James and the Giant Corn Rotating Header Image

agriculture

Where the superpowers of superweeds come from

Superman had the yellow sun of earth, spiderman had a radioactive spider-bite, but what about superweeds, where does their super power (surviving application of Round-up/glyphosate) come from?

To understand how superweeds survive, we first have to understand why normal weeds (the Jimmy Olsens and Lois Lanes of the plant world) die. <– last superhero reference of this post I promise. (more…)

Don’t judge the genetic diversity of a species by its cover

Photo: ekpatterson, flickr (click photo to see in original context)

There are more differences in the genomes of two unrelated corn plants than between the genomes of a human and a chimpanzee (two species separated by 3.5 million years of evolution).

On the other hand, two unrelated human beings, members of the same species, have more than four times as many genetic differences as two unrelated heirloom tomatoes.

Genetic Diversity:

Corn vs. Corn > Human vs. Chimpanzee >> Human vs. Human >> Heirloom Tomato vs. Heirloom Tomato

Now the fact that any two human beings are more closely related to each other than either is to a chimpanzee should be obvious to anyone who gives it a moments thought.

I plan to poll my sections tomorrow to see how many of them would put corn and heirloom tomatoes in the opposite positions, but many have figured out my feelings about corn, so they’ll probably guess it’s a trap.

BBC on drought tolerant maize/corn

There’s a new episode of BBC’s Discovery: Feeling the World out this morning. It’s only 26 minutes long, and the full piece is definitely worth a listen, but if you don’t have 26 minutes, the meat of the post can be summarized in 8 minutes:

3:20-7:54: Introducing the subject, developing drought tolerant varieties of maize in Africa, and the fact that the researchers working on it as using conventional breeding, marker assisted breeding and a genetically engineered trait Monsanto. When battling starvation, you use any tool that comes to hand.

18:40-21:20: This part is almost hard to listen to. You can hear the raw emotion in the researcher’s voice as the reporter keeps trying to make genetic engineering sound, at best, like a last resort. Couldn’t they just try irrigating more crop land she suggests?

25:10-end. Conclusion. I also thought this part was very powerful.

A few complaints: (more…)

The Most Studied Genes of Maize (and why we love kernel phenotypes)

Unique citations determined from papered linked to from MaizeGDB gene locus pages. Images of c1 and y1 segregating years by Gerald Neuffer and made available through MaizeGDB.

* = tied for number of citations

** = some mutant alleles have kernel phenotypes.

If you want to become one of the famous mutant corn genes, it helps if you have an effect that is visible in corn kernels instead of only from fully grown plants.

And here is why:

  • A geneticist could determine that the version of c1 that creates yellow kernels is recessive to the version that creates purple kernels just from looking at the ear of corn on left.
  • Furthermore, they could tell you that both the male parent (the plant that provided the pollen) and the female parent (the plant on which the ear of corn grew) were both heteryzygous for the c1 genes (they each had one dominant version of the genes and one recessive version), and therefore the corn kernels the parent plants were grown from were both purple.
  • They would know with certainty that all of the yellow kernels contain two recessive versions of the c1 gene.
  • While they couldn’t predict with absolute certainty whether a specific purple corn kernel on that ear carried two dominant versions of the c1 gene or one dominant and one recessive version, they would know there was a 1/3 chance that kernel has two dominant copies, and a 2/3 chance it had one dominant and one recessive copy.
  • That geneticist could make all sorts of predictions about what ears would look like in future generations depending on what colors of corn kernels were planted and which plants were mated with each other.

All this from a single picture of an ear of corn. For a phenotype seen in corn plants but not in kernels (like Knotted1), a geneticist would have to plant a row or more of corn seeds from an ear and examine the growing plants to get the same quantity of information.

And that is why mutations with kernel phenotypes have been so popular over a century of maize genetics research.

