Avena sativa, commonly known as oat grain, is a staple human food renowned for its substantial dietary fiber content, which confers significant health advantages. Recently, there has been a notable resurgence of interest in this crop, largely driven by its application as a foundational ingredient for plant-based milk alternatives. In contrast to numerous other cereal species, the scientific exploration of the oat genome is still in its nascent stages, with limited investigations into its structural genomic diversity and the variability of gene expression. A team of scientists has now successfully compiled and annotated the genomes of 33 distinct lines of wild and domesticated oats. Furthermore, they have developed an atlas detailing gene expression across six different tissue types and various developmental phases in 23 of these selected lines.
The oat (Avena sativa). Image credit: Krystian Win.
Oats, ranking as the world’s seventh most extensively cultivated cereal, are highly valued for their abundant dietary fiber, which has been demonstrably linked to considerable improvements in human well-being.
The global production of oats reached over 25 million metric tons in the years 2022 and 2023.
While genetically enhanced oat varieties hold the promise of boosting crop productivity and sustainability, a considerable portion of this promise remains untapped. Indeed, the initial reference sequences for the oat genome have only emerged in the past few years.
The inherent complexity of the oat genome is a significant factor contributing to the slow pace of progress in genomic research.
“The pangenome is fundamental to our comprehension of cultivated flora such as oats, as it comprehensively maps their entire genetic variability,” stated lead author Dr. Raz Avni, a researcher affiliated with the Leibniz Institute of Plant Genetics and Crop Plant Research, alongside his colleagues.
“It encompasses not only genes common to all plants but also those exclusive to specific species, effectively serving as an intricate genetic blueprint.”
“Concurrently, the pantranscriptome illuminates which genes are actively expressed in various plant tissues, including but not limited to leaves, roots, and seeds, and at different developmental junctures. It functions as a comprehensive gene expression directory.”
“Nevertheless, discerning how genetic disparities influence the specific characteristics of individual plants presents a considerable challenge, particularly in the context of oat genetics.”
“The oat genome is exceptionally intricate due to the plant’s hexaploid nature, possessing six sets of chromosomes derived from three distinct ancestral origins.”
Within the scope of their investigation, the researchers successfully sequenced and meticulously analyzed the genomes of 33 distinct oat varieties, encompassing both cultivated strains and their wild progenitors.
They further constructed the oat pantranscriptome by meticulously examining gene expression profiles across six different tissue types and at various stages of development in 23 of these oat specimens.
The primary objective was to pinpoint potential structural genomic alterations. These alterations can manifest as modifications in chromosome arrangement, such as inversions (regions that have undergone rotation) or translocations (segments that have been relocated to new chromosomal positions).
“Through the development of our pangenome, we have effectively showcased the full spectrum of genetic diversity present in oats,” Dr. Avni remarked.
“This endeavor significantly enhances our understanding of which genes play critical roles in yield, adaptability, and overall health.”
The research team also unearthed several unexpected findings during their meticulous work.
“For instance, we observed that a substantial number of genes had been lost from one of the three subgenomes,” the authors noted.
“However, the plant sustains its productivity because compensatory gene copies appear to assume the corresponding functions.”
“The deciphering of the oat pangenome underscores the profound impact modern genomics can have on advancing fundamental scientific inquiry and generating tangible benefits for human health, agriculture, and plant breeding,” commented senior author Dr. Martin Mascher, a researcher associated with the Leibniz Institute of Plant Genetics and Crop Plant Research, Murdoch University, and the German Centre for Integrative Biodiversity Research.
“We have also determined that structural variations within the genome influence genes that regulate the timing of flowering.”
The findings derived from this research team’s efforts are published in the esteemed journal Nature, accessible via the following link.
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R. Avni et al. A pangenome and pantranscriptome of hexaploid oat. Nature, published online October 29, 2025; doi: 10.1038/s41586-025-09676-7
