Tomatoes can be found in a wide range of colors (red, pink, orange, yellow, white, green, brown, purple, blue) at your local farmers' market or grocer. Those color differences represent differences in the types and proportions of biologically synthesized pigments. Because tomatoes are such an important crop and adding those pigments to our diet has been shown to give us positive health impacts, researchers have spent some time studying the pathway they use to build the various pigments.
Information about the pathway is spread across numerous papers encompassing decades of research. Not every paper examining the topic will contain all the details of the pathway and there are sometimes conflicting results that have to be negotiated.
The fortunate thing is that these days, more and more of the research behind any particular topic is being placed online. This gives amateur and professional researchers alike access to the same information and either can learn a great deal about many different subjects that may interest them. In general you shouldn't put too much stock in the results of any one paper, but when the results of multiple independent lines of inquiry happen to align, you can be more confident in the inferences you gain.
You might say I'm somewhat interested in the biology of the things I find around me. I decided to look into what was known about the interesting colors found in tomatoes.
The majority of pigments in the tomato are carotenoids. After a bit of research, I generated the figure (at right) to show the biosynthesis pathway which produces these pigments. It illustrates most of what I've learned about the pathway. The figure is probably not entirely comprehensive, as all biological systems are intricate, but it contains sufficient detail to help explain the range of fruit colors seen in tomatoes.
You can dig through the references at the end of this post if you're interested in where I got the information. In fact, I would highly recommend you do so, if you're interested in the biology of tomato color. If you've never read primary literature, you should be aware that you may have to read through dozens (or hundreds) of papers to get a solid grasp of a new topic in this way.
In my figure, I use double arrows to indicate higher reaction rates, as inferred from preferred branches of the reaction pathway or intermediates which are known but don't appear in large amounts. The colored components of the pathway are highlighted in something approaching their true colors in chromatography experiments (and in the fruit) to make it simpler to visualize how mutations might impact fruit color.
Energy flows through biosynthetic pathways. Though each enzymatic reaction is reversible, the overall progression of the pathway is driven by the enthalpy gradient across its components. When a mutation breaks part of a pathway, it blocks that flow of energy, resulting in a build-up of the chemical intermediates just before the break as well as a reduction or absence of those intermediates after the break.
The following figures are close-up versions of the main figure above, highlight the placement of a series of mutations in the pathway which result in color changes in the flesh of tomatoes. The mutations are indicated by a large negative or positive sign, highlighted in red, at the location of the change to the pathway.
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| Mutant : 'r' |
The first major mutation (left) is responsible for the difference between red and yellow tomatoes. The wild-type dominant allele of the gene leads to the production of lycopene, so the gene is named '
red' ('
R'). The recessive allele ('
r') results in an overall decrease in the production of carotenoids. The decrease is not uniform; some carotenoids are suppressed more than others, resulting in an overall yellow appearance.
 |
| Mutant : 'gf' |
The second major mutation (right), in combination with the '
r' mutation just described, is the most common cause of green-fleshed tomatoes. The recessive mutant allele leads to green flesh, so it is named '
green-flesh' ('
gf'). The wild-type dominant allele of the gene ('
Gf') allows the breakdown of chlorophyll and other photosynthetic components during the ripening process.
A minor mutation produces green ripe fruit by interfering with the ability of the fruit ripening system to respond to ethylene. Ethylene is a common plant hormone involved in maturation/ripening/senescence, so this mutation keeps some aspects of the normal fruit ripening from happening. This dominant mutant allele is called '
Green-ripe' ('
Gr') and results in a green tomato with a red heart. This mutation doesn't impact the pigment pathway, but instead where different components of it are activated. It is not clear if it interacts with the '
red' ('
r') locus in a similar way to the more common '
gf' mutation.
