What is C4 rice?
c4rice.irri.org
c4rice.irri.org
I genuinely think C4 rice the best shot we've got at alleviating a huge chunk of world hunger in one (extremely difficult) move.
Some key points:
- C4 plants (like maize and sugarcane) are generally about 50% more efficient at biomass accumulation than C3 plants (like rice and wheat). C4 rice could mean a yield increase for rice of up to 50% _with no increase in inputs_
- RuBisCO is by far the most abundant protein in plants. It accounts for the majority of the nitrogen required by C3 plants, and the inefficiency of C3 is the reason we have to use so much nitrogen fertiliser. C4 rice would require considerably less fertiliser than C3 rice.
- C4 plants use CO2 much more efficiently that C3 plants. This allows them to keep their stomata closed much more of the time, so they lose less water through transpiration. This makes C4 plants much more water efficient - C4 rice could require much less water than C3 rice, meaning it could be grown on land that is currently unsuitable for rice production.
- C4 is probably the most interesting example of convergent evolution we know about. It has evolved over 70 times independently. This is quite amazing - it's a complex trait that requires dozens of proteins to be organised in a particular temporal and spatial pattern, and needs a new cell type to be made. Yet it has evolved 70+ times.
- We are using the recurrent evolution pattern as our 'way in' to the problem of figuring out how to control C4 at the molecular level. We analyse gene expression on a massive scale in C4 and C3 sister species from all the evolutionary origins of the trait.
- This involves a lot of interesting software challenges that hn might be interested in. For example, we're working with so many species that we can't sequence all their genomes. But we can sequence their _transcriptomes_, which is all the genes that are expressed at a given time. The sequencing technology produces millions of tiny fragments of the original sequences, which have to be pieced back together to be useful (an NP-hard problem).
I couldn't agree more. I really hope this rampant science denialism that is getting traction in American society is just profoundly ignored by those in power.
It's not unscientific at all. Whether to perform extensive testing on foods is not a function of science but of public opinion.
The science tells us that all plant-derived foods outside a very small group of sources are extremely likely to be safe for the vast majority of people. There are very few exceptions, but there are some, like potatoes and tomatoes, which are both derived from poisonous wild ancestors so new strains need to be checked for reversion to the wild state. I say 'the vast majority of people', because some tiny number of people can have allergic reactions to any food, whether derived from a GMO or not.
We don't perform any testing at all on the majority of new foods introduced. This includes new plant strains bred by various mutagenesis strategies, where vast numbers of mutations are induced by chemicals or with x-rays. By comparison, GMO-derived foods receive extensive testing, but only due to public opinion, not because they are inherently more dangerous. They are in fact inherently more safe. In the process of producing a new strain by genetic modification, very few changes will be made to the genome, and they will tend to be highly predictable, whereas the conventional breeding process is highly unpredictable and introduces lots of unwanted effects. This has been demonstrated in dozens of studies.
> So, if you want to help the hungry, re-engineer the political and the economical system
This can only be said from a position of first-world comfort. It would be wonderful if we could solve the resource distribution problem. But let's not kid ourselves: it would be crazy to only try to fix the economics. What's the timescale on that change? A very long time. How likely is it to work? Not at all likely. Improving agricultural yields through technology is something we definitely can achieve, and the timescale is predictable. Hungry people will choose the technology that allows them to feed themselves now, not the promise that if the entire world economy changes they may one day get some food.
I'm not saying don't try to fix other things. I'm saying do both.
Most of the world's poor do not import food, they grow it in their immediate vicinity. Increased yields help them directly.
If you have a solution to the food distribution problem, by all means let's work on that at the same time. But there's no reason not to work on crop efficiency.
Part of the issue with 'GMO' is that many people see it as a way for 'Big Ag' to tighten its control on the food supply. This project is an example of GMO being used for humanitarian benefit on a massive scale, with no benefit to 'Big Ag'. However, that's not enough - Golden rice for example has been met with a deliberate campaign of resistance by Greenpeace.
The fundamentally important thing is that the farmers don't get fed misinformation. IRRI, who coordinate the C4 rice project, have a huge community outreach and participation program, and do an incredible amount of education with farmers. If the farmers want the technology, it will happen. And in the market, if people want the food, it will happen. Hungry people don't give a crap what Greenpeace say.
