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

November 17, 2009

Not Genetically Engineered: Watermelon

Filed under: agriculture,Crop Profiles,food,Plant breeding,Plants — James @ 2:45 am

I know I'm reusing images, but this is just a really gorgeous watermelon

I know I'm reusing images, but this is just a really gorgeous watermelon

Scientific Name: Citrullus lanatus

Purported Genetically Engineered Trait: Lack of seeds

The Reality:

Seedless watermelons grow on triploid (three copies of every chromosome) watermelon plants. Like the banana, triploid watermelons are seedless because it’s impossible to separate three copies of each chromosome into different different reproductive cells. Unlike bananas, seedless watermelons are grown from seed and must be fertilized by fertile (diploid) watermelons to produce fruit.

Where do farmers get seeds for a seedless plant? (more…)

November 16, 2009

Not Genetically Engineered: Domestic Cat

Filed under: Genetics — Tags: , , — James @ 5:29 pm

A non-transgenic cat. But then, so are all cats

A non-transgenic cat. But then, so are all cats so it wasn't a hard picture to find

Scientific Name: Felis silvestris ssp catus

Claimed Genetically Engineered Trait: Does not provoke allergic reactions (hypoallergenic)

The Reality: A company called Allerca used high thru-put screening to check lots and lots of cats to find one with a  broken copy of the gene that codes for one of the proteins people who are allergic to cats are most likely to react to.* After that they, presumably, used marker assisted breeding to introgress the broken gene copy into other cats, which they now sell for between $6,950 and $22,000.**

About Cats:

Siamese cat between two cool looking computers. Photo: Brian Landis, Flickr (click photo to view photostream)

Siamese cat between two cool looking computers. Photo: Brian Landis, Flickr (click photo to view photostream)

All of the felines in the world today shared a common ancestor between 10-15 million years ago. That’s comparable to the estimates of the most common ancestor of corn and sorghum two species of a plant that look much more similar than the house cat and the puma.

Cats with dark heads, tails, and legs (pattern associated with siamese cats) carry a mutant copy of a gene involved in the production of pigment. The gene can function normally, but only at slightly lower temperatures, and a cat’s extremities are generally bit cooler than its body. The coats of such cats will darken if they spend a lot of time outside during the winter, or, if you really wanted, you might be able to turn a siamese cat entirely white by keeping it in a sauna for months, though I’m not endorsing any attempt to verify that. (more…)

November 15, 2009

Indian Farmers

Filed under: agriculture,Feeding the world — Tags: , , — James @ 11:45 am

Over 60% of India’s workforce still works in the agricultural sector. Most are tenant farmers living in small villages, and a recent survey says a minimum of 40% of them would rather be doing something else rather than farming. At the same time the country is facing a looming crisis with as crop yields haven’t grown much since the green revolution, and population continues to. (more…)

Genetically Engineered Crops: Cotton

Filed under: agriculture,Crop Profiles — Tags: , , , — James @ 1:54 am

Field of Cotton in South Carolina. Photo: hdport, flickr

Field of Cotton in South Carolina. Photo: hdport, flickr

Scientific Name: Gossypium itscomplicated*

Genetically Engineered Traits: Insect Resistance (bt), Herbicide Resistance

Details of Genetic Engineering:

Cotton has been genetically engineered to resist both glyphosate (by Monsanto) and glufinsate (by Bayer CropScience) under the names Roundup Ready and LibertyLink respectively. As I’ve discussed in previous posts, there are both economic and scientific advantages to having more than one herbicide/herbicide resistance system as it tends to keep prices down, and slows the development of resistant weeds when any resistance they evolve to one herbicide will be useless if the farmer switches to the other for the next growing season.

But the big deal when it comes to genetically engineered cotton is bt cotton that substantially reduces insect damage (and insecticide applications). In the US both Monsanto and Dow AgroSciences sell their own versions of bt cotton using different bt proteins with different specificities. The Chinese government has also developed and deployed their own bt cotton varieties. Bt cotton is the most widely grown** type of genetically engineered plant in the world today, grown in countries like China, India***, and Australia, where other genetically modified crops are not yet approved, for the obvious reason that it’s harder to get people upset about wearing “unnatural” things than eating them.****

Cotton plant in Turkmenistan. Photo: flydime, flickr

Cotton plant in Turkmenistan. Photo: flydime, flickr

About Cotton: (more…)

November 14, 2009

The top two good keywords for this site are James and Corn!

