http://gcat.davidson.edu/GcatWiki/api.php?action=feedcontributions&feedformat=atom&user=LaheyerGcatWiki - User contributions [en]2026-05-17T20:55:38ZUser contributionsMediaWiki 1.28.2http://gcat.davidson.edu/GcatWiki/index.php?title=Time_of_bloom&diff=19289Time of bloom2021-08-12T16:44:29Z<p>Laheyer: </p>
<hr />
<div>Austin Mudd - Spring 2013<br />
<br/>Shortened URL: http://goo.gl/zuTkP<br />
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__TOC__<br />
<br />
==Introduction to Flowering==<br />
====The Process of Flowering====<br />
*Flowering is the "switch from vegetative growth (the production of stems and leaves) to reproductive growth (the production of flowers)" ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010065 Higgins ''et al.'', 2010])<br />
*The “shoot apical meristem starts to produce flowers instead of leaves” ([http://www.sciencedirect.com/science/article/pii/S0092867410004411 Fornara ''et al.'', 2010])<br />
*Occurs “when conditions for pollination and seed development are optimal and consequently most plants restrict flowering to a specific time of year” ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010065 Higgins ''et al.'', 2010])<br />
*”The genes and molecular mechanisms controlling flowering have been extensively studied in the model dicot <i>Arabidopsis thaliana</i>” ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010065 Higgins ''et al.'', 2010])<br />
*In <i>Arabidopsis thaliana</i>, “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” ([http://www.sciencedirect.com/science/article/pii/S0092867410004411 Fornara ''et al.'', 2010])<br />
<br />
[[File:Max_Planck_Institute_Pathway.png|thumb|right|alt=Diagram of pathways|The major pathways in the timing of flowering from Turck and Adrian at the [http://www.mpipz.mpg.de/305695/Project_1 Max Planck Institute for Plant Breeding Research]; permission granted]]<br />
====The Timing of Flowering====<br />
*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.” ([http://www.sciencedirect.com/science/article/pii/S0092867410004411 Fornara ''et al.'', 2010])<br />
*These “pathways converge to regulate a small number of ‘floral integrator genes,’ ... which govern flowering time by merging signals from multiple pathways” ([http://www.sciencedirect.com/science/article/pii/S0092867410004411 Fornara ''et al.'', 2010])<br />
<br />
====The Importance of Flowering====<br />
*”Flowering is one of the most important agronomic traits influencing crop yield” ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012])<br />
*”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” ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010065 Higgins ''et al.'', 2010])<br />
*“Adaptation to different environments and practices has been achieved by manipulation of flowering time responses” ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010065 Higgins ''et al.'', 2010])<br />
*The study of flowering is ”critical for the breeding of climate change resilient crop varieties” ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012])<br />
*Flowering is “an excellent system for comparison between and within domestic and wild species” ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010065 Higgins ''et al.'', 2010])<br />
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<br />
==Pathways Controlling Flowering==<br />
====Age Pathway====<br />
*"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" ([http://www.plantcell.org/content/early/2012/08/29/tpc.112.101014.full.pdf+html Yu ''et al.'', 2012])<br />
*5 <i>Arabidopsis</i> genes are involved in the age pathway: SPL3, SPL4, SPL5, SPL9, SPL10 ([http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2010.04148.x/pdf/ Amasino, 2010])<br />
<br />
====Ambient Temperature Pathway====<br />
*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" ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012])<br />
*16 <i>Arabidopsis</i> genes are involved in the ambient temperature pathway: AGL31, ATARP6, ATBZIP27, FCA, FD, FLC, FLD, FT, FVE, MAF1, MAF3, MAF4, MAF5, SVP, TFL1, TSF ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012])<br />
<br />
====Autonomous Pathway====<br />
*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 ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012])<br />
*17 <i>Arabidopsis</i> genes are involved in the autonomous pathway: CLF, FCA, FIE1, FLD, FLK, FPA, FVE, FY, LD, MSI1, SWN, VEL1, VEL2, VEL3, VIN3, VRN2, VRN5 ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012]) <br />
<br />
====Gibberellin Pathway====<br />
*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" ([http://www.plantcell.org/content/early/2012/08/29/tpc.112.101014.full.pdf+html Yu ''et al.'', 2012])<br />
*5 <i>Arabidopsis</i> genes are involved in the gibberellin pathway: GAI, GID1, RGA, RGL1, RGL2 ([http://www.plantcell.org/content/early/2012/08/29/tpc.112.101014.full.pdf+html Yu ''et al.'', 2012])<br />
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====Light Signaling Pathway====<br />
*"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" ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012])<br />
*48 <i>Arabidopsis</i> 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 ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012])<br />
<br />
====Polycomb Pathway====<br />
*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) ([http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002512 Kim ''et al.'', 2012])<br />
*10 <i>Arabidopsis</i> genes are involved in the polycomb pathway: CLF, EMF1, EMF2, FIE1, FIS2, LHP1, MEA, MSI1, SWN, VRN2 ([http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002512 Kim ''et al.'', 2012])<br />
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====Vernalization Pathway====<br />
*The vernalization pathway is the response to "prolonged periods of low temperature [that are required] to initiate flowering" ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012])<br />
*32 <i>Arabidopsis</i> 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 ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012])<br />
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<br />
==Gallery of <i>Arabidopsis</i> Flowering Pathways==<br />
<br />
<gallery widths="102px" heights="102px" perrow="6"><br />
File:Izawa_Pathway.jpeg|alt=Diagram of pathway from Izawa ''et al.'', 2003|[http://www.sciencedirect.com/science/article/pii/S1369526603000141 Izawa ''et al.'', 2003]; permission pending<br />
File:Sung_Pathway.gif|alt=Diagram of pathway from Sung ''et al.'', 2003|[http://www.sciencedirect.com/science/article/pii/S1369526602000146 Sung ''et al.'', 2003]; permission granted<br />
File:Boss_Pathway.gif|alt=Diagram of pathway from |[http://www.plantcell.org/content/16/suppl_1/S18/F2.expansion Boss ''et al.'', 2004]; permission granted<br />
File:Boss_Pathway_2.jpeg|alt=Diagram of pathway from Boss ''et al.'', 2004|[http://www.plantcell.org/content/16/suppl_1/S18/F3.expansion Boss ''et al.'', 2004]; permission granted<br />
File:Henderson_and_Dean_Pathway.jpeg|alt=Diagram of pathway from Henderson and Dean, 2004|[http://dev.biologists.org/content/131/16/3829/F1.expansion.html Henderson and Dean, 2004]; permission granted<br />
File:Amasino_Pathway.jpeg|alt=Diagram of pathway from Amasino, 2005|[http://www.sciencedirect.com/science/article/pii/S0958166905000273 Amasino, 2005]; permission granted<br />
File:He_and_Amasino_Pathway.jpeg|alt=Diagram of pathway from |[http://www.sciencedirect.com/science/article/pii/S1360138504002705 He and Amasino, 2005]; permission granted<br />
File:Yamaguchi_Pathway.jpeg|alt=Diagram of pathway from He and Amasino, 2005 |[http://pcp.oxfordjournals.org/content/46/8/1175/F7.expansion Yamaguchi ''et al.'', 2005]; permission pending<br />
File:Baurle_and_Dean_Pathway.jpeg|alt=Diagram of pathway from Yamaguchi ''et al.'', 2005|[http://www.sciencedirect.com/science/article/pii/S009286740600571X Bäurle and Dean, 2006]; permission granted<br />
File:Farrona_Pathway.jpeg|alt=Diagram of pathway from Farrona ''et al.'', 2008 |[http://www.sciencedirect.com/science/article/pii/S1084952108000566 Farrona ''et al.'', 2008]; permission granted<br />
File:Farrona_Pathway_2.jpeg|alt=Diagram of pathway from |[http://www.sciencedirect.com/science/article/pii/S1084952108000566 Farrona ''et al.'', 2008]; permission granted<br />
File:Amasino_Pathway_2.png|alt=Diagram of pathway from Amasino, 2010|[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2010.04148.x/pdf/ Amasino, 2010]; permission granted<br />
File:Higgins_Pathway.jpg|alt=Diagram of pathway from Higgins ''et al.'', 2010 |[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010065 Higgins ''et al.'', 2010]; permission granted<br />
File:Kim_and_Sung_Pathway.jpeg|alt=Pathway from Kim and Sung, 2010 |[http://www.pnas.org/content/107/39/17029/F6.expansion.html Kim and Sung, 2010]; permission pending<br />
File:Taiz_and_Zeiger_Pathway.jpeg|alt=Diagram of pathway from Taiz and Zeiger, 2010 |[http://5e.plantphys.net/article.php?ch=1&id=375 Taiz and Zeiger, 2010]; permission pending<br />
File:Ballerini_and_Kramer_Pathway.png|alt=Diagram of pathway from Ballerini and Kramer, 2011 |[http://dash.harvard.edu/bitstream/handle/1/4903810/Ballerini%20%26%20Kramer%202011.pdf?sequence=1 Ballerini and Kramer, 2011]; permission granted<br />
File:Ferrier_Pathway.jpeg|alt=Diagram of pathway from |[http://www.sciencedirect.com/science/article/pii/S0958166910002284 Ferrier ''et al.'', 2011]; permission pending<br />
File:Zhang_Pathway.png|alt=Diagram of pathway from Ferrier ''et al.'', 2011|[http://www.biomedcentral.com/1471-2164/12/63 Zhang ''et al.'', 2011]; permission granted<br />
File:Jung_Pathway.jpg|alt=Diagram of pathway from Jung ''et al.'', 2012 |[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012]; permission pending<br />
</gallery><br />
<br />
Additional figures:<br />
*[http://dev.biologists.org/content/136/20/3379/F3.expansion.html Figure 3 from Liu ''et al.'', 2009]<br />
*[http://www.els.net/WileyCDA/ElsArticle/refId-a0002053.html Figure 1 from Schneitz and Balasubramanian, 2009]<br />
*[http://www.sciencedirect.com/science/article/pii/S0168952510001873 Figure 1 from Wellmer and Riechmann, 2010]<br />
*[http://www.sciencedirect.com/science/article/pii/S1369526611001440 Figure 1 from Posé ''et al.'', 2012]<br />
<br />
<br />
==Methods==<br />
====Finding Genes====<br />
*I examined a variety of journal articles related to time of flowering in <i>Arabidopsis thaliana</i> and found a number of pathways related to flowering (see the gallery above). I came across a genomic analysis of soybean by [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012]. In this paper, they listed the "183 <i>Arabidopsis</i> genes that are known to take part in flowering regulatory pathways [taken] from previous studies." These 183 genes, plus "24 additional <i>Arabidopsis</i> 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 [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012] can be viewed here: [[File:Jung 207 Arabidopsis Flowering Genes.pdf]].<br />
*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.<br />
*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 [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2010.04148.x/pdf/ Amasino, 2010], [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012], [http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002512 Kim ''et al.'', 2012], and [http://www.plantcell.org/content/early/2012/08/29/tpc.112.101014.full.pdf+html Yu ''et al.'', 2012].<br />
*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." ([http://www.sciencedirect.com/science/article/pii/S0092867410004411 Fornara ''et al.'', 2010])<br />
<br />
====Finding SSRs====<br />
*A local database of the blueberry genome was created using the following coding:<br />
<PRE>./bin/makeblastdb -in BlueberryGenome.txt -input_type fasta -dbtype nucl -title blueberry_Genome</PRE><br />
*Amino acid sequences for all <i>Arabidopsis</i> genes were taken from [http://www.arabidopsis.org/index.jsp 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:<br />
<PRE>{ echo bin/tblastn -query AASequence.txt -db BlueberryGenome.txt; bin/tblastn -query <br />
AASequence.txt -db BlueberryGenome.txt; } >> AAOutput.txt</PRE><br />
*For each gene result, the best match was presumed to be the ortholog of the <i>Arabidopsis</i> gene in <i>Vaccinium corymbosum</i>. 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 <i>Vitis vinifera</i> ortholog of the <i>Arabidopsis</i> gene from [http://www.uniprot.org/uniprot/?query=organism%3A%22Vitis+vinifera+%5B29760%5D%22&sort=score UniProtKB (UniProt Consortium, 2012)] nomenclature search.<br />
*SSRs were determined by importing the best match scaffold into the [http://www.vaccinium.org/cgi-bin/vaccinium_ssr SSR Tool] at the [http://www.vaccinium.org/ Genome Database for Vaccinium]. Three di/trinucleotide SSRs near the gene location on the scaffold were chosen for each gene.<br />
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<br />
==SSR Results==<br />
All SSR results can be viewed on the [[Time of bloom SSR Results]] page. An abbreviated listing of the results is included below.<br />
<br/>[[File:Flowering_SSR_Results_Table.png]]<br />
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==Flowering Genes Of Interest==<br />
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." ([http://www.sciencedirect.com/science/article/pii/S0092867410004411 Fornara ''et al.'', 2010])<br />
<br />
{| class="wikitable sortable"<br />
|-<br />
! <i>Arabidopsis</i> Locus !! Other Names !! AA Source !! Pathway !! width="150px" |Top Hit ''Vaccinium'' Scaffold !! E Value<br />
|-<br />
| AT1G01060||LATE ELONGATED HYPOCOTYL, LATE ELONGATED HYPOCOTYL 1, LHY, LHY1||[http://arabidopsis.org/servlets/TairObject?id=137165&type=locus TAIR]||Light Signaling||Scaffold00140 (length 354209) at 234299||2e-19<br />
|-<br />
| AT1G02580||EMB173, EMBRYO DEFECTIVE 173, FERTILIZATION INDEPENDENT SEED 1, FIS1, MEA, MEDEA, SDG5, SET DOMAIN-CONTAINING PROTEIN 5||[http://arabidopsis.org/servlets/TairObject?id=136450&type=locus TAIR]||Polycomb||Scaffold00354 (length 215005) at 64805||4e-17<br />
|-<br />
| AT1G04400||AT-PHH1, ATCRY2, CRY2, CRYPTOCHROME 2, FHA, PHH1||[http://arabidopsis.org/servlets/TairObject?id=28374&type=locus TAIR]||Light Signaling||Scaffold00649 (length 159319) at 28296||1e-119<br />
|-<br />
| AT1G09570||ELONGATED HYPOCOTYL 8, FAR RED ELONGATED 1, FAR RED ELONGATED HYPOCOTYL 2, FHY2, FRE1, HY8, PHYA, PHYTOCHROME A||[http://arabidopsis.org/servlets/TairObject?id=27545&type=locus TAIR]||Light Signaling||Scaffold03861 (length 7403) at 3771||0.0<br />
|-<br />
| AT1G13260||EDF4, ETHYLENE RESPONSE DNA BINDING FACTOR 4, RAV1, RELATED TO ABI3/VP1 1||[http://arabidopsis.org/servlets/TairObject?id=137721&type=locus TAIR]||Light Signaling||Scaffold00930 (length 110378) at 63069||1e-103<br />
|-<br />
| AT1G14920||GAI, GIBBERELLIC ACID INSENSITIVE, RESTORATION ON GROWTH ON AMMONIA 2, RGA2||[http://arabidopsis.org/servlets/TairObject?id=26612&type=locus TAIR]||Gibberellin||Scaffold01360 (length 81306) at 51382||0.0<br />
|-<br />
| AT1G20330||COTYLEDON VASCULAR PATTERN 1, CVP1, FRILL1, FRL1, SMT2, STEROL METHYLTRANSFERASE 2||[http://arabidopsis.org/servlets/TairObject?id=27665&type=locus TAIR]||Vernalization||Scaffold02142 (length 46662) at 24743||9e-06<br />
|-<br />
| AT1G22770||FB, GI, GIGANTEA||[http://arabidopsis.org/servlets/TairObject?id=136959&type=locus TAIR]||Light Signaling||Scaffold00100 (length 346620) at 198329||0.0<br />
|-<br />
| AT1G25560||EDF1, ETHYLENE RESPONSE DNA BINDING FACTOR 1, TEM1, TEMPRANILLO 1||[http://arabidopsis.org/servlets/TairObject?id=30061&type=locus TAIR]||Light Signaling||Scaffold00930 (length 110378) at 63096||3e-99<br />
|-<br />
| AT1G26790||||[http://arabidopsis.org/servlets/TairObject?id=137136&type=locus TAIR]||Light Signaling||Scaffold00079 (length 471015) at 69048||6e-33<br />
|-<br />
| AT1G27370||SPL10, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 10||[http://arabidopsis.org/servlets/TairObject?id=28131&type=locus TAIR]||Age||Scaffold00127 (length 336847) at 165806||5e-33<br />
|-<br />
| AT1G29160||||[http://arabidopsis.org/servlets/TairObject?id=29883&type=locus TAIR]||Light Signaling||Scaffold00270 (length 246371) at 215229||4e-50<br />
|-<br />
| AT1G30970||SUF4, SUPPRESSOR OF FRIGIDA4||[http://arabidopsis.org/servlets/TairObject?id=28096&type=locus TAIR]||Vernalization||Scaffold00348 (length 210978) at 75279||1e-15<br />
|-<br />
| AT1G31814||FRIGIDA LIKE 2, FRL2||[http://arabidopsis.org/servlets/TairObject?id=226970&type=locus TAIR]||Vernalization||Scaffold00289 (length 259591) at 150896||2e-19<br />
|-<br />
| AT1G47250||20S PROTEASOME ALPHA SUBUNIT F2, PAF2||[http://arabidopsis.org/servlets/TairObject?id=30983&type=locus TAIR]||Vernalization||Scaffold00528 (length 197283) at 110933||3e-64<br />
|-<br />
| AT1G53090||SPA1-RELATED 4, SPA4||[http://arabidopsis.org/servlets/TairObject?id=31031&type=locus TAIR]||Light Signaling||Scaffold00734 (length 158513) at 143450||3e-129<br />
|-<br />
| AT1G53160||FLORAL TRANSITION AT THE MERISTEM6, FTM6, SPL4, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 4||[http://arabidopsis.org/servlets/TairObject?id=27097&type=locus TAIR]||Age||Scaffold00062 (length 451336) at 412489||1e-15<br />
|-<br />
| AT1G65480||FLOWERING LOCUS T, FT||[http://arabidopsis.org/servlets/TairObject?id=30541&type=locus TAIR]||Ambient Temperature||Scaffold00357 (length 260075) at 58774||6e-35<br />
|-<br />
| AT1G66350||RGA-LIKE 1, RGL, RGL1||[http://arabidopsis.org/servlets/TairObject?id=137244&type=locus TAIR]||Gibberellin||Scaffold00134 (length 346346) at 174707||0.0<br />
|-<br />
| AT1G68050||"FLAVIN-BINDING, KELCH REPEAT, F BOX 1", ADO3, FKF1||[http://arabidopsis.org/servlets/TairObject?id=137051&type=locus TAIR]||Light Signaling||Scaffold00110 (length 358202) at 120279||0.0<br />
|-<br />
| AT1G68840||ATRAV2, EDF2, ETHYLENE RESPONSE DNA BINDING FACTOR 2, RAP2.8, RAV2, RELATED TO ABI3/VP1 2, RELATED TO AP2 8, TEM2, TEMPRANILLO 2||[http://arabidopsis.org/servlets/TairObject?id=27570&type=locus TAIR]||Light Signaling||Scaffold00930 (length 110378) at 63096||5e-102<br />
|-<br />
| AT1G77080||AGAMOUS-LIKE 27, AGL27, FLM, FLOWERING LOCUS M, MADS AFFECTING FLOWERING 1, MAF1||[http://arabidopsis.org/servlets/TairObject?id=29106&type=locus TAIR]||Ambient Temperature, Vernalization||Scaffold10765 (length 2447) at 744||3e-13<br />
|-<br />
| AT1G77300||ASH1 HOMOLOG 2, ASHH2, CAROTENOID CHLOROPLAST REGULATORY1, CCR1, EARLY FLOWERING IN SHORT DAYS, EFS, LAZ2, LAZARUS 2, SDG8, SET DOMAIN GROUP 8||[http://arabidopsis.org/servlets/TairObject?id=136429&type=locus TAIR]||Vernalization||Scaffold00894 (length 114877) at 89213||1e-27<br />
|-<br />
| AT2G01570||REPRESSOR OF GA, REPRESSOR OF GA1-3 1, RGA, RGA1||[http://arabidopsis.org/servlets/TairObject?id=26549&type=locus TAIR]||Gibberellin||Scaffold01360 (length 81306) at 51382||0.0<br />
|-<br />
| AT2G06255||ELF4-L3, ELF4-LIKE 3||[http://arabidopsis.org/servlets/TairObject?id=500231553&type=locus TAIR]||Light Signaling||Scaffold00336 (length 230445) at 188137||1e-39<br />
|-<br />
| AT2G17770||ATBZIP27, BASIC REGION/LEUCINE ZIPPER MOTIF 27, BZIP27, FD PARALOG, FDP||[http://arabidopsis.org/servlets/TairObject?id=227228&type=locus TAIR]||Ambient Temperature||Scaffold00367 (length 240396) at 113139||7e-17<br />
|-<br />
| AT2G18790||HY3, OOP1, OUT OF PHASE 1, PHYB, PHYTOCHROME B||[http://arabidopsis.org/servlets/TairObject?id=26548&type=locus TAIR]||Light Signaling||Scaffold00751 (length 152548) at 83698||0.0<br />
|-<br />
| AT2G18870||VEL3, VERNALIZATION5/VIN3-LIKE 3, VIL4, VIN3-LIKE 4||[http://arabidopsis.org/servlets/TairObject?id=32249&type=locus TAIR]||Autonomous||Scaffold00396 (length 187979) at 73810||7e-19<br />
|-<br />
| AT2G18880||VEL2, VERNALIZATION5/VIN3-LIKE 2, VIL3, VIN3-LIKE 3||[http://arabidopsis.org/servlets/TairObject?id=32230&type=locus TAIR]||Autonomous||Scaffold00026 (length 499904) at 369396||6e-41<br />
|-<br />
| AT2G18915||ADAGIO 2, ADO2, LKP2, LOV KELCH PROTEIN 2||[http://arabidopsis.org/servlets/TairObject?id=500231567&type=locus TAIR]||Light Signaling||Scaffold00026 (length 499904) at 445582||0.0<br />
|-<br />
| AT2G19520||ACG1, ATMSI4, FVE, MSI4, MULTICOPY SUPPRESSOR OF IRA1 4, NFC04, NFC4||[http://arabidopsis.org/servlets/TairObject?id=33019&type=locus TAIR]||Ambient Temperature, Autonomous||Scaffold00728 (length 157708) at 8716||6e-21<br />
|-<br />
| AT2G22540||AGAMOUS-LIKE 22, AGL22, SHORT VEGETATIVE PHASE, SVP||[http://arabidopsis.org/servlets/TairObject?id=31694&type=locus TAIR]||Ambient Temperature, Vernalization||Scaffold01187 (length 101153) at 47701||2e-24<br />
|-<br />
| AT2G23380||CLF, CURLY LEAF, ICU1, INCURVATA 1, SDG1, SET1, SETDOMAIN 1, SETDOMAIN GROUP 1||[http://arabidopsis.org/servlets/TairObject?id=26534&type=locus TAIR]||Autonomous, Polycomb, Vernalization||Scaffold00354 (length 215005) at 64799||5e-41<br />
|-<br />
| AT2G25930||EARLY FLOWERING 3, ELF3, PYK20||[http://arabidopsis.org/servlets/TairObject?id=32082&type=locus TAIR]||Light Signaling||Scaffold00371 (length 223748) at 73111||6e-19<br />
|-<br />
| AT2G32950||ARABIDOPSIS THALIANA CONSTITUTIVE PHOTOMORPHOGENIC 1, ATCOP1, CONSTITUTIVE PHOTOMORPHOGENIC 1, COP1, DEETIOLATED MUTANT 340, DET340, EMB168, EMBRYO DEFECTIVE 168, FUS1, FUSCA 1||[http://arabidopsis.org/servlets/TairObject?id=34462&type=locus TAIR]||Light Signaling||Scaffold00734 (length 158513) at 142779||5e-62<br />
|-<br />
| AT2G33810||SPL3, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 3||[http://arabidopsis.org/servlets/TairObject?id=34194&type=locus TAIR]||Age||Scaffold00062 (length 451336) at 412489||2e-17<br />
|-<br />
| AT2G33835||FES1, FRIGIDA-ESSENTIAL 1||[http://arabidopsis.org/servlets/TairObject?id=500230872&type=locus TAIR]||Vernalization||Scaffold00102 (length 383343) at 88264||7e-17<br />
|-<br />
| AT2G34140||||[http://arabidopsis.org/servlets/TairObject?id=33865&type=locus TAIR]||Light Signaling||Scaffold00270 (length 246371) at 215217||7e-49<br />
|-<br />
| AT2G35670||FERTILIZATION INDEPENDENT SEED 2, FERTILIZATION-INDEPENDENT ENDOSPERM 2, FIE2, FIS2||[http://arabidopsis.org/servlets/TairObject?id=26543&type=locus TAIR]||Polycomb||Scaffold00857 (length 126644) at 55565||3e-04<br />
|-<br />
| AT2G40080||EARLY FLOWERING 4, ELF4||[http://arabidopsis.org/servlets/TairObject?id=34766&type=locus TAIR]||Light Signaling||Scaffold00254 (length 265810) at 228805||4e-24<br />
|-<br />
| AT2G42200||ATSPL9, SPL9, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 9||[http://arabidopsis.org/servlets/TairObject?id=34557&type=locus TAIR]||Age||Scaffold00691 (length 141413) at 61795||5e-21<br />
|-<br />
| AT2G43410||FPA||[http://arabidopsis.org/servlets/TairObject?id=34279&type=locus TAIR]||Autonomous||Scaffold01689 (length 75472) at 47663||4e-45<br />
|-<br />
| AT2G46340||SPA1, SUPPRESSOR OF PHYA-105 1||[http://arabidopsis.org/servlets/TairObject?id=31336&type=locus TAIR]||Light Signaling||Scaffold00734 (length 158513) at 142779||3e-69<br />
|-<br />
| AT2G46790||APRR9, ARABIDOPSIS PSEUDO-RESPONSE REGULATOR 9, PRR9, PSEUDO-RESPONSE REGULATOR 9, TL1, TOC1-LIKE PROTEIN 1||[http://arabidopsis.org/servlets/TairObject?id=32227&type=locus TAIR]||Light Signaling||Scaffold00001 (length 1030549) at 322801||1e-36<br />
|-<br />
| AT2G46830||ATCCA1, CCA1, CIRCADIAN CLOCK ASSOCIATED 1||[http://arabidopsis.org/servlets/TairObject?id=32221&type=locus TAIR]||Light Signaling||Scaffold00140 (length 354209) at 234299||7e-20<br />
|-<br />
| AT2G47700||RED AND FAR-RED INSENSITIVE 2, RFI2||[http://arabidopsis.org/servlets/TairObject?id=32070&type=locus TAIR]||Light Signaling||Scaffold01059 (length 101143) at 96557||1e-19<br />
|-<br />
| AT3G02380||ATCOL2, B-BOX DOMAIN PROTEIN 3, BBX3, COL2, CONSTANS-LIKE 2||[http://arabidopsis.org/servlets/TairObject?id=35635&type=locus TAIR]||Light Signaling||Scaffold01843 (length 51900) at 40767||3e-48<br />
|-<br />
| AT3G03450||RGA-LIKE 2, RGL2||[http://arabidopsis.org/servlets/TairObject?id=40021&type=locus TAIR]||Gibberellin||Scaffold00134 (length 346346) at 174722||0.0<br />
|-<br />
| AT3G04610||FLK, FLOWERING LOCUS KH DOMAIN||[http://arabidopsis.org/servlets/TairObject?id=37455&type=locus TAIR]||Autonomous||Scaffold01384 (length 81068) at 28309||4e-29<br />
|-<br />
| AT3G05120||ATGID1A, GA INSENSITIVE DWARF1A, GID1A||[http://arabidopsis.org/servlets/TairObject?id=39457&type=locus TAIR]||Gibberellin||Scaffold00101 (length 425332) at 398762||4e-175<br />
|-<br />
| AT3G07650||B-BOX DOMAIN PROTEIN 7, BBX7, COL9, CONSTANS-LIKE 9||[http://arabidopsis.org/servlets/TairObject?id=38550&type=locus TAIR]||Light Signaling||Scaffold00832 (length 123094) at 89599||1e-55<br />
|-<br />
| AT3G10390||FLD, FLOWERING LOCUS D||[http://arabidopsis.org/servlets/TairObject?id=35869&type=locus TAIR]||Ambient Temperature, Autonomous||Scaffold00232 (length 253418) at 139565||0.0<br />
|-<br />
| AT3G12810||CHR13, PHOTOPERIOD-INDEPENDENT EARLY FLOWERING 1, PIE1, SRCAP||[http://arabidopsis.org/servlets/TairObject?id=37964&type=locus TAIR]||Vernalization||Scaffold00147 (length 345970) at 30164||0.0<br />
|-<br />
| AT3G15270||SPL5, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 5||[http://arabidopsis.org/servlets/TairObject?id=37842&type=locus TAIR]||Age||Scaffold00105 (length 392037) at 147284||5e-16<br />
|-<br />
| AT3G15354||SPA1-RELATED 3, SPA3||[http://arabidopsis.org/servlets/TairObject?id=500230681&type=locus TAIR]||Light Signaling||Scaffold00734 (length 158513) at 143450||1e-144<br />
|-<br />
| AT3G18990||REDUCED VERNALIZATION RESPONSE 1, REM39, REPRODUCTIVE MERISTEM 39, VRN1||[http://arabidopsis.org/servlets/TairObject?id=37620&type=locus TAIR]||Vernalization||Scaffold00811 (length 108354) at 96661||2e-25<br />
|-<br />
| AT3G20740||FERTILIZATION-INDEPENDENT ENDOSPERM, FERTILIZATION-INDEPENDENT ENDOSPERM 1, FIE, FIE1, FIS3||[http://arabidopsis.org/servlets/TairObject?id=38691&type=locus TAIR]||Autonomous, Polycomb, Vernalization||Scaffold01670 (length 60304) at 9836||5e-20<br />
|-<br />
| AT3G21320||||[http://arabidopsis.org/servlets/TairObject?id=39170&type=locus TAIR]||Light Signaling||Scaffold00509 (length 192554) at 181887||1e-21<br />
|-<br />
| AT3G24440||VERNALIZATION 5, VIL1, VIN3-LIKE 1, VRN5||[http://arabidopsis.org/servlets/TairObject?id=39196&type=locus TAIR]||Autonomous, Vernalization||Scaffold00396 (length 187979) at 73795||2e-69<br />
|-<br />
| AT3G25730||EDF3, ETHYLENE RESPONSE DNA BINDING FACTOR 3||[http://arabidopsis.org/servlets/TairObject?id=37641&type=locus TAIR]||Light Signaling||Scaffold00930 (length 110378) at 63060||5e-100<br />
|-<br />
| AT3G33520||ACTIN-RELATED PROTEIN 6, ARP6, ATARP6, EARLY IN SHORT DAYS 1, ESD1, SUF3, SUPPRESSOR OF FRI 3||[http://arabidopsis.org/servlets/TairObject?id=40458&type=locus TAIR]||Ambient Temperature, Vernalization||Scaffold00246 (length 286612) at 268521||1e-53<br />
|-<br />
| AT3G46640||LUX, LUX ARRHYTHMO, PCL1, PHYTOCLOCK 1||[http://arabidopsis.org/servlets/TairObject?id=35747&type=locus TAIR]||Light Signaling||Scaffold01150 (length 88293) at 80272||3e-34<br />
|-<br />
| AT3G47500||CDF3, CYCLING DOF FACTOR 3||[http://arabidopsis.org/servlets/TairObject?id=36439&type=locus TAIR]||Light Signaling||Scaffold00079 (length 471015) at 68175||1e-85<br />
|-<br />
| AT4G00650||FLA, FLOWERING LOCUS A, FRI, FRIGIDA||[http://arabidopsis.org/servlets/TairObject?id=128299&type=locus TAIR]||Vernalization||Scaffold00039 (length 505275) at 216632||4e-50<br />
|-<br />
