Did oat domestication result in loss of simple repeat sequences?

Oat is one of the major cereals, especially important as a functional food. However, it is still an understudied crop. Genome repeat elements, known as simple sequence repeats (SSRs), can reveal genome dynamics and be used as markers for selection. SSRs across ancestral (Avena longiglumis and Avena insularis), wild hexaploid (Avena sterilis), and cultivated (Avena sativa) oat genomes were investigated to decouple the evolutionary impacts of polyploidization and domestication on genome architecture. The results revealed a two-step evolutionary trajectory: a "genomic shock" of allohexaploidization triggered a widespread expansion of repetitive elements in the wild A. sterilis, followed by artificial selection imposing a genetic bottleneck, resulting in a global contraction of SSRs in the cultivated A. sativa. In the AA subgenome, an asymmetric decrease of over 72,000 SSRs relative to its diploid ancestor was observed. Elimination of unstable mononucleotides in intergenic regions was observed, whereas conservation of GC-rich trinucleotides in some regions and localized expansion of SSR density within genic sequences on chromosome 3C were found. Genes exhibiting targeted SSR expansions were enriched for transcription factors and receptor-like kinases. Ultimately, these findings suggest that oat evolution is a dynamic structural reorganization driven by natural and artificial selection.