Popped corn Photo: D3 San Francisco, flickr (click to see photo in original context

Popping corn, or anything else, all comes down to pressure. Pop-corn has a particularly impermeable pericarp (the corn kernel’s shell), so as it is heated, the water inside the kernel vaporizes into steam and the starch turns into something close to a liquid. Eventually the heat creates enough pressure to split the pericarp and the starch of the corn kernel bursts out, resolidifying into the distinctive shape of popcorn. If there is even the smallest hole in the pericarp, the steam can escape from the kernel as it’s generated so the pressure never builds up enough to explode the pericarp — the reason some kernels will fail to pop in every batch. The explosive build up of steam is also the reason tea kettles need to be able to release steam while they’re used to boil water. The alternative would be exploding tea kettles which are a lot more dangerous (and a lot less tasty) than exploding corn kernels.

Un-popped popcorn photo: MissTessmacher, flickr (click to see photo in its original context)

It was this reason (along with my discovery of the website on April 1st) that I was so suspicious of the idea of popped sorghum a few days ago. Thanks to Party Cactus and Jeremy, I now know that sorghum does indeed pop like corn (there’s even a variety called “Tarahumara Popping”) and, in fact, thanks to the link Jeremy provided, I’ve discovered that most grains and even some other things (including cowpeas!) can be popped using the proper equipment.

By using a machine that is in some ways similar a pressure cooker, even grains without hard impermeable pericarps can be popped. The popping machine lets pressure rise equally inside and outside of whatever grain is being popped. When the outside pressure is released, the grains/kernels/seeds instantly pop.

It doesn’t sound as visually satisfying at the pop-corn popper I remember from my childhood, where half the fun was watching in anticipation for the first kernels to leap into the air, but a very cool invention never the less.

I’ll certainly be keeping an eye open for popped sorghum to show up out here in the bay area.

A. Normal popcorn kernel. Applying heat makes the pressure build up inside the kernel until the kernel pops open. B. A popcorn seed with a hole in the pericarp. Heat creates pressure, but it escapes through the hole so it never builds up enough to pop open the kernel. C. Even in grains with permiable pericarps, the pressure can build up inside, if the pressure outside is also high. Dropping the outside pressure suddenly still caused the grain to pop.

3:20-7:54: Introducing the subject, developing drought tolerant varieties of maize in Africa, and the fact that the researchers working on it as using conventional breeding, marker assisted breeding and a genetically engineered trait Monsanto. When battling starvation, you use any tool that comes to hand.

18:40-21:20: This part is almost hard to listen to. You can hear the raw emotion in the researcher’s voice as the reporter keeps trying to make genetic engineering sound, at best, like a last resort. Couldn’t they just try irrigating more crop land she suggests?

25:10-end. Conclusion. I also thought this part was very powerful.

A few complaints:

“It’s philanthropic but it can also be seen as a publicity stunt by {inset any person or organization here}” <– this statement would apply to pretty much any philanthropic act that’s not done anonymously wouldn’t it?

Marker assisted breeding is not “a kind of half-way house between breeding and genetic engineering”! Think of marker assisted breeding as GPS for plant breeders. All that changes is that plant breeders get more useful information faster.

I’m pretty sure the BBC reporter at one point calls ears of corn kernels, but if this is just a difference between american and british english, I’ll withdraw that complaint.

Obligatory greenpeace quote:

“We really question the use of say molecular markers and gm in the same plant together … And what would concern us, that is, that it would be undoing all the good effects of conventional breeding by then also crossing it with a GM crop.”

I talked about another BBC story that addressed the lack of acceptance of genetically engineered crops in europe back in December.

The relationships of the four grass species with sequenced genomes. The branches are NOT to scale with how long ago the species split apart. Green stars represent whole genome duplications. The most important one to notice in the one in the ancestry of maize/corn. That duplication means that every region in sorghum, rice, or brachypodium is equivalent to two different places in the maize genome, one descended from each of the two copies of the genome that existed after the duplication.

And this morning the dataset I drew that example from, 464 classical maize genes mapped onto the maize genome assembly plus syntenic orthologs in up to four grass species: sorghum, rice, brachypodium, and the other region of the maize genome created by the maize whole genome duplication (technically syntenic homeologs since we started in maize to begin with, by the principle is the same), went out to the maize genetics community (thank you MaizeGDB!).

A postdoc in our lab tells me more people have visited CoGe today than any day on record (and we hit that mark before noon!).

Anyway, thank you guys, it’s great to feel appreciated!

* = tied for number of citations

** = some mutant alleles have kernel phenotypes.

If you want to become one of the famous mutant corn genes, it helps if you have an effect that is visible in corn kernels instead of only from fully grown plants.

