HD3A (Heading date 3a; UniProt Q93WI9; Os06g0157700 / LOC_Os06g06320) is the rice florigen - the long-sought mobile flowering signal - and is the rice ortholog of Arabidopsis FLOWERING LOCUS T (FT). It is a small (179 aa) member of the phosphatidylethanolamine-binding protein (PEBP) family, FT-like subgroup. Hd3a is NOT an enzyme or transporter; its molecular mode of action is protein-protein interaction. Hd3a transcription is concentrated in leaf-blade vascular tissue, and the Hd3a protein is loaded into the phloem, transported long-distance to the shoot apical meristem (SAM), unloaded near the vascular termini, and enters SAM cells, where it triggers the vegetative-to-reproductive (floral) transition (Tamaki et al. 2007, PMID:17446351; deep-research falcon report). In SAM cells Hd3a first forms a cytoplasmic Hd3a-14-3-3 (GF14 family) subcomplex that becomes nuclear upon co-expression of the bZIP transcription factor OsFD1, assembling the "florigen activation complex" (FAC) that activates downstream floral-identity MADS-box genes (OsMADS14, OsMADS15). Hd3a acts downstream of the photoperiod regulators Hd1 and Ehd1 and promotes flowering specifically under inductive short-day conditions (Kojima et al. 2002, PMID:12407188). Functional perturbation produces large flowering-time phenotypes: Hd3a RNAi delays flowering by >30 days, and double suppression of Hd3a and RFT1 (the partly redundant second rice florigen) can prevent flowering for up to 300 days. The genuine core of Hd3a is therefore a florigenic, phloem-mobile, FAC-forming POSITIVE REGULATOR OF THE FLORAL TRANSITION (flowering time), not a differentiation factor and not an executor of flower-organ morphogenesis. Two retired SwissProt-keyword (GO_REF:0000043) annotations - "cell differentiation" (GO:0030154) and "flower development" (GO:0009908) - are over-annotations of this "timing signal != bare developmental process" type and are reviewed below.
Definition: The activity of a mobile FT-family flowering signal that promotes the floral transition by forming a transcriptional activation complex (with 14-3-3 receptors and FD/OsFD1) at the shoot apical meristem. There is currently no GO molecular-function term capturing this activity; Hd3a (and Arabidopsis FT) would be the canonical bearers of such a term. In its absence, Hd3a's molecular action is best approximated by 14-3-3 protein binding and its biological role by the floral-transition/timing process terms.
Justification: The PEBP-family namesake MF "phosphatidylethanolamine binding" (GO:0008429) is a misleading family-level inference with no demonstrated biological relevance for FT-like florigens, whose real molecular action is protein-protein interaction within the florigen activation complex.
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0030154 cell differentiation | IEA GO_REF:0000043 | REMOVE | Summary: SPKW (GO_REF:0000043) annotation derived from the UniProt keyword "Differentiation"; snapshot-only, removed in the current GOA release. Hd3a is a phloem-mobile flowering-time signal (florigen) that triggers the vegetative-to-reproductive transition by forming a transcriptional activation complex in the SAM - it is not a cell-differentiation factor. Reason: GOA's removal of this annotation was JUSTIFIED. "Cell differentiation" (GO:0030154) is a generic catch-all process term auto-mapped from the UniProt "Differentiation"/"Developmental protein" keyword. It does not describe Hd3a's molecular or biological role. Hd3a is "not an enzyme or transporter; its primary function is as a mobile signaling protein that controls flowering by forming a transcriptional activation complex in SAM cells" - it is synthesized in leaf vasculature, moves via the phloem, and acts in the SAM to switch the apex from vegetative to reproductive identity. That switch is most precisely captured by the transition/timing terms already in GOA (GO:0010228 vegetative to reproductive phase transition of meristem; GO:0048510 regulation of timing of transition from vegetative to reproductive phase), not by a blanket "cell differentiation" parent. There is no gene-specific evidence that Hd3a directs the differentiation of any particular cell type; the keyword-derived term adds no information and is an over-annotation. Supporting Evidence: file:ORYSJ/HD3A/HD3A-deep-research-falcon.md Hd3a is **not an enzyme or transporter**; its primary function is as a **mobile signaling protein** that controls flowering by forming a transcriptional activation complex in SAM cells. PMID:17446351 We show that the protein encoded by Hd3a, a rice ortholog of FT, moves from the leaf to the shoot apical meristem and induces flowering in rice. |
