Genetic and epigenetic changes of rDNA in a synthetic allotetraploid, Aegilops sharonensis  Ae. umbellulata A.B. Shcherban, E.D. Badaeva, A.V. Amosova, I.G. Adonina, and E.A. Salina Abstract: The synthetic allotetraploid Aegilops sharonensis  Ae. umbellulata (genomic formula S sh U) was used to study inheritance and expression of 45S rDNA during early stages of allopolyploid formation. Using silver staining, we revealed suppression of the NORs (nucleolar organizing regions) from the S sh genome in response to polyploidization. Most allo- polyploid plants of the S2–S4 generations retained the chromosomal location of 45S rDNA typical for the parental species, except for two S3 plants in which a deletion of the rDNA locus on one of the homologous 6S sh chromosomes was re- vealed. In addition, we found a decrease in NOR signal intensity on both 6S sh chromosomes in a portion of the S3 and S4 allopolyploid plants. As Southern hybridization showed, the allopolyploid plants demonstrated additive inheritance of pa- rental rDNA units together with contraction of copy number of some rDNA families inherited from Ae. sharonensis. Also, we identified a new variant of amplified rDNA unit with MspAI1 restriction sites characteristic of Ae. umbellulata. These genetic alterations in the allopolyploid were associated with comparative hypomethylation of the promoter region within the Ae. umbellulata–derived rDNA units. The fast uniparental elimination of rDNA observed in the synthetic allopolyploid agrees well with patterns observed previously in natural wheat allotetraploids. Key words: synthetic allotetraploid, 45S rRNA genes, wheat, Triticeae. Re ´sume ´: L’allote ´traploı ¨de synthe ´tique Aegilops sharonensis  Ae. umbellulata (de formule ge ´nomique S sh U) a e ´te ´ em- ploye ´ pour e ´tudier l’he ´re ´dite ´ et l’expression de l’ADNr 45S lors des premiers stades de la formation d’un allopolyploı ¨de. Par coloration a ` l’argent, les auteurs ont documente ´ la suppression des organisateurs nucle ´olaires (« NOR ») du ge ´nome S sh en re ´ponse a ` la polyploı ¨disation. Chez la majorite ´ des plantes allopolyploı ¨des des ge ´ne ´rations S 2 a `S 4 , l’emplacement chromosomique de l’ADNr 45S e ´tait typique de celui rencontre ´ chez les parents. Exceptionnellement, chez deux plantes S 3 , une de ´le ´tion du locus d’ADNr 45S a e ´te ´ observe ´e sur un des chromosomes homologues 6S sh . De plus, une re ´duction de l’intensite ´ du signal des NOR situe ´s sur les deux chromosomes 6S sh ae ´te ´ observe ´e chez une partie des allopolyploı ¨des S3 et S4. Des analyses Southern ont montre ´ une he ´re ´dite ´ additive des unite ´s d’ADNr 45S ainsi qu’une re ´duction du nombre de copies pour certaines familles d’ADNr he ´rite ´es de l’Ae. sharonensis. De plus, les auteurs ont identifie ´ un nouveau va- riant d’ADNr amplifie ´ posse ´dant des sites de restriction MspAI1 caracte ´ristiques de l’Ae. umbellulata. Ces modifications ge ´ne ´tiques chez l’allopolyploı ¨de e ´taient associe ´es a ` une hypome ´thylation relative de la re ´gion promotrice des ADNr prove- nant de l’Ae. umbellulata. L’e ´limination rapide et uniparentale de l’ADNr observe ´e chez les allopolyploı ¨des synthe ´tiques concorde avec ce qui a e ´te ´ observe ´e pre ´ce ´demment chez les allote ´traploı ¨des naturels chez le ble ´. Mots-cle ´s : allote ´traploı ¨des synthe ´tiques, ge `nes d’ARNr 45S, ble ´, horde ´es. [Traduit par la Re ´daction] Introduction There is considerable recent evidence for both extensive and rapid genome reorganization associated with allopoly- ploid formation (for review see Adams and Wendel 2005; Soltis et al. 2004; Leitch and Bennett 1997; Comai 2000; Rieseberg 2001). Synthetic allopolyploids can be used to an- alyze gene expression and genomic changes at early stages of polyploidization. The following alterations in genome structure have been found in synthetic wheat (Triticum  Aegilops), Brassica, Nicotiana, and Arabidopsis allopoly- ploids: (1) nonrandom elimination of coding and noncoding DNA sequences, (2) recombination between homoeologous chromosomes, (3) alterations in patterns of DNA methyla- tion and gene expression, and (4) activation or silencing of mobile elements (for review see Levy and Feldman 2004; Adams and Wendel 2005; Chen and Ni 2006). In contrast, synthetic cotton allotetraploids display negligible genomic changes (Liu et al. 2001), although there is some partition- ing in the expression of paralogs in different tissues (Adams et al. 2004). These data as a whole point to diverse ways that genomes respond to polyploidy. Ribosomal DNA (45S rDNA or rDNA) provides a valua- ble model to investigate molecular evolution in multigene families. The rDNA repeated units are located at nucleolus Received 6 June 2007. Accepted 7 January 2008. Published on the NRC Research Press Web site at genome.nrc.ca on 12 March 2008. A.B. Shcherban, 1 I.G. Adonina, and E.A. Salina. Institute of Cytology and Genetics, Lavrentiev ave. 10, Novosibirsk, 630090, Russia. E.D. Badaeva and A.V. Amosova. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, Moscow 119991, Russia. 1 Corresponding author (e-mail: atos@bionet.nsc.ru). 261 Genome 51: 261–271 (2008) doi:10.1139/G08-006 # 2008 NRC Canada