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ABC model of flower development

The ABC model of flower development is a genetic framework that explains the specification of floral organ identities in angiosperms through the combinatorial and overlapping expression of three classes of homeotic genes, designated A, B, and C functions, across the four concentric whorls of a flower.^[1] In this model, the outermost whorl (whorl 1) develops sepals due to A function alone, the second whorl (whorl 2) forms petals through the combined action of A and B functions, the third whorl (whorl 3) produces stamens via B and C functions, and the innermost whorl (whorl 4) yields carpels from C function alone.^[1] The model also incorporates mutual antagonism between A and C functions, where A represses C in the outer whorls and C represses A in the inner whorls, ensuring spatially restricted expression patterns.^[1] Proposed in 1991 by Enrico Coen and Elliot Meyerowitz, the ABC model emerged from genetic analyses of homeotic mutants in the model plants Arabidopsis thaliana and Antirrhinum majus, where alterations in floral organ identities revealed the underlying regulatory logic.^[1] These studies built on earlier observations of floral mutants dating back to the 19th century but integrated modern molecular cloning to identify the responsible genes, demonstrating conserved mechanisms across species.^[2] The model's predictive power was validated through double and triple mutant combinations; for instance, loss of B function transforms petals into sepals and stamens into carpels, while A mutants result in carpels replacing sepals and stamens replacing petals.^[1] Similarly, C mutants convert stamens to petals and carpels to sepals, often leading to indeterminate floral meristems with reiterated inner whorls.^[1] At the molecular level, A function is primarily mediated by the MADS-box transcription factor APETALA1 (AP1) and the AP2/ERF transcription factor APETALA2 (AP2), with AP1 also contributing to floral meristem identity.^[3] B function involves the MADS-box genes APETALA3 (AP3) and PISTILLATA (PI), which heterodimerize to activate downstream targets specifying petal and stamen development.^[3] C function is executed by AGAMOUS (AG), another MADS-box gene that not only defines inner whorl identities but also terminates the floral meristem to prevent indeterminacy.^[3] These genes belong to the floral quartet model, where protein complexes form higher-order structures to regulate organ-specific gene expression.^[4] While the classic ABC model provides a parsimonious explanation for core eudicot floral patterning, subsequent research has extended it to the ABCDE model, incorporating an E function mediated by SEPALLATA (SEP) MADS-box genes that are required in all whorls for proper organ identity specification.^[5] This refinement accounts for more complex mutant phenotypes and highlights the model's adaptability to evolutionary variations in floral morphology across angiosperms.^[5] The ABC framework remains influential in developmental biology, informing studies on gene regulatory networks, evo-devo, and applications in crop improvement.^[2]

Prerequisites for Flower Formation

Floral Transition

Floral transition refers to the developmental switch in plants where the shoot apical meristem (SAM) shifts from producing vegetative structures, such as leaves, to initiating reproductive structures, marking the onset of flowering.^[6] This process is crucial for ensuring reproduction occurs under optimal conditions and involves reprogramming the SAM's cellular activity to form floral meristems.^[7] The transition is triggered by a combination of environmental cues and internal signaling pathways. Key environmental factors include photoperiod, which responds to day length changes (e.g., long-day plants flower under extended daylight); vernalization, a prolonged cold exposure that promotes flowering in temperate species; and hormones like gibberellins, which can induce flowering independently or synergistically with other signals.^[8] Internally, the FLOWERING LOCUS T (FT) protein serves as a central integrator, synthesized in response to these cues and acting as a key mobile signal. The florigen signal, embodied primarily by the FT protein, plays a pivotal role in coordinating the transition by integrating diverse cues perceived in the leaves and transmitting them to the SAM. Produced in leaf phloem companion cells, FT travels through the vascular system to the meristem, where it forms complexes that activate floral identity genes, thereby committing the SAM to reproductive fate. This long-distance signaling ensures synchronized flowering across the plant.^[9] The concept of florigen originated in the 1930s through grafting experiments by Soviet plant physiologist Mikhail Chailakhyan, who demonstrated that a transmissible flowering stimulus could move from induced leaves to non-induced shoots, establishing the hormonal nature of the signal decades before its molecular identification.^[10] Following floral transition, the process leads to floral meristem initiation, where the reprogrammed SAM begins specifying inflorescence architecture. Recent studies as of 2025 emphasize the role of hormonal networks in coordinating these transitions to enhance plant resilience and yield under varying environmental conditions.^[11]