The Color of Corn and Cultural Values

MAT_kinase has sparked an interesting discussion about the associations people have with corn of different colors. I’d previously heard that yellow corn (where pre-vitamin A carotenoids are produced in the kernels) isn’t popular in Africa, with the reason usually being given as its association with American food aid.* If yellow corn comes predominantely from food aid, it eventually becomes associated with being poor and/or starving, so that when people have a choice they eat other varieties of corn. I can’t find where I read it, but I vividly remember reading an interview with a woman who talked about the shame of eating yellow food-aid corn, knowing that it had originally been intended to feed livestock in the US, not people.

MAT points out another more pragmatic reason yellow corn may not be favored in Africa that I hadn’t heard of before. Apparently the extra carotenoids make yellow corn more susceptiable to spoilage than white corn varieties, a very pertenent issue in areas without access to the kinds of storage facilities we take for granted in American agriculture.

Jeremy at the Agricultural Biodiversity Weblog picked up the torch, highlighting a number of their own previous posts relevant to the discussion, including one by fellow blogger Luigi that relates the reaction of his own wife, originally from Kenya, on ordering polenta** at a restuarant and receiving a yellow dish.

Fortunately breeds of corn that contain even more beta carotene (the carotenoid most easily converted into vitamin A by our bodies) aren’t even yellow all the time. Although I wasn’t able to find a freely available picture, sometimes they’re ORANGE.*** While it turns out the correlation between color and beta carotene content isn’t perfect****, there’s still reason to hope varieties bred for the highest pre-vitamin A content will end up a striking orange color. For a visual examples of how orange corn can get, check out check out Dr. Rocheford’s lab website.

Will the distinction between orange and yellow***** be enough to get over the Africa’s lack of enthusiasm for yellow corn? Will the benefits of a diet with more vitamin A be enough to outweight the issues with yellow corn going “off” if stored improperly? I certainly hope the answers to both these questions are yes, but we won’t know for sure until we try. And there are some hopeful signs. For example this segment in a story from NPR: (more…)

India and Bt Brinjal/Eggplant

India has delayed the introduction of their insect resistant eggplants.

Read about it in:

The Taste of Tomatoes + Tomato Mutagenesis

An anonymous indian tomato vendor in Chennai, Tamal Nadu. photo mckaysavage, flickr (click to see photo in it's original context)

First, since I didn’t explicitly state it in my previous post, the paper on the longer lasting tomatoes developed by India’s National Institute for Plant Genome Research didn’t report any data on how the RNAi knock-down tomatoes actually taste.* The tomatoes are nearly twice as firm as tomatoes in which these genes are NOT knocked down, so it’s possible they’d seem unpleasantly crunchy, I don’t know how doubling the firmness of a tomato translates into the feeling when a person bites into one.

On the other hand, if the tomatoes do turn out to be tasty and delicious, it’s quite possible the trait could be replicated without genetic engineering. And if that turns out to be true, it’s absolutely the approach anyone developing longer lasting farmers to Indian farmers, or farmers anywhere, should take (for why I’m saying this, check out the bit in bold further into this post). (more…)

Scientists at India’s NIPGR Create a Longer-Lasting Tomato (Studying The Regulation of Fruit Ripening)

ResearchBlogging.org

Author’s note: This would seem to be the week for vegetables I hated as a kid. Yesterday was onion, today tomato, if there’s a story about brinjal/eggplant in the next few days we’ll have hit all the big ones. 😉

Ripening tomatoes. Photo: Photos_by_Lina, fickr (click to see photo in its original context)

I was recently pointed to an early publication paper that went up on the Proceedings of the National Academy of Sciences website on Monday, where a research group at India’s National Institute of Plant Genome Research describes two genes from tomato that, when knocked down by RNAi*, result in tomatoes that can remain ripe but not spoiled for up to three times as long as tomatoes where these two genes function normally.

