Studying the genetic diversity that lies beneath

January 29, 2018

Graduate student Kevin Falk and Dr. Asheesh Singh inspecting soybean rootsDNA is everywhere, including the root system of plants. Up until now few have studied the genetic basis of root structure because it’s difficult to observe how roots grow underground.

Asheesh Singh, professor of agronomy, and his doctorate student Kevin Falk are two of the few doing it with help from Baskar Ganapathysubramanian, professor of mechanical engineering, and Gwyn Beattie, professor of plant pathology.

The idea to focus on researching root traits and their microbiome (the tiny community of microbes living on roots) came directly from a brainstorming session with farmers and Iowa State researchers at a workshop conducted by the Iowa Soybean Research Center.

“The lack of information about the genetics of root systems is limiting given how important they are to the health of the plant,” says Singh. “We want to understand the root genetic diversity in soybeans and hopefully link the information we get with what we know is happening above ground.”

Digging deep for data

Singh and Falk assembled 300 different types of soybeans from 19 different countries. They grew them in controlled environments and in Iowa farm fields. Then, they started digging.

“You can imagine the difficulty of digging up more than 1,000 samples by hand and carefully cleaning off soil and debris,” says Singh. “We take photos of each root system.”

It’s a team effort. There are 12 undergraduate employees, nine graduate students, four staff members and two postdoctoral researchers working on the project. Working in teams of eight to 10 people, it took hundreds of hours to dig up the root systems and properly clean them.

“I consider myself more of an archeologist than a ditch-digger,” says Falk. “Taking our time to extract the root in the best possible condition for high-quality data is difficult.”

Over 100,000 images will be taken in the team’s custom-designed photo booth using studio lighting and multiple cameras while rotating the root to different positions for multiple angles. Photos are uploaded into software created by Ganapathysubramanian’s team to analyze the architectural structure of the root system.

Tight research and microbial communities

“It is a challenging research topic, and we have a very vibrant collaboration between breeders, geneticists, engineers and computer and data scientists allowing us to work in this area,” says Singh. “We try to ask questions relating to real life applications and usefulness to farmers to improve their profitability.”

“The collaboration has allowed us agronomists to build technical skills including digital image processing, high-throughput pipeline development and data management,” says Falk.

In addition to the genetic traits, Gwyn Beattie, professor of plant pathology, is looking at the community of microbes found on and within the roots. “The roots are covered with diverse communities of microbes, which are influencing the plant in ways most people didn’t expect,” says Beattie.

These microscopic organisms are a city of activity within and along the root systems, affecting the plant in multiple ways. Combining that information with what’s happening above ground will give them a better understanding of how soybeans respond and why.

“Microbes tend to hang out together, like neighborhoods,” says Beattie. “Some are always together and others never hang out. If you take away one, does the whole neighborhood fall apart? We’re trying to find the organisms that are key to the structure of these communities and their ability to affect plant roots.”

Mapping roots’ microbiome

Up until recently the tools to take apart a microbial community didn’t exist. The DNA of these microbes, however, provides nametags to identify which ones and how many are there. With these nametags, Beattie can quantify and locate microbes on and within the root system as the roots grow through soil.

Creating a map of the microbiome on the different parts of a soybean root system, and seeing how this map changes as the plant grows, has not been done before. It is an important step toward identifying how microbes promote root growth, and therefore plant growth.

“We want to know which microbes are most useful for making soybeans tolerate things like low phosphorus, drought, high temperature stress,” says Beattie. “If we understand why things work the way they do, we can make them work better.”

The Singh research team will dig and photograph all of the root systems by the end of the year. In the following year, these photos will be analyzed using the software Ganapathysubramanian created, and Beattie and Amy Welty-Bernard, a postdoc driving the microbiome project, will draw the initial maps of the root microbes. What they’ve found so far is exciting.

“We see tremendous diversity for root traits, which is very encouraging,” says Singh. “Once we are able to connect root related traits with above ground traits we will be able to take the next steps in breeding and science for soybeans.”

Combining the genetics of the root systems with the microbial influences could provide tremendous opportunity for new varieties of soybeans. Developers could be able to strategically select genes for root features the way they select for growth above ground.

The project is funded by the Iowa Soybean Research Center, the Raymond F. Baker Center for Plant Breeding and the Monsanto Chair in Soybean Breeding.

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