Time of bloom - Revision history

Laheyer at 16:44, 12 August 2021

2021-08-12T16:44:29Z

Laheyer at 16:33, 12 August 2021

2021-08-12T16:33:57Z

Laheyer at 16:30, 12 August 2021

2021-08-12T16:30:17Z

Laheyer at 21:19, 11 August 2021

2021-08-11T21:19:13Z

Aumudd at 00:51, 30 April 2013

2013-04-30T00:51:19Z

Aumudd at 00:45, 30 April 2013

2013-04-30T00:45:09Z

Aumudd at 00:42, 30 April 2013

2013-04-30T00:42:39Z

Aumudd at 00:29, 30 April 2013

2013-04-30T00:29:48Z

Aumudd at 00:28, 30 April 2013

2013-04-30T00:28:35Z

Aumudd at 08:05, 29 April 2013

2013-04-29T08:05:51Z

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 *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])
-[[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]]
+[[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]]
 ====The Timing of Flowering====
 *Flowering is controlled by several “major pathways: the photoperiod and vernalization pathways control flowering in response to seasonal changes in day length and temperature; the ambient temperature pathway responds to daily growth temperatures; and the age, autonomous, and gibberellin pathways act more independently of environmental stimuli.” ([http://www.sciencedirect.com/science/article/pii/S0092867410004411 Fornara ''et al.'', 2010])
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 <gallery widths="102px" heights="102px" perrow="6">
-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
+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
-File:Sung_Pathway.gif|[http://www.sciencedirect.com/science/article/pii/S1369526602000146 Sung ''et al.'', 2003]; permission granted
+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
-File:Boss_Pathway.gif|[http://www.plantcell.org/content/16/suppl_1/S18/F2.expansion Boss ''et al.'', 2004]; permission granted
+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
-File:Boss_Pathway_2.jpeg|[http://www.plantcell.org/content/16/suppl_1/S18/F3.expansion Boss ''et al.'', 2004]; permission granted
+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
-File:Henderson_and_Dean_Pathway.jpeg|[http://dev.biologists.org/content/131/16/3829/F1.expansion.html Henderson and Dean, 2004]; permission granted
+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
-File:Amasino_Pathway.jpeg|[http://www.sciencedirect.com/science/article/pii/S0958166905000273 Amasino, 2005]; permission granted
+File:Amasino_Pathway.jpeg|alt=Diagram of pathway from Amasino, 2005|[http://www.sciencedirect.com/science/article/pii/S0958166905000273 Amasino, 2005]; permission granted
-File:He_and_Amasino_Pathway.jpeg|[http://www.sciencedirect.com/science/article/pii/S1360138504002705 He and Amasino, 2005]; permission granted
+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
-File:Yamaguchi_Pathway.jpeg|[http://pcp.oxfordjournals.org/content/46/8/1175/F7.expansion Yamaguchi ''et al.'', 2005]; permission pending
+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
-File:Baurle_and_Dean_Pathway.jpeg|[http://www.sciencedirect.com/science/article/pii/S009286740600571X Bäurle and Dean, 2006]; permission granted
+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
-File:Farrona_Pathway.jpeg|[http://www.sciencedirect.com/science/article/pii/S1084952108000566 Farrona ''et al.'', 2008]; permission granted
+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
-File:Farrona_Pathway_2.jpeg|[http://www.sciencedirect.com/science/article/pii/S1084952108000566 Farrona ''et al.'', 2008]; permission granted
+File:Farrona_Pathway_2.jpeg|alt=Diagram of pathway from |[http://www.sciencedirect.com/science/article/pii/S1084952108000566 Farrona ''et al.'', 2008]; permission granted
-File:Amasino_Pathway_2.png|[http://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2010.04148.x/pdf/ Amasino, 2010]; permission granted
+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
-File:Higgins_Pathway.jpg|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010065 Higgins ''et al.'', 2010]; permission granted
+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
-File:Kim_and_Sung_Pathway.jpeg|[http://www.pnas.org/content/107/39/17029/F6.expansion.html Kim and Sung, 2010]; permission pending
+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
-File:Taiz_and_Zeiger_Pathway.jpeg|[http://5e.plantphys.net/article.php?ch=1&id=375 Taiz and Zeiger, 2010]; permission pending
+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
-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
+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
-File:Ferrier_Pathway.jpeg|[http://www.sciencedirect.com/science/article/pii/S0958166910002284 Ferrier ''et al.'', 2011]; permission pending
+File:Ferrier_Pathway.jpeg|alt=Diagram of pathway from |[http://www.sciencedirect.com/science/article/pii/S0958166910002284 Ferrier ''et al.'', 2011]; permission pending
-File:Zhang_Pathway.png|[http://www.biomedcentral.com/1471-2164/12/63 Zhang ''et al.'', 2011]; permission granted
+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
-File:Jung_Pathway.jpg|[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038250 Jung ''et al.'', 2012]; permission pending
+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
 </gallery>

