Variations of form and function—that’s one of the things that fascinates Associate Professor Siobhan Brady about the world of plants. Glimpse the flora of a single landscape—say the foothills of the Sierras—and you’ll find an abundance of variation, species that have evolved to thrive in specific ecological niches.

“If you think about the solutions that each of those species have taken, it’s going to be so different,” said Brady, from the Department of Plant Biology. “I just love trying to understand how different species developed these solutions to adapt to the environment and to have this completely different form.”

Over the course of the 20th century, humanity’s plant knowledge grew and was harnessed to innovate agricultural technologies, ushering in The Green Revolution. The addition of nitrogen-containing fertilizers to the soil led to increases in crop production worldwide. But something else was growing among the rows, an environmental problem.

“We’ve dumped so much fertilizer containing nitrogen into the soil that it ends up having really adverse consequences, like agricultural runoff, for instance, in the water,” said Brady. “Algal blooms are a result of huge amounts of nitrogen and phosphorous from fertilizer.”

To curb the use of nitrogen-containing fertilizers, Brady is investigating the gene networks that govern nitrogen uptake in plants. On Oct. 24, 2018, Brady, her lab colleagues and her colleagues at New York’s Cold Spring Harbor Laboratory published “a core set of genes that are critical in nitrogen metabolism” in Nature. The research pushes plant breeders closer to producing crop varieties that grow more with less fertilizer or use fertilizer more efficiently.

For her research, Brady was recognized with the 2018-2019 College of Biological Sciences Faculty Research Award

“It’s a huge honor,” said Brady. “There is really incredible top-tier research at this university and in our College and so it feels awesome to be part of this group.”

“The fundamental research done at the College of Biological Sciences is paving the way for breakthroughs in industry," said College of Biological Sciences Dean Mark Winey. "Our crops are facing a crisis of our own creation when it comes to fertilizers. Associate Professor Siobhan Brady and her colleagues are getting to the core of plant genetics to help us understand how we might produce more efficient crops while curbing the use of resources.”

Nitrogen: essential to life

Nitrogen is essential for life and growth. It’s a part of our DNA, our RNA and our proteins.

“The majority of our nitrogen, if you trace it back, comes from plant-derived sources,” said Brady. “What plants do is take up nitrogen from the roots and then bring it up into the shoots and it is used for all these purposes to carry out basic biological processes.”

“Because nitrogen is important for all basic life processes,” she added, “we need to understand how plants produce and use nitrogen so that we will have enough food to eat.”

To understand nitrogen metabolism in plants, Brady and her colleagues investigated the transcription factors—or regulatory genes—that control nitrogen uptake. Since plants glean nitrogen from the soil, the team focused on roots, a hitherto understudied area of the plant. The team identified 21 transcription factors in the root and shoot system that facilitate both nitrogen metabolism and growth. The team also identified another avenue of feedback control within the root system.

“When nitrogen metabolism is perturbed genetically, we found that there is really dramatic changes in expression to the upstream transcriptional regulators,” said Brady. “That had never been described before.”

Breeding efficient crops for our future

This network of genes could prove pivotal to increasing agricultural productivity during a time of resource decline and growing food insecurity. Brady and her colleagues hope that by identifying and mapping these genetic networks, plant breeders will be able to cultivate plants with genes tailored to the make the most of the nitrogen resources in the soil environment.

The publication was the result of almost eight years of experimentation, analysis and writing. The effort was collaborative, with experiments performed by staff and students at the UC Davis Genome Center and the Cold Spring Harbor Laboratory. The research was supported by industry with additional support from the National Science Foundation, the Howard Hughes Medical Institute and University of California fellowships. 

Various projects have spun out of the research. Brady is currently working with Professor David Segal, UC Davis Genome Center, to use CRISPR technology to understand how the plant transcription factors necessary for nitrogen metabolism operate. The project is funded by United State Department of Agriculture’s Early Concept Grant for Exploratory Research program.  

“This is another example of how UC Davis is a wonderful place for collaboration,” said Brady. “David Segal is an expert in genome and epigenome editing in human disease. It’s only within the context of our campus and centers like the Genome Center that such opportunities could come about!”