HD3A

Existing Annotations Review

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.

Core Functions

Hd3a is the rice florigen: a phloem-mobile FT-family signaling protein produced in leaf-blade vascular tissue that moves long-distance to the shoot apical meristem and acts as a positive regulator of the floral transition, controlling the TIMING of the vegetative-to-reproductive switch (heading date / flowering time) under inductive short-day photoperiod.

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.
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.

In shoot-apical-meristem cells Hd3a executes its function by protein-protein interaction: it forms a cytoplasmic complex with 14-3-3 (GF14) proteins that, upon co-expression of the bZIP transcription factor OsFD1, becomes nuclear and assembles the florigen activation complex (FAC), which transcriptionally activates floral-identity MADS-box genes (OsMADS14, OsMADS15). The Hd3a-14-3-3 interaction is essential for activity. (Note: no GO molecular-function term for "florigen activity" exists; the relevant MF is 14-3-3/FAC-forming protein binding, and the family-namesake "phosphatidylethanolamine binding" is not a demonstrated function.)

Supporting Evidence:

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**. This complex provides the mechanistic bridge between Hd3a arrival and transcriptional activation of flowering genes.
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).

References

GO_REF:0000033

Annotation inferences using phylogenetic trees

FT/florigen (PEBP family) functions - vegetative-to-reproductive phase transition of meristem, regulation of timing of that transition, regulation of flower development and inflorescence development - are conserved across the FT-like phylogenetic group and were propagated to Hd3a by IBA.

GO_REF:0000043

Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping

SwissProt keyword-derived (SPKW) annotations present in an earlier keyword2GO snapshot but removed from the current GOA release after GOA retired the keyword2GO pipeline for cellular organisms.
For HD3A the keywords "Differentiation" and "Flowering"/"Developmental protein" mapped to GO:0030154 (cell differentiation) and GO:0009908 (flower development); both are over-general / mis-targeted for a mobile flowering-time signal and their removal was reasonable (cell differentiation) or warrants replacement with a regulatory term (flower development).

GO_REF:0000044

Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt

UniProt subcellular-location mapping assigns Nucleus (SL-0191) and Cytoplasm (SL-0086) to Hd3a, consistent with the cytoplasmic Hd3a-14-3-3 subcomplex and its nuclear FAC.

GO_REF:0000117

Electronic Gene Ontology annotations created by ARBA machine learning models

ARBA models assigned regulation of flower development, inflorescence development, regulation of timing of the vegetative-to-reproductive transition, and photoperiodism (flowering) to Hd3a; these duplicate or parallel the curated IBA/IMP annotations.

PMID:10583960

A pair of related genes with antagonistic roles in mediating flowering signals.

Characterizes Arabidopsis FT (the Hd3a ortholog) genetically - FT promotes flowering downstream of CONSTANS and acts antagonistically with TERMINAL FLOWER1 (TFL1); loss of FT delays flowering and FT overexpression causes precocious flowering.
Does not measure phosphatidylethanolamine binding; the ISS GO:0008429 annotation citing this paper is a PEBP-family-namesake inference, not an experimental MF.

PMID:12407188

Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering downstream of Hd1 under short-day conditions.

Identified Hd3a as an FT-like gene at a heading-date QTL; introduction of Hd3a caused an early-heading phenotype, Hd3a transcript increased under short days, and Hd3a mRNA is up-regulated by Hd1 under SD - Hd3a promotes heading under the control of Hd1.
Establishes the conserved function/regulatory relationship of Hd3a/FT with Hd1/CO between rice (SD plant) and Arabidopsis (LD plant).

PMID:12582636

Genetic dissection of a genomic region for a quantitative trait locus, Hd3, into two loci, Hd3a and Hd3b, controlling heading date in rice.

Genetically dissected the Hd3 region into two linked heading-date loci, Hd3a and Hd3b; the Kasalath allele at Hd3a promotes heading (flowering) under short-day conditions.
A flowering-time (heading-date) QTL study; provides no inflorescence-morphogenesis characterization.

PMID:17446351

Hd3a protein is a mobile flowering signal in rice.

Demonstrated that the Hd3a protein moves from the leaf to the shoot apical meristem and induces flowering - the key experimental evidence that Hd3a is the rice florigen (a mobile flowering signal).
Hd3a is expressed (protein level) in leaf-blade vascular tissue, stem and the inner region of the SAM, with circadian expression peaking at dawn under SD - consistent with a leaf-to-SAM long-distance signaling role.

file:ORYSJ/HD3A/HD3A-deep-research-falcon.md

Deep-research report (falcon / Edison Scientific Literature) - functional annotation of rice HD3A (Q93WI9).

Synthesizes the rice florigen literature, concluding Hd3a is the rice ortholog of Arabidopsis FT and a phloem-mobile florigen - synthesized in leaf vascular tissue, transported through the phloem, unloaded near the SAM, and entering the SAM to trigger the vegetative-to-reproductive transition.
Describes Hd3a's molecular mode of action as protein-protein interaction - it is not an enzyme or transporter - forming a cytoplasmic Hd3a-14-3-3 (GF14) subcomplex that becomes nuclear upon OsFD1 co-expression to assemble the florigen activation complex (FAC), which activates floral MADS-box genes OsMADS14/OsMADS15. The Hd3a-14-3-3 interaction is essential.
Documents large flowering-time phenotypes (Hd3a RNAi delays flowering >30 days; Hd3a+RFT1 double suppression prevents flowering up to 300 days) and a steep photoperiod response (Hd3a falls to <1/10 above ~13.5 h day length; a 10-min night break blocks induction); Hd3a acts downstream of Hd1 and Ehd1.

Suggested Experiments

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

Deep Research

Falcon

(HD3A-deep-research-falcon.md)

this with annotations you find in gene/protein databases, but these can be outdated or inaccurate. Falcon Edison Scientific Literature 31 citations 3 artifacts 2026-05-30T07:46:51.005771

Edison artifact artifact-00 (text/markdown)

## Context ID: pqac-00000008 Figure 1 on page 26 provides a model of Hd3a/FT protein action, illustrating its synthesis in the vascular tissue of leaves, its tr (image/png)

## Context ID: pqac-00000023 Figure 4 illustrates the rice florigen activation complex (FAC) and its role in the vegetative-to-reproductive phase transition in (image/png)

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Research report: Functional annotation of rice HD3A (UniProt Q93WI9; Os06g0157700; LOC_Os06g06320)

0) Target verification (mandatory)

The UniProt accession Q93WI9 corresponds to rice HD3A (Heading date 3a) (ordered locus name Os06g0157700 / LOC_Os06g06320) and is an FT-like member of the phosphatidylethanolamine-binding protein (PEBP) family. In the rice flowering literature, Hd3a is consistently described as the ortholog of Arabidopsis FLOWERING LOCUS T (FT) and as a mobile florigen produced in leaves and transported to the shoot apical meristem (SAM), matching the UniProt identity and domain/family context provided. (tsuji2008florigenandthe pages 1-2, zhou2021transcriptionalandpost‐transcriptional pages 2-3, sohail2023geneticandsignaling pages 1-3)

