by A new discovery, reported in a global study spanning more than a decade of research, could lead to the breeding of maize crops that can withstand drought and low-nitrogen soil conditions and ultimately reduce global food insecurity, according to with a Penn State. group of international researchers.
In findings published March 16 at Proceedings of the National Academy of Sciencesresearchers have identified a gene that encodes a transcription factor—a protein useful in converting DNA into RNA—that activates a genetic sequence responsible for the development of an important trait that allows corn roots to obtain more water and nutrients.
This observable characteristic, or phenotype, is called root cortical aerenchyma and results in the creation of air passages in the roots, according to research team leader Jonathan Lynch, distinguished professor of plant sciences. His team at Penn State showed that this phenotype makes roots metabolically cheaper, allowing them to better explore the soil and capture more water and nutrients from dry, infertile soil.
Now, identifying the genetic mechanism behind the trait creates a breeding target, noted Lynch, whose research team in the College of Agricultural Sciences studies root traits in corn and beans in the United States, Asia, Latin America , Europe and Africa for more than three decades, with the aim of improving crop yields.
This latest research was spearheaded by Hannah Schneider, a former PhD student and then postdoctoral fellow in the Lynch lab, now assistant professor of crop physiology at Wageningen University & Research, The Netherlands. In the study, he used powerful genetic tools developed in previous research at Penn State to achieve “high-throughput phenotyping” to measure traits of thousands of roots in a short period of time.
Using technologies such as Laser Ablation Tomography and the Anatomics Pipeline, along with genome-wide association studies, he found the gene — a “bHLH121 transcription factor” — that causes corn to express the root cortical airenchyma. But identifying and then validating the genetic underpinnings of the root trait required a sustained effort, Schneider pointed out.
“We first conducted the field experiments done in this study starting in 2010, growing more than 500 lines of corn at sites in Pennsylvania, Arizona, Wisconsin and South Africa,” he said. “I worked at all these sites. We saw compelling evidence that we had identified a gene associated with root cortical aerenchyma.”
But proof of concept took a long time, Schneider said. The researchers created multiple lines of maize mutants using genetic manipulation methods such as the CRISPR/Cas9 gene editing system and gene knockouts to show the causal relationship between the transcription factor and root cortex formation..
“It took years not only to create these lines, but also to phenotype them under different conditions to validate the function of this gene,” he said. “We spent 10 years on this, confirming and validating our results, to make sure that this is the gene and the specific transcription factor that controls the formation of the root aerenchyma cortex. Doing this kind of work in the field and digging up and phenotyping the roots of mature plants was a long process.”
In the paper, the researchers reported that functional studies revealed that the mutant maize line with the bHLH121 gene knocked out and a CRISPR/Cas9 mutant line in which the gene was edited to suppress its function both showed reduced root cortex formation. In contrast, an overexpression line showed significantly greater cortical root aerenchyma formation compared to the wild-type maize line.
Characterization of these lines under suboptimal water and nitrogen availability in multiple soil environments revealed that the bHLH121 gene is required for root aerenchyma cortex formation, according to the researchers. And the overall validation of the importance of the bHLH121 gene in root cortical aerenchyma formation, they suggest, provides a new marker for plant breeders to select cultivars with improved soil exploration, and therefore performance, under suboptimal conditions.
For Lynch, who plans to retire from the Department of Plant Sciences faculty at the end of this year, this research is the culmination of 30 years of work at Penn State.
“These findings are the result of many people at Penn State and beyond working with us, who have worked for many years,” he said. “We discovered the function of the aerenchyma trait and then the gene associated with it, and it came about because of technologies that have been invented here at Penn State, like Shovelomics — which discovers roots in the field — Laser Ablation Tomography and the Anatomics Pipeline. We put all of that together in this work.”
The results are important, Lynch continued, because finding a gene behind an important trait that will help plants have better drought tolerance and better nitrogen and phosphorus fixation looms large in the face of climate change.
“These are extremely important qualities — both here in the U.S. and around the world,” he said. “Droughts are the biggest risk to corn growers and are getting worse with climate change, and nitrogen is the biggest cost to growing corn, both economically and environmentally. Breeding corn lines more efficient at scavenging nutrients it would be a major development.”
Contributing to the research at Penn State were Kathleen Brown, professor of plant stress biology, now retired, Meredith Hanlon, postdoctoral fellow, Department of Plant Science. Stephanie Klein; PhD student in plant science. and Cody Depew, postdoctoral fellow, Department of Plant Science. and Vai Lor, Shawn Kaeppler, and Xia Zhang, Department of Agriculture and Wisconsin Crop Innovation Center, University of Wisconsin. Patompong Saengwilai, Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand. Jayne Davis, Rahul Bhosale and Malcolm Bennett, Future Food Beacon and School of Biosciences, University of Nottingham, Loughborough, UK. Aditi Borkar, School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK.
The US Department of Energy, the Howard G Buffett Foundation, and the US Department of Agriculture’s National Institute of Food and Agriculture supported this research.
