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

November 23, 2009

The Domestication of Maize

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)

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. (more…)

November 21, 2009

Of course plants are more genetically complex!

Filed under: biology,Genetics,Plants — Tags: , , , — James @ 4:12 pm

Let’s remember back to a time before the human genome project published it’s first draft assembly in 2001. The genome of C. elegans a tiny nematode had already been published with ~20,000 genes. The C. elegans genome is one 1/30 the size of the human genome and the tiny worms are so small that biologists have mapped the developmental fate of every single cell in their bodies (an adult C. elegans has exactly 959 or 1031 cells depending on gender), whereas the human body contains tens of trillions. How many genes would you guess humans have?

Estimates at the time ranged from 40,000 to 150,000 genes. (more…)

November 20, 2009

Bloggers on the Maize Genome

Filed under: Genetics,Link Posts,Plants — Tags: , , , , — James @ 3:31 pm

Update: PolITiGenomics just posted a piece on the corn genome as well.

You know I could keep talking about the maize genome all day (and I may very well do just that), but what are other bloggers saying about the most complicated plant genome ever published, of second most important single species for feeding people around the world? (Clearly I’m not at all excited) (more…)

Maize: The Genome Sequence Itself

Filed under: biology,Genetics,Plants — Tags: , , , , — James @ 1:45 pm

The corn genome is ~2.4 gigabases (2.4 billion As, Ts, Cs, and Gs) divided among ten chromosomes. The genome of sorghum, the most closely related species with a sequences genome to maize, is also divided into ten chromosomes, but it’s only less than 800 megabases long, approximately a third the size of maize.

What accounts for the size different? Well since their divergence, maize went through a whole genome duplication, doubling it’s genome to twenty chromosomes (which have since been reduced to ten again, as pieces of chromosomes broke apart and stuck to each other*). Since then a bunch of deletions have also occurred, so only sometimes like 20-30% of the genes from the ancestor of maize and sorghum can still be found in both duplicated regions. Clearly the genome duplication of maize is not responsibly (or at least not solely responsible) for the the enormous size of the maize genome. (more…)

About the Maize Genome Paper

Filed under: biology,Genetics,research stories — Tags: , , , — James @ 11:23 am

Looking at the maize genome paper in isolation it’d be easy to wonder what all the fuss was about. The paper itself is only four pages long with (plus a page of citations), with two figures, and as awesome as figure 1 is (and it really is very, VERY awesome), it doesn’t seem like an lot for a project that represents the work of more than 150 authors over four years. But the real fruits of the maize genome project are the sequences that can be found on either maizesequence.org or maizegdb.org and additional exciting research it is already enabling. And as the result of a quirk the way genome sequence is released to the research community, we can already get a sense of some of that other research. (more…)

The Family Tree Of Corn

Branches not to scale. Tree designed in Mesquite.

Branches lengths not remotely to scale. Tree designed in Mesquite.

This family tree shows the relationship of a few of the species in the grass family tree that I think people might be most familiar with. Genomes that were published before today are marked in green (there were only two, sorghum and rice), the maize genome which was just published today is marked in yellow, and brachypodium (which you shouldn’t feel at ALL bad if you haven’t heard of) is marked in grey as its genome project is in the final stages (a draft assembly was released to the public last winter) so it’ll probably be the next grass genome to be published. After that I’m less sure, I know there’s a foxtail millet genome project, but I don’t have any idea how far along the process of genome sequencing, assembly and annotation the genome project is.
What’s important to know about the relationship of the sequenced grasses? (more…)

Patrick Schnable on the Maize Genome

Filed under: Genetics,Plants — Tags: , , , , — James @ 1:25 am

Let me know if you have any trouble with the embedded video. The embedding code from ISU doesn’t seem to play well with wordpress.

I’ve got several posts on the maize genome coming out scheduled to go up later today. Living on the west coast (not to mention having a circadian clock that seems convinced I should actually be living on Honolulu time) it’s the only way to get information up in time for morning readers in most of the US.

Anyway, hopefully some of what I’ve written makes sense (I’ll be running a lot of long computational jobs at work so I’ll have plenty of time to answer questions in the comment sections about all the stuff I’ve written that doubtless makes no sense at all). But to start us off this morning, how about a short (<4 minutes) video from Patrick Schnable one of the two lead authors on the maize genome paper. After four years of talking about the corn genome project as well as it’s challenges and benefits, one gets very good at it.*

[flowplayer src=http://www.ag.iastate.edu/video/media/52/Sequencing_the_Maize_Genome.mp4]

See the video in it’s original context here. I’m assuming since ISU provides embedding code they’re ok with me showing it here.

*Fair disclosure, there are important reasons I may be biased in my evaluation.

