Genes, pathways, silencing, and why color behaves unpredictably
Copyright © Steve K. Lloyd
All Rights Reserved
This article explains how flower color works in modern dahlias at the level of genes, enzymes, and cellular regulation. Its purpose is to show why color can be stable, unstable, sharply patterned, or unexpectedly altered, without treating those outcomes as mysteries or accidents.
It does not attempt to catalog dahlia colors, cultivars, or historical breeding results, nor does it fully explore questions such as why true blue dahlias do not exist or why some white flowers appear ivory rather than snow white.
Those questions are best examined individually. Here, the focus is on the core biological machinery that governs pigment production and makes all of those outcomes understandable.
Why Dahlia Color Can Flip, Freeze, or Break Mid-Bloom
Modern dahlias do not change color because they are unpredictable plants. They change color because the biological machinery that produces pigment is tightly regulated and can be activated, suppressed, or locally shut down, sometimes within only part of a single petal. Once you understand how dahlia flower color is built, this behavior becomes much easier to explain.
At its core, dahlia color is produced by a single biochemical system called the flavonoid pathway. The flavonoid pathway is a sequence of chemical reactions inside plant cells that produces the pigments responsible for red, purple, black, yellow, and white flower colors. Every visible flower color in dahlias arises from differences in how this one pathway is regulated, not from different pigment systems competing with one another.
Understanding this pathway is not about memorizing chemistry. It is about recognizing that dahlia color behaves like a regulated system. When that regulation shifts, color outcomes shift with it.
All visible flower colors in modern dahlias arise from a single biochemical pathway, the flavonoid pathway. Differences in color reflect how pigment production is regulated within this pathway rather than the use of separate pigment systems. Depending on which branches are active or suppressed, the same pathway can produce red to black, yellow, or white flowers.
The Entry Point That Controls Everything
The flavonoid pathway begins with one critical enzyme called chalcone synthase. An enzyme is a protein that enables a specific chemical reaction to occur, and chalcone synthase carries out the first committed step that allows pigment production to begin at all. If chalcone synthase is active, the pathway can proceed. If chalcone synthase is suppressed, pigment production stops, even if every other step downstream remains functional.
This figure highlights chalcone synthase as the entry point that determines whether the flavonoid pathway is active in dahlia petal cells. When chalcone synthase activity is permitted, pigment production can proceed through multiple downstream branches. When chalcone synthase is suppressed, the pathway is effectively closed, even though the enzymes responsible for later steps remain present. This helps explain why white or unpigmented petals in dahlias often result from regulatory control rather than permanent genetic loss.
This control point matters especially in dahlias because modern dahlia hybrids are octoploid plants. Octoploid means they carry eight sets of chromosomes rather than two, which results in multiple copies of many pigment-related genes. Because of this redundancy, disabling a single gene copy is rarely enough to eliminate color. To fully shut pigment production down, the plant must suppress activity across several gene copies at once.
The practical consequence is easy to miss but important. Dramatic color changes in dahlias are usually not caused by broken genes. They are caused by regulation of gene activity. The plant is not losing the ability to make pigment. The plant is regulating pigment production at a molecular level not to use that ability in certain cells or at certain times.
When Color Disappears Without Mutation
On some dahlia plants, one flower may open fully pigmented while another flower opening later on the same plant shows large white sectors or appears entirely white. In other cases, a cultivar may consistently produce bicolor blooms and later revert to solid-colored flowers. In these situations, the genes required to make pigment are still present and structurally intact.
What changes is whether those genes are allowed to function.
In many dahlias, white or unpigmented petal tissue results from a process called post-transcriptional gene silencing of chalcone synthase. Post-transcriptional gene silencing is a normal regulatory mechanism in plants. It works by using very small RNA molecules to destroy messenger RNA after it is made. Messenger RNA is the intermediate message that carries instructions from a gene to the cellular machinery that builds an enzyme. When that message is destroyed, the enzyme is never produced, even though the gene itself remains unchanged.
In these dahlias, the plant produces small regulatory RNAs that specifically target the messages needed to make chalcone synthase. Those messages are eliminated before pigment production can begin. Because this silencing can switch on or off at the growing tip of the plant, or even in different regions of a developing petal, color expression can be unstable, patchy, or reversible over time.
This provides a molecular explanation for a long-standing breeder observation. Some color traits cannot be reliably fixed through breeding because the instability is regulatory rather than inherited through simple genetic segregation.
How Bicolor Patterns Stay Sharp
Bicolor petals in dahlias are not produced by a gradual fade in pigment production. They reflect a sharp boundary between two populations of cells that are behaving differently at the molecular level.
This can seem paradoxical. The same system that allows color to switch on and off over time can also lock color boundaries in place within a single petal. The resolution lies in how pigment metabolism interacts with gene regulation inside individual cells.
This photograph shows the bicolor dahlia ‘Edinburgh’ with sharply defined boundaries between pigmented and unpigmented petal regions. The clean transition illustrates that bicolor patterning in dahlias reflects neighboring cells operating under different regulatory states rather than gradual pigment dilution. Once established, these states can remain stable within a single petal, producing clear and repeatable patterning.