| GO:0009908 flower development | IEA GO_REF:0000043 | MODIFY | Summary: SPKW (GO_REF:0000043) annotation derived from the UniProt keyword "Flowering"; snapshot-only, removed in the current GOA release. Hd3a triggers the floral TRANSITION / induction of flowering (a timing function), and is a positive regulator upstream of floral-identity genes - it does not itself execute flower-organ development/morphogenesis. Reason: "Flower development" (GO:0009908) captures the right biological neighborhood but at the wrong altitude and the wrong part of the process. Hd3a is the florigen that induces the switch to flowering; it acts UPSTREAM of and POSITIVELY REGULATES the floral program rather than executing flower-organ morphogenesis. The accurate sense is "regulation of flower development" (GO:0009909) - already independently present in current GOA from IBA/IEA/IMP evidence - and, more specifically, "positive regulation of flower development" (GO:0009911), because Hd3a unambiguously promotes flowering (overexpression/introduction causes precocious flowering; loss/RNAi delays it). Hd3a acts "upstream of MADS14 and MADS15" and the FAC "activates flowering MADS-box genes", consistent with a positive regulatory role at the level of the floral transition rather than direct participation in flower-organ development. The keyword-derived bare developmental term should be replaced with the regulatory term(s). Proposed replacements: positive regulation of flower development regulation of flower development Supporting Evidence: file:ORYSJ/HD3A/HD3A-deep-research-falcon.md FAC formation leads to induction of floral identity and transition programs, including activation of **MADS-box genes**. PMID:12407188 Introduction of the gene caused an early-heading phenotype in rice. |
| GO:0010228 vegetative to reproductive phase transition of meristem | IBA GO_REF:0000033 | ACCEPT | Summary: IBA annotation propagated across the FT/florigen (PEBP) phylogenetic group. The vegetative-to-reproductive transition of the SAM is the defining biological process of Hd3a and the most accurate process term for the rice florigen. Reason: This is a core function and is at the right level of specificity. Hd3a is the mobile signal that, on arrival at the SAM, drives the switch of the apex from vegetative to reproductive identity - "an FT (or FT-ortholog) protein synthesized in leaves in response to inductive photoperiod and transported to the SAM, where it triggers the vegetative-to-reproductive transition." Tamaki et al. (2007) demonstrated experimentally that the Hd3a protein moves from leaf to SAM and induces flowering [PMID:17446351]. The IBA term is conserved across the florigen family and is strongly supported by rice-specific data. Supporting Evidence: file:ORYSJ/HD3A/HD3A-deep-research-falcon.md an **FT (or FT-ortholog) protein** synthesized in leaves in response to inductive photoperiod and transported to the SAM, where it triggers the vegetative-to-reproductive transition. PMID:17446351 the protein encoded by Hd3a, a rice ortholog of FT, moves from the leaf to the shoot apical meristem and induces flowering in rice. |
| GO:0048510 regulation of timing of transition from vegetative to reproductive phase | IBA GO_REF:0000033 | ACCEPT | Summary: IBA annotation: Hd3a regulates the TIMING of the floral transition (heading date / flowering time). This is a core function, supported by phylogeny and by direct rice genetics. (Three further annotations to this same term, by IEA and IMP, are reviewed below and share this rationale.) Reason: Core function. Hd3a was identified as the Heading date 3a quantitative trait locus controlling rice flowering time, and its expression level quantitatively sets flowering time: Hd3a transcription drops sharply under long days and a brief night-break blocks induction, while loss of Hd3a delays flowering by >30 days. The term is the precise regulatory process for a flowering-TIME signal and is conserved across the FT family. Supporting Evidence: file:ORYSJ/HD3A/HD3A-deep-research-falcon.md **Hd3a RNAi** delays flowering by **>30 days**, and **double RNAi suppressing both Hd3a and RFT1** prevented flowering up to **300 days** PMID:12407188 The transcript levels of Hd3a were increased under SD conditions. |
