As the planet warms, agricultural scientists are focusing on the root of the problem

Lisa m. Krieger Mercury News

SAN JOSE, Calif. — To feed a hotter, drier planet, Stanford scientists are building a smarter factory.

The team genetically reprogrammed plants, nurtured in a lab room, to grow long or short, branching or thin roots — traits that alter the ability to gather nutrients or water.

Controlling root growth could one day provide a powerful new tool for growers, especially in areas prone to drought or flooding with poor soils. Over the coming decades, experts say, we will need to grow crops that can produce unprecedented bounty in more extreme and unpredictable conditions, as populations grow. If improved root structures can increase the yield of a food crop, perhaps more food can be put on tables.

“The goal of all this work is to try to make plants that increase the sustainability of farming,” says plant systems biologist and Professor Jose Denene, whose work with Bioengineering Professor Jennifer Brophy is published in the journal Science.

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Scientists altered root structures by introducing DNA that alters a plant’s genetic circuits in response to environmental cues. Genetic circuits work like electrical circuits and can be turned on or off to adjust behaviour.

The goal is to engineer plants tailored to a specific environment — or, in the future, to give plants the ability to adjust themselves.

They tested their strategy on a type of mustard called Arabidopsis thaliana because it’s a fast and easy-to-grow plant. Now that the researchers have proven that the idea works, they plan to apply it to commercial crops.

Abroad, there may be less success. Organisms respond to the wild environment in unexpected ways. Other genes and genetic networks may require repair.

And critics like the Center for Food Safety argue that there are better ways to solve the problem, such as improving the soil or using traditional techniques to breed plants that can withstand the effects of climate change.

For years, researchers have tried to improve plants using traditional genetic engineering — inserting pieces of DNA from bacteria into a plant’s genome to alter a specific trait, such as resistance to pests and herbicides. Engineered to survive the herbicide Bulletin Report, corn, cotton and soybeans have become a standard on American fields.

But the emerging field of “synthetic biology” is accelerating research by offering more sophisticated tools. It is now possible to build or reprogram entire genomes—using gene parts custom-made from foundries, or “fab,” just as industry orders for cast and machined metal parts.

“The synthetic biology industry is booming in the Bay Area, with many entrepreneurs programming biological functions into living cells,” said John Kampers, founder and CEO of SynBioBeta, a global network of biological engineers. “We can now easily engineer an enzyme or cell to perform a specific function, such as making a new biochemical or substance.”

But, he said, until recently, the world of horticulture remained “largely beyond the reach of scientists.” “It’s one of the holy grails of bioengineering — how can we program plants to grow into whatever shape we desire?”

The Stanford technology provides precise and complex control, altering not just a single gene but the behavior of an entire group of plant genes to cause changes in root growth in diverse environmental conditions.

The team built synthetic DNA that changes circuits by creating a genetic switch, like a computer logic gate, to turn genes on and off.

The genetic switch allowed the team to adjust growth patterns, such as the number of branches in the root system, without changing the rest of the plant. For example, the “off” state created a layer of cells on the tip of a root that inhibited further growth.

The team envisions programming crops to develop root systems that are more angular, so that they sink deeper to find water or nitrogen, or more shallow, to prevent drowning during floods due to anoxia. Plants can be designed for density, sending up a single, long, non-infringing rootstock.

Between 1960 and 2010, the “Green Revolution” boosted world food production by 175% through improved use of fertilizers, high-yielding varieties, and irrigation techniques. But global crop yields are slowing.

Domestication has created plants that are inefficient at consuming water and nutrients, Denini said. They are designed for ideal environments.

He added that if yields are improved, it will help preserve what is left of our wilderness. “Unless we want to clear more forests to create more farmland, we are going to have to find ways to improve the way we grow plants for food,” he said.

But the project has been met with skepticism from critics such as Bill Friese, director of science at the Center for Food Safety.

“I have a feeling it’s a lot like the countless other examples of successes and failures, most of them misses, from research that I’ve seen,” he said. “I’ve seen a lot of ‘pie in the sky’ trials struggling because of technical hurdles.”

The promise has faded from some of the genetically modified plants, Friese said. For example, weeds are emerging resistant to the Roundup herbicide — so “Roundup Ready” engineered brands of corn and soybeans lose their usefulness. Farmers are now spending more on herbicides and the labor costs of tilling the land, according to a report from Harvard University.

Instead of genetic fixes, he said, we should focus on improving the environment, such as soil conditions. “If you step back from the genes and look more holistically at the environment in which the plant grows, you can sometimes find simpler, more direct solutions.”

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