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

February 26, 2010

One MORE reason pineapples are awesome

Filed under: Uncategorized — Tags: — James @ 10:00 am

Pineapple plant. photo: CameliaTWU, flickr (click photo to see in original context)

Pineapples use CAM photosynthesis. Normally plants have to open tiny holes in their leaves (called stomata) during the day to let in carbon dioxide that they use during photosynthesis. The problem they face is that when they’re letting carbon-dioxide in, plants also let water out.

CAM plants get around this water loss by collecting all their carbon dioxide at night (when it’s not as hot so they lose less water when they open their stomata) and storing it within their leaves until they need it during the day. This allows them to be much more efficient with water than normal plants (ones carry out plain old vanilla C3 photosynthesis.*)

Why do pineapple plants need to be so frugal when it comes to water? The fact that pineapples are native to paraguay and southern brazil is repeated across the internet, but as you can imagine, that description covers a wide range of climates and habitats some of which are much drier than others. Clearly more research on the subject is called for on my part.

The fact that pineapples do CAM photosynthesis came up in a discussion with another guy in my lab where we discussed the fact that pineapples would make an excellent comparison for grass genomes** and have a reasonably small genome at ~500 megabases***, half the size of the recently published soybean and sorghum genomes and less than a quarter the size of the maize genome.

With all these new third generation sequencing technologies coming out in 2010, hopefully someone will sequence the pineapple genome. If not, maybe the cost of sequencing will drop enough while I’m in grad school that I can sequence the genome myself ( a guy can dream).

For more on my long running admiration for pineapple (second only to my appreciation of corn itself):

Why Pineapples are Awesome.

Phylogeny of Pineapple, an further explanation of awesomeness.

*Let the record reflect that corn does C4 photosynthesis, which another awesome variation on the standard system of photosynthesis.

**In addition to both pineapple ¬†and grasses being monocots, they’re in the same order of plants, Poales, as grasses. The first non-grass monocot to be sequenced will almost certainly be the banana (in fact the process as already begun), but while bananas are monocots they belong to a different order¬†Zingiberales (which includes spice plants like ginger, cardamom, and tumeric).

***526 Megabases as cited in Patterson AH, Freeling M, Sasaki, T “Grains of Knowledge” Genome Research 10.1101/gr.3725905

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…)

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