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

February 7, 2010

Ford Denison on Why Creating Drought Resistant Crops Is Complicated

Filed under: Link Posts — James @ 2:54 pm

From the post in question:

… natural selection is unlikely to have missed simple, tradeoff-free improvements. So I’m always skeptical when someone speculates that we could double crop yield just by increasing the expression of some newly discovered “drought-resistance gene.” My rationale is that mutants with greater expression of any given gene are simple enough to have arisen repeatedly over the course of evolution.

Sounds grim doesn’t it, and I completely agree with his logic. Fortunately the author goes on to explain all sorts of loopholes where it should be possible to improve water use efficiency by looking at more complex traits or exploiting the differences in how natural selection (evolution) and artificial selection (farming and plant breeding) judge success.

One example being that in a whole field being grown for harvest we don’t care about the relative success of one plant compared to its neighbors (how natural selection normally works) but the success, or lack thereof of the whole field. So selecting against various traits that help in plant-plant competition, but reduce the efficiency of water use overall is probably a path worth being pursued if it isn’t already. This parallels the early work done in corn breeding that, sometimes unconsciously, selected for plants that didn’t compete with each other as much for light, as all the energy corn plants spent trying to outgrow their neighbors was wasted, from the point of view of the farmers. If you look at really old pictures of cornfields, you’ll notice the plants were much taller then than they are today. Modern cornfields are also planted much more densely, which would have provoked even more wasteful struggles for sunlight in old breeds of corn, but today ensures that even more of the sunlight that hits and acres of corn will fall upon the leaves of SOME corn plant.

The whole post is a great read, I highly recommend it and now Denison’s forthcoming book is on the long list of things I really want to find the time to read.

h/t to Agricultural Biodiversity Weblog

February 6, 2010

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

Filed under: agriculture,biology,Genetics,Plants — Tags: , , , , — James @ 6:24 pm


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…)

February 5, 2010

Not Genetically Engineered: The EverMild Onion

Filed under: food — Tags: , , — James @ 5:12 pm

Sprouting onions. Photo: J. C. Rojas, flickr (click to see photo in its original context)

This isn’t a lot that is biologically exciting about the EverMild onion from what I can tell. Hopefully there will be more details on Monday when these onions are officially announced on Monday, but the short version seems to be that plant breeders at Seminis have developed a variety of sweet onion that can be grown in the pacific northwest over the winter, supplying sweet onions grown within the US at a time when they normally must be shipped in from the tropics or southern hemisphere.

So plant breeding has produced a new hardier variety of sweet onion* and is taking part in the new trend towards “branded” breeds of produce (like the Jazzman rice I talked about earlier this year). This would normally hardly be news (Seminis sells over 3500 kinds of seeds and they’re adding one more), and if it was at all, would be a story of reducing the demand for imported food with new varieties adapted to the US (again there are parallels to the Jazzman rice story). But I expect we will be hearing a fair bit about the EverMild onion at some point, because Seminis was bought by Monsanto several years ago, and I’ve alreadying read comments from people convinced it is a “secret GMO.” Nevermind that sweet onions (onions breeds that are lower in sulpher) have been around for a century. (more…)

Some Evidence Suggests Trees Are Growing Faster

Filed under: biology — Tags: , — James @ 11:06 am

A Tree photo: me

In a Proceedings of the National Academy of Sciences paper from this week that has been picked up across the popular press, researchers in Maryland report that the trees they’re studying are growing measurably faster than they “should” be.

From US News and World Report:

During the past 22 years CO2 levels at SERC have risen 12%, the mean temperature has increased by nearly three-tenths of a degree and the growing season has lengthened by 7.8 days. The trees now have more CO2 and an extra week to put on weight. Parker and McMahon suggest that a combination of these three factors has caused the forest’s accelerated biomass gain.

These aren’t small changes either. The authors are quoted as saying the forests they’re taking measurements on are growing two to four times faster than they normally would. Very cool stuff. What I’d read previously suggested the increased temperatures brought about by an increase in CO2 in the atmosphere would more than cancel out the benefits to plants of having more CO2 available. Of course most of the work I read about has to do with food crops, not trees*, and trying to predict how plants will react to changes in the atmosphere and climate can get a bit circular since how plants react will also influence the state of the climate and atmosphere in decades to come.