1) Key concepts, definitions, and current understanding

1.1 Florigen and FT-like/PEBP proteins

Florigen is the long-sought systemic flowering signal: 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. In rice, Hd3a is one of the two principal florigen genes (with RFT1), encoding FT-like PEBP proteins. (tsuji2024thefunctionof pages 1-2, zhou2021transcriptionalandpost‐transcriptional pages 2-3)

1.2 Hd3a’s primary molecular function

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. Genetic and mechanistic studies summarized across sources support that Hd3a is synthesized in leaf vascular tissue, moves via the phloem, and then acts in the SAM to activate flowering gene expression programs. (tsuji2008florigenandthe pages 1-2, tsuji2008florigenandthe pages 2-4)

1.3 The florigen activation complex (FAC)

A central current concept is the florigen activation complex (FAC): in rice, Hd3a forms a complex with 14-3-3 proteins (GF14 family) and the SAM-expressed bZIP transcription factor OsFD1. This complex provides the mechanistic bridge between Hd3a arrival and transcriptional activation of flowering genes. (sohail2023geneticandsignaling pages 1-3, tsuji2024thefunctionof pages 6-7)

2) Expression, mobility, and localization of the Hd3a protein

2.1 Where Hd3a is expressed (tissue specificity)

Classic promoter/reporter and expression analyses show Hd3a transcription is localized to vascular cells of leaf blades, while Hd3a mRNA is extremely low in the shoot apex (reported as ~four orders of magnitude lower at the apex than in leaf blades). This supports a leaf-originating, long-distance signaling role rather than local SAM synthesis. (tsuji2008florigenandthe pages 1-2)

2.2 Long-distance mobility: leaf phloem → SAM

Transgenic localization experiments with Hd3a-GFP showed signal along the vascular system from leaf blade toward the upper stem and into the inner region beneath the SAM, supporting the model that Hd3a protein is synthesized in leaf vascular tissue, transported through the phloem, unloaded near the SAM, and enters the SAM. (tsuji2008florigenandthe pages 1-2)

A conceptual model figure from the same source summarizes this transport-and-action scheme (leaf vascular synthesis → phloem transport → SAM unloading and action). (tsuji2008florigenandthe media 72750ae5)

2.3 Subcellular localization and nuclear entry via FAC assembly (2024 synthesis)

A 2024 mechanistic review emphasizes a refined, cell-biological model for rice florigen action: Hd3a first forms an Hd3a–14-3-3 subcomplex in the cytoplasm of SAM cells. This subcomplex is described as large relative to nuclear pores and remains cytoplasmic until OsFD1 is co-expressed, at which point the complex localizes to the nucleus to activate downstream transcriptional programs. (tsuji2024thefunctionof pages 6-7)

A structural/functional depiction of the rice FAC (Hd3a/14-3-3/OsFD1) and its nucleus-associated activity is provided in a figure from this 2024 review. (tsuji2024thefunctionof media d2a973fd)

3) Molecular mechanism in pathways: regulators, partners, and targets

3.1 Core upstream regulators in photoperiodic flowering

Hd3a expression integrates photoperiod information via upstream factors including Hd1 and Ehd1 (positive regulation in inductive contexts), with additional modulation by circadian/photoperiod network components. (sohail2023geneticandsignaling pages 5-6, tsuji2008florigenandthe pages 7-8)

Quantitatively, Hd3a shows a strong photoperiod threshold response: one review reports Hd3a is expressed in the morning when day length is under ~13 hours, and Hd3a expression drops to <1/10 when day length exceeds 13.5 hours; a brief night-break (10 minutes) can prevent Hd3a induction and delay flowering. (zhou2021transcriptionalandpost‐transcriptional pages 2-3)

3.2 Interaction partners: 14-3-3 proteins and OsFD1

Multiple sources (including a 2023 review and a 2024 mechanistic review) converge on the model that Hd3a interacts with 14-3-3 proteins and with OsFD1 to form the FAC. The 2024 review further emphasizes that Hd3a–14-3-3 interaction is essential (mutants that cannot interact with 14-3-3 lose Hd3a function). (sohail2023geneticandsignaling pages 1-3, tsuji2024thefunctionof pages 6-7)

3.3 Downstream transcriptional targets

FAC formation leads to induction of floral identity and transition programs, including activation of MADS-box genes. A rice FT-like gene study explicitly states that Hd3a/RFT1 interact with 14-3-3 in the SAM cytoplasm, enter the nucleus, and combine with OsFD1 to form FAC, which induces OsMADS14 and OsMADS15. A 2023 review also emphasizes activation of OsMADS15 (AP1 homolog). (gu2022osftl4anftlike pages 1-2, sohail2023geneticandsignaling pages 1-3)

3.4 Antagonism and competitive binding within the PEBP/FT-like family

The florigen pathway is tunable via competitive interactions at the level of 14-3-3 binding. For example, one rice FT-like study reports that certain PEBP-family repressors (RCNs) can compete with Hd3a for 14-3-3 binding to form a florigen repression complex (FRC), and that another FT-like protein (OsFTL4) can compete with Hd3a for interactions with multiple 14-3-3 proteins. (gu2022osftl4anftlike pages 1-2)

4) Phenotypic evidence (statistics and data)

4.1 Large-effect genetic perturbations

A foundational rice florigen review reports strong phenotypes from suppression experiments: Hd3a RNAi delays flowering by >30 days, and double RNAi suppressing both Hd3a and RFT1 prevented flowering up to 300 days, underscoring that Hd3a is a major flowering promoter and partly redundant with RFT1. (tsuji2008florigenandthe pages 2-4)

4.2 Photoperiod-sensitive quantitative regulation

As noted above, Hd3a transcription shows a steep quantitative response around ~13–13.5 h day length (drop to <1/10 above 13.5 h), and a short night interruption can block induction. These quantitative regulatory features support the role of Hd3a as a photoperiod output node. (zhou2021transcriptionalandpost‐transcriptional pages 2-3)

5) Recent developments and latest research (prioritizing 2023–2024)

5.1 2024: refined subcellular model and key open questions

A 2024 Plant & Cell Physiology review consolidates mechanistic evidence and highlights unresolved issues: where and how florigen is unloaded at the base of the SAM, how Hd3a distribution within and around the SAM is established, how a spatially restricted Hd3a accumulation zone triggers a whole-SAM developmental switch, and which additional transport partners contribute to Hd3a movement and nuclear action. (tsuji2024thefunctionof pages 6-7, tsuji2024thefunctionof pages 1-2)

5.2 2023: pathway-centric synthesis and applied framing

A 2023 review reiterates Hd3a’s identity as a mobile FT-like florigen produced in leaf vasculature and unloaded into the SAM, acting via FAC with 14-3-3 and OsFD1 to activate OsMADS15; it also flags mechanistic uncertainties (e.g., details of trafficking) and emphasizes the relevance of this pathway for crop flowering-time manipulation. (sohail2023geneticandsignaling pages 1-3)

6) Current applications and real-world implementations (2024 examples)

Recent rice studies demonstrate practical “heading-date engineering” strategies that operate through, or converge on, Hd3a/RFT1 expression.