Floral Meristem Initiation

Floral meristem initiation in Arabidopsis thaliana, the primary model organism for studying flower development, occurs following the floral transition, where environmental and endogenous signals convert the shoot apical meristem into an inflorescence meristem that generates lateral floral primordia.^[12] The key regulators of this process are the transcription factors LEAFY (LFY) and APETALA1 (AP1), which act redundantly to specify floral meristem identity and promote the determinate growth characteristic of flowers.^[12] LFY, a plant-specific DNA-binding protein, is expressed early in presumptive floral primordia and directly activates downstream targets to enforce floral fate, preventing the formation of leaf-like structures; in lfy mutants, lateral meristems develop into partial inflorescences rather than flowers.^[13] AP1, a MADS-box transcription factor, complements LFY by repressing inflorescence identity genes and initiating floral programs, with ap1 mutants exhibiting bract-like organs subtending coflorescence-like structures on the main axis.^[14] A critical aspect of floral meristem initiation is the distinction between indeterminate and determinate meristems, which determines whether a structure produces multiple organs indefinitely or a fixed set before terminating. In Arabidopsis, the inflorescence meristem remains indeterminate, continuously generating successive floral primordia along the flanks, whereas each floral meristem becomes determinate, producing exactly four whorls of floral organs (sepals, petals, stamens, and carpels) and then exhausting its stem cell population.^[15] LFY and AP1 drive this determinacy by establishing boundaries and limiting meristem proliferation, ensuring the floral meristem consumes itself after organ formation rather than perpetuating growth.^[13] Auxin gradients play an essential role in positioning and initiating floral meristems within the inflorescence meristem, with local auxin maxima marking sites of primordium outgrowth. These gradients are established by polar auxin transport mediated by PIN-FORMED (PIN) efflux carriers, particularly PIN1, which directs auxin flow to create dynamic patterns that specify floral positions on the meristem periphery.^[16] The homeodomain transcription factor WUSCHEL (WUS), expressed in the underlying organizing center, maintains stem cell identity in the floral meristem by responding to these auxin signals and promoting cell proliferation non-cell-autonomously; wus mutants fail to sustain the central stem cell niche, resulting in arrested meristem development shortly after initiation.^[17] Together, auxin-WUS signaling integrates positional cues with genetic controls from LFY and AP1 to organize the nascent floral meristem into a structured precursor for organ patterning.^[18]

Core Principles of the ABC Model

Organ Identity Specification

The ABC model of flower development provides a combinatorial framework for specifying the identity of floral organs arranged in four concentric whorls, where each whorl's identity arises from the unique activity of three classes of regulatory genes designated A, B, and C. This model was originally formulated in the early 1990s based on genetic analyses in Arabidopsis thaliana, proposing that organ identities are determined by the overlapping expression domains of these gene classes within the floral meristem. Specifically, class A genes are active in whorls 1 and 2, class B genes in whorls 2 and 3, and class C genes in whorls 3 and 4, leading to distinct combinations that direct the development of sepals in whorl 1, petals in whorl 2, stamens in whorl 3, and carpels in whorl 4. Central to the model's mechanism is the mutual antagonism between class A and class C genes, which restricts their expression to non-overlapping domains and ensures proper organ specification across whorls. Class A activity represses class C in whorls 1 and 2, while class C represses class A in whorls 3 and 4, creating sharp boundaries that prevent ectopic organ formation. This antagonistic interaction, combined with the additive effects of class B, results in the following organ identities: class A alone specifies sepals in whorl 1; A plus B specifies petals in whorl 2; B plus C specifies stamens in whorl 3; and C alone specifies carpels in whorl 4. The whorl model can be visualized as a radial arrangement where gene activities overlap to generate diversity from a limited set of regulatory inputs, as evidenced by mutant phenotypes that transform organs according to predicted loss-of-function patterns. This framework underscores how spatial gene regulation establishes floral architecture without requiring separate genes for each organ type.

