Chromosome Research 1995, 3, 5-15 Organization of retro-element and stem-loop repeat families in the genomes and nuclei of cereals S. Abbo, R. P. Dunford, T. N. Foote, S. M. Reader, R. B. Flavell & G. Moore Received 11 April 1994; received in revised form 8 June 1994 Accepted for publication by J. S. (Pat) Heslop-Harrison 8 June 1994 Sequences homologous to the retro-element BIS-1 and the stem-loop repeat Hi-lO are present in the genomes of a number of cereal species. A detailed characterization of these elements indicated that they are non-randomly organized in the genomes of at least two of these species, namely barley and rye. In contrast to the BIS-1 retro-elements, the stem-loop repeats are also non-randomly organized into dis- crete domains in interphase nuclei from barley and rye. Features of the organization of these repeats along chromosomes and within interphase nuclei of rye, barley and rice are discussed. Key words: Interphase, physical organization, repeated se- quences Introduction The genomes of species in the Gramineae tribe Triticeae such as hexaploid wheat (Triticum aestivum L.), barley (Hordeum vulgare L.) and rye (Secale cereale L.) are 1.7 x 101° bp, 5 x 109 bp and 7 x 109 bp in size per 1C nucleus respectively (Bennett & Smith 1976). In contrast, the genomes of rice (Oryza sativa L.) and the wild grass, Brachypodium sylvaticum L., are much smaller, being 4--5 x 108 bp per 1C nucleus (Bennett & Smith 1991). Genetic mapping has revealed that the order of DNA markers along the homoeologous chro- mosomes of wheat, barley and rye is conserved (re- viewed by Moore et al. 1993a). Wheat and rice prob- ably diverged from a common ancestor 60 million years ago (Wolfe et al. 1989; Martin et al. 1989). The two species have different numbers of chromosomes and vary 40-fold in genome size. However, compari- son of the order of DNA markers on wheat and rice chromosomes reveals extensive collinearity (Kurata et al. 1994). Repetitive sequences account for most of the addi- tional DNA in Triticeae genomes when compared with rice chromosomes. Although most repetitive se- quences diverge significantly during speciation, evi- dence from mammalian genome studies suggests that some repeats may be conserved and are involved with chromatin organization at interphase (Manuelidis 1990). The analysis of cereal genomes should reveal whether the massive amounts of additional repetitive DNA has accumulated randomly or non-randomly, the nature of the sequences involved and if specific repeats have been conserved. Although the most repetitive sequences in the wheat and barley genomes are highly methylated, previous studies indicated the presence of unmethylated recognition sites for the restriction en- zymes MluI and NruI at non-random intervals (re- viewed in Moore et aI. 1993a). Hence, cleavage of wheat and barley DNA with these enzymes is partly discontinuous, generating a ladder of fragment size classes (FSCs). Families of repetitive sequences are distributed in similar proportions between the FSCs. However, it is unclear whether this distribution of unmethylated restriction sites reflects non-random organization of the bulk of the cereal genome and their association with a position-specific function, such as involvement in chromatin structure. This paper details the characterization of two re- peated elements found in cereal genomes. Their struc- ture, chromosomal distribution and organization within interphase nuclei are described and discussed with respect to the evolution of cereal genomes. Materials and methods Plant material Barley DNA used for pulsed-field gel electrophoretic (PFGE) analysis was prepared from cv. Betzes. DNA for two-dimensional (2-D) gel analysis was isolated from wheat-barley addition lines containing a single S. Abbo, R. P. Dunford, T. N. Foote, S. M. Reader, R. B. Flavell and G. Moore (corresponding author) are at the John Innes Centre, Colney Lane, Norwich NR4 7US, UK. Tel: (+44) 603 52571; Fax: (+44) 603 502241. (~ 1995 Rapid Communications of Oxford Ltd Chromosome Research Vol 3 1995 5