A new discovery, reported in a global study spanning more than a decade of research, could lead to growing corn crops that can withstand drought and nitrogen-poor soil conditions and ultimately reduce global food insecurity, a Penn State-led team of researchers said. international researchers.
In findings published March 16 in the Proceedings of the National Academy of Sciencethe 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 obtain more water and nutrients.
That observable characteristic, or phenotype, is called root cortical aerenchyma and results in air passages in the roots, according to research team leader Jonathan Lynch, distinguished professor of plant science. His team at Penn State has shown that this phenotype makes carrots metabolically cheaper, allowing them to better explore the soil and extract more water and nutrients from dry, infertile soil.
Now identifying the genetic mechanism behind the trait creates a breeding goal, noted Lynch, whose research group at the College of Agricultural Sciences has studied 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 performance.
This latest research was led by Hannah Schneider, formerly a PhD student and then a postdoctoral researcher in the Lynch lab, now an assistant professor of crop physiology at Wageningen University & Research, the Netherlands. In the study, she used powerful genetic tools developed in previous research at Penn State to achieve “high-throughput phenotyping” to measure characteristics of thousands of roots in a short period of time.
Using technologies such as laser ablation tomography and the anatomical pipeline, along with genome-wide association studies, she found the gene — a “bHLH121 transcription factor” — that causes corn to express root cortical aerenchyme. But locating and then validating the genetic underpinnings of the root trait required a lengthy effort, Schneider noted.
“We first conducted the field experiments devoted to this study in 2010, growing more than 500 corn lines at sites in Pennsylvania, Arizona, Wisconsin and South Africa,” she said. “I worked at all those sites. We saw compelling evidence that we had found a gene associated with root cortical aerenchyma.”
But proving the concept took a long time, Schneider said. The researchers created multiple mutated maize lines using genetic engineering methods such as the CRISPR/Cas9 gene editing system and gene knockouts to demonstrate the causal relationship between the transcription factor and root cortical aerenchyme formation..
“Not only did it take years to create those lines, but also to phenotype them under different conditions to validate the function of this gene. the gene and specific transcription factor that controls the formation of root cortical aerenchyma. Doing this kind of work in the field and excavating and phenotyping 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 turned off and a CRISPR/Cas9 mutant line in which the gene was edited to suppress its function both showed reduced root cortical aerenchyma formation. In contrast, an overexpressing line showed significantly greater root cortical 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 cortical aerenchyma formation, the researchers said. And the overall validation of the importance of the bHLH121 gene in root cortical aerenchyma formation, they argue, provides a new marker for plant breeders to select varieties with improved soil exploration, and thus yield, under sub-optimal conditions.
For Lynch, who plans to retire from the Department of Plant Sciences 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 who have worked with us over many years,” he said. “We discovered the function of the aerenchyma trait and then the gene associated with it, and it came about thanks to technologies invented here at Penn State, such as Shovelomics – digging up roots in the field – Laser Ablation Tomography and Anatomics Pipeline. We have all those brought together in this work.”
The results are significant, Lynch continued, because finding a gene behind an important trait that will help plants have better drought tolerance and better nitrogen and phosphorus uptake plays a big part in the face of climate change.
“Those are super important traits — both here in the US and around the world,” he said. “Drought is the biggest risk facing corn growers, exacerbated by climate change, and nitrogen is the biggest cost of growing corn, both from a financial and environmental point of view. It would be an important development to breed corn lines that are more efficient at scavenging the nutrient.”
Contributors to the research at Penn State were Kathleen Brown, professor of plant stress biology, now retired; Meredith Hanlon, postdoctoral scientist, Department of Plant Science; Stephanie Klein; doctorate in plant sciences; and Cody Depew, postdoctoral researcher, Department of Plant Science; and Vai Lor, Shawn Kaeppler, and Xia Zhang, Department of Agronomy 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 U.S. Department of Energy, the Howard G Buffett Foundation, and the U.S. Department of Agriculture’s National Institute of Food and Agriculture supported this research.