Crested wheatgrass (Agropyron cristatum
), a wild relative of wheat, is an attractive source of genes and alleles for their improvement. Our work has created new genomic resources and increased the knowledge about the genome/chromosome structure of A. cristatum
. Chromosome draft assemblies were created, and regions homologous to agronomically important genes were identified. The classification of repetitive DNA sequences revealed the centromere-specific LTR element Agrocen
, whose colocalization with histone CENH3 indicates its role in centromere function. We also demonstrate the potential of newly developed SSR markers for the rapid characterization of wheat–A. cristatum
introgression lines to accelerate introgression breeding programs.