And here is why:

• A geneticist could determine that the version of c1 that creates yellow kernels is recessive to the version that creates purple kernels just from looking at the ear of corn on left.
• Furthermore, they could tell you that both the male parent (the plant that provided the pollen) and the female parent (the plant on which the ear of corn grew) were both heteryzygous for the c1 genes (they each had one dominant version of the genes and one recessive version), and therefore the corn kernels the parent plants were grown from were both purple.
• They would know with certainty that all of the yellow kernels contain two recessive versions of the c1 gene.
• While they couldn’t predict with absolute certainty whether a specific purple corn kernel on that ear carried two dominant versions of the c1 gene or one dominant and one recessive version, they would know there was a 1/3 chance that kernel has two dominant copies, and a 2/3 chance it had one dominant and one recessive copy.
• That geneticist could make all sorts of predictions about what ears would look like in future generations depending on what colors of corn kernels were planted and which plants were mated with each other.

All this from a single picture of an ear of corn. For a phenotype seen in corn plants but not in kernels (like Knotted1), a geneticist would have to plant a row or more of corn seeds from an ear and examine the growing plants to get the same quantity of information.

And that is why mutations with kernel phenotypes have been so popular over a century of maize genetics research.

Corn Smut photo: oceandesetoiles, flickr (click to see photo in its original context)

And no that doesn’t mean corn pornography*. Corn smut, or Ustilago maydis, is a fungus that infects corn plants. It’s an old acquantance from my days working in the field. We always used to tell the new hires that corn smut was a rare delicacy in some countries (as we’d been told ourselves), but this was in the days before iPhones so until recently I never actually checked on this bit of received wisdom.

Turns out this particular bit of knowledge was true:

The immature galls, gathered two to three weeks after an ear of corn is infected, still retain moisture and, when cooked, have a flavor described as mushroom-like, sweet, savory, woody, and earthy.

More corn smut. Photo: moskatexugo, flickr (click to see photo in its original context)

I haven’t been able to figure out what the trade off in nutrition is between the ear of corn that is produced by a normal plant and the fungal galls that can be harvested from a plant infected with corn smut. I’d imagine corn smut provides more (and more complete) protein than an ear of corn (assuming corn smut is nutritionally similar to mushrooms.) But what’s the comparison in number of calories? The fungus is certainly sold at a higher price pound for pound.

My renewed interest in corn smut comes courtesy of a new paper** that came out in PLoS Biology describing how the fungus steals energy from infected corn plants without triggering the corn’s usual anti-fungal defenses. It’s an interesting read, you can check out the paper itself since PLoS Biology is open access, or Diane Kelley’s summary at “Science Made Cool.”

I’d seen a number of talks recently about another fungal parasite, powdery mildew in Arabidopsis, but somehow it’s much easier to focus on this stuff now that I can connect it back to corn. Even mammalian systems can be interesting*** once the make that connection.

*Please PLEASE don’t let that phrase start showing up in the search terms people use to find my site!

**Wahl R, Wippel K, Goos S, Kämper J, Sauer N (2010) A Novel High-Affinity Sucrose Transporter Is Required for Virulence of the Plant Pathogen Ustilago maydis. PLoS Biol 8(2): e1000303. doi:10.1371/journal.pbio.1000303

***The talk I’m practicing for Monday actually uses an example of a pheromone receptor in new world monkeys that was lost 23 million years ago in old world monkeys (including us humans).

But where was I? Oh yeah, gene counts. 32,690 high confidence genes*. Of those, how many have been studied individually?

While I don’t know that anyone knows the precise answer to that question, one indicator is how many maize genes were named before the maize genome was sequenced. People have been naming maize genes since before even the structure of DNA was known, based on the effect mutant version of the gene have on corn plants (for example: waxy1 or yellow stripe1). Later names might be based on the function of the gene (alcohol dehydrogenase1 or superoxide dismutase4), or anything else we know about the gene (wound induced protein1 or male flower specific18). The point being, if someone bothered to name a gene sometime during the last century of maize genetics, it was likely because they were studying it (to a greater or lesser extent). MaizeGDB keeps records of most of the named genes in maize and (excluding chloroplast and mitochondrial genes) I was able to find records of 1181 named genes in maize.

That’s less than 4% of the number of high confidence genes found within the maize genome, and at least a few of the named genes aren’t found within that group (see the first footnote for more details). Why is that number so low?

