The Genetics of Flower Color

Flower color is the result of pigment molecules accumulating in cells, but it's not as simple as just making pigment. The location, type of pigment, and amount produced, are all very important. These aspects are genetically controlled.

Two main groups of genes control flower color. One group includes genes that code for the protein machinery required to make pigment molecules. The other group includes genes that code for regulatory proteins. It's the regulatory proteins that control the location, type, and amount of pigment-producing machinery made.

The Rainbow Road

In flowers, anthocyanins and carotenoids are two of the major pigment types. They are built by a series of chemical reactions within cells.

Some flower color genes code for the protein machinery directly involved in the reactions. These proteins are called enzymes. An enzyme's job is to catalyze a biochemical reaction. They facilitate the attachment, removal, or rearrangement of a molecule's chemical groups. To build a pigment molecule, different enzymes make specific changes, one after the other, until the final product is formed. Enzymes working together in this way form the core of a biochemical pathway. A single biochemical pathway can require dozens or even hundres of enzymes.

In flowers, different groups of enzymes work together to make anthocyanin or carotenoid pigments. A specific set of genes code for the enzymes of the anthocyanin biosynthetic pathway. Another set code for the enzymes of the carotenoid biosynthetic pathway.

Related Content:

Anthocyanins and carotenoids are made by different protein machinery, and have different structures. Visit Chemistry of Flower Color to learn how the structure of pigment molecules determines the colors we see.

colors of anthocyanins

Anthocyanins and carotenoids are pigments that color many flowers.

Enzymes work together like an assembly line to build pigment molecules.

Fine Tuning

A second group of flower color genes code for proteins called transcription factors. Transcription factors are regulatory proteins. Each cell type has a unique set of transcription factors that control gene activity. In different types of flower cells, transcription factors turn genes in the anthocyanin and carotenoid pathways up or down. They also control the timing of gene activity. That's why even though all flower cells have the same genetic content, they aren't all the same color.

Transcription factors work through genetic switches. There are one or more switches controlling every gene. The switches aren't genes, but they're small stretches of DNA that affect gene activity. Transcription factors bind to a gene's switch, turning gene activity up or down.

Making a Pink and Yellow Monkeyflower

To clarify, let's explore how the monkeyflower Mimulus lewisii gets its color.M. lewisii flowers have pink petals from anthocyanins. They also have two yellow nectar guids, colored by carotenoids.

In a pink petal cell, transcription factors activate genes of the anthocyanin biosynthetic pathway. Many genes in the pathway have a similar switch, so they respond to the same transcription factors. Activated genes produce the protein enzymes they code for. The enzymes do their job of making anthocyanin pigment, and the petals are pink.

So far, researchers know three transcription factors that activate anthocyanin biosynthetic genes inM. lewisii . They are called MIWD40a, MlANbHLH1, and PELAN. All three work together as a group to activate genes.

A similar story explains whyM. lewisii's nectar guides are yellow. A transcription factor protein called RCP1 is in nectar guide cells, but not the other cells of the petal. RCP1 switches on genes whose protein products make carotenoid pigments. The nectar guides are yellow.

differences in gene expression that lead to color/pattern in M. lewisii

In most petal cells of this monkeyflower, transcription factors activate genes in the anthocyanin biosynthetic pathway. The cells make proteins that build pink pigments. In nectar guide cells, transcription factors activate genes in the carotenoid biosynthetic pathway. Proteins are made that build yellow pigments.

It's Not Just On or Off


The monkeyflower example describes how transcription factors activate genes, but they can also turn gene activity down. In the end, it is rarely as simple as turning the genes in a pathway on or off. It is usually a balance. A single cell type can also make more than one type of pigment, and levels can vary greatly. This complexity is part of what allows for the huge variety of flower colors that exist.

The petals of M. lewisii monkeyflowers usually have a combination of transcription factor proteins. They are light pink because some transcription factors turn gene activity "up", while others are turning it "down" at the same time. When one type of transcription factor is removed, the balance of gene activation shifts. Flower color changes.

