Effects of B Chromosomes on the A Genome Cytogenet Genome Res 106:320–324 (2004) DOI: 10.1159/000079306 Different numbers of rye B chromosomes induce identical compaction changes in distinct A chromosome domains M. Delgado, a,b A. Caperta, a,b T. Ribeiro, a W. Viegas, a R.N. Jones c and L. Morais-Cecı´lio a a Secça ˜o de Genética, Centro de Botânica Aplicada à Agricultura, Instituto Superior de Agronomia, Tapada da Ajuda; b Universidade Luso ´ fona de Humanidade e Tecnologias, Campo Grande, Lisboa (Portugal); c The University of Wales Aberystwyth, Institute of Biological Sciences, Aberystwyth, Wales (UK) Supported by the Fundaça ˜o para a Ciência e Tecnologia (project POCTI /1999/AGR/ 34000). M. Delgado was supported by a PhD grant from Fundaça ˜o para a Ciência e Tecnologia (PRAXIS XXI/BD/4522/94). Received 23 September 2003; manuscript accepted 3 December 2003. Request reprints from L. Morais-Cecı ´lio, Secça ˜o de Genética Centro de Botânica Aplicada à Agricultura Instituto Superior de Agronomia, Tapada da Ajuda 1349-017 Lisboa (Portugal); telephone: +351 21 365 32 81 fax: + 351 21 363 50 31; e-mail: lmorais@isa.utl.pt M.D. and A.C. contributed equally to this work ABC Fax + 41 61 306 12 34 E-mail karger@karger.ch www.karger.com © 2004 S. Karger AG, Basel 0301–0171/04/1064–0320$21.00/0 Accessible online at: www.karger.com/cgr Abstract. In rye each B chromosome (B) represents 5.5 % of the diploid A genome. Rye Bs have several nuclear to whole plant effects although they seem to bear no genes except for the ones that lead to their maintenance within a population. In this context, and considering that rye Bs are enriched in repetitive non-coding regions that build up heterochromatin (het), we investigated the influence of Bs on the organization of two chromatin fractions, namely the ribosomal DNA (facultative het) and satellite (non-het) domain of rye chromosome 1 by silver staining on root tip metaphase cells. The results show that rye Bs cause condensation both in the NOR and in the chromo- some 1 satellite domain. Since the silver staining technique used is indicative of the transcriptional activity of the NORs, the condensation observed at those loci demonstrates that the rRNA gene arrays are down-regulated in the presence of Bs, regardless of their number per individual. Furthermore, the organizational changes of metaphase NORs find parallel with the interphase organization of ribosomal chromatin, since the frequency of cells with intranucleolar condensed rDNA regions increases drastically and nuclear matrix attachment pattern is altered in the presence of the Bs. Our results show an identical effect of the Bs on the organization of two distinct chromosome domains displaying a presence/absence dichotomy. Copyright © 2004 S. Karger AG, Basel A number of endo- or exophenotype characteristics have been correlated with the presence of B chromosomes (Bs) in rye. Rye is notable for the frequent occurrence of these chromo- somes, which are found in many populations throughout its geographical range. The property of B non-disjunction at first mitosis in the male and female gametophytes, together with irregularities at meiosis, means that they can be either absent or present in distinct numbers between different individuals of the same population (for review see Jones and Puertas, 1993; Jones and Houben, 2003). Rye Bs appear to have both heterochromatic and euchro- matic domains, and whilst their profile is unique, they have no C-banding properties which distinguish them markedly from the As. The information so far available for DNA sequence composition shows that Bs are mostly composed of repeated DNA common to the As (Wilkes et al., 1995; Houben et al., 1996) with exception of two families of specific repetitive sequences, namely D1100 and E3900 (Sandery et al., 1990; Blunden et al., 1993; Langdon et al., 2000). These sequences exist in high copy number in the terminal part of the B long arm that corresponds to a characteristic prominent C-band. Accord- ing to this description of the molecular organization of the rye Bs, these supernumerary chromosomes represent additional content of repetitive DNA sequences that usually organize into heterochromatin (het) domains (Houben et al., 1996), although some may escape the cytological analysis (Redi et al., 2001). Considering the referred effects of B chromosomes on nucleo-