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

November 19, 2009

Why should you be excited about the corn genome?

Filed under: food,Plants,research stories — Tags: , , — James @ 5:36 pm

Virginia Walbot has ten reasons in the latest issue of PLOS genetics. PLOS journals are all open access so anyone can read it without a subscription.

The two reasons I think will be the most interesting to non-biologists are #1 and #10:

Corn was domesticated a short 10,000 years ago and domestication is normally a huge genetic bottleneck that results in the loss of much of the gene diversity found in the wild ancestor. (Modern tomatoes are more diverse than heirlooms because breeders are intentionally working to bring some of that diversity back over.) Yet two lines of corn, which certainly shared many common ancestors in the last 10,000 years, contain more genetic differences than humans and chimpanzees which have been evolving separately for 3.5 MILLION years. That’s 10,000 years vs 3,500,000 years!

Number ten drives home how essential corn is to the world today with statistics like American farmers growing so much corn last year than it works out to a metric ton for every man, woman, and child in this country. Or that corn and cornfeed animals feed a billion people around the globe (those aren’t rice numbers, but hopefully it drives home why corn has definitely earned it’s place as one of the big three grains that support civilization around the world).

h/t to the beekeeper (who I haven’t see around the blog in months) for pointing me at this PLOS genetics coverage of the maize genome papers coming out both there and in Science.

Not Genetically Engineered: Grapes

Filed under: Crop Profiles,Plant breeding,Plants — Tags: , , , , — James @ 11:19 am

New York Grapes. Concords I believe, though it's been several years so I may be remembering wrong.

New York Grapes. Concords I believe, though it's been several years so I may be remembering wrong.

Scientific Name: Vitis vinifera

Supposed Genetically Engineered Trait: Large size/seedlessness

The Real Story:

Seedless grapes are descended from several different mutations that all result in the developing embryos of grape seeds to abort prematurely*. You can still find the tiny dead remnants of seeds in seedless grapes. Of course being seedless raises a new question: How do plant breeders work with seedless grapes? (more…)

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 12, 2009

Genetically Engineered Crops: Papaya

Photo Reeding, Flickr (Click for photo stream)

Photo Reeding, Flickr (Click for photo stream)

Scientific Name: Carica papaya

Genetically Engineered Trait: Resistance to the papaya ringspot virus

Details of Genetic Engineering:

In the 1990s papaya ringspot virus was in the process of wiping out the Hawaiian papaya industry, then the second largest fruit industry in Hawaii. Conventional approaches such as selective breeding for resistant papayas or attempting to grow trees in isolation had failed. The virus is transmitted by small sap-sucking insects such as aphids. Infected papaya trees can be recognized by the discolored rings on their fruit (that the virus gets its name from) yellow leaves, and most importantly from a papaya farmer’s perpsective a 60-100%* loss of fruit production. (more…)

November 11, 2009

Genetically Engineered Crop: Blue Carnations

Filed under: Crop Profiles,Genetics,Plants — Tags: , , , , — James @ 2:08 am

Florigene's Moondust carnations, one of several violet and blue varieties they've created with genetic engineering. Photo by Pagemoral and licensed under the creative commons. Click to see the photo in its original context with license information

Florigene's Moondust carnations, one of several violet and blue varieties they've created with genetic engineering. Photo by Pagemoral and licensed under the creative commons. Click to see the photo in its original context with license information

Scientific Name: Dianthus caryophyllus

Genetically Engineered Trait: Anthocyanin biosynthesis (blue and violet plant pigments)

Details of Genetic Engineering:

The market in flowers with genetically engineered colors is (to my knowledge) occupied by a single Australian company called Florigene. They study anthocyanins, the class of plant pigments responsible for, among other things, the coloration of purple potatoes, purple carrots, black rice, purple corn, and many blue and purple berries. Anthocyanins are one of the key classes of plant pigments, found to greater or lesser extent in most flowering plants.* Florigene has been producing purple and sometimes blue carnations since the 1990s by adding key enzymes in the anthocyanin pathway from other plant species. While purple carnations are cool, the real goal of Florigene’s work has been blue (and purple, and violet) roses, something rose breeders have been trying and failing to create for centuries.