Combinatorial Gene Functions

The combinatorial code of the ABC model posits that floral organ identity arises from the unique combinations of gene activities across the four whorls of the flower, where spatial and temporal expression patterns ensure that specific organs form in defined positions. In the outermost whorl, activity of A-class genes alone specifies sepals; in the second whorl, the combination of A- and B-class genes specifies petals; in the third whorl, B- and C-class genes together specify stamens; and in the innermost whorl, C-class genes alone specify carpels. These patterns are established through overlapping domains of gene expression, with A-class genes active in the outer two whorls, B-class in the inner two of the outer three, and C-class in the inner two whorls, while temporal dynamics refine boundaries during development to prevent indeterminate growth and ensure sequential organ formation.^[1] Homeotic selector genes underlying the ABC classes function as master regulatory transcription factors that bind to cis-regulatory elements in the promoters and enhancers of downstream target genes, thereby activating or repressing cascades that dictate cell fate and morphogenesis in each whorl. These genes, primarily MADS-box transcription factors, recognize specific DNA motifs to orchestrate combinatorial interactions, allowing a limited set of regulators to generate diverse organ identities by integrating positional information from the floral meristem.^[1] A key aspect of maintaining the spatial precision of this combinatorial code is the mutual antagonism between A- and C-class genes, which establishes sharp boundaries between whorls by preventing ectopic expression; for instance, the C-class gene AGAMOUS represses the A-class gene APETALA1.^[19] This reciprocal repression ensures stable, heritable silencing across cell divisions, reinforcing the distinct gene combinations required for organ specification. The basic schematic of these interactions involves A-class genes promoting their own expression and repressing C-class in outer regions, while C-class genes reciprocate in inner regions, with B-class genes bridging the middle whorls without direct antagonism, thus generating a feedback network that locks in the combinatorial identities.^[1]

Discovery Through Genetic Analysis

Mutant Phenotype Analysis

The discovery of the ABC model relied on forward genetic screens conducted in the 1980s and 1990s in Arabidopsis thaliana by Elliot Meyerowitz's laboratory at Caltech and in Antirrhinum majus by Enrico Coen's laboratory at the John Innes Centre, which identified floral homeotic mutants through chemical mutagenesis such as ethyl methanesulfonate (EMS) and phenotypic screening for altered organ identities.^[20] These screens isolated key loss-of-function mutants in A-, B-, and C-class genes, revealing homeotic transformations that supported the combinatorial specification of floral organs in four whorls: sepals (whorl 1), petals (whorl 2), stamens (whorl 3), and carpels (whorl 4).^[2] Single mutants provided initial evidence for class-specific functions. In ap2 mutants (A-class), whorl 1 develops carpelloid structures instead of sepals, and whorl 2 produces stamen-like organs rather than petals, indicating loss of A function allows C-class activity to expand into outer whorls.^[2] B-class mutants, such as ap3 or pi, transform whorl 2 petals into sepals and whorl 3 stamens into carpels, demonstrating B genes are required for petal and stamen identity.^[20] For C-class, ag mutants convert whorl 3 stamens to petals and replace whorl 4 carpels with another flower, resulting in indeterminate proliferation of inner whorls.^[2] Analysis of double and triple mutants confirmed the combinatorial logic and mutual antagonism between A and C functions. In ap3 pi double mutants (B-class loss), whorls 2 and 3 become carpels while whorl 1 remains sepals and whorl 4 carpels, showing additive effects without B activity.^[20] The ap2 ag double mutant produces leaf-like organs in all whorls, as loss of both A and C eliminates floral identity, with sepals representing the default state.^[2] The ap2 ap3 pi ag triple mutant further demonstrates this by generating leaf-like structures across all whorls, underscoring that A, B, and C functions together impose floral organ identities on presumptive leaf-like primordia.^[2] These phenotypes align with gene expression patterns observed in wild-type flowers, where A is active in whorls 1 and 2, B in 2 and 3, and C in 3 and 4.^[20] Gain-of-function experiments via ectopic expression reinforced the model's predictions of antagonism. Constitutive expression of AG (C-class) under the 35S promoter in transgenic Arabidopsis suppresses A function, transforming sepals and petals into carpels and stamens, respectively, and confirming reciprocal repression between A and C genes.^[21] Similarly, ectopic B-class expression can convert sepals to petals, supporting the combinatorial requirements.^[2]