 |
| Mutant : 't' |
The third major mutation (left) is responsible for the most common form of orange tomato. The recessive mutant allele is named '
tangerine' ('
t') (after the orange variety
"Tangerine" where the gene was found). The wild-type dominant allele of the gene ('
T') allows the final synthesis of lycopene. The mutation results in the build-up of orange prolycopene, as well as zeta-carotene in smaller amounts.
 |
| Mutant : 'B' |
Another minor mutation (right) results in a less common types of orange tomato. The dominant allele is named '
beta-carotene' ('
Beta', '
B') because it leads to a large increase in beta-carotene and a decrease in lycopene. The position of this gene in the pathway and the mechanism of the mutation isn't entirely clear, but the data seems to suggest the gene is involved in the conversion of lycopene to gamma-carotene and the mutation results in increased activity.
The color of the epidermis also impacts the apparent color of tomatoes, but the mutations impacting this system are less well-understood. The typical red tomato has a transparent-yellow epidermis, giving the associated gene its name '
yellow' ('
Y'). A common recessive mutation ('
y') results in a clear epidermis. The epidermis color overlaid on the flesh color results in the perceptual differences is red/pink and brown/purple tomatoes.
Recently, breeders have been been working with genes that result in the production of dark purple anthocyanins in the skin of tomatoes. The two genes '
anthocyanin-fruit' ('
Aft') and '
atroviolaceum' ('
atv') were introgressed into cultivated tomatoes from
Solanum chilense and
Solanum cheesmaniae, respectively. A less common gene '
Abg' was introgressed into cultivated tomatoes from
Solanum lycopersicoides, but is less useful/available because it has a recessive lethal character. All three genes are described in Mes
et al, 2008.
There is evidence for lycopene production in the skin of some tomatoes, resulting in an opaque-red skin. The details of the genetics have yet to be worked out and published, but
Frogsleep Farms has found
some lovely examples. The fruit at right appears to have the genotype '
r' for yellow fruit flesh color, but has intense lycopene-red in the epidermis. (
The first photo on this page shows another fruit, illustrating high-lycopene opaque-red skin.)
In my personal gardening, I've noticed an opaque-red epidermis in fruit produced by the micro-tomato variety
'Tiny Tim'. This variety was derived in part from the wild tomato
Solanum pimpinellifolium, which also seems to have an opaque-red fruit epidermis. Potential variations might eventually be found which have opaque-yellow or opaque-orange skin, so I find the idea of exploring the traits of fruit skin color to be exciting.
 |
| wild-type |
Another set of genes impact where pigment is produced in the fruit. A wild-type tomato has a dark-green shoulder when immature, which delays ripening at the top of the fruit. Common modern market tomatoes have the '
uniform ripening' ('
u') trait which shows even ripening, but reduced overall color. This gene is a transcription factor which normally guides chlorophyll distribution and abundance in unripe fruit.
 |
| [dgdg] vs. [uu] |
The '
dark green' ('
dg') mutation produces a dark green immature fruit and increased levels of carotenoids in the ripe fruit. The '
high pigment 2' ('
hp2') mutant is now considered to be a different allele of the same gene as '
dg', which is now known to be the tomato homolog of the Arabidopsis DEETIOLATED1 gene. This gene is involved in the perception of light levels and impacts morphogenesis.
The cause of bicolor, striped, and spotted tomatoes are less well understood. Striped tomatoes using the '
green stripe' ('
gs') mutation are pretty common these days. Another type of striping is due to a dominant allele ('
Ufs') of the '
uniform ripening' gene. Spotting is generally considered a commercial defect, but the '
gold fleck' ('
Gfk') trait is an interesting look when it is highly expressed.
In the following section, I give limited descriptions of the different color categories of tomatoes. This description includes the genotypes and example varieties associated with them when they're commercially available.
 |
| 'RR' (Kachanovsky et al, 2012) |
Red Tomatoes
The typical red tomato is pigmented by a large amount of lycopene and lesser amounts of beta-carotene, driven by the '
red' ('
R') gene. The skin of these tomatoes also has a yellow pigment driven by the '
yellow' ('
Y') gene.
genotype = [RR; YY]
example = "Red Barn".