1. Each of the genes that has been studied in any detail probably represents some grad student’s doctoral thesis. While the tools have gotten better, the expectations for what is involved in characterizing a gene have risen too. I don’t have any statistics on how many maize genetics students earn their PhDs every year (and many of them will have worked on other kinds of projects than characterizing some new mutant gene), but it’s certainly not the thousands that would be required to characterize every gene in the genome in a short period of time.
2. Perhaps more importantly, the first genes to be studied are the ones with the best mutant phenotypes. To be a good mutant to study, breaking a gene should create something obviously different about the plant (it’s purple, or the tassel produces seeds like an ear instead of pollen, or the plants grow along the ground instead of standing upright), but not be so vital that embryos containing broken versions of the gene don’t develop at all. From a project that to knock out every gene in another plant Arabidopsis thaliana we know that many genes can be broken without any obvious effect on the plants that carry broken copies. That doesn’t mean there won’t be still be interesting things wrong with the plants when they’re studied in more detail, but such mutants were less likely to be identified early on. As for genes mutations are usually lethal, they can be studied (a friend in a lab downstairs is working with just such a mutant) but it certainly adds a whole new layer of difficulty to any research project so the genes better be involved in something interesting enough to justify the extra pain and suffering involved.

Now the situation isn’t nearly as grim as it might sound. Nature re-uses related genes over and over again both between and within species, so any time a researcher studies a new gene in detail, that information doesn’t just inform our knowledge of one particular gene in one particular species. Like a candle in a dark room, the information created by the study of a single gene will illuminate, to a greater or lesser extent, nearby genes (genes that have similar sequences to the gene being studied directly.) So even for a gene that’s never been studied in maize, we can make guesses about its function based on any related genes that have benefited from detailed study (either other genes in maize, in other grasses like barley or rice, other plants like arabidopsis or snapdragon, or even in animals or bacteria). While no geneticist worth their pollenating apron wouldn’t need experimental data before being CERTAIN of a gene’s function, knowing something about the functions of related genes is an excellent starting point.

I just finished some “free time” science looking at the classical genes of maize genetics (which displaced the time I normally spend writing for this site), so expect a couple more posts on related topics later this week.

*The good folks at maizesequence.org also produced a set of all the sequences they thought MIGHT be genes which, in addition to the filtered genes, includes ~70,000 more sequences that might or might not be genes. Many of these potential genes are computationally predicted, by programs that look at the underlying characteristics of the DNA sequence itself (how they work is outside my expertise and above my pay grade), but I can personally vouch for the fact that at least some of those “possible” maize genes are the real thing so the true number of genes contained within the maize genome is at least somewhat greater than the 32,690 reported with high confidence. This fact isn’t in any way a criticism of the people involved in sequencing and annotating the maize genome. The vast majority of the high confidence genes (called the filtered gene set) are real, and most of the other 70,000 genes (those included only in the working gene set (which also includes the genes from the filtered gene set)) are probably figments of a computer program’s imagination. Anywhere they chose to draw the line between the two groups was going to put some genes in the wrong category, and they did everything they could to minimize those miscategorizations.

**This doesn’t mean that the genes don’t have important jobs. You can imagine, for example, that genes involved in a plant’s ability to survive disease, water shortages, cold stress or heat stress all won’t create obvious problems for plants grown in the relatively pampered conditions we biologists try to provide for our research subjects when we aren’t actively studying what happens when we stress plants.

MAT points out another more pragmatic reason yellow corn may not be favored in Africa that I hadn’t heard of before. Apparently the extra carotenoids make yellow corn more susceptiable to spoilage than white corn varieties, a very pertenent issue in areas without access to the kinds of storage facilities we take for granted in American agriculture.

Jeremy at the Agricultural Biodiversity Weblog picked up the torch, highlighting a number of their own previous posts relevant to the discussion, including one by fellow blogger Luigi that relates the reaction of his own wife, originally from Kenya, on ordering polenta** at a restuarant and receiving a yellow dish.

Fortunately breeds of corn that contain even more beta carotene (the carotenoid most easily converted into vitamin A by our bodies) aren’t even yellow all the time. Although I wasn’t able to find a freely available picture, sometimes they’re ORANGE.*** While it turns out the correlation between color and beta carotene content isn’t perfect****, there’s still reason to hope varieties bred for the highest pre-vitamin A content will end up a striking orange color. For a visual examples of how orange corn can get, check out check out Dr. Rocheford’s lab website.

