Difference between revisions of "Time of bloom"

Latest revision as of 16:44, 12 August 2021

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)

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

• 

  Izawa et al., 2003; permission pending

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  Sung et al., 2003; permission granted

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  Boss et al., 2004; permission granted

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  Boss et al., 2004; permission granted

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  Henderson and Dean, 2004; permission granted

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  Amasino, 2005; permission granted

• 

  He and Amasino, 2005; permission granted

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  Yamaguchi et al., 2005; permission pending

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  Bäurle and Dean, 2006; permission granted

• 

  Farrona et al., 2008; permission granted

• 

  Farrona et al., 2008; permission granted

• 

  Amasino, 2010; permission granted

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  Higgins et al., 2010; permission granted

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  Kim and Sung, 2010; permission pending

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  Taiz and Zeiger, 2010; permission pending

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  Ballerini and Kramer, 2011; permission granted

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  Ferrier et al., 2011; permission pending

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  Zhang et al., 2011; permission granted

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  Jung et al., 2012; permission pending

Additional figures:

• Figure 3 from Liu et al., 2009
• Figure 1 from Schneitz and Balasubramanian, 2009
• Figure 1 from Wellmer and Riechmann, 2010
• Figure 1 from Posé et al., 2012

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

• Amino acid sequences for all Arabidopsis genes were taken from The Arabidopsis Information Resource (TAIR) (Huala et al., 2001). The amino acid sequences were run via tBLASTn against the blueberry scaffolds to find the closest match using the following coding:

{ 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 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)

References

• Amasino RM. Seasonal and developmental timing of flowering. Plant J, 61, 1001-1013 (2010).
• Amasino RM. Vernalization and flowering time. Curr Opin Plant Biol, 16, 154–158 (2005).
• Ballerini ES, Kramer EM. Environmental and molecular analysis of the floral transition in the lower eudicot Aquilegia formosa. Evodevo, 2, 1-20 (2011).
• Bäurle I, Dean C. The timing of developmental transitions in plants. Cell, 125, 655-664 (2006).
• Boss PK, Bastow RM, Mylne JS, Dean C. Multiple pathways in the decision to flower: enabling, promoting, and resetting. Plant Cell, 16, S18-S31 (2004).
• Farrona S, Coupland G, Turck F. The impact of chromatin regulation on the floral transition. Semin Cell Dev Biol, 19, 560-573 (2008).
• Ferrier T, Matus JT, Jin J, Riechmann JL. Arabidopsis paves the way: genomic and network analyses in crops. Curr Opin Biotechnol, 22, 260-270 (2011).
• Fornara F, de Montaigu A, Coupland G. SnapShot: Control of flowering in Arabidopsis. Cell, 141, 550-550.e2 (2010).
• Henderson IR, Dean C. Control of Arabidopsis flowering: the chill before the bloom. Development, 131, 3829-3838 (2004).
• He Y, Amasino RM. Role of chromatin modification in flowering-time control. Trends Plant Sci, 10, 30-35 (2005).
• Higgins JA, Bailey PC, Laurie DA. Comparative genomics of flowering time pathways using Brachypodium distachyon as a model for the temperate grasses. PLoS One, 5, e10065 (2010).
• Huala E, Dickerman AW, Garcia-Hernandez M, Weems D, Reiser L, LaFond F, Hanley D, Kiphart D, Zhuang M, Huang W, Mueller LA, Bhattacharyya D, Bhaya D, Sobral BW, Beavis W, Meinke DW, Town CD, Somerville C, Rhee SY. The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant. Nucleic Acids Res, 29, 102-105 (2001).
• Izawa T, Takahashi Y, Yano M. Comparative biology comes into bloom: genomic and genetic comparison of flowering pathways in rice and Arabidopsis. Curr Opin Plant Biol, 6, 113-120 (2003).
• Jung CH, Wong CE, Singh MB, Bhalla PL. Comparative genomic analysis of soybean flowering genes. PLoS One, 7, e38250 (2012).
• Kim DH, Sung S. The Plant Homeo Domain finger protein, VIN3-LIKE 2, is necessary for photoperiod-mediated epigenetic regulation of the floral repressor, MAF5. Proc Natl Acad Sci USA, 107, 17029-17034 (2010).
• Kim SY, Lee J, Eshed-Williams L, Zilberman D, Sung ZR. EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development. PLoS Genet, 8, e1002512 (2012).
• Liu C, Thong Z, Yu H. Coming into bloom: the specification of floral meristems. Development, 136, 3379-3391 (2009).
• Posé D, Yant L, Schmid M. The end of innocence: flowering networks explode in complexity. Curr Opin Plant Biol 15, 45-50 (2012).
• Schneitz K, Balasubramanian S. Floral Meristems. eLS (John Wiley & Sons Ltd, Chichester, 2009).
• SSR Tool. Genome Database for Vaccinium.
• Sung ZR, Chen L, Moon YH, Lertpiriyapong K. Mechanisms of floral repression in Arabidopsis. Curr Opin Plant Biol, 6, 29-35 (2003).
• Taiz L, Zeiger E. Plant Physiology Fifth Edition Ch. 20 (Sinauer Associates, Sunderland, MA, 2010).
• Turck F, Adrian J. A lesson in complexity: regulation of FLOWERING LOCUS T. Max Planck Institute for Plant Breeding Research.
• UniProt Consortium. Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res, 40, D71-D75 (2012).
• Wellmer F, Riechmann JL. Gene networks controlling the initiation of flower development. Trends Genet, 26, 519-527 (2010).
• Yamaguchi A, Kobayashi Y, Goto K, Abe M, Araki T. TWIN SISTER OF FT (TSF) acts as a floral pathway integrator redundantly with FT. Plant Cell Physiol, 46, 1175-1189 (2005).
• Yu S, Galvão VC, Zhang YC, Horrer D, Zhang TQ, Hao YH, Feng YQ, Wang S, Schmid M, Wang JW. Gibberellin regulates the Arabidopsis floral transition through miR156-targeted SQUAMOSA promoter binding-like transcription factors. Plant Cell, 24, 3320-3332 (2012).
• Zhang JZ, Ai XY, Sun LM, Zhang DL, Guo WW, Deng XX, Hu CG. Transcriptome profile analysis of flowering molecular processes of early flowering trifoliate orange mutant and the wild-type [Poncirus trifoliata (L.) Raf.] by massively parallel signature sequencing. BMC Genomics, 12, 63 (2011).