Pink Tomatoes
These have the lycopene (red) and beta-carotene (orange) of typical tomatoes, but they have clear skin from a recessive allele '
y'. This results in the tomatoes appearing pink when compared to the typical red tomato.
genotype = [RR; yy]
example = "Dwarf Champion Improved".
Orange Tomatoes
 |
| 'RR; tt' & 'rr; tt' (Kachanovsky et al, 2012) |
The most common type of orange tomato is caused by the '
tangerine' ('
t') mutation. The skin can be clear or yellow.
genotype = [RR; YY/yy; tt] or [rr; YY/yy; tt]
example = "Earl of Edgecombe", "Elbe", "Tangerine".
A less common type of orange tomato is caused by the '
Beta-carotene' ('
Beta','
B') mutation. The skin can be clear or yellow.
genotype = [RR; YY/yy; BB]
example = "Caro-Rich","Jaune Flammée".
 |
| 'rr' (Kachanovsky et al, 2012) |
Yellow/White Tomatoes
Yellow tomatoes are caused by a recessive allele ('
r') of the '
red' gene. The skin can be clear or yellow.
genotype = [rr; YY/yy; TT]
examples = "Yellow Pear".
White tomatoes appear to be caused by a stronger recessive allele ('
r-') of the '
red' gene.
genotype = [r-r-; YY/yy; TT]
example = "Dr Carolyn", "White Queen".
Green Tomatoes
 |
"Coeur de Surpriz" showing 'Gr'.
Grown by Mary Hope. |
The most common type of green tomato is caused by the recessive '
green-flesh' ('
gf') mutation in combination with the '
r' mutation.
genotype = [rr; YY/yy; TT; gfgf]
example = "Green Zebra".
A less common type of green tomato is caused by the dominant '
Green-ripe' ('
Gr') mutation. This mutation leaves the center of the fruit to ripen normally, resulting in green/'purple' outer regions and a yellow/red center. There are heirloom varieties around with this trait, but I haven't been able to find many specific names.
genotype = [GrGr]
example = "Coeur de Surpriz".
Brown Tomatoes
These are pigmented by a large amount of lycopene and lesser amounts of beta-carotene, driven by the '
red' ('
R') gene, as well as by chlorophyll from the '
green-flesh' ('
gf') gene. The skin of these tomatoes has a yellow pigment driven by the '
yellow' ('
Y') gene.
genotype = [RR; YY; TT; gfgf]
example = "Black Russian", "Brazilian Beauty".
Purple Tomatoes
These are pigmented by a large amount of lycopene and lesser amounts of beta-carotene, driven by the '
red' ('
R') gene, as well as by chlorophyll from the '
green-flesh' ('
gf') gene. The skin of these tomatoes is clear driven by the mutant allele ('
y') of the '
yellow' gene.
genotype = [RR; yy; TT; gfgf]
example = "Black Cherry", "Black Krim".
 |
| "Indigo Rose" showing 'Aft' and 'atv'. |
Blue Tomatoes
These have anthocyanin expression in the skin, driven by the combination of '
anthocyanin fruit' ('
Aft') and '
atroviolaceum' ('
atv') genes.
genotype = [AftAft; atvatv]
example = "Indigo Rose".
Black Tomatoes
There is no specific genetics to describe for this category. 'Black' is often used to describe those that I would call 'brown' or 'purple'. (The example varieties I list for the 'brown' and 'purple' groups have names starting with 'black'.) I wouldn't be surprised if the 'blue' tomatoes end up being described this way, since they're actually the closest to black we're likely to get.
Bicolor Tomatoes
The 'bicolor' trait is caused by an allele ('ry') of the 'R' gene which activates of the carotenoid pathway in some parts of the fruit and not others. This results in streaks of red and yellow throughout the fruit and skin.
genotype = [ryry]