| GO:0009909 regulation of flower development | IBA GO_REF:0000033 | ACCEPT | Summary: IBA annotation: Hd3a regulates (positively) flower development by inducing the floral transition. Accurate regulatory framing of the gene's role. (Two further annotations to this same term, by IEA and IMP, are reviewed below and share this rationale.) Reason: Correct and appropriately framed as a regulatory term. Hd3a acts upstream of the floral program - it forms the FAC that "activates flowering MADS-box genes" (OsMADS14/OsMADS15) and the UniProt FUNCTION statement places it "upstream of MADS14 and MADS15." Because Hd3a promotes flowering, the more specific "positive regulation of flower development" (GO:0009911) would be even more informative, but the parent regulatory term as annotated is accurate and is the correct sense for the retired "flower development" keyword (see SPKW MODIFY above). Proposed replacements: positive regulation of flower development Supporting Evidence: file:ORYSJ/HD3A/HD3A-deep-research-falcon.md FAC formation leads to induction of floral identity and transition programs, including activation of **MADS-box genes**. PMID:12407188 Introduction of the gene caused an early-heading phenotype in rice. |
| GO:0010229 inflorescence development | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA annotation: inflorescence (panicle) development is a downstream consequence of the Hd3a-triggered floral transition. (Five further annotations to this same term, by IEA and IMP, are reviewed below and share this rationale.) Reason: The annotation is not wrong - inducing flowering necessarily leads to inflorescence formation, and Hd3a perturbation alters panicle/inflorescence outcomes - but inflorescence morphogenesis is a downstream developmental CONSEQUENCE of the floral-transition timing signal rather than a process Hd3a directly executes. Hd3a's molecular role is upstream signaling/FAC formation that activates floral-identity genes; the actual organ patterning is carried out by downstream MADS-box and meristem-identity factors. Retain as a non-core developmental association; the core is the transition/timing role (GO:0010228, GO:0048510). Supporting Evidence: file:ORYSJ/HD3A/HD3A-deep-research-falcon.md The FAC activates flowering MADS-box genes, especially OsMADS15 and also OsMADS14/15 in rice, linking Hd3a arrival at the SAM to floral transition and meristem identity reprogramming. PMID:17446351 the protein encoded by Hd3a, a rice ortholog of FT, moves from the leaf to the shoot apical meristem and induces flowering in rice. |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: IEA annotation (UniProtKB-SubCell) for nuclear localization. Supported: the Hd3a-14-3-3-OsFD1 florigen activation complex localizes to the nucleus to activate transcription. Reason: Correct. The refined cell-biological model has Hd3a forming a cytoplasmic Hd3a-14-3-3 subcomplex that "localizes to the nucleus" once OsFD1 is co-expressed, where the FAC activates downstream transcriptional programs. UniProt lists Nucleus as a subcellular location. Nuclear localization is functionally meaningful because the FAC's transcriptional activation of MADS-box targets occurs there. Supporting Evidence: file:ORYSJ/HD3A/HD3A-deep-research-falcon.md remains cytoplasmic until **OsFD1 is co-expressed**, at which point the complex **localizes to the nucleus** to activate downstream transcriptional programs. |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: IEA annotation (UniProtKB-SubCell) for cytoplasmic localization. Supported: in SAM cells Hd3a first forms a cytoplasmic Hd3a-14-3-3 subcomplex before nuclear entry. Reason: Correct. The 2024 mechanistic model describes Hd3a first forming "an Hd3a-14-3-3 subcomplex in the cytoplasm of SAM cells" that remains cytoplasmic until OsFD1 is co-expressed. UniProt lists Cytoplasm as a subcellular location. Cytoplasmic residence (and phloem transport) is an integral part of the florigen mechanism, so this localization is accepted. Supporting Evidence: file:ORYSJ/HD3A/HD3A-deep-research-falcon.md Hd3a **first forms an Hd3a–14-3-3 subcomplex in the cytoplasm** of SAM cells. |
