The determining feature here is the skin color, each flesh color looks different when it is covered with a clear epidermis or a transparent-yellow epidermis. Thus, a tomato with red flesh and a clear epidermis appear pink on the outside, while a tomato with yellow skin and red flesh appears red. Tomatoes with purple flesh and clear epidermis are purple in color, while yellow epidermis on purple flesh will make the fruit brown. The skin color is controlled by a single recessive gene y – expressed in a recessive pairing (y y) results in clear skin in tomatoes. Wild type y+ is dominant. It results in yellow skin.
Anthocyanin can be seen both – on the fruit and on the plant (leaves and stems). Anthocyanin is a pigment found primarily in the epidermis of the fruit, although it’s been known to “bleed” slightly into the flesh on some varieties. It can also follow striping patterns when combined with the fruit strip (Fs) gene. Anthocyanin tomatoes can have any flesh color and also a yellow or clear epidermis.
The flesh pigment in browns comes from a combination of higher amounts of lycopene found in the red flesh “R” gene and chlorophyll promoted by the “gf,” or green flesh, gene. Brown tomatoes must have a yellow epidermis “Y”; this is what distinguishes them from purple (RR;YY;gfgf).
The fruit stripe gene (Fs) causes dark-green radial striping opposite the locules (seed cavities). These stripes may be more prominent when affected by environmental changes and tend to fade as the fruit matures. However, in some instances where this gene is found in combination with the anthocyanin fruit (Aft) gene, the anthocyanin pigmentation can express in the same manner (radial striping), but it doesn’t fade as the fruit ripens. Tomatoes with the Fs gene can have clear or yellow epidermis.
Bi-color tomatoes can have clear or yellow epidermis. The bicolor expression happens when the carotenoid pathway is triggered or expressed in parts of the tomato flesh but not all; we generally tend to see red streaks dispersed throughout the flesh of a different color. The gene responsible for this activity is a mutant allele of the “R” gene named “ry.” In a yellow flesh, the bicolor genotype would be labeled (ryry); however, in a green-fleshed fruit bicolor, the genotype label would be (ryry;gfgf).
Striped tomatoes can have any flesh color or combination of colors. One gene responsible for some stripes is a green stripe (gs), a recessive gene that causes uneven green striping to appear on unripe fruit. As the fruit ripens, these stripes retain chlorophyll for longer than other parts of the fruit, but they will eventually turn a paler shade of the ripe fruit color. This striping is only found within the fruit’s epidermis (skin). Another known gene, fruit stripe (Fs), causes dark-green radial striping opposite the locules (seed cavities). These stripes may be more prominent when affected by environmental changes and tend to fade as the fruit matures. However, in some instances where this gene is found in combination with the anthocyanin fruit (Aft) gene, the anthocyanin pigmentation can express in the same manner (radial striping), but it doesn’t fade as the fruit ripens. And lastly, there’s the uniform ripening (u) gene with the dominant allele of fruit stripe (Fs). This expression is similar to the Fs gene in its display, but it also expresses dark-green shoulders that run down into the radial stripes.
The most common type of green-fleshed tomato is caused by a combination of the recessive “r” (low lycopene promoting yellow flesh) and the recessive “gf,” or green-flesh mutation, which promotes continued chlorophyll production. This type of green can carry a yellow or clear epidermis (rr;YY;gfgf), (rr;yy;gfgf). The second type allows for a green flesh while still retaining a reddish core; the expression is from the dominant “Gr” (green ripe) mutation and can also have a yellow or clear epidermis (GrGr;YY), (GrGr;yy).
Orange tomatoes can be caused by several different expressions. The first critical enzyme in the carotenoid pathway is PSY1, which allows for orange flesh by way of the wild-type dominant allele “R” (RR or Rr) which enables the production of the PSY1 enzyme. The second type of orange expression can have a yellow or clear epidermis and is driven by the dominant beta-carotene allele “B” expressing higher levels of beta-carotene while reducing lycopene production (RR;YY;BB), (RR;yy;BB).
Pink tomato flesh contains lycopene and beta-carotene expressing the red gene “R,” but here the epidermis is clear, expressing the recessive allele “y” (RR;yy).
In purple tomatoes, the flesh is the same as described for browns, but the epidermis expresses the recessive “y” allele for clear skin (RR;yy;gfgf). Other expressions for brown and purple can also be affected by the expression of a high crimson (lycopene) mutation of the beta-carotene gene “Bc,” in combination with the “gf” chlorophyll promoter. The epidermis color allows for the brown or purple color to come through (BcBc;YY;gfgf), (BcBc;yy;gfgf).
Red tomato flesh is largely pigmented by lycopene (red) with lesser amounts of beta-carotene (orange), expressing the red gene “R.” The yellow skin pigment (chalconaringenin) is expressed here also, showing the “Y” gene (RR;YY). Red tomatoes have yellow epidermis.
Tri-color tomatoes can have clear or yellow epidermis. A characteristic feature of this type of fruit is that persistent chlorophyll in red and yellow bi-colored tomatoes is creating multiple colors in the flesh of the tomato.
A white tomato is caused by the flesh expressing an even stronger suppression of lycopene, the recessive allele of the red gene “r-.” A white tomato will always have a recessive clear skin “yy” (r-r-;yy).
Yellow tomato flesh is pigmented by a recessive allele of the red gene “r,” where the synthesis of lycopene is suppressed. Yellows can express either a clear skin “yy” or a yellow skin “YY.” (rr;YY) or (rr;yy)
