Cotton like Candy

Or Cottonseed you can Eat thanks to Genetic Engineering.
A few years ago, I read about a research group that had used genetic engineering to remove a poisonous compound from cotton seed. Now, it seems, they are one step closer to making a positive impact on the availability of food for people in developing countries and beyond. Time Magazine reports that Dr. Keerti Rathore and his team, who made the development years ago have now moved on to field trials, a necessary step to test the resilience and effectiveness of the trait in real-world conditions.

RNA that Interferes

Let me tell you how this works. They used a technique called RNA interference, or RNAi. When plants (and other organisms we are finding) are infected with a virus that uses RNA as its genetic material, they defend themselves by chopping up the offending molecule. Cells use the double-stranded DNA as genetic material, and use the very similar single-stranded RNA to carry information from the genes to the rest of the cell for making proteins. But the RNA that these viruses use is double-stranded, like DNA. Since plants don’t use RNA as a double-strand, this gives them something different to detect and destroy, and that’s what they do.

An enzyme called Dicer detects double-stranded RNA and chops it up into little pieces, about 20 bases long, and a complex of enzymes called the RNA Induced Silencing Complex (RISC) uses those short pieces to destroy any other RNA molecules that come along that match the sequence of those short pieces. These short pieces of RNA are called Small Interfering RNA or siRNA.

The goal of RNA-based viruses, or retroviruses, is to make DNA from their RNA genomes, and insert this DNA into the host cell where it can be used to make more viruses. So in addition to knocking out similar genes, a similar complex of enzymes called RITS (RNA-induced Transcriptional Silencing) can also find any genes in the cell’s DNA that match the siRNAs and ‘silence’ them by attaching small molecules called methyl groups to the DNA. This tells the cell’s enzymes to skip over the likely viral gene, protecting the cell from becoming a virus factory.
Once cells evolved this amazing defense mechanism, they put it to good use in their own evolution. (This is assuming the defense mechanism evolved first.) Now cells had a way to silence their own genes if need be. So if a gene produces an RNA molecule that doubles-back on itself, along comes Dicer to chop it up. The small pieces of RNA that are made in this fashion are called Micro RNAs, or miRNA. Any genes that match the sequence of this miRNA are doomed to be turned off.
In general, all it takes to get this silencing effect is to have an otherwise normal-looking gene with part of the gene duplicated and turned the other way around. This forms a ‘hairpin loop’ (looks like a bobby pin) in the RNA that gene produces, because the reversed part of the sequence can come back around and hook up with the forward part of the seqeunce. Now people with experience in RNAi will say, hey, it’s not that easy, but that’s the basic idea.
Micro RNAs are very cool, and they are rising in importance in genetics. When I was touring grad schools in 2007, one professor in Illinois showed me a picture of two soybeans, one green and one yellow, and asked me whether I thought the yellow soybean was caused by a dominant or recessive gene.
I answered, “Well, my first thought is that since the soybean lacks pigment, that it has a mutation in one of the genes in the pigment pathway that prevents the pigment from being formed, which is usually recessive.”
But I continued, “However if it is caused by a Micro RNA silencing one of those genes, then it would be dominant.” I was right, the yellow mutant was caused by a Micro RNA, that turned off one of the pigment genes in the way I described above.
“Ah, I tried to trick you!” She said. I forget whether she was holding her fist in the air as if to say, ‘foiled again,’ but it felt like that.
RNAi makes things just as if the gene it silences isn’t even there, kind of like if the gene was mutated so that it didn’t work anymore. But cells usually have two copies of every gene, one on each paired chromosome. Some plants have more than two of each chromosome, so they can have more. Usually, if you mutate a gene so that it doesn’t work anymore, the normal working copy or copies will still do the job in its absence. Such “knockouts” are therefore recessive, and you have to have every copy of the gene be non-functional to get your desired trait. Not with RNAi.
With RNAi, you usually only need one copy of the silencing gene, and it will turn off every copy of the target gene, and sometimes even similar genes in the same ‘gene family.’ Thus, MicroRNAs, whether natural or human-made, are dominant genes. One drop of miRNA does it.

The Gossypol Wall

Now let’s talk about the cotton. Cotton is grown for fiber, in fact every piece of clothing I am wearing right now is made from it. But sometimes, also, cottonseed is fed to ruminant cattle which can manage to digest it. But the rest of our farm animals, and us especially, cannot stomach it. That is because it contains a compound called Gossypol, which can cause low potassium levels and paralysis. (It can also apparently work as an effective male contraceptive… if you ignore the paralysis part.)
In the 1950s, researchers knew that cottonseed could be painstakingly processed to remove the poisonous gossypol, it made a suitable edible food. Cottonseed oil also finds its way into some foods today. So they decided that they would try to breed a gossypol-free cottonseed. By stacking up recessive nonfunctional or deleted gossypol genes in a cotton plant, they successfully made an edible cottonseed. The trouble was, it made a cotton plant that was itself quite edible for pests! Gossypol was necessary for plant defense througout the plant, so by knocking out the genes entirely it made a newly edible food that couldn’t be grown.
Fast forward fifty years to the work of Rathore et al. They realized that we have the technology to turn off the gossypol-making genes only in the seed, leaving the genes still working in the rest of the plant. Every gene has at least one promoter, a piece of DNA in front of it (or inside, and sometimes somewhere else), that tells the cell that there’s a gene there to express, and it also tells the cell when to express it. There are promoters that turn the gene on all the time, promoters that tell it to turn on only when a signal like an infection or insect attack is happening, promoters for stresses like drought, and promoters that turn the gene on only in certain tissues. Since all cells of the same plant have the same genes, the difference between each cell arises from which genes are being used and at what time.
Dr. Rathore and co. found a seed-specific promoter, one that turns on a gene only in the seed, and attached it to their RNAi construct that makes Micro RNAs. When they inserted it into a cotton plant and grew it, they found gossypol being produced in the leaves and stems as normal, and the compound was drastically reduced in the seeds. Success!

