Nucleolar dominance (ND) consists of the reversible silencing of 35S/45S rDNA loci inherited from one of the ancestors of an allopolyploid. The molecular mechanisms by which one ancestral rDNA set is selected for silencing remain unclear. We applied a combination of molecular (Southern blot hybridization and reverse-transcription cleaved amplified polymorphic sequence analysis), genomic (analysis of variants) and cytogenetic (fluorescence in situ hybridization) approaches to study the structure, expression and epigenetic landscape of 35S rDNA in an allotetraploid grass that exhibits ND, Brachypodium hybridum (genome composition DDSS), and its putative progenitors, Brachypodium distachyon (DD) and Brachypodium stacei (SS). In progenitor genomes, B. stacei showed a higher intragenomic heterogeneity of rDNA compared with B. distachyon. In all studied accessions of B. hybridum, there was a reduction in the copy number of S homoeologues, which was accompanied by their inactive transcriptional status. The involvement of DNA methylation in CG and CHG contexts in the silencing of the S-genome rDNA loci was revealed. In the B. hybridum allotetraploid, ND is stabilized towards the D-genome units, irrespective of the polyphyletic origin of the species, and does not seem to be influenced by homoeologous 35S rDNA ratios and developmental stage.

Department of Field Crops Faculty of Agriculture Tekirdag Namik Kemal University Suleymanpasa Tekirdag 59030 Turkey

Department of Molecular Epigenetics Institute of Biophysics Academy of Sciences of the Czech Republic v v i Královopolská 135 Brno 612 65 Czech Republic

Plant Cytogenetics and Molecular Biology Group Institute of Biology Biotechnology and Environmental Protection Faculty of Natural Sciences University of Silesia in Katowice Jagiellonska 28 Katowice 40 032 Poland

Tekirdag Anatolian High School Suleymanpasa Tekirdag 59030 Turkey

University California Berkeley Berkeley CA 94720 USA

US Department of Energy Berkeley CA 94720 USA

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