Precision Genetic Engineering Points to a Future of Sustainable Agriculture

As Earth's climate warms and changes, sustainable agricultural practices are critical for feeding a rapidly growing population. Can we genetically engineer crops to adapt to drought and other effects of a warming climate?

A roadmap for how new techniques and approaches in genomics and plant developmental biology can enable this is illustrated in a recent series of papers by Trevor Nolan, a plant developmental biologist and assistant professor of biology and biological engineering at Caltech. A new review paper in the journal Science outlines a path to improving and enhancing crops by using tools of basic biology research to understand the inner workings of plant cells. The paper is co-authored by Nolan in collaboration with researchers at the VIB Center for Plant Systems Biology at Ghent University in Belgium.

While general tools for modifying crops currently exist, Nolan and his colleagues propose a more precise approach. They suggest that making subtle tweaks to a plant's own gene expression could, for example, promote deeper root growth during drought, enhance water and nutrient uptake efficiency, or change leaf architecture to better capture light in crowded field conditions. 

"We want to be able to modulate plant growth with surgical-level precision, without side effects to the rest of the plant," Nolan says. "Being able to do this requires us to understand the context of exactly what the plant is doing on a cellular level."

Earlier this year, Nolan and collaborators reported in Cell that a particular class of plant hormones, brassinosteroids, orchestrate root growth through a dynamic cell-specific feedback network. Brassinosteroids are essential for plant development, regulating cell division and cell elongation. Still, when applied broadly to a plant, they can have the opposite effect, stunting growth by disrupting the delicate balance of hormone signaling between cells. Nolan explains that brassinosteroids exert a kind of Goldilocks effect on plants—growth only happens optimally with not too much, and not too little, in the right place at the right time.

The team discovered this by using cutting-edge techniques to see how individual cells express their genes in the model laboratory plant Arabidopsis thaliana. While each cell has the same genetic information stored in its genome, certain genes can be dialed on or off, like a set of light-dimmer switches, to give a cell different functions. Various gene-expression patterns can tell the cell to divide, for example, or to produce more hormones, or even to self-destruct. Techniques such as single-cell transcriptomics can measure gene expression across many cells simultaneously.

Nolan's laboratory is pioneering the integration of single-cell, spatial, and live-imaging technologies to visualize plant development with unprecedented resolution. Using a custom-built vertical confocal microscope and whole-root imaging pipelines, the team can now follow the developmental progression of individual cells—from their origin as stem cells in the root meristem through their differentiation into specialized tissues. By combining these live-imaging datasets with single-cell and spatial transcriptomic maps, the lab can trace how gene expression and hormone signaling vary over time and space, revealing how signals such as brassinosteroid hormones orchestrate growth, development, and stress responses.

Nolan now emphasizes that these techniques should be applied to the study of similar hormone- and stress-resilience mechanisms in crops.

"Our work shows that plants coordinate growth through remarkable spatial precision," says Nolan. "Once we understand these principles, we can start to engineer them in crops like rice, maize, and sorghum to make agriculture more resilient to heat and drought."

The paper is titled "Unlocking the potential of brassinosteroids: A path to precision plant engineering" and appears in Science on November 6. In addition to Nolan, co-authors are Nemanja Vukašinović and Eugenia Russinova of Ghent University in Belgium. Funding was provided by the Research Foundation of Flanders, the Shurl and Kay Curci Foundation, the Donna and Benjamin M. Rosen Bioengineering Center at Caltech, and Caltech.