6.1 Promoter editing of a florigen gene to fine-tune heading date (RFT1 promoter; 2024-02)

A 2024 Plant Growth Regulation study used CRISPR/Cas9 to edit a 0.5-kb region of the RFT1 promoter, generating multiple homozygous lines with mild-to-moderate heading delays of 1.4 to 9.2 days depending on line/background. Importantly for Hd3a annotation, Hd3a and RFT1 transcript levels were significantly reduced in the edited lines, linking this engineering intervention to the Hd3a-centered florigen network. (zhou2024genomeeditingof pages 1-4, zhou2024genomeeditingof pages 4-7)

6.2 Editing an upstream activator to delay heading while improving grain quality (OsMADS50; 2024-08)

A 2024 Plants paper edited the flowering activator OsMADS50 (CRISPR/Cas9) in the northern cultivar KenDao 12 to adapt it to southern regions. The edited line flowered ~1 week later, with reduced expression of multiple flowering genes including Hd3a and RFT1, and reported improved grain quality traits (e.g., increased length-to-width ratio, fat content, and seed transparency) with no yield penalty and a slight yield increase attributed mainly to more effective tillers. This is a concrete implementation example where manipulating an upstream regulator shifts Hd3a/RFT1 output to achieve agronomic goals. (liu2024improvingricequality pages 1-2)

6.3 Genome editing of a regulatory kinase to advance heading and improve yield traits (OsCKq1; 2024-08)

A 2024 Rice paper reports that OsCKq1 genome-edited (GE) lines headed ~3–5 days earlier than the background cultivar (Ilmi), accompanied by increased mRNA levels of Hd3a, Ehd1, and RFT1 under long-day conditions. The study also reports increases in grain size and yield-related metrics (grain length/width, 1,000-grain weight, overall yield) compared with Ilmi, positioning this as a translational strategy to create early-maturing, high-yielding cultivars via manipulating Hd3a pathway output. (kim2024osckq1regulatesheading pages 1-2)

7) Expert opinions / authoritative analysis (synthesis)

Across authoritative sources, there is strong consensus that Hd3a is the central mobile flowering signal in rice under inductive short-day conditions and that its key biochemical mode of action is protein–protein interaction culminating in FAC-dependent transcriptional activation of floral transition genes at the SAM. Recent expert synthesis (2024) stresses that while the FAC concept is well supported, the field still lacks a complete mechanistic account of transport partners, unloading routes, and spatial control of Hd3a within the SAM, which are now the major frontiers for research and crop-engineering leverage points. (tsuji2008florigenandthe pages 1-2, tsuji2024thefunctionof pages 6-7)

8) Evidence map (summary table)

The following table provides a compact evidence map for Hd3a functional annotation (identity → expression → transport → localization → mechanism → phenotype → applications).

Category	Key points	Evidence citation IDs
Identity/definition	HD3A in rice corresponds to Os06g0157700 and is the rice FT ortholog/florigen; it encodes a small FT-like phosphatidylethanolamine-binding protein (PEBP) family member that promotes flowering, especially under short days.	(sohail2023geneticandsignaling pages 1-3, zhou2021transcriptionalandpost‐transcriptional pages 2-3, tsuji2008florigenandthe pages 1-2)
Expression	Hd3a transcription is concentrated in leaf blade vascular tissue/phloem-associated cells and is very low in the shoot apex; expression is induced under short days and falls sharply under long days, with reported strong reduction when day length exceeds ~13.5 h.	(tsuji2008florigenandthe pages 1-2, zhou2021transcriptionalandpost‐transcriptional pages 2-3)
Mobility/transport	Hd3a protein is synthesized in leaves, loaded into phloem, transported long distance toward the shoot apical meristem (SAM), unloaded near the vascular termini, and then enters the SAM; transport is central to florigen function, while some trafficking steps remain unresolved.	(tsuji2008florigenandthe pages 1-2, tsuji2008florigenandthe pages 2-4, tsuji2024thefunctionof pages 6-7, colleoni2024floweringtimegenes pages 2-4)
Subcellular localization	In SAM cells, Hd3a first forms a cytoplasmic Hd3a–14-3-3 subcomplex; nuclear function depends on OsFD1 co-expression, and Hd3a accumulation in the SAM is spatially restricted during floral transition. Classic localization studies also detected Hd3a-GFP in vasculature and the inner SAM region.	(tsuji2024thefunctionof pages 6-7, tsuji2008florigenandthe pages 1-2)
Molecular interactions	Hd3a interacts with 14-3-3 proteins (GF14 family) and OsFD1 to form the florigen activation complex (FAC); 14-3-3 interaction is essential for activity. Antagonistic PEBP proteins such as RCNs/OsFTL4 can compete for 14-3-3 binding, forming repression complexes or attenuating florigen output.	(gu2022osftl4anftlike pages 1-2, sohail2023geneticandsignaling pages 1-3, tsuji2024thefunctionof pages 6-7)
Downstream targets	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.	(gu2022osftl4anftlike pages 1-2, sohail2023geneticandsignaling pages 1-3, sohail2023geneticandsignaling pages 6-7)
Upstream regulators	Hd3a is positively regulated by Hd1 and Ehd1; modulators include OsGI, OsMADS50, OsMADS51, Ghd7 and circadian/photoperiod inputs. Hd1 can activate or repress depending on daylength context, while Ehd1 is a major promoter of Hd3a expression.	(sohail2023geneticandsignaling pages 7-8, sohail2023geneticandsignaling pages 5-6, tsuji2008florigenandthe pages 7-8)
Quantitative phenotypes	Functional perturbation causes large flowering phenotypes: Hd3a RNAi delayed flowering by >30 days, and double suppression of Hd3a and RFT1 prevented flowering up to 300 days; Hd3a expression is reduced to <1/10 above ~13.5 h day length, and a 10-min night break can block induction and delay flowering.	(tsuji2008florigenandthe pages 2-4, zhou2021transcriptionalandpost‐transcriptional pages 2-3)
Recent developments 2023-2024	Recent reviews emphasize a refined model in which Hd3a forms the FAC after cytoplasmic interaction with 14-3-3, then acts in/around the SAM; major open questions include exact unloading routes, intra-SAM distribution, transport cofactors, and how a restricted Hd3a domain triggers whole-SAM transition.	(tsuji2024thefunctionof pages 6-7, colleoni2024floweringtimegenes pages 2-4, tsuji2024thefunctionof pages 1-2)
Applications	Hd3a-centered flowering networks are active targets for crop adaptation and breeding: recent studies manipulate upstream regulators or parallel florigen pathways to tune Hd3a/RFT1 expression and heading date for regional adaptation, quality, and yield; reviews highlight heading-date engineering as a practical route for rice improvement.	(sohail2023geneticandsignaling pages 1-3, giaume2022atripleflorigen pages 11-14)

Table: This table summarizes core functional-annotation evidence for rice HD3A/Os06g0157700, covering identity, mechanism, localization, regulation, phenotypes, and recent translational relevance. It is designed as a compact evidence map for use in a research report.

