Nucleolar dominance arises in Spartina homoploid hybrids and persists after allopolyploidization.

Allopolyploid C.E. Hubbard (2 = 120–124) has become recognized as a model system of recent allopolyploid speciation. It arose by interspecific hybridization between (2 = 62) introduced from North America and the native European (2 = 60) about 150 years ago. In addition, sterile first‐generation homoploid hybrids × and × (both 2 = 62) are still extant. In this study, we carried out a population‐level study of epigenetic silencing of 35S rDNA loci, also known as nucleolar dominance. Using molecular, genomic, and cytogenetic methods, we analyzed 75 individuals of (collected from 11 French populations and 5 UK populations), 34 individuals of (3 populations, all from the UK), and 2 individuals of from the south of France. We observed strong transcriptional dominance of ‐inherited rDNA in all hybrid and allopolyploid individuals. The dominant rDNA units were nearly devoid of methylation at CWG sites, in contrast to those of the silenced ‐inherited rDNA (M‐loci), which exhibited hypermethylation. At the DNA level, few (2%) individuals have completely lost M‐loci, indicating that rDNA diploidization proceeds extremely fast in , and such a process may be influenced by preceding epigenetic processes. We conclude that nucleolar dominance is already present in extant homoploid hybrid lineages and is largely maintained in , with occasional partial relaxation.