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Welcome to transposon week here at James and the Giant Corn!

I’m just about wrapped up with the big project I’ve been working on recently. Hope to be able to say more about it in the not-too-distant future. Having to be secretive in science sucks.

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: (more…)

BBC on drought tolerant maize/corn

There’s a new episode of BBC’s Discovery: Feeling the World out this morning. It’s only 26 minutes long, and the full piece is definitely worth a listen, but if you don’t have 26 minutes, the meat of the post can be summarized in 8 minutes:

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: (more…)

The two genomes of maize

I recently go back from the maize meeting. I mentioned before that big part of the reason to do poster presentations is to get comfortable discussing ones research with people who haven’t specialized in the exact same subject. In my case, my poster got a fair bit of interest which was great. (Although I was surprised which parts people were most interested in.) But there were also a couple of concepts I had a lot of trouble getting across.

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? (more…)

Wow!

Who could have predicted maize geneticists would be so interested in maize genes? The entry I posted last night on Purple plant1 and Colored aleurone1 easily received more traffic in its first day on the site (it’s still got a long way to go before it catches long term readership attractors like water chestnuts and the NIPGR tomatoes), than any entry since the heady days of the maize genome release back in November.

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!

Two classical maize genes, synteny, and the mystery of the missing gene

Colored aleurone1 and Purple plant1 are both genes with long histories in maize research and are involved in the regulation of anthocyanin biosynthesis.The mutant version of purple plant1 does exactly what it sounds like. (In the proper genetic background) it has plants producing anthocyanin (a purple plant pigment) everywhere, resulting in purple plants. The mutant form of colored aleurone1 was identified from a mutant that changed the color of individual corn kernels. Guess which of these two classic maize mutants made it into the top 15 most published on genes in maize, and which fell barely short.

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…)

The Most Studied Genes of Maize (and why we love kernel phenotypes)

Unique citations determined from papered linked to from MaizeGDB gene locus pages. Images of c1 and y1 segregating years by Gerald Neuffer and made available through MaizeGDB.

* = 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.

How many maize/corn genes have actually been studied? (Not a lot)

When the maize genome paper came out last November (see the summary of this blog’s maize day coverage) it included information on 32,690 genes within the maize genome.  These were the genes which the researchers involved in sequencing the genome were very confident really were genes. And by themselves those 30,000+ genes put the maize genome way ahead of our own. Of course EVERY plant genome ever sequenced has contained more genes than we do, so you’d think by now this wouldn’t be news any more. We’re not the most genetically complex creatures on the planet, and we’ll just have to learn to live with that fact.

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

How to Give an Interesting Research Talk?

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: (more…)

By The Numbers 12/19/09

In no way should any of the following statistics be taken as a dig against the people who study wheat. Wheat breeders have done so much with far few resources than have been invested in maize (corn) breeding. Ya’ll are amazing.
  • 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.

Summary of the Coverage of the Maize Genome here at J+TGC

Summarizing a couple of Virginia Walbot’s ten reasons you should care about the maize genome

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)