Florigene was granted a license to grow their first breed of genetically engineered blue rose this summer, (although as far as I can tell the roses aren’t yet for sale, so they don’t get their own post). For more on plant pigments, Florigene, and why the development of blue roses as foiled breeders for so long, check out this fascinating post by MAT Kinase.

Purple potatoes with orange carrots (and did you know most carrots where white when they were first domesticated?)

Purple potatoes with orange carrots (and did you know most carrots were white when they were first domesticated?)

About Carnations:

Carnations belong to the caryophyllales, an extended family of plants that include cacti (cool), rhubarb (tasty), and carnivorous plants like sundews and venus fly traps(awesome!). Beyond that, I’ll admit I don’t know much about their biology.

If you know someone who is into flower meanings (I used to date a girl who was), you’ll notice there is no definition on record for blue carnations. It makes them the perfect gift to say, “I like you, so I bought you flowers” without having to worry about any unintentional subtext beside: “I’m also a huge plant/genetics geek, and if you don’t ask me soon how they make the flowers blue I’m going to burst!”

*The extent of anthocyanin biosynthesis in flowering plants is a good indicator that the ancestor of all the flowering plants alive today (which lived sometime between 250 and 100 million years ago) already contained the genes needed to produce anthocyanins, and flowering plants which are unable to produce them today, like roses, cannot because their ancestors lost the ability.

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…)

November 9, 2009

Genetically Engineered Crops: Canola

Field of Canola in Bloom. Photo: Joe Shlabotnik, flickr (click photo to view Joe's photostream)

Field of Canola in Bloom. Photo: Joe Shlabotnik, flickr (click photo to view Joe's photostream)

Scientific name: Brassica napus

Genetically Engineered Traits: Herbicide Resistance.

Details of Genetic Engineering:

Two companies have produced canola that is resistant to different herbicides.
Monsanto sells canola (Roundup Ready canola) that is resistant to glyphosate, an herbicide monsanto sells under the brand name Roundup and lots of other companies sell under lots of other brand names since the herbicide itself recently came off patent (the resistance trait is still under patent.)
Bayer sells canola (Liberty Link canola) that resists the completely different, if similar sounding herbicide, glufosinate. Glufosinate is sold under a number of brand names (including, you guessed it, Liberty), but I wasn’t able to figure out whether or not it is still under patent.
About Canola:
Derived from the name “Canadian Oil” canola is an oilseed plant also known as rapeseed. The name change came in the 1970s when conventional breeding (this was approx. two decades before the first genetically engineered plants hit the market) created plants with healthier oil and without the bitter taste , and presumably someone to majored in advertising suggested that selling “Rape Oil” would be a good way to go bankrupt.

Two companies have produced canola that is resistant to different herbicides.

Monsanto sells canola (Roundup Ready canola) that is resistant to glyphosate, an herbicide Monsanto sells under the brand name Roundup and lots of other companies sell under lots of other brand names since the herbicide itself recently came off patent (the resistance trait is still under patent.)

Bayer sells canola (Liberty Link canola) that resists the completely different, if similar sounding herbicide, glufosinate. Glufosinate is sold under a number of brand names (including, you guessed it, Liberty), but I wasn’t able to figure out whether or not it is still under patent.

About Canola:

Derived from the name “Canadian Oil” canola is breed of the oilseed crop rapeseed. The name change came in the 1970s when conventional breeding (this was approx. two decades before the first genetically engineered plants hit the market) created plants with healthier oil and without the bitter taste people associated with rapeseed oil, and presumably someone to majored in advertising suggested that selling “Rape Oil” would be a good way to go bankrupt.

Close up of Canola Flowers. Photo: Pollobarca2, flickr (click photo to see pollobarca2's photostream)

Close up of Canola Flowers. Photo: Pollobarca2, flickr (click photo to see pollobarca2's photostream)

Rapeseed (the USDA doesn’t break out separate statistics for Canola) was the third biggest source of vegetable oils around the world in 2008-2009 at 20.5 million metric tons, coming in behind only soybeans and oil palms.