Gene Expression Detection Techniques

In situ hybridization emerged as the foundational technique for visualizing the spatial distribution of ABC gene mRNAs within floral tissues, enabling researchers to map expression patterns across whorls during early studies of flower development. This method involves hybridizing labeled RNA or DNA probes complementary to target transcripts in fixed tissue sections, allowing detection of mRNA localization at cellular resolution through colorimetric or fluorescent signals. In the context of the ABC model, in situ hybridization was instrumental in confirming whorl-specific expression, such as the overlapping domains of class A, B, and C genes, by revealing transcripts in precise regions of the developing Arabidopsis flower.^[22]^[23] Reporter gene fusions, particularly with β-glucuronidase (GUS) and green fluorescent protein (GFP), have been widely employed to assess promoter activity and protein localization for ABC genes. GUS fusions, where the reporter is driven by native promoters, produce a blue precipitate upon enzymatic reaction, facilitating histochemical staining to delineate regulatory elements active in specific floral whorls. GFP fusions, often translational, allow live-cell imaging of protein dynamics, providing insights into subcellular localization and timing of ABC gene products during organ specification. These approaches complemented in situ data by linking transcriptional regulation to functional protein distribution in model systems like Arabidopsis.^[24] Reverse transcription polymerase chain reaction (RT-PCR), including quantitative variants (qRT-PCR), offers a sensitive means for measuring ABC gene transcript levels across dissected floral tissues or developmental stages, quantifying expression without spatial resolution. RNA sequencing (RNA-seq) extends this by providing genome-wide profiles, identifying differentially expressed ABC-related transcripts and validating whorl-specific patterns through high-throughput reads mapped to reference genomes. These techniques have been crucial for confirming expression dynamics in diverse species, often cross-validating results with qRT-PCR to ensure accuracy in abundance measurements.^[25]^[26] The evolution of gene expression detection in ABC model research reflects a progression from 1990s-era in situ hybridization, which established foundational whorl maps in Arabidopsis, to contemporary high-resolution methods like single-cell RNA-seq (scRNA-seq). Early reliance on in situ provided qualitative snapshots but was labor-intensive; by the 2000s, RT-PCR and bulk RNA-seq enabled quantitative, genome-scale analysis. Recent scRNA-seq applications, including single-nucleus variants, have resolved cellular heterogeneity in floral meristems, reconstructing 3D expression atlases that refine ABC whorl boundaries and uncover subtle regulatory variations. This shift has enhanced validation of combinatorial gene functions across cell types.^[27]^[28]^[29]

Functions of Specific Gene Classes

A-Class Genes

In Arabidopsis thaliana, the primary A-class genes are APETALA1 (AP1) and APETALA2 (AP2), which specify sepal identity in the first floral whorl and contribute to petal identity in the second whorl while restricting C-class gene activity to the inner whorls. AP1 encodes a MADS-box transcription factor that functions both in establishing floral meristem identity during early flower development and in A-class organ specification, promoting the formation of sepals and petals through activation of downstream targets. In ap1 loss-of-function mutants, sepals develop as leaf-like or bract-like organs, and secondary flowers often form in the axils of first-whorl organs, highlighting AP1's role in maintaining proper floral structure. AP2, an AP2/ERF-domain transcription factor, is expressed broadly in developing flowers but exerts its A-class function primarily in whorls 1 and 2, where it directly represses the C-class gene AGAMOUS (AG) to prevent ectopic reproductive organ formation. This repression involves AP2 recruiting a corepressor complex, including TOPLESS and histone deacetylases, to AG regulatory regions, thereby maintaining boundaries between floral whorls.^[30] Additionally, AP2 levels are post-transcriptionally regulated by microRNA172 (miR172), which cleaves AP2 mRNA to limit its accumulation in inner whorls and refine A-class activity. In strong ap2 loss-of-function mutants, AG expression expands to whorls 1 and 2, resulting in carpel-like organs replacing sepals and stamen-like or absent petals. The expression patterns of AP1 and AP2 are established early in floral primordia, with both genes active in whorls 1 and 2; AP1 transcripts are detected shortly after floral induction, while AP2 mRNA persists throughout organogenesis in outer whorls. Together with B-class genes, A-class genes combinatorially specify petal identity in whorl 2. The core functions of A-class genes, including outer whorl specification and C-class antagonism, are evolutionarily conserved across eudicots, as evidenced by functional orthologs such as SQUAMOSA (AP1-like) in Antirrhinum majus that rescue Arabidopsis ap1 mutants and similarly pattern sepals and petals.^[2]