The research article itself is open access, meaning anyone can read it for free (without having to be associated with a major research university that holds an institutional subscription, which is how I normally get access). Click here and then click the Full Text (PDF) link on the right to grab the whole paper.

h/t to Greensparrow Gardens

*Not that trees can’t produce food.

February 4, 2010

Thanks Brassica oleracea

Filed under: Campus Life — Tags: , , , — James @ 11:01 am

My claim to 15 seconds of fame?

If you see a guy holding this stalk of brussels sprouts reciting the definition of qPCR in a promotional video from Agilent, it just might be me. (How many biologists carrying telegenic vegetables are they likely to find on campus? 😉 )

Edit: For the record, qPCR is a technique used to estimate the relative proportions of different DNA sequences in a sample. Perhaps most commonly, this is used to measure how strongly different genes are expressed. (Isolate RNA from a tissue, reverse transcribe it into DNA and measure how abundant your the sequence of your favorite gene is in the same.) When a plant needs more of a protein (say one that helps defend against fungal infection), it will produce more RNA copies of that gene’s sequence, each of which can be used over and over as a blueprint for ribosomes to make more copies of that particular protein. The acronym itself stands for quantitative Polymerase Chain Reaction.Which isn’t the most coherent explanation of a molecular biological technique I’ve ever written, but it has been a long day.

A Reminder: National Lab Mustache Day

Filed under: Campus Life — Tags: — James @ 12:28 am

… is coming up a week from tomorrow (Friday, February 12th). It’s been two and a half years since I last sported a mustache, but I recently found out about this holiday and it’s too awesome not to bring back the ‘stache. (Temporarily of course)

For more on National Lab Mustache Day, check out … the NLMD blog.

All sorts of bad hair choices on display here. Not that some people can't pull off the mustache, I'm just not one of them. 😉

February 3, 2010

We got to genetics in class today and the story of the shrunken 2 gene

Filed under: biology,Plants,Politics,teaching — Tags: , , , , — James @ 1:17 am

Arabidopsis that carries broken copies of both the AP1 (apetala1) and CAL (cauliflower) genes. The flower bearing stems have been replaced by these cauliflower-head-like growths. Image from "Genome-Wide Analysis of Gene Expression during Early Arabidopsis Flower Development" by Frank Wellmer et al (in PLOS Genetics a creative commons licensed journal). Article here: http://dx.doi.org/doi:10.1371/journal.pgen.0020117

Just in time for me to put together my worksheet for Thursday! I’ve managed to work in the CAL gene, which I talked about last week in my discussion of Cruciferous vegetables:

Cauliflower plants (and broccoflower plants) have broken copies of the CAL gene, which (when it isn’t broken) is helps the plant decide to switch from producing stems that were bear flowers to the flowers themselves. Without a functional version of CAL, cauliflowers just keep making denser and denser stems, producing the distinctive heads of cauliflower. If you have journal access, you can read more about the CAL gene at this science paper: http://dx.doi.org/10.1126/science.7824951

I also threw in a question that uses the shrunken2 gene (one of the two most common genes that convert normal starchy corn into sweet corn). From the question in question:

Note the shriveling of the yellow kernels that carry two broken copies of the shrunken2 gene, the purple kernels carry either one broken and one working copy of shrunken2, or two working copies. The change in color is controlled by another gene nearby on the same chromosome, shrunken2 itself has no effect on the color of corn kernels. Photo credit goes to MG Neuffer and MaizeGDB.

Corn kernels without a working copy of the shrunken2 gene can’t convert very much of the sugar provided by photosynthesis in the leaves of the corn plant into starch. Instead, sugar itself accumulates in the kernel making the corn taste quite sweet.

When sugary corn kernels are dried, they shrivel up, while starchy ones remain relatively round and smooth. This has to do with the fact that sugars are water soluble while starch is not. So, as I understand it, corn kernels with more sugar are also a greater percentage water than corn kernels that are made mostly of starch.

The mutant form of shrunken2 was identified by John Laughnan, a maize geneticist at the University of Illinois Urbana-Champaign. The story of the discovery as told in Maize Genetics and Breeding in the 20th Century by Peter Peterson and Angelo Bianchi: (more…)

February 2, 2010

Turkey Domestication

Filed under: agriculture — Tags: , — James @ 6:30 pm

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…)

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