Difference between revisions of "Time of bloom"
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| CDF3||Plant non-specific lipid-transfer proteins transfer phospholipids as well as galactolipids across membranes. May play a role in wax or cutin deposition in the cell walls of expanding epidermal cells and certain secretory tissues.||[http://www.uniprot.org/uniprot/Q9S7I3 UniProtKB]||L | | CDF3||Plant non-specific lipid-transfer proteins transfer phospholipids as well as galactolipids across membranes. May play a role in wax or cutin deposition in the cell walls of expanding epidermal cells and certain secretory tissues.||[http://www.uniprot.org/uniprot/Q9S7I3 UniProtKB]||L | ||
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| − | | CDF5||Cell growth defect factor||||L | + | | CDF5||Cell growth defect factor||-||L |
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| CHE||-||[http://www.uniprot.org/uniprot/Q9FTA2 UniProtKB]||L | | CHE||-||[http://www.uniprot.org/uniprot/Q9FTA2 UniProtKB]||L | ||
Revision as of 18:49, 19 February 2013
Contents
To Do
Note all Arabidopsis genes in File:Jung 207 Arabidopsis Flowering Genes.pdf from Jung et al., 2012.
Look for strawberry orthologs of Arabidopsis genes, such as in Mouhu et al., 2009.
Arabidopsis Flowering Pathway (2004-Present)
Overall pathway for the time of bloom from Henderson and Dean, 2004.
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Overall pathway for the time of bloom from Schneitz, 2009.
"The Arabidopsis floral transition network has been delineated as a result of extensive genetic analyses (depicted in a), but genome-wide studies have uncovered new molecular interactions and highlighted the role of AP1 as both a molecular switch and a network hub (shown in b)."
Overall pathway for the time of bloom from Wellmer and Riechmann, 2010 and Ferrier et al., 2011.
"Soybean genes marked with * are those that share the same clade with Arabidopsis genes but have not been investigated so far as flowering genes ... Arrows show promoting effects, T-bars show repressing effects. Environmental cues are shown as lower case letters in square boxes; ‘v’ is extended cold (vernalization); ‘ld’ is long days; ‘sd’ is short days; ‘am’ is ambient (non-vernalizing) temperature. Genes are shown in italics and proteins in non-italics in ovals. ‘Pfr’ indicates Pfr phytochrome signaling. Arabidopsis genes assigned to specific pathways are color-coded (photoperiod pathway in green, vernalization in blue and autonomous pathway in purple). Flowering pathway integrators are shown in red. Triple headed arrows indicate activation by red or blue light."
Overall pathway for the time of bloom from Jung et al., 2012.
All Arabidopsis Flowering Pathways
Henderson and Dean, 2004; Yamaguchi et al., 2005; Liu et al., 2009; Taiz and Zeiger, 2010; Boss et al., 2004; Zhang et al., 2011; Ballerini and Kramer, 2011; Posé et al., 2012; Kim and Sung, 2010; Wellmer and Riechmann, 2010; Farrona et al., 2008; He and Amasino, 2005; Max Planck Institute for Plant Breeding Research; Bäurle and Dean, 2006; Sung et al., 2003; Schneitz, 2009; Amasino, 2005; Ferrier et al., 2011; Izawa et al., 2003; Jung et al., 2012
Arabidopsis Flowering Genes
Note: All genes are compiled from Jung et al., 2012. 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 [ortholog groups] with known Arabidopsis flowering genes." Moreover, for pathways, "Am: Ambient temperature pathway, Au: Autonomous pathway, FPI: Flowering Pathway Intergrators, L: Light signaling pathway, MI: Meristem Identity, V: Vernalization pathway."
