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

December 7, 2009

To Accomplish the Impossible

Filed under: Plants,Politics — James @ 8:52 am

Here’s an inspirational quote about science:

“It was believed impossible to create a blue rose, since roses lack the gene to produce the color blue. However, a Japanese company spent 14 years in research and finally succeeded in developing the world’s first blue rose. I explained to President Obama how this blue rose, which holds the meaning ‘to accomplish the impossible,’ was created and said, ‘Let us work together to accomplish the impossible.’”

-Japanese Prime Minister Yukio Hatoyama as quoted here (and boy will I feel silly if the whole story is a hoax)

“To accomplish the impossible”. When it comes to assigning meanings to flowers (as well as picking life goals), I’d call that a pretty good one.

The blue rose was actually developed by an Australian company called Florigene which has been acquired by a Japanese company called Suntory. I went into more detail about Florigene’s products here.

December 2, 2009

Edible Cottonseed

Filed under: agriculture,Feeding the world,Plants — Tags: , , — James @ 1:26 am
Cotton and cotton seeds photo credit: Gonzalez's tongue, Flickr (click to see photo in it's original context)

Cotton and cotton seeds photo credit: Gonzalez's tongue, Flickr (click to see photo in it's original context)

Over 102 million bales of cotton (more than 24 million tons of cotton) were grown around the world last year. I wouldn’t surprise me to hear cotton called the single most important (and widely cultivated) food crop on the face of the planet. But does it have to be a non-food crop?

Clearly no one (nor any livestock) wants to eat the cotton fibers themselves, but they aren’t the only product of the plant. After to cotton plant flowers, the cotton fibers grow around the developing seeds. The combined mixture is harvested each year, after which the seeds are removed from the cotton fibers before the cotton is baled and sold.*

The seeds of the cotton plant are full of protein and oils and since cotton is already grown as a source of fiber (and the seeds are even harvested and sorted out of the cotton fibers already) adding them to the food supply** doesn’t require any further land to be cultivated or increased input costs. Obviously there is a catch… (more…)

November 26, 2009

Rainbow of Carrots!

Filed under: Photo Posts,Plants — Tags: , — James @ 1:11 am

Carrots ranging from yellow to almost black:

Carrots from pale yellow to black

At least five distinct colors: yellow, light orange, orange, purple, and near black

Still missing  dark red lycopene containing carrots, but it’s a wonderful range of colors. And there’s something different about the purple and black carrots. Check it out:

Yellow, orange, and purple carrots. Chopped onions too.

Yellow, orange, and purple carrots. Chopped onions too.

Notice how the purple carrots are still white in the centers? I want to know more about why!

November 23, 2009

The Domestication of Maize

Filed under: agriculture,biology,Genetics,Plants — Tags: , , , , , , , , — James @ 7:36 am

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…)

Transmitting DNA sequences to the stars

Filed under: Link Posts,Plants — Tags: , , — James @ 1:58 am

It’s a gloriously non-sensical project. To mark the 35th anniversary of the Drake-Sagan transmission, a guy named Joe Davis flew down to Puerto Rico and used the Arecibo radio telescope* to transmit the genetic sequence that encodes for the protein rubisco** to three nearby stars. While covering some awesomeness (using the most powerful radio transmitter on the planet to broadcast signals into space from an iPhone), and some criticisms (what is a DNA sequence going to mean to extra terrestrial life that almost certainly won’t contain DNA and absolutely wouldn’t use the same sequences to encode for the same amino acids), the author left one key question unanswered. Which plant’s rubisco sequence was shouted out to the cosmos?

Fortunately he posted the sequence here, and using BLAST it was easy to identify the gene as belonging to Nicotiana tabacum. The tobacco plant. Seriously? The gene that encodes for the rubisco protein is one of the more widely sequenced plant genes out there, as differences in the sequence are often used to study the relatedness of different plant species. He could pick from the sequences of organisms ranging from coconut to corn, from ferns to redwoods and the most worthy plant that came to mind was tobacco?

Oh well.

*Another awesome bit of science operated by Cornell

**Rubisco is the plant protein that plants use to grab CO2 molecules out of the air to turn into sugars. Providing us with both clean air and food to eat. It’s actually not very good at its job, which is why plants have to make so much of it. So much, in fact, that it truly is the single most abundant protein on the planet.

C4 plants like corn, sorghum, and sugar cane have actually redesigned their leaves and the way they do photosynthesis to get around the failings of rubisco.

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…)

The Family Tree Of Corn

Filed under: Genetics,Plants,research stories — Tags: , , , , , , — James @ 9:27 am
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.

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