The hardest thing is discovering how the system is fundamentally regulated, and we are making rapid progress. Our massively high throughput approach gives us huge lists of candidate genes with probabilities, so we can rank them and process them through a biological testing pipeline quite fast. Using this process we've discovered a whole lot in the last two years - for example we now have a toolbox of genes we can use to precisely time gene expression in the bundle sheath cell (the cell C4 plants concentrate RuBisCO in). Our computational systems are rapidly improving, and I think 2015 will be a big year for us. Final year of my PhD, and I intend to go out with a bang :).
The secondary challenge is building the system in rice, but unless everything we know about molecular biology is wrong, this will work. We've already started by putting the parts we do know about in the right places in separate plants, then breeding them together ('gene stacking'). This happens in parallel with the discovery.
The major uncertainty is in the timescale - 15 years is ambitious, but not unlikely. 20 years is likely. With a colleague at LSE, I did some simulations of what the impact of success would be at various timescales, and 20 years would still be a vast humanitarian win. Every year we can shave off the time to delivery potentially saves tens of thousands of lives and lifts another hundreds thousand or so people out of food scarcity.
[1] http://www.goldenrice.org/Content1-Who/who4_IP.php
[2] "low-income, food-deficit countries as defined by FAO" - see http://www.fao.org/countryprofiles/lifdc/en/
Are you talking about sequencing enough to get adequate coverage for reconstruction?
Also, what do you think of the criticism that it is difficult to know the potential effects of GMO on their ecosystems in the wild?
Including what I had until then assumed was the simple act of just sampling DNA material: multiple consistent sites on the plants were sampled and this context was important not just for gene expression, but overall sanity checking of final assemblies (speaking of sanity checks: flow cytometry as well). Then there was setting up Illumina and 454 sequencing experiments, which seemed to involve quite a few iterations/experimentation in developing primers, choosing bead configuration, amplification procedures and a whole lot of other stuff I don't understand...
And still, after all that, the literature did have a bunch of species that had already had a few genes sequenced using earlier methods and traditional PCRs, so the whole sample set was given this treatment as well, again as a sanity check and to get a strong reference to earlier results (1000+ of species, thousands of individual plants, each with multiple samples as I mentioned).
And still, after all that... the evolutionary history of this group of plants still looks slightly different depending on which genes you looked at.
And so now I know what a consensus tree is... and how much fun it is to see researchers have their software doing MCMC tree building run in just a few days on HPC compute clusters when they'd previously waited months :-)
Yes. Assembling a genome requires a lot of sequencing data or different kinds, and is expensive. Genomes (especially in plants) can be huge. We're only interested, at least in this specific example, in the things that are expressed. These make up a small proportion of the genome, and so we sequence only those things.
> Also, what do you think of the criticism that it is difficult to know the potential effects of GMO on their ecosystems in the wild?
Agriculture in general has a vast impact on the environment. This is true across the board - including organic, GMOs, 'conventional', etc. By its very nature agriculture is about shaping the environment so we can control a piece of it to optimise it for food production. Our responsibility is to try to predict and minimise the effects that might cause problems.
So far, GMOs have proven to have relatively little effect on the environment (compared to other drivers of agricultural productivity, like pesticide and herbicide use, for example).
In the case of C4 rice we can predict what the major potential issue might be: C4 rice plants might perform so well that they outcompete wild plants outside the field setting. `There are some technological tricks we can use to try to ensure plants don't do well outside the field.
Some plants developed with GMO technology might of course behave differently from other variants of same species; for instance if some GMO variantg grows up faster than previous seeds and is harvested faster and you can grow another crop in the same season and get a better yield, then there is of course more need for fertilizing etc. But that in itself does not come from something being GMO.
I should point out that herbicide resistance in weeds was widespread before GMOs by other mechanisms, and in fact the switch to glyphosate has been a great thing because we've massively reduced the application of harmful chemicals, while glyphosate is benign. But the fact remains that GMOs do carry their own specific risks that are a result of the technology and methodology, rather than the specific application.
In my experience most systems are a series of tradeoffs. Even though C4 has evolved over 70 times, are there advantages conveyed by C3 or is C3 just easier to evolve?
The evolutionary history goes something like this. 3.6 billion years ago, Earth's atmosphere was very rich in CO2 and had basically no O2. Then photosynthesis evolved in bacteria in the ocean, using the enzyme RuBisCO to trap CO2 into sugars. Those bacteria became incredibly successful and in the process released a lot of O2 into the atmosphere - over the next 2 billion years the atmosphere became oxygenated. Unfortunately, RuBisCO sometimes mistakes O2 for CO2 and accidentally creates a toxic product that wastes energy instead of storing it. So this new oxygen-rich atmosphere started to make photosynthesis more efficient. Eventually (42 million years ago) the atmosphere became so oxygen rich and CO2-depleted that this inefficiency was a major evolutionary pressure, and C4 started to pop up.
