Time of bloom

By Austin Mudd - Spring 2013

To Do

• Write introduction and procedure sections
• Aggregate all sequences into a single document in proper FASTA format

Introduction

The factors affecting time of flowering from the Max Planck Institute for Plant Breeding Research

• Higgins et al., 2010
• Jung et al., 2012
• General plant anatomy / process of flowering
• Why flowering is important to study / general impact
• Factors affecting time of flowering

Procedure

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

Gallery of Arabidopsis Flowering Pathways

• 

  Izawa et al., 2003

• 

  Sung et al., 2003

• 

  Boss et al., 2004

• 

  Boss et al., 2004

• 

  Henderson and Dean, 2004

• 

  Amasino, 2005

• 

  He and Amasino, 2005

• 

  Yamaguchi et al., 2005

• 

  Bäurle and Dean, 2006

• 

  Farrona et al., 2008

• 

  Farrona et al., 2008

• 

  Liu et al., 2009

• 

  Schneitz, 2009

• 

  Amasino, 2010

• 

  Higgins et al., 2010

• 

  Kim and Sung, 2010

• 

  Taiz and Zeiger, 2010

• 

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

• 

  Ballerini and Kramer, 2011

• 

  Zhang et al., 2011

• 

  Jung et al., 2012

• 

  Posé et al., 2012

105 Flowering Genes

The below table lists all of the genes involved in the ambient temperature, autonomous, light signaling, and vernalization pathways.

Note: All Arabidopsis genes are compiled from Jung et al., 2012. All potential orthologs are found via UniProt Grape or UniProt Strawberry nomenclature search. Formatting is the same as Jung et al., 2012 where a * indicates 1 of "24 Arabidopsis genes, which had not been previously investigated for their roles in flowering, [that] belong to [paralog groups] with known Arabidopsis flowering genes." Moreover, for pathways, "Am: Ambient temperature pathway, Au: Autonomous pathway, FPI: Flowering Pathway [Integrators], L: Light signaling pathway, MI: Meristem Identity, V: Vernalization pathway."

