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

November 1, 2009

Domestication Bottlenecks

Filed under: agriculture,Genetics,Plants — Tags: , , , , , — James @ 3:06 pm
Driveway tomato garden. How much diversity do these plants contain?

Driveway tomato garden. How much diversity do these plants contain?

Crops like tomatoes, even heirloom tomatoes, aren’t found in the wild. Domestication of crops usually involves only a relative handful of individual plants. Narrowing the species down to a few hundred (or possibly even a few dozen plants) means only a limited number of copies of each gene will be carried through and many of the variant copies of the genes present in the wild population won’t be included in that number. Keeping the population small for multiple generation reduces variability even more as by chance some rare version of genes in one generation won’t be passed to any of the offspring in the next.

Genetic bottlenecks happen in the animal world as well. Skin grafts between unrelated Cheetahs aren’t rejected because the animals are so genetically similar their immune system can’t distinguish the grafted skin as being different from its own skin. Even less fortunate are the tasmanian devils who have so little genetic diversity that they are being decimated by a transmissible cancer. After fighting with an infected devil, which has tumors on its face and neck, tiny bits of the cancer will get into an uninfected devil’s wounds, and since the immune system can’t distinguish the foreign cancer cells from the devil’s own cells, the cancer cells reproduce unchecked, the trait that makes normal cancers, produced by mutated versions of our own cells, so deadly. And the solution mentioned in the article, to save the species by protecting 200 individuals, while better than letting them all die, will sacrifice even more genetic variability by subjecting the already inbred devils to a new population (and genetic) bottleneck. (more…)

October 31, 2009

Predictable Spinning of Squash

Filed under: agriculture,biology,Plants — Tags: , , , , , , — James @ 2:01 am
I dont have any picture of pumpkins handy, so this watermelon (and fellow cucurbit) will have to do.

I don't have any picture of pumpkins handy, so this watermelon (and fellow cucurbit) will have to do.

What could be a more fitting topic for a Halloween post than cucurbits, the family of plants that (in addition to crops like watermelon and cucumber) include squash and pumpkins? Yeah, I know it’s a stretch.

A week ago a paper came out in PNAS (the proceedings of the national academy of sciences. A very prestigious journal, one step down from Science or Nature), that showed when an artificially inserted gene in squashes that provided virus resistance was introgressed into a wild related species it actually made them less fit. Short version: the wild squash also suffer from the virus which attacked domesticated squash but are also attacked by beetles, and the beetles prefer to eat squash without the virus. Tomorrow’s Table has a much better and more complete explanation of the research.

In that post the very first commenter predicted the result, that in this particular case a transgene (like most genes involved in domestication) was beneficial for farmers but not for wild plants, would be spun into “another failure for GMOs” when the real message is “we were worried about pollen drift, but in this case it turns out we didn’t have to be.”

He was right. (more…)

October 30, 2009

Mt. Tamalpais, Invasive Species, and Herbicides

Filed under: agriculture,Plants — Tags: , , , — James @ 4:20 pm
On the side of Mt. Tamalpais in in the summer.

On the side of Mt. Tamalpais in in the summer.

Mt. Tamalpais sits across the San Francisco bay from me, on a clear day you can even see it from the hills behind the Berkeley campus. Apparently, the region around Tamalpais is also home to species, especially plant species, found no where else. These local species are threatened by other, invasive, species that have been brought to northern California from all over the world. Some accidentally, but many more imported as ornamental species for private gardens.

Invasive species aren’t something I worry a lot about, but we had a great presentation in one of my classes on Tuesday by a woman who’d spent several years fighting the good fight against them across the bay.

Take French Broom, a woody shrub from the Mediterranean. California’s native habitat is quite similar to the Mediterranean climate and the species is thriving, growing so densely that it chokes out tree seedling before they can grow big enough to escape the thicket. The plant is out-competing FORESTS! And it’s also taking a bite out of the ecological niche currently occupied by alpine grasslands like the one pictured.

I like grasslands. (more…)

October 27, 2009

Banana Biology

Filed under: biology,Crop Profiles,Genetics,Plants — Tags: , , , , , — James @ 2:09 am

When I was giving my lecture to on phylogeny and tetraploidies, I found out not everyone knows why bananas don’t have seeds.