| GO:0009909 regulation of flower development | IEA GO_REF:0000117 | ACCEPT | Summary: IEA (ARBA machine-learning) annotation duplicating the IBA/IMP "regulation of flower development" term. Accepted on the same basis as the IBA annotation above. Reason: Duplicate of the curated IBA/IMP annotations to GO:0009909 and consistent with them. Hd3a positively regulates the floral transition (forms the FAC that activates MADS-box floral genes). Duplicate annotations with different evidence codes are acceptable; the more specific "positive regulation of flower development" (GO:0009911) is noted as a possible refinement. Proposed replacements: positive regulation of flower development Supporting Evidence: file:ORYSJ/HD3A/HD3A-deep-research-falcon.md FAC formation leads to induction of floral identity and transition programs, including activation of **MADS-box genes**. |
| GO:0010229 inflorescence development | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: IEA (ARBA) annotation duplicating the IBA/IMP "inflorescence development" term. Kept as non-core on the same basis as the IBA annotation above. Reason: Same rationale as the IBA GO:0010229 annotation: inflorescence (panicle) morphogenesis is a downstream consequence of the Hd3a-triggered floral transition rather than a process Hd3a directly executes. Retain as non-core; the core is the transition/timing role. Supporting Evidence: file:ORYSJ/HD3A/HD3A-deep-research-falcon.md linking Hd3a arrival at the SAM to floral transition and meristem identity reprogramming. |
| GO:0048510 regulation of timing of transition from vegetative to reproductive phase | IEA GO_REF:0000117 | ACCEPT | Summary: IEA (ARBA) annotation duplicating the IBA/IMP "regulation of timing of transition from vegetative to reproductive phase" term. Accepted as a core function. Reason: Duplicate of the curated IBA/IMP annotations to GO:0048510 and consistent with them. This is the core flowering-TIME regulatory process of Hd3a (heading date), supported by rice QTL/genetic and expression data. Supporting Evidence: PMID:12407188 The transcript levels of Hd3a were increased under SD conditions. |
| GO:0048573 photoperiodism, flowering | IEA GO_REF:0000117 | ACCEPT | Summary: IEA (ARBA) annotation: Hd3a integrates photoperiod into the flowering decision. Correct; a broad parent of the more specific short-day photoperiodism term (GO:0048575) also annotated. Reason: Correct. Hd3a is the photoperiodic output node of rice flowering: its expression integrates day-length information (induced under short days, sharply reduced above ~13.5 h day length, blocked by a 10-min night break) and is positively regulated by the photoperiod factors Hd1 and Ehd1. "Photoperiodism, flowering" is a valid broad term; the more specific "short-day photoperiodism, flowering" (GO:0048575, IMP) is also present and is the more informative term for the rice SD florigen. Supporting Evidence: file:ORYSJ/HD3A/HD3A-deep-research-falcon.md Hd3a expression integrates photoperiod information via upstream factors including **Hd1** and **Ehd1** (positive regulation in inductive contexts) PMID:12407188 the amount of Hd3a mRNA is up-regulated by Hd1 under SD conditions, suggesting that Hd3a promotes heading under the control of Hd1. |
| GO:0009909 regulation of flower development | IMP PMID:17446351 Hd3a protein is a mobile flowering signal in rice. | ACCEPT | Summary: IMP annotation from Tamaki et al. (2007), which showed Hd3a protein moves to the SAM and induces flowering - direct experimental support for Hd3a as a positive regulator of the floral program. Reason: Directly supported by the cited reference. Tamaki et al. (2007) demonstrated that the Hd3a protein moves from the leaf to the shoot apical meristem and induces flowering, establishing Hd3a as the mobile signal that regulates (promotes) the floral program [PMID:17446351]. The regulatory framing is correct; "positive regulation of flower development" (GO:0009911) would be a more specific refinement. Proposed replacements: positive regulation of flower development Supporting Evidence: PMID:17446351 the protein encoded by Hd3a, a rice ortholog of FT, moves from the leaf to the shoot apical meristem and induces flowering in rice. |
