A genetic secret lurks in America’s favorite snack

URBAN, Ill. — Popcorn, a seemingly simple snack, holds a hidden world of genetic diversity, according to researchers at the University of Illinois Urbana-Champaign. The study, led by agricultural science researchers, explored the genetic code of popcorn and uncovered a wealth of untapped secrets that could have implications for both consumers and the agricultural industry.

By analyzing 320 lines of publicly available popcorn, the researchers identified more than 308,000 variations in the genome. While these genetic differences may not immediately translate into a wider variety of popcorn for consumers, they have the potential to improve the agronomic performance of the crop. This diversity can be especially valuable for improving disease resistance and herbicide tolerance.

“This dataset opens up the possibility of germplasm diversification, which is crucial for improving culture traits. More work needs to be done to identify the specific traits of interest, but this research lays the groundwork for such advances,” says Tony Studer, associate professor and popcorn breeder in the Department of Crop Sciences, in a university release.

The team used a sequencing genotyping process to document genetic differences, focusing on the most informative regions of the genome. The variations, known as polymorphisms, occurred at the level of single nucleotides, which are the building blocks of DNA.

Different types of popcorn illustrate some of the genomic diversity found in a University of Illinois study.  The findings could facilitate future breeding efforts to create tastier, easier-to-grow versions of America's favorite snack.
Different types of popcorn illustrate some of the genomic diversity found in a University of Illinois study. The findings could facilitate future breeding efforts to create tastier, easier-to-grow versions of America’s favorite snack. (Credit:
Madsen Sullivan, University of Illinois)

To get a better understanding of the correlation between the different maize lines, the researchers grouped them according to single nucleotide polymorphism (SNP) patterns. This grouping allowed predictions of performance and potential line crossings.

“Knowing the genetic similarities and diversity within each group allows farmers to incorporate beneficial traits into their programs, benefiting both consumers and growers,” says Madsen Sullivan, a crop science doctoral student and first author of study.

In addition, the research team sought to unravel a long-standing mystery related to herbicide application labels. While nicosulfuron, a herbicide, has been used for decades for weed control in cornfields, its use is limited to yellow-stone hybrids, with caveats against applying it to white-stone popcorn. Co-author Marty Williams, a USDA-ARS ecologist, found this puzzling, as grain color shouldn’t be linked to herbicide sensitivity. Collaborating with Studer’s team, they conducted tests on 294 popcorn genotypes from both groups: Yellow Pearl and White Point, and Latinos.

Surprisingly, the researchers found that sensitivity to nicosulfuron was related to genetic makeup and population structure rather than bean color. Different types of popcorn showed different levels of sensitivity, with the pointed and Latin American types being the most sensitive. The study also revealed a different set of genes associated with nicosulfuron tolerance in popcorn, potentially pointing to an alternative mechanism for herbicide tolerance.

“This discovery opens up the possibility of understanding herbicide tolerance in popcorn via a different genetic pathway. We aim to explore this area further in our future research,” Studer reports.

The results of this study provide valuable insights into the untapped potential within the popcorn genetic code, paving the way for future advances in popcorn variety, agronomic performance, and herbicide tolerance.

The study is published in the journal Agricultural.

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