Will the distinction between orange and yellow***** be enough to get over the Africa’s lack of enthusiasm for yellow corn? Will the benefits of a diet with more vitamin A be enough to outweight the issues with yellow corn going “off” if stored improperly? I certainly hope the answers to both these questions are yes, but we won’t know for sure until we try. And there are some hopeful signs. For example this segment in a story from NPR:

Winter-Nelson and one of his graduate students took some of this orange corn to an open-air market in Mozambique for a taste test. The market-goers still preferred their white corn, but almost half of them agreed to exchange it for bags of orange corn when they heard it was more nutritious.”Probably the most encouraging part of it for me was that people who reported that they didn’t have much dietary diversity,” Winter-Nelson says. “People who reported that they didn’t eat very many fruits and vegetables, [or] that they very rarely ate animal products of any kind — eggs, meat, or chicken — were the most likely to take the trade.

“So, the ones who need it were attracted to it.”

So that’s a hopeful sign.

Two ears where some kernels received C1 from both parents, some from one parent and some from none. In a whole field full of C1 homozygotes, almost the kernels would be dark purple/black. Image courtesy of MaizeGDB and MG Neuffer

As I was proofing this post today, one other thing occurred to me. If the objection to yellow corn is primarily based on the color (let’s leave aside the issue of flavor for a moment), wouldn’t the simplest solution for the biofortified corn be to breed in an allele like C1 that turns corn kernels purple/black? There’d be absolutely no chance of the corn being mistaken for normal yellow corn, and since C1 acts on the production of anthocyanins, a completely different kind of plant pigments, it shouldn’t impact the level of beta carotene in the biofortified corn. Please point out in the comments if I’ve missed something obvious.

*This isn’t to say the food aid itself is unpopular, only that people prefer not to eat corn that resembles it when they’re NOT starving.

**A dish made of boiled corn meal, see photo below. A few years ago my mother discovered a lasagna recipe that substituted well cooked polenta for lasagna nuddles. About which, all I can say is that if you otherwise couldn’t eat lasagna (for example people who avoid eating gluten found in grains like wheat, barley, and rye by choice or necessity), polenta lasagna is a lot better than no lasagna at all.

Polenta. photo: Marilyn M., flickr (click to see photo in its original context)

***The amazing genetic diversity of maize also means these varietes can be produced without the need for genetic engineering. Which means getting the seeds to those would could most benefit from them would be faster and cheaper than something like golden rice which governments will hopefully approve someday.

****Harjes, C.E., Rocheford, T.R., Bai, L., Brutnell, T.P., Kandianis, C.B., Sowinski, S.G., Stapleton, A.E., Vallabhaneni, R., Williams, M., Wurtzel, E.T., Yan, J.B. and Buckler, E.S. (2008). Natural genetic variation in lycopene epsilon cyclase tapped for maize biofortification. Science DOI: 10.1126/science.1150255

****It occurs to me one factor in whether the distinction between yellow and orange is important may turn out to be whether different local languages contain a word for orange. Languages have been studied that contain as few as two words for colors (roughly: dark and light) and a color name describing orange is almost never found in languages with less than 7 color names. … sorry a distribution requirements class that I had to take in college just became arguable relevant. This is exciting!

Hear one of the lead authors of the maize genome paper explain how and why it was done in under four minutes.

Reviewing the quality of the genome sequence itself.

We can already see research made possible by the maize genome.

How maize fits in the family tree of grasses/grains

Read about how the maize genome project is helping researchers find more genes selected for during the domestication of maize.

Plants have more genes than people, why is this still news

Other people on the web react to the maize genome (also why different colors of corn are not different species)

The plant in question is studied internationally and while in America “corn” means those cool looking plants that you see me standing in front of one third of the time when you visit this blog, in british english the same word means any grain. I’ve never heard it explicitly said, but I assume the reason the geneticists who study the plant originally called it maize was to avoid confusion from those mixed definitions. It’s also possible “corn” was still considered a slang term back then, and not the sort of name a well educated scientist should be using regardless.

As a result of growing up in the midwest surrounded by corn and getting interested in comparative genomics by way of maize genetics, terms like “corn geneticist” and “corn genome” don’t sound right to my ear and ones like “maize plant” or “maize is selling for $5 a bushel” sound even worse. On the other hand, the sentence “Sequencing the maize genome is going to provide even more powerful tools to corn breeders” sounds fine, but I realize it can be confusing to people whose life experiences are different from my own.*

*An even weirder one: Back when I was still doing science that required writing with pen and paper instead of doing everything on the computer, without thinking about it I’d either cross my sevens or not depending on whether I was writing a number in a scientific context.

A crossed 7.

Theoretically a crossed 7 is easier to distinguish from a 1, especially on tassel bags and row stakes that are going to be outside, exposed to the elements for months. (And where a mistake has the potential to ruin a year or years of work. It’s not like maize geneticists can run down to Walmart and buy more seeds carrying the genotypes they’ve spent years putting together.)

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