| GO:0010229 inflorescence development | IMP PMID:17446351 Hd3a protein is a mobile flowering signal in rice. | KEEP AS NON CORE | Summary: IMP annotation (Tamaki et al. 2007) to inflorescence development. The reference shows Hd3a induces flowering; inflorescence formation is the downstream developmental outcome. Kept as non-core. Reason: The cited reference demonstrates that Hd3a induces flowering when it reaches the SAM [PMID:17446351]; the resulting inflorescence (panicle) development is a downstream consequence of that induction rather than a process Hd3a directly executes. The annotation is acceptable but non-core; the core role is the floral transition/timing (GO:0010228, GO:0048510). Supporting Evidence: PMID:17446351 the protein encoded by Hd3a, a rice ortholog of FT, moves from the leaf to the shoot apical meristem and induces flowering in rice. |
| GO:0048510 regulation of timing of transition from vegetative to reproductive phase | IMP PMID:17446351 Hd3a protein is a mobile flowering signal in rice. | ACCEPT | Summary: IMP annotation (Tamaki et al. 2007): the mobile Hd3a protein controls when flowering occurs. Core flowering-time regulatory function. Reason: Core function, directly supported. Tamaki et al. (2007) showed the Hd3a protein is the mobile flowering signal that moves from leaf to SAM and induces flowering [PMID:17446351], i.e. it regulates the timing of the vegetative-to-reproductive transition. This is the most accurate process term for the rice florigen. Supporting Evidence: PMID:17446351 Florigen, the mobile signal that moves from an induced leaf to the shoot apex and causes flowering |
| GO:0048575 short-day photoperiodism, flowering | IMP PMID:17446351 Hd3a protein is a mobile flowering signal in rice. | ACCEPT | Summary: IMP annotation (Tamaki et al. 2007): Hd3a is the florigen that promotes flowering under inductive short-day conditions. Core photoperiodic function for the rice SD florigen. Reason: Core function. Hd3a promotes flowering specifically under short-day (inductive) conditions in rice; its mRNA is up-regulated under SD and it acts downstream of Hd1 to promote heading under SD [PMID:12407188], and Tamaki et al. confirmed the protein is the mobile SD florigen [PMID:17446351]. "Short-day photoperiodism, flowering" is the precise, informative term. Supporting Evidence: PMID:12407188 The transcript levels of Hd3a were increased under SD conditions. file:ORYSJ/HD3A/HD3A-deep-research-falcon.md it encodes a small FT-like phosphatidylethanolamine-binding protein (PEBP) family member that promotes flowering, especially under short days. |
| GO:0008429 phosphatidylethanolamine binding | ISS PMID:10583960 A pair of related genes with antagonistic roles in mediating... | MARK AS OVER ANNOTATED | Summary: ISS annotation to the PEBP-family namesake molecular function, inferred from membership of the phosphatidylethanolamine-binding protein family (PMID:10583960 is the Arabidopsis FT/TFL1 paper). No demonstrated PE-binding biological role for Hd3a; the gene's actual molecular action is protein-protein interaction (14-3-3 / OsFD1) within the FAC. (A second ISS annotation to this term, citing PMID:12407188, is reviewed below and shares this rationale.) Reason: "Phosphatidylethanolamine binding" (GO:0008429) is the historical namesake activity of the PEBP fold and is assigned to FT-like proteins by family-level sequence similarity (ISS), not by any phospholipid-binding assay on Hd3a. The cited reference PMID:10583960 characterizes Arabidopsis FT/TFL1 genetics in flowering and does not demonstrate PE binding for the rice protein. The functionally relevant molecular action of Hd3a is NOT lipid binding but protein-protein interaction: it binds 14-3-3 (GF14) proteins and, via them, OsFD1 to form the florigen activation complex, and "Hd3a-14-3-3 interaction is essential" for activity. The PE-binding term is therefore an over-annotation propagated from the family name; the core MF is better described as 14-3-3 / FAC-forming protein binding (see proposed new terms and questions). Retaining a measured-looking MF that has no demonstrated role for this protein is misleading. Supporting Evidence: file:ORYSJ/HD3A/HD3A-deep-research-falcon.md The 2024 review further emphasizes that **Hd3a–14-3-3 interaction is essential** (mutants that cannot interact with 14-3-3 lose Hd3a function). PMID:10583960 FT acts in part downstream of CO and mediates signals for flowering in an antagonistic manner with its homologous gene, TERMINAL FLOWER1 (TFL1). |