| AT4G02020||EZA1, SDG10, SET DOMAIN-CONTAINING PROTEIN 10, SWINGER, SWN||[http://arabidopsis.org/servlets/TairObject?id=129104&type=locus TAIR]||Autonomous, Polycomb, Vernalization||Scaffold00354 (length 215005) at 64799||2e-48<br />
|-<br />
| AT4G02560||LD, LUMINIDEPENDENS||[http://arabidopsis.org/servlets/TairObject?id=26564&type=locus TAIR]||Autonomous||Scaffold00002 (length 840149) at 158601||4e-28<br />
|-<br />
| AT4G08920||ATCRY1, BLU1, BLUE LIGHT UNINHIBITED 1, CRY1, CRYPTOCHROME 1, ELONGATED HYPOCOTYL 4, HY4, OOP2, OUT OF PHASE 2||[http://arabidopsis.org/servlets/TairObject?id=129943&type=locus TAIR]||Light Signaling||Scaffold00331 (length 261439) at 124817||4e-128<br />
|-<br />
| AT4G11110||SPA1-RELATED 2, SPA2||[http://arabidopsis.org/servlets/TairObject?id=129633&type=locus TAIR]||Light Signaling||Scaffold01034 (length 107107) at 19205||2e-62<br />
|-<br />
| AT4G11880||AGAMOUS-LIKE 14, AGL14||[http://arabidopsis.org/servlets/TairObject?id=129748&type=locus TAIR]||Vernalization||Scaffold00249 (length 258199) at 131012||2e-29<br />
|-<br />
| AT4G16250||PHYD, PHYTOCHROME D||[http://arabidopsis.org/servlets/TairObject?id=26567&type=locus TAIR]||Light Signaling||Scaffold00751 (length 152548) at 83707||0.0<br />
|-<br />
| AT4G16280||FCA||[http://arabidopsis.org/servlets/TairObject?id=128853&type=locus TAIR]||Ambient Temperature, Autonomous||Scaffold00104 (length 360147) at 120318||5e-13<br />
|-<br />
| AT4G16845||REDUCED VERNALIZATION RESPONSE 2, VRN2||[http://arabidopsis.org/servlets/TairObject?id=228106&type=locus TAIR]||Autonomous, Polycomb, Vernalization||Scaffold00857 (length 126644) at 55203||3e-07<br />
|-<br />
| AT4G18130||PHYE, PHYTOCHROME E||[http://arabidopsis.org/servlets/TairObject?id=26568&type=locus TAIR]||Light Signaling||Scaffold00751 (length 152548) at 83749||0.0<br />
|-<br />
| AT4G20370||TSF, TWIN SISTER OF FT||[http://arabidopsis.org/servlets/TairObject?id=26553&type=locus TAIR]||Ambient Temperature||Scaffold00357 (length 260075) at 58807||1e-33<br />
|-<br />
| AT4G22950||AGAMOUS-LIKE 19, AGL19, GL19||[http://arabidopsis.org/servlets/TairObject?id=128336&type=locus TAIR]||Vernalization||Scaffold00249 (length 258199) at 131012||4e-28<br />
|-<br />
| AT4G24540||AGAMOUS-LIKE 24, AGL24||[http://arabidopsis.org/servlets/TairObject?id=127586&type=locus TAIR]||Vernalization||Scaffold01187 (length 101153) at 47701||2e-25<br />
|-<br />
| AT4G26000||PEP, PEPPER||[http://arabidopsis.org/servlets/TairObject?id=127403&type=locus TAIR]||Vernalization||Scaffold00021 (length 527983) at 157278||3e-29<br />
|-<br />
| AT4G30200||VEL1, VERNALIZATION5/VIN3-LIKE 1, VIL2, VIN3-LIKE 2||[http://arabidopsis.org/servlets/TairObject?id=128580&type=locus TAIR]||Autonomous, Vernalization||Scaffold00026 (length 499904) at 369417||7e-64<br />
|-<br />
| AT4G34530||CIB1, CRYPTOCHROME-INTERACTING BASIC-HELIX-LOOP-HELIX 1||[http://arabidopsis.org/servlets/TairObject?id=130033&type=locus TAIR]||Light Signaling||Scaffold01322 (length 99420) at 82955||2e-29<br />
|-<br />
| AT4G35900||ATBZIP14, FD, FD-1||[http://arabidopsis.org/servlets/TairObject?id=128068&type=locus TAIR]||Ambient Temperature||Scaffold00367 (length 240396) at 113139||1e-16<br />
|-<br />
| AT5G02810||APRR7, PRR7, PSEUDO-RESPONSE REGULATOR 7||[http://arabidopsis.org/servlets/TairObject?id=131538&type=locus TAIR]||Light Signaling||Scaffold00125 (length 356885) at 276518||1e-33<br />
|-<br />
| AT5G03840||TERMINAL FLOWER 1, TFL1||[http://arabidopsis.org/servlets/TairObject?id=131459&type=locus TAIR]||Ambient Temperature||Scaffold00181 (length 337602) at 12825||1e-28<br />
|-<br />
| AT5G08330||CCA1 HIKING EXPEDITION, CHE, TRANSCRIPTION FACTOR TCP21, TCP21||[http://www.uniprot.org/uniprot/Q9FTA2 UniProtKB]||Light Signaling||Scaffold00993 (length 109486) at 294||5e-27<br />
|-<br />
| AT5G10140||AGAMOUS-LIKE 25, AGL25, FLC, FLF, FLOWERING LOCUS C, FLOWERING LOCUS F||[http://arabidopsis.org/servlets/TairObject?id=136002&type=locus TAIR]||Ambient Temperature, Vernalization||Scaffold10765 (length 2447) at 708||8e-22<br />
|-<br />
| AT5G11530||EMBRYONIC FLOWER 1, EMF1||[http://arabidopsis.org/servlets/TairObject?id=130620&type=locus TAIR]||Polycomb||Scaffold00253 (length 240879) at 11069||1e-06<br />
|-<br />
| AT5G13480||FY||[http://arabidopsis.org/servlets/TairObject?id=136108&type=locus TAIR]||Autonomous||Scaffold00166 (length 328538) at 74796||2e-43<br />
|-<br />
| AT5G15840||B-BOX DOMAIN PROTEIN 1, BBX1, CO, CONSTANS, FG||[http://arabidopsis.org/servlets/TairObject?id=130492&type=locus TAIR]||Light Signaling||Scaffold01843 (length 51900) at 40767||3e-29<br />
|-<br />
| AT5G15850||ATCOL1, B-BOX DOMAIN PROTEIN 2, BBX2, COL1, CONSTANS-LIKE 1||[http://arabidopsis.org/servlets/TairObject?id=130495&type=locus TAIR]||Light Signaling||Scaffold01843 (length 51900) at 40767||5e-44<br />
|-<br />
| AT5G17690||ATLHP1, LHP1, LIKE HETEROCHROMATIN PROTEIN 1, TERMINAL FLOWER 2, TFL2||[http://arabidopsis.org/servlets/TairObject?id=134923&type=locus TAIR]||Polycomb||Scaffold00696 (length 140617) at 128983||7e-13<br />
|-<br />
| AT5G23150||ENHANCER OF AG-4 2, HUA2||[http://arabidopsis.org/servlets/TairObject?id=135220&type=locus TAIR]||Vernalization||Scaffold00686 (length 145647) at 102689||5e-42<br />
|-<br />
| AT5G24470||APRR5, PRR5, PSEUDO-RESPONSE REGULATOR 5||[http://arabidopsis.org/servlets/TairObject?id=135985&type=locus TAIR]||Light Signaling||Scaffold00001 (length 1030549) at 322798||3e-40<br />
|-<br />
| AT5G24930||ATCOL4, B-BOX DOMAIN PROTEIN 5, BBX5, COL4, CONSTANS-LIKE 4||[http://arabidopsis.org/servlets/TairObject?id=131285&type=locus TAIR]||Light Signaling||Scaffold11225 (length 3326) at 2816||8e-23<br />
|-<br />
| AT5G35840||PHYC, PHYTOCHROME C||[http://arabidopsis.org/servlets/TairObject?id=133466&type=locus TAIR]||Light Signaling||Scaffold01070 (length 102706) at 75395||0.0<br />
|-<br />
| AT5G37055||ATSWC6, SEF, SERRATED LEAVES AND EARLY FLOWERING||[http://arabidopsis.org/servlets/TairObject?id=500231974&type=locus TAIR]||Vernalization||Scaffold00925 (length 141061) at 38143||4e-29<br />
|-<br />
| AT5G39660||CDF2, CYCLING DOF FACTOR 2||[http://arabidopsis.org/servlets/TairObject?id=133414&type=locus TAIR]||Light Signaling||Scaffold00651 (length 145047) at 19066||1e-90<br />
|-<br />
| AT5G42790||ARS5, ARSENIC TOLERANCE 5, ATPSM30, PAF1, PROTEASOME ALPHA SUBUNIT F1||[http://arabidopsis.org/servlets/TairObject?id=133505&type=locus TAIR]||Vernalization||Scaffold00528 (length 197283) at 110933||5e-64<br />
|-<br />
| AT5G51230||ATEMF2, CYR1, CYTOKININ RESISTANT 1, EMBRYONIC FLOWER 2, EMF2, VEF2||[http://arabidopsis.org/servlets/TairObject?id=134952&type=locus TAIR]||Polycomb||Scaffold00857 (length 126644) at 44887||9e-19<br />
|-<br />
| AT5G57360||ADAGIO 1, ADO1, FKF1-LIKE PROTEIN 2, FKL2, LKP1, LOV KELCH PROTEIN 1, ZEITLUPE, ZTL||[http://arabidopsis.org/servlets/TairObject?id=134481&type=locus TAIR]||Light Signaling||Scaffold00026 (length 499904) at 445597||0.0<br />
|-<br />
| AT5G57380||VERNALIZATION INSENSITIVE 3, VIN3||[http://arabidopsis.org/servlets/TairObject?id=134483&type=locus TAIR]||Autonomous, Vernalization||Scaffold00026 (length 499904) at 369405||3e-48<br />
|-<br />
| AT5G57660||ATCOL5, B-BOX DOMAIN PROTEIN 6, BBX6, COL5, CONSTANS-LIKE 5||[http://arabidopsis.org/servlets/TairObject?id=134422&type=locus TAIR]||Light Signaling||Scaffold11225 (length 3326) at 2816||1e-25<br />
|-<br />
| AT5G58230||ARABIDOPSIS MULTICOPY SUPRESSOR OF IRA1, ATMSI1, MATERNAL EFFECT EMBRYO ARREST 70, MEE70, MSI1, MULTICOPY SUPRESSOR OF IRA1||[http://arabidopsis.org/servlets/TairObject?id=132921&type=locus TAIR]||Autonomous, Polycomb, Vernalization||Scaffold00615 (length 179658) at 161081||2e-61<br />
|-<br />
| AT5G60100||APRR3, PRR3, PSEUDO-RESPONSE REGULATOR 3||[http://arabidopsis.org/servlets/TairObject?id=133317&type=locus TAIR]||Light Signaling||Scaffold02075 (length 43325) at 14139||3e-25<br />
|-<br />
| AT5G61380||APRR1, ATTOC1, PRR1, PSEUDO-RESPONSE REGULATOR 1, TIMING OF CAB EXPRESSION 1, TOC1||[http://arabidopsis.org/servlets/TairObject?id=133196&type=locus TAIR]||Light Signaling||Scaffold00753 (length 123742) at 70468||2e-47<br />
|-<br />
| AT5G62430||CDF1, CYCLING DOF FACTOR 1||[http://arabidopsis.org/servlets/TairObject?id=131911&type=locus TAIR]||Light Signaling||Scaffold01102 (length 99830) at 51435||1e-59<br />
|-<br />
| AT5G65050||AGAMOUS-LIKE 31, AGL31, MADS AFFECTING FLOWERING 2, MAF2||[http://arabidopsis.org/servlets/TairObject?id=135154&type=locus TAIR]||Ambient Temperature, Vernalization||Scaffold10765 (length 2447) at 723||4e-20<br />
|-<br />
| AT5G65060||AGAMOUS-LIKE 70, AGL70, FCL3, MADS AFFECTING FLOWERING 3, MAF3||[http://arabidopsis.org/servlets/TairObject?id=130633&type=locus TAIR]||Ambient Temperature, Vernalization||Scaffold10765 (length 2447) at 639||7e-15<br />
|-<br />
| AT5G65070||AGAMOUS-LIKE 69, AGL69, FCL4, MADS AFFECTING FLOWERING 4, MAF4||[http://arabidopsis.org/servlets/TairObject?id=130634&type=locus TAIR]||Ambient Temperature, Vernalization||Scaffold10765 (length 2447) at 723||6e-20<br />
|-<br />
| AT5G65080||AGAMOUS-LIKE 68, AGL68, MADS AFFECTING FLOWERING 5, MAF5||[http://arabidopsis.org/servlets/TairObject?id=130635&type=locus TAIR]||Ambient Temperature, Vernalization||Scaffold10765 (length 2447) at 699||1e-18<br />
|}<br />
<br />
<br />
==References==<br />
*Amasino RM. Seasonal and developmental timing of flowering. ''Plant J,'' '''61,''' 1001-1013 (2010).<br />
*Amasino RM. Vernalization and flowering time. ''Curr Opin Plant Biol,'' '''16,''' 154–158 (2005).<br />
*Ballerini ES, Kramer EM. Environmental and molecular analysis of the floral transition in the lower eudicot Aquilegia formosa. ''Evodevo,'' '''2,''' 1-20 (2011).<br />
*Bäurle I, Dean C. The timing of developmental transitions in plants. ''Cell,'' '''125,''' 655-664 (2006).<br />
*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).<br />
*Farrona S, Coupland G, Turck F. The impact of chromatin regulation on the floral transition. ''Semin Cell Dev Biol,'' '''19,''' 560-573 (2008).<br />
*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).<br />
*Fornara F, de Montaigu A, Coupland G. SnapShot: Control of flowering in Arabidopsis. ''Cell,'' '''141,''' 550-550.e2 (2010).<br />
*Henderson IR, Dean C. Control of Arabidopsis flowering: the chill before the bloom. ''Development,'' '''131,''' 3829-3838 (2004).<br />
*He Y, Amasino RM. Role of chromatin modification in flowering-time control. ''Trends Plant Sci,'' '''10,''' 30-35 (2005).<br />
*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).<br />
*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).<br />
*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).<br />
*Jung CH, Wong CE, Singh MB, Bhalla PL. Comparative genomic analysis of soybean flowering genes. ''PLoS One,'' '''7,''' e38250 (2012).<br />
*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).<br />
*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).<br />
*Liu C, Thong Z, Yu H. Coming into bloom: the specification of floral meristems. ''Development,'' '''136,''' 3379-3391 (2009).<br />
*Posé D, Yant L, Schmid M. The end of innocence: flowering networks explode in complexity. ''Curr Opin Plant Biol'' '''15,''' 45-50 (2012).<br />
*Schneitz K, Balasubramanian S. Floral Meristems. ''eLS'' (John Wiley & Sons Ltd, Chichester, 2009).<br />
*SSR Tool. ''Genome Database for Vaccinium.''<br />
*Sung ZR, Chen L, Moon YH, Lertpiriyapong K. Mechanisms of floral repression in Arabidopsis. ''Curr Opin Plant Biol,'' '''6,''' 29-35 (2003).<br />
*Taiz L, Zeiger E. ''Plant Physiology Fifth Edition Ch. 20'' (Sinauer Associates, Sunderland, MA, 2010).<br />
*Turck F, Adrian J. A lesson in complexity: regulation of FLOWERING LOCUS T. ''Max Planck Institute for Plant Breeding Research.''<br />
*UniProt Consortium. Reorganizing the protein space at the Universal Protein Resource (UniProt). ''Nucleic Acids Res,'' '''40,''' D71-D75 (2012).<br />
*Wellmer F, Riechmann JL. Gene networks controlling the initiation of flower development. ''Trends Genet,'' '''26,''' 519-527 (2010).<br />
*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).<br />
*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).<br />
*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).</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=Time_of_bloom&diff=19288Time of bloom2021-08-12T16:33:57Z<p>Laheyer: </p>
<hr />
<div>Austin Mudd - Spring 2013<br />
<br/>Shortened URL: http://goo.gl/zuTkP<br />
<br />
<br />
__TOC__<br />
<br />
==Introduction to Flowering==<br />
====The Process of Flowering====<br />
*Flowering is the "switch from vegetative growth (the production of stems and leaves) to reproductive growth (the production of flowers)" ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010065 Higgins ''et al.'', 2010])<br />
*The “shoot apical meristem starts to produce flowers instead of leaves” ([http://www.sciencedirect.com/science/article/pii/S0092867410004411 Fornara ''et al.'', 2010])<br />
*Occurs “when conditions for pollination and seed development are optimal and consequently most plants restrict flowering to a specific time of year” ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010065 Higgins ''et al.'', 2010])<br />
*”The genes and molecular mechanisms controlling flowering have been extensively studied in the model dicot <i>Arabidopsis thaliana</i>” ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010065 Higgins ''et al.'', 2010])<br />
*In <i>Arabidopsis thaliana</i>, “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” ([http://www.sciencedirect.com/science/article/pii/S0092867410004411 Fornara ''et al.'', 2010])<br />
<br />
[[File:Max_Planck_Institute_Pathway.png|thumb|right|The major pathways in the timing of flowering from Turck and Adrian at the [http://www.mpipz.mpg.de/305695/Project_1 Max Planck Institute for Plant Breeding Research]; permission granted]]<br />
====The Timing of Flowering====<br />
*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.” ([http://www.sciencedirect.com/science/article/pii/S0092867410004411 Fornara ''et al.'', 2010])<br />
*These “pathways converge to regulate a small number of ‘floral integrator genes,’ ... which govern flowering time by merging signals from multiple pathways” ([http://www.sciencedirect.com/science/article/pii/S0092867410004411 Fornara ''et al.'', 2010])<br />
<br />
====The Importance of Flowering====<br />
*”Flowering is one of the most important agronomic traits influencing crop yield” ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012])<br />
*”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” ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010065 Higgins ''et al.'', 2010])<br />
*“Adaptation to different environments and practices has been achieved by manipulation of flowering time responses” ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010065 Higgins ''et al.'', 2010])<br />
*The study of flowering is ”critical for the breeding of climate change resilient crop varieties” ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012])<br />
*Flowering is “an excellent system for comparison between and within domestic and wild species” ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010065 Higgins ''et al.'', 2010])<br />
<br />
<br />
==Pathways Controlling Flowering==<br />
====Age Pathway====<br />
*"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" ([http://www.plantcell.org/content/early/2012/08/29/tpc.112.101014.full.pdf+html Yu ''et al.'', 2012])<br />
*5 <i>Arabidopsis</i> genes are involved in the age pathway: SPL3, SPL4, SPL5, SPL9, SPL10 ([http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2010.04148.x/pdf/ Amasino, 2010])<br />
<br />
====Ambient Temperature Pathway====<br />
*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" ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012])<br />
*16 <i>Arabidopsis</i> genes are involved in the ambient temperature pathway: AGL31, ATARP6, ATBZIP27, FCA, FD, FLC, FLD, FT, FVE, MAF1, MAF3, MAF4, MAF5, SVP, TFL1, TSF ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012])<br />
<br />
====Autonomous Pathway====<br />
*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 ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012])<br />
*17 <i>Arabidopsis</i> genes are involved in the autonomous pathway: CLF, FCA, FIE1, FLD, FLK, FPA, FVE, FY, LD, MSI1, SWN, VEL1, VEL2, VEL3, VIN3, VRN2, VRN5 ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012]) <br />
<br />
====Gibberellin Pathway====<br />
*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" ([http://www.plantcell.org/content/early/2012/08/29/tpc.112.101014.full.pdf+html Yu ''et al.'', 2012])<br />
*5 <i>Arabidopsis</i> genes are involved in the gibberellin pathway: GAI, GID1, RGA, RGL1, RGL2 ([http://www.plantcell.org/content/early/2012/08/29/tpc.112.101014.full.pdf+html Yu ''et al.'', 2012])<br />
<br />
====Light Signaling Pathway====<br />
*"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" ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012])<br />
*48 <i>Arabidopsis</i> 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 ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012])<br />
<br />
====Polycomb Pathway====<br />
*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) ([http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002512 Kim ''et al.'', 2012])<br />
*10 <i>Arabidopsis</i> genes are involved in the polycomb pathway: CLF, EMF1, EMF2, FIE1, FIS2, LHP1, MEA, MSI1, SWN, VRN2 ([http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002512 Kim ''et al.'', 2012])<br />
<br />
====Vernalization Pathway====<br />
*The vernalization pathway is the response to "prolonged periods of low temperature [that are required] to initiate flowering" ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012])<br />
*32 <i>Arabidopsis</i> 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 ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012])<br />
<br />
<br />
==Gallery of <i>Arabidopsis</i> Flowering Pathways==<br />
<br />
<gallery widths="102px" heights="102px" perrow="6"><br />
File:Izawa_Pathway.jpeg|alt=Izawa alt Pathway from Izawa ''et al.'', 2003|[http://www.sciencedirect.com/science/article/pii/S1369526603000141 Izawa ''et al.'', 2003]; permission pending<br />
File:Sung_Pathway.gif|[http://www.sciencedirect.com/science/article/pii/S1369526602000146 Sung ''et al.'', 2003]; permission granted<br />
File:Boss_Pathway.gif|[http://www.plantcell.org/content/16/suppl_1/S18/F2.expansion Boss ''et al.'', 2004]; permission granted<br />
File:Boss_Pathway_2.jpeg|[http://www.plantcell.org/content/16/suppl_1/S18/F3.expansion Boss ''et al.'', 2004]; permission granted<br />
File:Henderson_and_Dean_Pathway.jpeg|[http://dev.biologists.org/content/131/16/3829/F1.expansion.html Henderson and Dean, 2004]; permission granted<br />
File:Amasino_Pathway.jpeg|[http://www.sciencedirect.com/science/article/pii/S0958166905000273 Amasino, 2005]; permission granted<br />
File:He_and_Amasino_Pathway.jpeg|[http://www.sciencedirect.com/science/article/pii/S1360138504002705 He and Amasino, 2005]; permission granted<br />
File:Yamaguchi_Pathway.jpeg|[http://pcp.oxfordjournals.org/content/46/8/1175/F7.expansion Yamaguchi ''et al.'', 2005]; permission pending<br />
File:Baurle_and_Dean_Pathway.jpeg|[http://www.sciencedirect.com/science/article/pii/S009286740600571X Bäurle and Dean, 2006]; permission granted<br />
File:Farrona_Pathway.jpeg|[http://www.sciencedirect.com/science/article/pii/S1084952108000566 Farrona ''et al.'', 2008]; permission granted<br />
File:Farrona_Pathway_2.jpeg|[http://www.sciencedirect.com/science/article/pii/S1084952108000566 Farrona ''et al.'', 2008]; permission granted<br />
File:Amasino_Pathway_2.png|[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2010.04148.x/pdf/ Amasino, 2010]; permission granted<br />
File:Higgins_Pathway.jpg|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010065 Higgins ''et al.'', 2010]; permission granted<br />
File:Kim_and_Sung_Pathway.jpeg|[http://www.pnas.org/content/107/39/17029/F6.expansion.html Kim and Sung, 2010]; permission pending<br />
File:Taiz_and_Zeiger_Pathway.jpeg|[http://5e.plantphys.net/article.php?ch=1&id=375 Taiz and Zeiger, 2010]; permission pending<br />
File:Ballerini_and_Kramer_Pathway.png|[http://dash.harvard.edu/bitstream/handle/1/4903810/Ballerini%20%26%20Kramer%202011.pdf?sequence=1 Ballerini and Kramer, 2011]; permission granted<br />
File:Ferrier_Pathway.jpeg|[http://www.sciencedirect.com/science/article/pii/S0958166910002284 Ferrier ''et al.'', 2011]; permission pending<br />
File:Zhang_Pathway.png|[http://www.biomedcentral.com/1471-2164/12/63 Zhang ''et al.'', 2011]; permission granted<br />
File:Jung_Pathway.jpg|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012]; permission pending<br />
</gallery><br />
<br />
Additional figures:<br />
*[http://dev.biologists.org/content/136/20/3379/F3.expansion.html Figure 3 from Liu ''et al.'', 2009]<br />
*[http://www.els.net/WileyCDA/ElsArticle/refId-a0002053.html Figure 1 from Schneitz and Balasubramanian, 2009]<br />
*[http://www.sciencedirect.com/science/article/pii/S0168952510001873 Figure 1 from Wellmer and Riechmann, 2010]<br />
*[http://www.sciencedirect.com/science/article/pii/S1369526611001440 Figure 1 from Posé ''et al.'', 2012]<br />
<br />
<br />
==Methods==<br />
====Finding Genes====<br />
*I examined a variety of journal articles related to time of flowering in <i>Arabidopsis thaliana</i> and found a number of pathways related to flowering (see the gallery above). I came across a genomic analysis of soybean by [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012]. In this paper, they listed the "183 <i>Arabidopsis</i> genes that are known to take part in flowering regulatory pathways [taken] from previous studies." These 183 genes, plus "24 additional <i>Arabidopsis</i> 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 [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012] can be viewed here: [[File:Jung 207 Arabidopsis Flowering Genes.pdf]].<br />
*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.<br />
*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 [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2010.04148.x/pdf/ Amasino, 2010], [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012], [http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002512 Kim ''et al.'', 2012], and [http://www.plantcell.org/content/early/2012/08/29/tpc.112.101014.full.pdf+html Yu ''et al.'', 2012].<br />
*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." ([http://www.sciencedirect.com/science/article/pii/S0092867410004411 Fornara ''et al.'', 2010])<br />
<br />
====Finding SSRs====<br />
*A local database of the blueberry genome was created using the following coding:<br />
<PRE>./bin/makeblastdb -in BlueberryGenome.txt -input_type fasta -dbtype nucl -title blueberry_Genome</PRE><br />
*Amino acid sequences for all <i>Arabidopsis</i> genes were taken from [http://www.arabidopsis.org/index.jsp 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:<br />
<PRE>{ echo bin/tblastn -query AASequence.txt -db BlueberryGenome.txt; bin/tblastn -query <br />
AASequence.txt -db BlueberryGenome.txt; } >> AAOutput.txt</PRE><br />
*For each gene result, the best match was presumed to be the ortholog of the <i>Arabidopsis</i> gene in <i>Vaccinium corymbosum</i>. 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 <i>Vitis vinifera</i> ortholog of the <i>Arabidopsis</i> gene from [http://www.uniprot.org/uniprot/?query=organism%3A%22Vitis+vinifera+%5B29760%5D%22&sort=score UniProtKB (UniProt Consortium, 2012)] nomenclature search.<br />
*SSRs were determined by importing the best match scaffold into the [http://www.vaccinium.org/cgi-bin/vaccinium_ssr SSR Tool] at the [http://www.vaccinium.org/ Genome Database for Vaccinium]. Three di/trinucleotide SSRs near the gene location on the scaffold were chosen for each gene.<br />
<br />
<br />
==SSR Results==<br />
All SSR results can be viewed on the [[Time of bloom SSR Results]] page. An abbreviated listing of the results is included below.<br />
<br/>[[File:Flowering_SSR_Results_Table.png]]<br />
<br />
<br />
==Flowering Genes Of Interest==<br />
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." ([http://www.sciencedirect.com/science/article/pii/S0092867410004411 Fornara ''et al.'', 2010])<br />
<br />
{| class="wikitable sortable"<br />
|-<br />
! <i>Arabidopsis</i> Locus !! Other Names !! AA Source !! Pathway !! width="150px" |Top Hit ''Vaccinium'' Scaffold !! E Value<br />
|-<br />
| AT1G01060||LATE ELONGATED HYPOCOTYL, LATE ELONGATED HYPOCOTYL 1, LHY, LHY1||[http://arabidopsis.org/servlets/TairObject?id=137165&type=locus TAIR]||Light Signaling||Scaffold00140 (length 354209) at 234299||2e-19<br />
|-<br />
| AT1G02580||EMB173, EMBRYO DEFECTIVE 173, FERTILIZATION INDEPENDENT SEED 1, FIS1, MEA, MEDEA, SDG5, SET DOMAIN-CONTAINING PROTEIN 5||[http://arabidopsis.org/servlets/TairObject?id=136450&type=locus TAIR]||Polycomb||Scaffold00354 (length 215005) at 64805||4e-17<br />
|-<br />
| AT1G04400||AT-PHH1, ATCRY2, CRY2, CRYPTOCHROME 2, FHA, PHH1||[http://arabidopsis.org/servlets/TairObject?id=28374&type=locus TAIR]||Light Signaling||Scaffold00649 (length 159319) at 28296||1e-119<br />
|-<br />
| AT1G09570||ELONGATED HYPOCOTYL 8, FAR RED ELONGATED 1, FAR RED ELONGATED HYPOCOTYL 2, FHY2, FRE1, HY8, PHYA, PHYTOCHROME A||[http://arabidopsis.org/servlets/TairObject?id=27545&type=locus TAIR]||Light Signaling||Scaffold03861 (length 7403) at 3771||0.0<br />
|-<br />
| AT1G13260||EDF4, ETHYLENE RESPONSE DNA BINDING FACTOR 4, RAV1, RELATED TO ABI3/VP1 1||[http://arabidopsis.org/servlets/TairObject?id=137721&type=locus TAIR]||Light Signaling||Scaffold00930 (length 110378) at 63069||1e-103<br />
|-<br />
| AT1G14920||GAI, GIBBERELLIC ACID INSENSITIVE, RESTORATION ON GROWTH ON AMMONIA 2, RGA2||[http://arabidopsis.org/servlets/TairObject?id=26612&type=locus TAIR]||Gibberellin||Scaffold01360 (length 81306) at 51382||0.0<br />
|-<br />
| AT1G20330||COTYLEDON VASCULAR PATTERN 1, CVP1, FRILL1, FRL1, SMT2, STEROL METHYLTRANSFERASE 2||[http://arabidopsis.org/servlets/TairObject?id=27665&type=locus TAIR]||Vernalization||Scaffold02142 (length 46662) at 24743||9e-06<br />
|-<br />
| AT1G22770||FB, GI, GIGANTEA||[http://arabidopsis.org/servlets/TairObject?id=136959&type=locus TAIR]||Light Signaling||Scaffold00100 (length 346620) at 198329||0.0<br />
|-<br />
| AT1G25560||EDF1, ETHYLENE RESPONSE DNA BINDING FACTOR 1, TEM1, TEMPRANILLO 1||[http://arabidopsis.org/servlets/TairObject?id=30061&type=locus TAIR]||Light Signaling||Scaffold00930 (length 110378) at 63096||3e-99<br />
|-<br />
| AT1G26790||||[http://arabidopsis.org/servlets/TairObject?id=137136&type=locus TAIR]||Light Signaling||Scaffold00079 (length 471015) at 69048||6e-33<br />
|-<br />
| AT1G27370||SPL10, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 10||[http://arabidopsis.org/servlets/TairObject?id=28131&type=locus TAIR]||Age||Scaffold00127 (length 336847) at 165806||5e-33<br />
|-<br />
| AT1G29160||||[http://arabidopsis.org/servlets/TairObject?id=29883&type=locus TAIR]||Light Signaling||Scaffold00270 (length 246371) at 215229||4e-50<br />
|-<br />
| AT1G30970||SUF4, SUPPRESSOR OF FRIGIDA4||[http://arabidopsis.org/servlets/TairObject?id=28096&type=locus TAIR]||Vernalization||Scaffold00348 (length 210978) at 75279||1e-15<br />
|-<br />
| AT1G31814||FRIGIDA LIKE 2, FRL2||[http://arabidopsis.org/servlets/TairObject?id=226970&type=locus TAIR]||Vernalization||Scaffold00289 (length 259591) at 150896||2e-19<br />