9) Key figures supporting localization/mechanism (visual evidence)

A model figure depicts Hd3a synthesis in leaf vasculature, phloem transport, unloading near the SAM, and action in the SAM. (tsuji2008florigenandthe media 72750ae5)
A 2024 figure provides a structural model of the rice FAC (Hd3a/14-3-3/OsFD1) and depicts cytoplasmic subcomplex formation and nuclear localization upon OsFD1 expression. (tsuji2024thefunctionof media d2a973fd)

10) Selected references (with URLs and publication dates)

Tsuji H. et al. Florigen and the Photoperiodic Control of Flowering in Rice. Rice (Aug 2008). https://doi.org/10.1007/s12284-008-9005-8 (tsuji2008florigenandthe pages 1-2)
Zhou S. et al. Transcriptional and post-transcriptional regulation of heading date in rice. New Phytologist (Feb 2021). https://doi.org/10.1111/nph.17158 (zhou2021transcriptionalandpost‐transcriptional pages 2-3)
Sohail A. Genetic and signaling pathways of flowering regulation in rice. Brazilian Journal of Botany (Aug 2023). https://doi.org/10.1007/s40415-023-00910-y (sohail2023geneticandsignaling pages 1-3)
Tsuji H., Sato M. The Function of Florigen in the Vegetative-to-Reproductive Phase Transition… Plant and Cell Physiology (Jan 2024). https://doi.org/10.1093/pcp/pcae001 (tsuji2024thefunctionof pages 1-2)
Colleoni P.E. et al. Flowering time genes branching out. Journal of Experimental Botany (Mar 2024). https://doi.org/10.1093/jxb/erae112 (colleoni2024floweringtimegenes pages 2-4)
Zhou W. et al. Genome editing of RICE FLOWERING LOCUS T 1 promoter delayed flowering in rice. Plant Growth Regulation (Feb 2024). https://doi.org/10.1007/s10725-024-01118-0 (zhou2024genomeeditingof pages 1-4)
Kim E.-G. et al. OsCKq1 regulates heading date and grain weight in rice… Rice (Aug 2024). https://doi.org/10.1186/s12284-024-00726-8 (kim2024osckq1regulatesheading pages 1-2)
Liu J. et al. Improving Rice Quality by Regulating the Heading Dates… Plants (Aug 2024). https://doi.org/10.3390/plants13162221 (liu2024improvingricequality pages 1-2)

11) Limitations of this evidence package

Some mechanistic details alluded to in reviews (e.g., full molecular identity of all Hd3a transport cofactors, or comprehensive field-scale validation across environments) were not directly extractable from the retrieved excerpts and would require targeted retrieval of specific primary papers focused on florigen loading/unloading and long-distance transport machinery. (tsuji2024thefunctionof pages 6-7, tsuji2008florigenandthe pages 7-8)

