Whole genome harvesting

You think the human genome, with its three billion base pairs and 23 chromosome pairs, is too complex to unravel? Turns out, the wheat genome is six times as big and it's hexaploid, in other words, instead of chromosome pairs it's organized in chromosome sextets!

I've recently discussed genetically modified organisms, crops in particular, and while I still can't provide a definite answer on whether they are absolutely good or absolutely bad, one thing struck me as relevant as I was researching the topic: between climate changes and an exponentially growing population, we are making drastic changes to our planet and resources. While Mother Nature is usually able to buffer changes and constantly adapt to new environments, the changes human kind is bringing upon the planet are happening at such a fast rate that natural adaptation is unable to keep up.

I think at some point we will have to face a hard choice: either starve or give in to GMOs, where by GMOs I mean crops that are bioengineered to yield more in harsher conditions. Again, I'm not saying we should all embrace GMOs as they are healthy and good for us. I really don't know. What I'm saying is that we may not have a choice: in 2009 the FAO estimated that in order to meet the ever-growing demand, wheat production has to increase by 60% by 2050. In the 20th century, the Green Revolution met the increase in demand with the technology known at the time. Today, given the FAO estimate, we may face the need of a second Green Revolution.

With this in mind, you understand the importance of sequencing the wheat genome, a task that is complicated by the complexity of the genome itself. Its three sets of chromosome pairs originated first from the hybridization of two diploid wild grasses, which originated tetraploid wheats (two sets of chromosome pairs) like durum wheat. After thousand years of domestications, these underwent a further hybridization, yielding the hexaploid wheats commonly used today to make bread. Domestication led to a bottleneck in genome variety, nonetheless, the wheat genome has a high percentage of repeats (roughly 80%, mostly retroelements) that yield great variation in length and gene order, making it difficult to sequence.

Despite these obstacles, two papers [1,2] in the latest issue of Nature report using both whole-genome 454 sequencing and shotgun sequencing to assemble the genome of bread wheat and barley. Both sequencing methods have the shortcoming of being applicable to very short regions, and therefore additional work is required to reassemble the full genome out of the various short sequences.

Interestingly, the wheat genome appears to implement a lot of the variation mechanisms I've been extensively discussing here on the blog:

"Several classes of plant DNA transposons and retroelements create and amplify gene fragments, disrupt genes and create pseudogenes, which can influence gene expression through epigenetic mechanisms [1]."

Similarly, in barley:

"Abundant alternative splicing, premature termination codons and novel transcriptionally active regions suggest that post-transcriptional processing forms an important regulatory layer. Survey sequences from diverse accessions reveal a landscape of extensive single-nucleotide variation [2]."

Brenchley et al. [1] conclude:

"Major efforts are underway to improve wheat productivity by increasing genetic diversity in breeding materials and through genetic analysis of traits43. The genomic resources that we have developed promise to accelerate progress by facilitating the identification of useful variation in genes of wheat landraces and progenitor species, and by providing genomic landmarks to guide progeny selection. Analysis of complex polygenic traits such as yield and nutrient use efficiency will also be accelerated, contributing to sustainable increases in wheat crop production [1]."

[1] Brenchley, R., Spannagl, M., Pfeifer, M., Barker, G., D’Amore, R., Allen, A., McKenzie, N., Kramer, M., Kerhornou, A., Bolser, D., Kay, S., Waite, D., Trick, M., Bancroft, I., Gu, Y., Huo, N., Luo, M., Sehgal, S., et al. (2012). Analysis of the bread wheat genome using whole-genome shotgun sequencing Nature, 491 (7426), 705-710 DOI: 10.1038/nature11650

[2] Mayer, K., Waugh, R., Langridge, P., Close, T., Wise, R., Graner, A., Matsumoto, T., Sato, K., Schulman, A., et al. (2012). A physical, genetic and functional sequence assembly of the barley genome Nature DOI: 10.1038/nature11543

GMOs love me, GMOs love me not..

I've been asked to discuss genetically modified foods and I confess I've been procrastinating. Why? Because I don't have an answer on whether or not GMOs are good or bad, and I can't offer one. But, what I can do is offer a few thoughts. Food for thought is usually super-natural, organic, and pesticide-free, so here it goes. :-)

1. What are GMOs?
Technically, all domesticated plants and animals are "genetically modified" since, rather than letting the species evolve through natural selection, mankind has steadily selected offsprings according to some man-made criteria. However, today's technology allows us to artificially modify an organism's genome. The difference between the two is not just in time scale: when selecting crops, or, more in general, any organism, generation after generation based on phenotype, uncharacterized genes are introduced in the species. Genetically engineering, or bioengineering, however, introduces a few well-characterized genes (often from a different species) into the organism. In a way, this is no news: gene therapy creates genetically modified organisms. Humanized mice are created in labs to test drugs and other therapies. The question of whether or not GMOs are good arises in the food industry. Are they safe to eat?

2. The Cartagena Protocol on Biosafety
As California gets ready to cast its vote on Proposition 37 [1] (which would require foods to denote their GMO content on the labels), it is good to review what currently is in act to "protect" us from possible hazards. From Wikipedia:

"The Cartagena Protocol on Biosafety is an international agreement on biosafety, as a supplement to the Convention on Biological Diversity. The Biosafety Protocol seeks to protect biological diversity from the potential risks posed by genetically modified organisms resulting from modern biotechnology."