|-<br />
| AT1G47250||20S PROTEASOME ALPHA SUBUNIT F2, PAF2||[http://arabidopsis.org/servlets/TairObject?id=30983&type=locus TAIR]||Vernalization||Scaffold00528 (length 197283) at 110933||3e-64<br />
|-<br />
| AT1G53090||SPA1-RELATED 4, SPA4||[http://arabidopsis.org/servlets/TairObject?id=31031&type=locus TAIR]||Light Signaling||Scaffold00734 (length 158513) at 143450||3e-129<br />
|-<br />
| AT1G53160||FLORAL TRANSITION AT THE MERISTEM6, FTM6, SPL4, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 4||[http://arabidopsis.org/servlets/TairObject?id=27097&type=locus TAIR]||Age||Scaffold00062 (length 451336) at 412489||1e-15<br />
|-<br />
| AT1G65480||FLOWERING LOCUS T, FT||[http://arabidopsis.org/servlets/TairObject?id=30541&type=locus TAIR]||Ambient Temperature||Scaffold00357 (length 260075) at 58774||6e-35<br />
|-<br />
| AT1G66350||RGA-LIKE 1, RGL, RGL1||[http://arabidopsis.org/servlets/TairObject?id=137244&type=locus TAIR]||Gibberellin||Scaffold00134 (length 346346) at 174707||0.0<br />
|-<br />
| AT1G68050||"FLAVIN-BINDING, KELCH REPEAT, F BOX 1", ADO3, FKF1||[http://arabidopsis.org/servlets/TairObject?id=137051&type=locus TAIR]||Light Signaling||Scaffold00110 (length 358202) at 120279||0.0<br />
|-<br />
| AT1G68840||ATRAV2, EDF2, ETHYLENE RESPONSE DNA BINDING FACTOR 2, RAP2.8, RAV2, RELATED TO ABI3/VP1 2, RELATED TO AP2 8, TEM2, TEMPRANILLO 2||[http://arabidopsis.org/servlets/TairObject?id=27570&type=locus TAIR]||Light Signaling||Scaffold00930 (length 110378) at 63096||5e-102<br />
|-<br />
| AT1G77080||AGAMOUS-LIKE 27, AGL27, FLM, FLOWERING LOCUS M, MADS AFFECTING FLOWERING 1, MAF1||[http://arabidopsis.org/servlets/TairObject?id=29106&type=locus TAIR]||Ambient Temperature, Vernalization||Scaffold10765 (length 2447) at 744||3e-13<br />
|-<br />
| AT1G77300||ASH1 HOMOLOG 2, ASHH2, CAROTENOID CHLOROPLAST REGULATORY1, CCR1, EARLY FLOWERING IN SHORT DAYS, EFS, LAZ2, LAZARUS 2, SDG8, SET DOMAIN GROUP 8||[http://arabidopsis.org/servlets/TairObject?id=136429&type=locus TAIR]||Vernalization||Scaffold00894 (length 114877) at 89213||1e-27<br />
|-<br />
| AT2G01570||REPRESSOR OF GA, REPRESSOR OF GA1-3 1, RGA, RGA1||[http://arabidopsis.org/servlets/TairObject?id=26549&type=locus TAIR]||Gibberellin||Scaffold01360 (length 81306) at 51382||0.0<br />
|-<br />
| AT2G06255||ELF4-L3, ELF4-LIKE 3||[http://arabidopsis.org/servlets/TairObject?id=500231553&type=locus TAIR]||Light Signaling||Scaffold00336 (length 230445) at 188137||1e-39<br />
|-<br />
| AT2G17770||ATBZIP27, BASIC REGION/LEUCINE ZIPPER MOTIF 27, BZIP27, FD PARALOG, FDP||[http://arabidopsis.org/servlets/TairObject?id=227228&type=locus TAIR]||Ambient Temperature||Scaffold00367 (length 240396) at 113139||7e-17<br />
|-<br />
| AT2G18790||HY3, OOP1, OUT OF PHASE 1, PHYB, PHYTOCHROME B||[http://arabidopsis.org/servlets/TairObject?id=26548&type=locus TAIR]||Light Signaling||Scaffold00751 (length 152548) at 83698||0.0<br />
|-<br />
| AT2G18870||VEL3, VERNALIZATION5/VIN3-LIKE 3, VIL4, VIN3-LIKE 4||[http://arabidopsis.org/servlets/TairObject?id=32249&type=locus TAIR]||Autonomous||Scaffold00396 (length 187979) at 73810||7e-19<br />
|-<br />
| AT2G18880||VEL2, VERNALIZATION5/VIN3-LIKE 2, VIL3, VIN3-LIKE 3||[http://arabidopsis.org/servlets/TairObject?id=32230&type=locus TAIR]||Autonomous||Scaffold00026 (length 499904) at 369396||6e-41<br />
|-<br />
| AT2G18915||ADAGIO 2, ADO2, LKP2, LOV KELCH PROTEIN 2||[http://arabidopsis.org/servlets/TairObject?id=500231567&type=locus TAIR]||Light Signaling||Scaffold00026 (length 499904) at 445582||0.0<br />
|-<br />
| AT2G19520||ACG1, ATMSI4, FVE, MSI4, MULTICOPY SUPPRESSOR OF IRA1 4, NFC04, NFC4||[http://arabidopsis.org/servlets/TairObject?id=33019&type=locus TAIR]||Ambient Temperature, Autonomous||Scaffold00728 (length 157708) at 8716||6e-21<br />
|-<br />
| AT2G22540||AGAMOUS-LIKE 22, AGL22, SHORT VEGETATIVE PHASE, SVP||[http://arabidopsis.org/servlets/TairObject?id=31694&type=locus TAIR]||Ambient Temperature, Vernalization||Scaffold01187 (length 101153) at 47701||2e-24<br />
|-<br />
| AT2G23380||CLF, CURLY LEAF, ICU1, INCURVATA 1, SDG1, SET1, SETDOMAIN 1, SETDOMAIN GROUP 1||[http://arabidopsis.org/servlets/TairObject?id=26534&type=locus TAIR]||Autonomous, Polycomb, Vernalization||Scaffold00354 (length 215005) at 64799||5e-41<br />
|-<br />
| AT2G25930||EARLY FLOWERING 3, ELF3, PYK20||[http://arabidopsis.org/servlets/TairObject?id=32082&type=locus TAIR]||Light Signaling||Scaffold00371 (length 223748) at 73111||6e-19<br />
|-<br />
| AT2G32950||ARABIDOPSIS THALIANA CONSTITUTIVE PHOTOMORPHOGENIC 1, ATCOP1, CONSTITUTIVE PHOTOMORPHOGENIC 1, COP1, DEETIOLATED MUTANT 340, DET340, EMB168, EMBRYO DEFECTIVE 168, FUS1, FUSCA 1||[http://arabidopsis.org/servlets/TairObject?id=34462&type=locus TAIR]||Light Signaling||Scaffold00734 (length 158513) at 142779||5e-62<br />
|-<br />
| AT2G33810||SPL3, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 3||[http://arabidopsis.org/servlets/TairObject?id=34194&type=locus TAIR]||Age||Scaffold00062 (length 451336) at 412489||2e-17<br />
|-<br />
| AT2G33835||FES1, FRIGIDA-ESSENTIAL 1||[http://arabidopsis.org/servlets/TairObject?id=500230872&type=locus TAIR]||Vernalization||Scaffold00102 (length 383343) at 88264||7e-17<br />
|-<br />
| AT2G34140||||[http://arabidopsis.org/servlets/TairObject?id=33865&type=locus TAIR]||Light Signaling||Scaffold00270 (length 246371) at 215217||7e-49<br />
|-<br />
| AT2G35670||FERTILIZATION INDEPENDENT SEED 2, FERTILIZATION-INDEPENDENT ENDOSPERM 2, FIE2, FIS2||[http://arabidopsis.org/servlets/TairObject?id=26543&type=locus TAIR]||Polycomb||Scaffold00857 (length 126644) at 55565||3e-04<br />
|-<br />
| AT2G40080||EARLY FLOWERING 4, ELF4||[http://arabidopsis.org/servlets/TairObject?id=34766&type=locus TAIR]||Light Signaling||Scaffold00254 (length 265810) at 228805||4e-24<br />
|-<br />
| AT2G42200||ATSPL9, SPL9, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 9||[http://arabidopsis.org/servlets/TairObject?id=34557&type=locus TAIR]||Age||Scaffold00691 (length 141413) at 61795||5e-21<br />
|-<br />
| AT2G43410||FPA||[http://arabidopsis.org/servlets/TairObject?id=34279&type=locus TAIR]||Autonomous||Scaffold01689 (length 75472) at 47663||4e-45<br />
|-<br />
| AT2G46340||SPA1, SUPPRESSOR OF PHYA-105 1||[http://arabidopsis.org/servlets/TairObject?id=31336&type=locus TAIR]||Light Signaling||Scaffold00734 (length 158513) at 142779||3e-69<br />
|-<br />
| AT2G46790||APRR9, ARABIDOPSIS PSEUDO-RESPONSE REGULATOR 9, PRR9, PSEUDO-RESPONSE REGULATOR 9, TL1, TOC1-LIKE PROTEIN 1||[http://arabidopsis.org/servlets/TairObject?id=32227&type=locus TAIR]||Light Signaling||Scaffold00001 (length 1030549) at 322801||1e-36<br />
|-<br />
| AT2G46830||ATCCA1, CCA1, CIRCADIAN CLOCK ASSOCIATED 1||[http://arabidopsis.org/servlets/TairObject?id=32221&type=locus TAIR]||Light Signaling||Scaffold00140 (length 354209) at 234299||7e-20<br />
|-<br />
| AT2G47700||RED AND FAR-RED INSENSITIVE 2, RFI2||[http://arabidopsis.org/servlets/TairObject?id=32070&type=locus TAIR]||Light Signaling||Scaffold01059 (length 101143) at 96557||1e-19<br />
|-<br />
| AT3G02380||ATCOL2, B-BOX DOMAIN PROTEIN 3, BBX3, COL2, CONSTANS-LIKE 2||[http://arabidopsis.org/servlets/TairObject?id=35635&type=locus TAIR]||Light Signaling||Scaffold01843 (length 51900) at 40767||3e-48<br />
|-<br />
| AT3G03450||RGA-LIKE 2, RGL2||[http://arabidopsis.org/servlets/TairObject?id=40021&type=locus TAIR]||Gibberellin||Scaffold00134 (length 346346) at 174722||0.0<br />
|-<br />
| AT3G04610||FLK, FLOWERING LOCUS KH DOMAIN||[http://arabidopsis.org/servlets/TairObject?id=37455&type=locus TAIR]||Autonomous||Scaffold01384 (length 81068) at 28309||4e-29<br />
|-<br />
| AT3G05120||ATGID1A, GA INSENSITIVE DWARF1A, GID1A||[http://arabidopsis.org/servlets/TairObject?id=39457&type=locus TAIR]||Gibberellin||Scaffold00101 (length 425332) at 398762||4e-175<br />
|-<br />
| AT3G07650||B-BOX DOMAIN PROTEIN 7, BBX7, COL9, CONSTANS-LIKE 9||[http://arabidopsis.org/servlets/TairObject?id=38550&type=locus TAIR]||Light Signaling||Scaffold00832 (length 123094) at 89599||1e-55<br />
|-<br />
| AT3G10390||FLD, FLOWERING LOCUS D||[http://arabidopsis.org/servlets/TairObject?id=35869&type=locus TAIR]||Ambient Temperature, Autonomous||Scaffold00232 (length 253418) at 139565||0.0<br />
|-<br />
| AT3G12810||CHR13, PHOTOPERIOD-INDEPENDENT EARLY FLOWERING 1, PIE1, SRCAP||[http://arabidopsis.org/servlets/TairObject?id=37964&type=locus TAIR]||Vernalization||Scaffold00147 (length 345970) at 30164||0.0<br />
|-<br />
| AT3G15270||SPL5, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 5||[http://arabidopsis.org/servlets/TairObject?id=37842&type=locus TAIR]||Age||Scaffold00105 (length 392037) at 147284||5e-16<br />
|-<br />
| AT3G15354||SPA1-RELATED 3, SPA3||[http://arabidopsis.org/servlets/TairObject?id=500230681&type=locus TAIR]||Light Signaling||Scaffold00734 (length 158513) at 143450||1e-144<br />
|-<br />
| AT3G18990||REDUCED VERNALIZATION RESPONSE 1, REM39, REPRODUCTIVE MERISTEM 39, VRN1||[http://arabidopsis.org/servlets/TairObject?id=37620&type=locus TAIR]||Vernalization||Scaffold00811 (length 108354) at 96661||2e-25<br />
|-<br />
| AT3G20740||FERTILIZATION-INDEPENDENT ENDOSPERM, FERTILIZATION-INDEPENDENT ENDOSPERM 1, FIE, FIE1, FIS3||[http://arabidopsis.org/servlets/TairObject?id=38691&type=locus TAIR]||Autonomous, Polycomb, Vernalization||Scaffold01670 (length 60304) at 9836||5e-20<br />
|-<br />
| AT3G21320||||[http://arabidopsis.org/servlets/TairObject?id=39170&type=locus TAIR]||Light Signaling||Scaffold00509 (length 192554) at 181887||1e-21<br />
|-<br />
| AT3G24440||VERNALIZATION 5, VIL1, VIN3-LIKE 1, VRN5||[http://arabidopsis.org/servlets/TairObject?id=39196&type=locus TAIR]||Autonomous, Vernalization||Scaffold00396 (length 187979) at 73795||2e-69<br />
|-<br />
| AT3G25730||EDF3, ETHYLENE RESPONSE DNA BINDING FACTOR 3||[http://arabidopsis.org/servlets/TairObject?id=37641&type=locus TAIR]||Light Signaling||Scaffold00930 (length 110378) at 63060||5e-100<br />
|-<br />
| AT3G33520||ACTIN-RELATED PROTEIN 6, ARP6, ATARP6, EARLY IN SHORT DAYS 1, ESD1, SUF3, SUPPRESSOR OF FRI 3||[http://arabidopsis.org/servlets/TairObject?id=40458&type=locus TAIR]||Ambient Temperature, Vernalization||Scaffold00246 (length 286612) at 268521||1e-53<br />
|-<br />
| AT3G46640||LUX, LUX ARRHYTHMO, PCL1, PHYTOCLOCK 1||[http://arabidopsis.org/servlets/TairObject?id=35747&type=locus TAIR]||Light Signaling||Scaffold01150 (length 88293) at 80272||3e-34<br />
|-<br />
| AT3G47500||CDF3, CYCLING DOF FACTOR 3||[http://arabidopsis.org/servlets/TairObject?id=36439&type=locus TAIR]||Light Signaling||Scaffold00079 (length 471015) at 68175||1e-85<br />
|-<br />
| AT4G00650||FLA, FLOWERING LOCUS A, FRI, FRIGIDA||[http://arabidopsis.org/servlets/TairObject?id=128299&type=locus TAIR]||Vernalization||Scaffold00039 (length 505275) at 216632||4e-50<br />
|-<br />
| AT4G02020||EZA1, SDG10, SET DOMAIN-CONTAINING PROTEIN 10, SWINGER, SWN||[http://arabidopsis.org/servlets/TairObject?id=129104&type=locus TAIR]||Autonomous, Polycomb, Vernalization||Scaffold00354 (length 215005) at 64799||2e-48<br />
|-<br />
| AT4G02560||LD, LUMINIDEPENDENS||[http://arabidopsis.org/servlets/TairObject?id=26564&type=locus TAIR]||Autonomous||Scaffold00002 (length 840149) at 158601||4e-28<br />
|-<br />
| AT4G08920||ATCRY1, BLU1, BLUE LIGHT UNINHIBITED 1, CRY1, CRYPTOCHROME 1, ELONGATED HYPOCOTYL 4, HY4, OOP2, OUT OF PHASE 2||[http://arabidopsis.org/servlets/TairObject?id=129943&type=locus TAIR]||Light Signaling||Scaffold00331 (length 261439) at 124817||4e-128<br />
|-<br />
| AT4G11110||SPA1-RELATED 2, SPA2||[http://arabidopsis.org/servlets/TairObject?id=129633&type=locus TAIR]||Light Signaling||Scaffold01034 (length 107107) at 19205||2e-62<br />
|-<br />
| AT4G11880||AGAMOUS-LIKE 14, AGL14||[http://arabidopsis.org/servlets/TairObject?id=129748&type=locus TAIR]||Vernalization||Scaffold00249 (length 258199) at 131012||2e-29<br />
|-<br />
| AT4G16250||PHYD, PHYTOCHROME D||[http://arabidopsis.org/servlets/TairObject?id=26567&type=locus TAIR]||Light Signaling||Scaffold00751 (length 152548) at 83707||0.0<br />
|-<br />
| AT4G16280||FCA||[http://arabidopsis.org/servlets/TairObject?id=128853&type=locus TAIR]||Ambient Temperature, Autonomous||Scaffold00104 (length 360147) at 120318||5e-13<br />
|-<br />
| AT4G16845||REDUCED VERNALIZATION RESPONSE 2, VRN2||[http://arabidopsis.org/servlets/TairObject?id=228106&type=locus TAIR]||Autonomous, Polycomb, Vernalization||Scaffold00857 (length 126644) at 55203||3e-07<br />
|-<br />
| AT4G18130||PHYE, PHYTOCHROME E||[http://arabidopsis.org/servlets/TairObject?id=26568&type=locus TAIR]||Light Signaling||Scaffold00751 (length 152548) at 83749||0.0<br />
|-<br />
| AT4G20370||TSF, TWIN SISTER OF FT||[http://arabidopsis.org/servlets/TairObject?id=26553&type=locus TAIR]||Ambient Temperature||Scaffold00357 (length 260075) at 58807||1e-33<br />
|-<br />
| AT4G22950||AGAMOUS-LIKE 19, AGL19, GL19||[http://arabidopsis.org/servlets/TairObject?id=128336&type=locus TAIR]||Vernalization||Scaffold00249 (length 258199) at 131012||4e-28<br />
|-<br />
| AT4G24540||AGAMOUS-LIKE 24, AGL24||[http://arabidopsis.org/servlets/TairObject?id=127586&type=locus TAIR]||Vernalization||Scaffold01187 (length 101153) at 47701||2e-25<br />
|-<br />
| AT4G26000||PEP, PEPPER||[http://arabidopsis.org/servlets/TairObject?id=127403&type=locus TAIR]||Vernalization||Scaffold00021 (length 527983) at 157278||3e-29<br />
|-<br />
| AT4G30200||VEL1, VERNALIZATION5/VIN3-LIKE 1, VIL2, VIN3-LIKE 2||[http://arabidopsis.org/servlets/TairObject?id=128580&type=locus TAIR]||Autonomous, Vernalization||Scaffold00026 (length 499904) at 369417||7e-64<br />
|-<br />
| AT4G34530||CIB1, CRYPTOCHROME-INTERACTING BASIC-HELIX-LOOP-HELIX 1||[http://arabidopsis.org/servlets/TairObject?id=130033&type=locus TAIR]||Light Signaling||Scaffold01322 (length 99420) at 82955||2e-29<br />
|-<br />
| AT4G35900||ATBZIP14, FD, FD-1||[http://arabidopsis.org/servlets/TairObject?id=128068&type=locus TAIR]||Ambient Temperature||Scaffold00367 (length 240396) at 113139||1e-16<br />
|-<br />
| AT5G02810||APRR7, PRR7, PSEUDO-RESPONSE REGULATOR 7||[http://arabidopsis.org/servlets/TairObject?id=131538&type=locus TAIR]||Light Signaling||Scaffold00125 (length 356885) at 276518||1e-33<br />
|-<br />
| AT5G03840||TERMINAL FLOWER 1, TFL1||[http://arabidopsis.org/servlets/TairObject?id=131459&type=locus TAIR]||Ambient Temperature||Scaffold00181 (length 337602) at 12825||1e-28<br />
|-<br />
| AT5G08330||CCA1 HIKING EXPEDITION, CHE, TRANSCRIPTION FACTOR TCP21, TCP21||[http://www.uniprot.org/uniprot/Q9FTA2 UniProtKB]||Light Signaling||Scaffold00993 (length 109486) at 294||5e-27<br />
|-<br />
| AT5G10140||AGAMOUS-LIKE 25, AGL25, FLC, FLF, FLOWERING LOCUS C, FLOWERING LOCUS F||[http://arabidopsis.org/servlets/TairObject?id=136002&type=locus TAIR]||Ambient Temperature, Vernalization||Scaffold10765 (length 2447) at 708||8e-22<br />
|-<br />
| AT5G11530||EMBRYONIC FLOWER 1, EMF1||[http://arabidopsis.org/servlets/TairObject?id=130620&type=locus TAIR]||Polycomb||Scaffold00253 (length 240879) at 11069||1e-06<br />
|-<br />
| AT5G13480||FY||[http://arabidopsis.org/servlets/TairObject?id=136108&type=locus TAIR]||Autonomous||Scaffold00166 (length 328538) at 74796||2e-43<br />
|-<br />
| AT5G15840||B-BOX DOMAIN PROTEIN 1, BBX1, CO, CONSTANS, FG||[http://arabidopsis.org/servlets/TairObject?id=130492&type=locus TAIR]||Light Signaling||Scaffold01843 (length 51900) at 40767||3e-29<br />
|-<br />
| AT5G15850||ATCOL1, B-BOX DOMAIN PROTEIN 2, BBX2, COL1, CONSTANS-LIKE 1||[http://arabidopsis.org/servlets/TairObject?id=130495&type=locus TAIR]||Light Signaling||Scaffold01843 (length 51900) at 40767||5e-44<br />
|-<br />
| AT5G17690||ATLHP1, LHP1, LIKE HETEROCHROMATIN PROTEIN 1, TERMINAL FLOWER 2, TFL2||[http://arabidopsis.org/servlets/TairObject?id=134923&type=locus TAIR]||Polycomb||Scaffold00696 (length 140617) at 128983||7e-13<br />
|-<br />
| AT5G23150||ENHANCER OF AG-4 2, HUA2||[http://arabidopsis.org/servlets/TairObject?id=135220&type=locus TAIR]||Vernalization||Scaffold00686 (length 145647) at 102689||5e-42<br />
|-<br />
| AT5G24470||APRR5, PRR5, PSEUDO-RESPONSE REGULATOR 5||[http://arabidopsis.org/servlets/TairObject?id=135985&type=locus TAIR]||Light Signaling||Scaffold00001 (length 1030549) at 322798||3e-40<br />
|-<br />
| AT5G24930||ATCOL4, B-BOX DOMAIN PROTEIN 5, BBX5, COL4, CONSTANS-LIKE 4||[http://arabidopsis.org/servlets/TairObject?id=131285&type=locus TAIR]||Light Signaling||Scaffold11225 (length 3326) at 2816||8e-23<br />
|-<br />
| AT5G35840||PHYC, PHYTOCHROME C||[http://arabidopsis.org/servlets/TairObject?id=133466&type=locus TAIR]||Light Signaling||Scaffold01070 (length 102706) at 75395||0.0<br />
|-<br />
| AT5G37055||ATSWC6, SEF, SERRATED LEAVES AND EARLY FLOWERING||[http://arabidopsis.org/servlets/TairObject?id=500231974&type=locus TAIR]||Vernalization||Scaffold00925 (length 141061) at 38143||4e-29<br />
|-<br />
| AT5G39660||CDF2, CYCLING DOF FACTOR 2||[http://arabidopsis.org/servlets/TairObject?id=133414&type=locus TAIR]||Light Signaling||Scaffold00651 (length 145047) at 19066||1e-90<br />
|-<br />
| AT5G42790||ARS5, ARSENIC TOLERANCE 5, ATPSM30, PAF1, PROTEASOME ALPHA SUBUNIT F1||[http://arabidopsis.org/servlets/TairObject?id=133505&type=locus TAIR]||Vernalization||Scaffold00528 (length 197283) at 110933||5e-64<br />
|-<br />
| AT5G51230||ATEMF2, CYR1, CYTOKININ RESISTANT 1, EMBRYONIC FLOWER 2, EMF2, VEF2||[http://arabidopsis.org/servlets/TairObject?id=134952&type=locus TAIR]||Polycomb||Scaffold00857 (length 126644) at 44887||9e-19<br />
|-<br />
| AT5G57360||ADAGIO 1, ADO1, FKF1-LIKE PROTEIN 2, FKL2, LKP1, LOV KELCH PROTEIN 1, ZEITLUPE, ZTL||[http://arabidopsis.org/servlets/TairObject?id=134481&type=locus TAIR]||Light Signaling||Scaffold00026 (length 499904) at 445597||0.0<br />
|-<br />
| AT5G57380||VERNALIZATION INSENSITIVE 3, VIN3||[http://arabidopsis.org/servlets/TairObject?id=134483&type=locus TAIR]||Autonomous, Vernalization||Scaffold00026 (length 499904) at 369405||3e-48<br />
|-<br />
| AT5G57660||ATCOL5, B-BOX DOMAIN PROTEIN 6, BBX6, COL5, CONSTANS-LIKE 5||[http://arabidopsis.org/servlets/TairObject?id=134422&type=locus TAIR]||Light Signaling||Scaffold11225 (length 3326) at 2816||1e-25<br />
|-<br />
| AT5G58230||ARABIDOPSIS MULTICOPY SUPRESSOR OF IRA1, ATMSI1, MATERNAL EFFECT EMBRYO ARREST 70, MEE70, MSI1, MULTICOPY SUPRESSOR OF IRA1||[http://arabidopsis.org/servlets/TairObject?id=132921&type=locus TAIR]||Autonomous, Polycomb, Vernalization||Scaffold00615 (length 179658) at 161081||2e-61<br />
|-<br />
| AT5G60100||APRR3, PRR3, PSEUDO-RESPONSE REGULATOR 3||[http://arabidopsis.org/servlets/TairObject?id=133317&type=locus TAIR]||Light Signaling||Scaffold02075 (length 43325) at 14139||3e-25<br />
|-<br />
| AT5G61380||APRR1, ATTOC1, PRR1, PSEUDO-RESPONSE REGULATOR 1, TIMING OF CAB EXPRESSION 1, TOC1||[http://arabidopsis.org/servlets/TairObject?id=133196&type=locus TAIR]||Light Signaling||Scaffold00753 (length 123742) at 70468||2e-47<br />
|-<br />
| AT5G62430||CDF1, CYCLING DOF FACTOR 1||[http://arabidopsis.org/servlets/TairObject?id=131911&type=locus TAIR]||Light Signaling||Scaffold01102 (length 99830) at 51435||1e-59<br />
|-<br />
| AT5G65050||AGAMOUS-LIKE 31, AGL31, MADS AFFECTING FLOWERING 2, MAF2||[http://arabidopsis.org/servlets/TairObject?id=135154&type=locus TAIR]||Ambient Temperature, Vernalization||Scaffold10765 (length 2447) at 723||4e-20<br />
|-<br />
| AT5G65060||AGAMOUS-LIKE 70, AGL70, FCL3, MADS AFFECTING FLOWERING 3, MAF3||[http://arabidopsis.org/servlets/TairObject?id=130633&type=locus TAIR]||Ambient Temperature, Vernalization||Scaffold10765 (length 2447) at 639||7e-15<br />
|-<br />
| AT5G65070||AGAMOUS-LIKE 69, AGL69, FCL4, MADS AFFECTING FLOWERING 4, MAF4||[http://arabidopsis.org/servlets/TairObject?id=130634&type=locus TAIR]||Ambient Temperature, Vernalization||Scaffold10765 (length 2447) at 723||6e-20<br />
|-<br />
| AT5G65080||AGAMOUS-LIKE 68, AGL68, MADS AFFECTING FLOWERING 5, MAF5||[http://arabidopsis.org/servlets/TairObject?id=130635&type=locus TAIR]||Ambient Temperature, Vernalization||Scaffold10765 (length 2447) at 699||1e-18<br />
|}<br />
<br />
<br />
==References==<br />
*Amasino RM. Seasonal and developmental timing of flowering. ''Plant J,'' '''61,''' 1001-1013 (2010).<br />
*Amasino RM. Vernalization and flowering time. ''Curr Opin Plant Biol,'' '''16,''' 154–158 (2005).<br />
*Ballerini ES, Kramer EM. Environmental and molecular analysis of the floral transition in the lower eudicot Aquilegia formosa. ''Evodevo,'' '''2,''' 1-20 (2011).<br />
*Bäurle I, Dean C. The timing of developmental transitions in plants. ''Cell,'' '''125,''' 655-664 (2006).<br />
*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).<br />
*Farrona S, Coupland G, Turck F. The impact of chromatin regulation on the floral transition. ''Semin Cell Dev Biol,'' '''19,''' 560-573 (2008).<br />
*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).<br />
*Fornara F, de Montaigu A, Coupland G. SnapShot: Control of flowering in Arabidopsis. ''Cell,'' '''141,''' 550-550.e2 (2010).<br />
*Henderson IR, Dean C. Control of Arabidopsis flowering: the chill before the bloom. ''Development,'' '''131,''' 3829-3838 (2004).<br />
*He Y, Amasino RM. Role of chromatin modification in flowering-time control. ''Trends Plant Sci,'' '''10,''' 30-35 (2005).<br />
*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).<br />
*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).<br />
*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).<br />
*Jung CH, Wong CE, Singh MB, Bhalla PL. Comparative genomic analysis of soybean flowering genes. ''PLoS One,'' '''7,''' e38250 (2012).<br />
*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).<br />
*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).<br />
*Liu C, Thong Z, Yu H. Coming into bloom: the specification of floral meristems. ''Development,'' '''136,''' 3379-3391 (2009).<br />
*Posé D, Yant L, Schmid M. The end of innocence: flowering networks explode in complexity. ''Curr Opin Plant Biol'' '''15,''' 45-50 (2012).<br />
*Schneitz K, Balasubramanian S. Floral Meristems. ''eLS'' (John Wiley & Sons Ltd, Chichester, 2009).<br />
*SSR Tool. ''Genome Database for Vaccinium.''<br />
*Sung ZR, Chen L, Moon YH, Lertpiriyapong K. Mechanisms of floral repression in Arabidopsis. ''Curr Opin Plant Biol,'' '''6,''' 29-35 (2003).<br />
*Taiz L, Zeiger E. ''Plant Physiology Fifth Edition Ch. 20'' (Sinauer Associates, Sunderland, MA, 2010).<br />
*Turck F, Adrian J. A lesson in complexity: regulation of FLOWERING LOCUS T. ''Max Planck Institute for Plant Breeding Research.''<br />
*UniProt Consortium. Reorganizing the protein space at the Universal Protein Resource (UniProt). ''Nucleic Acids Res,'' '''40,''' D71-D75 (2012).<br />
*Wellmer F, Riechmann JL. Gene networks controlling the initiation of flower development. ''Trends Genet,'' '''26,''' 519-527 (2010).<br />
*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).<br />
*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).<br />
*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).</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=Time_of_bloom&diff=19287Time of bloom2021-08-12T16:30:17Z<p>Laheyer: </p>
<hr />
<div>Austin Mudd - Spring 2013<br />
<br/>Shortened URL: http://goo.gl/zuTkP<br />
<br />
<br />
__TOC__<br />
<br />
==Introduction to Flowering==<br />
====The Process of Flowering====<br />
*Flowering is the "switch from vegetative growth (the production of stems and leaves) to reproductive growth (the production of flowers)" ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010065 Higgins ''et al.'', 2010])<br />
*The “shoot apical meristem starts to produce flowers instead of leaves” ([http://www.sciencedirect.com/science/article/pii/S0092867410004411 Fornara ''et al.'', 2010])<br />
*Occurs “when conditions for pollination and seed development are optimal and consequently most plants restrict flowering to a specific time of year” ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010065 Higgins ''et al.'', 2010])<br />
*”The genes and molecular mechanisms controlling flowering have been extensively studied in the model dicot <i>Arabidopsis thaliana</i>” ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010065 Higgins ''et al.'', 2010])<br />
*In <i>Arabidopsis thaliana</i>, “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” ([http://www.sciencedirect.com/science/article/pii/S0092867410004411 Fornara ''et al.'', 2010])<br />
<br />
[[File:Max_Planck_Institute_Pathway.png|thumb|right|The major pathways in the timing of flowering from Turck and Adrian at the [http://www.mpipz.mpg.de/305695/Project_1 Max Planck Institute for Plant Breeding Research]; permission granted]]<br />
====The Timing of Flowering====<br />
*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.” ([http://www.sciencedirect.com/science/article/pii/S0092867410004411 Fornara ''et al.'', 2010])<br />
*These “pathways converge to regulate a small number of ‘floral integrator genes,’ ... which govern flowering time by merging signals from multiple pathways” ([http://www.sciencedirect.com/science/article/pii/S0092867410004411 Fornara ''et al.'', 2010])<br />
<br />
====The Importance of Flowering====<br />
*”Flowering is one of the most important agronomic traits influencing crop yield” ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012])<br />
*”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” ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010065 Higgins ''et al.'', 2010])<br />
*“Adaptation to different environments and practices has been achieved by manipulation of flowering time responses” ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010065 Higgins ''et al.'', 2010])<br />
*The study of flowering is ”critical for the breeding of climate change resilient crop varieties” ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012])<br />
*Flowering is “an excellent system for comparison between and within domestic and wild species” ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010065 Higgins ''et al.'', 2010])<br />
<br />
<br />
==Pathways Controlling Flowering==<br />
====Age Pathway====<br />
*"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" ([http://www.plantcell.org/content/early/2012/08/29/tpc.112.101014.full.pdf+html Yu ''et al.'', 2012])<br />
*5 <i>Arabidopsis</i> genes are involved in the age pathway: SPL3, SPL4, SPL5, SPL9, SPL10 ([http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2010.04148.x/pdf/ Amasino, 2010])<br />
<br />
====Ambient Temperature Pathway====<br />
*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" ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012])<br />
*16 <i>Arabidopsis</i> genes are involved in the ambient temperature pathway: AGL31, ATARP6, ATBZIP27, FCA, FD, FLC, FLD, FT, FVE, MAF1, MAF3, MAF4, MAF5, SVP, TFL1, TSF ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012])<br />
<br />
====Autonomous Pathway====<br />
*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 ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012])<br />
*17 <i>Arabidopsis</i> genes are involved in the autonomous pathway: CLF, FCA, FIE1, FLD, FLK, FPA, FVE, FY, LD, MSI1, SWN, VEL1, VEL2, VEL3, VIN3, VRN2, VRN5 ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012]) <br />
<br />
====Gibberellin Pathway====<br />
*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" ([http://www.plantcell.org/content/early/2012/08/29/tpc.112.101014.full.pdf+html Yu ''et al.'', 2012])<br />