| Arabidopsis Gene | Function (All function information is directly copied from the respective UniProtKB page) | AA Sequence | Pathway |
|---|---|---|---|
| ABF1 | Binds to the ABA-responsive element (ABRE). Could participate in abscisic acid-regulated gene expression. | UniProtKB | - |
| ABF2 | Involved in ABA and stress responses and acts as a positive component of glucose signal transduction. Functions as transcriptional activator in the ABA-inducible expression of rd29B. Binds specifically to the ABA-responsive element (ABRE) of the rd29B gene promoter. | UniProtKB | - |
| ABF3 | Binds to the ABA-responsive element (ABRE). Mediates stress-responsive ABA signaling. | UniProtKB | - |
| ABF4 | Functions as transcriptional activator in the ABA-inducible expression of rd29B. Binds specifically to the ABA-responsive element (ABRE) of the rd29B gene promoter. | UniProtKB | - |
| ABI5 | Participates in ABA-regulated gene expression during seed development and subsequent vegetative stage by acting as the major mediator of ABA repression of growth. Binds to the embryo specification element and the ABA-responsive element (ABRE) of the Dc3 gene promoter and to the ABRE of the Em1 and Em6 genes promoters. Can also trans-activate its own promoter, suggesting that it is autoregulated. Plays a role in sugar-mediated senescence. | UniProtKB | - |
| AG | Probable transcription factor involved in the control of organ identity during the early development of flowers. Is required for normal development of stamens and carpels in the wild-type flower. Plays a role in maintaining the determinacy of the floral meristem. Acts as C class cadastral protein by repressing the A class floral homeotic genes like APETALA1. Forms a heterodimer via the K-box domain with either SEPALATTA1/AGL2, SEPALATTA2/AGL4, SEPALLATA3/AGL9 or AGL6 that could be involved in genes regulation during floral meristem development. | UniProtKB | - |
| AGL14 | Probable transcription factor. | UniProtKB | V |
| AGL15 | Transcription factor involved in the negative regulation of flowering, probably through the photoperiodic pathway. Acts as both an activator and a repressor of transcription. Binds DNA in a sequence-specific manner in large CArG motif 5'-CC (A/T)8 GG-3'. Participates probably in the regulation of programs active during the early stages of embryo development. Prevents premature perianth senescence and abscission, fruits development and seed desiccation. Stimulates the expression of at least DTA4, LEC2, FUS3, ABI3, AT4G38680/CSP2 and GRP2B/CSP4. Can enhance somatic embryo development in vitro. | UniProtKB | - |
| AGL17 | Probable transcription factor. | UniProtKB | - |
| AGL18 | Probable transcription factor involved in the negative regulation of flowering, probably through the photoperiodic pathway. Prevents premature flowering. Downstream regulator of a subset of the MIKC* MADS-controlled genes required during pollen maturation. | UniProtKB | - |
| AGL19 | Probable transcription factor that promotes flowering, especially in response to vernalization by short periods of cold, in an FLC-inpedendent manner. | UniProtKB | V |
| AGL21* | Probable transcription factor. | UniProtKB | - |
| AGL24 | Transcription activator that mediates floral transition in response to vernalization. Promotes inflorescence fate in apical meristems. Acts in a dosage-dependent manner. Probably involved in the transduction of RLK-mediated signaling (e.g. IMK3 pathway). Together with AP1 and SVP, controls the identity of the floral meristem and regulates expression of class B, C and E genes. When associated with SOC1, mediates effect of gibberellins on flowering under short-day conditions, and regulates the expression of LEAFY (LFY), which links floral induction and floral development. Confers inflorescence characteristics to floral primordia and early flowering. | UniProtKB | V |
| AGL31 | Probable transcription factor that prevents vernalization by short periods of cold. Acts as a floral repressor. | UniProtKB | Am, FPI, V |
| AGL6 | Probable transcription factor. Forms a heterodimer via the K-box domain with AG, that could be involved in genes regulation during floral meristem development. | UniProtKB | - |
| AGL79 | - | UniProtKB | - |
