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Diploid  Aegilops umbellulata  and  Ae. comosa  and their natural allotetraploid hybrids  Ae. biuncialis  and  Ae. geniculata  are important wild gene sources for wheat. With the aim of assisting in alien gene transfer, this study provides gene-based conserved orthologous set (COS) markers for the U and M genome chromosomes. Out of the 140 markers tested on a series of wheat- Aegilops  chromosome introgression lines and flow-sorted subgenomic chromosome fractions, 100 were assigned to  Aegilops  chromosomes and six and seven duplications were identified in the U and M genomes, respectively. The marker-specific EST sequences were BLAST-ed to  Brachypodium  and rice genomic sequences to investigate macrosyntenic relationships between the U and M genomes of  Aegilops , wheat and the model species. Five syntenic regions of  Brachypodium  identified genome rearrangements differentiating the U genome from the M genome and from the D genome of wheat. All of them seem to have evolved at the diploid level and to have been modified differentially in the polyploid species  Ae. biuncialis  and  Ae. geniculata . A certain level of wheat– Aegilops  homology was detected for group 1, 2, 3 and 5 chromosomes, while a clearly rearranged structure was showed for the group 4, 6 and 7  Aegilops  chromosomes relative to wheat. The conserved orthologous set markers assigned to  Aegilops  chromosomes promise to accelerate gene introgression by facilitating the identification of alien chromatin. The syntenic relationships between the  Aegilops  species, wheat and model species will facilitate the targeted development of new markers specific for U and M genomic regions and will contribute to the understanding of molecular processes related to allopolyploidization.

Syntenic Relationships between the U and M Genomes of Aegilops, Wheat and the Model Species Brachypodium and Rice as Revealed by COS Markers