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 <gallery widths="102px" heights="102px" perrow="6">
-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
+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
 File:Sung_Pathway.gif|[http://www.sciencedirect.com/science/article/pii/S1369526602000146 Sung ''et al.'', 2003]; permission granted
 File:Boss_Pathway.gif|[http://www.plantcell.org/content/16/suppl_1/S18/F2.expansion Boss ''et al.'', 2004]; permission granted

@@ Line 59: / Line 59: @@
 <gallery widths="102px" heights="102px" perrow="6">
-File:Izawa_Pathway.jpeg|Pathway from Izawa ''et al.'', 2003|[http://www.sciencedirect.com/science/article/pii/S1369526603000141 Izawa ''et al.'', 2003]; permission pending
+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
 File:Sung_Pathway.gif|[http://www.sciencedirect.com/science/article/pii/S1369526602000146 Sung ''et al.'', 2003]; permission granted
 File:Boss_Pathway.gif|[http://www.plantcell.org/content/16/suppl_1/S18/F2.expansion Boss ''et al.'', 2004]; permission granted

@@ Line 59: / Line 59: @@
 <gallery widths="102px" heights="102px" perrow="6">
-File:Izawa_Pathway.jpeg|[http://www.sciencedirect.com/science/article/pii/S1369526603000141 Izawa ''et al.'', 2003]; permission pending
+File:Izawa_Pathway.jpeg|Pathway from Izawa ''et al.'', 2003|[http://www.sciencedirect.com/science/article/pii/S1369526603000141 Izawa ''et al.'', 2003]; permission pending
 File:Sung_Pathway.gif|[http://www.sciencedirect.com/science/article/pii/S1369526602000146 Sung ''et al.'', 2003]; permission granted
 File:Boss_Pathway.gif|[http://www.plantcell.org/content/16/suppl_1/S18/F2.expansion Boss ''et al.'', 2004]; permission granted

← Older revision		Revision as of 00:51, 30 April 2013
Line 4:		Line 4:

