Difference between revisions of "Time of bloom"

Revision as of 23:16, 12 March 2013

Austin Mudd - Spring 2013

To Do

• Write procedure section
• Conglomerate final list of amino acid sequences (each in individual txt files) to run

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

• 

  Izawa et al., 2003

• 

  Sung et al., 2003

• 

  Boss et al., 2004

• 

  Boss et al., 2004

• 

  Henderson and Dean, 2004

• 

  Amasino, 2005

• 

  He and Amasino, 2005

• 

  Yamaguchi et al., 2005

• 

  Bäurle and Dean, 2006

• 

  Farrona et al., 2008

• 

  Farrona et al., 2008

• 

  Liu et al., 2009

• 

  Schneitz, 2009

• 

  Amasino, 2010

• 

  Higgins et al., 2010

• 

  Kim and Sung, 2010

• 

  Taiz and Zeiger, 2010

• 

  Wellmer and Riechmann, 2010 and Ferrier et al., 2011

• 

  Ballerini and Kramer, 2011

• 

  Zhang et al., 2011

• 

  Jung et al., 2012

• 

  Posé et al., 2012

Procedure

• Overall procedure for finding the genes, running with GenSAS, determining SSRs, etc

Previous Examined Genes

• Constans (CO)
• Constitutive Photomorphogenic 1
• Crytochrome 1 (CRY1)
• Crytochrome 2 (CRY2)
• Cycling DOF Factor (CDF)
• Flowering Locus T (FT)
• Gigantea (GI)
• Phytochrome A (PHYA)
• Phytochrome B (PHYB)

108 Flowering Genes

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) All potential orthologs are found via UniProt Grape nomenclature search.