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

January 14, 2010

The Newly Published Soybean Genome and Fractionation

Here’s the key statistic: The maize genome paper estimated that roughly a quarter of maize genes are currently retained as duplicate pairs from maize’s whole genome duplication, while the soybean paper estimates just over half of soybean genes are similarly retained after soybean’s (apparently slightly older) duplication. <– had it buried at the end of this, but figured it’d be more fun to start out with something cool.

But first of all, let’s do this the right way this time. Here’s the paper in Nature describing the soybean genome. Here’s one of the places you can download the entire sequence from. Hopefully that establishes, beyond a reasonable doubt, that the soybean genome has, in fact, been published. (more…)

January 12, 2010

Strawberry Genome Sequenced (Correction included)

Filed under: biology,Genetics,Plants — Tags: , — James @ 3:10 pm

After already needing to correct this post, I must now invalidate the whole thing. Seems I’ve been taken in by a premature press release that was turned into reliable sounding articles on news sites and was then picked up by blogs like mine that took the those sites to be credible sources. It’s a big mess. ::sigh::

Among the many things I’m currently missing at the Plant and Animal Genome conference, in addition to an update on the banana genome I’ve just learned (thanks to Mary over at OpenHelix) that the sequencing of the woodland strawberry genome has been completed!

I don’t know yet if the sequence has been released to the public yet. Either way I can’t find the sequence so I can’t yet comment on the quality of the sequence, or any ancient duplications in the lineage (though we already know it must share the ancient hexaploidy of the rosids, possible all eudicots).

Wild diploid strawberry (left) and domesticated octoploid strawberry (right)

What we do know is that modern domesticated strawberries are octoploid, the result of two recent whole genome duplications, but the woodland strawberry doesn’t have any duplications modern enough to be obvious from cytogenetics, visually looking at chromosomes.

Sequencing a genome is a complicated process but it started out with the work of Janet Slovin, a USDA scientist who created the inbred line* used in sequencing and seems to be the front woman from the project (Janet was kind enough to comment and point out the original article was misleading on this point, check out the link she included as well!), she’s quoted in the linked article.
And if you know how I can get my hands on the sequence please PLEASE, drop me a line at jcs98 (at) jamesandthegiantcorn (dot) com.

January 9, 2010

Pumpernickel and Rye and Vavilovian Mimicry

Filed under: Crop Profiles,food,Plants — Tags: , , , — James @ 3:24 pm

Delicious pumpernickel bagel.

Its tasty but what is it? First, a disclaimer. I’m going to be discussing traditional pumpernickel bread. The kind pictured to the right is almost certainly modern pumpernickel which gets its color from dark substances like molasses or cocoa powder, and often is made with wheat flower rather than the traditional rye. But that’s a boring story. This one is more exciting!

(more…)

January 6, 2010

Biodiversity and Genetic Engineering Aren’t Mutually Exclusive!

Filed under: Feeding the world,Plants — Tags: , , , — James @ 8:28 pm

The work of plant breeders and the naturalists who catalog so much of the genetic diversity passed down over 400 generations*, have done far more to feed people than genetic engineering thus far. The reason I spend so much time talking about genetic engineering (and to a lesser extent mutation breeding) isn’t because I think the techniques are more important than breeding using the existing diversity of crop plants and their wild ancestors, it’s because genetic engineering (and once more to a lesser extent mutation breeding) are the techniques that are subject to the most misinformation and opposition. If I had to choose, for the entire world, between marker assisted selection and genetic engineering, I’d choose marker assisted selection in a heartbeat. But we don’t have to chose.

Consider three cases: (more…)

December 30, 2009

Why I’m so Excited About the Banana Genome

Filed under: biology,evolution,Genetics,Plants — Tags: , , , , — James @ 12:01 pm

The single most consumed fruit in America, yet in the tropics this bananas starchy relatives play an even more vital role in feeding whole nations.

At the Plant and Animal Genome Conference next month (which I really wish I was going to), there will be a workshop on banana genomics, but from the abstract submitted by Carine Charron (h/t to Jeremy at the Agricultural Biodiversity Weblog) I learned that:

The sequencing phase will be completed in early 2010 and automatic annotation will take place during the first semester of 2010.

Why is sequencing the banana genome important? Three reasons: (more…)

December 28, 2009

Not Genetically Engineered: Square Watermelons

Filed under: food,Plants — Tags: , , — James @ 4:28 am

Square watermelon. Photo: laughlin, flickr (click photo to see in original context)

This is an addendum to my previous post: Not Genetically Engineered: Watermelons

At the time I thought the only awesome thing about watermelons that people calling genetic engineering was seedlessness. It turns out there are also square watermelons. Are they genetically engineered? I guess my title does kind of give away the answer.