| AP1 | Transcription factor that promotes early floral meristem identity in synergy with LEAFY. Is required subsequently for the transition of an inflorescence meristem into a floral meristem. Is indispensable for normal development of sepals and petals in flowers. Regulates positively the B class homeotic proteins APETALA3 and PISTILLATA with the cooperation of LEAFY and UFO. Interacts with SEPALLATA3 or AP3/PI heterodimer to form complexes that could be involved in genes regulation during floral meristem development. Regulates positively AGAMOUS in cooperation with LEAFY. Displays a redundant function with CAULIFLOWER in the up-regulation of LEAFY. Together with AGL24 and SVP, controls the identity of the floral meristem and regulates expression of class B, C and E genes. Represses flowering time genes AGL24, SVP and SOC1 in emerging floral meristems. | UniProtKB | FPI, MI |
| AP2 | Probable transcriptional activator that promotes early floral meristem identity. Is required subsequently for the transition of an inflorescence meristem into a floral meristem. Plays a central role in the specification of floral identity, particularly for the normal development of sepals and petals in the wild-type flower. Acts as A class cadastral protein by repressing the C class floral homeotic gene AGAMOUS in association with other repressors like LEUNIG and SEUSS. It is also required during seed development. | UniProtKB | - |
| AP3 | Probable transcription factor involved in the genetic control of flower development. Is required for normal development of petals and stamens in the wild-type flower. Forms a heterodimer with PISTILLATA that is required for autoregulation of both AP3 and PI genes. AP3/PI heterodimer interacts with APETALA1 or SEPALLATA3 to form a ternary complex that could be responsible for the regulation of the genes involved in the flower development. AP3/PI heterodimer activates the expression of NAP. | UniProtKB | - |
| APRR3 | Controls photoperiodic flowering response. Component of the circadian clock. Controls the degradation of APRR1/TOC1 by the SCF(ZTL) complex. Expression of several members of the ARR-like family is controlled by circadian rhythm. The particular coordinated sequential expression of APRR9, APRR7, APRR5, APRR3 and APPR1 result to circadian waves that may be at the basis of the endogenous circadian clock. | UniProtKB | L |
| APRR5 | Controls photoperiodic flowering response. Seems to be one of the component of the circadian clock. Expression of several members of the ARR-like family is controlled by circadian rhythm. The particular coordinated sequential expression of APRR9, APRR7, APRR5, APRR3 and APPR1 result to circadian waves that may be at the basis of the endogenous circadian clock. | UniProtKB | L |
| APRR9 | Controls photoperiodic flowering response. Seems to be one of the component of the circadian clock. Expression of several members of the ARR-like family is controlled by circadian rhythm. The particular coordinated sequential expression of APRR9, APRR7, APRR5, APRR3 and APPR1 result to circadian waves that may be at the basis of the endogenous circadian clock. | UniProtKB | L |
| AREB3 | Binds to the embryo specification element and the ABA-responsive element (ABRE) of the Dc3 gene promoter. Could participate in abscisic acid-regulated gene expression during seed development. | UniProtKB | - |
| AT1G26790 | Transcription factor that binds specifically to a 5'-AA[AG]G-3' consensus core sequence. | UniProtKB | L |
| AT1G29160 | Transcription factor that binds specifically to a 5'-AA[AG]G-3' consensus core sequence. Acts as a negative regulator in the phytochrome-mediated light responses. Controls phyB-mediated end-of-day response and the phyA-mediated anthocyanin accumulation. | UniProtKB | L |
| AT1G50680 | Probably acts as a transcriptional activator. Binds to the GCC-box pathogenesis-related promoter element. May be involved in the regulation of gene expression by stress factors and by components of stress signal transduction pathways. | UniProtKB | - |
| AT1G51120 | Probably acts as a transcriptional activator. Binds to the GCC-box pathogenesis-related promoter element. May be involved in the regulation of gene expression by stress factors and by components of stress signal transduction pathways. | UniProtKB | - |
| AT2G23070 | Casein kinases are operationally defined by their preferential utilization of acidic proteins such as caseins as substrates. The alpha chain contains the catalytic site. May act as an ectokinase that phosphorylates several extracellular proteins. | UniProtKB | - |
| AT2G23080 | Casein kinases are operationally defined by their preferential utilization of acidic proteins such as caseins as substrates. The alpha chain contains the catalytic site. May act as an ectokinase that phosphorylates several extracellular proteins. | UniProtKB | - |
