But there’s a lot of be happy about! I’m done teaching for a long time. As much as I enjoyed working with the kids in my class, the other responsibilities of teaching (grading, sitting through lectures without the chance to break in for the discussions and arguments that make academia so fun, grading, designing assignments, grading) were really starting to wear me down.

And I’m only three weeks (June 22nd) from either passing my qualifying exam or becoming a beaten and broken shell of a man. For three hours four professors will question me on everything I’ve learned (or should have learned but didn’t) in my education up to this point, and everything I propose to spend the next few years of my life doing. This may not sound like a good thing, but it is. Because my qualifying exam has been hanging over my head all semester,

The lab has a new paper in press, having run the sequential gauntlets of Peer Review, Editorial Evaluation, and finally (and perhaps most dreaded) Your-Figures-Aren’t-High-Resolution-Enough e-mails from the journal’s publication department. But more on the details of that whenever the paper actually shows up.

But what was the point of this entry again? Oh yeah. Transposons. I have a soft spot from transposons (I’m guessing most people who work with maize genetics do). Today we may know that transposons are found in practically every genome under the sun, but they were discovered first in maize using old school genetics (breeding plants together and counting traits in the offspring), before DNA sequencing was a gleam in its inventor’s eye.

And on top of that, some delightfully high-copy number transposons are in the middle of proving a major scientific point for me, so I figured the least I could do was devote a week to them here on the site.

If you’re not a geneticist, should you still care about transposons? Absolutely! Transposons are one of the best arguments, not for why genetic engineering is safe, but for why, if anyone worried about hypothetical unintended consequences of genetic engineering should be worried about any food with DNA in it (and as far as I know, that’s all food.) To paraphrase a seinfield character: “No food for you!”

The week’s schedule:

• Tuesday: An introduction to transposons. Selfish (not junk) DNA.
• Wednesday: Transposon mutagenesis. In which we learn what happens when selfish DNA (transposons) goes head to head with DNA that has learned to cooperate with other DNA to build whole organisms (genes).
• Thursday: Transposons and gene regulation. How tiny transposons are changing the way rice genes respond to stress and where orange cauliflower comes from.
• Friday: Franken-gene! The terrifying (actually awesome) story of a new gene stitched together from pieces of lesser genes by (you guessed it) a transposon!

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.

It’s too late to do me any good at the maize meeting, but I have created the figure I think I needed to explain those ideas. Too late for the maize meeting, but maybe I can squeeze it into my qualifying exam proposal. Or maybe the next time I get a chance to give a talk on campus. Let’s just not get into how much of my morning I spent putting this together, and pretend it was a good investment of my time ok?

Click for full size.

Right after its whole genome duplication, the ancestor of maize had twenty chromosomes. Through rearrangements and fusions that number has since dropped back to ten, but it’s still possible to reconstruct the twenty paleo-chromosomes of maize by comparing the order of genes on the maize chromosomes to order of genes in sorghum, a related species of grass/grain that didn’t experience the same whole genome duplication and whose overall genome probably looks a fair bit like the unduplicated ancestor of maize.

The purple lines represent orthologous genes between maize and sorghum. Notice how you can trace a line of purple all the way from top to bottom for both maize1 and maize2 (except for maybe at the bottom of the maize2-region equivalent to sorghum chromosome 6 this looks like it was actually just a bug in the analysis).

This shows, in the most graphical way I can manage, that the genome of maize is made up of two genome copies, each equivalent to the whole genome of sorghum.

Nevertheless. I, through the power of Python*, have split the maize genome in twain. In those rare moments when the excitement about the actual research I do wanes I can still enjoy the fact that I know how to do dramatic, if not scientifically impressive, things like this.

Caveats:

• That doesn’t mean every single gene in sorghum has two copies in maize. After the duplication, many duplicate genes were lost, but the conserved order of genes remains.
• This is only one possible way of arranging the duplicated chromosomes of maize. I’ve grouped the paleo-chromosomes that have lost fewer genes relative to sorghum into maize 1 and the paleo-chromosomes that have lost more genes relative to sorghum into maize 2. But there’s no proof that’s a biologically relevant way to group them. There are 2^9 possible ways to arrange the pairs of chromosomes, and only one of those will accurately reflect the relationships of the chromosomes in the the original duplicated maize genome.

*As well as CoGe’s SynMap and all the various computational tools incorporated into synmap.

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!

Ears segregating for the colored aleurone mutant phenotype. Image courtesy of MG Neuffer via MaizeGDB.

Purple plant1's phenotype is highly variable depending on the genetic background the mutant is in. Images courtesy of MG Neuffer via MaizeGDB.

The two genes are also duplicates (homeologs) resulting from the maize whole genome duplication. From the picture below you can also see both the two genes and the regions they are in match up to single regions in rice and sorghum, two grasses that haven’t gone though a whole genome duplication since the great radiation of grass species that took place an estimated 50 million years ago (well after dinosaurs stopped walking the earth).

More interesting, at least to me, is the fact that there is NO gene equivalent to colored aleurone1 and purple plant1 in the region we’d expect to find such a gene in Brachypodium (the only other grass species with a sequenced genome)*. From all the genes that line up perfectly on either side we can predict the exact location the gene equivalent to colored aleurone1 and purple plant1 should be found in the Brachypodium genome. But the gene isn’t there…

The GEvo panel shown here can be regenerated at: http://tinyurl.com/yddlwor

The original version of this image had Pl1 mislabeled as C1. This version corrects that error.