References

(tsuji2008florigenandthe pages 1-2): Hiroyuki Tsuji, Shojiro Tamaki, Reina Komiya, and Ko Shimamoto. Florigen and the photoperiodic control of flowering in rice. Rice, 1:25-35, Aug 2008. URL: https://doi.org/10.1007/s12284-008-9005-8, doi:10.1007/s12284-008-9005-8. This article has 87 citations and is from a peer-reviewed journal.
(zhou2021transcriptionalandpost‐transcriptional pages 2-3): Shirong Zhou, Shanshan Zhu, Song Cui, Haigang Hou, Haoqin Wu, Benyuan Hao, Liang Cai, Zhuang Xu, Linglong Liu, Ling Jiang, Haiyang Wang, and Jianmin Wan. Transcriptional and post‐transcriptional regulation of heading date in rice. Feb 2021. URL: https://doi.org/10.1111/nph.17158, doi:10.1111/nph.17158. This article has 169 citations and is from a highest quality peer-reviewed journal.
(sohail2023geneticandsignaling pages 1-3): Amir Sohail. Genetic and signaling pathways of flowering regulation in rice (oryza sativa l.). Brazilian Journal of Botany, 46:599-608, Aug 2023. URL: https://doi.org/10.1007/s40415-023-00910-y, doi:10.1007/s40415-023-00910-y. This article has 10 citations.
(tsuji2024thefunctionof pages 1-2): Hiroyuki Tsuji and Moeko Sato. The function of florigen in the vegetative-to-reproductive phase transition in and around the shoot apical meristem. Plant and Cell Physiology, 65:322-337, Jan 2024. URL: https://doi.org/10.1093/pcp/pcae001, doi:10.1093/pcp/pcae001. This article has 27 citations and is from a domain leading peer-reviewed journal.
(tsuji2008florigenandthe pages 2-4): Hiroyuki Tsuji, Shojiro Tamaki, Reina Komiya, and Ko Shimamoto. Florigen and the photoperiodic control of flowering in rice. Rice, 1:25-35, Aug 2008. URL: https://doi.org/10.1007/s12284-008-9005-8, doi:10.1007/s12284-008-9005-8. This article has 87 citations and is from a peer-reviewed journal.
(tsuji2024thefunctionof pages 6-7): Hiroyuki Tsuji and Moeko Sato. The function of florigen in the vegetative-to-reproductive phase transition in and around the shoot apical meristem. Plant and Cell Physiology, 65:322-337, Jan 2024. URL: https://doi.org/10.1093/pcp/pcae001, doi:10.1093/pcp/pcae001. This article has 27 citations and is from a domain leading peer-reviewed journal.
(tsuji2008florigenandthe media 72750ae5): Hiroyuki Tsuji, Shojiro Tamaki, Reina Komiya, and Ko Shimamoto. Florigen and the photoperiodic control of flowering in rice. Rice, 1:25-35, Aug 2008. URL: https://doi.org/10.1007/s12284-008-9005-8, doi:10.1007/s12284-008-9005-8. This article has 87 citations and is from a peer-reviewed journal.
(tsuji2024thefunctionof media d2a973fd): Hiroyuki Tsuji and Moeko Sato. The function of florigen in the vegetative-to-reproductive phase transition in and around the shoot apical meristem. Plant and Cell Physiology, 65:322-337, Jan 2024. URL: https://doi.org/10.1093/pcp/pcae001, doi:10.1093/pcp/pcae001. This article has 27 citations and is from a domain leading peer-reviewed journal.
(sohail2023geneticandsignaling pages 5-6): Amir Sohail. Genetic and signaling pathways of flowering regulation in rice (oryza sativa l.). Brazilian Journal of Botany, 46:599-608, Aug 2023. URL: https://doi.org/10.1007/s40415-023-00910-y, doi:10.1007/s40415-023-00910-y. This article has 10 citations.
(tsuji2008florigenandthe pages 7-8): Hiroyuki Tsuji, Shojiro Tamaki, Reina Komiya, and Ko Shimamoto. Florigen and the photoperiodic control of flowering in rice. Rice, 1:25-35, Aug 2008. URL: https://doi.org/10.1007/s12284-008-9005-8, doi:10.1007/s12284-008-9005-8. This article has 87 citations and is from a peer-reviewed journal.
(gu2022osftl4anftlike pages 1-2): Houwen Gu, Kunming Zhang, Jie Chen, Sadia Gull, Chuyan Chen, Yafei Hou, Xiangbo Li, Jun Miao, Yong Zhou, and Guohua Liang. Osftl4, an ft-like gene, regulates flowering time and drought tolerance in rice (oryza sativa l.). Rice, Sep 2022. URL: https://doi.org/10.1186/s12284-022-00593-1, doi:10.1186/s12284-022-00593-1. This article has 42 citations and is from a peer-reviewed journal.
(zhou2024genomeeditingof pages 1-4): Wenyan Zhou, Mingliang He, Xiaojie Tian, Qingjie Guan, Xinglong Yu, Qingyun Bu, and Xiufeng Li. Genome editing of rice flowering locus t 1 promoter delayed flowering in rice. Plant Growth Regulation, 103(3):503-507, Feb 2024. URL: https://doi.org/10.1007/s10725-024-01118-0, doi:10.1007/s10725-024-01118-0. This article has 4 citations and is from a peer-reviewed journal.
(zhou2024genomeeditingof pages 4-7): Wenyan Zhou, Mingliang He, Xiaojie Tian, Qingjie Guan, Xinglong Yu, Qingyun Bu, and Xiufeng Li. Genome editing of rice flowering locus t 1 promoter delayed flowering in rice. Plant Growth Regulation, 103(3):503-507, Feb 2024. URL: https://doi.org/10.1007/s10725-024-01118-0, doi:10.1007/s10725-024-01118-0. This article has 4 citations and is from a peer-reviewed journal.
(liu2024improvingricequality pages 1-2): Jianguo Liu, Qinqin Yi, Guojun Dong, Yuyu Chen, Longbiao Guo, Zhenyu Gao, Li Zhu, Deyong Ren, Qiang Zhang, Qing Li, Jingyong Li, Qiangming Liu, Guangheng Zhang, Qian Qian, and Lan Shen. Improving rice quality by regulating the heading dates of rice varieties without yield penalties. Plants, 13:2221, Aug 2024. URL: https://doi.org/10.3390/plants13162221, doi:10.3390/plants13162221. This article has 8 citations.
(kim2024osckq1regulatesheading pages 1-2): Eun-Gyeong Kim, Yoon-Hee Jang, Jae-Ryoung Park, Xiao-Han Wang, Rahmatullah Jan, Muhammad Farooq, Sajjad Asaf, Saleem Asif, and Kyung-Min Kim. Osckq1 regulates heading date and grain weight in rice in response to day length. Rice, Aug 2024. URL: https://doi.org/10.1186/s12284-024-00726-8, doi:10.1186/s12284-024-00726-8. This article has 4 citations and is from a peer-reviewed journal.
(colleoni2024floweringtimegenes pages 2-4): Pierangela E Colleoni, Sam W van Es, Ton Winkelmolen, Richard G H Immink, and G Wilma van Esse. Flowering time genes branching out. Journal of Experimental Botany, 75:4195-4209, Mar 2024. URL: https://doi.org/10.1093/jxb/erae112, doi:10.1093/jxb/erae112. This article has 30 citations and is from a domain leading peer-reviewed journal.
(sohail2023geneticandsignaling pages 6-7): Amir Sohail. Genetic and signaling pathways of flowering regulation in rice (oryza sativa l.). Brazilian Journal of Botany, 46:599-608, Aug 2023. URL: https://doi.org/10.1007/s40415-023-00910-y, doi:10.1007/s40415-023-00910-y. This article has 10 citations.
(sohail2023geneticandsignaling pages 7-8): Amir Sohail. Genetic and signaling pathways of flowering regulation in rice (oryza sativa l.). Brazilian Journal of Botany, 46:599-608, Aug 2023. URL: https://doi.org/10.1007/s40415-023-00910-y, doi:10.1007/s40415-023-00910-y. This article has 10 citations.
(giaume2022atripleflorigen pages 11-14): F Giaume. A triple florigen system is essential for flowering and panicle architecture in rice. Unknown journal, 2022.

Artifacts

Edison artifact artifact-00

Citations

tsuji2008florigenandthe pages 1-2
tsuji2024thefunctionof pages 6-7
tsuji2008florigenandthe pages 2-4
sohail2023geneticandsignaling pages 1-3
liu2024improvingricequality pages 1-2
tsuji2024thefunctionof pages 1-2
colleoni2024floweringtimegenes pages 2-4
zhou2024genomeeditingof pages 1-4
sohail2023geneticandsignaling pages 5-6
tsuji2008florigenandthe pages 7-8
zhou2024genomeeditingof pages 4-7
sohail2023geneticandsignaling pages 6-7
sohail2023geneticandsignaling pages 7-8
giaume2022atripleflorigen pages 11-14
https://doi.org/10.1007/s12284-008-9005-8
https://doi.org/10.1111/nph.17158
https://doi.org/10.1007/s40415-023-00910-y
https://doi.org/10.1093/pcp/pcae001
https://doi.org/10.1093/jxb/erae112
https://doi.org/10.1007/s10725-024-01118-0
https://doi.org/10.1186/s12284-024-00726-8
https://doi.org/10.3390/plants13162221
https://doi.org/10.1007/s12284-008-9005-8,
https://doi.org/10.1111/nph.17158,
https://doi.org/10.1007/s40415-023-00910-y,
https://doi.org/10.1093/pcp/pcae001,
https://doi.org/10.1186/s12284-022-00593-1,
https://doi.org/10.1007/s10725-024-01118-0,
https://doi.org/10.3390/plants13162221,
https://doi.org/10.1186/s12284-024-00726-8,
https://doi.org/10.1093/jxb/erae112,