Coloring Fruits and Vegetables

It's Not Just On or Off

purple cauliflower

Transcription factors help control coloring in many plants, including fruits and vegetables.

What Activates the Transcription Factors?

blood oranges

The color of blood oranges is due to a mix of carotenoid and anthocyanin pigments. They contain an anthocyanin-activating transcription factor that is more active at low temperatures. This means anthocyanin accumulation - and blood oranges color - is different depending on temperature.

The monkeyflower example describes how transcription factors activate genes, but they can also turn gene activity down. In the end, it is rarely as simple as turning the genes in a pathway on or off. It is usually a balance. A single cell type can also make more than one type of pigment, and levels can vary greatly. This complexity is part of what allows for the huge variety of flower colors that exist.

Coloring Fruits and Vegetables

Transcription factors are also sensitive to signals from the environment. The signals can affect the amount of a transcription factor protein that is created, or ensure the protein acts at the right time and place after it is created. Cues from an organism's development, a cell's communication with its neighbors, and environmental signals like light, stress, and temperature, can all affect transcription factor activity.

Solving Old Puzzles

Because we understand so much about the genetics of color in monkeyflowers, we can use the knowledge to guide research into other questions. For example, researchers use monkeyflowers to study overdominance.

Overdominance is when the hybrid offspring of two parents have traits that are more extreme compared to either parent. It occurs in many different plants and animals, but it is very well-known in crops. Hybrid crop plants often have higher yields than their "purebred" parents. Farmers have used hybrid crops to improve yield for over a century, without fully understanding why it works. Knowing more might help us boost its effects.

overdominance in M. lewisii

This hybrid monkeyflower is darker than either of its parents.

In plants, aninbred line consists of individuals that are genetically very similar. They are established by either generations of strict crosses within the line, or self-pollination

Crossing two inbred lines gives hybrid offspring.

Overdominance in Monkeyflowers

monkeyflower color diagram

In the monkeyflowerM. lewisii , overdominance affects the intensity of flower color. If two specific inbred lines — one with light pink petals and one with very pale petals — are crossed, the hybrid offspring are dark pink. Researchers discovered the dark pink monkeyflower is a case of single-gene overdominance. It is dark pink because it has two forms (alleles) of a single gene. It gets one from each parent.

The gene responsible for the overdominance isFLAVONE SYNTHASE, orFNS. It codes for the proteinFNS.FNS interferes with an enzyme in the anthocyanin biosynthesis pathway. BothFNS and the enzyme use the same building material, but make different end products.FNS takes building material away from the anthocyanin pathway and uses it to make flavones. Flavones are also important for monkeyflower color. Once made, they bind and stabilize anthocyanins, preventing their breakdown.

Hybrid Vigor in Crop Plants

In crops, hybrid vigor (or heterosis) describes hybrid offspring that do better than their parents. For a long time, the molecular basis was unknown. Now we know at least a few cases are because of single-gene overdominance.

One example is tomato yield. The geneSINGLE FLOWER TRUSS (SFT) leads to the production of florigen protein, a hormone that tells plants that it is time to make flowers. Tomato plants are very sensitive to the amount of florigen produced. Too little, and they don't produce many flowers. Too much, and flower production slows down or ends. However, with one working and one non-working version of theSFT gene, florigen protein is produced at a level that allows plants to make more flowers. With more flowers, there are more tomatoes.

tomatoes on a vine

Hybrid tomatoes often produce more fruit.

Related Content:

The genetics behind flower color reveal there is a lot going on at the molecular level to determine a trait! This is true for most traits, in plants and in animals. In fact, the more we learn, the more we realize that familiar terms from classical genetics — like dominant and recessive — only tell a small part of the story. To learn more, visit What are Dominant and Recessive? and The Dominant/Recessive Problem.



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Genetic Science Learning Center. (2018, January 22) The Genetics of Flower Color. Retrieved September 27, 2021, from

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Genetic Science Learning Center. "The Genetics of Flower Color." Learn.Genetics. January 22, 2018. Accessed September 27, 2021.