44 Million Metric Tons of Fun

What are the potential implications for this development? First, it opens up a huge potential source of food, particularly protein. From the 2006 article:

“Very few people realize that for every pound of cotton fiber, the plant produces 1.6 pounds of seed,” Rathore pointed out. “The world produces 44 million metric tons of cottonseed each year. Cottonseed typically contains about 22 percent protein, and it’s a very high-quality protein.”
In all, about 10 million metric tons of protein are contained in that amount of seed, he said.

They did the math, and calculated that this is enough protein to meet the daily requirements of 500,000,000 people. Half a billion.
That’s almost 1/13th of the human population. Yeah, this could be a big deal someday.
Next, since cottonseed was considered mostly a waste product of farms, it now becomes a thing of value to the farmer. This means that cotton farming from the Third World to the New World can be more profitable.
Finally, this could also reduce the costs of processing cottonseed for oil and animal feed, which is fairly costly. Looks like this patent is going to be worth some money someday.
But the most important part in my opinion is what this means for farmers and other people in developing countries who will be able to directly benefit from additional food on the market. As cottonseed will compete against other commodities, it could also lower the cost of other foods at the same time.
The new development reported by Time Magazine is that since the research on this RNAi gossypol first came out, it has progressed from the greenhouse to full-fledged field trials. They found that it worked just as well in the field as in the greenhouse. There doesn’t appear to be a paper in publication yet, according to a Pubmed search, but when that happens I will be interested to find out more about how well it did.
The fact that they used RNAi also has other implications. If somehow, a mutant cotton plant was found that doesn’t produce gossypol in its seeds, chances are it would be a recessive mutation, as I explained above. If this was bred into a cotton variety and grown in a field it should work just fine, just like the genetically engineered one does. But if someone plants a normal, wild-type cotton field next to it, it could cross-pollinate the recessive gossypol-free plants. Since the genetics of seeds depend on both of their parents and not just one, some of the seeds on the recessive plants could have dominant genes in them, thus restoring the poisonous gossypol.
RNAi cotton would not have this problem. It would already have the same gossypol-producing genes as every other cotton, and would silence them all the same. Farmers could be confident that their cotton will produce edible seeds no matter what their neighbors grow.
Imagine a farmer in India with only a few acres that can now sell their once almost-worthless piles of cotton seed as a food commodity… or maybe cook and eat them!

Failure Repealed

This news reminds me about The Union of Concerned Scientists’ recent report, ‘Failure to Yield.‘ Rather, it reminds me about how limited in scope the report was, excluding everything but transgenic soybeans and corn from consideration. The author, Doug Gurian-Sherman, explained that cotton was excluded from the report because it was not enough of a food crop since it was grown for fiber and animal feed.

Failure to Yield was motivated in large part by the “global food crisis” of the past few years. So we wanted to examine the ability of GE to address the challenges for food production given a growing global population, changing consumption patterns, and climate change impacts. For this reason, we decided to look at major GE food or feed crops in the United States, and this means soybeans and corn. We didn’t include canola, an oilseed crop, because the acreage devoted to canola, about a million acres, is only 0.6 percent of the acreage devoted to corn and soybeans in 2008.
Cotton was excluded because it is primarily a fiber crop. Cotton seed meal may also be used as animal feed, and the plant itself as fodder in some places, but these uses are secondary to fiber production. In other words, we did not look at GE cotton because the report is intended to inform the solution of the global food crisis, not a global clothing crisis.

Har har. The first thing I thought of when I read this explanation was the 2006 paper, written long before the UCS report. I had no idea how far along the research was at the time, so this news brings the UCS report to the forefront again. Here we have a report purporting to analyze genetic engineering’s potential to aid in the global food crisis, yet totally ignoring the ways that genetic engineering can help people obtain more food (and protein in this case!) other than increases in yield. The above passage also makes several tenuous arguments to justify excluding increases in cotton (and canola) yield that Gurian-Sherman admits elsewhere are indeed real.

Bt cotton has been studied in developing-country settings but there’s been less study of Bt corn. Yield increases can often vary from about 10 to 40%, and sometimes more.

So therefore, if this RNAi trait is included in Bt cotton, those 10-40% (to 80% according to one study, mentioned here by Pam Ronald) yield increases in cotton can indeed contribute to the rising global demand for food. That is, yield increases after this genetically-engineered trait could already provide enough protein to feed half a billion people per year.

Nutty with a crunch?

This is a fascinating development, not only from a genetics perspective, or a food production standpoint, but also from the point of view of cuisines. According to Dr. Keerti Rathore, cottonseed “tastes like chickpeas.” I wonder what kind of foods cottonseed will lend itself well to? Could we find a cottonseed masala, or see it one day floating in chicken soup instead of barley? Or would a cottonseed pilaf be more in order, with orzo, pecans, mushrooms, and sage?
Since cotton is also widely grown in the US, perhaps I might soon get to find out how toasted “TAMU nuts“* taste.

*TAMU stands for Texas A&M University. Cute.