There's very little compromise with C4 - it's just better in a very wide range of commonly occurring environmental conditions.
> About 7,600 plant species use C4 carbon fixation, which represents about 3% of all terrestrial species of plants.
> These include the food crops maize, sugar cane, millet, and sorghum
(The section http://en.wikipedia.org/wiki/C4_carbon_fixation#C4_leaf_anat... is easier to read because it's not so technical.)
Is it easier to transform the rice in a C4 plant or to transfprm the rice fields to maize fields? [Disclaimer: My family is from the north of Argentina and we really like maize.]
A 50% yield increase in rice could alleviate starvation for the most starving continent on the planet.
My mother, however, grew up on a rice farm in Louisiana. C4 rice would be very welcome as long as there's plenty of hungry mouths to feed.
As far as the biology goes, not that I'm paying any attention to the field, this is the most ambitious genetic engineering project I've ever heard of. Hope they can pull it off.
0: http://en.wikipedia.org/wiki/Photosynthesis#Carbon_concentra...
In light of this, it should be questioned whether the use of optimized crop variants could be the right answer to the problem of feeding billions of people, and whether it can be a _sustainable_ solution. OK, let's say we can increase yield by 50%. What comes after that? (2)
I know it is a controversial and touchy subject, and also somewhat off-topic, but personally I'm quite convinced that the answer to current food shortages is not increased production, but rather the reduction of (over)consumption.
[1] The UNEP reports that "today, nearly half of the world’s cereals are being used for animal feed." - http://www.unep.org/pdf/FoodCrisis_lores.pdf
[2] It is interesting that the same UNEP report, among the seven options it proposes for dealing with food shortage (pp. 92-93), does not once mention GM crops or increasing yields as a possible solution.
However, this doesn't change the optimal strategy for feeding people in the medium term, for a bunch of reasons:
1. The arable land used for feeding animals would not necessarily be available for feeding people who are hungry now if it were to be freed up.
2. In general the world's poorest people grow their own food on small plots of land and don't produce a lot of meat. They care about the productivity of their plot of land.
3. Changing the world's eating habits is a gargantuan task. Are you suggesting we stop trying to feed people in the medium term using technology, and allow them to starve while we try to convince westerners not to eat meat? I know this is not what you're suggesting - but it serves to show that we should of course be pursuing all the available routes to alleviating hunger.
> OK, let's say we can increase yield by 50%. What comes after that?
That's enough to meet the entire calorific intake increase for rice-eating countries by the time population stabilises. By around 2050 the world population will have stopped growing. So what comes after that is that everyone is fed, and we can enjoy a world where very few people go hungry while we fix the much more difficult problems of economics and society.
Finally, the UNEP report doesn't talk about the potential for GM crops because it's out of scope - the report is about environmental factors in food production. They do say that their projections could be affected by improvements in GM technology.
Sure, growth rates would be slow, but the lack of need for irrigation and ability to utilize tracts of arid land might offset this.
I'm sure somebody at some point has looked into this. Any insight OP?
No offense (seriously), but this argument is the biggest load of bullshit.
Do you think there are any major food sources that just developed, as is, naturally? Pretty much every vegetable, fruit, grain, or pulse - has been selectively developed by humans, many over the course of thousands of years. The bananas we eat can't even reproduce without our direct intervention. Animals, too, both livestock and pets - that dachshund wasn't running wild in the forest before we tamed it.
We've been playing with nature as long as we've been able to do so. Genetic engineering is just a better set of tools for it. Somehow, though, people have convinced themselves that the selective breeding process is safer than direct genetic manipulation. Because, of course, breeding crops based on taste or visual appeal makes for safer and better development of crops - why pick the specific traits you want when you can just fumble about for generations without a clear idea of what you're gonna get?
Should we be careful? Sure, in this as in all things we do; but the fact that the technology is new isn't the reason why.
It just so happens that Asimov (the guy who wrote the series of short stories which inspired the title and character names of I, Robot) had something memorable to say about this kind of silliness:
Anti-intellectualism has been a constant thread winding its way
through our political and cultural life, nurtured by the false notion
that democracy means that 'my ignorance is just as good as your knowledge.'
- Asimov