Research shows that pigmented and unpigmented regions of a dahlia petal differ not only in pigment accumulation, but also in how RNA silencing operates within those cells. Cells that lack flavonoids, meaning they contain little or no pigment compounds, allow RNA silencing systems to remain active. Those silencing systems continue to suppress pigment production, keeping the cells colorless.
In contrast, cells that already contain flavonoids interfere with the RNA silencing machinery, preventing it from shutting pigment production down. Once a cell enters a pigmented state, it effectively disables the silencing system that would otherwise turn pigment off. Cells that remain unpigmented stay locked in the opposite state.
The result is a self-reinforcing feedback loop. Pigment accumulation suppresses gene silencing, while active gene silencing prevents pigment accumulation. Once established, this interaction creates a stable, sharply defined boundary that can persist across multiple flowers.
Sharply defined bicolor patterns in dahlia petals arise from differences in cellular regulation rather than gradual pigment dilution. Pigmented cells accumulate flavonoids that suppress RNA silencing and allow pigment production to continue, while adjacent unpigmented cells maintain active silencing and remain colorless. These opposing regulatory states reinforce one another, creating a stable and persistent boundary within a single petal.
Why Black Dahlias Are Not Simply Darker Reds
Black dahlias do not achieve their color by producing a new type of pigment. Instead, they achieve it by redirecting pigment production within the flavonoid pathway.
Black dahlia coloration arises from how pigment production is distributed within the flavonoid pathway rather than from the creation of a new pigment. When the branch that produces flavones is suppressed, shared precursor compounds are redirected toward anthocyanin production. The resulting high anthocyanin accumulation reduces light reflection, producing the deep, nearly black appearance seen in the darkest cultivars.
In these cultivars, production of flavones, a class of pale yellow flavonoid compounds, is strongly suppressed. This removes a competing branch of the flavonoid pathway and redirects the flow of raw materials within the cell toward extreme accumulation of anthocyanins. Anthocyanins are the red and purple pigments responsible for most dark flower colors.
When anthocyanins accumulate at very high concentrations, they absorb more light and reflect less of it back to the eye. This produces the deep, nearly black appearance of the darkest dahlia cultivars. Because this effect depends on regulatory suppression rather than permanent gene changes, it can be disrupted. When that happens, black flowers may abruptly shift toward purple or red.
These two cultivars illustrate how near-black dahlia coloration emerges from differences in pigment regulation rather than from entirely different pigments. The dark red bloom (‘Fidalgo Knight’) and the near-black bloom (‘Fidalgo Blacky’) are produced by the same underlying flavonoid pathway, but differ in how pigment production is distributed within that system. Extremely high anthocyanin accumulation reduces light reflection, creating the visual impression of black without introducing a distinct black pigment.
‘Fidalgo Blacky’ photo courtesy Mark Twyning. Used by permission.
Viruses, Silencing, and Sudden Color Shifts
Not all color changes in dahlias originate from the plant’s own regulatory systems.
Some plant viruses interfere directly with RNA silencing. When these viruses infect dahlias, they can disrupt the mechanisms that normally keep certain pigment genes suppressed. When that suppression is lifted, pigment production can change suddenly and dramatically, even though the plant’s genetic makeup has not changed.
For growers and breeders, this distinction matters. A sudden color break is not always a mutation or a genetic reversion. In some cases, it is the visible result of viral interference with gene regulation. The interaction between flower color and viral disease is complex enough to warrant focused discussion elsewhere, but its existence is essential for understanding why not all color changes should be interpreted as genetic events.
Dahlia Bloom Color as a Genetic Case Study
The behavior of flower color in dahlias is not an isolated curiosity. It reflects the same genetic structure described in Dahlia Genetics: An Introduction to the Science. The regulatory flexibility, gene redundancy, and reversibility seen in color expression arise from the broader architecture of the modern dahlia genome. Flower color simply makes those dynamics visible. Other traits are shaped by the same principles, even when their effects are less dramatic.
What This Means for Gardeners and Breeders
Dahlia flower color is not a single trait controlled by a single gene. It is an emergent outcome shaped by multiple interacting factors:
Control of pigment pathway entry
Post-transcriptional gene silencing
Feedback between pigments and regulatory enzymes
Environmental and biological disruptions
When color is understood this way, unpredictability stops looking like randomness. It becomes a natural consequence of a highly flexible regulatory system.
That flexibility explains why dahlias can surprise even experienced growers, sometimes within a single bloom.
Sources and Further Reading
This article draws on research spanning plant biochemistry, molecular genetics, and regulatory gene expression to explain how flower color is produced, suppressed, and stabilized in modern dahlias. Together, these studies show that dahlia bloom color is governed not by single genes or pigments, but by regulation within a shared flavonoid pathway, shaped by polyploidy, gene silencing, and feedback between pigments and cellular control systems.