For a couple more examples of comparisons between the four sequences grass genomes check out the Cogepedia post I spent this morning pulling together.

*The publication of which I celebrated just a little while ago.

* = 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.

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.

Corngrass1 a dominant mutant that keeps maize from making the transition to adult growth. The stalk of a normal maize plant is shown to the left for comparison. According to George Chuck, in some genetic backgrounds where they never flower, corngrass plants are potentially immortal, as cuttings of the stalk can be transplanted to new soil and simply continue to grow. (Normally corn plants are annuals, they stop growing once the end of their stalk turns into a tassel and eventually die off even if they're grown in temp. controlled greenhouses.) Photo courtesy of MaizeGDB.org

Just got back from a great talk given by George Chuck, who works on microRNAs that control the transitions between the juvinile and adult phases of plant development in maize at the USDA’s Plant Gene Expression Center. In trying to figure out why it was such a great talks (besides the obvious, that he had exciting data to present).

The obvious ones I could spot where:

• History. One of the mutants he was working on, corngrass1, was first discovered in a sweetcorn field before many in the audience had even been born, and he was able to tie the history of the mutant in with the history of the debate about corn’s relationship to teosinte the wild grass from which we now know corn was domesticated.
• Context. Starting out by discussing phase change in model organisms like C. elegans, as well as phase change in humans (more commonly known as puberty) before bringing it back to corn.
• Tiny unexpected things. The one datapoint he presented to suggest the system he’d found in corn might also be functioning in eudicts wasn’t the usual model system for eudicts (Arabidopsis thaliana, the first plant to have its genome sequenced). It was watermelon. “I’ve always wanted a reason to work with watermelons.” It was only the second time I’ve seen any biologic data on watermelons. (The first was the result of a fascinating discussion with my roommate about phloem loading in the cucurbits (a group of species that includes melons, squash, pumpkins and cucumbers).)
• I’m sure there were lots of other things I didn’t even notice. Like housekeeping, it’s what’s left undone or done badly is much easier to notice than what is taken care of perfectly. <– I don’t know how the analogy to housekeeping entered my vocabulary, sounds more like something a person who was alive for the 1950s would use.

Studying plant genetics (and probably a lot of other scientific fields as well) means seeing a lot of presentations that are difficult to follow, even though they’re presenting fascinating data, but it also means seeing the occasion speaker who has mastered both the concepts and methods of his or her field as well the techniques used hook an audience.

This isn’t true just of public speaking. I’ve heard people complain (though I haven’t formed an opinion of my own on the subject), that the papers that get published in Science and Nature, the two most prestigious scientific journals out there, don’t always represent the biggest scientific breakthroughs, but rather great science that’s been done by people who are the best at writing papers accessible and interesting to people not working in the exact same field as the authors. I’m still too unexperienced as a scientist to know if this is a real bias, or just represents bitterness by people whose papers don’t get accepted, but you can see how it would make sense if it were true, can’t you?

Science and Nature are both read by highly educated scientists across a wide range of disciplines. If you and I both make discoveries of equal scientific merit, but my paper is written up in such a way that NO one outside of plant science will be able to make heads or tails of it, and yours has a chance of being read and understood by people working in everything from the phylogenetics of archaea to human medicine, and maybe even get a few anthropologists interested enough to skim the figures, obviously your paper should have a higher priority for being published in journals that reach the widest audiences (like Science and Nature).

It really isn’t fair, but people who can do the research, and then turn around and effectively communicate their results clearly do have an advantage in science. That’s why I’m trying to make notes of what keeps me engaged during the best talks. My one attempt so far to present the results of my own research was an only slightly mitigated disaster.

As just for the record, unless you’ve already decided you want a 100% teaching position, great communication skills are NOT a substitute for actually producing interesting data. They’re complementary goods, not substitutes.

• Year in with the largest wheat harvest in the US: 1981-1982 (2.8 billion bushels)
• Year in with the largest wheat corn harvest in the US: 2007-2008(13 billion bushels)
• The US’s share of global wheat exports in 1973-1974: 50%
• The US’s share of global wheat exports today: 20%
• Percentage increase in yield per acre of wheat 1969-present: 45%
• Percentage increase in yield per acre of corn 1969-present: 90%
• Estimated earliest year a program to develop genetically engineered wheat, launched today, would be able to win regulatory approval for any variety of GM wheat: 2018
• Year in which Monsanto’s patent on their first generation Round-up Ready Soybeans expires: 2014
• Number of lawsuits filed by Monsanto against individual farmers it claims infringed on its seed patents in the past decade: 125 (same source as above)
• Number people threatened with legal action to force a settlement/sued by the RIAA in the same time period: more than 28,000
• Amount the RIAA sued the russian website allofmp3.com for in 2006: $1.65 trillion
• The gross domestic product of India in 2008: $1.2 trillion
• First time the world knew what the far side of the moon looked like: 1959

Check out the article in The Guardian about wheat farming and the future of genetically engineered wheat.

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)