Oats (Avena sativa) grain – This is a traditional human food, rich in fiber and helping to improve human health. Interest in this crop has increased sharply in recent years due to its use as a basis for plant milk analogues. Unlike many other cereal species, genomic research in oats is still at an early stage, and studies of genome structural diversity and gene expression variation are scarce. Scientists have collected and annotated genomes 33 lines of wild and domestic oatsas well as an atlas of gene expression in 6 tissues of different developmental stages in 23 of these lines.
Oats, the seventh most common grain crop in the world, are prized for their high dietary fiber content, which has been shown to provide significant health benefits.
More than 25 million tons were produced worldwide in 2022 and 2023.
Genetically improved varieties have the potential to make oat farming more productive and sustainable, but much of this potential remains unrealized and the first oat reference sequences have only been published in the last few years.
The complexity of the oat genome is partly to blame for the slow progress.
“The pangenome is central to our understanding of crop plants such as oats, as it maps their entire genetic diversity,” said first author Dr Raz Avni, a researcher at the Leibniz Institute of Plant Genetics and Crop Research, and colleagues.
“It covers not only genes that are found in all plants, but also those that are present only in certain species, serving as a kind of map.”
“In turn, the pantranscriptome shows which genes are active in different tissues, such as leaves, roots and seeds, and at different stages of development. It serves as an atlas of gene expression.”
“However, understanding how genetic differences influence individual plant traits is difficult, especially in the case of oats.”
“The oat genome is very complex because oats are a hexaploid plant with six sets of chromosomes derived from three different ancestors.”
In the study, the authors sequenced and analyzed the genomes of 33 oat lines, including cultivated varieties and their wild relatives.
They also created an oat pantranscriptome by examining gene expression patterns in six tissues and developmental stages of 23 of these oat lines.
The goal was to identify possible structural variations. These may include changes in the arrangement of chromosomes, such as inversions (ie, sections that have been rotated) or translocations (ie, sections that have been moved to another location).
“With our pangenome, we are demonstrating the true extent of genetic diversity in oats,” Dr. Avni said.
“This helps us better understand which genes are important for yield, adaptation and health.”
The researchers also discovered some surprising details in their work.
“For example, we found that many genes were lost in one of the three subgenomes,” they said.
“However, the plant remains productive because other copies of the gene appear to take over the appropriate tasks.”
“Deciphering the oat pangenome shows how modern genomics can advance basic research and have a direct impact on health, agriculture and breeding,” said senior author Dr Martin Mascher, researcher at the Leibniz Institute of Plant Genetics and Crop Research, Murdoch University and the German Center for Integrative Biodiversity Research.
“We also found that structural differences in the genome affect genes responsible for controlling flowering time.”
teams results appear in the magazine Nature.
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R. Avni etc.. Pangenome and pantranscriptome of hexaploid oats. Naturepublished online October 29, 2025; doi: 10.1038/s41586-025-09676-7