| AT2G25920 | Uncharacterized protein | UniProtKB | - |
| AT2G34140 | Transcription factor that binds specifically to a 5'-AA[AG]G-3' consensus core sequence. | UniProtKB | L |
| AT2G46670* | Putative uncharacterized protein | UniProtKB | L |
| AT3G21320 | Uncharacterized protein | UniProtKB | L |
| AT3G25730 | Probably acts as a transcriptional activator. Binds to the GCC-box pathogenesis-related promoter element. May be involved in the regulation of gene expression by stress factors and by components of stress signal transduction pathways. | UniProtKB | L |
| AT4G16810 | Putative uncharacterized protein | UniProtKB | - |
| AT5G08230* | Probable transcrition factor that seems to be involved in mRNA processing. | UniProtKB | V |
| AT5G10625* | Modulates the competence to flowering of apical meristems. | UniProtKB | - |
| AT5G23280* | Transcription factor | UniProtKB | L |
| AT5G27220 | Frigida-like protein | UniProtKB | - |
| AT5G42910 | Could participate in abscisic acid-regulated gene expression. | UniProtKB | - |
| AT5G44080 | Basic leucine zipper transcription factor | UniProtKB | - |
| AT5G48250* | Zinc finger protein Constans-like 10 | UniProtKB | L |
| AT5G59570* | Putative transcription factor | UniProtKB | L |
| AT5G62040 | May form complexes with phosphorylated ligands by interfering with kinases and their effectors. | UniProtKB | - |
| ATARP6 | Component of the SWR1 complex which mediates the ATP-dependent exchange of histone H2A for the H2A variant H2A.F/Z leading to transcriptional regulation of selected genes (e.g. FLC) by chromatin remodeling. Required for the activation of FLC and FLC/MAF genes expression to levels that inhibit flowering, through both histone H3 and H4 acetylation and methylation mechanisms. Involved in several developmental processes including organization of plant organs, leaves formation, flowering time repression, and fertility. Modulates photoperiod-dependent epidermal leaves cell development; promotes cell division in long days, and cell expansion/division in short days. May be involved in the regulation of pathogenesis-related proteins (PRs). | UniProtKB | Am, V |
| ATBZIP27 | Transcription factor | GenScript | Am, MI |
| ATC | May form complexes with phosphorylated ligands by interfering with kinases and their effectors. Can substitute for TERMINAL FLOWER 1 (in vitro). | UniProtKB | - |
| ATCOL4 | Sequence-specific DNA binding transcription factor activity, zinc ion binding. | Arabidopsis Information Resource | L |
| ATCOL5 | Sequence-specific DNA binding transcription factor activity, zinc ion binding. | Arabidopsis Information Resource | L |
| ATSWC6 | Encodes SERRATED LEAVES AND EARLY FLOWERING (SEF), an Arabidopsis homolog of the yeast SWC6 protein, a conserved subunit of the SWR1/SRCAP complex. SEF loss-of-function mutants have a pleiotropic phenotype characterized by serrated leaves, frequent absence of inflorescence internodes, bushy aspect, and flowers with altered number and size of organs. sef plants flower earlier than wild-type plants both under inductive and non-inductive photoperiods. SEF, ARP6 and PIE1 might form a molecular complex in Arabidopsis related to the SWR1/SRCAP complex identified in other eukaryotes. | Arabidopsis Information Resource | V |
| CAL | Probable transcription factor that promotes early floral meristem identity in synergy with APETALA1, FRUITFULL and LEAFY. Is required subsequently for the transition of an inflorescence meristem into a floral meristem. Seems to be partially redundant to the function of APETALA1. | UniProtKB | FPI, MI |
| CCA1 | Transcription factor involved in the circadian clock and in the phytochrome regulation. Binds to the promoter regions of APRR1/TOC1 and TCP21/CHE to repress their transcription. Binds to the promoter regions of CAB2A and CAB2B to promote their transcription. Represses both LHY and itself. | UniProtKB | L |
| CDF1 | Cell growth defect factor | UniProtKB | L |
| CDF2 | Cell growth defect factor | UniProtKB | L |
| CDF3 | Plant non-specific lipid-transfer proteins transfer phospholipids as well as galactolipids across membranes. May play a role in wax or cutin deposition in the cell walls of expanding epidermal cells and certain secretory tissues. | UniProtKB | L |
| CDF5 | Cell growth defect factor | - | L |
| CHE | - | UniProtKB | L |