Canola is the main oil I use in my own cooking. Canola is apparently one of the healthier sources of vegetable oils, but the two things I most appreciate about it are the high smoke point (it’s harder to burn the oil itself*), and low cost. Last time I checked I was able to find a 48 oz bottle of canola oil for 2.99 which was better than local prices for peanut or corn oil. (Olive oil of course comes in much smaller containers that cost $10 or more, not at all suitable for graduate students.)

*Good for someone who is both as indifferent a cook, and as easily distracted as I am.

November 8, 2009

Biological Control of Western Corn Rootworms

Filed under: agriculture,biology,Genetics,Plants — Tags: , , , , — James @ 8:52 pm
Face of the Enemy: Adult Western Corn Rootworm chewing on the silks of a corn ear. Picture from wikimedia, apparently in the public domain

Face of the Enemy: Adult Western Corn Rootworm chewing on the silks of a corn ear. Picture from wikimedia, apparently in the public domain

This post discusses the paper Degenhardt, J et al. (2009) “Restoring a maize root signal that attracts insect-killing nematodes to control a major pest”

The Western Corn Rootworm (which as you can see from the picture to the right are not actually worms) is estimated to cost farmers in the US alone one billion dollars a year in lost yield and pest control measures. The newly hatched larva begin feeding on root hairs and as they get bigger start attacking the main roots of a corn plant. The damage to the roots from the feeding itself is exacerbated by the open wounds becoming infected. The loss of roots both stresses the plant and reduces yield by decreasing the plant’s supply of nutrients and water, but also makes it much more vulnerable to lodging (getting blown down by a gust of wind). Oh, and did I mention the adults like to feed on the corn plant’s reproductive tissues, decreasing yield even further?

Rootworms are one of the pests controlled by plants genetically engineered to express BT a protein taken from organic agriculture. Without it, the 1 billion dollar price tag for rootworm damage and control would be even higher. But this isn’t an article about bt, it’s an article about how some corn already knows how to call for help when rootworms attack.

Rootworm larva may feast on the roots of maize, but they are in turn eaten by some species of nematodes.* And it turns out some kinds of corn know how to attract nematodes, and when they’re under attack by rootworms they do just that. The nematodes get a delicious meal of rootworms and the corn plant gets to keep more of its roots intact.

How do corn plants attract their, unintentional, nematode defenders? (more…)

November 3, 2009

Giant Vegetables and Fruit

Filed under: Link Posts,Plants — James @ 3:46 pm

Hey folks. I announce I’m going to be working on my NSF fellowship application all week and you all go break the daily traffic record. At this rate you’ll convince me to spend every week writing grant proposals!

What’s a guy gonna do? Apparently dig up more content to show you guys. Here are some cool pictures of giant fruits and vegetables. The giant pumpkin at the end is a particularly awesome 1725 pound monster.

There are also some pictures of things like giant burgers or giant pizzas but I just have trouble getting as exciting about huge versions of prepared food. Given sufficient money and time, humanity could produce a burger much heavier than 150 pounds or a pizza much wider than 42 inches. The size of these food items is limited solely by human motivation.

Cool mutants and horticultural tricks are way more exciting. 😉

Sugar Belle Citrus and Patents

Filed under: agriculture,biology,Plants — Tags: , , — James @ 2:02 am
Mandarin Orange (Not a Sugar Belle)

Mandarin Orange (Not a Sugar Belle) from dungodung on flickr

We’ve been talking about grains and genetic engineering strait for a few days, so I thought it’d be the perfect time to put up a story about conventionally bred citrus. The University of Florida put out a press release about a new mandarin orange breed developed by Fred Gmitter, called Sugar Belle. The fruit is of course described as delicious and it may well be, I can’t say one way or the other. Importantly to a different group of people (producers rather than consumers of citrus fruit), the fruit matures 4-6 weeks earlier than other varieties of mandarin, making the harvest better timed to cater to the demand for citrus around Christmas.

Fred has been developing the breed since 1985, when he found the tree Sugar Belle was bred from in the experimental plot of another plant breeder who’d just retired. That’s twenty-four years of research and development. 1985 is the year “new coke” was released. Soviet and Western forces still faced off against each other across the Berlin Wall. If Sugar Belle was a person, it’d already be old enough to be in grad school right now.

The lesson here (one of them) is that it takes a long time to breed fruit trees.

But that’s not the only interesting thing about this story. (more…)

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