📄 View Raw YAML

id: Q93WI9
gene_symbol: HD3A
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:39947
  label: Oryza sativa subsp. japonica
description: >
  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.
existing_annotations:
# --- SPKW keyword-mapping annotations (GO_REF:0000043) ---
# These two were derived from UniProt keywords ("Differentiation", "Flowering" /
# "Developmental protein") and were present in the keyword2GO (SPKW) snapshot, but were
# REMOVED from the current GOA release when GOA retired the keyword2GO pipeline for cellular
# organisms (~Apr 2026). They are re-added here for retrospective review to assess whether
# removal was justified. Both are over-specific/mis-targeted for a mobile flowering-TIME
# signal whose role is to trigger the floral transition, not to drive cell differentiation
# or flower-organ morphogenesis.
- term:
    id: GO:0030154
    label: cell differentiation
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  retired: true
  review:
    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.
    action: REMOVE
    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.
    supported_by:
    - reference_id: file:ORYSJ/HD3A/HD3A-deep-research-falcon.md
      supporting_text: >-
        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.
    - reference_id: PMID:17446351
      supporting_text: >-
        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.
- term:
    id: GO:0009908
    label: flower development
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  retired: true
  review:
    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.
    action: MODIFY
    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_replacement_terms:
    - id: GO:0009911
      label: positive regulation of flower development
    - id: GO:0009909
      label: regulation of flower development
    supported_by:
    - reference_id: file:ORYSJ/HD3A/HD3A-deep-research-falcon.md
      supporting_text: >-
        FAC formation leads to induction of floral identity and transition programs, including
        activation of **MADS-box genes**.
    - reference_id: PMID:12407188
      supporting_text: >-
        Introduction of the gene caused an early-heading phenotype in rice.
# --- Current GOA annotations (2026 release) ---
- term:
    id: GO:0010228
    label: vegetative to reproductive phase transition of meristem
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    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.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: file:ORYSJ/HD3A/HD3A-deep-research-falcon.md
      supporting_text: >-
        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.
    - reference_id: PMID:17446351
      supporting_text: >-
        the protein encoded by Hd3a, a rice ortholog of FT, moves from the leaf to the shoot
        apical meristem and induces flowering in rice.
- term:
    id: GO:0048510
    label: regulation of timing of transition from vegetative to reproductive phase
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    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.)
    action: ACCEPT
    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.
    supported_by:
    - reference_id: file:ORYSJ/HD3A/HD3A-deep-research-falcon.md
      supporting_text: >-
        **Hd3a RNAi** delays flowering by **>30 days**, and **double RNAi suppressing both Hd3a
        and RFT1** prevented flowering up to **300 days**
    - reference_id: PMID:12407188
      supporting_text: >-
        The transcript levels of Hd3a were increased under SD conditions.
- term:
    id: GO:0009909
    label: regulation of flower development
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    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.)
    action: ACCEPT
    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_replacement_terms:
    - id: GO:0009911
      label: positive regulation of flower development
    supported_by:
    - reference_id: file:ORYSJ/HD3A/HD3A-deep-research-falcon.md
      supporting_text: >-
        FAC formation leads to induction of floral identity and transition programs, including
        activation of **MADS-box genes**.
    - reference_id: PMID:12407188
      supporting_text: >-
        Introduction of the gene caused an early-heading phenotype in rice.
- term:
    id: GO:0010229
    label: inflorescence development
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    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.)
    action: KEEP_AS_NON_CORE
    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).
    supported_by:
    - reference_id: file:ORYSJ/HD3A/HD3A-deep-research-falcon.md
      supporting_text: >-
        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.
    - reference_id: PMID:17446351
      supporting_text: >-
        the protein encoded by Hd3a, a rice ortholog of FT, moves from the leaf to the shoot
        apical meristem and induces flowering in rice.
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  review:
    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.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: file:ORYSJ/HD3A/HD3A-deep-research-falcon.md
      supporting_text: >-
        remains cytoplasmic until **OsFD1 is co-expressed**, at which point the complex
        **localizes to the nucleus** to activate downstream transcriptional programs.
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  review:
    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.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: file:ORYSJ/HD3A/HD3A-deep-research-falcon.md
      supporting_text: >-
        Hd3a **first forms an Hd3a–14-3-3 subcomplex in the cytoplasm** of SAM cells.
- term:
    id: GO:0009909
    label: regulation of flower development
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: involved_in
  review:
    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.
    action: ACCEPT
    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_replacement_terms:
    - id: GO:0009911
      label: positive regulation of flower development
    supported_by:
    - reference_id: file:ORYSJ/HD3A/HD3A-deep-research-falcon.md
      supporting_text: >-
        FAC formation leads to induction of floral identity and transition programs, including
        activation of **MADS-box genes**.
- term:
    id: GO:0010229
    label: inflorescence development
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: involved_in
  review:
    summary: >
      IEA (ARBA) annotation duplicating the IBA/IMP "inflorescence development" term. Kept as
      non-core on the same basis as the IBA annotation above.
    action: KEEP_AS_NON_CORE
    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.
    supported_by:
    - reference_id: file:ORYSJ/HD3A/HD3A-deep-research-falcon.md
      supporting_text: >-
        linking Hd3a arrival at the SAM to floral transition and meristem identity reprogramming.
- term:
    id: GO:0048510
    label: regulation of timing of transition from vegetative to reproductive phase
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: involved_in
  review:
    summary: >
      IEA (ARBA) annotation duplicating the IBA/IMP "regulation of timing of transition from
      vegetative to reproductive phase" term. Accepted as a core function.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:12407188
      supporting_text: >-
        The transcript levels of Hd3a were increased under SD conditions.
- term:
    id: GO:0048573
    label: photoperiodism, flowering
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: involved_in
  review:
    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.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: file:ORYSJ/HD3A/HD3A-deep-research-falcon.md
      supporting_text: >-
        Hd3a expression integrates photoperiod information via upstream factors including
        **Hd1** and **Ehd1** (positive regulation in inductive contexts)
    - reference_id: PMID:12407188
      supporting_text: >-
        the amount of Hd3a mRNA is up-regulated by Hd1 under SD conditions, suggesting that Hd3a
        promotes heading under the control of Hd1.
- term:
    id: GO:0009909
    label: regulation of flower development
  evidence_type: IMP
  original_reference_id: PMID:17446351
  qualifier: involved_in
  review:
    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.
    action: ACCEPT
    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_replacement_terms:
    - id: GO:0009911
      label: positive regulation of flower development
    supported_by:
    - reference_id: PMID:17446351
      supporting_text: >-
        the protein encoded by Hd3a, a rice ortholog of FT, moves from the leaf to the shoot
        apical meristem and induces flowering in rice.
- term:
    id: GO:0010229
    label: inflorescence development
  evidence_type: IMP
  original_reference_id: PMID:17446351
  qualifier: involved_in
  review:
    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.
    action: KEEP_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).
    supported_by:
    - reference_id: PMID:17446351
      supporting_text: >-
        the protein encoded by Hd3a, a rice ortholog of FT, moves from the leaf to the shoot
        apical meristem and induces flowering in rice.
- term:
    id: GO:0048510
    label: regulation of timing of transition from vegetative to reproductive phase
  evidence_type: IMP
  original_reference_id: PMID:17446351
  qualifier: involved_in
  review:
    summary: >
      IMP annotation (Tamaki et al. 2007): the mobile Hd3a protein controls when flowering occurs.
      Core flowering-time regulatory function.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:17446351
      supporting_text: >-
        Florigen, the mobile signal that moves from an induced leaf to the shoot apex and causes
        flowering
- term:
    id: GO:0048575
    label: short-day photoperiodism, flowering
  evidence_type: IMP
  original_reference_id: PMID:17446351
  qualifier: involved_in
  review:
    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.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:12407188
      supporting_text: >-
        The transcript levels of Hd3a were increased under SD conditions.
    - reference_id: file:ORYSJ/HD3A/HD3A-deep-research-falcon.md
      supporting_text: >-
        it encodes a small FT-like phosphatidylethanolamine-binding protein (PEBP) family member
        that promotes flowering, especially under short days.
- term:
    id: GO:0008429
    label: phosphatidylethanolamine binding
  evidence_type: ISS
  original_reference_id: PMID:10583960
  qualifier: enables
  review:
    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.)
    action: MARK_AS_OVER_ANNOTATED
    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.
    supported_by:
    - reference_id: file:ORYSJ/HD3A/HD3A-deep-research-falcon.md
      supporting_text: >-
        The 2024 review further emphasizes that **Hd3a–14-3-3 interaction is essential** (mutants
        that cannot interact with 14-3-3 lose Hd3a function).
    - reference_id: PMID:10583960
      supporting_text: >-
        FT acts in part downstream of CO and mediates signals for flowering in an antagonistic
        manner with its homologous gene, TERMINAL FLOWER1 (TFL1).
- term:
    id: GO:0008429
    label: phosphatidylethanolamine binding
  evidence_type: ISS
  original_reference_id: PMID:12407188
  qualifier: enables
  review:
    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.
    action: MARK_AS_OVER_ANNOTATED
