Yabba Dabba Rabba Dopsis: A coming revolution in crop yields during times of drought?

July 25, 2012 |

Can new computational power, souped-up genetic knowledge and fresh algorithms usher in a new era in crop yields, and resistance to disease and drought?

Will a new model plant revolutionize energy grasses and food crops, and transform crop-based genetic engineers from a modern Stone Age family into Masters of the Digital Age?

Here we are, some 30+ years into the era of genetic modification of crops. The primary breadbasket of the world, the United States, is experiencing its most severe drought conditions in decades, and you might well ask how many new drought-resistant genetic traits are in commercial release around the world?

That would be zero.

As Tom Brutnell at the Missouri-based Danforth Center explains the problem, “In the long term outlook in climate change, the Midwest is not expected to be getting droughts frequently, but when they do come, the market is so tight that the effect is immediate. Monsanto and others have been investing quite heavily, in next-generation, drought tolerant crops, especially as we push production onto more marginal soils, and over time see more severe weather with climate change.

“These episodes of drought will hit China hardest, but everywhere will be more prolonged and more severe when they hit. Drought is the most abiotic stress that will affect their bottom line.”

So, where are the drought-resistant crops? Where, for that matter, are super yields, salt tolerance, super efficient use of, say, nitrogen, potassium and phosphorus – and so on and so on?

Not that much depends on the outcome. Only yields – the key to biomass as an energy platform. And, the fate of virtually every biofuels company, the availability of food amidst rising populations, land grabs in the South by worried nations from the North, the general availability of potable water, and agricultural productivity as the fundamental and abiding technology that powers advanced civilization.

As I said, not much depends on the outcome. Especially for those planning on interplanetary migration.

Part of the problem lies with one of the most useful plants ever discovered, and that is arabadopsis. Much of the rest of the problem lies with the tools that have been available to date to understand how plants work, as a total system, when it comes to system-wide responses such as the stress response to drought.

The Flintstone problem

Generally, what we have is a situation much like the Flintstones faced.

Yep, you remember that modern Stone Age family. Brilliant at exploiting the potential of some essentially primitive tools, like the foot-powered family car, or a dinosaur employed in quarrying operations. Well, it wasn’t exactly sound science, but it was good television, and illustrates a point.

Brutnell explains: “All transgenics to date, you take bacterial protein and express them in plants – take for example, disease resistance. You are working outside the plants’ system and that’s not to pooh-pooh earworm and root worm resistance, they have been critically important. But we are limited in the events we can find that work well.”

The limitations of the old ways

The limitations are to, some extent, imposed by our lack of the computational and genetic toolkits, and algorithms therein. No matter how brilliantly you innovate, you are limited by the power, speed and cost of the underlying tools – as was in the case down in Bedrock, too.

The result? Monsanto has “Drought Guard” in trial, a drought-tolerant corn, with 10,000 acres plamnted in a trial this year (and excellent conditions for analyzing rought response, we might add) and a first commercial release. But it’s a one-hit wonder gene, taking a bacterial cold shock protein, and trying to essentially infect the plant, thereby conferring the stress-resistant trait.

But, once the one-hit wonder works or does not, it’s right back to the lab to develop the next traits, one by one, hit or miss, hoping to find a winner – rather than taking a systemic approach to improving the genome.

Another limitation? The model plant that is most widely used for testing, arabidopsis, is not exactly a close cousin of the staple food crops and energy grasses in which we have the most interest. Arabidopsis, by the best estimates, diverged in evolutionary terms from the lines that make up today’s food and energy crops about 180 million years ago.

What we use arabidopsis for, generally, is a kind of “Mikey likes it” testing platform – to borrow an analogy from the LIFE cereal commercials over the years.

But imagine, instead of an older brother having Mikey try his cereal, imagine him using a duck-billed platypus – a line of animals that diverged from what became the human line about the same time that arabidopsis split off from the grasses.

So, why arabadopsis anyway. It’s remarkable well-understood, flowers quickly, goes seed to seed in a very short cycle, and we known how to put new genes in.

Over the past few years, a group of scientists have been working on developing a new model plant, brachypodium distaychon, and it has developed quite a following.

