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Siberian wild rye ( Elymus sibiricus  L.), an allotetraploid species, is a potentially high-quality perennial forage crop native to temperate regions. We used fluorescently conjugated oligonucleotides, representing ten repetitive sequences, including 6 microsatellite repeats, two satellite repeats, and two ribosomal DNAs, to characterize  E .  sibiricus  chromosomes, using sequential fluorescence  in situ  hybridization and genomic  in situ  hybridization assays. Our results showed that microsatellite repeats ( AAG ) 10  or ( AGG ) 10 , satellite repeats pAs1 and pSc119.2, and ribosomal 5S rDNA and 45S rDNA are specific markers for unique chromosomes. A referable karyotype ideogram was suggested, by further polymorphism screening, across different  E .  sibiricus  cultivars with a probe mixture of ( AAG ) 10 , Oligo-pAs1, and Oligo-pSc119.2. Chromosomal polymorphisms vary between different genomes and between different individual chromosomes. In particular, two distinct forms of chromosome E in H genome were identified in intra- and inter-populations. Here, the significance of these results, for  E .  sibiricus  genome research and breeding, and novel approaches to improve fluorescence  in situ  hybridization-based karyotyping are discussed.

Molecular karyotyping of Siberian wild rye (Elymus sibiricus L.) with oligonucleotide fluorescence in situ hybridization (FISH) probes