    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.
    supported_by:
    - reference_id: PMID:12407188
      supporting_text: >-
        we found a candidate gene that shows high similarity to the FLOWERING LOCUS T (FT) gene,
        which promotes flowering in Arabidopsis
    - reference_id: file:ORYSJ/HD3A/HD3A-deep-research-falcon.md
      supporting_text: >-
        in rice, Hd3a forms a complex with **14-3-3 proteins (GF14 family)** and the SAM-expressed
        bZIP transcription factor **OsFD1**.
- term:
    id: GO:0010229
    label: inflorescence development
  evidence_type: IMP
  original_reference_id: PMID:12407188
  qualifier: involved_in
  review:
    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.)
    action: KEEP_AS_NON_CORE
    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).
    supported_by:
    - reference_id: PMID:12407188
      supporting_text: >-
        Introduction of the gene caused an early-heading phenotype in rice.
- term:
    id: GO:0010229
    label: inflorescence development
  evidence_type: IMP
  original_reference_id: PMID:12582636
  qualifier: involved_in
  review:
    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.
    action: KEEP_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.
    supported_by:
    - reference_id: PMID:12582636
      supporting_text: >-
        the Kasalath allele at Hd3a promotes heading under short-day conditions
- term:
    id: GO:0048510
    label: regulation of timing of transition from vegetative to reproductive phase
  evidence_type: IMP
  original_reference_id: PMID:12407188
  qualifier: involved_in
  review:
    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.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:12407188
      supporting_text: >-
        the amount of Hd3a mRNA is up-regulated by Hd1 under SD conditions, suggesting that Hd3a
        promotes heading under the control of Hd1.
- term:
    id: GO:0048510
    label: regulation of timing of transition from vegetative to reproductive phase
  evidence_type: IMP
  original_reference_id: PMID:12582636
  qualifier: involved_in
  review:
    summary: >
      IMP annotation (Monna et al. 2002): the Hd3a allele controls heading date (flowering time).
      Core flowering-time regulatory function.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:12582636
      supporting_text: >-
        two tightly linked loci, Hd3a and Hd3b, were identified in the Hd3 region.
- term:
    id: GO:0048572
    label: short-day photoperiodism
  evidence_type: IMP
  original_reference_id: PMID:12407188
  qualifier: involved_in
  review:
    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.
    action: MODIFY
    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_replacement_terms:
    - id: GO:0048575
      label: short-day photoperiodism, flowering
    supported_by:
    - reference_id: PMID:12407188
      supporting_text: >-
        Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering
        downstream of Hd1 under short-day conditions.
references:
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings:
  - statement: FT/florigen (PEBP family) functions - vegetative-to-reproductive phase transition
      of meristem, regulation of timing of that transition, regulation of flower development and
      inflorescence development - are conserved across the FT-like phylogenetic group and were
      propagated to Hd3a by IBA.
- id: GO_REF:0000043
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
  findings:
  - statement: SwissProt keyword-derived (SPKW) annotations present in an earlier keyword2GO
      snapshot but removed from the current GOA release after GOA retired the keyword2GO pipeline
      for cellular organisms.
  - statement: For HD3A the keywords "Differentiation" and "Flowering"/"Developmental protein"
      mapped to GO:0030154 (cell differentiation) and GO:0009908 (flower development); both are
      over-general / mis-targeted for a mobile flowering-time signal and their removal was
      reasonable (cell differentiation) or warrants replacement with a regulatory term (flower
      development).
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary
    mapping, accompanied by conservative changes to GO terms applied by UniProt
  findings:
  - statement: UniProt subcellular-location mapping assigns Nucleus (SL-0191) and Cytoplasm
      (SL-0086) to Hd3a, consistent with the cytoplasmic Hd3a-14-3-3 subcomplex and its nuclear
      FAC.
- id: GO_REF:0000117
  title: Electronic Gene Ontology annotations created by ARBA machine learning models
  findings:
  - statement: ARBA models assigned regulation of flower development, inflorescence development,
      regulation of timing of the vegetative-to-reproductive transition, and photoperiodism
      (flowering) to Hd3a; these duplicate or parallel the curated IBA/IMP annotations.
- id: PMID:10583960
  title: A pair of related genes with antagonistic roles in mediating flowering signals.
  findings:
  - statement: Characterizes Arabidopsis FT (the Hd3a ortholog) genetically - FT promotes
      flowering downstream of CONSTANS and acts antagonistically with TERMINAL FLOWER1 (TFL1);
      loss of FT delays flowering and FT overexpression causes precocious flowering.
  - statement: Does not measure phosphatidylethanolamine binding; the ISS GO:0008429 annotation
      citing this paper is a PEBP-family-namesake inference, not an experimental MF.
- id: PMID:12407188
  title: Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering
    downstream of Hd1 under short-day conditions.
  findings:
  - statement: Identified Hd3a as an FT-like gene at a heading-date QTL; introduction of Hd3a
      caused an early-heading phenotype, Hd3a transcript increased under short days, and Hd3a mRNA
      is up-regulated by Hd1 under SD - Hd3a promotes heading under the control of Hd1.
  - statement: Establishes the conserved function/regulatory relationship of Hd3a/FT with Hd1/CO
      between rice (SD plant) and Arabidopsis (LD plant).
- id: PMID:12582636
  title: Genetic dissection of a genomic region for a quantitative trait locus, Hd3, into two
    loci, Hd3a and Hd3b, controlling heading date in rice.
  findings:
  - statement: Genetically dissected the Hd3 region into two linked heading-date loci, Hd3a and
      Hd3b; the Kasalath allele at Hd3a promotes heading (flowering) under short-day conditions.
  - statement: A flowering-time (heading-date) QTL study; provides no inflorescence-morphogenesis
      characterization.
- id: PMID:17446351
  title: Hd3a protein is a mobile flowering signal in rice.
  findings:
  - statement: Demonstrated that the Hd3a protein moves from the leaf to the shoot apical meristem
      and induces flowering - the key experimental evidence that Hd3a is the rice florigen (a
      mobile flowering signal).
  - statement: Hd3a is expressed (protein level) in leaf-blade vascular tissue, stem and the inner
      region of the SAM, with circadian expression peaking at dawn under SD - consistent with a
      leaf-to-SAM long-distance signaling role.
- id: file:ORYSJ/HD3A/HD3A-deep-research-falcon.md
  title: Deep-research report (falcon / Edison Scientific Literature) - functional annotation of
    rice HD3A (Q93WI9).
  findings:
  - statement: Synthesizes the rice florigen literature, concluding Hd3a is the rice ortholog of
      Arabidopsis FT and a phloem-mobile florigen - synthesized in leaf vascular tissue,
      transported through the phloem, unloaded near the SAM, and entering the SAM to trigger the
      vegetative-to-reproductive transition.
  - statement: Describes Hd3a's molecular mode of action as protein-protein interaction - it is
      not an enzyme or transporter - forming a cytoplasmic Hd3a-14-3-3 (GF14) subcomplex that
      becomes nuclear upon OsFD1 co-expression to assemble the florigen activation complex (FAC),
      which activates floral MADS-box genes OsMADS14/OsMADS15. The Hd3a-14-3-3 interaction is
      essential.
  - statement: Documents large flowering-time phenotypes (Hd3a RNAi delays flowering >30 days;
      Hd3a+RFT1 double suppression prevents flowering up to 300 days) and a steep photoperiod
      response (Hd3a falls to <1/10 above ~13.5 h day length; a 10-min night break blocks
      induction); Hd3a acts downstream of Hd1 and Ehd1.
core_functions:
- description: >
    Hd3a is the rice florigen: a phloem-mobile FT-family signaling protein produced in
    leaf-blade vascular tissue that moves long-distance to the shoot apical meristem and acts as
    a positive regulator of the floral transition, controlling the TIMING of the
    vegetative-to-reproductive switch (heading date / flowering time) under inductive short-day
    photoperiod.
  supported_by:
  - reference_id: PMID:17446351
    supporting_text: >-
      the protein encoded by Hd3a, a rice ortholog of FT, moves from the leaf to the shoot apical
      meristem and induces flowering in rice.
  - reference_id: file:ORYSJ/HD3A/HD3A-deep-research-falcon.md
    supporting_text: >-
      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.
- description: >
    In shoot-apical-meristem cells Hd3a executes its function by protein-protein interaction:
    it forms a cytoplasmic complex with 14-3-3 (GF14) proteins that, upon co-expression of the
    bZIP transcription factor OsFD1, becomes nuclear and assembles the florigen activation
    complex (FAC), which transcriptionally activates floral-identity MADS-box genes (OsMADS14,
    OsMADS15). The Hd3a-14-3-3 interaction is essential for activity. (Note: no GO molecular-function
    term for "florigen activity" exists; the relevant MF is 14-3-3/FAC-forming protein binding,
    and the family-namesake "phosphatidylethanolamine binding" is not a demonstrated function.)
  supported_by:
  - reference_id: file:ORYSJ/HD3A/HD3A-deep-research-falcon.md
    supporting_text: >-
      in rice, Hd3a forms a complex with **14-3-3 proteins (GF14 family)** and the SAM-expressed
      bZIP transcription factor **OsFD1**. This complex provides the mechanistic bridge between
      Hd3a arrival and transcriptional activation of flowering genes.
  - reference_id: file:ORYSJ/HD3A/HD3A-deep-research-falcon.md
    supporting_text: >-
      The 2024 review further emphasizes that **Hd3a–14-3-3 interaction is essential** (mutants
      that cannot interact with 14-3-3 lose Hd3a function).
proposed_new_terms:
- proposed_name: florigen activity
  proposed_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.
  supported_by:
  - reference_id: file:ORYSJ/HD3A/HD3A-deep-research-falcon.md
    supporting_text: >-
      its key biochemical mode of action is **protein–protein interaction** culminating in
      FAC-dependent transcriptional activation of floral transition genes at the SAM.
suggested_questions:
- question: 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?
  experts:
  - Hiroyuki Tsuji
- question: 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?
  experts:
  - Ko Shimamoto
- question: 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?
  experts:
  - Hiroyuki Tsuji
suggested_experiments:
- description: 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.
  experiment_type: in planta live imaging of a mobile signaling protein
- description: 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.
  experiment_type: complex reconstitution and transcriptional-activation assay
- description: 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.
  experiment_type: in vitro lipid-binding (liposome / protein-lipid overlay) assay

