The Biologist Is In: The Color of Peppers

Since writing this post, I took some nice photos of chiles I collected or grew this year, found more interesting mutations to talk about, and have generally filled out my understanding of the story of pepper color genetics. All this has been included in a new post at: the-biologist-is-in.blogspot.com/2015/11/the-color-of-peppers-2.html

I previously posted about some of the genetics involved in determining the color of tomatoes (http://the-biologist-is-in.blogspot.com/2014/04/the-color-of-tomatoes.html). Here we'll be looking at the colors of chile peppers.

Ripe chile peppers come in a very similar range of colors to ripe tomatoes. Both vegetables (along with potatoes, tomatillos, and ground-cherries) belong to the Solanaceae family of plants. Because of the close relationship of the plants, there are strong similarities in how the basic biology of color operates in each of them.

The red color of a classic ripe tomato is due to lycopene. The red color of a classic ripe pepper is not due to lycopene, but instead due to a combination of Capsanthin and Capsorubin. These are produced by the carotenoid pathway like lycopene, but they're produced further along the pathway. The figure at right illustrates the carotenoid pathway in peppers, to the degree I've been able to learn about it from reading primary research literature. Most of the pathway here is identical to that seen in tomatoes (and other plants), but with an extension after Zeaxanthin.

Compared with tomatoes, there is less research available to elucidate the genetics of color in pepper. The following figures are close-up versions of the main figure above, highlighting the placement of a series of mutations in the pathway which result in color changes. The mutations are indicated by a large negative, highlighted in red, at the location of the change to the pathway.

Mutant "y".

The first major mutation (left) is responsible for the difference between red and most yellow-orange peppers. The recessive mutant generating the "yellow" ("y") trait is caused by a defect in the gene Capsanthin-Capsorubin Synthase (CSS), which normally converts lighter colored Antheraxanthin and Violaxanthin into the Capsanthin and Capsorubin which are responsible for the typical rich red color.

Papers discussing mutations in CSS refer to the resulting fruit as yellow or sometimes orange. I'm pretty sure this is due to the actual color ranging between orange and yellow depending on the actions of other genes (like those described below).

The next major color mutations are abbreviated as "c1" and "c2". The "c1" trait results in a reduction in red pigment to about 1/10 of the wild-type level. The "c2" trait results in a reduction in red pigment to about 1/100 of the wild-type level. In an otherwise red fruit (with the "Y" allele), the actions of these two genes can result in a range of colors from light-red, to orange and pale-orange. In an otherwise yellow fruit (with the "y" allele), the actions of these two genes can result in a range of colors from pale-orange-yellow, to lemon-yellow and white.

Mutant "c2".

The "c2" mutation has been determined to likely be a defect in the Phytoene Synthase gene. This interferes with the production of a very early stage of the carotenoid pathway, resulting in a strong suppression of every later product in the pathway. Mutations in the same gene in tomatoes is also responsible for the production of yellow and white fruit. Though the phenotypes are different in the two species, they share the common aspect of having a much reduced output of the carotenoid pathway.

Mutant "bc".

Another mutation that results in an orange pepper and doesn't have the complications of the "y"/"c1"/"c2" genes is associated with a large increase in β-Carotene. This mutation is in the β-Carotene Hydroxylase 2 (BCH2) gene and interferes with the conversion of β-Carotene into β-Cryptoxanthin. Because of the increase in β-Carotene, the trait is called "bc".

There's also a pair of genes, called "B" and "t" that interact to result in a high level of β-Carotene, but so far I haven't been able to find any useful research to clarify how the mutations do so.

Mutant "cl".

The chlorophyll that makes a typical immature pepper green is broken down during maturation of the fruit. A mutation that interferes with this breakdown is called "chlorophyll retainer" ("cl"). When it is found in an otherwise red pepper, the result is a ripe pepper with a chocolate-brown color. When it is found in an otherwise yellow pepper, the result is a ripe pepper with an olive-green color.

There are several pepper varieties that have purple or black immature fruit. This trait is driven by two genes. The first mutant ("A") allows the plant to produce anthocyanin pigments in its leaves, stems, and purple immature fruit. The second mutant is a modifier of "A" ("MoA") that increases the amount of anthocyanins produced and results in a black immature fruit. These anthocyanins are broken down as the fruit matures. There is a very rare trait which interferes with this breakdown (seen in variety "Pimenta De Neyde") and so results in ripe fruit that remain purple. I haven't been able to find any publications describing this trait, so I've decided to refer to it as "anthocyanin retainer" and abbreviate as "an". I think it is likely to be a recessive trait, but I'll have to perform some crosses to be sure.

Looking at the β-Carotene enhancing mutant 'bc' in the pathway, I wonder if there are any mutations around which interfere with the conversion of Lycopene into β-Carotene. Such a mutation wouldn't be visible in the normal genetic backround of red peppers, as the red color of Lycopene is very similar to the red color of Capsanthin and Capsorubin. However, such a mutation would be very visible in the bright-orange background of a strain with the 'bc' trait.

Alternately, instead of searching for such a mutation, one could be engineered into the lycopene-cyclase gene to slow down its activity and result in a fruit which has a mix of Lycopene, Capsanthin, and Capsorubin.

pale-orange; orange; red.

Habanero-type chiles exist in a wide range of shades. I'd really like to breed up some standard-shaped Habanero chiles in the few missing colors (white, lilac, purple, and black). There is a variety called "Habanero White", but it doesn't have the shape of the classic Habanero. There is also a variety called "Black Habanero", but it has a rich brown color instead of black because it lacks the anthocyanin pigments necessary to generate the most darkly-colored fruit.

Pepper color genotypes I have.
y	cl	c1	c2	A	*MoA*	an	-	ripe-fruit-color
+	+	+	+	+	+	+		red ("Habanero" from Dominican Republic)
+	+	+	c2	+	+	+		orange ("Habanero" from grocer)
+	+	c1	c2	+	+	+		pale-orange ("Habanero" from grocer)
y	+	+	c2	+	+	+		lemon-yellow ("Devil's Tongue"; "Datil")
+	+	+	+	A	MoA	an		purple ("Pimenta De Neyde")
-
Habanero color genotypes I'd like to have.
y	cl	c1	c2	A	*MoA*	an	-	ripe-fruit-color
y	+	c1	c2	+	+	+		white
y	+	c1	c2	A	+	an		lilac
+	+	+	+	A	MoA	an		purple
+	cl	+	+	A	MoA	an		black

I expect different combinations of the "y", "c1", "c2", and "MoA" genes would result in a range of shades between a light lilac all the way to a visually black fruit.

I don't have any pictures of the various pepper colors, but I am growing several peppers this year and expect to get a few nice photos. I have red, pale-orange, and purple fruited plants well-established and I'll soon be starting some of the orange and lemon-yellow types I have seed for.

If I can get my gardens built soon enough, as well as find a way to keep them protected from deer, I'll be able to think about doing some of the initial crosses I would need to make progress towards the few remaining novelty colors.

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