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 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 29, 2009

By The Numbers 12/19/09

Filed under: agriculture,Fun With Numbers,Politics — Tags: , , , , , , — James @ 1:22 am
In no way should any of the following statistics be taken as a dig against the people who study wheat. Wheat breeders have done so much with far few resources than have been invested in maize (corn) breeding. Ya’ll are amazing.
  • Year in with the largest wheat harvest in the US: 1981-1982 (2.8 billion bushels)
  • Year in with the largest wheat corn harvest in the US: 2007-2008(13 billion bushels)
  • The US’s share of global wheat exports in 1973-1974: 50%
  • The US’s share of global wheat exports today: 20%
  • Percentage increase in yield per acre of wheat 1969-present: 45%
  • Percentage increase in yield per acre of corn 1969-present: 90%
  • Estimated earliest year a program to develop genetically engineered wheat, launched today, would be able to win regulatory approval for any variety of GM wheat: 2018
  • Year in which Monsanto’s patent on their first generation Round-up Ready Soybeans expires: 2014
  • Number of lawsuits filed by Monsanto against individual farmers it claims infringed on its seed patents in the past decade: 125 (same source as above)
  • Number people threatened with legal action to force a settlement/sued by the RIAA in the same time period: more than 28,000
  • Amount the RIAA sued the russian website allofmp3.com for in 2006: $1.65 trillion
  • The gross domestic product of India in 2008: $1.2 trillion
  • First time the world knew what the far side of the moon looked like: 1959

Check out the article in The Guardian about wheat farming and the future of genetically engineered wheat.

November 10, 2009

Genetically Engineered Crops: Soybean

Soybean field. Photo: Big Grey Mare, Flickr (click photo to view photostream)

Soybean field. Photo: Big Grey Mare, Flickr (click photo to view photostream)

Scientific Name: Glycine max

Genetically Engineered Traits: Herbicide Resistance

Details of Genetic Engineering:

The genetic engineering of soybeans is pretty similar to that of Canola. Roundup Ready soybeans (produced by Monsanto) have been on the market for some time. The soybeans, which allowed farmers to spray an herbicide that kills all the plants in the field besides the soybeans themselves, have been a huge hit with market shares >90%. The benefit here is that being able to use herbicide resistant soybeans has been linked to increased use of no-till farming.* Bayer CropScience recently received regulatory approval for LibertyLink soybeans, their own herbicide + resistance system. Having another system is good for two reasons:

  1. Competition brings down prices for farmers
  2. Being able to rotate between two different herbicides prolongs the usefulness of both. Even if weeds develop some resistance to glyphosate (the active ingredient Roundup Ready crops are resistant to) the weeds are killed next year when the farmer sprays Glufosinate (the active ingredient that Liberty Link crops are resistant to).

About Soybeans: (more…)

October 28, 2009

I’m disappointed in the Des Moines Register

Filed under: agriculture — Tags: , , , — James @ 10:45 pm

Normally the Des Moines Register is pretty good about getting their facts straight when it comes to crop breeding and genetic engineering. After all of the major newspapers left in this country, their readership is probably the most likely to catch any slip ups.

So I was surprised when reading a story about a small breeder who’d developed soybeans resistant to nematodes to find this:

The seed industry has battled the parasite in the usual way, with genetically modified seeds designed to resist the parasites. As has happened in the age of genetic engineering, the nematodes* gradually evolve to overcome the biotech resistances.

I have no idea where Dan Piller, the author of this piece, got this information. Unlike new media outlets like blogs, newspapers don’t ever have to cite sources, the assumption being that they’re reliable enough to be taken at their word. But I defy the Register in general, Dan Piller in particular, or any of the people already linking to this piece to name a seed company currently selling seed genetically engineered to resist nematodes. It would be a very beneficial trait. When I worked at the Danforth Center, Chris Taylor was studying how nematodes interact with their prey. I’m also told Monsanto recently announced that they have been working on nematode resistance using RNAi (though I couldn’t find any internet sources to back that up). Even so that’s a trait still in development, and this article gives the impression transgenic nematode resistance has already been commercially sold and failed.

That said, nematode resistant soybeans would be a Very Good Thing™ regardless of whether the resistance is the result of transgenes or conventional breeding. Nematodes are a big problem for yield. However, whether the trait is transgenic or non-transgenic, any single resistance trait will eventually be overcome by the continued evolution of whatever organism it is protecting against.  One of my plant breeding instructors in undergrad said that a good resistance allele (talking about conventional breeding, not genetic engineering) is one that protects a crop from a disease or pest for a decade after the trait becomes widely available.

That window can be stretched with proper care. Bt crops that resist against specific insect pests have been on the market for ~15 years and the development of resistant insects has been slowed planting refuges of non-resistant crops.

*Nematodes are microscopic worms that live in the soil. They latch onto the roots of crops (and other plants) and suck out nutrients. They’re the plant equivalent of tapeworms. With all that energy going to feed parasites, plants have less energy left to … well produce food for us humans.

January 18, 2008

The Day of the Thousand Interviews

Filed under: University Visits — Tags: , , , , — James @ 9:04 pm

Well five actually, but everything in due course.

Actually I’m just going to hit the major high lights:

The computer support they’ve got is amazing. On our tour of one of the facilities we walked into a room built for pure computational biologists. There where giant metal sleeves of cables running up from the center of every table surface, and looking up I saw giant bundles of ethernet cables running overhead. The only word that comes to mind is awesome.

Plenty of growth chambers and greenhouses of course.

I learned a lot about soybeans. Which was good. I got something to call my interest: crop genomics.

At the poster session they had this evening I met a guy who was working with wild rice, which is only in the earliest stages of domestication. The two things that struck me where the creativity he was forced into, given the extremely limited resources the government provides for such a small crop, and the fact that a big percentage of the money he gets comes from the wild rice growers themselves, and in return he goes out and meets with the grower association. He’s only of literally four people doing work in wild rice and the only molecular biologist. So it was really cool to talk to him.

Coolest Title I’ve ever heard of: Lichenologist (The Lichens that grown on rocks and trees, not the werewolves in Underworld)

Saddest realization: Not only is it a lot more work to cross soybeans than corn, but after you’ve made that cross, you get MAYBE 5 seeds. Not the 50-200 you’d normally get from an ear of corn. It seems to me that would change the way you’d have to do experiments in all sorts of ways, though I’m not having a lot of success thinking of what they are yet.

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