Arabidopsis Locus	Other Names	AA Sequence	Pathway	Potential Ortholog
AT1G04400	AT-PHH1, ATCRY2, CRY2, CRYPTOCHROME 2, FHA, PHH1	TAIR	L
AT1G26790		TAIR	L
AT1G29160		TAIR	L
AT2G17770	ATBZIP27, BASIC REGION/LEUCINE ZIPPER MOTIF 27, BZIP27, FD PARALOG, FDP	TAIR	Am, MI
AT2G23380	CLF, CURLY LEAF, ICU1, INCURVATA 1, SDG1, SET1, SETDOMAIN 1, SETDOMAIN GROUP 1	TAIR	Au, V
AT2G32950	ARABIDOPSIS THALIANA CONSTITUTIVE PHOTOMORPHOGENIC 1, ATCOP1, CONSTITUTIVE PHOTOMORPHOGENIC 1, COP1, DEETIOLATED MUTANT 340, DET340, EMB168, EMBRYO DEFECTIVE 168, FUS1, FUSCA 1	TAIR	L
AT2G34140		TAIR	L
AT2G46670*		TAIR	L
AT2G46790	APRR9, ARABIDOPSIS PSEUDO-RESPONSE REGULATOR 9, PRR9, PSEUDO-RESPONSE REGULATOR 9, TL1, TOC1-LIKE PROTEIN 1	TAIR	L
AT2G46830	ATCCA1, CCA1, CIRCADIAN CLOCK ASSOCIATED 1	TAIR	L
AT3G02380	ATCOL2, B-BOX DOMAIN PROTEIN 3, BBX3, COL2, CONSTANS-LIKE 2	TAIR	FPI, L
AT3G07650	B-BOX DOMAIN PROTEIN 7, BBX7, COL9, CONSTANS-LIKE 9	TAIR	L
AT3G21320		TAIR	L
AT3G25730	EDF3, ETHYLENE RESPONSE DNA BINDING FACTOR 3	TAIR	L
AT3G33520	ACTIN-RELATED PROTEIN 6, ARP6, ATARP6, EARLY IN SHORT DAYS 1, ESD1, SUF3, SUPPRESSOR OF FRI 3	TAIR	Am, V
AT3G47500	CDF3, CYCLING DOF FACTOR 3	TAIR	L
AT4G08920	ATCRY1, BLU1, BLUE LIGHT UNINHIBITED 1, CRY1, CRYPTOCHROME 1, ELONGATED HYPOCOTYL 4, HY4, OOP2, OUT OF PHASE 2	TAIR	L	Grape
AT4G11880	AGAMOUS-LIKE 14, AGL14	TAIR	V
AT4G22950	"AGAMOUS-LIKE 19, AGL19, GL19
"	TAIR	V
AT4G24540	AGAMOUS-LIKE 24, AGL24	TAIR	V
AT4G34530	CIB1, CRYPTOCHROME-INTERACTING BASIC-HELIX-LOOP-HELIX 1	TAIR	L
AT5G08230*		TAIR	V
AT5G08330	CCA1 HIKING EXPEDITION, CHE, TRANSCRIPTION FACTOR TCP21, TCP21	UniProtKB	L
AT5G15840	B-BOX DOMAIN PROTEIN 1, BBX1, CO, CONSTANS, FG	TAIR	FPI, L
AT5G15850	ATCOL1, B-BOX DOMAIN PROTEIN 2, BBX2, COL1, CONSTANS-LIKE 1	TAIR	FPI, L
AT5G23280*		TAIR	L
AT5G24470	APRR5, PRR5, PSEUDO-RESPONSE REGULATOR 5	TAIR	L
AT5G24930	ATCOL4, B-BOX DOMAIN PROTEIN 5, BBX5, COL4, CONSTANS-LIKE 4	TAIR	L
AT5G37055	ATSWC6, SEF, SERRATED LEAVES AND EARLY FLOWERING	TAIR	V
AT5G39660	CDF2, CYCLING DOF FACTOR 2	TAIR	L
AT5G48250*	B-BOX DOMAIN PROTEIN 8, BBX8	TAIR	L
AT5G57660	ATCOL5, B-BOX DOMAIN PROTEIN 6, BBX6, COL5, CONSTANS-LIKE 5	TAIR	L
AT5G59570*	BOA, BROTHER OF LUX ARRHYTHMO	TAIR	L
AT5G60100	APRR3, PRR3, PSEUDO-RESPONSE REGULATOR 3	TAIR	L
AT5G62430	CDF1, CYCLING DOF FACTOR 1	TAIR	L
AT5G65050	AGAMOUS-LIKE 31, AGL31, MADS AFFECTING FLOWERING 2, MAF2	TAIR	Am, FPI, V
AT1G77300	ASH1 HOMOLOG 2, ASHH2, CAROTENOID CHLOROPLAST REGULATORY1, CCR1, EARLY FLOWERING IN SHORT DAYS, EFS, LAZ2, LAZARUS 2, SDG8, SET DOMAIN GROUP 8	TAIR	V
AT2G25930	EARLY FLOWERING 3, ELF3, PYK20	TAIR	L
AT2G40080	EARLY FLOWERING 4, ELF4	TAIR	L
AT2G06255	ELF4-L3, ELF4-LIKE 3	TAIR	L
AT4G16280	FCA	TAIR	Am, Au	Grape
AT4G35900	ATBZIP14, FD, FD-1	TAIR	Am, MI
AT2G33835	FES1, FRIGIDA-ESSENTIAL 1	TAIR	V
AT3G20740	FERTILIZATION-INDEPENDENT ENDOSPERM, FERTILIZATION-INDEPENDENT ENDOSPERM 1, FIE, FIE1, FIS3	TAIR	Au, V
AT1G68050	"FLAVIN-BINDING, KELCH REPEAT, F BOX 1", ADO3, FKF1	TAIR	L
FLC		TAIR	Am, FPI, V	Grape
FLD		TAIR	Am, Au
FLK		TAIR	Au
FPA		TAIR	Au
FRI		TAIR	V
FRL1		TAIR	V
FRL2		TAIR	V
FT		TAIR	Am, FPI	Grape, Strawberry
FVE		TAIR	Am, Au
FY		TAIR	Au
GI		TAIR	L
HUA2		TAIR	V
LD		TAIR	Au
LDL1*		TAIR	Am, Au
LDL2*		TAIR	Am, Au
LHY		TAIR	L
LKP2		TAIR	L
LUX		TAIR	L
MAF1		TAIR	Am, FPI, V
MAF3		TAIR	Am, FPI, V
MAF4		TAIR	Am, FPI, V
MAF5		TAIR	Am, FPI, V
MEA*		TAIR	Au, V
MSI1		TAIR	Au, V
MSI2*		TAIR	Au, V
MSI3*		TAIR	Au, V
NFC5*		TAIR	Am, Au
PAF1		TAIR	V
PAF2		TAIR	V
PEP		TAIR	V
PHYA		TAIR	L	Grape
PHYB		TAIR	L	Grape
PHYC		TAIR	L	Grape
PHYD		TAIR	L
PHYE		TAIR	L	Grape
PIE1		TAIR	V
PRR7		TAIR	L
RAV1		TAIR	L
RFI2		TAIR	L
SPA1		TAIR	L
SPA2		TAIR	L
SPA3		TAIR	L
SPA4		TAIR	L
SUF4		TAIR	V
SVP		TAIR	Am, V	Grape
SWN		TAIR	Au, V
TEM1		TAIR	L
TEM2		TAIR	L
TFL1		TAIR	Am, FPI	Grape, Strawberry
TOC1		TAIR	L
TSF		TAIR	Am, FPI
UVR3*		TAIR	L
VEL1		TAIR	Au, V
VEL2		TAIR	Au
VEL3		TAIR	Au
VIN3		TAIR	Au, V
VRN1		TAIR	V
VRN2		TAIR	Au, V
VRN5		TAIR	Au, V
ZTL		TAIR	L