Identification and physical mapping of induced translocation breakpoints involving chromosome 1R in rye S. Catarino 1 , E. Alvarez 2 , A. Campa 2 , R. Vieira 1 , A. Roca 2 & R. Giraldez 2 * 1 Instituto Botaˆnico, Universidade de Coimbra, 3000-000 Coimbra, Portugal; 2 Departamento de Biologı´a Funcional, Universidad de Oviedo, 33006 Oviedo, Spain; Tel: +34-985103594; Fax: +34-985103534; E-mail: giraldez@uniovi.es S. Catarino and E. Alvarez contributed equally to this work * Correspondence Received 6 July 2006. Received in revised form and accepted for publication by Steve Stack 8 September 2006 Key words: physical mapping, rye, synaptonemal complex, translocation breakpoint Abstract To obtain translocations involving specific chromosomes in rye, pollen of a line in which chromosome 1R has large C-bands on its two telomeres, but which lacks C-bands (or has very small ones) on the telomeres of the remaining chromosomes, was X-irradiated. All translocations involving the labelled chromosome (1R) could be easily recognized in C-banded mitotic metaphases. The non-labelled chromosome involved in each translocation was identified either from mitotic C-banding analysis or from the meiotic configurations observed in some specific progenies. A physical map including 40 translocation breakpoints has been developed by means of synaptonemal complex (SC) analysis of well-paired pachytene quadrivalents. The results agree with the hypothesis of chromosomes 2R to 7R having similar probabilities of participating in translocations with chromosome 1R. However, the locations of the breakpoints are not entirely random: an excess of translocation breakpoints located on the short arm of chromosome 1R was obtained, and the two acentric translocated segments of each translocation show a trend towards having similar sizes. The possible reasons for these two non-random situations are discussed. Introduction Chromosome rearrangements, like translocations or deletions, are useful tools for the development of physical maps in plants. Since only polyploid plants can tolerate the majority of the deletions, trans- locations have been the mutations most extensively used in cytogenetic mapping of diploid plants (de Vries & Sybenga 1984, Linde-Laursen 1988, Hoisington & Coe 1990, Sybenga et al. 1990, Alonso-Blanco et al. 1993a,b, 1994, Sorokin et al. 1994, Ku ¨nzel et al. 2000). A translocation set covering all seven rye chro- mosomes was constructed by Sybenga & Wolters (1972). This set was extended by Ramulu & Sybenga (1985), and a few translocations of spontaneous ori- gin were later described by Alvarez et al. (1994). However, the collection of translocations in rye is much smaller than in barley (Linde-Laursen 1988, Ku ¨nzel 1992) or maize (Longley 1961) in which a high degree of saturation for all chromosomes has been reached. Rye translocations may be efficiently induced by pol- len irradiation with X-rays (Sybenga & Wolters 1972) but their later identification may represent a laborious and difficult task. Since most rye chromosomes show small differences in their C-band patterns, only reciprocal exchanges giving rise to size differences in the translocated chromosomes can be unequivocally Chromosome Research (2006) 14:755–765 # Springer 2006 DOI: 10.1007/s10577-006-1089-7