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

<div><p>Diploid <i>Aegilops umbellulata</i> and <i>Ae. comosa</i> and their natural allotetraploid hybrids <i>Ae. biuncialis</i> and <i>Ae. geniculata</i> 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-<i>Aegilops</i> chromosome introgression lines and flow-sorted subgenomic chromosome fractions, 100 were assigned to <i>Aegilops</i> chromosomes and six and seven duplications were identified in the U and M genomes, respectively. The marker-specific EST sequences were BLAST-ed to <i>Brachypodium</i> and rice genomic sequences to investigate macrosyntenic relationships between the U and M genomes of <i>Aegilops</i>, wheat and the model species. Five syntenic regions of <i>Brachypodium</i> 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 <i>Ae. biuncialis</i> and <i>Ae. geniculata</i>. A certain level of wheat–<i>Aegilops</i> 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 <i>Aegilops</i> chromosomes relative to wheat. The conserved orthologous set markers assigned to <i>Aegilops</i> chromosomes promise to accelerate gene introgression by facilitating the identification of alien chromatin. The syntenic relationships between the <i>Aegilops</i> 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.</p>