How did carrots evolve from ghostly white vegetables into the dayglow orange things we’re used to seeing in Bugs Bunny’s hand?

Philipp Simon, a research geneticist for the U.S. Department of Agriculture and the University of Wisconsin at Madison, had the same question. He has been studying carrots for about 35 years, looking at their reproductive habits, their relationship to other vegetables (celery and fennel are close cousins, grapes have been evolving away from them for 113 million years) and their coloring. See, the carotenoids that give carrots their vibrant hue are also what make them healthy for humans: Those chemicals are sources of vitamin A.

If you ask Simon what got him interested in carrots, he responds in a tone of polite indignation (he is from the Midwest, after all).

“You wouldn’t ask someone who studies corn that question,” he said.

The reality is that the USDA has scientists studying pretty much every crop imaginable, all of them looking for ways to make produce bigger, healthier and more resilient. “Anything that you can breed,” Simon said, “somewhere in the world there are breeders working on it.”

The community of carrot breeders may be small, but as Simon shows, it’s plenty hardy. Recently, he and 20 other scientists scraped together the vegetable’s genome – a string of DNA more than 32,000 genes long.

Their results, published Monday in the journal Nature Genetics, help explain how carrots evolved from their wild white form to the one we know today. The find could give a boost to breeders looking to make related vegetables – say, the colorless parsnip or cassava – as rich in nutrients as carrots are. Given the world’s booming population and ever-growing nutritional needs, this will undoubtedly come in handy in the future.

But sequencing a genome is also a way of traveling back in time, of figuring where and when things started and how and why they changed. The carrot genome has some interesting things to tell scientists about the history of the plant – and the humans who cultivated it.

At 32,000 genes, the carrot genome is a good deal longer than ours (somewhere between 20,000 and 25,000 genes). It’s not actually surprising that a lowly carrot’s DNA would have to be more sophisticated than a human’s, Simon said. After all, plants can’t choose or change their environments, so they need to prepare for all contingencies, stocking their genome with traits that can be turned on or off depending on changing environmental circumstances.

From that crazy long string of DNA, Simon was able to tease out a gene thought to be responsible for making carrots orange. It’s still just a candidate, he cautioned. “Like with the election. You’ve got your favorite candidate but in the end it may turn out to be a different gene,” Simon said.

He paused, and chuckled: “Though there’s maybe more certainty about carrots than about the election.”

The gene in question is known as DCAR_032551, or the “Y gene” for short. It’s found in plenty of other plants as well; it causes red, orange and yellow pigments to accumulate in leaves, where they help with photosynthesis. We see the Y gene at work in the fall, when green chlorophyll drains from tree leaves and only the colorful carotenoids remain.

But sometime about 1,100 years ago, farmers living in what is now Afghanistan took advantage of a mutation in the Y gene that put it to work down in their carrots’ roots. In the process of domesticating the white, wild carrot, they turned it yellow.

Six hundred years later in Europe, cultivation took another turn, and carrots deepened in hue from yellow to dark orange. Simon knows this from his examinations of carrot DNA, but you can also see for yourself by visiting an art museum. Before the 16th century or so, carrots were painted yellow. Afterward, they were orange. They also became a fixture of artwork from the Netherlands – not because the Dutch were particularly carrot crazy, but because painters wanted to honor their royal family, who were members of the House of Orange. (If you’re into carrot artwork, or vegetable history in general, check out the World Carrot Museum website, which is chock-full of both.)

So now Simon knows when carrots got their color, and has a pretty good idea of how that happened. But he still can’t figure out why.

“There’s no good biological reason for carrots to be orange except one,” he said. “And it’s that people have been diddling around with carrots for 1,000 years.”

It’s obvious that farmers were selecting for the mutation that concentrated carotenoids in the carrot root. It’s a good thing they did so, too, since it made carrots much more nutritious. But health can’t have been bygone breeders’ motivation – no one in the 9th century knew what a carotenoid was, let alone that it was a source of a vitamin that’s good for our eyes, immune systems and other organs.

So Simon examined flavor, to see if colorful carrots tasted better. Again, no dice: Orange carrots and their white counterparts taste pretty much the same. There are other possibilities – perhaps the gene for color is linked to one for size, or hardiness. Or perhaps historic humans just liked the way yellow and orange carrots looked.

Is it possible that this is one question best answered by people, rather than carrots?

Simon demurred. There’s a lot of genome left to explore – he’s not ready to give up on carrots yet.