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Oats are having a moment. As a highly nutritious cereal crop with well-documented health benefits, it's no surprise oat-based foods are popular alternates to dairy and wheat products. They contain compounds that help lower cholesterol and reduce the risk of metabolic diseases, and they are less likely to trigger allergies. With improved crop breeding, future oat varieties could become even more nutritious, productive, and sustainable.

But for years now, oat breeders have been uncertain why progress in improving yield and quality has been slower than in other major crops. It turns out that the oat's exceptionally large and complex genome has been a major factor limiting that progress.

BYU plant and wildlife professors Rick Jellen and Jeff Maughan, together with an international consortium of researchers, have taken a major step toward unraveling this complexity. Their new research—published in Nature and Nature Communications—ushers in a new era for oat genetics and breeding. The studies describe the full scope of genetic diversity across a wide panel of oat varieties, showing how specific genes are expressed, how they influence key traits and how chromosomal rearrangements affect heredity and adaptation.

"Sequencing the first oat genome [in 2022] gave us the book," said Maughan, whose expertise lies in gene sequencing. "Sequencing many oat genomes allowed us to see how the story changes from one variety to another."

For the , the researchers developed the pangenome, a comprehensive map of the genetic diversity found in modern oats. This reference includes 33 wild and domesticated oat lines and identifies genes that are shared across all varieties as well as those unique to individual types. The pangenome is essential because it reveals the full spectrum of genes present across different oat varieties.

"By studying only one variety, we miss much of the genetic diversity that could be valuable for improving oats in the future," Maughan said.

Building on the pangenome, the team also created a panscriptome—a gene expression atlas that shows which genes are active in different plant tissues (such as leaves, roots, and seeds) at various developmental stages.

Using BYU's DNA Sequencing Center, the researchers examined gene activity across six tissue types and developmental stages in 23 oat lines. They also explored large-scale structural variations in the oat genome, including chromosomal inversions (segments flipped in orientation) and translocations (segments moved to new locations).

"The oat genome is relatively dynamic in terms of the way the chromosomes break and rearrange themselves," said Jellen, an expert in chromosomal structure and heredity. "We confirmed that these chromosomal rearrangements are partially responsible for the lack of breeding progress in oats."

In the , the international team analyzed roughly 9,000 oat samples from around the world to study population structure and genomic regions associated with local adaptation. Remarkably, some of the same chromosomal rearrangements identified in the Nature study were also linked to environmental adaptation—validating their adaptive and breeding significance.

Maughan emphasized the essential role of BYU's DNA Sequencing Center and the strength of global collaboration in achieving these results.

"For me, the most exciting part of this project was the collaboration and the opportunity to work with some of the world's leading crop geneticists," Maughan said. "These aren't just experts in oats—they're among the best in their respective fields."

With the new genetic reference panels, gene expression data, and detailed chromosomal maps now available, researchers and plant breeders will be able to select more precisely for desirable traits. For example, beta-glucan—a compound known to promote heart health—can be prioritized, while traits such as plant height, flowering time, and drought tolerance can be optimized to improve adaptation and productivity in specific environments.

"In my opinion, these are some of the most important papers ever published on oats," Jellen said. "They clarify key questions about oat evolution and domestication and will greatly influence the future of oat breeding. Researchers in agronomy and crop genetics now have a tremendous resource to build upon."