The reason the bananas we eat don’t have seeds is that they are all sterile. A long time ago the Cavendish bananas first came into being when a tetraploid banana (that is a plant that has four copies of every chromosome instead of the normal two) mated with a normal diploid banana. The result, a banana with three copies of every chromosome couldn’t mate or produce seeds. One of the steps in making reproductive cells (the analog of human sperm and egg cells) is the even dividing of a plant’s chromosomes into two reproductive cells.* Normal diploid cells can easily divide into two cells (one copy of each chromosome in each cell), tetraploid plants can divide the same way (two copies of each chromosome in each cell). Hexaploid, three copies in each and so on. Odd numbers of chromosomes don’t work. The plants can’t successfully make the cells it needs to reproduce, if it can’t reproduce it can’t make seeds, and that is why bananas (or seedless watermelons) don’t have seeds. (more…)

October 25, 2009

Bananas: The Original Not-From-Here Fruit

Filed under: agriculture,Crop Profiles,food,Plants — Tags: , , — James @ 6:03 pm
A banana storage room in Salt Lake City in 1913.

A banana storage room in Salt Lake City in 1913.

As early as 1905 the United States was importing 33 million bunches of bananas a year. Bunches averaged more than 100 individual bananas. Billions of bananas were being consumed in America before the Ford Model-T car was first produced. (more…)

October 20, 2009

Grafting

Filed under: agriculture,Plants — Tags: , , , , , , — James @ 1:13 am
Grafted Apple Tree

Grafted Apple Tree

Imagine if all it took to replace a lost leg was to put another leg against the amputation site, tie up the wound and let the two grow together. We can do that with plants! We’ve been doing it for thousands of years and it is an important part of crops production for woody plants (think fruit trees).

The technique is called grafting and it really is almost that simple. A branch or stalk* from one plant is cut and attached to another plant of the same or a related species**, making sure to line up the vascular tissue*** of the cut branch and host plant. That connection is covered with grafting wax or grafting compound which keeps the exposed ends of the cuts from drying out which would stress or kill the cells. (more…)

October 16, 2009

World Food Prize

Filed under: agriculture,Feeding the world,Plants — James @ 6:41 pm
Iowa sorghum field.

Iowa sorghum field.

The World Food Prize, an award set up by Norman Borlaug to honor others who fought against hunger, was held in Des Moines this week.* The prize went to Gebisa Ejeta, an Ethopian-American plant breeder and geneticist, who developed new breeds of sorghum that increase yields as much as fourfold.

His sorghum breeds deal better with drought, a trait that will become only more important around the world as competition for fresh water increases. Perhaps even more importantly though, they are resistant to striga**, a parasitic weed that attaches to the roots of crops, drawing off nutrients and severely decreasing yield (20-80% less than uninfected fields). Each plant produces tens of thousands of tiny seeds than can lie dormant in the soil for up to twenty years waiting for the best moment to strike, so once a field is infected with striga, it isn’t going away. The common name for striga is witchweed which fits the species perfectly. Striga resistant sorghum is a very good thing.

My appreciation and congratulations go out to Gebisa Ejeta.

*This is the first time the prize has been awarded since Dr. Borlaug passed away.

**On the more basic research side, the study of striga lead to the discovery of a new class of plant signaling molecules strigolactones.

October 14, 2009

Potato Breeding

Filed under: agriculture,biology,Crop Profiles,food,Genetics,Plants — Tags: , , , , , , , — James @ 2:08 pm
Unfortunately the purple potatoes aren't a Cornell Breed

Unfortunately these purple potatoes aren't one of the Cornell breeds

A lot of people may not share my enthusiasm for the potato genome, hopefully you all enjoy eating potatoes. The stereotype of potatoes is lots of boring sameness one identical to the next.* Reality, as usual, is much more complicated. Tens of thousands of cultivars can still be found in the South American regions where potatoes were first domesticated. In America, breeders are constantly working to bring in desirable traits from those (often really cool looking) breeds and even wild relatives of the potato. They face both genetic barriers (species barriers are bad enough normally, but trying to introgress genes across a tetraploidy can be a mess) and consumer acceptance ones.

This was driven home in a story at the NYtimes about Cornell potato breeders who have developed breeds which grow much better in upstate New York, but run into problems because the potatoes look and taste different than the couple of varieties of potatoes consumers and restaurants are used to (most notably Idaho grown Russet Burbanks**). Cornell Extension has been working on overcoming that barrier providing the potatoes to restaurants and, in what I think is a genius move, culinary schools throughout the region.

