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MIT Better World

By Stephanie M. McPherson

And certain aspects of climate change, such as variable weather patterns and increased levels of carbon dioxide, are likely to create more difficult conditions for crops, making the food security crisis even worse.

“Frankly, the danger has been understated. It’s a really, really big issue that people aren’t talking about enough and certainly aren’t acting on enough,” says David Des Marais, the Walter Henry Gale Career Development Assistant Professor in MIT’s Department of Civil and Environmental Engineering. “To address this, we’re going to have to think bigger about the future of farming.”

That’s exactly what Des Marais is doing in a collaborative project supported by the Abdul Latif Jameel Water and Food Systems Lab (J-WAFS). J-WAFS was founded in 2014 to catalyze MIT research that addresses global food and water systems challenges brought about by climate change, rising populations, and urbanization.

Building genetic resilience
Des Marais and his co-investigator, Caroline Uhler, an associate professor in the Department of Electrical Engineering and Computer Science as well as in the Institute for Data, Systems and Society, are studying how plants respond to the environment on a molecular level and exploring how tweaking cellular pathways could help plants adapt to unpredictable circumstances. “We are developing a more nuanced understanding of how plants perceive and respond to environmental cues,” says Des Marais.

Right now, crops in even moderate drought conditions will drop their leaves and abort their seeds, thereby destroying any chance of recovery for that season, even if much-needed rain materializes. Some of the major crop seed manufacturers have produced cereal grains that thrive on much less water than their traditional counterparts with the expectation that climate change will create all-around drier growing regions. But in many locations, weather will likely be much more variable than that. Crops will need to be engineered to be able to handle a short-term drought, but also be able to thrive in wet conditions when the rain returns. Engineering this type of variable drought resilience has been tricky.

“The real challenge is teaching a plant how, genetically, to understand, ‘you got water today, so grow great, but tomorrow there’s going to be a little less, and don’t freak out, just hang in there, because chances are, there’s more rain coming,’” says Des Marais.

In their pilot J-WAFS project, Des Marais and Uhler focused on addressing unpredictable rainfall, one of the many issues associated with climate change. Des Marais used the lab-friendly grass Brachypodium—a good analog for classic cereal grains—to understand how intermittent drought affects plants at a molecular level.

In all living things, the functions of genes can be turned on or off or rendered more or less active based on environmental influences. These changes are controlled by gene expression pathways. If something is altered at the top of the pathway, it can cause a domino effect that modifies how genes down the line perform. These changes can be seen in how much of a given protein is made before, during, and after the external stressors. As a proxy for the number of proteins, researchers measure RNA transcripts—or the blueprints for different proteins—which can be sequenced in single cells in a high-throughput manner.

Des Marais’s lab grew the plants in increasingly drought-like conditions and sequenced their RNA at various time points. He then sent the sequences to Uhler, who used her machine-learning expertise to build a novel algorithm that modeled the molecular action of the plants. This algorithm was able to pinpoint where Brachypodium changed its cellular pathways when exposed to drought conditions. It could also identify how these pathways affected the plant’s response to environmental stress and predict ways in which genetic modifications might create more drought-resilient plants.

This analysis revealed that when Brachypodium received less water than was ideal, the plants altered how they metabolized carbohydrates. In follow-up studies, the researchers plan to explore the specifics of this—for example, what does a plant do when it needs extra sugar? Does it pull from reserves, or does it steal from another process such as respiration? They will model possible genetic tweaks using the algorithm and then will apply the most promising adjustments to the plants using gene editing.

Further details of the work will be reported in an upcoming paper.

A biotech toolkit
Adjusting the genetic pathways of plants is no longer a prohibitive undertaking, thanks to the advent of CRISPR and other such genetic engineering techniques. Des Marais hopes that, once perfected, Uhler’s algorithms can be used to inform improvements in crops grown by smallholder farmers around the world.

“We want to provide a toolkit that allows us to say, ‘OK, grow crops in the field and measure these things.’ Then we provide the statistical pipeline, and this algorithm will help researchers to develop hypotheses about what they need to do in biotech” to create more resilient crops, says Des Marais.

This project, marrying molecular biology and machine learning to help the world’s food supply adapt to climate change, is illustrative of the types of boundary-pushing endeavors J-WAFS was created to support.

“J-WAFS lets us take those ideas that are good, but maybe not quite ready to sell to the US Department of Agriculture and try them out in a pretty low-stress setting,” says Des Marais.

“Now that we have some proof of concept, we can push this further,” says Uhler. “That’s the really exciting thing about a J-WAFS grant. We couldn’t have done this work otherwise.”