*5 <i>Arabidopsis</i> genes are involved in the gibberellin pathway: GAI, GID1, RGA, RGL1, RGL2 ([http://www.plantcell.org/content/early/2012/08/29/tpc.112.101014.full.pdf+html Yu ''et al.'', 2012])<br />
<br />
====Light Signaling Pathway====<br />
*"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" ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012])<br />
*48 <i>Arabidopsis</i> 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 ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012])<br />
<br />
====Polycomb Pathway====<br />
*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) ([http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002512 Kim ''et al.'', 2012])<br />
*10 <i>Arabidopsis</i> genes are involved in the polycomb pathway: CLF, EMF1, EMF2, FIE1, FIS2, LHP1, MEA, MSI1, SWN, VRN2 ([http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002512 Kim ''et al.'', 2012])<br />
<br />
====Vernalization Pathway====<br />
*The vernalization pathway is the response to "prolonged periods of low temperature [that are required] to initiate flowering" ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012])<br />
*32 <i>Arabidopsis</i> 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 ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012])<br />
<br />
<br />
==Gallery of <i>Arabidopsis</i> Flowering Pathways==<br />
<br />
<gallery widths="102px" heights="102px" perrow="6"><br />
File:Izawa_Pathway.jpeg|alt Pathway from Izawa ''et al.'', 2003|[http://www.sciencedirect.com/science/article/pii/S1369526603000141 Izawa ''et al.'', 2003]; permission pending<br />
File:Sung_Pathway.gif|[http://www.sciencedirect.com/science/article/pii/S1369526602000146 Sung ''et al.'', 2003]; permission granted<br />
File:Boss_Pathway.gif|[http://www.plantcell.org/content/16/suppl_1/S18/F2.expansion Boss ''et al.'', 2004]; permission granted<br />
File:Boss_Pathway_2.jpeg|[http://www.plantcell.org/content/16/suppl_1/S18/F3.expansion Boss ''et al.'', 2004]; permission granted<br />
File:Henderson_and_Dean_Pathway.jpeg|[http://dev.biologists.org/content/131/16/3829/F1.expansion.html Henderson and Dean, 2004]; permission granted<br />
File:Amasino_Pathway.jpeg|[http://www.sciencedirect.com/science/article/pii/S0958166905000273 Amasino, 2005]; permission granted<br />
File:He_and_Amasino_Pathway.jpeg|[http://www.sciencedirect.com/science/article/pii/S1360138504002705 He and Amasino, 2005]; permission granted<br />
File:Yamaguchi_Pathway.jpeg|[http://pcp.oxfordjournals.org/content/46/8/1175/F7.expansion Yamaguchi ''et al.'', 2005]; permission pending<br />
File:Baurle_and_Dean_Pathway.jpeg|[http://www.sciencedirect.com/science/article/pii/S009286740600571X Bäurle and Dean, 2006]; permission granted<br />
File:Farrona_Pathway.jpeg|[http://www.sciencedirect.com/science/article/pii/S1084952108000566 Farrona ''et al.'', 2008]; permission granted<br />
File:Farrona_Pathway_2.jpeg|[http://www.sciencedirect.com/science/article/pii/S1084952108000566 Farrona ''et al.'', 2008]; permission granted<br />
File:Amasino_Pathway_2.png|[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2010.04148.x/pdf/ Amasino, 2010]; permission granted<br />
File:Higgins_Pathway.jpg|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010065 Higgins ''et al.'', 2010]; permission granted<br />
File:Kim_and_Sung_Pathway.jpeg|[http://www.pnas.org/content/107/39/17029/F6.expansion.html Kim and Sung, 2010]; permission pending<br />
File:Taiz_and_Zeiger_Pathway.jpeg|[http://5e.plantphys.net/article.php?ch=1&id=375 Taiz and Zeiger, 2010]; permission pending<br />
File:Ballerini_and_Kramer_Pathway.png|[http://dash.harvard.edu/bitstream/handle/1/4903810/Ballerini%20%26%20Kramer%202011.pdf?sequence=1 Ballerini and Kramer, 2011]; permission granted<br />
File:Ferrier_Pathway.jpeg|[http://www.sciencedirect.com/science/article/pii/S0958166910002284 Ferrier ''et al.'', 2011]; permission pending<br />
File:Zhang_Pathway.png|[http://www.biomedcentral.com/1471-2164/12/63 Zhang ''et al.'', 2011]; permission granted<br />
File:Jung_Pathway.jpg|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012]; permission pending<br />
</gallery><br />
<br />
Additional figures:<br />
*[http://dev.biologists.org/content/136/20/3379/F3.expansion.html Figure 3 from Liu ''et al.'', 2009]<br />
*[http://www.els.net/WileyCDA/ElsArticle/refId-a0002053.html Figure 1 from Schneitz and Balasubramanian, 2009]<br />
*[http://www.sciencedirect.com/science/article/pii/S0168952510001873 Figure 1 from Wellmer and Riechmann, 2010]<br />
*[http://www.sciencedirect.com/science/article/pii/S1369526611001440 Figure 1 from Posé ''et al.'', 2012]<br />
<br />
<br />
==Methods==<br />
====Finding Genes====<br />
*I examined a variety of journal articles related to time of flowering in <i>Arabidopsis thaliana</i> and found a number of pathways related to flowering (see the gallery above). I came across a genomic analysis of soybean by [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012]. In this paper, they listed the "183 <i>Arabidopsis</i> genes that are known to take part in flowering regulatory pathways [taken] from previous studies." These 183 genes, plus "24 additional <i>Arabidopsis</i> 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 [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012] can be viewed here: [[File:Jung 207 Arabidopsis Flowering Genes.pdf]].<br />
*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.<br />
*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 [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2010.04148.x/pdf/ Amasino, 2010], [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012], [http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002512 Kim ''et al.'', 2012], and [http://www.plantcell.org/content/early/2012/08/29/tpc.112.101014.full.pdf+html Yu ''et al.'', 2012].<br />
*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." ([http://www.sciencedirect.com/science/article/pii/S0092867410004411 Fornara ''et al.'', 2010])<br />
<br />
====Finding SSRs====<br />
*A local database of the blueberry genome was created using the following coding:<br />
<PRE>./bin/makeblastdb -in BlueberryGenome.txt -input_type fasta -dbtype nucl -title blueberry_Genome</PRE><br />
*Amino acid sequences for all <i>Arabidopsis</i> genes were taken from [http://www.arabidopsis.org/index.jsp 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:<br />
<PRE>{ echo bin/tblastn -query AASequence.txt -db BlueberryGenome.txt; bin/tblastn -query <br />
AASequence.txt -db BlueberryGenome.txt; } >> AAOutput.txt</PRE><br />
*For each gene result, the best match was presumed to be the ortholog of the <i>Arabidopsis</i> gene in <i>Vaccinium corymbosum</i>. 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 <i>Vitis vinifera</i> ortholog of the <i>Arabidopsis</i> gene from [http://www.uniprot.org/uniprot/?query=organism%3A%22Vitis+vinifera+%5B29760%5D%22&sort=score UniProtKB (UniProt Consortium, 2012)] nomenclature search.<br />
*SSRs were determined by importing the best match scaffold into the [http://www.vaccinium.org/cgi-bin/vaccinium_ssr SSR Tool] at the [http://www.vaccinium.org/ Genome Database for Vaccinium]. Three di/trinucleotide SSRs near the gene location on the scaffold were chosen for each gene.<br />
<br />
<br />
==SSR Results==<br />
All SSR results can be viewed on the [[Time of bloom SSR Results]] page. An abbreviated listing of the results is included below.<br />
<br/>[[File:Flowering_SSR_Results_Table.png]]<br />
<br />
<br />
==Flowering Genes Of Interest==<br />
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." ([http://www.sciencedirect.com/science/article/pii/S0092867410004411 Fornara ''et al.'', 2010])<br />
<br />
{| class="wikitable sortable"<br />
|-<br />
! <i>Arabidopsis</i> Locus !! Other Names !! AA Source !! Pathway !! width="150px" |Top Hit ''Vaccinium'' Scaffold !! E Value<br />
|-<br />
| AT1G01060||LATE ELONGATED HYPOCOTYL, LATE ELONGATED HYPOCOTYL 1, LHY, LHY1||[http://arabidopsis.org/servlets/TairObject?id=137165&type=locus TAIR]||Light Signaling||Scaffold00140 (length 354209) at 234299||2e-19<br />
|-<br />
| AT1G02580||EMB173, EMBRYO DEFECTIVE 173, FERTILIZATION INDEPENDENT SEED 1, FIS1, MEA, MEDEA, SDG5, SET DOMAIN-CONTAINING PROTEIN 5||[http://arabidopsis.org/servlets/TairObject?id=136450&type=locus TAIR]||Polycomb||Scaffold00354 (length 215005) at 64805||4e-17<br />
|-<br />
| AT1G04400||AT-PHH1, ATCRY2, CRY2, CRYPTOCHROME 2, FHA, PHH1||[http://arabidopsis.org/servlets/TairObject?id=28374&type=locus TAIR]||Light Signaling||Scaffold00649 (length 159319) at 28296||1e-119<br />
|-<br />
| AT1G09570||ELONGATED HYPOCOTYL 8, FAR RED ELONGATED 1, FAR RED ELONGATED HYPOCOTYL 2, FHY2, FRE1, HY8, PHYA, PHYTOCHROME A||[http://arabidopsis.org/servlets/TairObject?id=27545&type=locus TAIR]||Light Signaling||Scaffold03861 (length 7403) at 3771||0.0<br />
|-<br />
| AT1G13260||EDF4, ETHYLENE RESPONSE DNA BINDING FACTOR 4, RAV1, RELATED TO ABI3/VP1 1||[http://arabidopsis.org/servlets/TairObject?id=137721&type=locus TAIR]||Light Signaling||Scaffold00930 (length 110378) at 63069||1e-103<br />
|-<br />
| AT1G14920||GAI, GIBBERELLIC ACID INSENSITIVE, RESTORATION ON GROWTH ON AMMONIA 2, RGA2||[http://arabidopsis.org/servlets/TairObject?id=26612&type=locus TAIR]||Gibberellin||Scaffold01360 (length 81306) at 51382||0.0<br />
|-<br />
| AT1G20330||COTYLEDON VASCULAR PATTERN 1, CVP1, FRILL1, FRL1, SMT2, STEROL METHYLTRANSFERASE 2||[http://arabidopsis.org/servlets/TairObject?id=27665&type=locus TAIR]||Vernalization||Scaffold02142 (length 46662) at 24743||9e-06<br />
|-<br />
| AT1G22770||FB, GI, GIGANTEA||[http://arabidopsis.org/servlets/TairObject?id=136959&type=locus TAIR]||Light Signaling||Scaffold00100 (length 346620) at 198329||0.0<br />
|-<br />
| AT1G25560||EDF1, ETHYLENE RESPONSE DNA BINDING FACTOR 1, TEM1, TEMPRANILLO 1||[http://arabidopsis.org/servlets/TairObject?id=30061&type=locus TAIR]||Light Signaling||Scaffold00930 (length 110378) at 63096||3e-99<br />
|-<br />
| AT1G26790||||[http://arabidopsis.org/servlets/TairObject?id=137136&type=locus TAIR]||Light Signaling||Scaffold00079 (length 471015) at 69048||6e-33<br />
|-<br />
| AT1G27370||SPL10, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 10||[http://arabidopsis.org/servlets/TairObject?id=28131&type=locus TAIR]||Age||Scaffold00127 (length 336847) at 165806||5e-33<br />
|-<br />
| AT1G29160||||[http://arabidopsis.org/servlets/TairObject?id=29883&type=locus TAIR]||Light Signaling||Scaffold00270 (length 246371) at 215229||4e-50<br />
|-<br />
| AT1G30970||SUF4, SUPPRESSOR OF FRIGIDA4||[http://arabidopsis.org/servlets/TairObject?id=28096&type=locus TAIR]||Vernalization||Scaffold00348 (length 210978) at 75279||1e-15<br />
|-<br />
| AT1G31814||FRIGIDA LIKE 2, FRL2||[http://arabidopsis.org/servlets/TairObject?id=226970&type=locus TAIR]||Vernalization||Scaffold00289 (length 259591) at 150896||2e-19<br />
|-<br />
| AT1G47250||20S PROTEASOME ALPHA SUBUNIT F2, PAF2||[http://arabidopsis.org/servlets/TairObject?id=30983&type=locus TAIR]||Vernalization||Scaffold00528 (length 197283) at 110933||3e-64<br />
|-<br />
| AT1G53090||SPA1-RELATED 4, SPA4||[http://arabidopsis.org/servlets/TairObject?id=31031&type=locus TAIR]||Light Signaling||Scaffold00734 (length 158513) at 143450||3e-129<br />
|-<br />
| AT1G53160||FLORAL TRANSITION AT THE MERISTEM6, FTM6, SPL4, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 4||[http://arabidopsis.org/servlets/TairObject?id=27097&type=locus TAIR]||Age||Scaffold00062 (length 451336) at 412489||1e-15<br />
|-<br />
| AT1G65480||FLOWERING LOCUS T, FT||[http://arabidopsis.org/servlets/TairObject?id=30541&type=locus TAIR]||Ambient Temperature||Scaffold00357 (length 260075) at 58774||6e-35<br />
|-<br />
| AT1G66350||RGA-LIKE 1, RGL, RGL1||[http://arabidopsis.org/servlets/TairObject?id=137244&type=locus TAIR]||Gibberellin||Scaffold00134 (length 346346) at 174707||0.0<br />
|-<br />
| AT1G68050||"FLAVIN-BINDING, KELCH REPEAT, F BOX 1", ADO3, FKF1||[http://arabidopsis.org/servlets/TairObject?id=137051&type=locus TAIR]||Light Signaling||Scaffold00110 (length 358202) at 120279||0.0<br />
|-<br />
| AT1G68840||ATRAV2, EDF2, ETHYLENE RESPONSE DNA BINDING FACTOR 2, RAP2.8, RAV2, RELATED TO ABI3/VP1 2, RELATED TO AP2 8, TEM2, TEMPRANILLO 2||[http://arabidopsis.org/servlets/TairObject?id=27570&type=locus TAIR]||Light Signaling||Scaffold00930 (length 110378) at 63096||5e-102<br />
|-<br />
| AT1G77080||AGAMOUS-LIKE 27, AGL27, FLM, FLOWERING LOCUS M, MADS AFFECTING FLOWERING 1, MAF1||[http://arabidopsis.org/servlets/TairObject?id=29106&type=locus TAIR]||Ambient Temperature, Vernalization||Scaffold10765 (length 2447) at 744||3e-13<br />
|-<br />
| AT1G77300||ASH1 HOMOLOG 2, ASHH2, CAROTENOID CHLOROPLAST REGULATORY1, CCR1, EARLY FLOWERING IN SHORT DAYS, EFS, LAZ2, LAZARUS 2, SDG8, SET DOMAIN GROUP 8||[http://arabidopsis.org/servlets/TairObject?id=136429&type=locus TAIR]||Vernalization||Scaffold00894 (length 114877) at 89213||1e-27<br />
|-<br />
| AT2G01570||REPRESSOR OF GA, REPRESSOR OF GA1-3 1, RGA, RGA1||[http://arabidopsis.org/servlets/TairObject?id=26549&type=locus TAIR]||Gibberellin||Scaffold01360 (length 81306) at 51382||0.0<br />
|-<br />
| AT2G06255||ELF4-L3, ELF4-LIKE 3||[http://arabidopsis.org/servlets/TairObject?id=500231553&type=locus TAIR]||Light Signaling||Scaffold00336 (length 230445) at 188137||1e-39<br />
|-<br />
| AT2G17770||ATBZIP27, BASIC REGION/LEUCINE ZIPPER MOTIF 27, BZIP27, FD PARALOG, FDP||[http://arabidopsis.org/servlets/TairObject?id=227228&type=locus TAIR]||Ambient Temperature||Scaffold00367 (length 240396) at 113139||7e-17<br />
|-<br />
| AT2G18790||HY3, OOP1, OUT OF PHASE 1, PHYB, PHYTOCHROME B||[http://arabidopsis.org/servlets/TairObject?id=26548&type=locus TAIR]||Light Signaling||Scaffold00751 (length 152548) at 83698||0.0<br />
|-<br />
| AT2G18870||VEL3, VERNALIZATION5/VIN3-LIKE 3, VIL4, VIN3-LIKE 4||[http://arabidopsis.org/servlets/TairObject?id=32249&type=locus TAIR]||Autonomous||Scaffold00396 (length 187979) at 73810||7e-19<br />
|-<br />
| AT2G18880||VEL2, VERNALIZATION5/VIN3-LIKE 2, VIL3, VIN3-LIKE 3||[http://arabidopsis.org/servlets/TairObject?id=32230&type=locus TAIR]||Autonomous||Scaffold00026 (length 499904) at 369396||6e-41<br />
|-<br />
| AT2G18915||ADAGIO 2, ADO2, LKP2, LOV KELCH PROTEIN 2||[http://arabidopsis.org/servlets/TairObject?id=500231567&type=locus TAIR]||Light Signaling||Scaffold00026 (length 499904) at 445582||0.0<br />
|-<br />
| AT2G19520||ACG1, ATMSI4, FVE, MSI4, MULTICOPY SUPPRESSOR OF IRA1 4, NFC04, NFC4||[http://arabidopsis.org/servlets/TairObject?id=33019&type=locus TAIR]||Ambient Temperature, Autonomous||Scaffold00728 (length 157708) at 8716||6e-21<br />
|-<br />
| AT2G22540||AGAMOUS-LIKE 22, AGL22, SHORT VEGETATIVE PHASE, SVP||[http://arabidopsis.org/servlets/TairObject?id=31694&type=locus TAIR]||Ambient Temperature, Vernalization||Scaffold01187 (length 101153) at 47701||2e-24<br />
|-<br />
| AT2G23380||CLF, CURLY LEAF, ICU1, INCURVATA 1, SDG1, SET1, SETDOMAIN 1, SETDOMAIN GROUP 1||[http://arabidopsis.org/servlets/TairObject?id=26534&type=locus TAIR]||Autonomous, Polycomb, Vernalization||Scaffold00354 (length 215005) at 64799||5e-41<br />
|-<br />
| AT2G25930||EARLY FLOWERING 3, ELF3, PYK20||[http://arabidopsis.org/servlets/TairObject?id=32082&type=locus TAIR]||Light Signaling||Scaffold00371 (length 223748) at 73111||6e-19<br />
|-<br />
| AT2G32950||ARABIDOPSIS THALIANA CONSTITUTIVE PHOTOMORPHOGENIC 1, ATCOP1, CONSTITUTIVE PHOTOMORPHOGENIC 1, COP1, DEETIOLATED MUTANT 340, DET340, EMB168, EMBRYO DEFECTIVE 168, FUS1, FUSCA 1||[http://arabidopsis.org/servlets/TairObject?id=34462&type=locus TAIR]||Light Signaling||Scaffold00734 (length 158513) at 142779||5e-62<br />
|-<br />
| AT2G33810||SPL3, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 3||[http://arabidopsis.org/servlets/TairObject?id=34194&type=locus TAIR]||Age||Scaffold00062 (length 451336) at 412489||2e-17<br />
|-<br />
| AT2G33835||FES1, FRIGIDA-ESSENTIAL 1||[http://arabidopsis.org/servlets/TairObject?id=500230872&type=locus TAIR]||Vernalization||Scaffold00102 (length 383343) at 88264||7e-17<br />
|-<br />
| AT2G34140||||[http://arabidopsis.org/servlets/TairObject?id=33865&type=locus TAIR]||Light Signaling||Scaffold00270 (length 246371) at 215217||7e-49<br />
|-<br />
| AT2G35670||FERTILIZATION INDEPENDENT SEED 2, FERTILIZATION-INDEPENDENT ENDOSPERM 2, FIE2, FIS2||[http://arabidopsis.org/servlets/TairObject?id=26543&type=locus TAIR]||Polycomb||Scaffold00857 (length 126644) at 55565||3e-04<br />
|-<br />
| AT2G40080||EARLY FLOWERING 4, ELF4||[http://arabidopsis.org/servlets/TairObject?id=34766&type=locus TAIR]||Light Signaling||Scaffold00254 (length 265810) at 228805||4e-24<br />
|-<br />
| AT2G42200||ATSPL9, SPL9, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 9||[http://arabidopsis.org/servlets/TairObject?id=34557&type=locus TAIR]||Age||Scaffold00691 (length 141413) at 61795||5e-21<br />
|-<br />
| AT2G43410||FPA||[http://arabidopsis.org/servlets/TairObject?id=34279&type=locus TAIR]||Autonomous||Scaffold01689 (length 75472) at 47663||4e-45<br />
|-<br />
| AT2G46340||SPA1, SUPPRESSOR OF PHYA-105 1||[http://arabidopsis.org/servlets/TairObject?id=31336&type=locus TAIR]||Light Signaling||Scaffold00734 (length 158513) at 142779||3e-69<br />
|-<br />
| AT2G46790||APRR9, ARABIDOPSIS PSEUDO-RESPONSE REGULATOR 9, PRR9, PSEUDO-RESPONSE REGULATOR 9, TL1, TOC1-LIKE PROTEIN 1||[http://arabidopsis.org/servlets/TairObject?id=32227&type=locus TAIR]||Light Signaling||Scaffold00001 (length 1030549) at 322801||1e-36<br />
|-<br />
| AT2G46830||ATCCA1, CCA1, CIRCADIAN CLOCK ASSOCIATED 1||[http://arabidopsis.org/servlets/TairObject?id=32221&type=locus TAIR]||Light Signaling||Scaffold00140 (length 354209) at 234299||7e-20<br />
|-<br />
| AT2G47700||RED AND FAR-RED INSENSITIVE 2, RFI2||[http://arabidopsis.org/servlets/TairObject?id=32070&type=locus TAIR]||Light Signaling||Scaffold01059 (length 101143) at 96557||1e-19<br />
|-<br />
| AT3G02380||ATCOL2, B-BOX DOMAIN PROTEIN 3, BBX3, COL2, CONSTANS-LIKE 2||[http://arabidopsis.org/servlets/TairObject?id=35635&type=locus TAIR]||Light Signaling||Scaffold01843 (length 51900) at 40767||3e-48<br />
|-<br />
| AT3G03450||RGA-LIKE 2, RGL2||[http://arabidopsis.org/servlets/TairObject?id=40021&type=locus TAIR]||Gibberellin||Scaffold00134 (length 346346) at 174722||0.0<br />
|-<br />
| AT3G04610||FLK, FLOWERING LOCUS KH DOMAIN||[http://arabidopsis.org/servlets/TairObject?id=37455&type=locus TAIR]||Autonomous||Scaffold01384 (length 81068) at 28309||4e-29<br />
|-<br />
| AT3G05120||ATGID1A, GA INSENSITIVE DWARF1A, GID1A||[http://arabidopsis.org/servlets/TairObject?id=39457&type=locus TAIR]||Gibberellin||Scaffold00101 (length 425332) at 398762||4e-175<br />
|-<br />
| AT3G07650||B-BOX DOMAIN PROTEIN 7, BBX7, COL9, CONSTANS-LIKE 9||[http://arabidopsis.org/servlets/TairObject?id=38550&type=locus TAIR]||Light Signaling||Scaffold00832 (length 123094) at 89599||1e-55<br />
|-<br />
| AT3G10390||FLD, FLOWERING LOCUS D||[http://arabidopsis.org/servlets/TairObject?id=35869&type=locus TAIR]||Ambient Temperature, Autonomous||Scaffold00232 (length 253418) at 139565||0.0<br />
|-<br />
| AT3G12810||CHR13, PHOTOPERIOD-INDEPENDENT EARLY FLOWERING 1, PIE1, SRCAP||[http://arabidopsis.org/servlets/TairObject?id=37964&type=locus TAIR]||Vernalization||Scaffold00147 (length 345970) at 30164||0.0<br />
|-<br />
| AT3G15270||SPL5, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 5||[http://arabidopsis.org/servlets/TairObject?id=37842&type=locus TAIR]||Age||Scaffold00105 (length 392037) at 147284||5e-16<br />
|-<br />
| AT3G15354||SPA1-RELATED 3, SPA3||[http://arabidopsis.org/servlets/TairObject?id=500230681&type=locus TAIR]||Light Signaling||Scaffold00734 (length 158513) at 143450||1e-144<br />
|-<br />
| AT3G18990||REDUCED VERNALIZATION RESPONSE 1, REM39, REPRODUCTIVE MERISTEM 39, VRN1||[http://arabidopsis.org/servlets/TairObject?id=37620&type=locus TAIR]||Vernalization||Scaffold00811 (length 108354) at 96661||2e-25<br />
|-<br />
| AT3G20740||FERTILIZATION-INDEPENDENT ENDOSPERM, FERTILIZATION-INDEPENDENT ENDOSPERM 1, FIE, FIE1, FIS3||[http://arabidopsis.org/servlets/TairObject?id=38691&type=locus TAIR]||Autonomous, Polycomb, Vernalization||Scaffold01670 (length 60304) at 9836||5e-20<br />
|-<br />
| AT3G21320||||[http://arabidopsis.org/servlets/TairObject?id=39170&type=locus TAIR]||Light Signaling||Scaffold00509 (length 192554) at 181887||1e-21<br />
|-<br />
| AT3G24440||VERNALIZATION 5, VIL1, VIN3-LIKE 1, VRN5||[http://arabidopsis.org/servlets/TairObject?id=39196&type=locus TAIR]||Autonomous, Vernalization||Scaffold00396 (length 187979) at 73795||2e-69<br />
|-<br />
| AT3G25730||EDF3, ETHYLENE RESPONSE DNA BINDING FACTOR 3||[http://arabidopsis.org/servlets/TairObject?id=37641&type=locus TAIR]||Light Signaling||Scaffold00930 (length 110378) at 63060||5e-100<br />
|-<br />
| AT3G33520||ACTIN-RELATED PROTEIN 6, ARP6, ATARP6, EARLY IN SHORT DAYS 1, ESD1, SUF3, SUPPRESSOR OF FRI 3||[http://arabidopsis.org/servlets/TairObject?id=40458&type=locus TAIR]||Ambient Temperature, Vernalization||Scaffold00246 (length 286612) at 268521||1e-53<br />
|-<br />
| AT3G46640||LUX, LUX ARRHYTHMO, PCL1, PHYTOCLOCK 1||[http://arabidopsis.org/servlets/TairObject?id=35747&type=locus TAIR]||Light Signaling||Scaffold01150 (length 88293) at 80272||3e-34<br />
|-<br />
| AT3G47500||CDF3, CYCLING DOF FACTOR 3||[http://arabidopsis.org/servlets/TairObject?id=36439&type=locus TAIR]||Light Signaling||Scaffold00079 (length 471015) at 68175||1e-85<br />
|-<br />
| AT4G00650||FLA, FLOWERING LOCUS A, FRI, FRIGIDA||[http://arabidopsis.org/servlets/TairObject?id=128299&type=locus TAIR]||Vernalization||Scaffold00039 (length 505275) at 216632||4e-50<br />
|-<br />
| AT4G02020||EZA1, SDG10, SET DOMAIN-CONTAINING PROTEIN 10, SWINGER, SWN||[http://arabidopsis.org/servlets/TairObject?id=129104&type=locus TAIR]||Autonomous, Polycomb, Vernalization||Scaffold00354 (length 215005) at 64799||2e-48<br />
|-<br />
| AT4G02560||LD, LUMINIDEPENDENS||[http://arabidopsis.org/servlets/TairObject?id=26564&type=locus TAIR]||Autonomous||Scaffold00002 (length 840149) at 158601||4e-28<br />
|-<br />
| AT4G08920||ATCRY1, BLU1, BLUE LIGHT UNINHIBITED 1, CRY1, CRYPTOCHROME 1, ELONGATED HYPOCOTYL 4, HY4, OOP2, OUT OF PHASE 2||[http://arabidopsis.org/servlets/TairObject?id=129943&type=locus TAIR]||Light Signaling||Scaffold00331 (length 261439) at 124817||4e-128<br />
|-<br />
| AT4G11110||SPA1-RELATED 2, SPA2||[http://arabidopsis.org/servlets/TairObject?id=129633&type=locus TAIR]||Light Signaling||Scaffold01034 (length 107107) at 19205||2e-62<br />
|-<br />
| AT4G11880||AGAMOUS-LIKE 14, AGL14||[http://arabidopsis.org/servlets/TairObject?id=129748&type=locus TAIR]||Vernalization||Scaffold00249 (length 258199) at 131012||2e-29<br />
|-<br />
| AT4G16250||PHYD, PHYTOCHROME D||[http://arabidopsis.org/servlets/TairObject?id=26567&type=locus TAIR]||Light Signaling||Scaffold00751 (length 152548) at 83707||0.0<br />
|-<br />
| AT4G16280||FCA||[http://arabidopsis.org/servlets/TairObject?id=128853&type=locus TAIR]||Ambient Temperature, Autonomous||Scaffold00104 (length 360147) at 120318||5e-13<br />
|-<br />
| AT4G16845||REDUCED VERNALIZATION RESPONSE 2, VRN2||[http://arabidopsis.org/servlets/TairObject?id=228106&type=locus TAIR]||Autonomous, Polycomb, Vernalization||Scaffold00857 (length 126644) at 55203||3e-07<br />
|-<br />
| AT4G18130||PHYE, PHYTOCHROME E||[http://arabidopsis.org/servlets/TairObject?id=26568&type=locus TAIR]||Light Signaling||Scaffold00751 (length 152548) at 83749||0.0<br />
|-<br />
| AT4G20370||TSF, TWIN SISTER OF FT||[http://arabidopsis.org/servlets/TairObject?id=26553&type=locus TAIR]||Ambient Temperature||Scaffold00357 (length 260075) at 58807||1e-33<br />
|-<br />
| AT4G22950||AGAMOUS-LIKE 19, AGL19, GL19||[http://arabidopsis.org/servlets/TairObject?id=128336&type=locus TAIR]||Vernalization||Scaffold00249 (length 258199) at 131012||4e-28<br />
|-<br />
| AT4G24540||AGAMOUS-LIKE 24, AGL24||[http://arabidopsis.org/servlets/TairObject?id=127586&type=locus TAIR]||Vernalization||Scaffold01187 (length 101153) at 47701||2e-25<br />
|-<br />
| AT4G26000||PEP, PEPPER||[http://arabidopsis.org/servlets/TairObject?id=127403&type=locus TAIR]||Vernalization||Scaffold00021 (length 527983) at 157278||3e-29<br />
|-<br />
| AT4G30200||VEL1, VERNALIZATION5/VIN3-LIKE 1, VIL2, VIN3-LIKE 2||[http://arabidopsis.org/servlets/TairObject?id=128580&type=locus TAIR]||Autonomous, Vernalization||Scaffold00026 (length 499904) at 369417||7e-64<br />
|-<br />
| AT4G34530||CIB1, CRYPTOCHROME-INTERACTING BASIC-HELIX-LOOP-HELIX 1||[http://arabidopsis.org/servlets/TairObject?id=130033&type=locus TAIR]||Light Signaling||Scaffold01322 (length 99420) at 82955||2e-29<br />
|-<br />
| AT4G35900||ATBZIP14, FD, FD-1||[http://arabidopsis.org/servlets/TairObject?id=128068&type=locus TAIR]||Ambient Temperature||Scaffold00367 (length 240396) at 113139||1e-16<br />
|-<br />
| AT5G02810||APRR7, PRR7, PSEUDO-RESPONSE REGULATOR 7||[http://arabidopsis.org/servlets/TairObject?id=131538&type=locus TAIR]||Light Signaling||Scaffold00125 (length 356885) at 276518||1e-33<br />
|-<br />
| AT5G03840||TERMINAL FLOWER 1, TFL1||[http://arabidopsis.org/servlets/TairObject?id=131459&type=locus TAIR]||Ambient Temperature||Scaffold00181 (length 337602) at 12825||1e-28<br />
|-<br />
| AT5G08330||CCA1 HIKING EXPEDITION, CHE, TRANSCRIPTION FACTOR TCP21, TCP21||[http://www.uniprot.org/uniprot/Q9FTA2 UniProtKB]||Light Signaling||Scaffold00993 (length 109486) at 294||5e-27<br />
|-<br />
| AT5G10140||AGAMOUS-LIKE 25, AGL25, FLC, FLF, FLOWERING LOCUS C, FLOWERING LOCUS F||[http://arabidopsis.org/servlets/TairObject?id=136002&type=locus TAIR]||Ambient Temperature, Vernalization||Scaffold10765 (length 2447) at 708||8e-22<br />
|-<br />
| AT5G11530||EMBRYONIC FLOWER 1, EMF1||[http://arabidopsis.org/servlets/TairObject?id=130620&type=locus TAIR]||Polycomb||Scaffold00253 (length 240879) at 11069||1e-06<br />
|-<br />
| AT5G13480||FY||[http://arabidopsis.org/servlets/TairObject?id=136108&type=locus TAIR]||Autonomous||Scaffold00166 (length 328538) at 74796||2e-43<br />
|-<br />
| AT5G15840||B-BOX DOMAIN PROTEIN 1, BBX1, CO, CONSTANS, FG||[http://arabidopsis.org/servlets/TairObject?id=130492&type=locus TAIR]||Light Signaling||Scaffold01843 (length 51900) at 40767||3e-29<br />
|-<br />
| AT5G15850||ATCOL1, B-BOX DOMAIN PROTEIN 2, BBX2, COL1, CONSTANS-LIKE 1||[http://arabidopsis.org/servlets/TairObject?id=130495&type=locus TAIR]||Light Signaling||Scaffold01843 (length 51900) at 40767||5e-44<br />
|-<br />
| AT5G17690||ATLHP1, LHP1, LIKE HETEROCHROMATIN PROTEIN 1, TERMINAL FLOWER 2, TFL2||[http://arabidopsis.org/servlets/TairObject?id=134923&type=locus TAIR]||Polycomb||Scaffold00696 (length 140617) at 128983||7e-13<br />
|-<br />
| AT5G23150||ENHANCER OF AG-4 2, HUA2||[http://arabidopsis.org/servlets/TairObject?id=135220&type=locus TAIR]||Vernalization||Scaffold00686 (length 145647) at 102689||5e-42<br />
|-<br />
| AT5G24470||APRR5, PRR5, PSEUDO-RESPONSE REGULATOR 5||[http://arabidopsis.org/servlets/TairObject?id=135985&type=locus TAIR]||Light Signaling||Scaffold00001 (length 1030549) at 322798||3e-40<br />
|-<br />
| AT5G24930||ATCOL4, B-BOX DOMAIN PROTEIN 5, BBX5, COL4, CONSTANS-LIKE 4||[http://arabidopsis.org/servlets/TairObject?id=131285&type=locus TAIR]||Light Signaling||Scaffold11225 (length 3326) at 2816||8e-23<br />
|-<br />
| AT5G35840||PHYC, PHYTOCHROME C||[http://arabidopsis.org/servlets/TairObject?id=133466&type=locus TAIR]||Light Signaling||Scaffold01070 (length 102706) at 75395||0.0<br />
