The fate of 35S rRNA genes in the allotetraploid grass Brachypodium hybridum

Nucleolar dominance (ND) consists of the reversible silencing of 35/45S 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 hybridisation, RT-CAPS), genomic (analysis of variants) and cytogenetic (FISH) 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, B. distachyon (DD) and B. stacei (SS). In progenitor genomes, B. stacei showed a higher intragenomic heterogeneity of rDNA compared to 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 silencing of the S-genome rDNA loci was revealed. The nucleolar dominance in the B. hybridum allotetraploid is stabilised 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.