Nucleolar dominance is an epigenetic phenomenon that describes the formation of nucleoli around rRNA genes inherited from only one parent in the progeny of an interspecific hybrid. Despite numerous cytogenetic studies, little is known about nucleolar dominance at the level of rRNA gene expression in plants. We used S1 nuclease protection and primer extension assays to define nucleolar dominance at a molecular level in the plant genus Brassica. rRNA transcription start sites were mapped in three diploids and in three allotetraploids (amphidiploids) and one allohexaploid species derived from these diploid progenitors. rRNA transcripts of only one progenitor were detected in vegetative tissues of each polyploid. Dominance was independent of maternal effect, ploidy, or rRNA gene dosage. Natural and newly synthesized amphidiploids yielded the same results, arguing against substantial evolutionary effects. The hypothesis that nucleolar dominance in plants is correlated with physical characteristics of rRNA gene intergenic spacers is not supported in Brassica. Furthermore, in Brassica napus, rRNA genes silenced in vegetative tissues were found to be expressed in all f loral organs, including sepals and petals, arguing against the hypothesis that passage through meiosis is needed to reactivate suppressed genes. Instead, the transition of inf lorescence to f loral meristem appears to be a developmental stage when silenced genes can be derepressed.Ribosomal RNA genes (rRNA genes, rDNA) in eukaryotes are tandemly arrayed in hundreds (to thousands) of copies at chromosomal loci known as nucleolus organizer regions (NORs) (1). Each rRNA gene can be transcribed within the nucleolus by RNA polymerase I to produce a primary transcript that is processed to form the 18S, 5.8S, and 25-27S rRNAs (the size depends on species). To form ribosomes, these RNAs are assembled with 5S rRNA transcribed by RNA polymerase III and Ϸ80 proteins whose mRNAs are transcribed by RNA polymerase II. Because ribosome production directly affects the protein synthetic capacity of the cell, proper regulation of rRNA gene transcription is critical (2-9).The study of rRNA gene regulation in eukaryotes has focused primarily on in vitro analyses of transcriptional activation of individual rRNA genes and the biochemical characterization of transcription factors (6). However, cytogenetic evidence for rRNA gene regulation on a larger scale has accumulated for nearly 70 years on the basis of studies of nucleolar dominance. Nucleolar dominance occurs in organisms as diverse as insects, amphibians, and mammals (10) but was first described in the plant genus Crepis (11-13), followed by studies in Salix, Ribes, Solanum, Hordeum, Avena, Agropyron, Triticum, and Zea, and in intergeneric crosses such as Triticale (wheat ϫ rye; reviewed in refs. 10 and 14). In wheat, changes in the methylation status and DNase I hypersensitivity of dominant and underdominant (the term recessive is inappropriate) rRNA genes suggest that inactive genes are packaged into a transcri...