B-Class Genes

B-class genes in the ABC model of flower development are MADS-box transcription factors that specify petal identity in the second whorl and stamen identity in the third whorl, in combination with A-class genes for petals and C-class genes for stamens. In Arabidopsis thaliana, the primary B-class genes are APETALA3 (AP3) and PISTILLATA (PI), which were identified through genetic screens for floral mutants exhibiting homeotic transformations. The AP3 gene was cloned in 1992, revealing it encodes a MADS-domain protein essential for these organ identities. Similarly, PI was cloned in 1994, confirming its role as a paralogous MADS-box gene required alongside AP3.^[31] These genes function through the formation of obligate heterodimers between the AP3 and PI proteins, which is necessary for specific DNA binding to CArG-box sequences in target gene promoters. This heterodimerization is mediated primarily by the K-domain of the MADS proteins and represents a unique protein-protein interaction characteristic of B-class factors, enabling combinatorial control of downstream targets that promote petal and stamen development. AP3 and PI are expressed specifically in whorls 2 and 3 of the floral meristem, restricting their activity to these regions and ensuring proper organ specification without ectopic effects in whorls 1 or 4.^[32]^[33]^[34] Mutations in AP3 or PI result in similar loss-of-function phenotypes, where the second-whorl organs develop as sepals instead of petals and the third-whorl organs as carpels instead of stamens, demonstrating their redundant yet essential roles. Ectopic expression experiments have shown that AP3 and PI are sufficient to confer B-class function, converting sepals and carpels into petals and stamens when misexpressed, underscoring their deterministic role in organ identity. B-class genes also contribute to mutual antagonism with C-class genes, preventing C activity from expanding into whorl 2.^[35]^[34]

C-Class Genes

C-class genes in the ABC model of flower development are primarily responsible for specifying stamen identity in the third whorl and carpel identity in the fourth whorl, while also repressing A-class gene activity in the inner whorls to establish proper floral boundaries. In Arabidopsis thaliana, the canonical C-class gene is AGAMOUS (AG), which encodes a MADS-box transcription factor belonging to the MIKC-type subfamily.^[36] This gene was cloned and characterized through genetic mapping and sequencing, revealing its structural similarity to known transcription factors involved in developmental regulation.^[36] AG expression initiates in the presumptive third and fourth whorls during early floral stages and persists through organ differentiation, ensuring the correct identity of reproductive organs. In the third whorl, AG cooperates with B-class genes such as APETALA3 and PISTILLATA to promote stamen formation, while in the fourth whorl, it acts alone to specify carpels. A key function of AG is the termination of floral meristem activity; it directly represses the stem cell regulator WUSCHEL (WUS) through recruitment of Polycomb group proteins, thereby limiting proliferation and promoting determinacy.^[37] A chromatin loop further contributes to this repression by excluding the WUS promoter from activating enhancers.^[38] Mutations in AG result in striking phenotypes, including the transformation of stamens into petals in the third whorl and replacement of the single carpel in the fourth whorl with another flower that reiterates the outer whorls (sepals and petals), leading to indeterminate, "double-flower" structures with repeated whorls 1 and 2.^[36] This loss of determinacy underscores AG's role in meristem termination. Furthermore, AG represses A-class genes like APETALA1 (AP1) in whorls 3 and 4, as evidenced by ectopic AP1 expression in ag mutants, which helps maintain spatial restrictions of perianth identity. Although the precise mechanism for AP1 repression remains under investigation, AG employs chromatin modifications, such as those mediated by Polycomb group proteins and SWI/SNF complexes, to silence target loci including WUS, suggesting similar regulatory strategies may apply to A-class genes.^[39]