If you happen to visit New York farmers markets take a moment to ask sellers about the breeds of potatoes they have for sale.*** The potatoes covered in the story are Salem, Eva (both white potatoes), Lehigh, Keuka Gold (yellow breeds), Adirondack Blue and Adirondack Red (both of which are just the color you’d expect from the name.) Purple potatoes in particular just look really cool, see image above.

*There was a saying about accepting differences that I vaguely remember from a childhood TV show, something along the lines of “People aren’t the same like potatoes, and that’s a good thing because potatoes are boring.”

**The Russett Burbank was developed by a truck gardener outside of New York City called Luther Burbank in the 1800s who was initially inspired to become involved in plant breeding by Charles Darwin’s 1868 The Variation of Animals and Plants Under Domestication. He later moved to California where he became famous plant breeder and, among other things championed the practice of grafting (connecting a cutting from one plant (usually a tree) to the stem of another, which, if done properly grows the two together and the cutting will grow flower and produce fruit like it would normally) a practice at the time condemned as unnatural. <– This info from Mendel in the Kitchen by Nina Fedoroff and Nancy Brown a great resource

***In fact, whenever you’re buying directly from a farmer, if you get a chance, ask about the breed of whatever you’re buying. More often than you’d expect there’s an interesting story about why he or she is growing that particular breed and where it came from.

October 13, 2009

Potato Genome!

Filed under: biology,Plants,research stories — Tags: , , , , , — James @ 7:26 pm
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Photo from graibeard

Sort of anyway. What was released was a pre-publication scaffold of the genome. A final, published, version might include more primary sequence data, will have fewer gaps, and most importantly of all, people will be able publish their own work which draws on the potato genome.

Overall I have mixed feelings on the current practice of releasing genome sequences prior to publication. As someone who does comparative genomics, having access to more genomes is great, but the agreements they’re released under severely limit how they can be used in publications prior to the publication of the genome paper itself (which can be a LONG time).

Within the grasses four genomes are available (Maize(corn), Sorghum, Rice and Brachypodium) however only two of them, Rice and Sorghum, are published. Any paper making use of whole genome analysis of all four cannot be published before the Maize and Brachy papers come out (hopefully before the end of this year!).

That said having even a rough draft of the potato genome is cool. Potato is a great plant for a lot of reasons. Potatoes are the fourth staple crop (behind only rice, maize and wheat) that provided enough food for people to build civilizations and probably the most important non-grass crop in the world. Currently there are no GMO-potatoes on the market, as I mentioned here. Domesticated potatoes are tetraploid and rarely breed true (their offspring aren’t much like the parents).* And I still owe it a post of its own.

Another reason to be interested in potatoes are is the family tree of the species. Potato can claim tomatoes, eggplant, and deadly nightshade as close relatives.** That whole group of species belongs to a different branch of the family tree of plants (the Asterids) from the early non-grass genomes (Arabidopsis, Papaya, and Grape) which were all in a group called the Rosids. These two groups are responsible for a lot of the diversity of species within the Eudicots*** so it’s good we are starting to starting to see Asterid genomes.

*Potatoes grown from seed not sharing many characteristics with their parents is why most cultivation of potatoes is done by planting pieces of potatoes instead of seed. The plant that sprouts out of a potato is genetically identical to the plant that grew the potato. It’s a clone. Apples actually face a similar issue with apple seeds not being much like their parents. That’s why breeds of apples are propagated by grafting. A breeder cuts off a piece of a branch from one tree and carefully connects it to the stem of an unrelated apple tree. If the graft is done properly the branch will grow, flower, and produce fruit just as it would normally. So all apples of the same variety (say Gala, Macintosh, or my new favorite Cripps Pink) are clones of each other.

**The obvious family resemblance to deadly nightshade was one of the reasons Europeans originally believed tomatoes and potatoes to be toxic when they were introduced from the Americas.

***For a sense of how Eudicots fit into the family tree of all plants, check out Phylogeny of Pineapple, a further explanation of awesomeness

October 2, 2009

The Real GM Tomato

Filed under: agriculture,Plants — Tags: , , — James @ 11:10 am

In my previous post I mentioned that the only people who actually knew what GM tomatoes tasted like where a few who’d lived in California in the mid-90s. That was when Calgene, a biotech start-up founded in the university town of UC-Davis, introduced a tomato that would last longer without tasting like cardboard. And the trait wasn’t the result of a gene from fish or deadly nightshade* but simply a copy of a gene already in tomatoes, reversed so it would reduce the effect of the existing copies. But how did it taste? Click read more to find out: (more…)

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