Genome reveals why carrots are so orange

The new genome sequence reveals how the orange color occurs and which genes are involved, and also shows that carrot color is not genetically connected to flavor. (Credit: Brett Forsyth/Flickr)

Scientists have deciphered the full genetic code of carrots and are learning lots of details about their domestication, their color, and why they’re so good for us.

“The carrot has a good reputation as a crop, and we know its a significant source of nutrition—vitamin A, in particular,” says lead researcher Phil Simon, a horticulture professor and US Department of Agriculture geneticist at the University of Wisconsin–Madison. “Now, we have the chance to dig deeper, and it’s a nice addition to the toolbox for improving the crop.”

The results, published in Nature Genetics, could also lead to the improvement of similar crops, such as parsnips and the yellow-fleshed cassava, a staple food throughout much of Africa.

The history of carrots

Cultivated carrots were first documented 1,100 years ago in Central Asia. Unlike wild carrots, which are white, those first domestic carrots were purple and yellow. The canonical orange carrot appeared in Europe in the 1500s, as shown in German and Spanish art of the time.

The new genome sequence reveals how the orange color occurs and which genes are involved, and also shows that carrot color is not genetically connected to flavor.

It is fortuitous that colored carrots became popular, because the pigments are what make carrots nutritious, and orange carrots are the most nutritious of all.

32,000 genes

The research team used the Nantes carrot—a bright orange variety named for a city in France—to assemble and analyze the full genetic sequence and peer into the vegetable’s evolution.

The carrot genome contains more than 32,000 genes arranged among nine chromosomes, which code for pest and disease resistance, colorful carotenoids, and more. Carotenoids, like alpha- and beta-carotene, were first discovered in carrots.

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The study confirms that the “Y” gene is responsible for the difference between white carrots and yellow or orange carrots. It also identifies a new, previously unknown gene that contributes to the accumulation of the colorful compounds. The newly discovered gene is actually a defect in a metabolic pathway that appears to be related to light sensing, the researchers say.

The researchers also uncovered features traced to distantly related plant species, from grapes and tomatoes to kiwi and potatoes. Carrots more recently split from lettuce, and they are in the same family as spice crops, like parsley and fennel.

Domesticated in the Middle East

The researchers also sequenced 35 different types of carrots to compare them to their wild ancestors. They showed that carrots were first domesticated in the Middle East and Central Asia.

The research team traced carrot evolution as far back as the dinosaurs. Sometime between the Cretaceous and Paleogene periods—roughly around the time dinosaurs went extinct—carrots, along with other plants of the era, picked up genetic advantages that allowed them to thrive.

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Global carrot consumption quadrupled between 1976 and 2013, and over the last 40 years, breeding has led to more nutritious carrots with the selection of ever more intensely orange crops. In fact, carrots have 50 percent more carotene today than they did in 1970.

In addition to Van Deynze and Simon, the study included co-authors from Michigan State University and around the world, including Poland, Spain, Italy, Turkey, China, and Argentina.

The carrot industry and the following seed companies funded the study: Rijk Zwaan BV, Bejo BV, Monsanto Co., Nunhems USA, Takii Co., Vilmorin, Suminak, and Carosem. Funds also came from the US Department of Agriculture’s Agricultural Research Service, National Science Foundation, the Polish National Science Center, and the Polish Ministry of Science and Higher Education.

Source: UC Davis