D- and E-Class Genes

The D-class genes extend the ABC model by specifying ovule identity within the carpels of the fourth whorl, addressing a limitation of the original framework that did not fully account for reproductive structure development inside the gynoecium. In Arabidopsis thaliana, the primary D-class genes are SHATTERPROOF1 (SHP1) and SHATTERPROOF2 (SHP2), which were identified in the late 1990s through genetic screens for mutants affecting fruit dehiscence, and SEEDSTICK (STK), discovered in the early 2000s. SHP1 and SHP2, closely related MADS-box transcription factors, redundantly promote ovule development alongside STK, a paralog in the AGAMOUS (AG) clade. Triple mutants lacking SHP1, SHP2, and STK exhibit carpels filled with leaf-like or carpel-like structures instead of ovules, demonstrating their essential, redundant role in conferring ovule identity. Ectopic expression of STK or SHP genes can induce ovule formation on ectopic carpels, further confirming their determinative function.^[40] The E-class genes, represented by the four SEPALLATA (SEP) MADS-box factors SEP1 through SEP4, were identified in the late 1990s and early 2000s to explain the biochemical basis of floral organ specification across all whorls, revealing that ABC-class proteins alone are insufficient without E-class partners.^[41] SEP genes act redundantly to enable the formation of higher-order protein complexes, specifically tetrameric quartets, where two SEP proteins dimerize with pairs of A-, B-, or C-class proteins to activate organ-specific transcriptional programs. This "floral quartet model," building on the combinatorial logic of the ABC model, posits that sepal identity arises from APETALA1 (AP1; A-class) and SEP quartets, petal identity from APETALA3/PISTILLATA (AP3/PI; B-class) with SEP, stamen identity from AP3/PI and AG (C-class) with SEP, and carpel/ovule identity from AG and SEP quartets, often incorporating D-class inputs for ovules. SEP1, SEP2, and SEP3 were first characterized as essential for B- and C-class functions, with triple mutants (sep1 sep2 sep3) converting petals, stamens, and carpels into sepal-like or leaf-like organs, while sepals remain largely unaffected.^[41] SEP4, identified subsequently, provides additional redundancy across all floral organs and contributes to floral meristem determinacy.^[42] In quadruple sep1 sep2 sep3 sep4 mutants, all floral organs transform into leaf-like structures, underscoring the collective E-class requirement for suppressing vegetative identity and promoting floral fate throughout the flower.^[42] The discovery of D- and E-class genes in the 2000s thus refined the ABC model into the ABCDE framework, integrating ovule specification and protein quaternary structures as critical for comprehensive floral organogenesis.^[4]

Extensions and Recent Developments

ABCDE Model Integration

The original ABC model of floral organ identity was extended into the ABCDE framework in the early 2000s to account for the specification of ovules by D-class genes and the broad requirement of E-class genes for all floral organs via MADS-domain protein complexes.^[43] D-class genes, such as SEEDSTICK (STK), were identified as promoting ovule development within the fourth whorl, while E-class genes, including the redundant SEPALLATA (SEP) family, facilitate the formation of higher-order protein interactions necessary for organ differentiation across whorls one through four.^[41] In the updated ABCDE model, combinatorial rules specify organ identities through tetrameric complexes: sepals arise from A + E activity, petals from A + B + E, stamens from B + C + E, carpels from C + E, and placental ovules from C + D + E, with E-class proteins enabling the quartet formations essential for all whorls.^[44] This integration highlights the universal role of E function, as its absence disrupts floral patterning entirely, and the specialized D function for ovule primordia within carpels.00815-2) Evidence supporting the necessity of the full ABCDE model comes from mutant analyses, such as the sep1 sep2 sep3 triple mutants, where B- and C-class functions fail without E activity, resulting in flowers composed primarily of sepal-like organs, and combinations involving shatterproof (shp) mutants that, when layered with other disruptions, enhance leaf-like transformations and underscore the interdependent roles in ovule and carpel specification.^[41] Similarly, the stk shp1 shp2 triple mutant lacks ovules entirely, with carpel walls producing leaf- or stamen-like structures instead, confirming D-class redundancy and requirement for ovule identity. These phenotypes demonstrate that isolated A, B, or C functions are insufficient without D and E integration. Refinements in the 2000s, led by Theissen and colleagues, further unified the model through the floral quartet hypothesis, proposing that E-class SEP proteins dimerize with A/B/C/D partners to form DNA-binding tetramers that activate organ-specific genes, as validated by protein interaction studies and ectopic expression experiments.^[44] Subsequent work, including the identification of SEP4's redundant role in the sep1 sep2 sep3 sep4 quadruple mutant—where all organs convert to leaves—solidified E's pan-floral necessity and refined the quartet mechanism for precise regulatory control.00815-2)