| CIB1 | Encodes a transcription factor CIB1 (cryptochrome-interacting basic-helix-loop-helix). CIB1 interacts with CRY2 (cryptochrome 2) in a blue light-specific manner in yeast and Arabidopsis cells, and it acts together with additional CIB1-related proteins to promote CRY2-dependent floral initiation. CIB1 positively regulates FT expression. | Arabidopsis Information Resource | L |
| CKA1 | Casein kinase II (CK2) catalytic subunit (alpha 1). One known substrate of CK2 is Phytochrome Interacting Factor 1 (PIF1). CK2-mediated phosphorylation enhances the light-induced degradation of PIF1 to promote photomorphogenesis. | Arabidopsis Information Resource | - |
| CKA2 | Encodes the casein kinase II (CK2) catalytic subunit (alpha). | Arabidopsis Information Resource | - |
| CLF | Similar to the product of the Polycomb-group gene Enhancer of zeste. Required for stable repression of AG and AP3. Putative role in cell fate determination. Involved in the control of leaf morphogenesis. mutants exhibit curled, involute leaves. AGAMOUS and APETALA3 are ectopically expressed in the mutant. | Arabidopsis Information Resource | Au, V |
| CO | Encodes a protein showing similarities to zinc finger transcription factors, involved in regulation of flowering under long days. Acts upstream of FT and SOC1. | Arabidopsis Information Resource | FPI, L |
| COL1 | Homologous to the flowering-time gene CONSTANS. | Arabidopsis Information Resource | FPI, L |
| COL2 | Homologous to the flowering-time gene CONSTANS (CO) encoding zinc-finger proteins | Arabidopsis Information Resource | FPI, L |
| COL3 | Positive regulator of photomorphogenesis that acts downstream of COP1 but can promote lateral root development independently of COP1 and also function as a daylength-sensitive regulator of shoot branching. | Arabidopsis Information Resource | - |
| COL9 | This gene belongs to the CO (CONSTANS) gene family. This gene family is divided in three subgroups: groups III, to which COL9 belongs, is characterised by one B-box (supposed to regulate protein-protein interactions) and a second diverged zinc finger. COL9 downregulates expression of CO (CONSTANS) as well as FT and SOC1 which are known regulatory targets of CO. | Arabidopsis Information Resource | L |
| COP1 | Represses photomorphogenesis and induces skotomorphogenesis in the dark. Contains a ring finger zinc-binding motif, a coiled-coil domain, and several WD-40 repeats, similar to G-beta proteins. The C-terminus has homology to TAFII80, a subunit of the TFIID component of the RNA polymerase II of Drosophila. Nuclear localization in the dark and cytoplasmic in the light. | Arabidopsis Information Resource | L |
| CRY1 | Encodes CRY1, a flavin-type blue-light photoreceptor with ATP binding and autophosphorylation activity. Functions in perception of blue / green ratio of light. The photoreceptor may be involved in electron transport. Mutant phenotype displays a blue light-dependent inhibition of hypocotyl elongation. Photoreceptor activity requires light-induced homodimerisation of the N-terminal CNT1 domains of CRY1. Involved in blue-light induced stomatal opening. The C-terminal domain of the protein undergoes a light dependent conformational change. Also involved in response to circadian rhythm. Mutants exhibit long hypocotyl under blue light and are out of phase in their response to circadian rhythm. CRY1 is present in the nucleus and cytoplasm. Different subcellular pools of CRY1 have different functions during photomorphogenesis of Arabidopsis seedlings. | Arabidopsis Information Resource | L |
| CRY2 | Blue light receptor mediating blue-light regulated cotyledon expansion and flowering time. Positive regulator of the flowering-time gene CONSTANS. This gene possesses a light-induced CNT2 N-terminal homodimerisation domain.Involved in blue-light induced stomatal opening. Involved in triggering chromatin decondensation. An 80-residue motif (NC80) is sufficient to confer CRY2's physiological function. It is proposed that the PHR domain and the C-terminal tail of the unphosphorylated CRY2 form a "closed" conformation to suppress the NC80 motif in the absence of light. In response to blue light, the C-terminal tail of CRY2 is phosphorylated and electrostatically repelled from the surface of the PHR domain to form an "open" conformation, resulting in derepression of the NC80 motif and signal transduction to trigger photomorphogenic responses. Cry2 phosphorylation and degradation both occur in the nucleus. | Arabidopsis Information Resource | L |
| DPBF2 | Basic leucine zipper transcription factor (BZIP67), identical to basic leucine zipper transcription factor GI:18656053 from (Arabidopsis thaliana); identical to cDNA basic leucine zipper transcription factor (atbzip67 gene) GI:18656052. Located in the nucleus and expressed during seed maturation in the cotyledons. | Arabidopsis Information Resource | - |