November 19, 2009

Corn Genome

Filed under: biology,Genetics — Tags: , , — James @ 3:25 pm

So I was mixed up and didn’t think this could be publically mentioned until tomorrow, but the finalized corn genome has come out. Edited this link to point to the ISU coverage which seems to be more detailed than the release from Wash U. If Wash U can mention it, so can I. Expect tomorrow to be a day of corn here at Jamesandthegiantcorn (though it would have been more fun if I could had started the day of corn before this news was publically announced.)

Lots of corn … and maybe some genomics. Consider yourselves forwarned!

November 16, 2009

Not Genetically Engineered: Domestic Cat

Filed under: Genetics — Tags: , , — James @ 5:29 pm

A non-transgenic cat. But then, so are all cats

A non-transgenic cat. But then, so are all cats so it wasn't a hard picture to find

Scientific Name: Felis silvestris ssp catus

Claimed Genetically Engineered Trait: Does not provoke allergic reactions (hypoallergenic)

The Reality: A company called Allerca used high thru-put screening to check lots and lots of cats to find one with a  broken copy of the gene that codes for one of the proteins people who are allergic to cats are most likely to react to.* After that they, presumably, used marker assisted breeding to introgress the broken gene copy into other cats, which they now sell for between $6,950 and $22,000.**

About Cats:

Siamese cat between two cool looking computers. Photo: Brian Landis, Flickr (click photo to view photostream)

Siamese cat between two cool looking computers. Photo: Brian Landis, Flickr (click photo to view photostream)

All of the felines in the world today shared a common ancestor between 10-15 million years ago. That’s comparable to the estimates of the most common ancestor of corn and sorghum two species of a plant that look much more similar than the house cat and the puma.

Cats with dark heads, tails, and legs (pattern associated with siamese cats) carry a mutant copy of a gene involved in the production of pigment. The gene can function normally, but only at slightly lower temperatures, and a cat’s extremities are generally bit cooler than its body. The coats of such cats will darken if they spend a lot of time outside during the winter, or, if you really wanted, you might be able to turn a siamese cat entirely white by keeping it in a sauna for months, though I’m not endorsing any attempt to verify that. (more…)

November 11, 2009

Genetically Engineered Crop: Blue Carnations

Filed under: Crop Profiles,Genetics,Plants — Tags: , , , , — James @ 2:08 am

Florigene's Moondust carnations, one of several violet and blue varieties they've created with genetic engineering. Photo by Pagemoral and licensed under the creative commons. Click to see the photo in its original context with license information

Florigene's Moondust carnations, one of several violet and blue varieties they've created with genetic engineering. Photo by Pagemoral and licensed under the creative commons. Click to see the photo in its original context with license information

Scientific Name: Dianthus caryophyllus

Genetically Engineered Trait: Anthocyanin biosynthesis (blue and violet plant pigments)

Details of Genetic Engineering:

The market in flowers with genetically engineered colors is (to my knowledge) occupied by a single Australian company called Florigene. They study anthocyanins, the class of plant pigments responsible for, among other things, the coloration of purple potatoes, purple carrots, black rice, purple corn, and many blue and purple berries. Anthocyanins are one of the key classes of plant pigments, found to greater or lesser extent in most flowering plants.* Florigene has been producing purple and sometimes blue carnations since the 1990s by adding key enzymes in the anthocyanin pathway from other plant species. While purple carnations are cool, the real goal of Florigene’s work has been blue (and purple, and violet) roses, something rose breeders have been trying and failing to create for centuries.

Florigene was granted a license to grow their first breed of genetically engineered blue rose this summer, (although as far as I can tell the roses aren’t yet for sale, so they don’t get their own post). For more on plant pigments, Florigene, and why the development of blue roses as foiled breeders for so long, check out this fascinating post by MAT Kinase.

Purple potatoes with orange carrots (and did you know most carrots where white when they were first domesticated?)

Purple potatoes with orange carrots (and did you know most carrots were white when they were first domesticated?)

About Carnations:

Carnations belong to the caryophyllales, an extended family of plants that include cacti (cool), rhubarb (tasty), and carnivorous plants like sundews and venus fly traps(awesome!). Beyond that, I’ll admit I don’t know much about their biology.

If you know someone who is into flower meanings (I used to date a girl who was), you’ll notice there is no definition on record for blue carnations. It makes them the perfect gift to say, “I like you, so I bought you flowers” without having to worry about any unintentional subtext beside: “I’m also a huge plant/genetics geek, and if you don’t ask me soon how they make the flowers blue I’m going to burst!”

*The extent of anthocyanin biosynthesis in flowering plants is a good indicator that the ancestor of all the flowering plants alive today (which lived sometime between 250 and 100 million years ago) already contained the genes needed to produce anthocyanins, and flowering plants which are unable to produce them today, like roses, cannot because their ancestors lost the ability.

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