Researchers Discover a Novel Gene that could lead to More Resilient Corn Crops

The researchers identified a gene encoding a transcription factor (a protein useful for converting DNA into RNA) that activates a genetic sequence responsible for the development of an important trait that allows corn roots to acquire more water and nutrients, according to findings published in the Proceedings of the National Academy of Science.

According to research team leader Jonathan Lynch, distinguished professor of plant science, that observable property, or phenotype, is called root cortical aerenchyma and results in the formation of air passageways in the roots. His Penn State colleagues discovered that this genotype makes roots metabolically cheaper, allowing them to better explore the soil and acquire more water and nutrients from dry, barren soil.

Identifying the genetic mechanism underlying the trait now creates a breeding target, according to Lynch, whose research group in the College of Agricultural Sciences has been studying root traits in corn and beans for more than three decades in the United States, Asia, Latin America, Europe, and Africa with the goal of improving crop performance.

Hannah Schneider, a former PhD student and postdoctoral scholar in the Lynch lab, is now an assistant professor of crop physiology at Wageningen University & Research in the Netherlands. In the work, she employed strong genetic techniques created in prior Penn State research to do "high-throughput phenotyping" on thousands of roots in a short period of time.

She discovered the gene- a "bHLH121 transcription factor"- that causes corn to express root cortical aerenchyma using technologies such as Laser Ablation Tomography and the Anatomics Pipeline, as well as genome-wide association analyses. However, Schneider noted that finding and then verifying the genetic foundations of the root feature took time.

"We began the field studies that led to this study in 2010, cultivating over 500 lines of maize at sites in Pennsylvania, Arizona, Wisconsin, and South Africa," she explained. "I worked at all of those places. We noticed compelling evidence that we had discovered a gene linked to root cortical aerenchyma."

Yet, according to Schneider, demonstrating the concept took a long time. To demonstrate the causal relationship between the transcription factor and the establishment of root cortical aerenchyma, the researchers produced numerous mutant corn lines utilising genetic manipulation technologies such as the CRISPR/Cas9 gene-editing system and gene knockouts.

"Not only did it take years to produce those lines, but it also required years to phenotype them in different settings to validate the function of this gene," she explained. "We worked on this for ten years, confirming and validating our findings to ensure that this is the gene and transcription factor that governs root cortical aerenchyma production. Working in the field, digging up and phenotyping mature plant roots, was a time-consuming task."

Functional investigations demonstrated that a mutant corn line with the bHLH121 gene knocked out and a CRISPR/Cas9 mutant line with the gene altered to decrease its function both showed reduced root cortical aerenchyma development, according to the researchers. When compared to the wildtype corn line, an overexpression line formed considerably more root cortical aerenchyma.

According to the researchers, characterization of these lines under poor water and nitrogen availability in diverse soil settings demonstrated that the bHLH121 gene is necessary for root cortical aerenchyma development. Furthermore, they believe that the overall validation of the bHLH121 gene's role in root cortical aerenchyma formation gives a new marker for plant breeders to choose cultivars with increased soil exploration, and consequently yield, under poor conditions.

This discovery represents the conclusion of 30 years of work at Penn State for Lynch, who prepares to retire from the Department of Plant Sciences faculty at the end of this year.

"These findings are the result of many people at Penn State and elsewhere working with us over many years," he explained. "We discovered the aerenchyma trait's function and then the gene connected with it. It was made possible by technology developed at Penn State, such as Shovelomics (digging up roots in the field), Laser Ablation Tomography, and the Anatomics Pipeline. We combined all of those in this work."

Lynch went on to say that the findings are crucial because uncovering a gene responsible for an important characteristic that will assist plants have improved drought tolerance and nitrogen and phosphorus collection is critical in the face of climate change.

"They are extremely significant skills, both here in the United States and around the world," he remarked. "Droughts pose the greatest risk to corn growers and are worsening as a result of climate change, and nitrogen is the most expensive component of corn production, both financially and environmentally. Breeding maize lines that are more efficient at scavenging for nutrients would be a significant advancement."

Kathleen Brown, now retired professor of plant stress biology, Meredith Hanlon, postdoctoral scholar, Department of Plant Science, Stephanie Klein, doctoral student in plant science, and Cody Depew, postdoctoral scholar, Department of Plant Science; and Vai Lor, Shawn Kaeppler, and Xia Zhang, Department of Agronomy and Wisconsin Crop Innovation Center, University of Wisconsin; and Patompong Saengwilai, Department of Biology, Jayne Davis, Rahul Bhosale, and Malcolm Bennett, Future Food Beacon and Department of Biosciences, University of Nottingham, Loughborough, UK; and Aditi Borkar, School of Veterinary Medicine & Science, University of Nottingham, Sutton Bonington, UK.

This research was funded by the US Department of Energy, the Howard G Buffett Foundation, and the US Department of Agriculture's National Institute of Food and Agriculture.

(Source: Penn State)