|-<br />
| AT5G37055||ATSWC6, SEF, SERRATED LEAVES AND EARLY FLOWERING||[http://arabidopsis.org/servlets/TairObject?id=500231974&type=locus TAIR]||Vernalization||Scaffold00925 (length 141061) at 38143||4e-29<br />
|-<br />
| AT5G39660||CDF2, CYCLING DOF FACTOR 2||[http://arabidopsis.org/servlets/TairObject?id=133414&type=locus TAIR]||Light Signaling||Scaffold00651 (length 145047) at 19066||1e-90<br />
|-<br />
| AT5G42790||ARS5, ARSENIC TOLERANCE 5, ATPSM30, PAF1, PROTEASOME ALPHA SUBUNIT F1||[http://arabidopsis.org/servlets/TairObject?id=133505&type=locus TAIR]||Vernalization||Scaffold00528 (length 197283) at 110933||5e-64<br />
|-<br />
| AT5G51230||ATEMF2, CYR1, CYTOKININ RESISTANT 1, EMBRYONIC FLOWER 2, EMF2, VEF2||[http://arabidopsis.org/servlets/TairObject?id=134952&type=locus TAIR]||Polycomb||Scaffold00857 (length 126644) at 44887||9e-19<br />
|-<br />
| AT5G57360||ADAGIO 1, ADO1, FKF1-LIKE PROTEIN 2, FKL2, LKP1, LOV KELCH PROTEIN 1, ZEITLUPE, ZTL||[http://arabidopsis.org/servlets/TairObject?id=134481&type=locus TAIR]||Light Signaling||Scaffold00026 (length 499904) at 445597||0.0<br />
|-<br />
| AT5G57380||VERNALIZATION INSENSITIVE 3, VIN3||[http://arabidopsis.org/servlets/TairObject?id=134483&type=locus TAIR]||Autonomous, Vernalization||Scaffold00026 (length 499904) at 369405||3e-48<br />
|-<br />
| AT5G57660||ATCOL5, B-BOX DOMAIN PROTEIN 6, BBX6, COL5, CONSTANS-LIKE 5||[http://arabidopsis.org/servlets/TairObject?id=134422&type=locus TAIR]||Light Signaling||Scaffold11225 (length 3326) at 2816||1e-25<br />
|-<br />
| AT5G58230||ARABIDOPSIS MULTICOPY SUPRESSOR OF IRA1, ATMSI1, MATERNAL EFFECT EMBRYO ARREST 70, MEE70, MSI1, MULTICOPY SUPRESSOR OF IRA1||[http://arabidopsis.org/servlets/TairObject?id=132921&type=locus TAIR]||Autonomous, Polycomb, Vernalization||Scaffold00615 (length 179658) at 161081||2e-61<br />
|-<br />
| AT5G60100||APRR3, PRR3, PSEUDO-RESPONSE REGULATOR 3||[http://arabidopsis.org/servlets/TairObject?id=133317&type=locus TAIR]||Light Signaling||Scaffold02075 (length 43325) at 14139||3e-25<br />
|-<br />
| AT5G61380||APRR1, ATTOC1, PRR1, PSEUDO-RESPONSE REGULATOR 1, TIMING OF CAB EXPRESSION 1, TOC1||[http://arabidopsis.org/servlets/TairObject?id=133196&type=locus TAIR]||Light Signaling||Scaffold00753 (length 123742) at 70468||2e-47<br />
|-<br />
| AT5G62430||CDF1, CYCLING DOF FACTOR 1||[http://arabidopsis.org/servlets/TairObject?id=131911&type=locus TAIR]||Light Signaling||Scaffold01102 (length 99830) at 51435||1e-59<br />
|-<br />
| AT5G65050||AGAMOUS-LIKE 31, AGL31, MADS AFFECTING FLOWERING 2, MAF2||[http://arabidopsis.org/servlets/TairObject?id=135154&type=locus TAIR]||Ambient Temperature, Vernalization||Scaffold10765 (length 2447) at 723||4e-20<br />
|-<br />
| AT5G65060||AGAMOUS-LIKE 70, AGL70, FCL3, MADS AFFECTING FLOWERING 3, MAF3||[http://arabidopsis.org/servlets/TairObject?id=130633&type=locus TAIR]||Ambient Temperature, Vernalization||Scaffold10765 (length 2447) at 639||7e-15<br />
|-<br />
| AT5G65070||AGAMOUS-LIKE 69, AGL69, FCL4, MADS AFFECTING FLOWERING 4, MAF4||[http://arabidopsis.org/servlets/TairObject?id=130634&type=locus TAIR]||Ambient Temperature, Vernalization||Scaffold10765 (length 2447) at 723||6e-20<br />
|-<br />
| AT5G65080||AGAMOUS-LIKE 68, AGL68, MADS AFFECTING FLOWERING 5, MAF5||[http://arabidopsis.org/servlets/TairObject?id=130635&type=locus TAIR]||Ambient Temperature, Vernalization||Scaffold10765 (length 2447) at 699||1e-18<br />
|}<br />
<br />
<br />
==References==<br />
*Amasino RM. Seasonal and developmental timing of flowering. ''Plant J,'' '''61,''' 1001-1013 (2010).<br />
*Amasino RM. Vernalization and flowering time. ''Curr Opin Plant Biol,'' '''16,''' 154–158 (2005).<br />
*Ballerini ES, Kramer EM. Environmental and molecular analysis of the floral transition in the lower eudicot Aquilegia formosa. ''Evodevo,'' '''2,''' 1-20 (2011).<br />
*Bäurle I, Dean C. The timing of developmental transitions in plants. ''Cell,'' '''125,''' 655-664 (2006).<br />
*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).<br />
*Farrona S, Coupland G, Turck F. The impact of chromatin regulation on the floral transition. ''Semin Cell Dev Biol,'' '''19,''' 560-573 (2008).<br />
*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).<br />
*Fornara F, de Montaigu A, Coupland G. SnapShot: Control of flowering in Arabidopsis. ''Cell,'' '''141,''' 550-550.e2 (2010).<br />
*Henderson IR, Dean C. Control of Arabidopsis flowering: the chill before the bloom. ''Development,'' '''131,''' 3829-3838 (2004).<br />
*He Y, Amasino RM. Role of chromatin modification in flowering-time control. ''Trends Plant Sci,'' '''10,''' 30-35 (2005).<br />
*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).<br />
*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).<br />
*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).<br />
*Jung CH, Wong CE, Singh MB, Bhalla PL. Comparative genomic analysis of soybean flowering genes. ''PLoS One,'' '''7,''' e38250 (2012).<br />
*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).<br />
*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).<br />
*Liu C, Thong Z, Yu H. Coming into bloom: the specification of floral meristems. ''Development,'' '''136,''' 3379-3391 (2009).<br />
*Posé D, Yant L, Schmid M. The end of innocence: flowering networks explode in complexity. ''Curr Opin Plant Biol'' '''15,''' 45-50 (2012).<br />
*Schneitz K, Balasubramanian S. Floral Meristems. ''eLS'' (John Wiley & Sons Ltd, Chichester, 2009).<br />
*SSR Tool. ''Genome Database for Vaccinium.''<br />
*Sung ZR, Chen L, Moon YH, Lertpiriyapong K. Mechanisms of floral repression in Arabidopsis. ''Curr Opin Plant Biol,'' '''6,''' 29-35 (2003).<br />
*Taiz L, Zeiger E. ''Plant Physiology Fifth Edition Ch. 20'' (Sinauer Associates, Sunderland, MA, 2010).<br />
*Turck F, Adrian J. A lesson in complexity: regulation of FLOWERING LOCUS T. ''Max Planck Institute for Plant Breeding Research.''<br />
*UniProt Consortium. Reorganizing the protein space at the Universal Protein Resource (UniProt). ''Nucleic Acids Res,'' '''40,''' D71-D75 (2012).<br />
*Wellmer F, Riechmann JL. Gene networks controlling the initiation of flower development. ''Trends Genet,'' '''26,''' 519-527 (2010).<br />
*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).<br />
*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).<br />
*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).</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=Time_of_bloom&diff=19286Time of bloom2021-08-11T21:19:13Z<p>Laheyer: </p>
<hr />
<div>Austin Mudd - Spring 2013<br />
<br/>Shortened URL: http://goo.gl/zuTkP<br />
<br />
<br />
__TOC__<br />
<br />
==Introduction to Flowering==<br />
====The Process of Flowering====<br />
*Flowering is the "switch from vegetative growth (the production of stems and leaves) to reproductive growth (the production of flowers)" ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010065 Higgins ''et al.'', 2010])<br />
*The “shoot apical meristem starts to produce flowers instead of leaves” ([http://www.sciencedirect.com/science/article/pii/S0092867410004411 Fornara ''et al.'', 2010])<br />
*Occurs “when conditions for pollination and seed development are optimal and consequently most plants restrict flowering to a specific time of year” ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010065 Higgins ''et al.'', 2010])<br />
*”The genes and molecular mechanisms controlling flowering have been extensively studied in the model dicot <i>Arabidopsis thaliana</i>” ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010065 Higgins ''et al.'', 2010])<br />
*In <i>Arabidopsis thaliana</i>, “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” ([http://www.sciencedirect.com/science/article/pii/S0092867410004411 Fornara ''et al.'', 2010])<br />
<br />
[[File:Max_Planck_Institute_Pathway.png|thumb|right|The major pathways in the timing of flowering from Turck and Adrian at the [http://www.mpipz.mpg.de/305695/Project_1 Max Planck Institute for Plant Breeding Research]; permission granted]]<br />
====The Timing of Flowering====<br />
*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.” ([http://www.sciencedirect.com/science/article/pii/S0092867410004411 Fornara ''et al.'', 2010])<br />
*These “pathways converge to regulate a small number of ‘floral integrator genes,’ ... which govern flowering time by merging signals from multiple pathways” ([http://www.sciencedirect.com/science/article/pii/S0092867410004411 Fornara ''et al.'', 2010])<br />
<br />
====The Importance of Flowering====<br />
*”Flowering is one of the most important agronomic traits influencing crop yield” ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012])<br />
*”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” ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010065 Higgins ''et al.'', 2010])<br />
*“Adaptation to different environments and practices has been achieved by manipulation of flowering time responses” ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010065 Higgins ''et al.'', 2010])<br />
*The study of flowering is ”critical for the breeding of climate change resilient crop varieties” ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012])<br />
*Flowering is “an excellent system for comparison between and within domestic and wild species” ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010065 Higgins ''et al.'', 2010])<br />
<br />
<br />
==Pathways Controlling Flowering==<br />
====Age Pathway====<br />
*"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" ([http://www.plantcell.org/content/early/2012/08/29/tpc.112.101014.full.pdf+html Yu ''et al.'', 2012])<br />
*5 <i>Arabidopsis</i> genes are involved in the age pathway: SPL3, SPL4, SPL5, SPL9, SPL10 ([http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2010.04148.x/pdf/ Amasino, 2010])<br />
<br />
====Ambient Temperature Pathway====<br />
*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" ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012])<br />
*16 <i>Arabidopsis</i> genes are involved in the ambient temperature pathway: AGL31, ATARP6, ATBZIP27, FCA, FD, FLC, FLD, FT, FVE, MAF1, MAF3, MAF4, MAF5, SVP, TFL1, TSF ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012])<br />
<br />
====Autonomous Pathway====<br />
*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 ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012])<br />
*17 <i>Arabidopsis</i> genes are involved in the autonomous pathway: CLF, FCA, FIE1, FLD, FLK, FPA, FVE, FY, LD, MSI1, SWN, VEL1, VEL2, VEL3, VIN3, VRN2, VRN5 ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012]) <br />
<br />
====Gibberellin Pathway====<br />
*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" ([http://www.plantcell.org/content/early/2012/08/29/tpc.112.101014.full.pdf+html Yu ''et al.'', 2012])<br />
*5 <i>Arabidopsis</i> genes are involved in the gibberellin pathway: GAI, GID1, RGA, RGL1, RGL2 ([http://www.plantcell.org/content/early/2012/08/29/tpc.112.101014.full.pdf+html Yu ''et al.'', 2012])<br />
<br />
====Light Signaling Pathway====<br />
*"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" ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012])<br />
*48 <i>Arabidopsis</i> 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 ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012])<br />
<br />
====Polycomb Pathway====<br />
*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) ([http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002512 Kim ''et al.'', 2012])<br />
*10 <i>Arabidopsis</i> genes are involved in the polycomb pathway: CLF, EMF1, EMF2, FIE1, FIS2, LHP1, MEA, MSI1, SWN, VRN2 ([http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002512 Kim ''et al.'', 2012])<br />
<br />
====Vernalization Pathway====<br />
*The vernalization pathway is the response to "prolonged periods of low temperature [that are required] to initiate flowering" ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012])<br />
*32 <i>Arabidopsis</i> 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 ([http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012])<br />
<br />
<br />
==Gallery of <i>Arabidopsis</i> Flowering Pathways==<br />
<br />
<gallery widths="102px" heights="102px" perrow="6"><br />
File:Izawa_Pathway.jpeg|Pathway from Izawa ''et al.'', 2003|[http://www.sciencedirect.com/science/article/pii/S1369526603000141 Izawa ''et al.'', 2003]; permission pending<br />
File:Sung_Pathway.gif|[http://www.sciencedirect.com/science/article/pii/S1369526602000146 Sung ''et al.'', 2003]; permission granted<br />
File:Boss_Pathway.gif|[http://www.plantcell.org/content/16/suppl_1/S18/F2.expansion Boss ''et al.'', 2004]; permission granted<br />
File:Boss_Pathway_2.jpeg|[http://www.plantcell.org/content/16/suppl_1/S18/F3.expansion Boss ''et al.'', 2004]; permission granted<br />
File:Henderson_and_Dean_Pathway.jpeg|[http://dev.biologists.org/content/131/16/3829/F1.expansion.html Henderson and Dean, 2004]; permission granted<br />
File:Amasino_Pathway.jpeg|[http://www.sciencedirect.com/science/article/pii/S0958166905000273 Amasino, 2005]; permission granted<br />
File:He_and_Amasino_Pathway.jpeg|[http://www.sciencedirect.com/science/article/pii/S1360138504002705 He and Amasino, 2005]; permission granted<br />
File:Yamaguchi_Pathway.jpeg|[http://pcp.oxfordjournals.org/content/46/8/1175/F7.expansion Yamaguchi ''et al.'', 2005]; permission pending<br />
File:Baurle_and_Dean_Pathway.jpeg|[http://www.sciencedirect.com/science/article/pii/S009286740600571X Bäurle and Dean, 2006]; permission granted<br />
File:Farrona_Pathway.jpeg|[http://www.sciencedirect.com/science/article/pii/S1084952108000566 Farrona ''et al.'', 2008]; permission granted<br />
File:Farrona_Pathway_2.jpeg|[http://www.sciencedirect.com/science/article/pii/S1084952108000566 Farrona ''et al.'', 2008]; permission granted<br />
File:Amasino_Pathway_2.png|[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2010.04148.x/pdf/ Amasino, 2010]; permission granted<br />
File:Higgins_Pathway.jpg|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010065 Higgins ''et al.'', 2010]; permission granted<br />
File:Kim_and_Sung_Pathway.jpeg|[http://www.pnas.org/content/107/39/17029/F6.expansion.html Kim and Sung, 2010]; permission pending<br />
File:Taiz_and_Zeiger_Pathway.jpeg|[http://5e.plantphys.net/article.php?ch=1&id=375 Taiz and Zeiger, 2010]; permission pending<br />
File:Ballerini_and_Kramer_Pathway.png|[http://dash.harvard.edu/bitstream/handle/1/4903810/Ballerini%20%26%20Kramer%202011.pdf?sequence=1 Ballerini and Kramer, 2011]; permission granted<br />
File:Ferrier_Pathway.jpeg|[http://www.sciencedirect.com/science/article/pii/S0958166910002284 Ferrier ''et al.'', 2011]; permission pending<br />
File:Zhang_Pathway.png|[http://www.biomedcentral.com/1471-2164/12/63 Zhang ''et al.'', 2011]; permission granted<br />
File:Jung_Pathway.jpg|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012]; permission pending<br />
</gallery><br />
<br />
Additional figures:<br />
*[http://dev.biologists.org/content/136/20/3379/F3.expansion.html Figure 3 from Liu ''et al.'', 2009]<br />
*[http://www.els.net/WileyCDA/ElsArticle/refId-a0002053.html Figure 1 from Schneitz and Balasubramanian, 2009]<br />
*[http://www.sciencedirect.com/science/article/pii/S0168952510001873 Figure 1 from Wellmer and Riechmann, 2010]<br />
*[http://www.sciencedirect.com/science/article/pii/S1369526611001440 Figure 1 from Posé ''et al.'', 2012]<br />
<br />
<br />
==Methods==<br />
====Finding Genes====<br />
*I examined a variety of journal articles related to time of flowering in <i>Arabidopsis thaliana</i> and found a number of pathways related to flowering (see the gallery above). I came across a genomic analysis of soybean by [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012]. In this paper, they listed the "183 <i>Arabidopsis</i> genes that are known to take part in flowering regulatory pathways [taken] from previous studies." These 183 genes, plus "24 additional <i>Arabidopsis</i> 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 [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012] can be viewed here: [[File:Jung 207 Arabidopsis Flowering Genes.pdf]].<br />
*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.<br />
*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 [http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2010.04148.x/pdf/ Amasino, 2010], [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012], [http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002512 Kim ''et al.'', 2012], and [http://www.plantcell.org/content/early/2012/08/29/tpc.112.101014.full.pdf+html Yu ''et al.'', 2012].<br />
*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." ([http://www.sciencedirect.com/science/article/pii/S0092867410004411 Fornara ''et al.'', 2010])<br />
<br />
====Finding SSRs====<br />
*A local database of the blueberry genome was created using the following coding:<br />
<PRE>./bin/makeblastdb -in BlueberryGenome.txt -input_type fasta -dbtype nucl -title blueberry_Genome</PRE><br />
*Amino acid sequences for all <i>Arabidopsis</i> genes were taken from [http://www.arabidopsis.org/index.jsp 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:<br />
<PRE>{ echo bin/tblastn -query AASequence.txt -db BlueberryGenome.txt; bin/tblastn -query <br />
AASequence.txt -db BlueberryGenome.txt; } >> AAOutput.txt</PRE><br />
*For each gene result, the best match was presumed to be the ortholog of the <i>Arabidopsis</i> gene in <i>Vaccinium corymbosum</i>. 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 <i>Vitis vinifera</i> ortholog of the <i>Arabidopsis</i> gene from [http://www.uniprot.org/uniprot/?query=organism%3A%22Vitis+vinifera+%5B29760%5D%22&sort=score UniProtKB (UniProt Consortium, 2012)] nomenclature search.<br />
*SSRs were determined by importing the best match scaffold into the [http://www.vaccinium.org/cgi-bin/vaccinium_ssr SSR Tool] at the [http://www.vaccinium.org/ Genome Database for Vaccinium]. Three di/trinucleotide SSRs near the gene location on the scaffold were chosen for each gene.<br />
<br />
<br />
==SSR Results==<br />
All SSR results can be viewed on the [[Time of bloom SSR Results]] page. An abbreviated listing of the results is included below.<br />
<br/>[[File:Flowering_SSR_Results_Table.png]]<br />
<br />
<br />
==Flowering Genes Of Interest==<br />
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." ([http://www.sciencedirect.com/science/article/pii/S0092867410004411 Fornara ''et al.'', 2010])<br />
<br />
{| class="wikitable sortable"<br />
|-<br />
! <i>Arabidopsis</i> Locus !! Other Names !! AA Source !! Pathway !! width="150px" |Top Hit ''Vaccinium'' Scaffold !! E Value<br />
|-<br />
| AT1G01060||LATE ELONGATED HYPOCOTYL, LATE ELONGATED HYPOCOTYL 1, LHY, LHY1||[http://arabidopsis.org/servlets/TairObject?id=137165&type=locus TAIR]||Light Signaling||Scaffold00140 (length 354209) at 234299||2e-19<br />
|-<br />
| AT1G02580||EMB173, EMBRYO DEFECTIVE 173, FERTILIZATION INDEPENDENT SEED 1, FIS1, MEA, MEDEA, SDG5, SET DOMAIN-CONTAINING PROTEIN 5||[http://arabidopsis.org/servlets/TairObject?id=136450&type=locus TAIR]||Polycomb||Scaffold00354 (length 215005) at 64805||4e-17<br />
|-<br />
| AT1G04400||AT-PHH1, ATCRY2, CRY2, CRYPTOCHROME 2, FHA, PHH1||[http://arabidopsis.org/servlets/TairObject?id=28374&type=locus TAIR]||Light Signaling||Scaffold00649 (length 159319) at 28296||1e-119<br />
|-<br />
| AT1G09570||ELONGATED HYPOCOTYL 8, FAR RED ELONGATED 1, FAR RED ELONGATED HYPOCOTYL 2, FHY2, FRE1, HY8, PHYA, PHYTOCHROME A||[http://arabidopsis.org/servlets/TairObject?id=27545&type=locus TAIR]||Light Signaling||Scaffold03861 (length 7403) at 3771||0.0<br />
|-<br />
| AT1G13260||EDF4, ETHYLENE RESPONSE DNA BINDING FACTOR 4, RAV1, RELATED TO ABI3/VP1 1||[http://arabidopsis.org/servlets/TairObject?id=137721&type=locus TAIR]||Light Signaling||Scaffold00930 (length 110378) at 63069||1e-103<br />
|-<br />
| AT1G14920||GAI, GIBBERELLIC ACID INSENSITIVE, RESTORATION ON GROWTH ON AMMONIA 2, RGA2||[http://arabidopsis.org/servlets/TairObject?id=26612&type=locus TAIR]||Gibberellin||Scaffold01360 (length 81306) at 51382||0.0<br />
|-<br />
| AT1G20330||COTYLEDON VASCULAR PATTERN 1, CVP1, FRILL1, FRL1, SMT2, STEROL METHYLTRANSFERASE 2||[http://arabidopsis.org/servlets/TairObject?id=27665&type=locus TAIR]||Vernalization||Scaffold02142 (length 46662) at 24743||9e-06<br />
|-<br />
| AT1G22770||FB, GI, GIGANTEA||[http://arabidopsis.org/servlets/TairObject?id=136959&type=locus TAIR]||Light Signaling||Scaffold00100 (length 346620) at 198329||0.0<br />
|-<br />
| AT1G25560||EDF1, ETHYLENE RESPONSE DNA BINDING FACTOR 1, TEM1, TEMPRANILLO 1||[http://arabidopsis.org/servlets/TairObject?id=30061&type=locus TAIR]||Light Signaling||Scaffold00930 (length 110378) at 63096||3e-99<br />
|-<br />
| AT1G26790||||[http://arabidopsis.org/servlets/TairObject?id=137136&type=locus TAIR]||Light Signaling||Scaffold00079 (length 471015) at 69048||6e-33<br />
|-<br />
| AT1G27370||SPL10, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 10||[http://arabidopsis.org/servlets/TairObject?id=28131&type=locus TAIR]||Age||Scaffold00127 (length 336847) at 165806||5e-33<br />
|-<br />
| AT1G29160||||[http://arabidopsis.org/servlets/TairObject?id=29883&type=locus TAIR]||Light Signaling||Scaffold00270 (length 246371) at 215229||4e-50<br />
|-<br />
| AT1G30970||SUF4, SUPPRESSOR OF FRIGIDA4||[http://arabidopsis.org/servlets/TairObject?id=28096&type=locus TAIR]||Vernalization||Scaffold00348 (length 210978) at 75279||1e-15<br />
|-<br />
| AT1G31814||FRIGIDA LIKE 2, FRL2||[http://arabidopsis.org/servlets/TairObject?id=226970&type=locus TAIR]||Vernalization||Scaffold00289 (length 259591) at 150896||2e-19<br />
|-<br />
| AT1G47250||20S PROTEASOME ALPHA SUBUNIT F2, PAF2||[http://arabidopsis.org/servlets/TairObject?id=30983&type=locus TAIR]||Vernalization||Scaffold00528 (length 197283) at 110933||3e-64<br />
|-<br />
| AT1G53090||SPA1-RELATED 4, SPA4||[http://arabidopsis.org/servlets/TairObject?id=31031&type=locus TAIR]||Light Signaling||Scaffold00734 (length 158513) at 143450||3e-129<br />
|-<br />
| AT1G53160||FLORAL TRANSITION AT THE MERISTEM6, FTM6, SPL4, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 4||[http://arabidopsis.org/servlets/TairObject?id=27097&type=locus TAIR]||Age||Scaffold00062 (length 451336) at 412489||1e-15<br />
|-<br />
| AT1G65480||FLOWERING LOCUS T, FT||[http://arabidopsis.org/servlets/TairObject?id=30541&type=locus TAIR]||Ambient Temperature||Scaffold00357 (length 260075) at 58774||6e-35<br />
|-<br />
| AT1G66350||RGA-LIKE 1, RGL, RGL1||[http://arabidopsis.org/servlets/TairObject?id=137244&type=locus TAIR]||Gibberellin||Scaffold00134 (length 346346) at 174707||0.0<br />
|-<br />
| AT1G68050||"FLAVIN-BINDING, KELCH REPEAT, F BOX 1", ADO3, FKF1||[http://arabidopsis.org/servlets/TairObject?id=137051&type=locus TAIR]||Light Signaling||Scaffold00110 (length 358202) at 120279||0.0<br />
|-<br />
| AT1G68840||ATRAV2, EDF2, ETHYLENE RESPONSE DNA BINDING FACTOR 2, RAP2.8, RAV2, RELATED TO ABI3/VP1 2, RELATED TO AP2 8, TEM2, TEMPRANILLO 2||[http://arabidopsis.org/servlets/TairObject?id=27570&type=locus TAIR]||Light Signaling||Scaffold00930 (length 110378) at 63096||5e-102<br />
|-<br />
| AT1G77080||AGAMOUS-LIKE 27, AGL27, FLM, FLOWERING LOCUS M, MADS AFFECTING FLOWERING 1, MAF1||[http://arabidopsis.org/servlets/TairObject?id=29106&type=locus TAIR]||Ambient Temperature, Vernalization||Scaffold10765 (length 2447) at 744||3e-13<br />
|-<br />
| AT1G77300||ASH1 HOMOLOG 2, ASHH2, CAROTENOID CHLOROPLAST REGULATORY1, CCR1, EARLY FLOWERING IN SHORT DAYS, EFS, LAZ2, LAZARUS 2, SDG8, SET DOMAIN GROUP 8||[http://arabidopsis.org/servlets/TairObject?id=136429&type=locus TAIR]||Vernalization||Scaffold00894 (length 114877) at 89213||1e-27<br />
|-<br />
| AT2G01570||REPRESSOR OF GA, REPRESSOR OF GA1-3 1, RGA, RGA1||[http://arabidopsis.org/servlets/TairObject?id=26549&type=locus TAIR]||Gibberellin||Scaffold01360 (length 81306) at 51382||0.0<br />
|-<br />
| AT2G06255||ELF4-L3, ELF4-LIKE 3||[http://arabidopsis.org/servlets/TairObject?id=500231553&type=locus TAIR]||Light Signaling||Scaffold00336 (length 230445) at 188137||1e-39<br />
|-<br />
| AT2G17770||ATBZIP27, BASIC REGION/LEUCINE ZIPPER MOTIF 27, BZIP27, FD PARALOG, FDP||[http://arabidopsis.org/servlets/TairObject?id=227228&type=locus TAIR]||Ambient Temperature||Scaffold00367 (length 240396) at 113139||7e-17<br />
|-<br />
| AT2G18790||HY3, OOP1, OUT OF PHASE 1, PHYB, PHYTOCHROME B||[http://arabidopsis.org/servlets/TairObject?id=26548&type=locus TAIR]||Light Signaling||Scaffold00751 (length 152548) at 83698||0.0<br />
|-<br />
| AT2G18870||VEL3, VERNALIZATION5/VIN3-LIKE 3, VIL4, VIN3-LIKE 4||[http://arabidopsis.org/servlets/TairObject?id=32249&type=locus TAIR]||Autonomous||Scaffold00396 (length 187979) at 73810||7e-19<br />
|-<br />
| AT2G18880||VEL2, VERNALIZATION5/VIN3-LIKE 2, VIL3, VIN3-LIKE 3||[http://arabidopsis.org/servlets/TairObject?id=32230&type=locus TAIR]||Autonomous||Scaffold00026 (length 499904) at 369396||6e-41<br />
|-<br />
| AT2G18915||ADAGIO 2, ADO2, LKP2, LOV KELCH PROTEIN 2||[http://arabidopsis.org/servlets/TairObject?id=500231567&type=locus TAIR]||Light Signaling||Scaffold00026 (length 499904) at 445582||0.0<br />
|-<br />
| AT2G19520||ACG1, ATMSI4, FVE, MSI4, MULTICOPY SUPPRESSOR OF IRA1 4, NFC04, NFC4||[http://arabidopsis.org/servlets/TairObject?id=33019&type=locus TAIR]||Ambient Temperature, Autonomous||Scaffold00728 (length 157708) at 8716||6e-21<br />
|-<br />
| AT2G22540||AGAMOUS-LIKE 22, AGL22, SHORT VEGETATIVE PHASE, SVP||[http://arabidopsis.org/servlets/TairObject?id=31694&type=locus TAIR]||Ambient Temperature, Vernalization||Scaffold01187 (length 101153) at 47701||2e-24<br />
|-<br />
| AT2G23380||CLF, CURLY LEAF, ICU1, INCURVATA 1, SDG1, SET1, SETDOMAIN 1, SETDOMAIN GROUP 1||[http://arabidopsis.org/servlets/TairObject?id=26534&type=locus TAIR]||Autonomous, Polycomb, Vernalization||Scaffold00354 (length 215005) at 64799||5e-41<br />
|-<br />
| AT2G25930||EARLY FLOWERING 3, ELF3, PYK20||[http://arabidopsis.org/servlets/TairObject?id=32082&type=locus TAIR]||Light Signaling||Scaffold00371 (length 223748) at 73111||6e-19<br />
|-<br />
| AT2G32950||ARABIDOPSIS THALIANA CONSTITUTIVE PHOTOMORPHOGENIC 1, ATCOP1, CONSTITUTIVE PHOTOMORPHOGENIC 1, COP1, DEETIOLATED MUTANT 340, DET340, EMB168, EMBRYO DEFECTIVE 168, FUS1, FUSCA 1||[http://arabidopsis.org/servlets/TairObject?id=34462&type=locus TAIR]||Light Signaling||Scaffold00734 (length 158513) at 142779||5e-62<br />
|-<br />
| AT2G33810||SPL3, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 3||[http://arabidopsis.org/servlets/TairObject?id=34194&type=locus TAIR]||Age||Scaffold00062 (length 451336) at 412489||2e-17<br />
|-<br />
| AT2G33835||FES1, FRIGIDA-ESSENTIAL 1||[http://arabidopsis.org/servlets/TairObject?id=500230872&type=locus TAIR]||Vernalization||Scaffold00102 (length 383343) at 88264||7e-17<br />
|-<br />
| AT2G34140||||[http://arabidopsis.org/servlets/TairObject?id=33865&type=locus TAIR]||Light Signaling||Scaffold00270 (length 246371) at 215217||7e-49<br />
|-<br />
| AT2G35670||FERTILIZATION INDEPENDENT SEED 2, FERTILIZATION-INDEPENDENT ENDOSPERM 2, FIE2, FIS2||[http://arabidopsis.org/servlets/TairObject?id=26543&type=locus TAIR]||Polycomb||Scaffold00857 (length 126644) at 55565||3e-04<br />
|-<br />
