Genotype to phenotype: Carrington takes charge at Danforth Plant Center

April 4, 2011 |

The Danforth Center's new President, James C. Carrington

Recently, the Donald Danforth Plant Science Center announced that Dr. James C. Carrington, will become the next President Center. Carrington is the Director of the Center for Genome Research and Biocomputing (CGRB), the Stewart Professor for Gene Research, and Distinguished Professor of Botany and Plant Pathology at Oregon State University in Corvallis, Oregon. Jim Carrington took some time out to talk with the Digest about his goals.

“There are so few centers of this scale focused on plant science,” says Jim Carrington, the new head of the Donald Danforth Plant Sciences Center in St. Louis, “where you have the opportunity to help humanity by providing more and better food, and improving the environment.”

With idealistic vision, but practical plans, Carrington is taking charge in St. Louis, after a stretch at Oregon State University.

“The resources convinced me to come,” he said, “all these generous donors, and the record of achievement, the number of things that the scientists are already doing. It’s a very good facility, yet we have maxed out the capacity, so we are expanding.”

“Five new principal investigators, including one focused on algal biofuels, looking at the big questions, with interactive collaboration. That’s what it will be about,” Carrington says.

What are the big questions?

“The big arching question? In this age of genomic science, when we can sequence, in days, thousands of variants: how does genomic structure relate to phenotype. Genotype to phenotype, that’s the biggest, broadest question out there in plant biology.

“What are the genetic traits than confer yield, drought resistance, flood tolerance, more efficient in using nitrogen, phosphorus and potassium. We don’t understand that nearly enough.

“Take a phenotype into two different environmental conditions. There’s a different time to flower, different time to granulate. The interactions of genotypes are causing different phenotypes.

“The other big question. Absolutely, the how of yield.”

What about biofuels?

“With biofuels, the way we do them in the US, the good news ois that we make a significant amount of ethanol, and on the surface that is a good thing. In practice, all things considered, there is a minimal, marginal environmental benefit, and ethanol from corn is probably not sustainable, because it is in direct competition with the food supply.

Even with first generation ethanol that is not in direct competition, such as sugarcane,, there are still other problems. There is just not enough energy output to make it sustainable.

“Now, the price of the corn crop, wheat soy, is not entirely due to biofuel, there are a lot of intersecting issues, and a perfect storm can develop.

Issues?

“Floods in Australia, drought in Russia. Also, 16 percent of corn crop goes to China, where it is used primarily for animal feed. And then, here in the US we don’t have strategic grain reserve, and there’s been hoarding. All kinds of things are factoring in.

Climate Change?

“Climate change is quite clearly occurring, that’s indisputable, and we can increasingly forecast the impact with a fair degree of confidence. The trends tell us that it will directly affect agriculture in many ways. Some land will become suitable, other land will become unsuitable.

“There will be increasing complications over land and land use, and water is going to become more critical. Not only water use but water patterns. Having said that, short term phenomena, like the floods and droughts in Australia and Russia are the result of weather. The models tell us that these natural phenomena will become more frequent, and more severe. That means that agricultural productivity will depend on our ability to forecast effects, plan ahead, and mitigate those impacts to the extent we can.”

Scarce resources?

“In addition to water, there’s fertilizer. We’ve had very impressive gains in yield, but these have in turn caused dramatic NPK [nitrogen, phosphorus, potassium] increases. If you draw the curves out, particularly for phosphorus, at current yields, it’s a pretty grim prospect a few decades out. Our systems are not sustainable in the long term and we have to learn to tap genetics, to use available genes.

Abundant and increasing public scrutiny

“When you talk about fertilizer, well, the average person is not thinking about fertilizer. They didn’t used to think much about food prices, 4 years ago. Now we have this set of societal issues, and we have two issues on fertilizer. First there is the issue of the price of price of mined fertilizer.

“The other is a plant’s nitrogen need, given that what we have is an energy intensive process. In many ways, the limiting input is natural gas, how cheaply we can mine or synthesize fertilizer from natural gas. Plus, in the past we have over fertilized, some mechanical, spot application or targeted, when it was in our benefit to use the genetics much better.”

What about genetic modification?

“That’s a good segue from fertilizer, because we went through this with Roundup Ready crops. GMO does not hit home with the public, because it is viewed as an optional thing that we can do without. For example, there are the organic farms. But the truth is that mechanized, industrial, high tech agriculture will require genetic modification.

“In the early days, the 1970s, of genetic engineering, there were lots of concerns. But the early beneficiaries — in the case of biomedical, drugs, therapeutics — embraced GMO. You don’t hear as much about GM with therapeutics, because there is a perception of the benefits.

“So one of the key things we have to do is to address the problem, and raise awareness. For biofuels, we will have to hit on why they are important.”

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