James and the Giant Corn Genetics: Studying the Source Code of Nature

Twenty thousand years ago, not a single crop species existed in its current form. Almost* every bite of food you eat today is the result huge amounts of human artificial selection, both unconsciously and intentionally by farmers and plant breeders. Sometimes the obvious changes are minor, for example between wild and domesticated strawberries:

Wild strawberry (left) and domesticated strawberry (right)

Clearly one of the major traits early strawberry growers selected for was bigger fruits. Which makes sense since it takes about the same amount of time an effort to pick a strawberry either way, but if you’re picking the ones on the right you’ll have more pounds of fruit picked at the end of the day.

But even in this case, the similarity in form hides major changes at the genome left. Strawberries went through two whole genome duplications during domestication (looks like it’s more complicated than I made it sound see comments), so each of the cells in the strawberries on the right contain eight copies of each chromosome, while the strawberry on the left contains the more standard two copies of each chromosome.

On the other end of the spectrum is maize. Maize is like nothing else on this earth, and for the longest time, many botanists and agronomists were convinced it must have been domesticated from a wild species that had since gone extinct. In fact the wild ancestor, a species of teosinte, of maize is so closely related to corn they can still mate with each other, the key definition of a species.

Teosinte was initially disregarded as the ancestor of corn because the two plants look very different. I could show you this if I’d been able to find a public domain photo of teosinte (or taken a picture of some of the plants when I rotated in a lab that was growing them). As is, you’ll have to take my word for it. To my eye a corn plant (at least up until it flowers) looks more like sorghum than it does like teosinte. The ears of corn also bear little resemblance to the tiny row of seeds produced by the female flowers of teosinte. (For a comparison of the two, look at the picture on the left here.)

Anyway, long before the corn genome came out, the fact corn had been domesticated from teosinte had been established. Some really clever classical genetics** suggested that 5-6 major genetic changes were responsible for most of the obvious physical changes between teosinte and corn. The Doebley lab actually mapped at least two of those changes, teosinte branched 1 (TB1) and teosinte glum architecture (TGA1).

Teosinte branched1 was one of the first genes that got me really excited about maize genetics. In fact it was this specific paper, assigned to me by an awesome post doc who refused to let me work for him until I know what I was talking about. The teosinte branched1 gene is actually expressed more in domesticated corn than in corn’s teosinte ancestors the result of a mutation in front of the gene. The gene’s job is to turn off clusters of cells near the base of each leaf which otherwise would develop into whole new stalks. The result is obvious:

From left to right mutant teosinte branched1 corn (where the tb1 gene doesn't work properly), normal corn, and sorghum. Key point: notice how the teosinte branched1 mutant corn and sorghum plants both have many stalks, while most corn has a single big one. The photo of the tb1 plant comes from maizeGDB the other two are my own.

But domestication isn’t just about a few big physical changes, there are a bunch of traits that farmers and farming select for both intentionally and unintentionally. Everything from when a crop flowers to how it tastes is under constant selection. So while 5-6 major traits may explain a lot of the obvious changes, the story of corn’s domestication includes many more genes. The publication of the corn genome is making it easier to track down those other domestication genes. Ed Buckler’s group is already identifying many of them.

When a single form of a gene which creates some desirable trait and is selected for, it displaces all the other variations of that gene. A telltale sign of selection for a particular gene is that comparing the versions of the gene from different individuals shows fewer differences than expected. Ed Buckler’s group generated more than 32,000,000,000 bases (the equivalent of 13 whole maize genomes) from 27 maize lines around the world. They identified 148 regions that where very similar between all 27 lines, a glaring difference from the normally incredible genetic diversity of corn. Finding these new candidates for domestication genes (I’ll be fascinated to learn more about which genes are on that list) were made possible by three things:

• The corn genome sequencing project
• The current generation of massively parallel sequencing technologies that make generating 32 gigabases of sequence possible for less than millions of dollars
• The hard work of people like Michael Gore and Jer-ming Chia the two lead authors on this paper.

*The single biggest exception is probably seafood. Also venison, and other wild game, and well as a few forms of wild berries and nuts.

**Classical genetics is the kind you can do without a sequenced genome or most of the modern molecular biology tools that make life so much easier for biologists of my generation. In this case, by mating corn and teosinte and looking at the ratios of traits in the grandchildren