	__TOC__		__TOC__
−
−	~~==To Do==~~
−	*Cite TAIR and Vaccinium SSR
−	*Revision of paper
−

	==Introduction to Flowering==		==Introduction to Flowering==

@@ Line 105: / Line 105: @@
 <PRE>{ echo bin/tblastn -query AASequence.txt -db BlueberryGenome.txt; bin/tblastn -query
 AASequence.txt -db BlueberryGenome.txt; } >> AAOutput.txt</PRE>
-*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] nomenclature search.
+*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.
 *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.
@@ Line 344: / Line 344: @@
 *Ballerini ES, Kramer EM. Environmental and molecular analysis of the floral transition in the lower eudicot Aquilegia formosa. ''Evodevo,'' '''2,''' 1-20 (2011).
 *Bäurle I, Dean C. The timing of developmental transitions in plants. ''Cell,'' '''125,''' 655-664 (2006).
-*Boss PK, Bastow RM, Mylne JS, Dean C. Multiple pathways in the decision to flower: enabling, promoting, and resetting. ''Plant Cell,'' '''16,''' Suppl:S18-S31 (2004).
+*Boss PK, Bastow RM, Mylne JS, Dean C. Multiple pathways in the decision to flower: enabling, promoting, and resetting. ''Plant Cell,'' '''16,''' S18-S31 (2004).
 *Farrona S, Coupland G, Turck F. The impact of chromatin regulation on the floral transition. ''Semin Cell Dev Biol,'' '''19,''' 560-573 (2008).
 *Ferrier T, Matus JT, Jin J, Riechmann JL. Arabidopsis paves the way: genomic and network analyses in crops. ''Curr Opin Biotechnol,'' '''22,''' 260-270 (2011).
@@ Line 363: / Line 363: @@
 *Taiz L, Zeiger E. ''Plant Physiology Fifth Edition Ch. 20'' (Sinauer Associates, Sunderland, MA, 2010).
 *Turck F, Adrian J. A lesson in complexity: regulation of FLOWERING LOCUS T. ''Max Planck Institute for Plant Breeding Research.''
-*UniProt Consortium. Reorganizing the protein space at the Universal Protein Resource (UniProt). ''Nucleic Acids Res,'' '''40,''' Database:D71-D75 (2012).
+*UniProt Consortium. Reorganizing the protein space at the Universal Protein Resource (UniProt). ''Nucleic Acids Res,'' '''40,''' D71-D75 (2012).
 *Wellmer F, Riechmann JL. Gene networks controlling the initiation of flower development. ''Trends Genet,'' '''26,''' 519-527 (2010).
 *Yamaguchi A, Kobayashi Y, Goto K, Abe M, Araki T. TWIN SISTER OF FT (TSF) acts as a floral pathway integrator redundantly with FT. ''Plant Cell Physiol,'' '''46,''' 1175-1189 (2005).
 *Yu S, Galvão VC, Zhang YC, Horrer D, Zhang TQ, Hao YH, Feng YQ, Wang S, Schmid M, Wang JW. Gibberellin regulates the Arabidopsis floral transition through miR156-targeted SQUAMOSA promoter binding-like transcription factors. ''Plant Cell,'' '''24,''' 3320-3332 (2012).
 *Zhang JZ, Ai XY, Sun LM, Zhang DL, Guo WW, Deng XX, Hu CG. Transcriptome profile analysis of flowering molecular processes of early flowering trifoliate orange mutant and the wild-type [Poncirus trifoliata (L.) Raf.] by massively parallel signature sequencing. ''BMC Genomics,'' '''12,''' 63 (2011).

@@ Line 102: / Line 102: @@
 *A local database of the blueberry genome was created using the following coding:
 <PRE>./bin/makeblastdb -in BlueberryGenome.txt -input_type fasta -dbtype nucl -title blueberry_Genome</PRE>
-*Amino acid sequences for all <i>Arabidopsis</i> genes were taken from [http://www.arabidopsis.org/index.jsp The Arabidopsis Information Resource (TAIR)]. The amino acid sequences were run via tBLASTn against the blueberry scaffolds to find the closest match using the following coding:
+*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:
 <PRE>{ echo bin/tblastn -query AASequence.txt -db BlueberryGenome.txt; bin/tblastn -query
 AASequence.txt -db BlueberryGenome.txt; } >> AAOutput.txt</PRE>

@@ Line 351: / Line 351: @@
 *He Y, Amasino RM. Role of chromatin modification in flowering-time control. ''Trends Plant Sci,'' '''10,''' 30-35 (2005).
 *Higgins JA, Bailey PC, Laurie DA. Comparative genomics of flowering time pathways using Brachypodium distachyon as a model for the temperate grasses. ''PLoS One,'' '''5,''' e10065 (2010).
 *Izawa T, Takahashi Y, Yano M. Comparative biology comes into bloom: genomic and genetic comparison of flowering pathways in rice and Arabidopsis. ''Curr Opin Plant Biol,'' '''6,''' 113-120 (2003).
 *Jung CH, Wong CE, Singh MB, Bhalla PL. Comparative genomic analysis of soybean flowering genes. ''PLoS One,'' '''7,''' e38250 (2012).

← Older revision		Revision as of 08:05, 29 April 2013
Line 4:		Line 4:

	__TOC__		__TOC__
		+
		+	==To Do==
		+	*Cite TAIR and Vaccinium SSR
		+	*Revision of paper
		+

	==Introduction to Flowering==		==Introduction to Flowering==