Christopher Topp,

PhD

Associate Member

Roots

Growing up in Chino, California, Chris Topp describes himself as very much a suburban kid:

“I knew that food came from 7-11. I never thought about where water comes from, where food really comes from.” It wasn’t until age 19, when he had an uncomfortable revelation about his chicken sandwich, that he became interested in the origins of things—and became a vegetarian.

While at the University of Georgia pursuing a genetics degree, Chris began studying plant pathogens. Interested in cutting-edge and emerging technologies, he worked as a research tech in an NSF-funded plant science lab to develop artificial chromosomes, an example of early synthetic biology. In grad school, he focused on maize, realizing that this crop could have the biggest impact: “In the U.S., there are about 90 million acres of corn planted each year. At an average density of 30,000 plants per acre, that’s 2.7 trillion corn plants. It’s been said there are more corn seeds are planted each year than stars in the Milky Way.”

After launching his professional career at Duke University, Chris is today a principal investigator at the Danforth Center. Together with his lab, he’s trying to unlock the secrets of the hidden half of plants.

The Hidden Half

Roots are the foundation of plant health and productivity—even Darwin was interested in them—but so much is still unknown about this “hidden half” of plants. Roots are buried underground, sometimes by as much as dozens of feet of soil. Studies of roots growing in soil typically require killing the plant by removing it from the ground. Such studies are not able to capture the dynamic nature of root growth and soil interactions.

So when Chris learned about specialized 3D X-ray computed tomography (X-ray CT) systems for very large objects used in the aerospace industry, he saw a new potential application. In 2016, a partnership with Valent BioSciences, along with funding from the National Science Foundation, brought one of these 8-ton machines to the Danforth Center. The success of this instrument soon led to a smaller, but more powerful X-ray microscope to look at root-microbial interactions. Now the Topp lab can see the 3D subterranean world of roots nondestructively, at least for plants growing in large containers. The Topp lab’s X-ray CT and microscope facility for plant science at the Danforth Center is unique in the world.

Emerging Results

Already the work is yielding results in the sphere of "rhizo-economics," the study of the microbial ecology fostered by plant root systems, including symbiotic interactions of mycorrhizal fungi. Chris and his team are studying the effects of drought and other stressors. They can observe how different treatments lead to changes in root system growth. They can learn more about carbon sequestration.

The eye-popping three-dimensional imagery generated by the facility has another impact as well: education. The Topp lab, working with the Danforth Center science education and outreach team, has developed a virtual reality tour of a plant's root system—a “worm's-eye” view—called “Get Rooted.” It is used in partnership with the St. Louis Science Center to turn kids on to the wonders of plant science.

Get in touch with Christopher Topp

Research Team
Research Summary

The Topp laboratory deploys X-ray-based imaging and analysis of corn and other root systems to develop more robust and sustainable crops.

Christopher Topp

Principal Investigator, Associate Member

Adam Bray

Graduate Student

Eddie Campell

Lab Assistant

Renee Dale

Postdoctoral Associate

Tyler Dowd

Postdoctoral Associate

Keith Duncan

Research Scientist

Shayla Gunn

Senior Lab Technician

Ni Jiang

Senior Computational Scientist

Elisa Morales

Senior Laboratory Technician

Timothy Parker

Mitchell Sellers

Mon-Ray Shao

Postdoctoral Associate

Gus Thies

Plant Imaging Technician

Dhineshkumar Thiruppathi

Research Scientist

Alicia Zhang

Christopher Topp

Principal Investigator, Associate Member

Adam Bray

Graduate Student

Eddie Campell

Lab Assistant

Renee Dale

Postdoctoral Associate

Tyler Dowd

Postdoctoral Associate

Keith Duncan

Research Scientist

Shayla Gunn

Senior Lab Technician

Ni Jiang

Senior Computational Scientist

Elisa Morales

Senior Laboratory Technician

Timothy Parker

Mitchell Sellers

Mon-Ray Shao

Postdoctoral Associate

Gus Thies

Plant Imaging Technician

Dhineshkumar Thiruppathi

Research Scientist

Alicia Zhang

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Chris’s current research interests are subterranean phenotyping and characterizing the environmental and genetic factors that condition root growth. As a postdoctoral scholar, he led the development of a high-throughput 3D root imaging and analysis pipeline, and applied it to map regions of the rice genome controlling root architecture. Long-term, he aims to understand how genotype directs phenotype for agriculturally important traits.