| AT2G40080||EARLY FLOWERING 4, ELF4||[http://arabidopsis.org/servlets/TairObject?id=34766&type=locus TAIR]||Light Signaling||Scaffold00254 (length 265810) at 228805||4e-24<br />
|-<br />
| AT2G42200||ATSPL9, SPL9, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 9||[http://arabidopsis.org/servlets/TairObject?id=34557&type=locus TAIR]||Age||Scaffold00691 (length 141413) at 61795||5e-21<br />
|-<br />
| AT2G43410||FPA||[http://arabidopsis.org/servlets/TairObject?id=34279&type=locus TAIR]||Autonomous||Scaffold01689 (length 75472) at 47663||4e-45<br />
|-<br />
| AT2G46340||SPA1, SUPPRESSOR OF PHYA-105 1||[http://arabidopsis.org/servlets/TairObject?id=31336&type=locus TAIR]||Light Signaling||Scaffold00734 (length 158513) at 142779||3e-69<br />
|-<br />
| AT2G46790||APRR9, ARABIDOPSIS PSEUDO-RESPONSE REGULATOR 9, PRR9, PSEUDO-RESPONSE REGULATOR 9, TL1, TOC1-LIKE PROTEIN 1||[http://arabidopsis.org/servlets/TairObject?id=32227&type=locus TAIR]||Light Signaling||Scaffold00001 (length 1030549) at 322801||1e-36<br />
|-<br />
| AT2G46830||ATCCA1, CCA1, CIRCADIAN CLOCK ASSOCIATED 1||[http://arabidopsis.org/servlets/TairObject?id=32221&type=locus TAIR]||Light Signaling||Scaffold00140 (length 354209) at 234299||7e-20<br />
|-<br />
| AT2G47700||RED AND FAR-RED INSENSITIVE 2, RFI2||[http://arabidopsis.org/servlets/TairObject?id=32070&type=locus TAIR]||Light Signaling||Scaffold01059 (length 101143) at 96557||1e-19<br />
|-<br />
| AT3G02380||ATCOL2, B-BOX DOMAIN PROTEIN 3, BBX3, COL2, CONSTANS-LIKE 2||[http://arabidopsis.org/servlets/TairObject?id=35635&type=locus TAIR]||Light Signaling||Scaffold01843 (length 51900) at 40767||3e-48<br />
|-<br />
| AT3G03450||RGA-LIKE 2, RGL2||[http://arabidopsis.org/servlets/TairObject?id=40021&type=locus TAIR]||Gibberellin||Scaffold00134 (length 346346) at 174722||0.0<br />
|-<br />
| AT3G04610||FLK, FLOWERING LOCUS KH DOMAIN||[http://arabidopsis.org/servlets/TairObject?id=37455&type=locus TAIR]||Autonomous||Scaffold01384 (length 81068) at 28309||4e-29<br />
|-<br />
| AT3G05120||ATGID1A, GA INSENSITIVE DWARF1A, GID1A||[http://arabidopsis.org/servlets/TairObject?id=39457&type=locus TAIR]||Gibberellin||Scaffold00101 (length 425332) at 398762||4e-175<br />
|-<br />
| AT3G07650||B-BOX DOMAIN PROTEIN 7, BBX7, COL9, CONSTANS-LIKE 9||[http://arabidopsis.org/servlets/TairObject?id=38550&type=locus TAIR]||Light Signaling||Scaffold00832 (length 123094) at 89599||1e-55<br />
|-<br />
| AT3G10390||FLD, FLOWERING LOCUS D||[http://arabidopsis.org/servlets/TairObject?id=35869&type=locus TAIR]||Ambient Temperature, Autonomous||Scaffold00232 (length 253418) at 139565||0.0<br />
|-<br />
| AT3G12810||CHR13, PHOTOPERIOD-INDEPENDENT EARLY FLOWERING 1, PIE1, SRCAP||[http://arabidopsis.org/servlets/TairObject?id=37964&type=locus TAIR]||Vernalization||Scaffold00147 (length 345970) at 30164||0.0<br />
|-<br />
| AT3G15270||SPL5, SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 5||[http://arabidopsis.org/servlets/TairObject?id=37842&type=locus TAIR]||Age||Scaffold00105 (length 392037) at 147284||5e-16<br />
|-<br />
| AT3G15354||SPA1-RELATED 3, SPA3||[http://arabidopsis.org/servlets/TairObject?id=500230681&type=locus TAIR]||Light Signaling||Scaffold00734 (length 158513) at 143450||1e-144<br />
|-<br />
| AT3G18990||REDUCED VERNALIZATION RESPONSE 1, REM39, REPRODUCTIVE MERISTEM 39, VRN1||[http://arabidopsis.org/servlets/TairObject?id=37620&type=locus TAIR]||Vernalization||Scaffold00811 (length 108354) at 96661||2e-25<br />
|-<br />
| AT3G20740||FERTILIZATION-INDEPENDENT ENDOSPERM, FERTILIZATION-INDEPENDENT ENDOSPERM 1, FIE, FIE1, FIS3||[http://arabidopsis.org/servlets/TairObject?id=38691&type=locus TAIR]||Autonomous, Polycomb, Vernalization||Scaffold01670 (length 60304) at 9836||5e-20<br />
|-<br />
| AT3G21320||||[http://arabidopsis.org/servlets/TairObject?id=39170&type=locus TAIR]||Light Signaling||Scaffold00509 (length 192554) at 181887||1e-21<br />
|-<br />
| AT3G24440||VERNALIZATION 5, VIL1, VIN3-LIKE 1, VRN5||[http://arabidopsis.org/servlets/TairObject?id=39196&type=locus TAIR]||Autonomous, Vernalization||Scaffold00396 (length 187979) at 73795||2e-69<br />
|-<br />
| AT3G25730||EDF3, ETHYLENE RESPONSE DNA BINDING FACTOR 3||[http://arabidopsis.org/servlets/TairObject?id=37641&type=locus TAIR]||Light Signaling||Scaffold00930 (length 110378) at 63060||5e-100<br />
|-<br />
| AT3G33520||ACTIN-RELATED PROTEIN 6, ARP6, ATARP6, EARLY IN SHORT DAYS 1, ESD1, SUF3, SUPPRESSOR OF FRI 3||[http://arabidopsis.org/servlets/TairObject?id=40458&type=locus TAIR]||Ambient Temperature, Vernalization||Scaffold00246 (length 286612) at 268521||1e-53<br />
|-<br />
| AT3G46640||LUX, LUX ARRHYTHMO, PCL1, PHYTOCLOCK 1||[http://arabidopsis.org/servlets/TairObject?id=35747&type=locus TAIR]||Light Signaling||Scaffold01150 (length 88293) at 80272||3e-34<br />
|-<br />
| AT3G47500||CDF3, CYCLING DOF FACTOR 3||[http://arabidopsis.org/servlets/TairObject?id=36439&type=locus TAIR]||Light Signaling||Scaffold00079 (length 471015) at 68175||1e-85<br />
|-<br />
| AT4G00650||FLA, FLOWERING LOCUS A, FRI, FRIGIDA||[http://arabidopsis.org/servlets/TairObject?id=128299&type=locus TAIR]||Vernalization||Scaffold00039 (length 505275) at 216632||4e-50<br />
|-<br />
| AT4G02020||EZA1, SDG10, SET DOMAIN-CONTAINING PROTEIN 10, SWINGER, SWN||[http://arabidopsis.org/servlets/TairObject?id=129104&type=locus TAIR]||Autonomous, Polycomb, Vernalization||Scaffold00354 (length 215005) at 64799||2e-48<br />
|-<br />
| AT4G02560||LD, LUMINIDEPENDENS||[http://arabidopsis.org/servlets/TairObject?id=26564&type=locus TAIR]||Autonomous||Scaffold00002 (length 840149) at 158601||4e-28<br />
|-<br />
| AT4G08920||ATCRY1, BLU1, BLUE LIGHT UNINHIBITED 1, CRY1, CRYPTOCHROME 1, ELONGATED HYPOCOTYL 4, HY4, OOP2, OUT OF PHASE 2||[http://arabidopsis.org/servlets/TairObject?id=129943&type=locus TAIR]||Light Signaling||Scaffold00331 (length 261439) at 124817||4e-128<br />
|-<br />
| AT4G11110||SPA1-RELATED 2, SPA2||[http://arabidopsis.org/servlets/TairObject?id=129633&type=locus TAIR]||Light Signaling||Scaffold01034 (length 107107) at 19205||2e-62<br />
|-<br />
| AT4G11880||AGAMOUS-LIKE 14, AGL14||[http://arabidopsis.org/servlets/TairObject?id=129748&type=locus TAIR]||Vernalization||Scaffold00249 (length 258199) at 131012||2e-29<br />
|-<br />
| AT4G16250||PHYD, PHYTOCHROME D||[http://arabidopsis.org/servlets/TairObject?id=26567&type=locus TAIR]||Light Signaling||Scaffold00751 (length 152548) at 83707||0.0<br />
|-<br />
| AT4G16280||FCA||[http://arabidopsis.org/servlets/TairObject?id=128853&type=locus TAIR]||Ambient Temperature, Autonomous||Scaffold00104 (length 360147) at 120318||5e-13<br />
|-<br />
| AT4G16845||REDUCED VERNALIZATION RESPONSE 2, VRN2||[http://arabidopsis.org/servlets/TairObject?id=228106&type=locus TAIR]||Autonomous, Polycomb, Vernalization||Scaffold00857 (length 126644) at 55203||3e-07<br />
|-<br />
| AT4G18130||PHYE, PHYTOCHROME E||[http://arabidopsis.org/servlets/TairObject?id=26568&type=locus TAIR]||Light Signaling||Scaffold00751 (length 152548) at 83749||0.0<br />
|-<br />
| AT4G20370||TSF, TWIN SISTER OF FT||[http://arabidopsis.org/servlets/TairObject?id=26553&type=locus TAIR]||Ambient Temperature||Scaffold00357 (length 260075) at 58807||1e-33<br />
|-<br />
| AT4G22950||AGAMOUS-LIKE 19, AGL19, GL19||[http://arabidopsis.org/servlets/TairObject?id=128336&type=locus TAIR]||Vernalization||Scaffold00249 (length 258199) at 131012||4e-28<br />
|-<br />
| AT4G24540||AGAMOUS-LIKE 24, AGL24||[http://arabidopsis.org/servlets/TairObject?id=127586&type=locus TAIR]||Vernalization||Scaffold01187 (length 101153) at 47701||2e-25<br />
|-<br />
| AT4G26000||PEP, PEPPER||[http://arabidopsis.org/servlets/TairObject?id=127403&type=locus TAIR]||Vernalization||Scaffold00021 (length 527983) at 157278||3e-29<br />
|-<br />
| AT4G30200||VEL1, VERNALIZATION5/VIN3-LIKE 1, VIL2, VIN3-LIKE 2||[http://arabidopsis.org/servlets/TairObject?id=128580&type=locus TAIR]||Autonomous, Vernalization||Scaffold00026 (length 499904) at 369417||7e-64<br />
|-<br />
| AT4G34530||CIB1, CRYPTOCHROME-INTERACTING BASIC-HELIX-LOOP-HELIX 1||[http://arabidopsis.org/servlets/TairObject?id=130033&type=locus TAIR]||Light Signaling||Scaffold01322 (length 99420) at 82955||2e-29<br />
|-<br />
| AT4G35900||ATBZIP14, FD, FD-1||[http://arabidopsis.org/servlets/TairObject?id=128068&type=locus TAIR]||Ambient Temperature||Scaffold00367 (length 240396) at 113139||1e-16<br />
|-<br />
| AT5G02810||APRR7, PRR7, PSEUDO-RESPONSE REGULATOR 7||[http://arabidopsis.org/servlets/TairObject?id=131538&type=locus TAIR]||Light Signaling||Scaffold00125 (length 356885) at 276518||1e-33<br />
|-<br />
| AT5G03840||TERMINAL FLOWER 1, TFL1||[http://arabidopsis.org/servlets/TairObject?id=131459&type=locus TAIR]||Ambient Temperature||Scaffold00181 (length 337602) at 12825||1e-28<br />
|-<br />
| AT5G08330||CCA1 HIKING EXPEDITION, CHE, TRANSCRIPTION FACTOR TCP21, TCP21||[http://www.uniprot.org/uniprot/Q9FTA2 UniProtKB]||Light Signaling||Scaffold00993 (length 109486) at 294||5e-27<br />
|-<br />
| AT5G10140||AGAMOUS-LIKE 25, AGL25, FLC, FLF, FLOWERING LOCUS C, FLOWERING LOCUS F||[http://arabidopsis.org/servlets/TairObject?id=136002&type=locus TAIR]||Ambient Temperature, Vernalization||Scaffold10765 (length 2447) at 708||8e-22<br />
|-<br />
| AT5G11530||EMBRYONIC FLOWER 1, EMF1||[http://arabidopsis.org/servlets/TairObject?id=130620&type=locus TAIR]||Polycomb||Scaffold00253 (length 240879) at 11069||1e-06<br />
|-<br />
| AT5G13480||FY||[http://arabidopsis.org/servlets/TairObject?id=136108&type=locus TAIR]||Autonomous||Scaffold00166 (length 328538) at 74796||2e-43<br />
|-<br />
| AT5G15840||B-BOX DOMAIN PROTEIN 1, BBX1, CO, CONSTANS, FG||[http://arabidopsis.org/servlets/TairObject?id=130492&type=locus TAIR]||Light Signaling||Scaffold01843 (length 51900) at 40767||3e-29<br />
|-<br />
| AT5G15850||ATCOL1, B-BOX DOMAIN PROTEIN 2, BBX2, COL1, CONSTANS-LIKE 1||[http://arabidopsis.org/servlets/TairObject?id=130495&type=locus TAIR]||Light Signaling||Scaffold01843 (length 51900) at 40767||5e-44<br />
|-<br />
| AT5G17690||ATLHP1, LHP1, LIKE HETEROCHROMATIN PROTEIN 1, TERMINAL FLOWER 2, TFL2||[http://arabidopsis.org/servlets/TairObject?id=134923&type=locus TAIR]||Polycomb||Scaffold00696 (length 140617) at 128983||7e-13<br />
|-<br />
| AT5G23150||ENHANCER OF AG-4 2, HUA2||[http://arabidopsis.org/servlets/TairObject?id=135220&type=locus TAIR]||Vernalization||Scaffold00686 (length 145647) at 102689||5e-42<br />
|-<br />
| AT5G24470||APRR5, PRR5, PSEUDO-RESPONSE REGULATOR 5||[http://arabidopsis.org/servlets/TairObject?id=135985&type=locus TAIR]||Light Signaling||Scaffold00001 (length 1030549) at 322798||3e-40<br />
|-<br />
| AT5G24930||ATCOL4, B-BOX DOMAIN PROTEIN 5, BBX5, COL4, CONSTANS-LIKE 4||[http://arabidopsis.org/servlets/TairObject?id=131285&type=locus TAIR]||Light Signaling||Scaffold11225 (length 3326) at 2816||8e-23<br />
|-<br />
| AT5G35840||PHYC, PHYTOCHROME C||[http://arabidopsis.org/servlets/TairObject?id=133466&type=locus TAIR]||Light Signaling||Scaffold01070 (length 102706) at 75395||0.0<br />
|-<br />
| AT5G37055||ATSWC6, SEF, SERRATED LEAVES AND EARLY FLOWERING||[http://arabidopsis.org/servlets/TairObject?id=500231974&type=locus TAIR]||Vernalization||Scaffold00925 (length 141061) at 38143||4e-29<br />
|-<br />
| AT5G39660||CDF2, CYCLING DOF FACTOR 2||[http://arabidopsis.org/servlets/TairObject?id=133414&type=locus TAIR]||Light Signaling||Scaffold00651 (length 145047) at 19066||1e-90<br />
|-<br />
| AT5G42790||ARS5, ARSENIC TOLERANCE 5, ATPSM30, PAF1, PROTEASOME ALPHA SUBUNIT F1||[http://arabidopsis.org/servlets/TairObject?id=133505&type=locus TAIR]||Vernalization||Scaffold00528 (length 197283) at 110933||5e-64<br />
|-<br />
| AT5G51230||ATEMF2, CYR1, CYTOKININ RESISTANT 1, EMBRYONIC FLOWER 2, EMF2, VEF2||[http://arabidopsis.org/servlets/TairObject?id=134952&type=locus TAIR]||Polycomb||Scaffold00857 (length 126644) at 44887||9e-19<br />
|-<br />
| AT5G57360||ADAGIO 1, ADO1, FKF1-LIKE PROTEIN 2, FKL2, LKP1, LOV KELCH PROTEIN 1, ZEITLUPE, ZTL||[http://arabidopsis.org/servlets/TairObject?id=134481&type=locus TAIR]||Light Signaling||Scaffold00026 (length 499904) at 445597||0.0<br />
|-<br />
| AT5G57380||VERNALIZATION INSENSITIVE 3, VIN3||[http://arabidopsis.org/servlets/TairObject?id=134483&type=locus TAIR]||Autonomous, Vernalization||Scaffold00026 (length 499904) at 369405||3e-48<br />
|-<br />
| AT5G57660||ATCOL5, B-BOX DOMAIN PROTEIN 6, BBX6, COL5, CONSTANS-LIKE 5||[http://arabidopsis.org/servlets/TairObject?id=134422&type=locus TAIR]||Light Signaling||Scaffold11225 (length 3326) at 2816||1e-25<br />
|-<br />
| AT5G58230||ARABIDOPSIS MULTICOPY SUPRESSOR OF IRA1, ATMSI1, MATERNAL EFFECT EMBRYO ARREST 70, MEE70, MSI1, MULTICOPY SUPRESSOR OF IRA1||[http://arabidopsis.org/servlets/TairObject?id=132921&type=locus TAIR]||Autonomous, Polycomb, Vernalization||Scaffold00615 (length 179658) at 161081||2e-61<br />
|-<br />
| AT5G60100||APRR3, PRR3, PSEUDO-RESPONSE REGULATOR 3||[http://arabidopsis.org/servlets/TairObject?id=133317&type=locus TAIR]||Light Signaling||Scaffold02075 (length 43325) at 14139||3e-25<br />
|-<br />
| AT5G61380||APRR1, ATTOC1, PRR1, PSEUDO-RESPONSE REGULATOR 1, TIMING OF CAB EXPRESSION 1, TOC1||[http://arabidopsis.org/servlets/TairObject?id=133196&type=locus TAIR]||Light Signaling||Scaffold00753 (length 123742) at 70468||2e-47<br />
|-<br />
| AT5G62430||CDF1, CYCLING DOF FACTOR 1||[http://arabidopsis.org/servlets/TairObject?id=131911&type=locus TAIR]||Light Signaling||Scaffold01102 (length 99830) at 51435||1e-59<br />
|-<br />
| AT5G65050||AGAMOUS-LIKE 31, AGL31, MADS AFFECTING FLOWERING 2, MAF2||[http://arabidopsis.org/servlets/TairObject?id=135154&type=locus TAIR]||Ambient Temperature, Vernalization||Scaffold10765 (length 2447) at 723||4e-20<br />
|-<br />
| AT5G65060||AGAMOUS-LIKE 70, AGL70, FCL3, MADS AFFECTING FLOWERING 3, MAF3||[http://arabidopsis.org/servlets/TairObject?id=130633&type=locus TAIR]||Ambient Temperature, Vernalization||Scaffold10765 (length 2447) at 639||7e-15<br />
|-<br />
| AT5G65070||AGAMOUS-LIKE 69, AGL69, FCL4, MADS AFFECTING FLOWERING 4, MAF4||[http://arabidopsis.org/servlets/TairObject?id=130634&type=locus TAIR]||Ambient Temperature, Vernalization||Scaffold10765 (length 2447) at 723||6e-20<br />
|-<br />
| AT5G65080||AGAMOUS-LIKE 68, AGL68, MADS AFFECTING FLOWERING 5, MAF5||[http://arabidopsis.org/servlets/TairObject?id=130635&type=locus TAIR]||Ambient Temperature, Vernalization||Scaffold10765 (length 2447) at 699||1e-18<br />
|}<br />
<br />
<br />
==References==<br />
*Amasino RM. Seasonal and developmental timing of flowering. ''Plant J,'' '''61,''' 1001-1013 (2010).<br />
*Amasino RM. Vernalization and flowering time. ''Curr Opin Plant Biol,'' '''16,''' 154–158 (2005).<br />
*Ballerini ES, Kramer EM. Environmental and molecular analysis of the floral transition in the lower eudicot Aquilegia formosa. ''Evodevo,'' '''2,''' 1-20 (2011).<br />
*Bäurle I, Dean C. The timing of developmental transitions in plants. ''Cell,'' '''125,''' 655-664 (2006).<br />
*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).<br />
*Farrona S, Coupland G, Turck F. The impact of chromatin regulation on the floral transition. ''Semin Cell Dev Biol,'' '''19,''' 560-573 (2008).<br />
*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).<br />
*Fornara F, de Montaigu A, Coupland G. SnapShot: Control of flowering in Arabidopsis. ''Cell,'' '''141,''' 550-550.e2 (2010).<br />
*Henderson IR, Dean C. Control of Arabidopsis flowering: the chill before the bloom. ''Development,'' '''131,''' 3829-3838 (2004).<br />
*He Y, Amasino RM. Role of chromatin modification in flowering-time control. ''Trends Plant Sci,'' '''10,''' 30-35 (2005).<br />
*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).<br />
*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).<br />
*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).<br />
*Jung CH, Wong CE, Singh MB, Bhalla PL. Comparative genomic analysis of soybean flowering genes. ''PLoS One,'' '''7,''' e38250 (2012).<br />
*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).<br />
*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).<br />
*Liu C, Thong Z, Yu H. Coming into bloom: the specification of floral meristems. ''Development,'' '''136,''' 3379-3391 (2009).<br />
*Posé D, Yant L, Schmid M. The end of innocence: flowering networks explode in complexity. ''Curr Opin Plant Biol'' '''15,''' 45-50 (2012).<br />
*Schneitz K, Balasubramanian S. Floral Meristems. ''eLS'' (John Wiley & Sons Ltd, Chichester, 2009).<br />
*SSR Tool. ''Genome Database for Vaccinium.''<br />
*Sung ZR, Chen L, Moon YH, Lertpiriyapong K. Mechanisms of floral repression in Arabidopsis. ''Curr Opin Plant Biol,'' '''6,''' 29-35 (2003).<br />
*Taiz L, Zeiger E. ''Plant Physiology Fifth Edition Ch. 20'' (Sinauer Associates, Sunderland, MA, 2010).<br />
*Turck F, Adrian J. A lesson in complexity: regulation of FLOWERING LOCUS T. ''Max Planck Institute for Plant Breeding Research.''<br />
*UniProt Consortium. Reorganizing the protein space at the Universal Protein Resource (UniProt). ''Nucleic Acids Res,'' '''40,''' D71-D75 (2012).<br />
*Wellmer F, Riechmann JL. Gene networks controlling the initiation of flower development. ''Trends Genet,'' '''26,''' 519-527 (2010).<br />
*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).<br />
*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).<br />
*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).</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=Summer_2014_SynBio_Project_(Davidson_and_MWSU)&diff=17351Summer 2014 SynBio Project (Davidson and MWSU)2014-05-29T14:40:36Z<p>Laheyer: </p>
<hr />
<div><br />
=== Presentations during MWSU visit to Davidson ===<br />
<br />
Central Dogma presentation [[File:Central_dogma.pptx]]<br />
<br />
PCR presentation [[File:PCR.pptx]]<br />
<br />
Cloning presentation [[File:Cloning.pptx]]<br />
<br />
Riboswitch presentation [[File:Riboswitch_function.pptx]]<br />
<br />
Agent based modeling presentation [[File:AgentBased_Modeling.pptx]]<br />
<br />
Competition presentation [[File:Competition_Modeling.xlsx]]<br />
<br />
Programmed evolution presentation [[File:Programmed_Evolution.pdf]]<br />
<br />
Caffeine results [[File:Caffeine_Disk.pptx]]<br />
<br />
Ammeline presentation [[File:Ammeline.pptx]]<br />
<br />
Repressilator modeling exercises [[File:repressilator_modeling.docx]]<br />
<br />
Repressilator modeling Excel file [[File:Repressilator_model.xls]]<br />
<br />
Repressilator modeling Netlogo file [[File:Repressilator_mod.nlogo.zip]]<br />
<br />
=== Biology Files ===<br />
<br />
Chaperone plasmid DNA sequences [[File:Chaperone_plasmid_DNA_sequences.docx]]<br />
<br />
Origin PCR Gels 5-26-14[[File:5-26-14 Orig PCR Elecpho Gel Pic.doc]]<br />
<br />
Chaperone PCR and Repeat Origin PCR 5-27-14[[File:5-27-14_Chap_PCR_and_Repeat_Ori_PCR.doc]]<br />
<br />
Chaperone PCR of original clones 5-27-14[[File:5-27-14_chaperone_pcr_clones_1-24.doc]]<br />
<br />
Origin PCR of original clones 5-27-14[[File:5-27-14 Ori PCR 1-24.doc ]]<br />
<br />
New Chap PCR clones 1-5[[File:5-28-14_New_Chap_PCR_1-5.doc (]]<br />
<br />
Combinations Labeling System [[File:Labeling.xlsx]]<br />
<br />
ThyA Fitness Module [[File:ThyA fitness module.docx]]<br />
<br />
===Sub-pages on various topics===<br />
'''<br />
[[MATH]]<br />
'''<br />
<br />
[[Catherine Doyle Thesis Materials]]<br />
<br />
[[Repeating 20 Clone Experiments]]<br />
<br />
[[Extending theophylline application]]<br />
<br />
[[Melamine iteration]]<br />
<br />
[[Ramping up Programmed Evolution]]<br />
<br />
[[Rational Design of Riboswitches: papers to read]]</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=Rational_Design_of_Riboswitches:_papers_to_read&diff=17350Rational Design of Riboswitches: papers to read2014-05-29T14:37:06Z<p>Laheyer: </p>
<hr />
<div>Wachsmuth, et al - [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3575828/ De novo design of a synthetic riboswitch that regulates transcription termination]<br />
* engineered switch terminates '''transcription''' in the absence of theophylline (6.5 fold induction in presence of theophylline)<br />
* model folding of many candidate switches in steps of 5-10 nt (to simulate different elongation speeds) using RNAfold<br />
* find distribution of MFE in shuffled sequences to characterize those structures more/less stable than expected by chance<br />
<br />
Beisel and Smolke - [http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000363 Design Principles for Riboswitch Function]<br />
<br />
Dixon, et al - [http://www.pnas.org/content/107/7/2830.full#ref-19 Reengineering Orthogonally Selective Riboswitches]<br />
<br />
Rieder, et al (referenced by Dixon)- [http://onlinelibrary.wiley.com/doi/10.1002/cbic.200700057/full Ligand-Induced Folding of the Adenosine Deaminase A-Riboswitch and Implications on Riboswitch Translational Control]<br />
<br />
Perdizet, et al - [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3295289/ Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch]<br />
<br />
Ceres, et al (Mar 2013) - [http://pubs.acs.org/doi/ipdf/10.1021/sb4000096 Modularity of Select Riboswitch Expression Platforms Enables Facile Engineering of Novel Genetic Regulatory Devices]<br />
* OFF switches<br />
<br />
Ceres, Trausch and Batey (Dec 2013) - [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3905868/ Engineering modular ‘ON’ RNA switches using biological components]</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=Rational_Design_of_Riboswitches:_papers_to_read&diff=17349Rational Design of Riboswitches: papers to read2014-05-29T14:33:33Z<p>Laheyer: </p>
<hr />
<div>Wachsmuth, et al - [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3575828/ De novo design of a synthetic riboswitch that regulates transcription termination]<br />
* engineered switch terminates '''transcription''' in the absence of theophylline (6.5 fold induction in presence of theophylline)<br />
* model folding of many candidate switches in steps of 5-10 nt (to simulate different elongation speeds) using RNAfold<br />
* find distribution of MFE in shuffled sequences to characterize those structures more/less stable than expected by chance<br />
<br />
Beisel and Smolke - [http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000363 Design Principles for Riboswitch Function]<br />
<br />
Dixon, et al - [http://www.pnas.org/content/107/7/2830.full#ref-19 Reengineering Orthogonally Selective Riboswitches]<br />
<br />
Rieder, et al (referenced by Dixon)- [http://onlinelibrary.wiley.com/doi/10.1002/cbic.200700057/full Ligand-Induced Folding of the Adenosine Deaminase A-Riboswitch and Implications on Riboswitch Translational Control]<br />
<br />
Ceres, Trausch and Batey (Dec 2013) - [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3905868/ Engineering modular ‘ON’ RNA switches using biological components]<br />
<br />
Perdizet, et al - [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3295289/ Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch]<br />
<br />
Ceres, et al (Mar 2013) - [http://pubs.acs.org/doi/ipdf/10.1021/sb4000096 Modularity of Select Riboswitch Expression Platforms Enables Facile Engineering of Novel Genetic Regulatory Devices]</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=Rational_Design_of_Riboswitches:_papers_to_read&diff=17348Rational Design of Riboswitches: papers to read2014-05-29T14:28:38Z<p>Laheyer: </p>
<hr />
<div>Wachsmuth, et al - [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3575828/ De novo design of a synthetic riboswitch that regulates transcription termination]<br />
* engineered switch terminates '''transcription''' in the absence of theophylline<br />
* model folding of many candidate switches in steps of 5-10 nt (to simulate different elongation speeds) using RNAfold<br />
* find distribution of MFE in shuffled sequences to characterize those structures more/less stable than expected by chance<br />
<br />
Beisel and Smolke - [http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000363 Design Principles for Riboswitch Function]<br />
<br />
Dixon, et al - [http://www.pnas.org/content/107/7/2830.full#ref-19 Reengineering Orthogonally Selective Riboswitches]<br />
<br />
Rieder, et al (referenced by Dixon)- [http://onlinelibrary.wiley.com/doi/10.1002/cbic.200700057/full Ligand-Induced Folding of the Adenosine Deaminase A-Riboswitch and Implications on Riboswitch Translational Control]<br />
<br />
Ceres, Trausch and Batey (Dec 2013) - [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3905868/ Engineering modular ‘ON’ RNA switches using biological components]<br />
<br />
Perdizet, et al - [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3295289/ Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch]<br />
<br />
Ceres, et al (Mar 2013) - [http://pubs.acs.org/doi/ipdf/10.1021/sb4000096 Modularity of Select Riboswitch Expression Platforms Enables Facile Engineering of Novel Genetic Regulatory Devices]</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=Rational_Design_of_Riboswitches:_papers_to_read&diff=17346Rational Design of Riboswitches: papers to read2014-05-29T13:54:00Z<p>Laheyer: Created page with "Beisel and Smolke - [http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000363 Design Principles for Riboswitch Function]"</p>
<hr />
<div>Beisel and Smolke - [http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000363 Design Principles for Riboswitch Function]</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=Summer_2014_SynBio_Project_(Davidson_and_MWSU)&diff=17186Summer 2014 SynBio Project (Davidson and MWSU)2014-05-20T20:20:20Z<p>Laheyer: </p>
<hr />
<div>Central Dogma presentation [[File:Central_dogma.pptx]]<br />
<br />
PCR presentation [[File:PCR.pptx]]<br />
<br />
Cloning presentation [[File:Cloning.pptx]]<br />
<br />
Riboswitch presentation [[File:Riboswitch_function.pptx]]<br />
<br />
Agent based modeling presentation [[File:AgentBased_Modeling.pptx]]<br />
<br />
Competition presentation [[File:Competition_Modeling.xlsx]]<br />
<br />
Programmed evolution presentation [[File:Programmed_Evolution.pdf]]<br />
<br />
Caffeine results [[File:Caffeine_Disk.pptx]]<br />
<br />
Ammeline presentation [[File:Ammeline.pptx]]<br />
<br />
Repressilator modeling exercises [[File:repressilator_modeling.docx]]<br />
<br />
Repressilator modeling Excel file [[File:Repressilator_model.xls]]<br />
<br />
Repressilator modeling Netlogo file [[File:Repressilator_mod.nlogo.zip]]</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=File:Repressilator_mod.nlogo.zip&diff=17185File:Repressilator mod.nlogo.zip2014-05-20T20:20:00Z<p>Laheyer: </p>
<hr />
<div></div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=Summer_2014_SynBio_Project_(Davidson_and_MWSU)&diff=17184Summer 2014 SynBio Project (Davidson and MWSU)2014-05-20T20:06:44Z<p>Laheyer: </p>
<hr />
<div>Central Dogma presentation [[File:Central_dogma.pptx]]<br />
<br />
PCR presentation [[File:PCR.pptx]]<br />
<br />
Cloning presentation [[File:Cloning.pptx]]<br />
<br />
Riboswitch presentation [[File:Riboswitch_function.pptx]]<br />
<br />
Agent based modeling presentation [[File:AgentBased_Modeling.pptx]]<br />
<br />
Competition presentation [[File:Competition_Modeling.xlsx]]<br />
<br />
Programmed evolution presentation [[File:Programmed_Evolution.pdf]]<br />
<br />
Caffeine results [[File:Caffeine_Disk.pptx]]<br />
<br />
Ammeline presentation [[File:Ammeline.pptx]]<br />
<br />
Repressilator modeling exercises [[File:repressilator_modeling.docx]]<br />
<br />
