Illinois study reveals genetic secrets of America’s favorite snack

In its simplest form, popcorn is pretty basic. Most supermarket strains offer a choice of two bean colors, yellow or white, and two bean shapes, pointed or pearly. When popped, the flake typically expands into one of two shapes: mushroom or butterfly. But there’s more to popcorn than meets the eye. New research from the University of Illinois Urbana-Champaign reveals a wealth of untapped diversity lurking in popcorn’s genetic code.

Analyzing 320 publicly available popcorn lines, crop science researchers found variations at more than 308,000 locations across the genome. This diversity may or may not translate into a greater variety of popcorn for consumers, but some of the differences may be important in improving the agronomic performance of the crop.

“This could be useful if popcorn companies wanted to bring in material to diversify their germplasm, which is hugely important for things like disease resistance and herbicide tolerance. More work needs to be done to identify the traits of interest, but this dataset opens up those possibilities,” says study co-author Tony Studer, an associate professor and popcorn breeder in the Department of Crop Sciences, part of the Illinois College of Agricultural, Consumer and Environmental Sciences.

Studer’s team documented genetic differences in a process known as sequencing genotyping, which narrows the focus of genetic sequencing efforts to the most information-rich parts of the genome. Differences, or polymorphisms, between the maize lines occurred at the level of single nucleotides, the building blocks of DNA.


Popcorn kernels of different colors arranged in a spiral on a black background

popcorn populations

After identifying hundreds of thousands of differences, the team could then group the maize lines based on single nucleotide polymorphism (SNP) patterns, allowing the researchers to draw conclusions about relatedness. According to the analysis, North American popcorn falls into two groups: one composed primarily of yellow pearl types, with white-tipped and Latin American types falling into a second group.

“Grouping popcorn based on genetic similarities allows us to examine the diversity present in each group and better predict the performance of crosses between lines. Also, if a gene is found that enhances performance, knowing its group membership will help the farmers to incorporate it into their program, something I hope popcorn companies will take advantage of to improve their products on both the consumer and grower side,” says Madsen Sullivan, PhD student in Crop Science and first author of the study.

The results showed a high level of inbreeding among yellow pearl popcorn. This means less genetic diversity and more relatedness among that group. Even if this led to better popping traits, the other group’s material will likely contain versions of genes that might be useful but aren’t present in yellow pearl popcorn.

The analysis also provides a starting point from which to discover the long history of the popcorn movement in North America and around the world. Studer says the first people to consume corn probably ate it popped, not buttered on the cob. He is working to trace popcorn’s early origins in a follow-up study.

Demystifying Popcorn’s Herbicide Tolerance

With popcorn’s genetic code explained, researchers were eager to tackle a long-standing mystery surrounding herbicide application labels. Nicosulfuron has been killing weeds in cornfields since the early 1990s, but is only labeled for yellow-core hybrids; farmers are specifically warned not to use it on white-grain popcorn.

“This was a red flag for me, because grain color should have nothing to do with herbicide sensitivity,” says co-author Marty Williams, a USDA-ARS ecologist and affiliate professor of crop science at the University of California. Illinois. “Hazelnut color is controlled by genes in a completely different part of the genome.”

Williams worked with Studer’s team to test 294 popcorn genotypes from both populations, the yellow pearl group and the white-pointed and Latino group; incidentally, neither group is exclusively yellow or white, despite their names. The researchers applied nicosulfuron to the test group as well as sensitive and tolerant popcorn and sweetcorn hybrids as controls.

While nicosulfuron damaged more popcorn with white kernels, the effect had nothing to do with the color of the kernel itself. Instead, susceptibility to nicosulfuron was related to genetic makeup and population structure. Pointy and Latin American types were more sensitive than yellow pearls. In dent maize, nicosulfuron is detoxified by a gene known as nsf1. The researchers immediately looked for the same gene in popcorn, assuming it was active in tolerant genotypes.

“We expected nsf1 to arrive in popcorn, but instead we found a completely different set of genes that appeared to be related to nicosulfuron tolerance,” Studer says. “This opens up the possibility of an alternative mechanism for herbicide tolerance in popcorn, and we’re planning to follow up on that.”

Next steps

Williams recommends popcorn farmers use this research to improve tolerance to nicosulfuron, and possibly other herbicides, in their existing and new cultivars. So herbicide labels could eventually be updated to reflect tolerance across the crop, regardless of grain color.

Could the results of the genome study improve the agronomic characteristics of popcorn? Studer says it will take more work to examine the dataset for desirable traits, but elite popcorn lines could eventually be developed and commercialized by popcorn companies.

The study, “North American popcorn germplasm genetic diversity and the effect of population structure on nicosulfuron response,” is published in Crop Science [DOI: 10.1002/csc2.21039]. Madsen Sullivan, Marty Williams and Tony Studer are authors. The research received funding from the University of Illinois and Sullivan was supported by a grant from the Illinois Corn Growers Association.

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