The Topp Lab takes a phenomics approach to study crop root growth dynamics in response to environmental stress such as drought and rhizosphere competition, and as a consequence of artificial selection for agronomically important traits such as Nitrogen uptake. Studying roots requires the development of imaging technologies, computational infrastructure, and statistical methods that can capture and analyze morphologically complex networks over time and at high-throughput. Thus the lab combines expertise in imaging (optical, X-ray CT, PET, etc.), computational analysis, and quantitative genetics with molecular biology to understand root growth and physiology.

 

What is the genetic basis of root system architecture (RSA)?

‘Root system architecture’ encompasses the spatial and temporal organization of roots in the growth medium, and thus greatly influences the resource capturing abilities of a plant. However, root architecture traits are notoriously difficult to measure due to the opacity of soil and a complex morphology that is environmentally sensitive. The Topp lab uses a semi-automated optical tomography (OPT) system to phenotype crop root systems in 3D as they grow in environmentally controlled conditions. By comparing different genotypes that were bred or naturally selected for different growth traits and combining with molecular analysis, we aim to identify genes that can help generate more stress resistant and sustainable crops. In one project, we are exploring the genetic basis of enhanced Nitrogen uptake. The Illinois High and Low Protein maize lines have been recurrently selected for over 100 years for high or low seed protein content; during this time the IHP lines have evolved enhanced Nitrogen scavenging abilities. We phenotyped the two lines with OPT to reveal major architectural differences, including lateral root density. Work is underway to identify the responsible genes in a high-resolution mapping population using field and lab based phenotyping tools combined with ionomics.

 

How do roots communicate and distinguish self from non-self?

Roots exude an array of chemicals into the rhizosphere to modify the chemical composition of the soil, as well as to communicate with microbes and other root systems. The lab is interested in the nature of these exudates in root-root and root-microbe interactions, and their effects on plant health and productivity. In one project, we are comparing the effects of long-term adaptation to high planting density on maize root-root interactions. A primary factor driving the approximately 8-fold increase in US maize production over the past 80 years has been the ability of modern varieties to maintain high grain yields at increasing planting densities. The Topp lab has shown that density selected maize has a dampened inhibition to intraspecific root competition, likely through a change in root exudations. We are combining transcriptome profiling (RNAseq), and OPT with PET, which can image the dynamics of carbon allocation in real time. In this way, we can identify transcriptional, morphological, and physiological responses to root competition in real time. In another project we have used OPT-PET to study the growth promoting properties of roots infected with different fungal isolates.

 

Fine scale dynamics: How is the growth of individual roots coordinated with the whole?

A fundamental question arises in the study of any biological network, “Is the network topology purely an emergent property of local patterns, or is there coordination at a higher level?” We ask the same question of root growth dynamics, and are investigating relationships between local root growth patterns, global architecture traits, and gene expression with high spatiotemporal resolution. Using an automated system that images roots 24/7, we are generating several dozen high-density time series data sets during approximately two weeks of maize root growth. With collaborators at the IST, the lab is using these data sets to map the growth rates, angles, curvatures, and branching patterns of each root back to their respective global architectures. They will then extend these analyses to functional studies of root growth response to nitrogen availability in the high and low protein lines, as well as response to neighboring roots in the historical versus modern maize material.

 

What is perenniality?

The perennial life form offers a number of desirable traits for agriculture, including rapid early season growth for increased biomass, and an established root system for increased stress resistance and growth in marginal soil by providing access to greater water and nutrient resources. Despite the fact that each major crop variety has a close perennial relative, little is known about the mechanisms that confer perenniality outside of a few studies that suggest a handful of major genes condition the trait. The Topp lab is applying subterranean phenomics methods to identifying the genes controlling perenniality in maize x teosinte (wild relative) and Sorghum bicolor x S.propinquum (wild relative) mapping populations.