The new discovery, reported in a global study spanning more than a decade of research, could lead to the development of corn crops that can withstand drought and low soil nitrogen and ultimately ease global food security, according to Pennsylvania State Dept. a group of international researchers.
In the conclusions published on March 16 in Proceedings of the National Academy of Sciencesresearchers have identified a gene that encodes a transcription factor – a protein useful for converting DNA into RNA – that triggers a genetic sequence responsible for the development of an important trait that allows corn roots to obtain more water and nutrients.
This trait, or phenotype, is called root cortical arenchyma and leads to the formation of air passages in the roots, according to research team leader Jonathan Lynch, a distinguished professor of plant engineering. 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 underlying the trait creates a breeding target, said Lynch, whose research group in the College of Agricultural Sciences studies root characteristics of corn and beans in the United States, Asia, Latin America, Europe and Africa. for more than three decades with the aim of improving crops.
This latest study was led by Hannah Schneider, a former postdoctoral fellow in Lynch’s lab who is now an assistant professor in the Department of Crop Physiology at Wageningen University and Research in the Netherlands. In the study, she used powerful genetic tools developed during previous research in Pennsylvania to perform “high-throughput phenotyping” to measure the characteristics of thousands of roots in a short time.
Using technologies such as laser ablation tomography and an anatomical pipeline, along with genome-wide association studies, she found a gene – “transcription factor bHLH121” – that causes maize to express root aerenchyma. But locating and then verifying the genetic basis of the root trait requires a sustained effort, Schneider noted.
“We first conducted the field experiments included in this study starting in 2010, growing more than 500 lines of corn at sites in Pennsylvania, Arizona, Wisconsin and South Africa,” she said. “I’ve worked in all these places. We saw compelling evidence that we found a gene associated with cortical arenchyma.”
But proof of concept took a long time, Schneider said. The researchers created several mutant lines of maize using genetic manipulation techniques such as the CRISPR/Cas9 gene editing system and gene knockouts to show the causal relationship between the transcription factor and the formation of cortical root arenchyma..
“It took years not only to generate these lines, but also to phenotype them under different conditions to confirm the function of this gene,” she said. “We spent 10 years on this, validating and validating our results to make sure that this is a gene and a specific transcription factor that controls the formation of aerenchyma of the root 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 report that functional studies showed that a mutant maize line with the bHLH121 gene knocked out and a CRISPR/Cas9 mutant line in which the gene had been edited to suppress its function showed reduced cortical aerenchyma formation. In contrast, the overexpression line showed significantly greater formation of root cortical arenchyma compared to the wild-type maize line.
Characterization of these lines under suboptimal water and nitrogen availability in different soil environments showed that the bHLH121 gene is required for cortical root aerenchyma formation, according to the researchers. And the general confirmation of the importance of the bHLH121 gene in the formation of the aerenchyma of the root cortex, they believe, provides breeders with a new marker for the selection of varieties with improved soil learning and thus yield in suboptimal conditions.
For Lynch, who plans to retire from the plant department at the end of this year, the research is the culmination of 30 years of work at Pennsylvania.
“These findings are the result of many years of collaboration with many people in Pennsylvania and beyond who have worked with us over the years,” he said. “We discovered the function of the aerenchyma trait and then the gene associated with it, and that’s thanks to technologies that have been developed here at Penn State, such as Shovelomics — root digging in the field — laser ablation tomography and the Anatomics Pipeline. We bring it all together in this work.”
The results are significant, Lynch continued, because the search for a gene that underlies an important trait that helps plants better tolerate drought and take up nitrogen and phosphorus is approaching climate change.
“These are very important qualities — both here in the U.S. and around the world,” he said. “Droughts are the biggest risk to corn producers and are getting worse with climate change, and nitrogen is the biggest cost to growing corn, both financially and environmentally. Breeding maize lines more efficient at scavenging nutrients would be an important development. “
Contributors to the Penn study were Kathleen Brown, now retired professor of plant stress biology, Meredith Hanlon, a postdoctoral fellow in the department of plant engineering; Stephanie Klein; doctoral student in plant science; and Cody Depew, graduate student in the Department of Crop Science; and Wai Lor, Shawn Kepler, and Xia Zhang, Department of Agronomy and Wisconsin Plant Innovation Center, University of Wisconsin; Patompong Saengwilai, Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand; Jane Davies, Rahul Bosale and Malcolm Bennett, Future Food Beacon and School of Life Sciences, University of Nottingham, Loughborough, UK; Aditi Borkar, School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonnington, UK.
US Department of Energy, Howard J. Buffett and the USDA’s National Institute of Food and Agriculture supported this research.