"The Biosafety Protocol makes clear that products from new technologies must be based on the precautionary principle and allow developing nations to balance public health against economic benefits. It will for example let countries ban imports of a genetically modified organism if they feel there is not enough scientific evidence that the product is safe and requires exporters to label shipments containing genetically altered commodities such as corn or cotton."

3. Why are foods genetically modified?
For a number of reasons, some good and some not so good. Some are just practical reasons in a world that, whether we like it or not, is getting more and more "globalized": the first bioengineered produce was a tomato designed to have a prolonged shelf life. Some crops are genetically modified to resist harsher herbicides and pesticides. Others, are genetically modified to desist bugs from eating them. For example, genes producing Bt toxins have been introduced in cotton and corn. These toxins kill caterpillars that would otherwise eat up the whole crop. Notably, the modification benefits not only the genetically modified crops, but, since it reduces the global population of harmful caterpillars, it also benefits the non-modified crops.

I expect foods that can resist herbicides to be soaked in chemicals. On the other hand, if a crop is genetically modified so its flowers/fruits/seeds no longer offer a viable environment to certain parasites, I expect those foods to be pesticide-free. Yes, I'll take a few modified genes over harmful chemicals. Bottom line: NOTING WHETHER OR NOT A CERTAIN FOOD CONTAINS GMOs DOES NOT HELP. What you should really demand in a label is WHY SUCH FOOD WAS MODIFIED AND WHAT WAS ACHIEVED THROUGH THE BIOENGINEERING. Notice that while the Food and Drug administration currently does not impose any GMO labeling, their guideline recommendations state that the GMO content be noted, as well as the reason why the food was modified, and what was achieved through the modification.

4. Genetic homogeneity is bad
Rice is one of the most consumed crops in the world. Again, from Wikipedia:

"As of 2009 world food consumption of rice was 531,639 thousands metric tons of paddy equivalent (354,603 of milled equivalent), while the far largest consumers were China consuming 156,312 thousands metric tons of paddy equivalent (29.4% of the world consumption) and India consuming 123,508 thousands metric tons of paddy equivalent (23.3% of the world consumption). Between 1961 and 2002, per capita consumption of rice increased by 40%."

Rice is also highly "domesticated", as it has been selected over thousands of years to fit human needs. Currently, there are 20 different kinds of rice, but, according to FAO, the Food and Agriculture Organization, "It is estimated that not even 15 percent of the potential diversity has been utilized." This is a THREAT to food security. If a pesticide-resistant parasite were to attack rice crops, it'd be lethal to the vast majority of rice varieties currently harvested. Heavy use of pesticides favors the selection of pesticide-resistant organisms, while domestication favors genetic homogeneity in crops. This is NOT a good combination. Another reason why, between GMOs and pesticides, I'd favor GMOs. And if GMO research can prevent a pesticide-resistant organism to wipe out 50% of the world-wide food, hey, who's to complain?

5. Knowledge is NOT power if that knowledge is poorly understood
We live in a strange era when technology leaps forward at a higher speed than our ability to comprehend its output, especially in the field of genetics. We have loads of data we don't quite know how to store, let alone analyze. It's getting cheaper and cheaper to have a full human genome typed and companies are advocating that we do it for every individual. But are we capable of understanding the data? Last week I posted a shocking story of a boy discriminated because he carries a recessive mutation for a disease he doesn't have and he's at no risk of contracting (that's what recessive means). The Internet is full of bogus info on genes, genetics, mutations, etc. There's more noise than ever, giving people the illusion that they know when in fact they don't. I fear that the same will happen for GMOs. Once those labels come out, will people be able to understand what they mean? If Prop 37 will only require a "content" statement without a "reason", for example, will the information be really useful or will it just generate a stigma?

You now see why I cannot tell you whether GMOs are good or bad. They can be both! (Aren't we all?)

Food always has a higher impact than other things, but if you think about it, there are so many things that we've introduced in our daily lives in the past few decades that we simply don't know whether or not they are good IN THE LONG RUN: wi-fi, for example. Cell phones. Chemicals in skin products, from sun protection to cosmetics. I'm afraid the next generation will be the test. So the real question is: do we want to experiment with our children as guinea pigs? Sadly, when you put it in these terms, it seems to me it's too late to go back. The experiment has already begun.

If these few thoughts weren't depressing enough, read Pamela Ronald's review, referenced below [2]. One of the great points Ronald makes is that we are changing our climate and environment much faster than ever before (thanks to climate change and an exponentially growing population). Natural selection can't keep up with the pace, hence

"an important goal for genetic improvement of agricultural crops is to adapt our existing food crops to increasing temperatures, decreased water availability in some places and flooding in others, rising salinity, and changing pathogen and insect threats."

The review is clearly biased in favor of GMOs and it lists several benefits from such procedures. While advocating for adequate testing on every newly modified organisms, it also reports that all genetically modified crops tested so far have been deemed safe and substantially no different than conventionally selected crops "in terms of unintended consequences to human health and the environment."

Bottom line: I can't tell you what to vote on Prop 37 and I can't tell you whether or not you should avoid GMOs. Just read as much as you can and be sure to form your own opinion.

REFERENCES:

[1] Baker, M. (2012). Companies set to fight food-label plan Nature, 488 (7412), 443-443 DOI: 10.1038/488443a

[2] Ronald, P. (2011). Plant Genetics, Sustainable Agriculture and Global Food Security Genetics, 188 (1), 11-20 DOI: 10.1534/genetics.111.128553