Filed under: Site Business — James @ 9:09 pm

Looks like the search engine is finally letting me put the annoying hacking of this site over the summer behind me.

Marker Assisted Breeding

Filed under: agriculture,Plant breeding — Tags: , , , — James @ 5:03 pm
Some traits are easy to select for. It’s easy to tell which plants have a gene that turns them purple, or one that turns a single stalk of corn into a, for lack of a better word, corn bush. (links) When I was an undergrad some of the world I did was with a gene that (when it wasn’t knocked out by a transposon) turned corn kernals dark purple. Traits like that one (the R gene) that can be identified just from looking at a seed are the easiest of all.
Other traits are not so easy to select for. How do you pick out which plants in a row carry a gene variant that increases yield by 6%. Or worse yet, yields 6% more under drought conditions, but has no effect otherwise? For improving crops a plant breeder will need to track gene variants for many generations under in all sorts of growing conditions.
The solution, made possible by modern genomics and molecular biology, is to use differences in the genetics code between individuals in the same species to track what what happens to different pieces of DNA from one generation to the next.
Today a plant breeder can take a piece of leaf from every plant in his field, and find out a huge amount about which parts of their genomes they inherited from which parents. So even if it’s not a dry year, he or she can still tell which plants carry the gene variant previously identified as better surviving drought. A breeder can check for dozens or hundreds of of different genes in each plant from that same small piece of leaf.
Some companies are even setting up systems to scrape little pieces off of individual corn kernals and do the same kinds of analysis. Then only the kernals with promising combinations of gene variants are planted, either further study or breeding with other kinds of corn carrying other promising traits identified and mapped by breeders.
The system can also work to discover useful new traits, something called quantitative trait mapping. A bunch of plants that are the mixed descendants of two known breeds are measured for some trait, for this example let’s use flowering time. The same plants are also analyzed using known genetic varations between their two ancestors to see which parts of their genomes come from which of the ancestral breeds. A region of the genome that contains a gene that effects flowering time will show a pattern. More of the plants which flower earliest will have inherited that region from one of their ancestors, and more of the plants which flower later will have inherited that region from the other ancestor. Regions of the genome what don’t contain genes that have an effect on when plants flower will be randomly distributed between the earlier and later flowering plants
Doing some complicated math that I don’t even want to think about can reveal regions on individual chromosomes which contains genes that control flowering time.  Depending on how much they’re able to narrow the region down, breeders will often use the regions they identify (called QTLs: quantitative trait loci) to bread improved crops without ever having to identifiy the exact gene responsible. (And flowering time can be important for breeders, for example when adapting a breed of soybeans grown in Georgia to be grown in North Dakota, a breeder will want to select for soybeans that flower faster because the growing season is shorter farther north.)

Some traits are easy to select for. It’s easy to tell which plants have a gene that turns them purple, or almost any of the mutants seen in the mutants of corn garden at cornell. When I was an undergrad some of the world I did was with a gene that (when it wasn’t knocked out by a transposon) turned corn kernals dark purple. Traits like that one (the R gene) that can be identified just from looking at a seed are the easiest of all.

Other traits are not so easy to select for. How do you pick out which plants in a row carry a gene variant that increases yield by 6%? Or worse yet, yields 6% more under drought conditions, but has no effect otherwise? For improving crops a plant breeder will need to track gene variants for many generations under in all sorts of growing conditions. (more…)

Genetically Engineered Crops: Rice

Filed under: agriculture,Crop Profiles — Tags: , , — James @ 1:49 am
IMG_4625_nEO_IMG

Rice photo: flickr,毛利人

Scientific name: Orzya sativa

Genetically Engineered Traits: Herbicide tolerance, insect resistance (bt), increased vitamin A content

Details of Genetic Engineering:

Rice genetically engineered to be resistant to glufosinate (developed by Bayer CropScience) has been approved (deregulated) in the US but is not yet for sale commercially as the company attempts to get approval in countries which import rice from the US as well.