| GO:0008429 phosphatidylethanolamine binding | ISS PMID:12407188 Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes t... | MARK AS OVER ANNOTATED | Summary: Second ISS annotation to the PEBP-family namesake MF, citing the rice Hd3a QTL paper (PMID:12407188), which reports cloning and an early-heading phenotype but no phosphatidylethanolamine-binding assay. Over-annotation from family membership. Reason: As for the other ISS annotation to GO:0008429, this is a family-namesake molecular function assigned by sequence similarity, not by experiment. The cited paper PMID:12407188 reports identification of Hd3a as an FT-like gene and an early-heading phenotype upon introduction; it contains no phospholipid-binding measurement. Hd3a's biologically relevant molecular action is protein-protein interaction in the FAC (14-3-3/OsFD1), not PE binding. Mark as over-annotated. Supporting Evidence: PMID:12407188 we found a candidate gene that shows high similarity to the FLOWERING LOCUS T (FT) gene, which promotes flowering in Arabidopsis file:ORYSJ/HD3A/HD3A-deep-research-falcon.md in rice, Hd3a forms a complex with **14-3-3 proteins (GF14 family)** and the SAM-expressed bZIP transcription factor **OsFD1**. |
| GO:0010229 inflorescence development | IMP PMID:12407188 Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes t... | KEEP AS NON CORE | Summary: IMP annotation (Kojima et al. 2002) to inflorescence development. The reference reports an early-heading (flowering-time) phenotype, not inflorescence morphogenesis per se. Kept as non-core. (A further IMP annotation to this term citing PMID:12582636 is reviewed below and shares this rationale.) Reason: PMID:12407188 reports that introduction of Hd3a caused an early-heading phenotype and that Hd3a promotes the transition to flowering downstream of Hd1 under short days - this is a flowering-TIME effect. Any inflorescence development consequence is downstream of the Hd3a-triggered floral transition. The annotation is acceptable but non-core; the core is the transition/timing role (GO:0048510, GO:0048575). Supporting Evidence: PMID:12407188 Introduction of the gene caused an early-heading phenotype in rice. |
| GO:0010229 inflorescence development | IMP PMID:12582636 Genetic dissection of a genomic region for a quantitative tr... | KEEP AS NON CORE | Summary: IMP annotation (Monna et al. 2002) to inflorescence development. This reference is the genetic dissection of the Hd3 QTL into Hd3a and Hd3b controlling heading date - a flowering-time study, not an inflorescence-morphogenesis study. Kept as non-core. Reason: PMID:12582636 maps Hd3a as a heading-date (flowering-time) QTL whose Kasalath allele promotes heading under short days; it does not characterize inflorescence development per se. Inflorescence formation is a downstream developmental consequence of the Hd3a-controlled floral transition. Retain as non-core; the core flowering-time role is better captured by GO:0048510 and GO:0048575. Supporting Evidence: PMID:12582636 the Kasalath allele at Hd3a promotes heading under short-day conditions |
| GO:0048510 regulation of timing of transition from vegetative to reproductive phase | IMP PMID:12407188 Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes t... | ACCEPT | Summary: IMP annotation (Kojima et al. 2002): Hd3a promotes the transition to flowering downstream of Hd1 under short days. Core flowering-time regulatory function, directly supported. Reason: Core function, directly supported by the cited reference. Kojima et al. (2002) showed that introduction of Hd3a caused early heading and that Hd3a mRNA is up-regulated by Hd1 under SD, establishing Hd3a as a regulator of the timing of the vegetative-to-reproductive transition [PMID:12407188]. The term is at the right level of specificity. Supporting Evidence: PMID:12407188 the amount of Hd3a mRNA is up-regulated by Hd1 under SD conditions, suggesting that Hd3a promotes heading under the control of Hd1. |
