Technical Abstract: Genome research on oat (Avena sativa) has received less attention than wheat and barley because it is a less prominent component of the food chain. To assess the potential of the model grass Brachypodium as a surrogate for oat genome research, the whole genome sequence (WGS) of Brachypodium was employed for comparative analysis with oat genetic linkage maps. Sequences of mapped molecular markers from one diploid Avena and two oat maps were aligned to the Brachypodium WGS to infer syntenic relationships. Diploid Avena and Brachypodium exhibit a high degree of synteny with 18 syntenic blocks covering 87% of the oat genome, which permitted postulation of an ancestral Aveneae chromosome structure. Synteny between oat and Brachypodium was also prevalent, with 50 syntenic blocks covering 76.6% of the Kanota x Ogle linkage map. Co-alignment of diploid and hexaploid maps to Brachypodium helped resolve homoeologous relationships between different oat linkage groups, as well as revealing many major rearrangements in oat subgenomes. Extending the analysis to a second oat linkage map (Ogle x TAM) identified several putative homologous linkage groups across the two oat populations. These results indicate that the Brachypodium genome sequence will be a useful resource to assist genetics and genomics research in oat. The analytical strategy employed here should be applicable for genome research in other cool season grass crops with modest amounts of genomic data.