Time of bloom

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Austin Mudd - Spring 2013


To Do

  • Write procedure section
  • Run amino acid sequences


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)
The major pathways in the timing of flowering from the Max Planck Institute for Plant Breeding Research

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


Procedure

Finding Genes

  • I examined a variety of journal articles related to time of flowering in Arabidopsis thaliana. I came across
  • Overall procedure for finding the genes, running with GenSAS, determining SSRs, etc


Previous Examined Genes


61 Flowering Genes

This table lists 61 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
AT1G02580 EMB173, EMBRYO DEFECTIVE 173, FERTILIZATION INDEPENDENT SEED 1, FIS1, MEA, MEDEA, SDG5, SET DOMAIN-CONTAINING PROTEIN 5 TAIR Polycomb
AT1G14920 GAI, GIBBERELLIC ACID INSENSITIVE, RESTORATION ON GROWTH ON AMMONIA 2, RGA2 TAIR Gibberellin
AT1G20330 COTYLEDON VASCULAR PATTERN 1, CVP1, FRILL1, FRL1, SMT2, STEROL METHYLTRANSFERASE 2 TAIR Vernalization
AT1G27370 SPL10, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 10 TAIR Age
AT1G30970 SUF4, SUPPRESSOR OF FRIGIDA4 TAIR Vernalization
AT1G31814 FRIGIDA LIKE 2, FRL2 TAIR Vernalization
AT1G47250 20S PROTEASOME ALPHA SUBUNIT F2, PAF2 TAIR Vernalization
AT1G53160 FLORAL TRANSITION AT THE MERISTEM6, FTM6, SPL4, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 4 TAIR Age
AT1G65480 FLOWERING LOCUS T, FT TAIR Ambient Temperature
AT1G66350 RGA-LIKE 1, RGL, RGL1 TAIR Gibberellin
AT1G77080 AGAMOUS-LIKE 27, AGL27, FLM, FLOWERING LOCUS M, MADS AFFECTING FLOWERING 1, MAF1 TAIR Ambient Temperature, 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
AT2G01570 REPRESSOR OF GA, REPRESSOR OF GA1-3 1, RGA, RGA1 TAIR Gibberellin
AT2G17770 ATBZIP27, BASIC REGION/LEUCINE ZIPPER MOTIF 27, BZIP27, FD PARALOG, FDP TAIR Ambient Temperature
AT2G18870 VEL3, VERNALIZATION5/VIN3-LIKE 3, VIL4, VIN3-LIKE 4 TAIR Autonomous
AT2G18880 VEL2, VERNALIZATION5/VIN3-LIKE 2, VIL3, VIN3-LIKE 3 TAIR Autonomous
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
AT2G23380 CLF, CURLY LEAF, ICU1, INCURVATA 1, SDG1, SET1, SETDOMAIN 1, SETDOMAIN GROUP 1 TAIR Autonomous, Polycomb, Vernalization
AT2G33810 SPL3, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 3 TAIR Age
AT2G33835 FES1, FRIGIDA-ESSENTIAL 1 TAIR Vernalization
AT2G35670 FERTILIZATION INDEPENDENT SEED 2, FERTILIZATION-INDEPENDENT ENDOSPERM 2, FIE2, FIS2 TAIR Polycomb
AT2G42200 ATSPL9, SPL9, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 9 TAIR Age
AT2G43410 FPA TAIR Autonomous
AT3G03450 RGA-LIKE 2, RGL2 TAIR Gibberellin
AT3G04610 FLK, FLOWERING LOCUS KH DOMAIN TAIR Autonomous
AT3G05120 ATGID1A, GA INSENSITIVE DWARF1A, GID1A TAIR Gibberellin
