Chromosomal Organization and Subgenomic Differentiation of Satellite Repeats in Hexaploid Elymus tsukushiensis

The hexaploid grass Elymus tsukushiensis (2n = 42, StStHHYY) provides a suitable system for investigating the chromosomal organization and subgenomic differentiation of repetitive DNA in an allopolyploid genome. In this study, we determined the chromosomal localization of 16 previously characterized repetitive families (E1–E16) derived from satellite DNA and used as FISH probes and subsequently identified the H-, St-, and Y-subgenomes with Oligo-HvCSR and St2-80 probes. FISH mapping revealed pronounced differences among subgenomes: large arrays of E7 and E9 were associated with the St-subgenome; E10 was detected exclusively on Y-chromosomes; E12 and E16 showed preferential localization in the H-subgenome; the remaining repeats exhibited two- or multisubgenomic distribution. Comparison of FISH patterns with previously established relative copy numbers showed that quantitative abundance and physical organization are not strictly proportional: the high copy number of E9 coincided with local accumulation on one pair of St-chromosomes, whereas the low abundance of E16 did not preclude the formation of reproducible FISH loci primarily in the H-subgenome. Repeatome analysis indicated that repetitive DNA constitutes 50.36% of the E. tsukushiensis genome, including 38.42% mobile elements and 1.41% satellite DNA. Our results demonstrate that combining quantitative and cytogenetic approaches provides a more complete characterization of subgenomic organization of satellite repeats and identifies E9, E10, E12, and E16 as promising candidates for further evaluation as cytogenetic markers in Triticeae.