Readers who wish to explore the underlying research in greater depth are encouraged to consult the original publications directly. While not all sources listed here are open access, abstracts and previews are often available online, and full texts can frequently be located by searching the citations exactly as shown in Google Scholar.
Flavonoid Pathway and Pigment Biochemistry
Tanaka, Y., Sasaki, N., & Ohmiya, A. (2008).
Biosynthesis of plant pigments: Anthocyanins, betalains and carotenoids.
The Plant Journal, 54(4), 733–749.
A comprehensive review of pigment biosynthesis pathways, clarifying how multiple flower colors arise from regulation within a shared biochemical framework rather than from independent pigment systems.
Davies, K. M., Albert, N. W., & Schwinn, K. E. (2012).
From landing lights to mimicry: The molecular regulation of flower colouration and mechanisms for pigmentation patterning.
Functional Plant Biology, 39(8), 619–638.
Examines how regulatory control, spatial gene expression, and pathway branching generate stable patterns, including bicolor and sectoring effects, in ornamental flowers.
Chalcone Synthase and Pathway Entry Control
Forkmann, G., & Ruhnau, B. (1987).
Distinct substrate specificity of chalcone synthase from flowers of Petunia hybrida.
Zeitschrift für Naturforschung C, 42(9–10), 1146–1148.
An early biochemical demonstration of chalcone synthase as the gateway enzyme controlling entry into flavonoid biosynthesis.
Holton, T. A., & Cornish, E. C. (1995).
Genetics and biochemistry of anthocyanin biosynthesis.
The Plant Cell, 7(7), 1071–1083.
A foundational synthesis linking chalcone synthase activity to downstream pigment outcomes and showing why suppression at this step has system-wide effects.
Post-Transcriptional Gene Silencing and Color Loss
Napoli, C., Lemieux, C., & Jorgensen, R. (1990).
Introduction of a chimeric chalcone synthase gene into petunia results in reversible co-suppression of homologous genes in trans.
The Plant Cell, 2(4), 279–289.
The landmark paper demonstrating post-transcriptional gene silencing of chalcone synthase, providing the conceptual basis for understanding white sectors and unstable coloration in ornamentals.
van der Krol, A. R., Mur, L. A., de Lange, P., Mol, J. N., & Stuitje, A. R. (1990).
Inhibition of flower pigmentation by antisense CHS genes.
The Plant Cell, 2(4), 291–299.
Established that pigment loss can occur without gene mutation, reinforcing the distinction between gene presence and gene expression.
Pattern Stability, Bicolor Boundaries, and Feedback
Koes, R., Verweij, W., & Quattrocchio, F. (2005).
Flavonoids: A colorful model for the regulation and evolution of biochemical pathways.
Trends in Plant Science, 10(5), 236–242.
Explores how flavonoid accumulation can influence regulatory processes, helping explain stable pattern boundaries and feedback-driven color states.
Kuriyama, K., Ohno, S., Yamazaki, N., Tabara, M., Koiwa, H., Moriyam, H., & Fukuhara, T. (2023).
Bidirectional feedforward regulatory loop of Dicer-like 4 and flavonoids causes floral bicolor patterning in petunia and dahlia.
bioRxiv.
Provides direct experimental evidence linking flavonoids, RNA silencing, and stable bicolor patterning in dahlias and related ornamentals.
Dark and Near-Black Flower Coloration
Tanaka, Y., Katsumoto, Y., Brugliera, F., & Mason, J. (2005).
Genetic engineering in floriculture.
Plant Cell, Tissue and Organ Culture, 80(1), 1–24.
Discusses how shifts in pathway flux and suppression of competing branches alter pigment concentration and visual outcome, including near-black coloration.
Noda, N. (2018).
Recent advances in the research and development of blue flowers.
Breeding Science, 68(1), 79–87.
Although focused on blue coloration, this review clarifies structural limits of flavonoid pigments and why extreme dark colors arise from concentration and light absorption rather than novel pigments.
Viral Interference and Regulatory Disruption
Hull, R. (2014).
Plant virology (5th ed.).
Academic Press.
A comprehensive reference on how plant viruses interfere with RNA silencing pathways, providing context for sudden, non-genetic color breaks in ornamentals.
AI Collaboration Transparency
This article was created collaboratively by the author, a dahlia grower and educator, and an AI language model.
The author directed the structure, tone, scope, and emphasis of the piece; supplied all scientific sources; and retained full editorial control over the final text. The AI assisted with summarizing complex technical material, suggesting phrasing, and organizing relationships among peer-reviewed sources provided by the author. It did not independently select sources or introduce unsupported claims.
All content was carefully reviewed, edited, and refined by the author to ensure scientific accuracy, clarity, and alignment with the Dahlia Doctor approach to evidence-based horticultural education.
Illustrations and diagrams appearing in this article were created with the assistance of AI tools under the author’s direction.
These visuals are conceptual and explanatory in nature. They are intended to help readers visualize structural relationships described in the text, not to serve as data figures or predictive models. All diagrams reflect scientific concepts supported by the cited literature and were reviewed by the author for accuracy and clarity.
