHR13, PHOTOPERIOD-INDEPENDENT EARLY FLOWERING 1, PIE1, SRCAP TAIR Vernalization Scaffold00147 (length 345970) at 30164 0.0
AT3G15270 SPL5, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 5 TAIR Age Scaffold00105 (length 392037) at 147284 5e-16
AT3G15354 SPA1-RELATED 3, SPA3 TAIR Light Signaling Scaffold00734 (length 158513) at 143450 1e-144
AT3G18990 REDUCED VERNALIZATION RESPONSE 1, REM39, REPRODUCTIVE MERISTEM 39, VRN1 TAIR Vernalization Scaffold00811 (length 108354) at 96661 2e-25
AT3G20740 FERTILIZATION-INDEPENDENT ENDOSPERM, FERTILIZATION-INDEPENDENT ENDOSPERM 1, FIE, FIE1, FIS3 TAIR Autonomous, Polycomb, Vernalization Scaffold01670 (length 60304) at 9836 5e-20
AT3G21320 TAIR Light Signaling Scaffold00509 (length 192554) at 181887 1e-21
AT3G24440 VERNALIZATION 5, VIL1, VIN3-LIKE 1, VRN5 TAIR Autonomous, Vernalization Scaffold00396 (length 187979) at 73795 2e-69
AT3G25730 EDF3, ETHYLENE RESPONSE DNA BINDING FACTOR 3 TAIR Light Signaling Scaffold00930 (length 110378) at 63060 5e-100
AT3G33520 ACTIN-RELATED PROTEIN 6, ARP6, ATARP6, EARLY IN SHORT DAYS 1, ESD1, SUF3, SUPPRESSOR OF FRI 3 TAIR Ambient Temperature, Vernalization Scaffold00246 (length 286612) at 268521 1e-53
AT3G46640 LUX, LUX ARRHYTHMO, PCL1, PHYTOCLOCK 1 TAIR Light Signaling Scaffold01150 (length 88293) at 80272 3e-34
AT3G47500 CDF3, CYCLING DOF FACTOR 3 TAIR Light Signaling Scaffold00079 (length 471015) at 68175 1e-85
AT4G00650 FLA, FLOWERING LOCUS A, FRI, FRIGIDA TAIR Vernalization Scaffold00039 (length 505275) at 216632 4e-50
AT4G02020 EZA1, SDG10, SET DOMAIN-CONTAINING PROTEIN 10, SWINGER, SWN TAIR Autonomous, Polycomb, Vernalization Scaffold00354 (length 215005) at 64799 2e-48
AT4G02560 LD, LUMINIDEPENDENS TAIR Autonomous Scaffold00002 (length 840149) at 158601 4e-28
AT4G08920 ATCRY1, BLU1, BLUE LIGHT UNINHIBITED 1, CRY1, CRYPTOCHROME 1, ELONGATED HYPOCOTYL 4, HY4, OOP2, OUT OF PHASE 2 TAIR Light Signaling Scaffold00331 (length 261439) at 124817 4e-128
AT4G11110 SPA1-RELATED 2, SPA2 TAIR Light Signaling Scaffold01034 (length 107107) at 19205 2e-62
AT4G11880 AGAMOUS-LIKE 14, AGL14 TAIR Vernalization Scaffold00249 (length 258199) at 131012 2e-29
AT4G16250 PHYD, PHYTOCHROME D TAIR Light Signaling Scaffold00751 (length 152548) at 83707 0.0
AT4G16280 FCA TAIR Ambient Temperature, Autonomous Scaffold00104 (length 360147) at 120318 5e-13
AT4G16845 REDUCED VERNALIZATION RESPONSE 2, VRN2 TAIR Autonomous, Polycomb, Vernalization Scaffold00857 (length 126644) at 55203 3e-07
AT4G18130 PHYE, PHYTOCHROME E TAIR Light Signaling Scaffold00751 (length 152548) at 83749 0.0
AT4G20370 TSF, TWIN SISTER OF FT TAIR Ambient Temperature Scaffold00357 (length 260075) at 58807 1e-33
AT4G22950 AGAMOUS-LIKE 19, AGL19, GL19 TAIR Vernalization Scaffold00249 (length 258199) at 131012 4e-28
AT4G24540 AGAMOUS-LIKE 24, AGL24 TAIR Vernalization Scaffold01187 (length 101153) at 47701 2e-25
AT4G26000 PEP, PEPPER TAIR Vernalization Scaffold00021 (length 527983) at 157278 3e-29
AT4G30200 VEL1, VERNALIZATION5/VIN3-LIKE 1, VIL2, VIN3-LIKE 2 TAIR Autonomous, Vernalization Scaffold00026 (length 499904) at 369417 7e-64
AT4G34530 CIB1, CRYPTOCHROME-INTERACTING BASIC-HELIX-LOOP-HELIX 1 TAIR Light Signaling Scaffold01322 (length 99420) at 82955 2e-29
AT4G35900 ATBZIP14, FD, FD-1 TAIR Ambient Temperature Scaffold00367 (length 240396) at 113139 1e-16
AT5G02810 APRR7, PRR7, PSEUDO-RESPONSE REGULATOR 7 TAIR Light Signaling Scaffold00125 (length 356885) at 276518 1e-33
AT5G03840 TERMINAL FLOWER 1, TFL1 TAIR Ambient Temperature Scaffold00181 (length 337602) at 12825 1e-28