Their approach targets specific genes involved in breaking down certain proteins found in the cell walls of tomatoes (in fact in the cell walls of all plants). Breaking down the cell wall is a key part of ripening in fruits (which the tomato is, botanically if not culinarily). Which makes sense if you’ll think about it for a moment. One of the traits we associate with ripening is getting softer, from bananas to peaches if it’s still crunchy when you bite into it, it wasn’t ripe. What makes plants stiff and crunchy? The strength of their cell walls. Since, unlike vegetables, fruits WANT to be eaten**, as they ripen they begin to break down their cell walls to make themselves more appealing to passing animals. Unfortunately, ripening and spoiling are, in a lot of ways, the same process. If fruits aren’t eaten when they become ripe, they continue to get softer, transitioning from delicious looking -> unappetizing -> inedible -> a puddle of mush on your kitchen counter.

Preventing ripening entirely is relatively easy, and there are plenty of known mutants in tomatoes and other species that never ripen (these naturally mutant tomatoes stay green and hard no matter how long you wait). But getting part of the way to ripeness but stopping before crossing the line into spoiled is a much less tractable problem. (more…)

Turkey Domestication

Wild turkeys photo: sanbeiji, flickr (click to see in original context)

When I first saw the headline I was hoping I’d find an article describing the first fruits of the turkey genome project (which I talked about back in november.) Instead, and still interestingly, what was just published in the Proceedings of the National Academy of Sciences was a study showing that wild turkeys have been domesticated twice by different cultures in the Americas.

The turkeys we eat today come from a breed domesticated by the Aztecs, living in present day Mexico (or proceeding cultures occupying that region). However this study, looking purely at mitochondrial DNA sequences was able to use DNA isolated from bones and turkey droppings to determine that turkeys kept by indigenous farmers in what is now the American southwest represented an independent domestication of wild turkeys from one of a couple of wild turkey subspecies found in North America. Given the uncertainties of archeological dating, the most recent evidence for the existence of this second form of domesticated turkey could be as early as 1400 AD or as late as 1840 AD.

The Cliff Palace, the largest of the ancient villages in Mesa Verde Park. Photo: j-fi, flickr (click to see photo in original context)

What’s fascinating to me is (more…)

An Interview with Roger Beachy

Pam Ronald, writing at Tomorrow’s Table points out an interesting interview with Roger Beachy the new head of the National Institute of Food and Agriculture (itself a newly created government organization) in Nature Biotechnology. He talks about everything from restoring support for the, very successful, programs that used to fund the training of plant breeders and plant biologists from around the world* to increasing the number of research grants that have specific money set aside for education and outreach. I’m guessing this is the comment that will get the most play if the interview gets noticed by the popular press:

In the early days of agbiotech, regulations were fairly minimal, which kept development costs low. The safety of a product was judged on the product itself and not the method used to develop it. Regulatory agencies have lost some of that focus in the past ten years. … I am very interested in having a regulatory structure that is science based and gets back to what we originally had.

I continue to be impressed with President Obama’s choice to head up the new agency, as I have been since the appointment of Roger Beachy was first announced. Though I will say I got this part wrong in my original post about Beachy’s appointment:

And on top of that, he’s spent his entire life working in the public and non-profit sectors (places like Cornell, Wash U, the Scripps Institute, and most recently president of the Danforth Plant Science Center). Can you imagine the screaming if Obama had picked someone who’d ever worked in industry to head up the NIFA?

As we’ve seen from the reaction to Roger Beachy’s appointment, finding a respected scientist who has done both basic and applied research, with proven skills as an administrator (plenty of great researchers make horrible administrators) and who’d spent his entire like working in the public and non-profit sectors instead provoked so much screams one might have thought President Obama had appointed Hugh Grant (the CEO of Monsanto, not the actor) to head the NIFA instead of Roger Beachy.

*Such funding contributed to the training of, among others, Gebisa Ejeta, who won the World Food Prize in 2009 for his work developing striga resistant sorghum, and who, from his testimony to the senate foreign relations committee, sounds like he would agree with this goal.