Bring on the new age

But last week in Missouri, the U.S. Department of Energy (DOE) awarded a five year, $12.1 million grant to researchers at the Donald Danforth Plant Science Center and their collaborators at the Carnegie Institution for Science, the University of Illinois, Urbana-Champaign, the University of Minnesota and Washington State University to develop a new model plant system, Setaria viridis, to advance bioenergy grasses as a sustainable source of renewable fuels.

As the DOE explained, “to engineer bioenergy grasses with the desirable traits needed for large scale production, it is necessary to develop model plant systems that are closely related to bioenergy feedstocks, but which are more amenable to genetic analysis. One of the most promising model species is the grass Setaria viridis.

Brutnell and his colleagues will utilize genomic, computational and engineering tools to begin the genetic dissection of drought and density response in S. viridis. The research team will produce one of the most extensive molecular characterizations of plant growth in the field to date, generating several million data points that will be collected from physiological and molecular genetic studies.

In doing so, they hope to discover the mechanisms that underlie drought responses and identify candidate genes and pathways for improving the closely related feedstock grasses. The ability of bioenergy feedstocks to use water efficiently and to produce abundant yields at high density will be major drivers in the development of improved varieties that can serve as a replacement for petroleum-based fuels.

A total of nine principal investigators and and co-principals will be working on the project.

What’s the big deal with Setaria?

There are two factors to consider. First, setaria is much closer to the grasses – which are the source of energy crops and staple food crops, than arabidopsis.

As Brutnell explains, “With arbidopsis, the wiring is very different from corn. Setaria viridis is more closely related to corn and miscanthus, and is a sister to switchgrass, with only 9-13 million years of evolution from switchgrass. So it looks fairly similar, and it is likely that likely setaria will deal with drought in the same way. If we can understand the process by which it moves resources in reponse to stress, then we can potentially engineer and breed for increased tolerance, based on a systems level understanding that takes into account micronutrient responses, water transport, and the gene regulation network by which genes are turned on and off.”

Second, more cost effective. To lay down a new gene in corn, it takes 1-2 years and around $5,000 – it can become prohibitive to the university-based researcher.

Brutnell explains. “We can do the same in setaria and its an order of magnitude less in cost, and could be as little as five days, and no more than 6 months, to get the same result.

What’s the other big win for this project?

It’s very much a project for now. That is to say, the mathematical, computational and genetic tools are just being invented now, or are just invented, that make such an effort possible.

“These are massive data sets,” said Brutness, “with millions of data points. Managing those data points is, among other things, a challenge of building computational systems. In the course of this project we will go from nothing to having one of most sophisticated collections of data on an organism.”

“It’s a very timely project where we are going with informatics, developing novel algorithms for doing the data analysis. It is a very exciting grant in resource development. And as we build these tools, we can use them to work on any plant.”

Yabba Dabba Doo: the bottom line

In transforming the food, energy and bio-based material platforms, there are the “tip of the iceberg” events in applied sciences.

Such as figuring out how to produce jet fuel from a synthesis of CO2, sunlight and brackish water in an affordable, sustainable system. Or, how to train algae to produce dielectric fluids that are worth quite a lot to companies like Dow that market them. Or how to squeeze more ethanol out of corn, or how to separate biobutanol from the broth, or get algae out of the water.

Then, there are the platform discoveries, such as new traits in plants, and bringing forward transformational new varietals of food and energy crops. They have been hard to develop – only a couple of companies like Ceres, SG Biofuels, Chromatin, Mendel Biotechnology and Agrisoma have been able to afford and get done the “hard yards” of development in energy crops. On the food side, giants like Monsanto, Dupont and Syngenta have been hard at it for a long time, but successes are expensive.

Two wins in prospect with this project. First, the establishment of setaria itself as a model plant system. Second – and we think even more importantly – the advancement of the toolkits in biology that will continue to power a sustainable driving force for cost-reduction and yield enhancement for bio-based systems. In the big battle between bio and more traditional forms of chemical engineering — and look at the impact that, say, fracking technology is having — a platform for robust improvement of the basic yields in photosynthesis is, to put it mildly, huge.

Or, as Fred Flintstone might exclaim, “Yabba Dabba Doo!”

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