| E12A11 | Encodes a member of the FT and TFL1 family of phosphatidylethanolamine-binding proteins. It is expressed in seeds and up-regulated in response to ABA. Loss of function mutants show decreased rate of germination in the presence of ABA. ABA dependent regulation is mediated by both ABI3 and ABI5. ABI5 promotes MFT expression, primarily in the radicle-hypocotyl transition zone and ABI3 suppresses it in the seed. | Arabidopsis Information Resource | - |
| EEL | Transcription factor homologous to ABI5. Regulates AtEm1 expression by binding directly at the AtEm1 promoter. Located in the nucleus and expressed during seed maturation in the cotyledons and later in the whole embryo. | Arabidopsis Information Resource | - |
| EFS | Encodes a protein with histone lysine N-methyltransferase activity required specifically for the trimethylation of H3-K4 in FLC chromatin (and not in H3-K36 dimethylation). Acts as an inhibitor of flowering specifically involved in the autonomous promotion pathway. EFS also regulates the expression of genes involved in carotenoid biosynthesis.Modification of histone methylation at the CRTISO locus reduces transcript levels 90%. The increased shoot branching seen in some EFS mutants is likely due to the carotenoid biosynthesis defect having an effect on stringolactones.Required for ovule, embryo sac, anther and pollen development. | Arabidopsis Information Resource | V |
| ELF3 | Encodes a nuclear protein that is expressed rhythmically and interacts with phytochrome B to control plant development and flowering through a signal transduction pathway. Required component of the core circadian clock regardless of light conditions. | Arabidopsis Information Resource | L |
| ELF4 | Encodes a novel nuclear 111 amino-acid phytochrome-regulated component of a negative feedback loop involving the circadian clock central oscillator components CCA1 and LHY. ELF4 is necessary for light-induced expression of both CCA1 and LHY, and conversely, CCA1 and LHY act negatively on light-induced ELF4 expression. ELF4 promotes clock accuracy and is required for sustained rhythms in the absence of daily light/dark cycles. It is involved in the phyB-mediated constant red light induced seedling de-etiolation process and may function to coregulate the expression of a subset of phyB-regulated genes. | Arabidopsis Information Resource | L |
| ELF4-L3 | Protein of unknown function | Arabidopsis Information Resource | - |
| ELF4-L2 | Protein of unknown function | Arabidopsis Information Resource | - |
| ELF4-L3 | Protein of unknown function | Arabidopsis Information Resource | L |
| ELF4-L4 | Protein of unknown function | Arabidopsis Information Resource | - |
| ELF5 | Nuclear targeted protein involved in flowering time regulation that affects flowering time independent of FLC | Arabidopsis Information Resource | - |
| ELF6 | Early Flowering 6 (ELF6) encodes a Jumonji N/C and zinc finger domain-containing protein that acts as a repressor in the photoperiod pathway. ELF6 interacts with BES1 in a Y2H assay, in vitro, and in Arabidosis protoplasts (based on BiFC). ELF6 may play a role in brassinosteroid signaling by affecting histone methylation in the promoters of BR-responsive genes. | Arabidopsis Information Resource | - |
| ELF9 | Encodes a RNA binding protein ELF9 (EARLY FLOWERING9). Loss of ELF9 function in the Wassilewskija ecotype causes early flowering in short days. ELF9 reduces SOC1 (SUPPRESSOR OF OVEREXPRESSION OF CO1) transcript levels, possibly via nonsense-mediated mRNA decay. | Arabidopsis Information Resource | FPI |
| EMF1 | Involved in regulating reproductive development | Arabidopsis Information Resource | - |
| EMF2 | Polycomb group protein with zinc finger domain involved in negative regulation of reproductive development. Forms a complex with FIE, CLF, and MSI1. This complex modulates the expression of target genes including AG, PI and AP3. | Arabidopsis Information Resource | - |
| ESD4 | EARLY IN SHORT DAYS 4 Arabidopsis mutant shows extreme early flowering and alterations in shoot development. It encodes a SUMO protease, located predominantly at the periphery of the nucleus. Accelerates the transition from vegetative growth to flowering. Probably acts in the same pathway as NUA in affecting flowering time, vegetative and inflorescence development. | Arabidopsis Information Resource | - |
