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…)

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

Why should you be excited about the corn genome?

Filed under: food,Plants,research stories — Tags: , , — James @ 5:36 pm

Virginia Walbot has ten reasons in the latest issue of PLOS genetics. PLOS journals are all open access so anyone can read it without a subscription.

The two reasons I think will be the most interesting to non-biologists are #1 and #10:

Corn was domesticated a short 10,000 years ago and domestication is normally a huge genetic bottleneck that results in the loss of much of the gene diversity found in the wild ancestor. (Modern tomatoes are more diverse than heirlooms because breeders are intentionally working to bring some of that diversity back over.) Yet two lines of corn, which certainly shared many common ancestors in the last 10,000 years, contain more genetic differences than humans and chimpanzees which have been evolving separately for 3.5 MILLION years. That’s 10,000 years vs 3,500,000 years!

Number ten drives home how essential corn is to the world today with statistics like American farmers growing so much corn last year than it works out to a metric ton for every man, woman, and child in this country. Or that corn and cornfeed animals feed a billion people around the globe (those aren’t rice numbers, but hopefully it drives home why corn has definitely earned it’s place as one of the big three grains that support civilization around the world).

h/t to the beekeeper (who I haven’t see around the blog in months) for pointing me at this PLOS genetics coverage of the maize genome papers coming out both there and in Science.

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 12, 2009

Hawaiian Pineapples and the Seed Industry

Filed under: agriculture,Fun With Numbers — Tags: , , , — James @ 2:37 pm
Pineapple. Wish I'd thought to check for a country of origin...

Pineapple. Wish I'd thought to check for a country of origin...

Since today seems to have a tropical theme, here’s another post about Hawaii:

The corn breeding industry is expanding in Hawaii*. The pineapple industry is contracting. People seem to be blaming the second on the first, and are passing this article around. My reading of the article, and some other statistics I looked, don’t seem to agree with the story line (evil GMO seed companies driving out the pineapple industry) that people seem to be suggesting.

Yes, Monsanto did buy out one of Hawaii’s three remaining large pineapple growers several years ago (as of 2007 there were also 49 small pineapple producers growing pineapples on 1-15 acres and a single medium sized grower with between 100-250 acres), but Maui Land & Pineapple Co., the company this article talks about, isn’t selling out to a seed company, they’re switching to the production of other crops instead of pineapples. One company sells its land and shuts down, another stays in the farming business but gives up on pineapples and announced plans to grow a more diverse range of crops. To me, that suggests it is becoming harder and harder to make a profit growing pineapples in Hawaii. (more…)

November 8, 2009

Biological Control of Western Corn Rootworms

Filed under: agriculture,biology,Genetics,Plants — Tags: , , , , — James @ 8:52 pm
Face of the Enemy: Adult Western Corn Rootworm chewing on the silks of a corn ear. Picture from wikimedia, apparently in the public domain

Face of the Enemy: Adult Western Corn Rootworm chewing on the silks of a corn ear. Picture from wikimedia, apparently in the public domain

This post discusses the paper Degenhardt, J et al. (2009) “Restoring a maize root signal that attracts insect-killing nematodes to control a major pest”

The Western Corn Rootworm (which as you can see from the picture to the right are not actually worms) is estimated to cost farmers in the US alone one billion dollars a year in lost yield and pest control measures. The newly hatched larva begin feeding on root hairs and as they get bigger start attacking the main roots of a corn plant. The damage to the roots from the feeding itself is exacerbated by the open wounds becoming infected. The loss of roots both stresses the plant and reduces yield by decreasing the plant’s supply of nutrients and water, but also makes it much more vulnerable to lodging (getting blown down by a gust of wind). Oh, and did I mention the adults like to feed on the corn plant’s reproductive tissues, decreasing yield even further?

Rootworms are one of the pests controlled by plants genetically engineered to express BT a protein taken from organic agriculture. Without it, the 1 billion dollar price tag for rootworm damage and control would be even higher. But this isn’t an article about bt, it’s an article about how some corn already knows how to call for help when rootworms attack.

Rootworm larva may feast on the roots of maize, but they are in turn eaten by some species of nematodes.* And it turns out some kinds of corn know how to attract nematodes, and when they’re under attack by rootworms they do just that. The nematodes get a delicious meal of rootworms and the corn plant gets to keep more of its roots intact.

How do corn plants attract their, unintentional, nematode defenders? (more…)

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