URBANA, Ill. (U.S.A.) — A new study led by University of Illinois Urbana-Champaign scientists reveals critically low genetic variation in one of the country’s primary breeding stocks for corn. The finding relates specifically to grain yield in intermediate-maturity hybrids, which dominate commercial production in the U.S. and represent nearly a third of the world’s corn production.

The researchers say it’s a crisis waiting to happen.

"Our study reveals a significant genetic weakness that threatens maize breeders' ability to develop high-yielding hybrids, especially in the context of climatic challenges projected for the U.S. Corn Belt,” said the study’s lead author, Jenifer Camila Godoy dos Santos, a postdoctoral researcher in the Department of Crop Sciences, part of the College of Agricultural, Consumer and Environmental Sciences at U. of I.

Modern corn breeding relies on heterosis, also known as hybrid vigor. This means that when parents from different genetic, or heterotic, groups are crossed, the hybrid offspring far outstrips either parent’s performance in the field.

For several decades, new corn hybrids have been generated by crossing parents from two specific heterotic groups: stiff-stalk (SS) and non-stiff-stalk (NSS). These groups are genetically distinct from one another — a necessary ingredient to ensure the most productive corn hybrids — but the inbred lines within each group are genetically similar. And therein lies the problem.

Over time, breeders have selected and reused the strongest performing lines as parents, gradually reducing the overall variability within each heterotic group. Theoretically, with lower in-group variation, crosses between the groups would no longer guarantee strong hybrids.

Godoy dos Santos and her collaborators suspected variation was waning, but didn’t know by how much and how it might affect certain traits.

To answer these questions, they evaluated the genetic variation underlying multiple plant traits in 13 SS and 28 NSS inbreds representing early-, intermediate-, and late-maturing (flowering) types. Specifically, they focused on variation related to grain yield, plant height, and days to silking and anthesis.

The big takeaway? Genetic variability related to yield was lacking in intermediate-maturity SS lines, the most commonly grown maturity group in the U.S. Corn Belt. The researchers say this important heterotic group could fail to contribute to the development of new hybrids that meet yield goals under future challenges.

On a more positive note, they found plenty of genetic variability remaining across traits in early- and late-maturing inbreds in both SS and NSS groups. There was also sufficient variability for yield in intermediate-maturity inbreds in the NSS group.

Project origins

This project has been in the works for more than a decade. In 2013, a group of U.S. university corn breeders realized their work would be more powerful if they worked together. Thus, the Genomes to Fields (G2F) initiative was born. The researchers not only began trading breeding materials to test in multiple growing environments across the nation, they also tackled some of the thorniest issues facing the industry.

“In 2015 or 2016, we started asking whether we still have genetic variation in our breeding germplasm. That's important because if we don't have variation, then we don't make progress. Without variation, we can’t adapt our germplasm to changing growing conditions, climate change, or diseases that might come up. And most importantly, we can’t produce hybrids that are high-yielding in these new environments,” said Martin Bohn, corn breeder and crop sciences professor at U. of I.

To characterize the remaining genetic diversity, the team started making crosses between SS and NSS inbred lines. They grew 162 single-cross hybrids in more than 30 U.S. and Canadian locations, gathering phenotypic data across maturity groups. Then, they handed this mountain of data over to computational experts Godoy dos Santos and Alex Lipka, a statistical geneticist and professor of biometry at U. of I.

The path forward

“Our analysis can be distilled to a very powerful take-home message about the depletion of the genetic variability in an important group of corn: We are lining ourselves up for an emergency,” Lipka said. “The fact that we’ve observed insignificant genetic variability for yield in this heterotic group should be viewed as a canary in a coal mine. We have to do something about it.”

The researchers say corn breeders should take purposeful steps to reintroduce genetic variability into the breeding pool. Bohn suggests the USDA Agricultural Research Service’s Germplasm Enhancement of Maize program, a publicly funded effort that strategically introduces germplasm from around the world into elite heterotic groups.

“While this study is a warning sign, it does not signify the end of maize breeding, which has been making tremendous progress for more than 100 years,” Godoy dos Santos said. “Our study reminds us of the importance of protecting and broadening the genetic diversity available to breeders. By introducing new sources of genetic diversity, breeding programs can continue developing better maize hybrids for future generations.”

The study, “Dissecting genetic variance structure and evaluating genomic prediction models for single-cross hybrids derived from Stiff Stalk and Non-Stiff Stalk maize heterotic groups,” is published in G3 Genes|Genomes|Genetics [DOI: 10.1093/g3journal/jkag163].

Research in the College of ACES is made possible in part by Hatch funding from USDA’s National Institute of Food and Agriculture. This study was also supported by competitive funding from NIFA [project no. 2024-67013-42588] and from the USDA’s Agricultural Research Service [project no. 5030-21000-073-000D].