Evolutionary and Regulatory Advances

The ABCDE model of flower development, originally elucidated in eudicots like Arabidopsis thaliana, exhibits significant conservation across angiosperms but also notable variations in non-eudicot lineages. In monocots such as tulips and lilies, B-class gene expression extends to the outer perianth whorls, promoting petaloid characteristics in both tepal whorls and effectively modifying the standard ABC framework to an "fading borders" model.^[45] In basal angiosperms like Aquilegia (a basal eudicot), B-class genes maintain conserved roles in specifying petals and stamens, supporting the model's applicability beyond core eudicots.^[46] However, some basal angiosperms, such as Amborella, show deviations including potential loss or reduced function of B-class activity, leading to simpler perianth structures without distinct petals.^[47] In gymnosperms, orthologs of MADS-box genes exist but lack the combinatorial ABCDE logic, instead contributing to ovule and pollen organ development without true floral whorls.^[48] Evolutionary milestones in the ABCDE model trace back to gene duplications in the MADS-box family following the radiation of angiosperms around 140 million years ago. Whole-genome duplications (WGDs) post-angiosperm origin generated paralogs of MIKC-type MADS genes, enabling subfunctionalization into A-, B-, C-, D-, and E-classes that underpin floral organ diversity.^[49] For instance, the AGAMOUS (C-class) subfamily duplicated early, with members controlling reproductive organs in both gymnosperms and angiosperms, facilitating the transition to enclosed seeds and complex flowers.^[50] These duplications, often linked to nested radiations and polyploidy events, correlate with increased diversification rates in angiosperm lineages.^[51] Recent regulatory advances have revealed intricate hormonal and transcriptional controls modulating ABCDE gene activity. Studies from 2023–2025 highlight the role of cytokinins in regulating the floral transition and gynoecium development, where root-derived cytokinins promote flowering time through the two-component signaling pathway and age pathway components, influencing the activation of floral identity genes.^[52] Additionally, confocal imaging has shown cytokinin signaling gradients correlating with cell proliferation in early floral stages, fine-tuning whorl-specific patterning in Arabidopsis.^[53] Transcriptionally, a 2023 study identified ZINC FINGER PROTEIN 1 (ZP1) and ZFP8 as repressors of B- and C-class genes (AP3, PI, AG) in vegetative tissues; their downregulation by LEAFY (LFY) and APETALA1 (AP1) in floral meristems derepresses these homeotic genes, ensuring precise activation during flower initiation.^[54] These insights have practical applications in crop improvement, particularly for ornamentals with petaloid modifications. Manipulating ABCDE regulators, such as ectopic expression of B-class genes, has enabled the development of novel flower forms in species like petunias and chrysanthemums, enhancing petal color and symmetry for commercial breeding.^[55] Translational efforts leverage the model's conserved elements to engineer tepal-like structures in monocot ornamentals, boosting aesthetic value and market traits without disrupting fertility.^[56]