AT3G10390 FLD, FLOWERING LOCUS D TAIR Ambient Temperature, Autonomous
AT3G12810 CHR13, PHOTOPERIOD-INDEPENDENT EARLY FLOWERING 1, PIE1, SRCAP TAIR Vernalization
AT3G15270 SPL5, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 5 TAIR Age
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, Polycomb, Vernalization
AT3G24440 VERNALIZATION 5, VIL1, VIN3-LIKE 1, VRN5 TAIR Autonomous, Vernalization
AT3G33520 ACTIN-RELATED PROTEIN 6, ARP6, ATARP6, EARLY IN SHORT DAYS 1, ESD1, SUF3, SUPPRESSOR OF FRI 3 TAIR Ambient Temperature, Vernalization
AT4G00650 FLA, FLOWERING LOCUS A, FRI, FRIGIDA TAIR Vernalization
AT4G02020 EZA1, SDG10, SET DOMAIN-CONTAINING PROTEIN 10, SWINGER, SWN TAIR Autonomous, Polycomb, Vernalization
AT4G02560 LD, LUMINIDEPENDENS TAIR Autonomous
AT4G11880 AGAMOUS-LIKE 14, AGL14 TAIR Vernalization
AT4G16280 FCA TAIR Ambient Temperature, Autonomous
AT4G16845 REDUCED VERNALIZATION RESPONSE 2, VRN2 TAIR Autonomous, Polycomb, Vernalization
AT4G20370 TSF, TWIN SISTER OF FT TAIR Ambient Temperature
AT4G22950 AGAMOUS-LIKE 19, AGL19, GL19 TAIR Vernalization
AT4G24540 AGAMOUS-LIKE 24, AGL24 TAIR Vernalization
AT4G26000 PEP, PEPPER TAIR Vernalization
AT4G30200 VEL1, VERNALIZATION5/VIN3-LIKE 1, VIL2, VIN3-LIKE 2 TAIR Autonomous, Vernalization
AT4G35900 ATBZIP14, FD, FD-1 TAIR Ambient Temperature
AT5G03840 TERMINAL FLOWER 1, TFL1 TAIR Ambient Temperature
AT5G10140 AGAMOUS-LIKE 25, AGL25, FLC, FLF, FLOWERING LOCUS C, FLOWERING LOCUS F TAIR Ambient Temperature, Vernalization
AT5G11530 EMBRYONIC FLOWER 1, EMF1 TAIR Polycomb
AT5G13480 FY TAIR Autonomous
AT5G17690 ATLHP1, LHP1, LIKE HETEROCHROMATIN PROTEIN 1, TERMINAL FLOWER 2, TFL2 TAIR Polycomb
AT5G23150 ENHANCER OF AG-4 2, HUA2 TAIR Vernalization
AT5G37055 ATSWC6, SEF, SERRATED LEAVES AND EARLY FLOWERING TAIR Vernalization
AT5G42790 ARS5, ARSENIC TOLERANCE 5, ATPSM30, PAF1, PROTEASOME ALPHA SUBUNIT F1 TAIR Vernalization
AT5G51230 ATEMF2, CYR1, CYTOKININ RESISTANT 1, EMBRYONIC FLOWER 2, EMF2, VEF2 TAIR Polycomb
AT5G57380 VERNALIZATION INSENSITIVE 3, VIN3 TAIR Autonomous, Vernalization
AT5G58230 ARABIDOPSIS MULTICOPY SUPRESSOR OF IRA1, ATMSI1, MATERNAL EFFECT EMBRYO ARREST 70, MEE70, MSI1, MULTICOPY SUPRESSOR OF IRA1 TAIR Autonomous, Polycomb, Vernalization
AT5G65050 AGAMOUS-LIKE 31, AGL31, MADS AFFECTING FLOWERING 2, MAF2 TAIR Ambient Temperature, Vernalization
AT5G65060 AGAMOUS-LIKE 70, AGL70, FCL3, MADS AFFECTING FLOWERING 3, MAF3 TAIR Ambient Temperature, Vernalization
AT5G65070 AGAMOUS-LIKE 69, AGL69, FCL4, MADS AFFECTING FLOWERING 4, MAF4 TAIR Ambient Temperature, Vernalization
AT5G65080 AGAMOUS-LIKE 68, AGL68, MADS AFFECTING FLOWERING 5, MAF5 TAIR Ambient Temperature, Vernalization
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