Repressilator modeling Excel file [[File:Repressilator_model.xls]]<br />
<br />
Repressilator modeling Netlogo file [[File:Repressilator_model.xls.zip]]</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=File:Repressilator_model.xls.zip&diff=17183File:Repressilator model.xls.zip2014-05-20T20:06:02Z<p>Laheyer: </p>
<hr />
<div></div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=Summer_2014_SynBio_Project_(Davidson_and_MWSU)&diff=17182Summer 2014 SynBio Project (Davidson and MWSU)2014-05-20T20:04:21Z<p>Laheyer: </p>
<hr />
<div>Central Dogma presentation [[File:Central_dogma.pptx]]<br />
<br />
PCR presentation [[File:PCR.pptx]]<br />
<br />
Cloning presentation [[File:Cloning.pptx]]<br />
<br />
Riboswitch presentation [[File:Riboswitch_function.pptx]]<br />
<br />
Agent based modeling presentation [[File:AgentBased_Modeling.pptx]]<br />
<br />
Competition presentation [[File:Competition_Modeling.xlsx]]<br />
<br />
Programmed evolution presentation [[File:Programmed_Evolution.pdf]]<br />
<br />
Caffeine results [[File:Caffeine_Disk.pptx]]<br />
<br />
Ammeline presentation [[File:Ammeline.pptx]]<br />
<br />
Repressilator modeling exercises [[File:repressilator_modeling.docx]]<br />
<br />
Repressilator modeling Excel file [[File:Repressilator_model.xls]]</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=File:Repressilator_model.xls&diff=17181File:Repressilator model.xls2014-05-20T20:03:54Z<p>Laheyer: </p>
<hr />
<div></div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=Summer_2014_SynBio_Project_(Davidson_and_MWSU)&diff=17180Summer 2014 SynBio Project (Davidson and MWSU)2014-05-20T19:59:48Z<p>Laheyer: </p>
<hr />
<div>Central Dogma presentation [[File:Central_dogma.pptx]]<br />
<br />
PCR presentation [[File:PCR.pptx]]<br />
<br />
Cloning presentation [[File:Cloning.pptx]]<br />
<br />
Riboswitch presentation [[File:Riboswitch_function.pptx]]<br />
<br />
Agent based modeling presentation [[File:AgentBased_Modeling.pptx]]<br />
<br />
Competition presentation [[File:Competition_Modeling.xlsx]]<br />
<br />
Programmed evolution presentation [[File:Programmed_Evolution.pdf]]<br />
<br />
Caffeine results [[File:Caffeine_Disk.pptx]]<br />
<br />
Ammeline presentation [[File:Ammeline.pptx]]<br />
<br />
Repressilator modeling exercises [[File:repressilator_modeling.docx]]<br />
<br />
Repressilator modeling Excel file [[File:]]</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=Summer_2014_SynBio_Project_(Davidson_and_MWSU)&diff=17179Summer 2014 SynBio Project (Davidson and MWSU)2014-05-20T19:58:13Z<p>Laheyer: </p>
<hr />
<div>Central Dogma presentation [[File:Central_dogma.pptx]]<br />
<br />
PCR presentation [[File:PCR.pptx]]<br />
<br />
Cloning presentation [[File:Cloning.pptx]]<br />
<br />
Riboswitch presentation [[File:Riboswitch_function.pptx]]<br />
<br />
Agent based modeling presentation [[File:AgentBased_Modeling.pptx]]<br />
<br />
Competition presentation [[File:Competition_Modeling.xlsx]]<br />
<br />
Programmed evolution presentation [[File:Programmed_Evolution.pdf]]<br />
<br />
Caffeine results [[File:Caffeine_Disk.pptx]]<br />
<br />
Ammeline presentation [[File:Ammeline.pptx]]<br />
<br />
Repressilator modeling exercises [[File:repressilator_modeling.docx]]</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=File:Repressilator_modeling.docx&diff=17178File:Repressilator modeling.docx2014-05-20T19:57:13Z<p>Laheyer: </p>
<hr />
<div></div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=Biology&diff=16470Biology2013-06-03T15:58:06Z<p>Laheyer: </p>
<hr />
<div>[[Davidson Protocols]] <br><br />
[[MWSU_protocols]] <br><br />
<br />
[[J-GGA Scaffold Sequences]]<br />
<br />
[[File:Gelpouring.jpg|200px|thumb|right|Look, Mom, no EtBr!]]<br />
<br />
'''Topics to Investigate'''<br />
<br />
<u>High Priority = more people</u><br />
<br />
* '''Phoebe and Claire:''' eCDM8 working to make theophylline with biosensor and fitness modules (Tet<sup>R</sup>) to report out. <br><br />
Which plasmid carries which device?<br><br />
Biosensor<br><br />
Fitness (tetA)<br><br />
feeds into stress module<br><br />
* '''Sachii and Jess:''' Determine the junction sequences and associated primers<br><br />
(use existing rules)<br><br />
build scaffold for insert segments<br><br />
include orI (collaborate with copy number research)<br><br />
include drug resistance gene<br><br />
test JGG design<br><br />
* '''Spencer and Sara:''' test fitness module with adhE<br />
compare with tetA<br><br />
fine tune tetA resistance<br><br />
combine with tetA<br><br />
Does theophylline diffuse across the membrane and thus the system fails?<br><br />
* '''Brandon and Erich:''' Copy number of plasmids <br><br />
Can we alter Ori to produce a range of plasmid densities in ''E. coli''? <br><br />
<br />
<br />
<u>Second Order Priority = one person</u><br />
* produce different CDM alleles<br />
* swap out different components (promoters, RBS, alleles)<br />
* test out programmed evolution<br />
* Stress module needs more work (see eCDM8 outputs)<br></div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=File:Gelpouring.jpg&diff=16469File:Gelpouring.jpg2013-06-03T15:46:26Z<p>Laheyer: First ever non-EtBr gel</p>
<hr />
<div>First ever non-EtBr gel</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=File:CHA-A02_scaled.pdf&diff=14323File:CHA-A02 scaled.pdf2012-04-26T16:43:08Z<p>Laheyer: </p>
<hr />
<div></div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=IRobot_Energy_Saver_Project&diff=14322IRobot Energy Saver Project2012-04-26T16:42:54Z<p>Laheyer: /* Dr. Heyer's To Do */</p>
<hr />
<div>==Team Pages==<br />
[[Team R2D2]] <br><br />
[[Team Commando]]<br />
<br />
==Tools/Packages==<br />
*[http://www.usna.edu/Users/weapsys/esposito/roomba.matlab/ MatLab Package]<br />
*[http://www.rose-hulman.edu/class/csse/resources/Robotics/ PyCreate]<br />
*[http://cgi.cs.duke.edu/~mac/flail/index.cgi?page=home FLAIL]<br />
<br />
==Useful Links==<br />
*[http://www.irobot.com/hrd_right_rail/create_rr/create_fam/createFam_rr_manuals.html All Manuals]<br />
**May be really useful to command module team<br />
*[http://www.elementdirect.com/files/10542B.pdf BAM documentation]<br />
*[http://www.usna.edu/Users/weapsys/esposito/roomba.matlab/Matlab_Toolbox_iRobot_create_doc.pdf MATLAB Create Toolbox User Guide]<br />
*[http://teyvoniathomas.com/index.php/projects/55-opticalflow.html Theory and practice], visual navigation on the iRobot Create<br />
*[http://www.cs.hmc.edu/~dodds/erdos/ College iRobot Project]<br />
*[http://myroombud.com/ Roomba Costumes]<br />
*[http://gicl.cs.drexel.edu/wiki/LearningRoomba Learning Roomba] excellent set of tutorials<br />
<br />
==General To Do==<br />
*Navigation<br />
**Check out this SLAM [http://ocw.mit.edu/courses/aeronautics-and-astronautics/16-412j-cognitive-robotics-spring-2005/projects/1aslam_blas_repo.pdf tutorial]<br />
*Aiming Camera<br />
**[http://www.ez-robot.com/Robots/iRobot-Roomba-Hack Camera option?]<br />
**[http://www.dmcinfo.com/Blog/articleType/ArticleView/articleId/1327/Office-Autonomous-Robot.aspx Autonomous Office Robot] has wireless camera, uses RoboRealm<br />
*Image Processing<br />
<br />
==Dr. Heyer's To Do==<br />
<br />
* Working on camera options. Both groups should continue to keep me posted on their camera requirements.<br />
<br />
* Got maps of Chambers, scale drawings of 2nd [[Media:CHA-A02_scaled.pdf]] and 3rd floor [[Media:CHA-A03_scaled.pdf]], connected to CAD guy on campus if we need more.</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=File:CHA-A03_scaled.pdf&diff=14321File:CHA-A03 scaled.pdf2012-04-26T16:41:58Z<p>Laheyer: </p>
<hr />
<div></div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=IRobot_Energy_Saver_Project&diff=14320IRobot Energy Saver Project2012-04-26T16:41:35Z<p>Laheyer: /* Dr. Heyer's To Do */</p>
<hr />
<div>==Team Pages==<br />
[[Team R2D2]] <br><br />
[[Team Commando]]<br />
<br />
==Tools/Packages==<br />
*[http://www.usna.edu/Users/weapsys/esposito/roomba.matlab/ MatLab Package]<br />
*[http://www.rose-hulman.edu/class/csse/resources/Robotics/ PyCreate]<br />
*[http://cgi.cs.duke.edu/~mac/flail/index.cgi?page=home FLAIL]<br />
<br />
==Useful Links==<br />
*[http://www.irobot.com/hrd_right_rail/create_rr/create_fam/createFam_rr_manuals.html All Manuals]<br />
**May be really useful to command module team<br />
*[http://www.elementdirect.com/files/10542B.pdf BAM documentation]<br />
*[http://www.usna.edu/Users/weapsys/esposito/roomba.matlab/Matlab_Toolbox_iRobot_create_doc.pdf MATLAB Create Toolbox User Guide]<br />
*[http://teyvoniathomas.com/index.php/projects/55-opticalflow.html Theory and practice], visual navigation on the iRobot Create<br />
*[http://www.cs.hmc.edu/~dodds/erdos/ College iRobot Project]<br />
*[http://myroombud.com/ Roomba Costumes]<br />
*[http://gicl.cs.drexel.edu/wiki/LearningRoomba Learning Roomba] excellent set of tutorials<br />
<br />
==General To Do==<br />
*Navigation<br />
**Check out this SLAM [http://ocw.mit.edu/courses/aeronautics-and-astronautics/16-412j-cognitive-robotics-spring-2005/projects/1aslam_blas_repo.pdf tutorial]<br />
*Aiming Camera<br />
**[http://www.ez-robot.com/Robots/iRobot-Roomba-Hack Camera option?]<br />
**[http://www.dmcinfo.com/Blog/articleType/ArticleView/articleId/1327/Office-Autonomous-Robot.aspx Autonomous Office Robot] has wireless camera, uses RoboRealm<br />
*Image Processing<br />
<br />
==Dr. Heyer's To Do==<br />
<br />
* Working on camera options. Both groups should continue to keep me posted on their camera requirements.<br />
<br />
* Got maps of Chambers, scale drawings of 2nd [[Media:CHA-A03_scaled.pdf]] and 3rd floor, connected to CAD guy on campus if we need more.</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=IRobot_Energy_Saver_Project&diff=14319IRobot Energy Saver Project2012-04-26T16:38:13Z<p>Laheyer: /* Dr. Heyer's To Do */</p>
<hr />
<div>==Team Pages==<br />
[[Team R2D2]] <br><br />
[[Team Commando]]<br />
<br />
==Tools/Packages==<br />
*[http://www.usna.edu/Users/weapsys/esposito/roomba.matlab/ MatLab Package]<br />
*[http://www.rose-hulman.edu/class/csse/resources/Robotics/ PyCreate]<br />
*[http://cgi.cs.duke.edu/~mac/flail/index.cgi?page=home FLAIL]<br />
<br />
==Useful Links==<br />
*[http://www.irobot.com/hrd_right_rail/create_rr/create_fam/createFam_rr_manuals.html All Manuals]<br />
**May be really useful to command module team<br />
*[http://www.elementdirect.com/files/10542B.pdf BAM documentation]<br />
*[http://www.usna.edu/Users/weapsys/esposito/roomba.matlab/Matlab_Toolbox_iRobot_create_doc.pdf MATLAB Create Toolbox User Guide]<br />
*[http://teyvoniathomas.com/index.php/projects/55-opticalflow.html Theory and practice], visual navigation on the iRobot Create<br />
*[http://www.cs.hmc.edu/~dodds/erdos/ College iRobot Project]<br />
*[http://myroombud.com/ Roomba Costumes]<br />
*[http://gicl.cs.drexel.edu/wiki/LearningRoomba Learning Roomba] excellent set of tutorials<br />
<br />
==General To Do==<br />
*Navigation<br />
**Check out this SLAM [http://ocw.mit.edu/courses/aeronautics-and-astronautics/16-412j-cognitive-robotics-spring-2005/projects/1aslam_blas_repo.pdf tutorial]<br />
*Aiming Camera<br />
**[http://www.ez-robot.com/Robots/iRobot-Roomba-Hack Camera option?]<br />
**[http://www.dmcinfo.com/Blog/articleType/ArticleView/articleId/1327/Office-Autonomous-Robot.aspx Autonomous Office Robot] has wireless camera, uses RoboRealm<br />
*Image Processing<br />
<br />
==Dr. Heyer's To Do==<br />
<br />
* Working on camera options. Both groups should continue to keep me posted on their camera requirements.<br />
<br />
* Got maps of Chambers, scale drawings of 2nd and 3rd floor, connected to CAD guy on campus if we need more.</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=File:CHM-A02_scaled.pdf&diff=14318File:CHM-A02 scaled.pdf2012-04-26T16:36:14Z<p>Laheyer: </p>
<hr />
<div></div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=IRobot_Energy_Saver_Project&diff=14317IRobot Energy Saver Project2012-04-26T02:20:10Z<p>Laheyer: /* General To Do */</p>
<hr />
<div>==Team Pages==<br />
[[Team R2D2]] <br><br />
[[Team Commando]]<br />
<br />
==Tools/Packages==<br />
*[http://www.usna.edu/Users/weapsys/esposito/roomba.matlab/ MatLab Package]<br />
*[http://www.rose-hulman.edu/class/csse/resources/Robotics/ PyCreate]<br />
*[http://cgi.cs.duke.edu/~mac/flail/index.cgi?page=home FLAIL]<br />
<br />
==Useful Links==<br />
*[http://www.irobot.com/hrd_right_rail/create_rr/create_fam/createFam_rr_manuals.html All Manuals]<br />
**May be really useful to command module team<br />
*[http://www.elementdirect.com/files/10542B.pdf BAM documentation]<br />
*[http://www.usna.edu/Users/weapsys/esposito/roomba.matlab/Matlab_Toolbox_iRobot_create_doc.pdf MATLAB Create Toolbox User Guide]<br />
*[http://teyvoniathomas.com/index.php/projects/55-opticalflow.html Theory and practice], visual navigation on the iRobot Create<br />
*[http://www.cs.hmc.edu/~dodds/erdos/ College iRobot Project]<br />
*[http://myroombud.com/ Roomba Costumes]<br />
*[http://gicl.cs.drexel.edu/wiki/LearningRoomba Learning Roomba] excellent set of tutorials<br />
<br />
==General To Do==<br />
*Navigation<br />
**Check out this SLAM [http://ocw.mit.edu/courses/aeronautics-and-astronautics/16-412j-cognitive-robotics-spring-2005/projects/1aslam_blas_repo.pdf tutorial]<br />
*Aiming Camera<br />
**[http://www.ez-robot.com/Robots/iRobot-Roomba-Hack Camera option?]<br />
**[http://www.dmcinfo.com/Blog/articleType/ArticleView/articleId/1327/Office-Autonomous-Robot.aspx Autonomous Office Robot] has wireless camera, uses RoboRealm<br />
*Image Processing<br />
<br />
==Dr. Heyer's To Do==<br />
<br />
* Working on camera options. Both groups should continue to keep me posted on their camera requirements.</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=IRobot_Energy_Saver_Project&diff=14316IRobot Energy Saver Project2012-04-26T02:18:13Z<p>Laheyer: /* Useful Links */</p>
<hr />
<div>==Team Pages==<br />
[[Team R2D2]] <br><br />
[[Team Commando]]<br />
<br />
==Tools/Packages==<br />
*[http://www.usna.edu/Users/weapsys/esposito/roomba.matlab/ MatLab Package]<br />
*[http://www.rose-hulman.edu/class/csse/resources/Robotics/ PyCreate]<br />
*[http://cgi.cs.duke.edu/~mac/flail/index.cgi?page=home FLAIL]<br />
<br />
==Useful Links==<br />
*[http://www.irobot.com/hrd_right_rail/create_rr/create_fam/createFam_rr_manuals.html All Manuals]<br />
**May be really useful to command module team<br />
*[http://www.elementdirect.com/files/10542B.pdf BAM documentation]<br />
*[http://www.usna.edu/Users/weapsys/esposito/roomba.matlab/Matlab_Toolbox_iRobot_create_doc.pdf MATLAB Create Toolbox User Guide]<br />
*[http://teyvoniathomas.com/index.php/projects/55-opticalflow.html Theory and practice], visual navigation on the iRobot Create<br />
*[http://www.cs.hmc.edu/~dodds/erdos/ College iRobot Project]<br />
*[http://myroombud.com/ Roomba Costumes]<br />
*[http://gicl.cs.drexel.edu/wiki/LearningRoomba Learning Roomba] excellent set of tutorials<br />
<br />
==General To Do==<br />
*Navigation<br />
**Check out this SLAM [http://ocw.mit.edu/courses/aeronautics-and-astronautics/16-412j-cognitive-robotics-spring-2005/projects/1aslam_blas_repo.pdf tutorial]<br />
*Aiming Camera<br />
**[http://www.ez-robot.com/Robots/iRobot-Roomba-Hack Camera option?]<br />
*Image Processing<br />
<br />
==Dr. Heyer's To Do==<br />
<br />
* Working on camera options. Both groups should continue to keep me posted on their camera requirements.</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=IRobot_Energy_Saver_Project&diff=14315IRobot Energy Saver Project2012-04-26T02:17:53Z<p>Laheyer: /* Useful Links */</p>
<hr />
<div>==Team Pages==<br />
[[Team R2D2]] <br><br />
[[Team Commando]]<br />
<br />
==Tools/Packages==<br />
*[http://www.usna.edu/Users/weapsys/esposito/roomba.matlab/ MatLab Package]<br />
*[http://www.rose-hulman.edu/class/csse/resources/Robotics/ PyCreate]<br />
*[http://cgi.cs.duke.edu/~mac/flail/index.cgi?page=home FLAIL]<br />
<br />
==Useful Links==<br />
*[http://www.irobot.com/hrd_right_rail/create_rr/create_fam/createFam_rr_manuals.html All Manuals]<br />
**May be really useful to command module team<br />
*[http://www.elementdirect.com/files/10542B.pdf BAM documentation]<br />
*[http://www.usna.edu/Users/weapsys/esposito/roomba.matlab/Matlab_Toolbox_iRobot_create_doc.pdf MATLAB Create Toolbox User Guide]<br />
*[http://teyvoniathomas.com/index.php/projects/55-opticalflow.html Theory and practice], visual navigation on the iRobot Create<br />
*[http://www.cs.hmc.edu/~dodds/erdos/ College iRobot Project]<br />
*[http://myroombud.com/ Roomba Costumes]<br />
*{http://gicl.cs.drexel.edu/wiki/LearningRoomba Learning Roomba] excellent set of tutorials<br />
<br />
==General To Do==<br />
*Navigation<br />
**Check out this SLAM [http://ocw.mit.edu/courses/aeronautics-and-astronautics/16-412j-cognitive-robotics-spring-2005/projects/1aslam_blas_repo.pdf tutorial]<br />
*Aiming Camera<br />
**[http://www.ez-robot.com/Robots/iRobot-Roomba-Hack Camera option?]<br />
*Image Processing<br />
<br />
==Dr. Heyer's To Do==<br />
<br />
* Working on camera options. Both groups should continue to keep me posted on their camera requirements.</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=IRobot_Energy_Saver_Project&diff=14306IRobot Energy Saver Project2012-04-25T01:49:24Z<p>Laheyer: /* Dr. Heyer's To Do */</p>
<hr />
<div>==Team Pages==<br />
[[Team R2D2]] <br><br />
[[Team Commando]]<br />
<br />
==Tools/Packages==<br />
*[http://www.usna.edu/Users/weapsys/esposito/roomba.matlab/ MatLab Package]<br />
*[http://www.rose-hulman.edu/class/csse/resources/Robotics/ PyCreate]<br />
*[http://cgi.cs.duke.edu/~mac/flail/index.cgi?page=home FLAIL]<br />
<br />
==Useful Links==<br />
*[http://www.irobot.com/hrd_right_rail/create_rr/create_fam/createFam_rr_manuals.html All Manuals]<br />
**May be really useful to command module team<br />
*[http://www.elementdirect.com/files/10542B.pdf BAM documentation]<br />
*[http://www.robotiklubi.ee/_media/kursused/roomba_sumo/failid/hacking_roomba.pdf iRobot Hacking Guide]<br />
*[http://www.usna.edu/Users/weapsys/esposito/roomba.matlab/Matlab_Toolbox_iRobot_create_doc.pdf MATLAB Create Toolbox User Guide]<br />
*[http://teyvoniathomas.com/index.php/projects/55-opticalflow.html Theory and practice], visual navigation on the iRobot Create<br />
<br />
==General To Do==<br />
*Navigation<br />
**Check out this SLAM [http://ocw.mit.edu/courses/aeronautics-and-astronautics/16-412j-cognitive-robotics-spring-2005/projects/1aslam_blas_repo.pdf tutorial]<br />
*Aiming Camera<br />
**[http://www.ez-robot.com/Robots/iRobot-Roomba-Hack Camera option?]<br />
*Image Processing<br />
<br />
==Dr. Heyer's To Do==<br />
<br />
* Working on camera options. Both groups should continue to keep me posted on their camera requirements.</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=IRobot_Energy_Saver_Project&diff=14305IRobot Energy Saver Project2012-04-25T01:48:30Z<p>Laheyer: /* Useful Links */</p>
<hr />
<div>==Team Pages==<br />
[[Team R2D2]] <br><br />
[[Team Commando]]<br />
<br />
==Tools/Packages==<br />
*[http://www.usna.edu/Users/weapsys/esposito/roomba.matlab/ MatLab Package]<br />
*[http://www.rose-hulman.edu/class/csse/resources/Robotics/ PyCreate]<br />
*[http://cgi.cs.duke.edu/~mac/flail/index.cgi?page=home FLAIL]<br />
<br />
==Useful Links==<br />
*[http://www.irobot.com/hrd_right_rail/create_rr/create_fam/createFam_rr_manuals.html All Manuals]<br />
**May be really useful to command module team<br />
*[http://www.elementdirect.com/files/10542B.pdf BAM documentation]<br />
*[http://www.robotiklubi.ee/_media/kursused/roomba_sumo/failid/hacking_roomba.pdf iRobot Hacking Guide]<br />
*[http://www.usna.edu/Users/weapsys/esposito/roomba.matlab/Matlab_Toolbox_iRobot_create_doc.pdf MATLAB Create Toolbox User Guide]<br />
*[http://teyvoniathomas.com/index.php/projects/55-opticalflow.html Theory and practice], visual navigation on the iRobot Create<br />
<br />
==General To Do==<br />
*Navigation<br />
**Check out this SLAM [http://ocw.mit.edu/courses/aeronautics-and-astronautics/16-412j-cognitive-robotics-spring-2005/projects/1aslam_blas_repo.pdf tutorial]<br />
*Aiming Camera<br />
**[http://www.ez-robot.com/Robots/iRobot-Roomba-Hack Camera option?]<br />
*Image Processing<br />
<br />
==Dr. Heyer's To Do==<br />
<br />
* Laptops are in the cabinet, along with the robots and all accessories. <br />
**Macbook is for BAM group (R2D2) and Dell laptop is for Command module group (Commandos) <br />
**MATLAB and statistics toolbox are installed and now (as of 4-22-12) activated on both<br />
**Cyrus, Leland and Duke are already admin on Macbook, others can be made admin by them<br />
**All Commandos are admin on Dell<br />
**EVERYONE must log in once on wired connection before wireless will work<br />
<br />
* Standing by for camera specs. Need to figure this out soon.<br />
<br />
*Wiki accounts have been requested, coming soon</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=IRobot_Energy_Saver_Project&diff=14304IRobot Energy Saver Project2012-04-24T18:58:07Z<p>Laheyer: /* General To Do */</p>
<hr />
<div>==Team Pages==<br />
[[Team R2D2]] <br><br />
[[Team Commando]]<br />
<br />
==Tools/Packages==<br />
*[http://www.usna.edu/Users/weapsys/esposito/roomba.matlab/ MatLab Package]<br />
*[http://www.rose-hulman.edu/class/csse/resources/Robotics/ PyCreate]<br />
*[http://cgi.cs.duke.edu/~mac/flail/index.cgi?page=home FLAIL]<br />
<br />
==Useful Links==<br />
*[http://www.irobot.com/hrd_right_rail/create_rr/create_fam/createFam_rr_manuals.html All Manuals]<br />
**May be really useful to command module team<br />
*[http://www.elementdirect.com/files/10542B.pdf BAM documentation]<br />
*[http://www.robotiklubi.ee/_media/kursused/roomba_sumo/failid/hacking_roomba.pdf iRobot Hacking Guide]<br />
*[http://www.usna.edu/Users/weapsys/esposito/roomba.matlab/Matlab_Toolbox_iRobot_create_doc.pdf MATLAB Create Toolbox User Guide]<br />
<br />
==General To Do==<br />
*Navigation<br />
**Check out this SLAM [http://ocw.mit.edu/courses/aeronautics-and-astronautics/16-412j-cognitive-robotics-spring-2005/projects/1aslam_blas_repo.pdf tutorial]<br />
*Aiming Camera<br />
**[http://www.ez-robot.com/Robots/iRobot-Roomba-Hack Camera option?]<br />
*Image Processing<br />
<br />
==Dr. Heyer's To Do==<br />
<br />
* Laptops are in the cabinet, along with the robots and all accessories. <br />
**Macbook is for BAM group (R2D2) and Dell laptop is for Command module group (Commandos) <br />
**MATLAB and statistics toolbox are installed and now (as of 4-22-12) activated on both<br />
**Cyrus, Leland and Duke are already admin on Macbook, others can be made admin by them<br />
**All Commandos are admin on Dell<br />
**EVERYONE must log in once on wired connection before wireless will work<br />
<br />
* Standing by for camera specs. Need to figure this out soon.<br />
<br />
*Wiki accounts have been requested, coming soon</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=IRobot_Energy_Saver_Project&diff=14285IRobot Energy Saver Project2012-04-22T22:48:25Z<p>Laheyer: /* Dr. Heyer's To Do */</p>
<hr />
<div>==Team Pages==<br />
[[Team R2D2]] <br><br />
[[Team Commando]]<br />
<br />
==Tools/Packages==<br />
*[http://www.usna.edu/Users/weapsys/esposito/roomba.matlab/ MatLab Package]<br />
*[http://www.rose-hulman.edu/class/csse/resources/Robotics/ PyCreate]<br />
*[http://cgi.cs.duke.edu/~mac/flail/index.cgi?page=home FLAIL]<br />
<br />
==Useful Links==<br />
*[http://www.irobot.com/hrd_right_rail/create_rr/create_fam/createFam_rr_manuals.html All Manuals]<br />
**May be really useful to command module team<br />
*[http://www.elementdirect.com/files/10542B.pdf BAM documentation]<br />
<br />
==General To Do==<br />
*Navigation<br />
**Check out this SLAM [http://ocw.mit.edu/courses/aeronautics-and-astronautics/16-412j-cognitive-robotics-spring-2005/projects/1aslam_blas_repo.pdf tutorial]<br />
*Aiming Camera<br />
*Image Processing<br />
<br />
==Dr. Heyer's To Do==<br />
<br />
* Laptops are in the cabinet, along with the robots and all accessories. <br />
**Macbook is for BAM group (R2D2) and Dell laptop is for Command module group (Commandos) <br />
**MATLAB and statistics toolbox are installed and now (as of 4-22-12) activated on both<br />
**Cyrus, Leland and Duke are already admin on Macbook, others can be made admin by them<br />
**All Commandos are admin on Dell<br />
**EVERYONE must log in once on wired connection before wireless will work<br />
<br />
* Standing by for camera specs. Need to figure this out soon.<br />
<br />
*Wiki accounts have been requested, coming soon</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=IRobot_Energy_Saver_Project&diff=14284IRobot Energy Saver Project2012-04-22T22:48:03Z<p>Laheyer: /* General To Do */</p>
<hr />
<div>==Team Pages==<br />
[[Team R2D2]] <br><br />
[[Team Commando]]<br />
<br />
==Tools/Packages==<br />
*[http://www.usna.edu/Users/weapsys/esposito/roomba.matlab/ MatLab Package]<br />
*[http://www.rose-hulman.edu/class/csse/resources/Robotics/ PyCreate]<br />
*[http://cgi.cs.duke.edu/~mac/flail/index.cgi?page=home FLAIL]<br />
<br />
==Useful Links==<br />
*[http://www.irobot.com/hrd_right_rail/create_rr/create_fam/createFam_rr_manuals.html All Manuals]<br />
**May be really useful to command module team<br />
*[http://www.elementdirect.com/files/10542B.pdf BAM documentation]<br />
<br />
==General To Do==<br />
*Navigation<br />
**Check out this SLAM [http://ocw.mit.edu/courses/aeronautics-and-astronautics/16-412j-cognitive-robotics-spring-2005/projects/1aslam_blas_repo.pdf tutorial]<br />
*Aiming Camera<br />
*Image Processing<br />
<br />
==Dr. Heyer's To Do==<br />
<br />
* Laptops are in the cabinet, along with the robots and all accessories. <br />
**Macbook is for BAM group (R2D2) and Dell laptop is for Command module group (Commandos) <br />
**MATLAB and statistics toolbox are installed and now (as of 4-22-12) activated on both<br />
**Cyrus, Leland and Duke are already admin on Macbook, others can be made admin by them<br />
**All Commandos are admin on Dell<br />
**EVERYONE must log in once on wired connection before wireless will work<br />
<br />
<br />
* Standing by for camera specs. Need to figure this out soon.<br />
<br />
*Wiki accounts have been requested, coming soon</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=IRobot_Energy_Saver_Project&diff=14283IRobot Energy Saver Project2012-04-22T22:47:44Z<p>Laheyer: /* General To Do */</p>
<hr />
<div>==Team Pages==<br />
[[Team R2D2]] <br><br />
[[Team Commando]]<br />
<br />
==Tools/Packages==<br />
*[http://www.usna.edu/Users/weapsys/esposito/roomba.matlab/ MatLab Package]<br />
*[http://www.rose-hulman.edu/class/csse/resources/Robotics/ PyCreate]<br />
*[http://cgi.cs.duke.edu/~mac/flail/index.cgi?page=home FLAIL]<br />
<br />
==Useful Links==<br />
*[http://www.irobot.com/hrd_right_rail/create_rr/create_fam/createFam_rr_manuals.html All Manuals]<br />
**May be really useful to command module team<br />
*[http://www.elementdirect.com/files/10542B.pdf BAM documentation]<br />
<br />
==General To Do==<br />
*Navigation<br />
**Check out this [http://ocw.mit.edu/courses/aeronautics-and-astronautics/16-412j-cognitive-robotics-spring-2005/projects/1aslam_blas_repo.pdf tutorial]<br />
*Aiming Camera<br />
*Image Processing<br />
<br />
==Dr. Heyer's To Do==<br />
<br />
* Laptops are in the cabinet, along with the robots and all accessories. <br />
