Fifteen years after the first draft of the corn genome was published, the roles of 98% of its nearly 40,000 genes remain unknown. Conventional gene characterization methods have been slow and expensive.

Scientists from the University of Nebraska-Lincoln (UNL) are at the forefront of tackling this problem. Their innovative work, published in The Plant Journal, has the potential to revolutionize the development of resilient corn varieties, thereby making enhanced crops more accessible to farmers.

Led by postdoctoral associate Vladimir Torres-Rodriguez and Professor James Schnable, the team's innovative approach was RNA-based. Each gene or transcript abundance was linked to a phenotype, and genome-wide association was conducted using a published resequencing-based genetic marker data approach. Their technique identified ten times more genes affecting flowering time than traditional DNA-based methods. By identifying the functions of individual corn genes more rapidly and accurately, this breakthrough will reduce the cost of developing new gene-edited corn varieties and increase broader producer access to improved crops. This has the potential to lower prices for farmers, offering a brighter future for the agricultural industry and the global food supply.

The project was not without its challenges, requiring the development of new and unique lab and field techniques. These included rapid sample collection and flash freezing to preserve RNA integrity, as well as the use of special equipment designed by Jonathan Turkus using 3D printing. Torres-Rodriguez also played a pivotal role in developing a software pipeline for data analysis, repurposing tools, and creating new quality control steps.

The goal, Schnable said, is “to make sure that, decades from now, when a Nebraska farmer is driving his tractor, the corn being planted has the genetics to perform well and tolerate harsher conditions.”
Supported by a $650,000 grant from the U.S. Department of Energy’s Advanced Research Projects Agency-Energy program, this project positions UNL as a leading research institution for corn genetics. Collaborations with private-sector scientists like Brad Zamft, the project lead of a stealth plant biology project at X, Alphabet’s “moonshot factory” division that explores a range of scientific innovations, make the future even more promising.

“The expertise that we have experienced and the collaborations that we have engaged in have been delightfully productive, and I think could have a real impact on the world. There is no doubt in my mind the University of Nebraska is an agricultural technology powerhouse”, Zamft said, to underscore UNL’s potential to impact not just local or regional agriculture, but the global agricultural technology landscape.

By harnessing the power of RNA precision and specificity, this innovation could positively impact the development of climate-smart corn varieties that can adapt to sub-optimal conditions worldwide.