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Validation of RNA-seq data by quantitative real-time PCR (qRT-PCR). We selected six genes in the pepper ABCDE model for qRT-PCR analysis. Specific primers ...
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Reflections on the ABC model of flower development - PMC
Simply stated, the ABC model postulates 3 distinct gene activities (A, B, and C), each of which are present in 2 adjacent whorls of the Arabidopsis flower, act ...
[21]
Architecture of gene regulatory networks controlling flower ... - Nature
Oct 31, 2018 · In this model, sepals are specified by a complex consisting of AP1 and SEP proteins, while AP1, AP3, PISTILLATA (PI), and SEP form a higher- ...Results · Mirna-Mediated Grns And... · Organ-Specific Grns<|control11|><|separator|>
[22]
APETALA2 negatively regulates multiple floral organ identity genes ...
Specifically, we show that AP2 directly represses AG by recruiting a transcriptional co-repressor and a histone deacetylase. This AP2 repressor complex also ...
[23]
The homeotic gene APETALA3 of Arabidopsis thaliana encodes a ...
Mutations in the APETALA3 (AP3) gene of A. thaliana result in homeotic transformations of petals to sepals and stamens to carpels. We have cloned the AP3 ...
[24]
Molecular basis for the specification of floral organs by APETALA3 ...
AP3 and PI are closely related MADS domain proteins that are thought to act as obligate heterodimers (12–14). Only few direct target genes of AP3/PI have been ...
[25]
Molecular basis for the specification of floral organs by APETALA3 ...
We studied the function of the homeotic selector genes APETALA3 (AP3) and PISTILLATA (PI), which control the formation of petals and stamens during Arabidopsis ...Results · Functions Of Ap3/pi In... · Spatial And Temporal...Missing: class seminal
[26]
The Arabidopsis homeotic genes APETALA3 and PISTILLATA are ...
Jan 1, 1996 · The class B organ identity genes, APETALA3 and PISTILLATA, are required to specify petal and stamen identity in the Arabidopsis flower.Missing: seminal | Show results with:seminal
[27]
Functional divergence within the APETALA3/PISTILLATA floral ...
Mutations in the two genes exhibit similar phenotypes in which the second-whorl petals are transformed into sepals and the third-whorl stamens are transformed ...
[28]
The protein encoded by the Arabidopsis homeotic gene agamous ...
Jul 5, 1990 · Cloning and sequence analysis of agamous suggest that it encodes a protein with a high degree of sequence similarity to the DNA-binding region ...Missing: original | Show results with:original
[29]
AGAMOUS Controls GIANT KILLER, a Multifunctional Chromatin ...
The ABC model predicts that the combinatorial action of ABC floral homeotic genes controls floral organ identity. The ABC genes, A class for APETALA1 ... AGAMOUS ...
[30]
MADS-box protein complexes control carpel and ovule development ...
We show that ectopic expression of either the STK or SHP gene is sufficient to induce the transformation of sepals into carpeloid organs bearing ovules.
[31]
B and C floral organ identity functions require SEPALLATA ... - Nature
May 11, 2000 · Here we show that the activities of the B and C organ-identity genes require the activities of three closely related and functionally redundant MADS-box genes, ...
[32]
Reflections on the ABC model of flower development | The Plant Cell
The model immediately suggests phenotypes for most double and triple mutants (Fig. 2, J to M). While most double mutant combinations were additive, the key ...
[33]
Floral quartets | Nature
Jan 25, 2001 · It seems that four genes involved in plant development must be expressed together to turn leaves into floral organs.
[34]
[PDF] Changes in the floral ABCs in angiosperms
Nov 22, 2009 · Angiosperms display a huge variety of floral forms. The development of the ABC-model for floral organ identity, almost 20 years ago, ...
[35]
Conservation of B-class floral homeotic gene function between ...
Dec 15, 2004 · The ABC model of flower development, established through studies in eudicot model species, proposes that petal and stamen identity are under ...Missing: variations | Show results with:variations
[36]
The ABC Model and its Applicability to Basal Angiosperms - PMC
The ABC model has long been the unifying paradigm for floral developmental genetics, but it is based on phylogenetically derived eudicot models.
[37]
The naked and the dead: The ABCs of gymnosperm reproduction ...
20 years after establishment of the ABC model many of the molecular mechanisms underlying development of the angiosperm flower are relatively well understood.Missing: variations | Show results with:variations
[38]
Patterns of gene duplication and functional evolution during ... - NIH
Members of the AGAMOUS (AG) subfamily of MIKC-type MADS-box genes appear to control the development of reproductive organs in both gymnosperms and angiosperms.
[39]
Patterns of gene duplication and functional evolution during the ...
Members of the AGAMOUS (AG) subfamily of MIKC-type MADS-box genes appear to control the development of reproductive organs in both gymnosperms and angiosperms.
[40]
Nested radiations and the pulse of angiosperm diversification ...
Jun 4, 2015 · Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications.
[41]
Root-derived cytokinin regulates Arabidopsis flowering time through ...
Jun 25, 2025 · Root-borne phytohormone cytokinin regulates flowering time through distinct elements of the two-component signaling pathway, components of ...
[42]
Confocal imaging of the cell cycle and cytokinin signaling during ...
Jun 24, 2025 · Here, we use confocal imaging to study the cell cycle, the proliferation of internal tissues, and the relationship with cytokinin signaling.
[43]
LEAFY and APETALA1 down-regulate ZINC FINGER PROTEIN 1 ...
May 22, 2023 · We show that ZP1 and ZFP8 repress these floral homeotic genes in leaves. LFY and AP1 down-regulate ZP1 and ZFP8 in floral meristems, lifting the repression on ...Missing: via | Show results with:via
[44]
[PDF] Strategies for the development of unique flower forms in ornamental ...
Oct 2, 2017 · These mutations were used in the model plant Arabidopsis thaliana to determine the model for floral development. Plants with mutated ABC genes ...
[45]
ABC flower model: Floral identity guide - Jupiter Science
Final takeaway: the ABC flower model provides a vocabulary to predict outcomes of genetic perturbations, guiding both basic science and crop improvement. As ...