AT5G08330 CCA1 HIKING EXPEDITION, CHE, TRANSCRIPTION FACTOR TCP21, TCP21 UniProtKB Light Signaling Scaffold00993 (length 109486) at 294 5e-27
AT5G10140 AGAMOUS-LIKE 25, AGL25, FLC, FLF, FLOWERING LOCUS C, FLOWERING LOCUS F TAIR Ambient Temperature, Vernalization Scaffold10765 (length 2447) at 708 8e-22
AT5G11530 EMBRYONIC FLOWER 1, EMF1 TAIR Polycomb Scaffold00253 (length 240879) at 11069 1e-06
AT5G13480 FY TAIR Autonomous Scaffold00166 (length 328538) at 74796 2e-43
AT5G15840 B-BOX DOMAIN PROTEIN 1, BBX1, CO, CONSTANS, FG TAIR Light Signaling Scaffold01843 (length 51900) at 40767 3e-29
AT5G15850 ATCOL1, B-BOX DOMAIN PROTEIN 2, BBX2, COL1, CONSTANS-LIKE 1 TAIR Light Signaling Scaffold01843 (length 51900) at 40767 5e-44
AT5G17690 ATLHP1, LHP1, LIKE HETEROCHROMATIN PROTEIN 1, TERMINAL FLOWER 2, TFL2 TAIR Polycomb Scaffold00696 (length 140617) at 128983 7e-13
AT5G23150 ENHANCER OF AG-4 2, HUA2 TAIR Vernalization Scaffold00686 (length 145647) at 102689 5e-42
AT5G24470 APRR5, PRR5, PSEUDO-RESPONSE REGULATOR 5 TAIR Light Signaling Scaffold00001 (length 1030549) at 322798 3e-40
AT5G24930 ATCOL4, B-BOX DOMAIN PROTEIN 5, BBX5, COL4, CONSTANS-LIKE 4 TAIR Light Signaling Scaffold11225 (length 3326) at 2816 8e-23
AT5G35840 PHYC, PHYTOCHROME C TAIR Light Signaling Scaffold01070 (length 102706) at 75395 0.0
AT5G37055 ATSWC6, SEF, SERRATED LEAVES AND EARLY FLOWERING TAIR Vernalization Scaffold00925 (length 141061) at 38143 4e-29
AT5G39660 CDF2, CYCLING DOF FACTOR 2 TAIR Light Signaling Scaffold00651 (length 145047) at 19066 1e-90
AT5G42790 ARS5, ARSENIC TOLERANCE 5, ATPSM30, PAF1, PROTEASOME ALPHA SUBUNIT F1 TAIR Vernalization Scaffold00528 (length 197283) at 110933 5e-64
AT5G51230 ATEMF2, CYR1, CYTOKININ RESISTANT 1, EMBRYONIC FLOWER 2, EMF2, VEF2 TAIR Polycomb Scaffold00857 (length 126644) at 44887 9e-19
AT5G57360 ADAGIO 1, ADO1, FKF1-LIKE PROTEIN 2, FKL2, LKP1, LOV KELCH PROTEIN 1, ZEITLUPE, ZTL TAIR Light Signaling Scaffold00026 (length 499904) at 445597 0.0
AT5G57380 VERNALIZATION INSENSITIVE 3, VIN3 TAIR Autonomous, Vernalization Scaffold00026 (length 499904) at 369405 3e-48
AT5G57660 ATCOL5, B-BOX DOMAIN PROTEIN 6, BBX6, COL5, CONSTANS-LIKE 5 TAIR Light Signaling Scaffold11225 (length 3326) at 2816 1e-25
AT5G58230 ARABIDOPSIS MULTICOPY SUPRESSOR OF IRA1, ATMSI1, MATERNAL EFFECT EMBRYO ARREST 70, MEE70, MSI1, MULTICOPY SUPRESSOR OF IRA1 TAIR Autonomous, Polycomb, Vernalization Scaffold00615 (length 179658) at 161081 2e-61
AT5G60100 APRR3, PRR3, PSEUDO-RESPONSE REGULATOR 3 TAIR Light Signaling Scaffold02075 (length 43325) at 14139 3e-25
AT5G61380 APRR1, ATTOC1, PRR1, PSEUDO-RESPONSE REGULATOR 1, TIMING OF CAB EXPRESSION 1, TOC1 TAIR Light Signaling Scaffold00753 (length 123742) at 70468 2e-47
AT5G62430 CDF1, CYCLING DOF FACTOR 1 TAIR Light Signaling Scaffold01102 (length 99830) at 51435 1e-59
AT5G65050 AGAMOUS-LIKE 31, AGL31, MADS AFFECTING FLOWERING 2, MAF2 TAIR Ambient Temperature, Vernalization Scaffold10765 (length 2447) at 723 4e-20
AT5G65060 AGAMOUS-LIKE 70, AGL70, FCL3, MADS AFFECTING FLOWERING 3, MAF3 TAIR Ambient Temperature, Vernalization Scaffold10765 (length 2447) at 639 7e-15
AT5G65070 AGAMOUS-LIKE 69, AGL69, FCL4, MADS AFFECTING FLOWERING 4, MAF4 TAIR Ambient Temperature, Vernalization Scaffold10765 (length 2447) at 723 6e-20
AT5G65080 AGAMOUS-LIKE 68, AGL68, MADS AFFECTING FLOWERING 5, MAF5 TAIR Ambient Temperature, Vernalization Scaffold10765 (length 2447) at 699 1e-18


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