The pangenome is central to our understanding of cultivated plants such as oats, as it maps their entire genetic diversity. It encompasses not only genes that occur in all plants, but also those that are only present 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 a gene expression atlas. However, understanding how genetic differences influence individual plant traits is challenging, particularly in the case of oats. The oat genome is very complex because oats are a hexaploid plant with six sets of chromosomes originating from three different ancestors.
In their journey towards the pangenome, the team sequenced and analysed the genomes of 33 oat lines, encompassing cultivated varieties and their wild relatives. To create the pantranscriptome, they examined the gene expression patterns in six tissues and developmental stages of 23 of these oat lines. State-of-the-art sequencing technologies were used for this purpose. The aim was to identify possible structural variations. These can involve changes in the arrangement of chromosomes, such as inversions (i.e. sections that have been rotated) or translocations (i.e. sections that have been moved to a different location).
"With our pangenome, we demonstrate the true extent of the genetic diversity in oats. This helps us to better understand which genes are important for yield, adaptation, and health," says Dr. Raz Avni, first author of the study. The research team also came across some surprising details in their work. "For instance, we found that many genes had been lost in one of the three subgenomes. However, the plant remains productive because other gene copies apparently take over the corresponding tasks."
"Decoding the oat pangenome shows how modern genomics can advance basic research and have a direct impact on health, agriculture, and breeding," explains Dr. Martin Mascher, head of the "Domestication Genomics" research group at the IPK. He immediately gives an example. "We have also found that structural variation in the genome affects genes responsible for controlling flowering time," says Dr. Mascher, who is also coordinator of the international PanOat consortium.
