Carbon dioxide (CO2)  levels are higher than at any point in the past 800,000 years and in 2017, the global average amount of CO2  hit a new record: 405 parts per million, according to a report issued by the National Oceanic Atmospheric Association. A unique interdisciplinary collaboration between scientists at the Donald Danforth Plant Science Center and Washington University in St. Louis have developed a four-year research project that garnered $3 million in support from the National Science Foundation to study how plants react to increased levels of CO2  over generations. Not only are they monitoring the plants themselves, but they will also explore how the increased level of CO2  affects their offspring. Understanding plant responses to environmental stress are important to secure our future national interest in maintaining agricultural productivity and preserving the environment.

The research, led by Keith Slotkin, Ph.D., associate member, Danforth Center and associate professor, Division of Biological Sciences, University of Missouri-Columbia, will result in a unique model that helps predict the lasting effects of environmental challenges on a plant’s genome and physical growth. If successful, this new knowledge could help equip farmers with the information they need to make better decisions when it comes to growing food on a large scale. For example, if increased levels of CO2  result in generations of leafier, wider plants, farmers could plan to plant their crops farther apart.

When Slotkin joined the Danforth Center in 2018, he was inspired by the incredible advances his colleagues had made analyzing 3D shapes of whole plants. The transformative aspect of this new research project is the novelty of the data analysis. The analysis of genome regulation hasn’t changed for a decade and is stuck in 2D. Slotkin’s team has cutting-edge expertise in the mathematical and computational analysis of plant form in 3D space and this will be used to elevate the standard genomic analysis to 3D, therefore opening doors to new discoveries based on the relation between genome regulation and plant form. Using shape analysis and machine learning, the data collected on a broad array of plant species will provide a computational model that describes how the 3D genome and phenome respond to environmental challenge.

“This project is important because we can take technology advancements that scientists in the field of phenomics (simultaneous study of many physical traits) utilize to be successful, apply it to this research, and transform the field of genomics in the process,” explains Slotkin. “Knowledge gained will help us prepare for the future, so once we get there we don’t have to go through trial and error. We can try to avoid learning difficult lessons.”

The research team will use image analysis technology to monitor how a plant’s chromosomes alter their shape over time when exposed to extreme levels of CO2 , and how the difference in chromosome shape effects the plant’s phenotype. They are including six diverse plants in their study, chosen for ease of work and variation among plants, so that their findings could prove a “rule of life” discovery that is true across the plant kingdom.

Slotkin specializes in genomics, a branch of molecular biology that focuses on an organism’s genomes (a complete set of DNA). To tackle this research, he is collaborating with Danforth Center Principal Investigators, Malia Gehan, Ph.D., Noah Fahlgren, Ph.D., Blake Meyers, Ph.D., Sona Pandey, Ph.D., and Chris Topp, Ph.D. to tap their expertise in phenomics and Washington University computer scientists, Tao Ju, Ph.D.and Ayan Chakrabarti, Ph.D., who bring cutting-edge computation and machine learning expertise to the project.

“The ultimate goal is to have a predictive model where we can provide an idea of how challenges in the environment will change the genetic configuration of a plant,” said Chakrabarti, Ph.D., assistant professor of computer science & engineering in the McKelvey School of Engineering. “We will look at how the environmental changes change the plant form and whether that change is going to be passed on to future generations.”

The research project also includes an education component for high school students who participate in the Danforth Center’s successful Mutant Millets outreach program, which brings inquiry-based learning and real research in modern plant science and agriculture into the classroom. Since 2013, Mutant Millets has been disseminated into 35 high schools in Missouri, Illinois, Kentucky and Ohio, providing over 4,000 students and 50 teachers with scientific training and hands-on STEM experiences.