As far as I know, no company in the US has produced bt rice, which has less to do with consumer fears than with the small amount of rice production in the US rather than consumer rejection, but that’s just a guess. The Chinese government has developed breeds of bt rice, but doesn’t grow them commercially because of the risk to their export markets, which is primarily to countries that reject genetic engineering (although Chinese rice exports are declining drastically as more and more of their production is needed to feed their own people).

White and Golden Rice Respectively

White and Golden Rice Respectively

Golden rice, which has betacarotene, which human bodies need to make vitamin A, was developed by in Swizerland in the 1990s. Almost all plants produce carotenoids like betacarotene in their leaves as part of the biological machinery that makes photosynthesis possible. Breeders can sometimes identify and propogate natural mutations which lead to the expression of carotenoids in other parts of the plant, two key examples are orange carrots* and orange cauliflower. Vitamin A deficiency is a major issue** in many countries were rice is the primary crop, so breeders have searched for decades for natural mutations at would create orange rice, without success.*** The initial breed of golden rice which used two genes, one from daffodile to promote the expression of carotenoids in the grains of rice was attacked as requiring people to eat more than a dozen bowls of rice a day to get their daily recommended vitamin A intake, new versions that replaced the gene taken from daffodil with a version of the same gene taken from corn have more than twenty times as much beta carotene. Golden rice is also not currently grown commercially as it, like ringspot resistant papaya, doesn’t have a powerful for-profit corporation to shepherd it through the complex approval processes of various nations.

About Rice:
(more…)

November 13, 2009

Greenpeace offers marker assisted breeding

Greenpeace on Friday called on the International Rice Research Institute to abandon its genetic engineering program as the environmental activist group offers marker assisted breeding as a safe alternative to bioengineering.

Source.

Dear Greenpeace,

I would like to call upon you to abandon your campaign against genetic engineering and offer up an alternative priority your organization could focus on to the greater benefit of the world we all share: Fighting man-made global warming.

-James

Now you could argue greenpeace already is opposed to global warming. And you’d be right. They are. I guess my offering it to them looks pretty stupid doesn’t it?

The same could be said of greenpeace offering marker assisted selection to the plant breeding community that pioneered the technique and is taking full advantage of it, and has been for years in both the private and public sectors. Case in point: (more…)

Genetically Engineered Crops: Sugar Beet

Filed under: agriculture,Crop Profiles — Tags: , , , — James @ 7:57 am

Two sugar beets. From the USDA via wikipedia. (USDA you are awesome)

Two sugar beets. From the USDA via wikipedia. (USDA you continue to be awesome)

Scientific Name: Beta vulgaris*

Genetically Engineered Trait: Herbicide resistance.

Details of Genetic Engineering:

Sugar beets tolerant of the herbicide glyphosate (created by Monsanto) were de-regulated by the USDA in 2005**.  The beets were first grown commercially in 2008. Before the first seeds were even in the ground, the USDA was being sued in California for approving their cultivation. This fall (2009), a federal judge named Jeffery White ruled that the study of the environmental impacts of glyphosate tolerant beets (part of the data the USDA considered in its decision to deregulate the beets) should have considered the economic impacts of the herbicide tolerant beets on organic farmers. Since the ruling came at the end of the growing season,*** there was no time to breed new conventional seed to plant next spring. There may be enough seed next year, but if so it’ll be a stretch.

I’m keeping sugar beets on the list of genetically engineered crops, because there’s a still chance the plants will be grown next year. The judge still hasn’t decided if his own ruling should result in a ban on growing the beets. That’s all the detail I have room for here, but if you’re interested in the court case and the science behind it, I’d recommend checking out Anastasia’s excellent in depth follow up to the judge’s ruling.

About Sugar Beets: (more…)

Oops

Filed under: Site Business — James @ 2:26 am

If you’re seeing this, it means I stayed out to late doing important science (read: hanging out in Calvin) and didn’t write and schedule my nightly genetically engineered crop profile. Sorry folks.

Here’s a review of the series thusfar:

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