Dynamic evolution and hierarchical regulation of rDNA in polyploid oat

Ribosomal DNA (rDNA) encodes the RNA core of ribosomes, yet it remains one of the least understood components of eukaryotic genomes, particularly in complex polyploids. Here, we present a comprehensive analysis of rDNA organization, evolution, and transcription across the Avena genus. We show that rDNA copy number varies extensively across loci and genotypes, and is partially structured by populations. Despite widespread sequence polymorphism, rRNA coding regions exhibit greater sequence conservation than noncoding regions, which retain considerably high levels of sequence diversity. Comparative analyses across ploidy levels further reveal that rDNA evolution is highly structured, lineage-specific, and asymmetric, with polyploidization accompanied by extensive remodeling of rDNA composition and preferential retention of particular subgenome-derived variants. At the transcriptional level, rDNA arrays are not used uniformly, but instead show context-dependent expression of specific variants across developmental and environmental conditions. Using oat-maize addition lines, we further demonstrate complete silencing of alien maize rDNA, while endogenous oat rDNA preserves a stable internal transcriptional hierarchy. Together, these findings establish rDNA as a dynamic genomic system shaped by genome merger, selection, and hierarchical regulation during polyploid evolution. More broadly, they provide a framework for understanding how ribosomal gene diversity contributes to regulatory plasticity, genome stability, and cellular robustness in complex crop genomes.