Gene Description

Proposed New Ontology Terms

florigen activity

Existing Annotations Review

Core Functions

References

Suggested Questions for Experts

Suggested Experiments

Deep Research

Falcon

Research report: Functional annotation of rice HD3A (UniProt Q93WI9; Os06g0157700; LOC_Os06g06320)

0) Target verification (mandatory)

1) Key concepts, definitions, and current understanding

1.1 Florigen and FT-like/PEBP proteins

1.2 Hd3a’s primary molecular function

1.3 The florigen activation complex (FAC)

2) Expression, mobility, and localization of the Hd3a protein

2.1 Where Hd3a is expressed (tissue specificity)

2.2 Long-distance mobility: leaf phloem → SAM

2.3 Subcellular localization and nuclear entry via FAC assembly (2024 synthesis)

3) Molecular mechanism in pathways: regulators, partners, and targets

3.1 Core upstream regulators in photoperiodic flowering

3.2 Interaction partners: 14-3-3 proteins and OsFD1

3.3 Downstream transcriptional targets

3.4 Antagonism and competitive binding within the PEBP/FT-like family

4) Phenotypic evidence (statistics and data)

4.1 Large-effect genetic perturbations

4.2 Photoperiod-sensitive quantitative regulation

5) Recent developments and latest research (prioritizing 2023–2024)

5.1 2024: refined subcellular model and key open questions

5.2 2023: pathway-centric synthesis and applied framing

6) Current applications and real-world implementations (2024 examples)

6.1 Promoter editing of a florigen gene to fine-tune heading date (RFT1 promoter; 2024-02)

6.2 Editing an upstream activator to delay heading while improving grain quality (OsMADS50; 2024-08)

6.3 Genome editing of a regulatory kinase to advance heading and improve yield traits (OsCKq1; 2024-08)

7) Expert opinions / authoritative analysis (synthesis)

8) Evidence map (summary table)

9) Key figures supporting localization/mechanism (visual evidence)

10) Selected references (with URLs and publication dates)

11) Limitations of this evidence package

Artifacts

Citations

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