Gene identified that will help develop plants to fight climate change

Plants with deep, robust roots can store more carbon underground for longer periods of time, reducing the amount of CO2 in the atmosphere. However, the genetic and molecular mechanisms that regulate remain largely unknown. The lab of Wolfgang Busch, which moved from the GMI to the Salk Institute in 2017, has identified a gene that determines whether roots grow deep or shallow.

Left: Normal Arabidopsis plant with shallow root system architecture. Right: Arabidopsis mutant showing deeper root system architecture. (Roots are colored yellow in the image for better visibility.)

These results will also make it possible to develop plants that can help combat climate change as part of Salk's Harnessing Plants Inititiative. "One of the great challenges of our time is to reduce the amount of CO2 in the atmosphere. Working on a solution means a lot to me. This is why I am so enthusiastic about this first result," says Wolfgang Busch, Associate Professor and member of the Salk's Plant Molecular and Cellular Biology Laboratory. Busch was previously group leader at the GMI, where much of the research on this project took place. 

Wolfgang's team used Arabidopsis to identify genes and their variants that regulate the way auxin, a hormone that is a key factor in controlling the root system architecture, works. Though auxin was known to influence almost all aspects of plant growth, it was not known which factors determined how it specifically affects root system architecture. 

“In order to better view the root growth, I developed and optimized a novel method for studying plant root systems in soil,” says first author Takehiko Ogura, a postdoctoral fellow in the Busch lab. “The roots of A. thaliana are incredibly small so they are not easily visible, but by slicing the plant in half we could better observe and measure the root distributions in the soil.”

The team found that one gene, called EXOCYST70A3, directly regulates root system architecture by controlling the auxin pathway without disrupting other pathways. EXOCYST70A3 does this by affecting the distribution of PIN4, a protein known to influence auxin transport. When the researchers altered the EXOCYST70A3 gene, they found that the orientation of the root system shifted and more roots grew deeper into the soil.

“Biological systems are incredibly complex, so it can be difficult to connect plants’ molecular mechanisms to an environmental response,” says Ogura. “By linking how this gene influences root behavior, we have revealed an important step in how plants adapt to changing environments through the auxin pathway.”

In addition to enabling the team to develop plants that can grow deeper root systems to store more carbon, this discovery could help scientists understand how plants address seasonal variance in rainfall and how to help plants adapt to changing climates.

“We hope to use this knowledge of the auxin pathway as a way to uncover more components that are related to these genes and their effect on root system architecture,” adds Busch. “This will help us create better, more adaptable crop plants, such as soybean and corn, that farmers can grow to produce more food for a growing world population.”

The work was funded by funds from the Austrian Academy of Sciences through the Gregor Mendel Institute along with a grant from the Austrian Science Fund (FWF P27163-B22).

A video describing the work in more detail is available here.


Ogura T, Goeschl C, ... Busch W (2019) Root system depth in Arabidopsis is shaped by EXOCYST70A3 via the dynamic modulation of auxin transport. Cell 178(2):400-12.

Press release (German .pdf)