Square watermelons aren’t the product of genetic engineering, or radiation mutagenesis, nor even conventional breeding. (more…)

December 26, 2009

Name That Plant: Nondescript Root Edition

Filed under: Photo Posts,Plants — Tags: — James @ 4:31 am

Do you have any idea how long it’s been since we’ve had a name that plant post? The last one was almost a year ago on January 11th. So rather than let the tradition go a year untouched, this is an special edition of Name… that… Plant!

Can you name this root vegetable?

If you guess it correctly (and I’ve no idea if this one will be hard or easy but prior experience suggests someone will know within the first couple of comments, though on this other hand this isn’t a great picture) I’ll let you know as soon as I see the comment. If no one gets it by new year’s eve I’ll update again with the answer (and a better picture that gives it away).

This is what my part of California looked like on the Monday before Christmas! Glad I'm celebrating the holidays somewhere with snow.

December 25, 2009

Merry Christmas

Filed under: Photo Posts,Plants — Tags: , , — James @ 5:24 am

I hope everyone is having a great holiday (even if you don’t celebrate Christmas, if you live in the US it’s hard to get much work done today).

Right before I left town to celebrate the holidays with my folks, my zygocactus decided to flower for the first time ever*. I guess it really is a christmas cactus!

Christmas cactus in bloom!

Wishing all a safe and happy holiday!

*Well since it’s been a free living plant. As previously mentioned, the plant goes back at least four human generations propagated by cuttings.

December 12, 2009

The Water Chestnut

Filed under: Crop Profiles,food,Plants — Tags: — James @ 7:45 pm
Botanical illustration of Eleocharis dulcis, the Water Chestnut

Botanical illustration of Eleocharis dulcis, the Water Chestnut

The water chestnut is one of those foods I’ve eaten my whole life without knowing anything more about it than flavor and appearance (and that only because it so often shows up in frozen vegetable mixes).

The scientific name for the Water Chestnut is Eleocharis dulcis, and it’s often classified as a sedge.* It’s also a quite awesome plant. Consider:

  • The visible parts of a water chestnut plant are leafless stems that perform photosynthesis. (The water chestnut has almost completely abandoned leaves!)
  • The edible part of the plant is a botanical structure called a corm** which is a modified underground stem used by a plant to store energy (water chestnut plants are very much about stems). Not to be confused with bulbs like those of onions and garlic, which can look similar, but are instead made up mostly of leaves
  • The reason water chestnuts remain so crunchy after cooking is that their cell walls are reinforced by special phenolic compounds, the same class of molecules as capsaicin, the molecule that makes chilli peppers spicy.

The genus Eleocharis also contains species like Eleocharis vivapara which switch between C3 and C4 forms of photosynthesis depending on whether they’re grown on dry land or in swamps. The relative advantages and costs of these two different forms of photosynthesis are worth a post on their own, but I’d always assumed it was an either/or choice and didn’t realize ANY plant species could pick to use whichever system was best suited to the local environment.[citation]

Domestication: (more…)

December 8, 2009

My Zygocactus is Getting Ready to Bloom

Filed under: Photo Posts,Plants — Tags: , , — James @ 11:51 am

Some background: as an exciting and awesome plant scientist as myself might be expected to maintain a wide range of plants around the house. Instead I have exactly one*, a Christmas Cactus that’s been clonally** in my family for four generations (human generations, my Christmas Cactus is only a third generation plant).

My Christmas Cactus is not happy. At my old apartment I had it on the kitchen table, where…someone… had an accident involving it and a pressure cooker. Right after we moved I left it on a windowsill with the window open and the blinds (blowing in the wind) cut into it even more. On top of all that, the new place offers only north facing windows***.

So needless to say I wasn’t expecting so much as a single flower given everything it’s been through. Which is why I was so surprised when I went to water it and discovered…

Christmas Cactus blooming... also a sample of the less than thrilling view out my bedroom window.

Christmas Cactus blooming... also a sample of the less than thrilling view out my bedroom window.

Before I rotated the plant, those two branch tips were pressed right against the window, which makes me think something like a vernalization response (temperature dependent) is involved in signaling to a Christmas Cactus that it’s time to flower. There are buds on many of the rest of the branches, but they’re still tiny.

Thanks to Mr. Subjunctive for introducing me to the name Zygocactus, even if it was in a post about how he was giving up on the (awesome sounding) name in favor of Schlumbergera.

I also want to name-drop Liza of Good to Grow. My plan is to continue following her site and use it as inspiration to increase my plant collection so by next year my Christmas Cactus won’t be so alone.

*This is what happens when you’ve moved into a new place six times times in the past six years, plus two moves of ~1000 and ~3000 miles respectively.

**The easiest way to make new Christmas cactuses is to break off several of the segments that make up one of it’s branches, put them in water to root and then plant the new plant in soil. Since the new plant is genetically identical to the old (after all it grew from a PIECE of the old plant), in other words it’s a clone. Cloning plants is much easier than cloning animals…

***When it warms up I’m planning a commando raid to sneak the poor plant onto my roommate’s balcony for a bit more sun.

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