**Macbook is for BAM group (R2D2) and Dell laptop is for Command module group (Commandos) <br />
**MATLAB and statistics toolbox are installed and now (as of 4-22-12) activated on both<br />
**Cyrus, Leland and Duke are already admin on Macbook, others can be made admin by them<br />
**All Commandos are admin on Dell<br />
**EVERYONE must log in once on wired connection before wireless will work<br />
<br />
<br />
* Standing by for camera specs. Need to figure this out soon.<br />
<br />
*Wiki accounts have been requested, coming soon</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=IRobot_Energy_Saver_Project&diff=14282IRobot Energy Saver Project2012-04-22T22:47:11Z<p>Laheyer: /* General To Do */</p>
<hr />
<div>==Team Pages==<br />
[[Team R2D2]] <br><br />
[[Team Commando]]<br />
<br />
==Tools/Packages==<br />
*[http://www.usna.edu/Users/weapsys/esposito/roomba.matlab/ MatLab Package]<br />
*[http://www.rose-hulman.edu/class/csse/resources/Robotics/ PyCreate]<br />
*[http://cgi.cs.duke.edu/~mac/flail/index.cgi?page=home FLAIL]<br />
<br />
==Useful Links==<br />
*[http://www.irobot.com/hrd_right_rail/create_rr/create_fam/createFam_rr_manuals.html All Manuals]<br />
**May be really useful to command module team<br />
*[http://www.elementdirect.com/files/10542B.pdf BAM documentation]<br />
<br />
==General To Do==<br />
*Navigation<br />
**Check out this tutorial: <br />
*Aiming Camera<br />
*Image Processing<br />
<br />
==Dr. Heyer's To Do==<br />
<br />
* Laptops are in the cabinet, along with the robots and all accessories. <br />
**Macbook is for BAM group (R2D2) and Dell laptop is for Command module group (Commandos) <br />
**MATLAB and statistics toolbox are installed and now (as of 4-22-12) activated on both<br />
**Cyrus, Leland and Duke are already admin on Macbook, others can be made admin by them<br />
**All Commandos are admin on Dell<br />
**EVERYONE must log in once on wired connection before wireless will work<br />
<br />
<br />
* Standing by for camera specs. Need to figure this out soon.<br />
<br />
*Wiki accounts have been requested, coming soon</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=IRobot_Energy_Saver_Project&diff=14280IRobot Energy Saver Project2012-04-22T18:41:04Z<p>Laheyer: /* Dr. Heyer's To Do */</p>
<hr />
<div>==Team Pages==<br />
[[Team R2D2]] <br><br />
[[Team Commando]]<br />
<br />
==Tools/Packages==<br />
*[http://www.usna.edu/Users/weapsys/esposito/roomba.matlab/ MatLab Package]<br />
*[http://www.rose-hulman.edu/class/csse/resources/Robotics/ PyCreate]<br />
*[http://cgi.cs.duke.edu/~mac/flail/index.cgi?page=home FLAIL]<br />
<br />
==Useful Links==<br />
*[http://www.irobot.com/hrd_right_rail/create_rr/create_fam/createFam_rr_manuals.html All Manuals]<br />
**May be really useful to command module team<br />
<br />
==General To Do==<br />
*Navigation<br />
*Aiming Camera<br />
*Image Processing<br />
<br />
==Dr. Heyer's To Do==<br />
<br />
* Laptops are in the cabinet, along with the robots and all accessories. <br />
**Macbook is for BAM group (R2D2) and Dell laptop is for Command module group (Commandos) <br />
**MATLAB and statistics toolbox are installed and now (as of 4-22-12) activated on both<br />
**Cyrus, Leland and Duke are already admin on Macbook, others can be made admin by them<br />
**All Commandos are admin on Dell<br />
**EVERYONE must log in once on wired connection before wireless will work<br />
<br />
<br />
* Standing by for camera specs. Need to figure this out soon.<br />
<br />
*Wiki accounts have been requested, coming soon</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=IRobot_Energy_Saver_Project&diff=14279IRobot Energy Saver Project2012-04-22T18:40:09Z<p>Laheyer: /* Dr. Heyer's To Do */</p>
<hr />
<div>==Team Pages==<br />
[[Team R2D2]] <br><br />
[[Team Commando]]<br />
<br />
==Tools/Packages==<br />
*[http://www.usna.edu/Users/weapsys/esposito/roomba.matlab/ MatLab Package]<br />
*[http://www.rose-hulman.edu/class/csse/resources/Robotics/ PyCreate]<br />
*[http://cgi.cs.duke.edu/~mac/flail/index.cgi?page=home FLAIL]<br />
<br />
==Useful Links==<br />
*[http://www.irobot.com/hrd_right_rail/create_rr/create_fam/createFam_rr_manuals.html All Manuals]<br />
**May be really useful to command module team<br />
<br />
==General To Do==<br />
*Navigation<br />
*Aiming Camera<br />
*Image Processing<br />
<br />
==Dr. Heyer's To Do==<br />
<br />
* Laptops are in the cabinet, along with the robots and all accessories. <br />
**Macbook is for BAM group (R2D2) and Dell laptop is for Command module group (Commandos) <br />
**MATLAB and statistics toolbox are installed and now (as of 4-22-12) activated on both<br />
**Cyrus, Leland and Duke are already admin on Macbook, others can be made admin by them<br />
**All Commandos are admin on Dell<br />
**EVERYONE must log in once on wired connection before wireless will work<br />
<br />
<br />
* Standing by for camera specs. Need to figure this out soon.</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=IRobot_Energy_Saver_Project&diff=14278IRobot Energy Saver Project2012-04-22T18:35:20Z<p>Laheyer: /* Dr. Heyer's To Do */</p>
<hr />
<div>==Team Pages==<br />
[[Team R2D2]] <br><br />
[[Team Commando]]<br />
<br />
==Tools/Packages==<br />
*[http://www.usna.edu/Users/weapsys/esposito/roomba.matlab/ MatLab Package]<br />
*[http://www.rose-hulman.edu/class/csse/resources/Robotics/ PyCreate]<br />
*[http://cgi.cs.duke.edu/~mac/flail/index.cgi?page=home FLAIL]<br />
<br />
==Useful Links==<br />
*[http://www.irobot.com/hrd_right_rail/create_rr/create_fam/createFam_rr_manuals.html All Manuals]<br />
**May be really useful to command module team<br />
<br />
==General To Do==<br />
*Navigation<br />
*Aiming Camera<br />
*Image Processing<br />
<br />
==Dr. Heyer's To Do==<br />
<br />
* Laptops are in the cabinet, along with the robots and all accessories. <br />
**Macbook is for BAM group (R2D2) and Dell is for Command module group (Commandos) <br />
**MATLAB and statistics toolbox are installed and now (as of 4-22-12) activated on both<br />
**Cyrus, Leland and Duke are already admin on Macbook, others can be made admin by them<br />
<br />
**EVERYONE must log in once on wired connection before wireless will work<br />
<br />
<br />
* Standing by for camera specs. Need to figure this out soon.</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=WEEK_FIFTEEN_(April_23_-_27)&diff=14079WEEK FIFTEEN (April 23 - 27)2012-03-31T20:10:15Z<p>Laheyer: </p>
<hr />
<div>Work on your personal research proposal.<br />
<br />
'''Last day for feedback on your proposal: Wed, April 25.'''</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=WEEK_TWELVE_(April_2_-_6)&diff=14078WEEK TWELVE (April 2 - 6)2012-03-31T20:07:15Z<p>Laheyer: </p>
<hr />
<div>Discuss what we have learned so far and start thinking about project for this summer. <br />
<br />
What can be done in small pilot projects to generate preliminary data? Remember that we do not have to complete the project in one summer.<br />
<br />
Journals due at Friday meeting, 3:00 p.m.<br />
<br />
'''Meet in Think Tank at 3:00. Video conference with MWSU 3:30 - 4:30 eastern.'''<br />
<br />
Be prepared to answer questions from MWSU and have questions to ask them.<br />
<br />
Discuss this paper about [http://www.jbioleng.org/content/pdf/1754-1611-5-12.pdf data sheets for standardized parts].<br />
<br />
<br />
<br />
<br />
'''Relevant PRESENTATIONS'''<br><br />
This PPT file contains all the slides from student presentations addressing the idea proposed by MWSU. <br><br />
[[Media:Reports_on_Circuits.pptx]]<br />
<br />
<br />
This PPT contains slides summarizing some of the best and most complicated papers. <br><br />
[[Media:Week_11.pptx]]</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=WEEK_TEN_(March_19_-_23)&diff=13950WEEK TEN (March 19 - 23)2012-03-11T19:02:25Z<p>Laheyer: </p>
<hr />
<div>This week, you will be working in one of four teams.<br />
<br />
'''Monday 4:30 - 5:30: pm Alex and Dancho''' = explain C. dog protein expression system [[Media:C_dog_concept.pdf]]<br />
<br />
'''Tuesday 9:45 - 10:45 am Duke and Ben''' = improve double cloning using type IIs enzymes. Remember Missouri Western PPT and [http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/cleavage_olignucleotides.asp#.T1e7HJjufqE How close to the edge can a restriction enzyme cut?]<br />
<br />
'''Tuesday 4:30 - 5:30 pm Ellen, Nishita and Erich''' = summarize noise issues and describe optimal pathway characteristics. Add to existing PPT presentation but make a new version when you do this. [[Synthetic_Biology_Network_Research#MWSU]]<br><br />
<br />
'''Wednesday 4:30 - 5:30 pm Becca and Kirsten''' = explain how CRIM and transposons in bacteria work in ''E. coli''. <br />
<br />
'''Friday 2:30 - 4:00 pm''' 4 presentations by the four groups.</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=WEEK_ELEVEN_(March_26_-_30)&diff=13949WEEK ELEVEN (March 26 - 30)2012-03-11T19:01:39Z<p>Laheyer: </p>
<hr />
<div>This week, you will be working in the same team as last week.<br />
<br />
'''Monday 4:30 - 5:30: pm Alex and Dancho''' = [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3053042/?tool=pubmed Multichromatic Control of Gene Expression]<br />
<br />
'''Tuesday 9:45 - 10:45 am Duke and Ben''' = [http://www.nature.com/nature/journal/v469/n7329/full/nature09565.html Chemical Wires]<br />
<br />
'''Tuesday 4:30 - 5:30 pm Ellen, Nishita and Erich''' = [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2782888/?tool=pubmed Synthetic RBSs]<br />
<br />
'''Wednesday 4:30 - 5:30 pm Becca and Kirsten''' = [http://www.nature.com/nature/journal/v481/n7379/full/nature10722.html BioPixels]<br />
<br />
'''Friday 2:30 - 4:00 pm''' 4 presentations by the four groups.</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=WEEK_ELEVEN_(March_26_-_30)&diff=13948WEEK ELEVEN (March 26 - 30)2012-03-11T01:59:34Z<p>Laheyer: </p>
<hr />
<div>This week, you will be working in the same team as last week.<br />
<br />
'''Monday 4:30 - 5:30: pm Alex and Dancho''' = [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3053042/?tool=pubmed Multichromatic Control of Gene Expression]<br />
<br />
'''Tuesday 9:45 - 10:45 am Duke and Ben''' = [http://www.nature.com/nature/journal/v469/n7329/full/nature09565.html Chemical Wires]<br />
<br />
'''Tuesday 4:30 - 5:30 pm Kirsten, Nishita and Erich''' = [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2782888/?tool=pubmed Synthetic RBSs]<br />
<br />
'''Wednesday 4:30 - 5:30 pm Becca and Ellen''' = [http://www.nature.com/nature/journal/v481/n7379/full/nature10722.html BioPixels]<br />
<br />
'''Friday 2:30 - 4:00 pm''' 4 presentations by the four groups.</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=WEEK_TEN_(March_19_-_23)&diff=13947WEEK TEN (March 19 - 23)2012-03-11T01:51:04Z<p>Laheyer: </p>
<hr />
<div>This week, you will be working in one of four teams.<br />
<br />
'''Monday 4:30 - 5:30: pm Alex and Dancho''' = explain C. dog protein expression system [[Media:C_dog_concept.pdf]]<br />
<br />
'''Tuesday 9:45 - 10:45 am Duke and Ben''' = improve double cloning using type IIs enzymes. Remember Missouri Western PPT and [http://www.neb.com/nebecomm/tech_reference/restriction_enzymes/cleavage_olignucleotides.asp#.T1e7HJjufqE How close to the edge can a restriction enzyme cut?]<br />
<br />
'''Tuesday 4:30 - 5:30 pm Kirsten, Nishita and Erich''' = summarize noise issues and describe optimal pathway characteristics. Add to existing PPT presentation but make a new version when you do this. [[Synthetic_Biology_Network_Research#MWSU]]<br><br />
<br />
'''Wednesday 4:30 - 5:30 pm Becca and Ellen''' = explain how CRIM and transposons in bacteria work in ''E. coli''. <br />
<br />
'''Friday 2:30 - 4:00 pm''' 4 presentations by the four groups.</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=WEEK_THREE_(January_30_-_February_3)&diff=13647WEEK THREE (January 30 - February 3)2012-01-26T01:05:13Z<p>Laheyer: </p>
<hr />
<div>We have an X-prize type of challenge for you. <br />
<br />
We are wondering if there are a set of [http://www.neb.com/nebecomm/EnzymeFinderSearchByTypeIIs.asp type IIs restriction enzymes] within which you could embed other type IIs restriction site(s) to do something useful or interesting. Perhaps you could improve upon Golden Gate assembly, or other methods in the paper reviewed by Becca [http://gcat.davidson.edu/mediawiki-1.15.0/images/c/ca/Synthetic_assembly_overview.pdf Tom Ellis,*ab Tom Adieac and Geoff S. Baldwin]. Or perhaps you can think of a way to represent a mathematical problem with combinations of sites.<br />
<br />
You can work solo or in teams of your design. However, everyone must participate in this challenge.<br />
<br />
<br />
Ethics paper for discussion in large group (all read):<br />
<br />
'''Talking the Talk''' <br><br />
Colin Mcilswain <br><br />
Nature. Vol 465, page 867.<br />
<br />
<br />
Paper Presentations for Week Three:<br />
<br />
Team 1 MONDAY = Alex, Nishita, Erich<br><br />
'''Noise in Gene Expression: Origins, Consequences, and Control''' <br><br />
Jonathan M. Raser and Erin K. O’Shea <br><br />
Science. Vol. 309, page 2010<br />
<br />
Team 2 TUESDAY = Ellen, Dancho, Kirsten<br><br />
'''Synthetic Biology: Integrated Gene Circuits''' <br><br />
Nagarajan Nandagopal and Michael B. Elowitz<br><br />
Science. Vol. 333, page 1244. <br />
<br />
Team 3 WEDNESDAY = Duke, Becca, Ben <br><br />
'''Network Motifs: Simple Building<br />
Blocks of Complex Networks''' <br><br />
R. Milo, S. Shen-Orr, et al<br><br />
Science. Vol. 298, page 824.</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=WEEK_THREE_(January_30_-_February_3)&diff=13646WEEK THREE (January 30 - February 3)2012-01-26T00:51:53Z<p>Laheyer: </p>
<hr />
<div>We have an X-prize type of challenge for you. <br />
<br />
We are wondering if there are a set of [http://www.neb.com/nebecomm/EnzymeFinderSearchByTypeIIs.asp type IIs restriction enzymes] within which you could embed other type IIs restriction site(s) to do something useful or interesting. Perhaps you could improve upon Golden Gate assembly, or other methods in the paper reviewed by Becca [http://gcat.davidson.edu/mediawiki-1.15.0/images/c/ca/Synthetic_assembly_overview.pdf Tom Ellis,*ab Tom Adieac and Geoff S. Baldwin]. Or perhaps you can think of a way to represent a mathematical problem with combinations of sites.<br />
<br />
You can work solo or in teams of your design. However, everyone must participate in this challenge.<br />
<br />
Paper Presentations for Week Three:<br />
<br />
Team 1 = Duke, Becca, Ben<br><br />
'''Synthetic Biology: Integrated Gene Circuits''' <br><br />
Nagarajan Nandagopal and Michael B. Elowitz<br><br />
Science. Vol. 333, page 1244. <br />
<br />
<br />
Team 2 = Alex, Dancho Kirsten<br><br />
<br />
<br />
<br />
Team 3 = Ellen, Nishita, Erich<br></div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=Synthetic_Biology_Network_Research&diff=13645Synthetic Biology Network Research2012-01-26T00:50:00Z<p>Laheyer: </p>
<hr />
<div>This page is designed as a community page for students at MWSU and Davidson College who are using synthetic biology to learn more about graph theory and network topology. <br />
<br />
==Davidson College==<br />
Our first meeting will be on Thursday, January 19, 2012. We will meet at 11 am (the common hour) in the Think Tank in the back of Belk computer lab. <br />
<br />
'''Grading'''<br />
* Weekly Journals (your own paper summary and those of others) = 30% final grade<br />
* Weekly Presentations = 30% final grade<br />
* Research Proposal by teams = 40% final grade<br />
<br />
You must keep hard copies of your weekly journal entries in a 3-ring binder. We will grade these periodically during the semester. You will also keep copies of your papers, any drawings of ideas you have, protocols used in lab, etc. <br />
<br />
'''Scheduling with [http://doodle.com/xkssebxsv4g3rwxk Doodle]'''<br />
<br />
<br />
[[WEEK ONE (January 17 - 20)]]<br />
<br />
<br />
[[WEEK TWO (January 23 - 27)]]<br />
<br />
<br />
[[WEEK THREE (January 30 - February 3)]]<br />
<br />
<br />
[[WEEK FOUR (February 6 - 10)]] '''WET LAB WEEK'''<br />
<br />
<br />
[[WEEK FIVE (February 13 - 17)]]<br />
<br />
<br />
[[WEEK SIX (January 20 - 24)]]<br />
<br />
<br />
[[WEEK SEVEN (February 27 - March 2)]]<br />
<br />
<br />
[[WEEK EIGHT (March 5 - 9)]] '''SPRING BREAK'''<br />
<br />
<br />
<br />
Over the next 14 weeks, we will read a series of papers. We have chosen some to help us get started, but as the semester progresses, you will take the lead in identifying papers. Some of these papers will be easy for you, but others will be more difficult. We will work as a group to understand what is going on. In all cases, we will use these papers to help us frame a research project that will be conducted this summer by 8 Davidson students. <br />
<br />
We will need to become experts in the [http://2011.igem.org/Team:Washington/Magnetosomes/Magnet_Toolkit magnetosome] produced by bacteria. We will need to identify key papers to understand what is known so far. We also need to understand what UW-Seattle iGEM2011 did with this project. <br />
<br />
<br />
<center>'''Some possible papers'''</center><br />
* '''The creativity crisis'''. <br><br />
Po Bronson and Ashley Merryman <br><br />
Newsweek. July 19, 2010. page 44. <br />
<br />
* '''Synthetic Biology Moving into the Clinic'''<br><br />
Warren C. Ruder,* Ting Lu,* James J. Collins<br><br />
Science. Vol. 333. page 1248. <br />
<br />
* '''Engineering bacteria to solve the Burnt Pancake Problem'''. <br><br />
[http://www.jbioleng.org/content/2/1/8 Haynes, Karmella, et al.]<br><br />
Journal of Biological Engineering. Vol. 2(8): 1 – 12.<br />
<br />
* '''Solving a Hamiltonian Path Problem with a Bacterial Computer'''. <br><br />
[http://www.jbioleng.org/content/3/1/11 Baumgardner, Jordan et al.]<br><br />
Journal of Biological Engineering. Vol. 3:11<br />
<br />
* '''Bacterial Hash Function Using DNA-Based XOR Logic Reveals Unexpected Behavior of the LuxR Promoter'''.<br><br />
[http://www.ibc7.org/article/journal_v.php?sid=265 Brianna Pearson*, Kin H. Lau* et al.] <br><br />
Interdisciplinary Bio Central. Vol. 3, article no. 10<br />
<br />
* '''DNA assembly for synthetic biology: from parts to pathways and beyond'''<br><br />
[http://gcat.davidson.edu/mediawiki-1.15.0/images/c/ca/Synthetic_assembly_overview.pdf Tom Ellis,*ab Tom Adieac and Geoff S. Baldwin] <br><br />
Integr. Biol., 2011, 3, 109–118<br />
<br />
* '''Information Transduction Capacity of Noisy Biochemical Signaling Networks'''<br><br />
Raymond Cheong, Alex Rhee, Chiaochun Joanne Wang, Ilya Nemenman, Andre Levchenko<br><br />
Science. Vol. 334, page 354. <br />
<br />
* '''Synthetic Biology: Regulating Industry Uses of New Biotechnologies'''<br><br />
Brent Erickson, Rina Singh, Paul Winters<br><br />
Science. Vol. 333, page 1254. <br />
<br />
* '''Synthetic Biology: Integrated Gene Circuits''' <br><br />
Nagarajan Nandagopal and Michael B. Elowitz<br><br />
Science. Vol. 333, page 1244. <br />
<br />
* '''Community Structure in Time-Dependent, Multiscale, and Multiplex Networks''' <br><br />
Peter J. Mucha, Thomas Richardson, Kevin Macon, Mason A. Porter, and Jukka-Pekka Onnela <br><br />
Science. Vol. 328. page 876-878.<br />
<br />
* '''Stochastic Pulse Regulation in Bacterial Stress Response'''<br><br />
James C. W. Locke,* Jonathan W. Young,* Michelle Fontes, María Jesús Hernández Jiménez, Michael B. Elowitz<br><br />
Science. Vol. 334. page 366. <br />
<br />
* '''Synthetic biology: applications come of age'''<br><br />
Ahmad S. Khalil* and James J. Collins<br><br />
Nature Review Genetics. Vol. 11. page 367. <br />
<br />
* '''A Cultured Greigite-Producing Magnetotactic Bacterium in a Novel Group of Sulfate-Reducing Bacteria'''<br><br />
Christopher T. Lefèvre, et al.<br><br />
Science. Vol. 334. page 1720.<br />
<br />
* '''Five hard truths for synthetic biology'''. <br><br />
Roberta Kwok<br><br />
Nature. Vol. 463. page 288. <br />
<br />
* '''Controllability of complex networks'''<br><br />
Yang-Yu Liu1,2, Jean-Jacques Slotine3,4 & Albert-La ́szlo ́ Baraba ́si<br><br />
Nature. Vol. 473. page 167. <br />
<br />
<br />
<br />
<br />
<br />
==MWSU==</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=Synthetic_Biology_Network_Research&diff=13644Synthetic Biology Network Research2012-01-26T00:49:42Z<p>Laheyer: </p>
<hr />
<div>This page is designed as a community page for students at MWSU and Davidson College who are using synthetic biology to learn more about graph theory and network topology. <br />
<br />
==Davidson College==<br />
Our first meeting will be on Thursday, January 19, 2012. We will meet at 11 am (the common hour) in the Think Tank in the back of Belk computer lab. <br />
<br />
'''Grading'''<br />
* Weekly Journals (your own paper summary and those of others) = 30% final grade<br />
* Weekly Presentations = 30% final grade<br />
* Research Proposal by teams = 40% final grade<br />
<br />
You must keep hard copies of your weekly journal entries in a 3-ring binder. We will grade these periodically during the semester. You will also keep copies of your papers, any drawings of ideas you have, protocols used in lab, etc. <br />
<br />
'''Scheduling with [http://doodle.com/xkssebxsv4g3rwxk Doodle]'''<br />
<br />
[[WEEK ONE (January 17 - 20)]]<br />
<br />
<br />
[[WEEK TWO (January 23 - 27)]]<br />
<br />
<br />
[[WEEK THREE (January 30 - February 3)]]<br />
<br />
<br />
[[WEEK FOUR (February 6 - 10)]] '''WET LAB WEEK'''<br />
<br />
<br />
[[WEEK FIVE (February 13 - 17)]]<br />
<br />
<br />
[[WEEK SIX (January 20 - 24)]]<br />
<br />
<br />
[[WEEK SEVEN (February 27 - March 2)]]<br />
<br />
<br />
[[WEEK EIGHT (March 5 - 9)]] '''SPRING BREAK'''<br />
<br />
<br />
<br />
Over the next 14 weeks, we will read a series of papers. We have chosen some to help us get started, but as the semester progresses, you will take the lead in identifying papers. Some of these papers will be easy for you, but others will be more difficult. We will work as a group to understand what is going on. In all cases, we will use these papers to help us frame a research project that will be conducted this summer by 8 Davidson students. <br />
<br />
We will need to become experts in the [http://2011.igem.org/Team:Washington/Magnetosomes/Magnet_Toolkit magnetosome] produced by bacteria. We will need to identify key papers to understand what is known so far. We also need to understand what UW-Seattle iGEM2011 did with this project. <br />
<br />
<br />
<center>'''Some possible papers'''</center><br />
* '''The creativity crisis'''. <br><br />
Po Bronson and Ashley Merryman <br><br />
Newsweek. July 19, 2010. page 44. <br />
<br />
* '''Synthetic Biology Moving into the Clinic'''<br><br />
Warren C. Ruder,* Ting Lu,* James J. Collins<br><br />
Science. Vol. 333. page 1248. <br />
<br />
* '''Engineering bacteria to solve the Burnt Pancake Problem'''. <br><br />
[http://www.jbioleng.org/content/2/1/8 Haynes, Karmella, et al.]<br><br />
Journal of Biological Engineering. Vol. 2(8): 1 – 12.<br />
<br />
* '''Solving a Hamiltonian Path Problem with a Bacterial Computer'''. <br><br />
[http://www.jbioleng.org/content/3/1/11 Baumgardner, Jordan et al.]<br><br />
Journal of Biological Engineering. Vol. 3:11<br />
<br />
* '''Bacterial Hash Function Using DNA-Based XOR Logic Reveals Unexpected Behavior of the LuxR Promoter'''.<br><br />
[http://www.ibc7.org/article/journal_v.php?sid=265 Brianna Pearson*, Kin H. Lau* et al.] <br><br />
Interdisciplinary Bio Central. Vol. 3, article no. 10<br />
<br />
* '''DNA assembly for synthetic biology: from parts to pathways and beyond'''<br><br />
[http://gcat.davidson.edu/mediawiki-1.15.0/images/c/ca/Synthetic_assembly_overview.pdf Tom Ellis,*ab Tom Adieac and Geoff S. Baldwin] <br><br />
Integr. Biol., 2011, 3, 109–118<br />
<br />
* '''Information Transduction Capacity of Noisy Biochemical Signaling Networks'''<br><br />
Raymond Cheong, Alex Rhee, Chiaochun Joanne Wang, Ilya Nemenman, Andre Levchenko<br><br />
Science. Vol. 334, page 354. <br />
<br />
* '''Synthetic Biology: Regulating Industry Uses of New Biotechnologies'''<br><br />
Brent Erickson, Rina Singh, Paul Winters<br><br />
Science. Vol. 333, page 1254. <br />
<br />
* '''Synthetic Biology: Integrated Gene Circuits''' <br><br />
Nagarajan Nandagopal and Michael B. Elowitz<br><br />
Science. Vol. 333, page 1244. <br />
<br />
* '''Community Structure in Time-Dependent, Multiscale, and Multiplex Networks''' <br><br />
Peter J. Mucha, Thomas Richardson, Kevin Macon, Mason A. Porter, and Jukka-Pekka Onnela <br><br />
Science. Vol. 328. page 876-878.<br />
<br />
* '''Stochastic Pulse Regulation in Bacterial Stress Response'''<br><br />
James C. W. Locke,* Jonathan W. Young,* Michelle Fontes, María Jesús Hernández Jiménez, Michael B. Elowitz<br><br />
Science. Vol. 334. page 366. <br />
<br />
* '''Synthetic biology: applications come of age'''<br><br />
Ahmad S. Khalil* and James J. Collins<br><br />
Nature Review Genetics. Vol. 11. page 367. <br />
<br />
* '''A Cultured Greigite-Producing Magnetotactic Bacterium in a Novel Group of Sulfate-Reducing Bacteria'''<br><br />
Christopher T. Lefèvre, et al.<br><br />
Science. Vol. 334. page 1720.<br />
<br />
* '''Five hard truths for synthetic biology'''. <br><br />
Roberta Kwok<br><br />
Nature. Vol. 463. page 288. <br />
<br />
* '''Controllability of complex networks'''<br><br />
Yang-Yu Liu1,2, Jean-Jacques Slotine3,4 & Albert-La ́szlo ́ Baraba ́si<br><br />
Nature. Vol. 473. page 167. <br />
<br />
<br />
<br />
<br />
<br />
==MWSU==</div>Laheyerhttp://gcat.davidson.edu/GcatWiki/index.php?title=WEEK_THREE_(January_30_-_February_3)&diff=13643WEEK THREE (January 30 - February 3)2012-01-26T00:45:13Z<p>Laheyer: </p>
<hr />
<div>We have an X-prize type of challenge for you. <br />
<br />
We are wondering if there are a set of [http://www.neb.com/nebecomm/EnzymeFinderSearchByTypeIIs.asp type IIs restriction enzymes] within which you could embed other type IIs restriction site(s) to do something useful or interesting. Perhaps you could improve upon Golden Gate assembly, or other methods in the paper reviewed by Becca [http://gcat.davidson.edu/mediawiki-1.15.0/images/c/ca/Synthetic_assembly_overview.pdf Tom Ellis,*ab Tom Adieac and Geoff S. Baldwin]. Or perhaps you can think of a way to represent a mathematical problem with combinations of sites.<br />
<br />
You can work solo or in teams of your design. However, everyone must participate in this challenge.<br />
<br />
Paper Presentations for Week Three:<br />
<br />
Team 1 Monday = Duke, Alex, Ellen<br><br />
'''Engineering bacteria to solve the Burnt Pancake Problem'''. <br><br />
[http://www.jbioleng.org/content/2/1/8 Haynes, Karmella, et al.]<br><br />
Journal of Biological Engineering. Vol. 2(8): 1 – 12.<br />
<br />
<br />
Team 2 Tuesday = Dancho and Nishita<br><br />
'''Solving a Hamiltonian Path Problem with a Bacterial Computer'''. <br><br />
[http://www.jbioleng.org/content/3/1/11 Baumgardner, Jordan et al.]<br><br />
Journal of Biological Engineering. Vol. 3:11<br />
<br />
<br />
Team 3 Wednesday = Ben, Kirsten, Erich<br><br />
'''Bacterial Hash Function Using DNA-Based XOR Logic Reveals Unexpected Behavior of the LuxR Promoter'''.<br><br />
[http://www.ibc7.org/article/journal_v.php?sid=265 Brianna Pearson*, Kin H. Lau* et al.] <br><br />
Interdisciplinary Bio Central. Vol. 3, article no. 10.<br></div>Laheyer