| GO:0048510 regulation of timing of transition from vegetative to reproductive phase | IMP PMID:12582636 Genetic dissection of a genomic region for a quantitative tr... | ACCEPT | Summary: IMP annotation (Monna et al. 2002): the Hd3a allele controls heading date (flowering time). Core flowering-time regulatory function. Reason: Core function. Monna et al. (2002) genetically dissected the Hd3 region and showed the Hd3a locus controls heading date, with the Kasalath allele promoting heading under short days [PMID:12582636]. This directly supports a role in regulating the timing of the vegetative-to-reproductive transition. Supporting Evidence: PMID:12582636 two tightly linked loci, Hd3a and Hd3b, were identified in the Hd3 region. |
| GO:0048572 short-day photoperiodism | IMP PMID:12407188 Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes t... | MODIFY | Summary: IMP annotation (Kojima et al. 2002) to "short-day photoperiodism". Correct, but the flowering-specific child term GO:0048575 (short-day photoperiodism, flowering) is more informative. Reason: The annotation is biologically correct - Hd3a mediates the short-day photoperiodic response that promotes rice flowering (its mRNA is induced under SD; it promotes heading under SD downstream of Hd1) [PMID:12407188]. However, "short-day photoperiodism" (GO:0048572) is the broad parent; the flowering-specific child "short-day photoperiodism, flowering" (GO:0048575) - already annotated by IMP from PMID:17446351 - is the precise, informative term for this florigen and should be used instead. Proposed replacements: short-day photoperiodism, flowering Supporting Evidence: PMID:12407188 Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering downstream of Hd1 under short-day conditions. |
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Download this section (compressed HTML)Q: What is the most appropriate GO molecular-function representation for florigen (FT-family) activity - 14-3-3 protein binding plus transcription coactivator-like activity within the FAC - given that the PEBP-family "phosphatidylethanolamine binding" term is a namesake inference with no demonstrated role for Hd3a?
Suggested experts: Hiroyuki Tsuji
Q: Should the rice florigen Hd3a carry a cellular-component annotation for the florigen activation complex (Hd3a/14-3-3/OsFD1), and is there a suitable GO complex term, analogous to how transcription-factor complexes are annotated?
Suggested experts: Ko Shimamoto
Q: How is the long-distance, phloem-mediated movement of Hd3a from leaf to SAM best annotated - does it warrant a protein-transport / intercellular-signaling process term in addition to the floral-transition terms?
Suggested experts: Hiroyuki Tsuji
Experiment: Quantitatively map Hd3a protein movement and unloading at the base of the SAM using tissue-specific, switchable Hd3a-fluorescent fusions combined with live imaging, to define the spatial Hd3a accumulation zone that triggers the whole-SAM developmental switch.
Hypothesis: A spatially restricted zone of Hd3a accumulation near the SAM periphery is sufficient to trigger a whole-meristem vegetative-to-reproductive transition.
Type: in planta live imaging of a mobile signaling protein
Experiment: Reconstitute the rice florigen activation complex (Hd3a + 14-3-3/GF14 + OsFD1) in vitro and in SAM protoplasts, and test 14-3-3-binding-deficient Hd3a variants for FAC assembly, nuclear localization and OsMADS14/OsMADS15 activation.
Hypothesis: Hd3a's molecular function is 14-3-3-dependent FAC assembly and consequent transcriptional activation of floral MADS-box genes, not phospholipid binding.
Type: complex reconstitution and transcriptional-activation assay
Experiment: Directly test whether purified Hd3a binds phosphatidylethanolamine (or other phospholipids) under physiological conditions, to determine whether the PEBP-family-namesake GO:0008429 annotation has any biochemical basis for the rice florigen.
Hypothesis: Hd3a does not bind phosphatidylethanolamine in a functionally relevant manner; the ISS annotation is a family-name artefact.
Type: in vitro lipid-binding (liposome / protein-lipid overlay) assay
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